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WO1998035029A1 - Synthetic genes for recombinant mycobacterium proteins - Google Patents

Synthetic genes for recombinant mycobacterium proteins Download PDF

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Publication number
WO1998035029A1
WO1998035029A1 PCT/US1998/002341 US9802341W WO9835029A1 WO 1998035029 A1 WO1998035029 A1 WO 1998035029A1 US 9802341 W US9802341 W US 9802341W WO 9835029 A1 WO9835029 A1 WO 9835029A1
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WO
WIPO (PCT)
Prior art keywords
nucleic acid
mycobacterium
antigen
codon
altered
Prior art date
Application number
PCT/US1998/002341
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French (fr)
Inventor
David Lakey
Douglas S. Kernodle
Kathryn M. Edwards
Rama K. R. Voladri
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Vanderbilt University
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Publication date
Application filed by Vanderbilt University filed Critical Vanderbilt University
Priority to AU61487/98A priority Critical patent/AU6148798A/en
Publication of WO1998035029A1 publication Critical patent/WO1998035029A1/en

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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/195—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria
    • C07K14/35—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria from Mycobacteriaceae (F)
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/51—Medicinal preparations containing antigens or antibodies comprising whole cells, viruses or DNA/RNA
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies

Definitions

  • Tuberculosis is the world's leading cause of death from a single infectious agent. An estimated one-third of the world's population, 1.7 billion people, are infected with tuberculosis.
  • BCG Bacillus Calmette-Guerin
  • BCG blood pressure
  • lymphadenopathy a progressive fibroblast growth factor
  • skeletal infections a progressive fibroblast growth factor
  • visceral granulomas in apparently healthy individuals have been described.
  • disseminated BCG infections have been reported in patients with congenital and acquired immunodeficiencies.
  • a BCG strain from the blood of a four year old HIV-infected Brazilian child immunized with BCG at birth was recently isolated, which has renewed the concern for the safety of BCG vaccine in HIV-infected persons. ⁇ Edwards et al. Ped. Infect. Dis J. 15:836-838, 1996). Because of concerns of vaccine efficacy and safety, a new vaccine against tuberculosis is badly needed.
  • a subunit vaccine consisting of one or more mycobacterial antigens has the advantage of eliminating problems associated with live vaccines.
  • the leading candidates for a subunit vaccine include protein antigens that have been shown to be associated with a strong cell- mediated immune response. Persons infected with M. tuberculosis respond to a variety of mycobacterial antigens. Protective immunity appears to involve predominately T cell responses, the production of cytokines, and the activation of macrophages.
  • a leading candidate for a subunit vaccine against M. tuberculosis is the antigen 85 complex of proteins.
  • Antigen 85 was described, purified, and recognized as immunogenic by 1965 (Yoneda et al. Amer Rev Resp Dis 92:9-18, 1965). It is quantitatively the most important secreted protein of M. tuberculosis and includes three cross-reactive antigens, 85A, 85B, and 85C, which are encoded by three distinct chromosomal genes.
  • the quantitatively major antigens, 85B and 85A comprise 35 to 40% of the total extracellular protein harvested from cultures of M. tuberculosis.
  • the 85Ag proteins induce strong cell-mediated immune responses including T lymphocyte proliferation and gamma-interferon production, in animals and in man (De Bruyn et al. Microbial Pathogenesis 2:351-366, 1987; Huygen et al. Scand J Immunol 27:187-194; 1988).
  • Two recent studies have established that immunization with antigen 85B purified directly from M. tuberculosis or with naked DNA encoding antigen 85B confers partial protection against disease following challenge with M. tuberculosis in animal models (Horwitz et al. Proc Natl Acad Sci. 92:1530-1534, 1995 and Huygen et al. Nature Medicine 2:893-898, 1996).
  • antigen 85 Because of this low expression, published work involving antigen 85 including the recent study which demonstrated that 85B confers partial protective immunity against tuberculosis in guinea pigs generally has required antigen 85 to be purified directly from M. tuberculosis. (Horwitz et al. Proc Natl Acad Sci. 92:1530-1534, 1995). This is an inefficient process, with approximately 150 liters of broth culture containing M. tuberculosis and grown for 2 to 3 weeks required to produce 100 mg of purified antigen 85B. (Horwitz et al. and Harth et al. Infect Immun 64:3038-3047, 1996).
  • this invention in one aspect, relates to a compound comprising a nucleic acid encoding an 85 antigen of Mycobacterium, wherein at least one codon of the nucleic acid encoding the 85 antigen is altered whereby expression of the 85 antigen in an expression system is increased over expression in the same expression system of a nucleic acid sequence having a wild-type codon at the same position as the altered codon.
  • the invention also provides an isolated nucleic acid encoding an 85 antigen of Mycobacterium comprising at least one altered codon which is designed to increase expression of the 85 antigen in an Escherichia coli expression system, wherein the codon is selected from the group consisting of AGG, AGA, ATA, CTA, CGG, CTT, CTC, GGG, and GGA.
  • the invention also provides an isolated nucleic acid encoding an 85A protein of Mycobacterium tuberculosis comprising at least one altered codon which is selected to increase expression of the 85 A antigen in an Escherichia coli expression system, wherein the codon is selected from the codons consisting of positions 3, 6, 15, 17, 24, 28, 33, 34, 39, 64, 67, 69, 76, 85, 107, 113, 115, 117, 119, 122, 123, 125, 126, 131, 134, 140, 144, 147, 150, 153, 155, 161, 195, 197, 198, 207, 217, 229, 234, 261, 271, 276, 280, 285, 286, 289, 290, and 292.
  • the invention also provides an isolated nucleic acid encoding an 85B antigen of Mycobacterium tuberculosis comprising at least one altered codon which is selected to increase expression of the 85B antigen in an Escherichia coli expression system, wherein the codon is selected from the codons consisting of positions 3, 5, 8, 15, 30, 33, 34, 39, 64, 65, 67, 68, 69, 72, 74, 109, 113, 117, 125, 126, 130, 131, 135, 140, 150, 155, 158, 160, 161, 166, 182, 183, 184, 193, 194, 198, 201, 206, 207, 212, 219, 224, 225, 229, 249, 258, 261, 271, 280, and 282.
  • the invention further provides an isolated nucleic acid encoding an 85C antigen o ⁇ Mycobacterium tuberculosis comprising at least one altered codon which is selected to increase expression of the 85C antigen in an Escherichia coli expression system, wherein the codon is selected from the codons consisting of positions 3, 4, 6, 17, 24, 30, 36, 39, 43, 64, 65, 66, 67, 71, 77, 85, 86, 101, 103, 106, 109, 118, 125, 126, 128, 148, 149, 150, 153, 162, 171, 198, 201, 206, 215, 216, 219, 224, 232, 241, 249, 252, 258, 260, 261, 263, 265, 272, 282, 286, 287, and 291.
  • the examples and strategy described herein for increasing the production of recombinant antigen 85 is not limited to E. coli but can be applied to other bacterial organisms, including Bacillus subtilis, Salmonella, humans and other mammals.
  • the invention therefore further provides an isolated nucleic acid encoding an 85 antigen of Mycobacterium tuberculosis comprising at least one altered codon which is selected to increase expression of the 85 antigen in a mammalian or mammalian-derived expression system.
  • the invention also provides an improved method of producing a Mycobacterium protein in a host cell comprising altering a codon of a nucleic acid encoding the Mycobacterium protein so that the codon of the altered nucleic acid is one preferred by the host and introducing the nucleic acid containing the altered codon into the host, whereby the host expresses the nucleic acid thereby producing the Mycobacterium protein.
  • the invention also provides an isolated nucleic acid encoding a protein of Mycobacterium comprising at least one altered codon which is designed to increase expression of the protein in an Escherichia coli expression system, wherein the codon is selected from the group consisting of AGG, AGA, ATA, CGA, CTA, CGG, CTT, CTC, GGG, and GGA.
  • Figure 1 shows a coomasie blue-stained polyacrylamide gel of recombinant antigen 85B recovered from 50 ml of broth containing E. coli transformed with wild-type and mutant 85B genes. Five one ml fractions were eluted off the nickel resin affinity column. As ten ⁇ l of each fraction were applied to a lane, the protein on the gel corresponds to that harvested from 0.5 ml of the original broth culture.
  • Figure 2 shows a coomasie blue-stained PAGE gel of recombinant antigen 85 A recovered from E. coli containing the wild-type and mutant 85A genes. Lane numbers represent the fractions eluted off the nickel resin affinity column, and the protein on the gel corresponds to that harvested from 0.5 ml of the original broth culture.
  • the invention relates to a compound comprising a nucleic acid encoding an 85 antigen o ⁇ Mycobacterium, wherein at least one codon of the nucleic acid encoding the 85 antigen is altered whereby expression of the 85 antigen in an expression system is increased over expression in the same expression system of a nucleic acid sequence having a wild-type codon at the same position as the altered codon.
  • altered is used herein to describe changing the primary sequence of the nucleic acid from a particular codon to a synonymous codon. Because of the degeneracy of the genetic code, certain amino acids are designated by more than one nucleic acid triplet.
  • the codon CGG for example, is one of 6 possible codons coding for the amino acid arginine. This codon can be "altered" to one of the remaining five codons coding for arginine.
  • the expression of the particular gene therefore, can be maximized by determining which codons, when altered from their wild-type sequence to a synonymous codon, result in increased expression of the gene.
  • a “gene” refers to the entire portion of DNA that is involved in the synthesis of a particular protein. This includes a structural region including a coding region of the nucleic acid which begins at the 5' end of the translational start codon (usually ATG) and extends to the stop codon (TAG, TGA, or TAA) at the 3' end.
  • the gene may also contain a promoter region which is usually located upstream of the start codon of the structural region, as well as other regulatory regions such as a transcriptional terminator.
  • Expression refers to the transcription and translation of a gene to yield the encoded protein, in particular a Mycobacterium protein.
  • the synthetic nucleic acids of the present invention are expressed at a higher level in a particular expression system, E. coli for example, than the corresponding wild-type nucleic acids.
  • E. coli E. coli
  • expression of nucleic acids containing altered codons in a particular expression system should be compared to the expression of the wild-type nucleic acids using the same regulatory sequences, the promoter for example, and the same type of host cells. It will also be apparent that analogous means of accessing the level of expression of the nucleic acids should also be used for any comparisons.
  • the structural region of the gene encoding a particular protein can be from one type of organism; a particular Mycobacterium for example.
  • the Mycobacterium from which a nucleic acid encoding an 85 antigen is derived, wherein at least one codon of the nucleic acid encoding the 85 antigen is altered whereby expression of the 85 antigen in an expression system is increased over expression in the same expression system of a nucleic acid sequence having a wild-type codon at the same position as the altered codon can be Mycobacterium tuberculosis.
  • the Mycobacterium can be Mycobacterium bovis.
  • the Mycobacterium can be Mycobacterium africanum.
  • the Mycobacterium can be Mycobacterium leprae.
  • Mycobacterium species include Mycobacterium agr, Mycobacterium aichiense, Mycobacterium asiaticum, Mycobacterium aurum, Mycobacterium avium, Mycobacterium avium-intracellulare, Mycobacterium celatum, Mycobacterium chelonae, Mycobacterium chitae, Mycobacterium chlorophenolicum, Mycobacterium chlorophenolicus, Mycobacterium chubuense, Mycobacterium co ⁇ fluentis, Mycobacterium cookii, Mycobacterium diernhoferi, Mycobacterium duvalii, Mycobacterium fallax, Mycobacterium farcinogenes, Mycobacterium flavescens, ycobacterium fortuitum, Mycobacterium gadium, Mycobacterium gastri, Mycobacterium genavense, Mycobacterium,
  • the structural region may comprise sequences from a plurality of organisms, such as different species o ⁇ Mycobacterium, or organisms of different genera, such as E. coli and Mycobacterium for example.
  • a protein from Mycobacterium is to be expressed in an organism other than a Mycobacterium, such as E. coli
  • one can substitute particular E. coli sequences such as a 5' untranslated region for the corresponding Mycobacterium sequences to design a nucleic acid for expression in E. coli.
  • the expressed nucleic acid could contain a coding region corresponding to the Mycobacterium protein and a leader region containing an E. coli ribosome binding region.
  • the Mycobacterium sequence can be a monocistronic sequence or a polycistronic sequence. Where the Mycobacterium sequence is monocistronic, the leader and the trailer can be from Mycobacterium or another organism. Where the Mycobacterium sequence is polycistronic, in addition to the leader and the trailer being either from Mycobacterium or another organism, the intercistronic sequence can also be from either Mycobacterium or another organism.
  • the structural region can also be from more than one type o ⁇ Mycobacterium.
  • fusion proteins can be constructed using standard techniques such as gene cloning or gene synthesis to construct a nucleic acid encoding a hybrid protein.
  • a nucleic acid encoding a hybrid 85 antigen which may be a hybrid between 85A and 85B antigens, a hybrid between 85B and 85C antigens, a hybrid between 85A and 85C antigens, or a hybrid between 85A, 85B, and 85C antigens.
  • the structural gene may also contain one or more modifications in sequences other than the protein coding regions which could affect the biological activity or the chemical structure of the expression product, the rate of expression or the manner of expression control.
  • modifications include, but are not limited to, mutations, insertions, deletions and substitutions of one or more nucleotides.
  • the 85 antigen o ⁇ Mycobacterium comprises three different proteins; the 85A antigen, the 85B antigen, and the 85C antigen, which are set forth in the Sequence Listing as SEQ ID NO: 1 , SEQ ID NO: 2, and SEQ ID NO:3, respectfully.
  • the nucleic acid sequence encoding an 85 antigen of Mycobacterium wherein at least one codon of the nucleic acid encoding the 85 antigen is altered whereby expression of the 85 antigen in an expression system is increased over expression in the same expression system of a nucleic acid sequence having a wild-type codon at the same position as the altered codon is selected from the group consisting of 85A antigen, 85B antigen, and 85C antigen.
  • the compound comprising a nucleic acid encoding an 85 antigen o ⁇ Mycobacterium wherein at least one codon of the nucleic acid encoding the 85 antigen is altered whereby expression of the 85 antigen in an expression system is increased over expression in the same expression system of a nucleic acid having a wild-type codon at the same position as the altered codon comprises the nucleic acid encoding the 85A antigen and the altered codon is selected from the group consisting of positions 3, 113, 115, 117, and 119.
  • the nucleic acid comprises the nucleic acid encoding the 85B antigen and the altered codon is selected from the group consisting of positions 3, 5, 206, 207, 224, and 225.
  • the nucleic acid comprises the nucleic acid encoding the 85B antigen and the altered codon is selected from the group consisting of positions 3, 5, 113, 206, and 207.
  • the nucleic acid comprises the nucleic acid encoding the 85C antigen and the altered codon is selected from the group consisting of positions 3, 4, 6, 101, 103, 109, and 224.
  • the nucleic acid comprises the nucleic acid encoding the 85A antigen and the altered codon is selected from the group consisting of positions 3, 6, 15, 17, 24, 28, 33, 34, 39, 64, 67, 69, 76, 85, 107, 113, 115, 117, 119, 122, 123, 125, 126, 131, 134, 140, 144, 147, 150, 153, 155, 161, 195, 197, 198, 207, 217, 229, 234, 261, 271, 276, 280, 285, 286, 289, 290, and 292.
  • the nucleic acid comprises the nucleic acid encoding the 85B antigen and the altered codon is selected from the group consisting of positions 3, 5, 8, 15, 30, 33, 34, 39, 64, 65, 67, 68, 69, 72, 74, 109, 113, 117, 125, 126, 130, 131, 135, 140, 150, 155, 158, 160, 161, 166, 182, 183, 184, 193, 194, 198, 201, 206, 207, 212, 219, 224, 225, 229, 249, 258, 261, 271, 280, and 282.
  • the nucleic acid comprises the nucleic acid encoding the 85C antigen and the altered codon is selected from the group consisting of positions 3, 4, 6, 17, 24, 30, 36, 39, 43, 64, 65, 66, 67, 71, 77, 85, 86, 101, 103, 106, 109, 118, 125, 126, 128, 148, 149, 150, 153, 162, 171, 198, 201, 206, 215, 216, 219, 224, 232, 241, 249, 252, 258, 260, 261, 263, 265, 272, 282, 286, 287, and 291.
  • the nucleic acid encodes a Mycobacterium tuberculosis or a.
  • Mycobacterium bovis 85 A antigen and the nucleic acid comprises at least one altered codon selected from the group consisting of positions 3, 113, 115, 117, and 119.
  • the nucleic acid encodes a Mycobacterium tuberculosis or a Mycobacterium bovis 85A antigen and the nucleic acid comprises at least two altered codons selected from the group consisting of positions 3, 113, 115, 117, and 119.
  • the nucleic acid encodes a.
  • the nucleic acid comprises at least three altered codons selected from the group consisting of positions 3, 113, 115, 117, and 119.
  • the nucleic acid encodes a Mycobacterium tuberculosis or a Mycobacterium bovis 85A antigen and the nucleic acid comprises at least four altered codons selected from the group consisting of positions 3, 113, 115, 117, and 119.
  • the nucleic acid encodes a Mycobacterium tuberculosis or a Mycobacterium bovis 85A antigen and the nucleic acid comprises five altered codons wherein the codons are at positions 3, 113, 115, 117, and 119.
  • the nucleic acid encodes a Mycobacterium tuberculosis or a Mycobacterium bovis 85B antigen and the nucleic acid comprises at least one altered codon selected from the group consisting of positions 3, 5, 206, 207, 224, and 225.
  • the nucleic acid encodes a Mycobacterium tuberculosis or a Mycobacterium bovis 85B antigen and the nucleic acid comprises at least two altered codons selected from the group consisting of positions 3, 5, 206, 207, 224, and 225.
  • the nucleic acid encodes a Mycobacterium tuberculosis or a Mycobacterium bovis 85B antigen and the nucleic acid comprises at least three altered codons selected from the group consisting of positions 3, 5, 206, 207, 224, and 225.
  • the nucleic acid encodes a Mycobacterium tuberculosis or a Mycobacterium bovis 85B antigen and the nucleic acid comprises at least four altered codons selected from the group consisting of positions 3, 5, 206, 207, 224, and 225.
  • the nucleic acid encodes a Mycobacterium tuberculosis or a Mycobacterium bovis 85B antigen and the nucleic acid comprises at least five altered codons selected from the group consisting of positions 3, 5, 206, 207, 224, and 225.
  • the nucleic acid encodes a Mycobacterium tuberculosis or a Mycobacterium bovis 85B antigen and the nucleic acid comprises six altered codons wherein the codons are at positions 3, 5, 206, 207, 224, and 225.
  • the nucleic acid encodes a Mycobacterium 85B antigen and the nucleic acid comprises at least one altered codon selected from the group consisting of positions 3, 5, 113, 206, and 207.
  • the nucleic acid encodes a Mycobacterium 85B antigen and the nucleic acid comprises at least two altered codons selected from the group consisting of positions 3, 5, 113, 206, and 207.
  • the nucleic acid encodes a Mycobacterium 85B antigen and the nucleic acid comprises at least three altered codons selected from the group consisting of positions 3, 5, 113, 206, and 207.
  • the nucleic acid encodes a Mycobacterium 85B antigen and the nucleic acid comprises at least four altered codons selected from the group consisting of positions 3, 5, 113, 206, and 207.
  • the nucleic acid encodes a Mycobacterium 85B antigen and the nucleic acid comprises five altered codons wherein the codons are at positions 3, 5, 113, 206, and 207.
  • codon numbering used herein corresponds to the most favorable alignment of the 85 antigen genes.
  • the codon at position 26 in SEQ ID NO.1-5 is TTC and the codon at position 39 in these same sequences is CTC despite the fact that SEQ ID NO.3 is six nucleotides shorter than SEQ ID NO. 1, SEQ ID NO.2, SEQ ID NO.4, and SEQ ID NO.5 in this same region.
  • the six nucleotides may therefore be represented in a sequence alignment as a six bas gap; however the above-discussed CTC codon in SEQ ID NO.3 aligns with the other sequences at their codon position 39 and is referenced herein as codon 39, not codon 37.
  • the present invention provides an isolated nucleic acid encoding a protein o ⁇ Mycobacterium comprising at least one codon altered to increase expression of the nucleic acid wherein the codon is selected from the group consisting of AGG, AGA, ATA, CGA, CTA, CGG, CTT, CTC, GGG, and GGA.
  • the codons AGG, CGG, CGA, and AGA in a Mycobacterium protein can be altered to CGT or CGC.
  • the codon ATA in a Mycobacterium protein can be altered to ATT or ATC.
  • the codons CTT, CTA, and CTC in a Mycobacterium protein can be altered to CTG.
  • the codon GGG and GGA in a Mycobacterium protein can be altered to GGT or GGC.
  • nucleic acids encoding a Mycobacterium 85 antigen as described in the Example contained herein do not contain the arginine codon CGA. Accordingly, the present invention also specifically provides an isolated nucleic acid encoding an 85 antigen o ⁇ Mycobacterium comprising at least one codon altered to increase expression of the nucleic acid wherein the codon is selected from the group consisting of AGG, AGA, ATA, CTA, CGG, CTT, CTC, GGG, and GGA.
  • the wild-type nucleic acids encoding a Mycobacterium 85 A antigen, an 85B antigen, and an 85C antigen have the specific nucleic acid sequences disclosed herein as SEQ ID NO: 1, SEQ ID NO:2, and SEQ ID NO:3, respectfully. Therefore these nucleic acids can be altered at specific codon locations rather than altered at specific codon sequences.
  • the present invention provides an isolated nucleic acid encoding an 85 A protein o ⁇ Mycobacterium tuberculosis or Mycobacterium bovis comprising at least one codon altered to increase expression of the nucleic acid wherein the codon is selected from the codons consisting of positions 3, 6, 15, 17, 24, 28, 33, 34, 39, 64, 67, 69, 76, 85, 107, 113, 115, 117, 119, 122, 123, 125, 126, 131, 134, 140, 144, 147, 150, 153, 155, 161, 195, 197, 198, 207, 217, 229, 234, 261, 271, 276, 280, 285, 286, 289, 290, and 292.
  • the present invention provides an isolated nucleic acid encoding an 85B antigen o ⁇ Mycobacterium tuberculosis ox Mycobacterium bovis comprising at least one codon altered to increase expression of the nucleic acid wherein the codon is selected from the codons consisting of positions 3, 5, 8, 15, 30, 33, 34, 39, 64, 65, 67, 68, 69, 72, 74, 109, 113, 117, 125, 126, 130, 131, 135, 140, 150, 155, 158, 160, 161, 166, 182, 183, 184, 193, 194, 198, 201, 206, 207, 212, 219, 224, 225, 229, 249, 258, 261, 271, 280, and 282.
  • the present invention provides an isolated nucleic acid encoding an
  • 85C antigen o ⁇ Mycobacterium tuberculosis or Mycobacterium bovis comprising at least one codon altered to increase expression of the nucleic acid wherein the codon is selected from the codons consisting of positions 3, 4, 6, 17, 24, 30, 36, 39, 43, 64, 65, 66, 67, 71, 77, 85, 86, 101, 103, 106, 109, 118, 125, 126, 128, 148, 149, 150, 153, 162, 171, 198, 201, 206, 215, 216, 219, 224, 232, 241, 249, 252, 258, 260, 261, 263, 265, 272, 282, 286, 287, and 291.
  • the codons altered to increase expression of a nucleic acid encoding a Mycobacterium protein can also differ. Accordingly, the present invention provides an isolated nucleic acid encoding a protein o ⁇ Mycobacterium comprising at least one codon altered to increase expression of the nucleic acid in a mammalian or mammalian-derived expression system wherein the codon is selected from the group consisting of GCG, CGT, CGA, GGT, ATA, TTA, CTA, TTG, CTT, CCG, TCG, AGT, TCA, TCT, ACG, GTA, and GTT.
  • the codon GCG in a Mycobacterium protein can be altered to GCC, GCT, or GCA.
  • the codons CGT and CGA in a Mycobacterium protein can be altered to AGG, AGA, CGG, or CGC.
  • the codon GGT in a Mycobacterium protein can be altered to GGC, GGA, or GGG.
  • the codon ATA in a Mycobacterium protein can be altered to ATT or ATC.
  • the codons TTA, CTA, TTG, and CTT in a Mycobacterium protein can be altered to CTG or CTC.
  • the codon CCG in a Mycobacterium protein can be altered to CCC, CCT, or CCA.
  • the codons TCG, AGT, TCA, and TCT in a Mycobacterium protein can be altered to AGC or TCC. Additionally, the codon ACG in a Mycobacterium protein can be altered to ACC, ACA, or ACT. Additionally, the codons GTA and GTT in a Mycobacterium protein can be altered to GTG or GTC.
  • the present invention also provides an isolated nucleic acid encoding an 85 A protein o ⁇ Mycobacterium tuberculosis or Mycobacterium bovis comprising at least one codon altered to increase expression of the nucleic acid in a mammalian or mammalian-derived expression system wherein the codon is selected from the codons consisting of positions 4, 6, 7, 14, 15, 16, 17, 20, 28, 29, 30, 33, 44, 56, 57, 64, 67, 71, 73, 76, 91, 106, 124, 125, 126, 130, 131, 132, 134, 136, 146, 148, 150, 153, 158, 160, 167, 169, 182, 186, 187, 193, 195, 216, 217, 220, 225, 247, 257, 260, 261, 269, 283, 285, and 291.
  • the present invention also provides an isolated nucleic acid encoding an 85B protein o ⁇ Mycobacterium tuberculosis or Mycobacterium bovis comprising at least one codon altered to increase expression of the nucleic acid in a mammalian or mammalian-derived expression system wherein the codon is selected from the codons consisting of positions 4, 7, 14, 15, 16, 17, 24, 29, 33, 35, 36, 56, 57, 64, 67, 68, 71, 85, 88, 106, 109, 125, 126, 130, 131, 135, 148, 150, 156, 167, 169, 173, 181, 183, 184, 186, 194, 207, 209, 216, 219, 221, 224, 229, 233, 234, 243, 247, 257, 261, 276, 280, 281, and 282.
  • the present invention also provides an isolated nucleic acid encoding an 85C protein o ⁇ Mycobacterium tuberculosis or Mycobacterium bovis comprising at least one codon altered to increase expression of the nucleic acid in a mammalian or mammalian-derived expression system wherein the codon is selected from the codons consisting of positions 2, 5, 6, 16, 17, 31, 35, 41, 56, 64, 66, 67, 77, 86, 101, 109, 117, 121, 122, 124, 125, 126, 128, 130, 132, 137, 140, 144, 147, 148, 149, 150, 155, 161, 162, 167, 171, 173, 181, 182, 186, 195, 212, 224, 225, 226, 245, 248, 257, 263, 285, 288, 293, and 294.
  • nucleic acid sequence encoding an 85 antigen of Mycobacterium wherein at least one codon of the nucleic acid encoding the 85 antigen is altered whereby expression of the 85 antigen in an expression system is increased over expression in the same expression system of a nucleic acid sequence having a wild-type codon at the same position as the altered codon.
  • One method of obtaining the nucleic acid is by constructing the nucleic acid by synthesizing a recombinant DNA molecule. For example, oligonucleotide synthesis procedures are routine in the art and oligonucleotides coding for a particular protein or regulatory region are readily obtainable through automated DNA synthesis.
  • a nucleic acid for one strand of a double-stranded molecule can be synthesized and hybridized to its complementary strand.
  • Double-stranded molecules coding for relatively large proteins or regulatory regions can be synthesized by first constructing several different double-stranded molecules that code for particular regions of the protein or regulatory region, followed by ligating these DNA molecules together. For example, Cunningham, et al, "Receptor and Antibody Epitopes in Human Growth Hormone Identified by Homolog-Scanning Mutagenesis," Science, Vol.
  • a DNA or cDNA library can be constructed and screened for the presence of the nucleic acid of interest.
  • nucleic acid can be directly cloned into an appropriate vector, or if necessary, be modified to facilitate the subsequent cloning steps.
  • modification steps are routine, an example of which is the addition of oligonucleotide linkers which contain restriction sites to the termini of the nucleic acid.
  • the amplification step may be combined with a mutation step, using primers not completely homologous to the target nucleic acid for example, to simultaneously amplify the nucleic acid and alter specific positions of the nucleic acid.
  • An example of this method of constructing a nucleic acid sequence encoding an 85 antigen o ⁇ Mycobacterium wherein at least one codon of the nucleic acid encoding the 85 antigen is altered is contained and described in the Example contained herein, where the wild-type nucleic acids were previously available, but the desired mutant nucleic acids were generated from this wild-type template using PCR.
  • the nucleic acid sequence encoding an 85 antigen o ⁇ Mycobacterium wherein at least one codon of the nucleic acid encoding the 85 antigen is altered whereby expression of the 85 antigen in an expression system is increased over expression in the same expression system of a nucleic acid sequence having a wild-type codon at the same position as the altered codon may be introduced into a host cell for expression of that nucleic acid by any number of methods that are familiar to one skilled in the art.
  • DNA may be introduced into a host by calcium chloride transformation of the host, by protoplast transformation, by prokaryotic transduction, electroporation, or via the use of phage vectors. (Sambrook et al.)
  • Other methods more commonly used for other hosts include calcium phosphate transfection, liposome delivery, DEAE-dextran mediated transfection, lipofectin-mediated transfection, injection, or viral vectors.
  • E. coli may be used as the host expression system.
  • Other hosts can alternatively be used for the expression system for the nucleic acids and methods of the present invention.
  • other bacterial hosts such as Bacillus can be used as the host for expressing the nucleic acid.
  • Other hosts may also be used as the expression host.
  • yeast hosts, plant hosts, mammalian hosts, insect hosts, and other various viral hosts may be used. These types of host expression systems are well known in the art. For an example of a plant expression, see U.S. Patent No.
  • the expression system used to express the nucleic acids of the present invention can comprise a human or human-derived expression system.
  • E. coli vectors that are available for expressing nucleic acids.
  • E. coli vectors that are available for expressing nucleic acids.
  • an E. coli vector used for expressing a nucleic acid wherein at least one codon of the nucleic acid encoding the 85 antigen is altered whereby expression of the 85 antigen in the E. coli expression system is increased over expression in the same E. coli expression system of a nucleic acid sequence having a wild-type codon at the same position as the altered codon is the vector pTrcHisB.
  • retroviral vector systems which can package a recombinant retroviral genome.
  • retroviral vector systems which can package a recombinant retroviral genome.
  • the produced recombinant retrovirus can then be used to infect and thereby deliver to the infected cells a nucleic acid sequence encoding an 85 antigen o ⁇ Mycobacterium wherein at least one codon of the nucleic acid encoding the 85 antigen is altered to increase expression of the 85 antigen.
  • the exact method of introducing the altered nucleic acid into mammalian cells is, of course, not limited to the use of retroviral vectors. Other techniques are widely available for this procedure including the use of adenoviral vectors (Mitani et al. "Transduction of human bone marrow by adenoviral vector.” Human Gene Therapy 5:941-948 (1994)), adenoassociated viral vectors (Goodman et al.
  • the various vectors and hosts used to express the nucleic acids of the present invention may be used to express the nucleic acids in culture.
  • a vector comprising a nucleic acid provided by the present invention may be introduced into a tissue culture cell line, such as COS cells, and expressed whereby the nucleic acid is expressed in culture.
  • various vectors and hosts used to express the nucleic acids of the present invention may be used to express the nucleic acids in vivo.
  • a vector comprising a nucleic acid provided by the present invention may be introduced into cells of the eukaryotic host which is being administered a nucleic acid provided by the present invention to provide a polypeptide for purposes of eliciting an immune response by the host.
  • the nucleic acids provided by the present invention may, therefore, be used as templates for the production of proteins which may be used to vaccinate a subject against Mycobacterium infection since the primary sequences of the polypeptides encoded by the nucleic acids provided by the present invention are identical to the corresponding wild-type Mycobacterium polypeptides.
  • One skilled in the art will recognize there are also various techniques for introducing the nucleic acids comprising the nucleic acids provided by the present invention into host cells in vivo, such as, but not limited to, liposome delivery and "naked DNA" techniques.
  • the present invention also provides a Mycobacterium
  • 85B antigen wherein at least 20mg of this protein are produced per liter of cell culture using an expression system described herein.
  • a composition comprising at least 20mg o ⁇ a Mycobacterium antigen obtained per liter of the cell culture is provided.
  • similar high expression levels o ⁇ the Mycobacterium 85A antigen and the Mycobacterium 85C antigen using an expression systems described herein are provided.
  • Similar compositions of 85A and 85C antigens are also provided.
  • the proteins provided by the present invention may also be used to treat an existing Mycobacterial infection, to provide a vaccine, as well as provide a Mycobacterium protein that can be used as a therapeutic. Additionally, the proteins may be reintroduced into a Mycobacterium which may be used as a whole organism vaccine or therapeutic.
  • various vectors and hosts used to express the nucleic acids of the present invention may be used to express the nucleic acids ex vivo.
  • a vector comprising a nucleic acid provided by the present invention may be introduced into cells of the host which have, previous to the introduction of the nucleic acid, been removed from the host.
  • the cells of the host comprising those cells containing the introduced nucleic acid can then be used to express the nucleic acid and therefore produce the polypeptide in culture, or the cells of the host comprising those cells containing the introduced nucleic acid can then be reintroduced into the host and thereby used to express the nucleic acid and therefore produce the polypeptide in vivo.
  • codons selected to be altered to increase the expression of the nucleic acid relative to the wild-type nucleic acid will vary depending on which expression system is used to express the nucleic acid.
  • the codon preference for E. coli is different than the codon preference for mammals. Therefore one can design a nucleic acid with an altered codon(s) for expression in one expression system which may be different from a nucleic acid with an altered codon(s) in a different expression system while both nucleic acids encode the same polypeptide.
  • the invention relates to a method of producing a
  • Mycobacterium protein in a host cell comprising altering a codon of a nucleic acid encoding the Mycobacterium protein so that the altered codon of the nucleic acid is one preferred by the host and introducing the nucleic acid containing the altered codon into the host, whereby the host expresses the nucleic acid thereby producing the Mycobacterium protein.
  • the nucleic acid encoding a Mycobacterium protein in which a codon is altered to be one preferred by the host may comprise any Mycobacterium nucleic acid encoding any Mycobacterium protein.
  • the nucleic acid used in the improved method of producing a Mycobacterium protein encodes an 85 antigen o ⁇ Mycobacterium selected from the group consisting of 85 A antigen, 85B antigen, and 85C antigen.
  • the nucleic acid used in the improved method of producing a Mycobacterium protein encodes an 85 antigen which is a hybrid 85 antigen selected from the group consisting of an 85A/85B hybrid, an 85A/85C hybrid, an 85B/85C hybrid, and an 85/A/85B/85C hybrid.
  • the particular Mycobacterium is selected from the group consisting o ⁇ Mycobacterium tuberculosis, Mycobacterium bovis, Mycobacterium africanum, and Mycobacterium leprae. Therefore the improved method described herein may be used to produce different Mycobacterium proteins for various applications. For example, a Mycobacterium protein derived from Mycobacterium tuberculosis may be used to elicit an immune response from a subject. This particular utility therefore may be directed toward immunizing a subject from subsequent infection by Mycobacterium tuberculosis.
  • nucleic acid from Mycobacterium leprae may be used in the improved method to produce a protein encoded by that nucleic acid for a similar use.
  • a nucleic acid from Mycobacterium bovis may be used in the improved method to produce a protein encoded by that nucleic acid to elicit an immune response from a bovine subject and a human subject.
  • an antigen from one species can be used to elicit an immune response in a subject that is infected with a different species of Mycobacterium.
  • an 85 antigen from Mycobacterium bovis can be used to elicit an immune response in a human subject.
  • the nucleic acid o ⁇ Mycobacterium used in the method described herein can encode any number of proteins.
  • the nucleic acid can encode a Mycobacterium virulence factor, or a gene or genes involved in cellular metabolism or cellular biosynthesis.
  • the following list is a partial list of other genes of tuberculosis orM. bovis that may be altered to increase expression of those nucleic acids:
  • RNA polymerase beta subunit C (rpoC gene) MT11452
  • RNA polymerase beta subunit B (rpoB gene) MT 12205 14 kDa antigen MT14KA
  • MTAT10S at9s gene MTAT9S biotin carboxyl carrier protein MTBCARBCP diaminopimelate decarboxylase (lysA) MTCAPDC heat-shock protein genes (dnaK, grpE, and dnaJ) MTDNAGRP, MTDNAJ esat ⁇ (early secreted antigen of tuberculosis) MTESAT6 dihydrofolate reductase MTFOLA groE gene for KCS and 10-kDa products MTGROEOP DNA gyrase A and B subunits MTGYRAB mce gene MTMCE
  • MPT40 protein and phospholipase C MTMTP40, MTMTP40A mycocerosic acid synthase MTMYACSYN antigen B MTPABA
  • MTTCWPA thymidilate synthase MTTHYA elongation factor TU MTTUF orotidine-5'-monophosphate decarboxylase (uraA) MB072 20 kD antigen protein MB19KD alcohol dehydrogenase MBADH ornithine carbamoyltransferase MBARGF meso-diaminopimelate biosynthetic pathway (dapB) MBDAPB immunogenic protein MPB57 MBMPB57, MBBPB57A antigen MPB70 MBMPBAA ribosomal protein L7/L 12 MBRPLL ribosomal protein S12 and S7 MBRPS127X putative host cell receptor binding protein S46909
  • the protein produced by the method described herein can be used in a number of other applications as well.
  • the proteins can also be used as reagents in applications such as immunodiagnostic assays, for example to detect the presence of antigens.
  • the proteins can also be used in therapeutic applications, such as to generate antibodies to the protein which can be administered to a subject infected with an organism whose genome encodes the protein.
  • oligonucleotide primers were constructed and used to amplify via the polymerase chain reaction (PCR) each of the three wild-type 85 antigen genes individually.
  • the 5' oligonucleotides contained an EcoRI endonuclease restriction site, while the 3' oligonucleotides contained a BamW. restriction site to facilitate subsequent cloning.
  • the PCR products were cleaved with BamH ⁇ and EcoRI and cloned into the BamHl and Ec ⁇ Rl sites of the plasmid pBCSK + (Stratagene, La Jolla CA), and then transformed into E. coli strain DH5 ⁇ . Plasmid DNA was isolated from these transformants.
  • the expression plasmid pTrcHisB (Invitrogen) contains the trp and lac promoter upstream to the multiple cloning site and a sequence that encodes an N-terminal fusion peptide. This sequence also codes for an ATG initiation codon, six histidine residues in series that function as a metal binding domain in the translated protein, and an enterokinase cleavage recognition site. This expression plasmid was digested with BamHl and EcoRI, which have single restriction sites in the multiple cloning site of pTrcHisB and the 85 antigen genes then individually ligated in-frame between these sites.
  • Each recombinant expression plasmid therefore contained a powerful promoter followed by an initiation codon, the six histidines, the enterokinase cleavage site, one of the three individual 85 antigen genes, and a stop codon.
  • Six such plasmids were constructed, one for each of the following proteins: BCG 85A, BCG 85C, M. tuberculosis H37Rv 85 A, M. tuberculosis H37Rv 85B, and tuberculosis H37Rv 85C.
  • the recombinant 85 antigen was then eluted by further lowering the pH.
  • the column was repeatedly washed with phosphate buffer. Proteins were then eluted from the nickel resin column by increasing concentrations of imidazole, which displaces the histidine from the nickel column.
  • CGG-CTA a region of the 85B gene containing two adjacent unpreferred codons, i.e., CGG-CTA at codon positions 206- 207 of the antigen 85B gene sequence.
  • CGG encodes for arginine (R) and CTA encodes for leucine (L).
  • CGG is a nonpreferred codon that is used by E. coli only 10% of the time that arginine is encoded.
  • CGT (CGU) and CGC are preferred codons for arginine, encoding for 37% and 38% of E. coli arginine respectively.
  • CTA is an unpreferred codon for leucine, encoding for only 4% of __. coli leucine.
  • Other codons for leucine are CTG, CTT, CTC, TTG, and TTA which encode for 50%), 11%), 10%, 12%, and 13% of E. coli leucine respectively.
  • This primer encodes for a BamHl restriction site followed by the first 24 nucleotides (8 codons; nucleotides 1-24) corresponding to the mature exoenzyme form of the 85B antigen.
  • Nucleotide #1 is numbered.
  • [b] 85B R626 mut AAC-CCA-CAG-ACG-CGT-GTT-GTT-TGC-GAC-CAG- CTT-GGG-GAT- CTG (SEQ ID NO.7).
  • This is an antisense primer encoding for nucleotides number 627 through 586, but containing the mutations noted above to produce the desired codon changes and to introduce the Mlul restriction site.
  • Nucleotides 621, 618, and 615 were changed to produce the mutant 85B antigen gene and are underlined.
  • GGC-ACC- CCG SEQ ID NO.8. This is a sense primer from nucleotide 613 through 648 that also contains the mutations noted above to produce the desired codon changes and to introduce the ⁇ _7./I restriction site. Nucleotides 615, 618, and 621 were changed to produce the mutant 85B antigen gene and are underlined.
  • 85B R102 GATGAATTC-TCA-GCC-GGC-GCC-TAA-CGA-ACT-CTG- CAG (SEQ ID NO.9). This is an antisense primer containing an EcoRI restriction site followed by a stop codon and the last 24 nucleotides of the 85B gene.
  • Primers 85B L211 and 85B R626 mut were used to amplify the first 627 nucleotides of the portion of the 85B gene that encodes the mature exoenzyme form of the antigen (corresponding to nucleotides 1 through 627 as numbered in SEQ ID NO:2).
  • the product of this PCR contained the nucleotide substitutions at bases 615, 618, and 621.
  • Primers 85B L612 mut and 85B R102 were used to amplify the nucleotides from base 613 to the end of the 85B gene. Again, this PCR product contained the nucleotide changes at bases 615, 618, and 621. These two PCR products contained 15 bases of overlap (bases 613 through 627).
  • PCR was repeated using the two original PCR products along with primers 85B L211 and 85B R102.
  • the product of this PCR was a full length fragment which contained the nucleotide changes at bases 615, 618, and 621.
  • This PCR product was ligated into the BamHl and EcoRI restriction sites of plasmid pTrcHisB, and transformed into the E. coli strain TOP 10. The bacterial cells were grown to an OD 600 of 0.6, induced with ImM isopropylthio- ⁇ -D-galactoside (IPTG), and harvested after 5 hours of growth.
  • IPTG ImM isopropylthio- ⁇ -D-galactoside
  • a 50 ml culture produced approximately 1.4 mg of recombinant antigen 85B, which is equivalent to 27 mg per liter.
  • a polyacrylamide gel comparing the protein harvested from transformants carrying the wild-type and the mutated antigen 85B genes in pTrcHisB expression plasmids is shown in Figure 1.
  • PCR was the 85A gene (SEQ ID NO:l) amplified from M tuberculosis strain H37Rv and cloned into the pTrcHisB expression vector.
  • the names and sequences of the primers are as follows:
  • GTG-GAG (SEQ ID NO.10). This primer encodes for a BamHl restriction site followed by the first 27 nucleotides (9 codons) of the mature secreted 85 A protein. It includes the mutation noted above to produce the desired change in codon 3. Nucleotide #1 is numbered.
  • 85AR 360 m t ACC-GGT-CGG-CTT-AAC-GTG-ACG-GTT-GGC-CTG- CAG-CCA-CCC (SEQ ID NO.1 1).
  • This antisense primer encodes for nucleotides number 357-319 and contains the mutations noted above to produce the desired changes in codons 113, 115, 117, and 119.
  • Nucleotides 337, 339, 345, 351, and 357 were changed to produce the desired mutant 85A antigen gene and are underlined.
  • 85AL mut 339 C(337)GT-CAC-GTT-AAG-CCG-ACC-GGT-AGC- GCC-GTC-GTC-GGT-CTT (SEQ ID NO.12).
  • This sense primer encodes for nucleotides number 337-375 and contains the mutations noted above to produce the desired changes in codons 113, 115, 1 17, and 119.
  • Nucleotides 337, 339, 345, 351, and 357 were changed to produce the desired mutant 85 A antigen gene and are underlined.
  • 85AR 100 GATGAATTC-CTA-GGC-GCC-CTG-CGG-CGG-GCC-CGG (SEQ ID NO.13). This is an antisense primer containing an EcoRl restriction site followed by the stop codon and the last 7 codons (numbers 288-295) of the 85A gene.
  • the primers 85 A L mut2 and 85AR360 mut were used to amplify the first 357 bases of the mutant 85A gene.
  • the primers 85AL mut 339 and 85AR 100 were used to amplify the last 548 bases of the mutant 85A gene. These two products were purified on a low-melt agarose gel. A final PCR was then preformed using these two PCR products with the primers 85AL mut 339 and 85AR 100. The product from this PCR was the desired 85A mutant gene.
  • This product was digested with BamHl and EcoRI, and ligated into pTrcHisB.
  • This plasmid was transformed into the Top 10 strain of E. coli. Expression was induced with IPTG and the recombinant antigen 85 A protein was harvested and purified as previously described.
  • a polyacrylamide gel comparing the protein harvested from transformants carrying the wild-type (15-20 mg per liter) and the mutated (> 60 mg per liter) antigen 85A genes in pTrcHisB expression plasmids is shown in Figure 2.
  • Codons which may have the greatest adverse effect on the production of recombinant proteins in E. coli include AGG, AGA, ATA, CGA, CTA, CGG, CTT, CTC, GGG, and GGA. Except for CGA, each of these codons is found in one or more of the antigen 85 genes. The replacement of these codons should result in an increased yield of recombinant antigen 85 when the genes are expressed in E. coli.
  • NAME SPRATT, Gwendolyn D.
  • MOLECULE TYPE DNA (genomic)
  • MOLECULE TYPE DNA (genomic)
  • CAGCAGTTCA TCTACGCCGG CTCGCTGTCG GCCCTGCTGG ACCCCTCTCA GGGGATGGGG 480
  • MOLECULE TYPE DNA (genomic)
  • MOLECULE TYPE DNA (genomic)
  • MOLECULE TYPE DNA (genomic)
  • CAGCAGTTCA TCTACGCCGG CTCGCTGTCG GCCCTGCTGG ACCCCTCTCA GGGGATGGGG 480 CCTAGCCTGA TCGGCCTCGC GATGGGTGAC GCCGGCGGTT ACAAGGCCGC AGACATGTGG 540
  • MOLECULE TYPE DNA (oligonucleotide)
  • MOLECULE TYPE DNA (oligonucleotide)
  • MOLECULE TYPE DNA (oligonucleotide)
  • MOLECULE TYPE DNA (oligonucleotide)
  • SEQUENCE DESCRIPTION SEQ ID NO : 9 :
  • MOLECULE TYPE DNA (oligonucleotide)
  • MOLECULE TYPE DNA (oligonucleotide)
  • MOLECULE TYPE DNA (oligonucleotide)
  • MOLECULE TYPE DNA (oligonucleotide)
  • SEQUENCE DESCRIPTION SEQ ID NO: 13: GATGAATTCC TAGGCGCCCT GCGGCGGGCC CGG 33

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Abstract

The invention provides a compound comprising a nucleic acid encoding an 85 antigen of Mycobacterium, wherein at least one codon of the nucleic acid encoding the 85 antigen is altered whereby expression of the 85 antigen in an expression system is increased over expression in the same expression system of a nucleic acid having a wild-type codon at the same position as the altered codon. Specifically, the invention provides an isolated nucleic acid encoding a protein of Mycobacterium comprising at least one codon altered to increase expression of the nucleic acid, wherein the codon is selected from the group consisting of AGG, AGA, ATA, CGA, CTA, CGG, CTT, CTC, GGG, and GGA and an isolated nucleic acid encoding an 85 antigen of Mycobacterium comprising at least one codon altered to increase expression of the nucleic acid, wherein the codon is selected from the group consisting of AGG, AGA, ATA, CTA, CGC, CTT, CTC, GGG, and GGA. Also provided is an improved method of producing a Mycobacterium protein in a host cell comprising altering a codon of a nucleic acid encoding the Mycobacterium protein so that the altered codon of the nucleic acid is one preferred by the host and introducing the nucleic acid containing the altered codon into the host, whereby the host expresses the nucleic acid thereby producing the Mycobacterium protein.

Description

SYNTHETIC GENES FOR RECOMBINANT MYCOBACTERIUM PROTEINS
BACKGROUND OF THE INVENTION This work was supported by National Institutes of Health Grants AI35250 and AI37871. The government has certain rights in the invention. FIELD OF THE INVENTION
Tuberculosis is the world's leading cause of death from a single infectious agent. An estimated one-third of the world's population, 1.7 billion people, are infected with tuberculosis.
The most effective method of controlling many infectious diseases has been through vaccine development. The only currently-available vaccine for tuberculosis is the live-attenuated BCG (Bacille Calmette-Guerin) vaccine, derived from a live strain of Mycobacterium bovis attenuated through serial in vitro passage. First administered to humans in 1921, many BCG vaccines have been subsequently derived from the original strain. These strains vary in growth characteristics, associated reactogenicity, and ability to induce positive purified protein derivative (PPD) skin test responses in vaccinees. Analysis of previous efficacy trials indicate that immunization with a BCG vaccine confers about 75% protection from miliary disease in infants and children but less than 50% protection from pulmonary tuberculosis, with the overall efficacy varying widely from ineffective to 80% effective. Efficacy rates have also varied with the vaccine strains ~ the vaccines that confer greater degrees of protection have been reported to induce the most adverse reactions.
An additional concern regarding BCG involves the safety of the vaccine. Local swelling and pustule formation are common complications, and lymphadenopathy, skeletal infections, and visceral granulomas in apparently healthy individuals have been described. Recently, disseminated BCG infections have been reported in patients with congenital and acquired immunodeficiencies. A BCG strain from the blood of a four year old HIV-infected Brazilian child immunized with BCG at birth was recently isolated, which has renewed the concern for the safety of BCG vaccine in HIV-infected persons. {Edwards et al. Ped. Infect. Dis J. 15:836-838, 1996). Because of concerns of vaccine efficacy and safety, a new vaccine against tuberculosis is badly needed.
One alternative to the use of live-attenuated BCG as a vaccine for tuberculosis is to develop a new vaccine based on subunits of M. tuberculosis. A subunit vaccine consisting of one or more mycobacterial antigens has the advantage of eliminating problems associated with live vaccines. The leading candidates for a subunit vaccine include protein antigens that have been shown to be associated with a strong cell- mediated immune response. Persons infected with M. tuberculosis respond to a variety of mycobacterial antigens. Protective immunity appears to involve predominately T cell responses, the production of cytokines, and the activation of macrophages.
Several immunodominant antigens of M. tuberculosis have been identified {Andersen et al. "Proteins and antigens of Mycobacterium tuberculosis" In: Bloom B.R. (ed.), "Tuberculosis: Pathogenesis, Protection, and Control" American Society for Microbiology, Washington, DC. 1994). These include secreted proteins as well as cell- surface proteins. The strong immunogenicity of proteins recovered from broth culture filtrates (i.e., secreted proteins) of M. tuberculosis was reported in 1932 by Seibert & Mundy (Am Rev Tuberc 25:724, 1932). There is a precedent for the use of secreted proteins to make vaccines in that the toxoided extracellular toxins of Clostridium tetani and Corynebacterium diptheriae (tetanus and diptheria toxins) are used to induce antibody-mediated protection against tetanus and diphtheria. Also, the idea that secreted antigens may be an important component of any effective tuberculosis vaccine has been well-established in the tuberculosis literature since at least 1986 (Rook et al. Clin. Exp. Immunol. 63:105-110, 1986, Wiker et al. Int Archs Allergy appl. Immunol. 81:307-314, 1986, Rook GAW. Clin. Exp. Immunol. 69:1-9, 1987, Orme lM. J. Immunol. 138:293-298, 1987, and Collins et al. Infect Immun 56:1260-1266, 1988).
A leading candidate for a subunit vaccine against M. tuberculosis is the antigen 85 complex of proteins. Antigen 85 was described, purified, and recognized as immunogenic by 1965 (Yoneda et al. Amer Rev Resp Dis 92:9-18, 1965). It is quantitatively the most important secreted protein of M. tuberculosis and includes three cross-reactive antigens, 85A, 85B, and 85C, which are encoded by three distinct chromosomal genes. The quantitatively major antigens, 85B and 85A, comprise 35 to 40% of the total extracellular protein harvested from cultures of M. tuberculosis. The 85Ag proteins induce strong cell-mediated immune responses including T lymphocyte proliferation and gamma-interferon production, in animals and in man (De Bruyn et al. Microbial Pathogenesis 2:351-366, 1987; Huygen et al. Scand J Immunol 27:187-194; 1988). Two recent studies have established that immunization with antigen 85B purified directly from M. tuberculosis or with naked DNA encoding antigen 85B confers partial protection against disease following challenge with M. tuberculosis in animal models (Horwitz et al. Proc Natl Acad Sci. 92:1530-1534, 1995 and Huygen et al. Nature Medicine 2:893-898, 1996).
One of the difficulties encountered in attempting to develop an antigen 85-based subunit vaccine for tuberculosis has been the low yield of many M. tuberculosis proteins in E. c o/z-based expression systems. Dale and Patki note that: "Initial attempts to clone and express mycobacterial antigens in Escherichia coli were met with a considerable degree of skepticism. (Dale JW and Patki A. "Mycobacterial gene expression and regulation" pp. 173-198. In: McFadden J (ed.), "Molecular Biology of the Mycobacteria" Surrey University Press, London, 1990). This skepticism, reinforced by frequent failures in attempts to produce recombinant mycobacterial proteins in E. co/t-based systems has led some investigators to abandon these expression systems.
As there are substantial differences in the promoter regions of many mycobacterial and E. coli genes, the strategy of cloning genes behind a strong E. coli promoter has enabled even more recombinant M. tuberculosis proteins to be produced in E. coli. However with some mycobacterial genes the problems in expression have continued despite such efforts. For example, although the gene encoding antigen 85B was originally sequenced and cloned behind a trc promoter in an E. coli overexpression system in 1988, the yield of recombinant 85B production was poor at less than 0.5 mg per liter (Matsuo et al. J Bacteriol 170:3847-3854, 1988). Because of this low expression, published work involving antigen 85 including the recent study which demonstrated that 85B confers partial protective immunity against tuberculosis in guinea pigs generally has required antigen 85 to be purified directly from M. tuberculosis. (Horwitz et al. Proc Natl Acad Sci. 92:1530-1534, 1995). This is an inefficient process, with approximately 150 liters of broth culture containing M. tuberculosis and grown for 2 to 3 weeks required to produce 100 mg of purified antigen 85B. (Horwitz et al. and Harth et al. Infect Immun 64:3038-3047, 1996). A more recent attempt to overexpress the antigen 85 genes behind a stronger T7 promoter was somewhat more promising with yields of 10 to 20 mg per liter reported. (Harth et al). However, to be valuable as a reagent for wide-scale immunization, there needs to be a way to obtain these proteins in a relatively large scale, which necessitates a system for overexpressing the nucleic acids encoding these proteins.
There exists a need, therefore, for an improved method of producing a Mycobacterium protein in a host by overexpressing a nucleic acid encoding that protein. This is necessary in order to be able to produce these proteins in larger quantities than prior methods so that these proteins can realistically provide adequate quantities of antigens for immunization techniques as well as other techniques such as immunodiagnostics. This invention provides this method as well as providing the altered nucleic acids encoding these proteins.
SUMMARY OF THE INVENTION
In accordance with the purpose(s) of this invention, as embodied and broadly described herein, this invention, in one aspect, relates to a compound comprising a nucleic acid encoding an 85 antigen of Mycobacterium, wherein at least one codon of the nucleic acid encoding the 85 antigen is altered whereby expression of the 85 antigen in an expression system is increased over expression in the same expression system of a nucleic acid sequence having a wild-type codon at the same position as the altered codon.
The invention also provides an isolated nucleic acid encoding an 85 antigen of Mycobacterium comprising at least one altered codon which is designed to increase expression of the 85 antigen in an Escherichia coli expression system, wherein the codon is selected from the group consisting of AGG, AGA, ATA, CTA, CGG, CTT, CTC, GGG, and GGA.
The invention also provides an isolated nucleic acid encoding an 85A protein of Mycobacterium tuberculosis comprising at least one altered codon which is selected to increase expression of the 85 A antigen in an Escherichia coli expression system, wherein the codon is selected from the codons consisting of positions 3, 6, 15, 17, 24, 28, 33, 34, 39, 64, 67, 69, 76, 85, 107, 113, 115, 117, 119, 122, 123, 125, 126, 131, 134, 140, 144, 147, 150, 153, 155, 161, 195, 197, 198, 207, 217, 229, 234, 261, 271, 276, 280, 285, 286, 289, 290, and 292.
The invention also provides an isolated nucleic acid encoding an 85B antigen of Mycobacterium tuberculosis comprising at least one altered codon which is selected to increase expression of the 85B antigen in an Escherichia coli expression system, wherein the codon is selected from the codons consisting of positions 3, 5, 8, 15, 30, 33, 34, 39, 64, 65, 67, 68, 69, 72, 74, 109, 113, 117, 125, 126, 130, 131, 135, 140, 150, 155, 158, 160, 161, 166, 182, 183, 184, 193, 194, 198, 201, 206, 207, 212, 219, 224, 225, 229, 249, 258, 261, 271, 280, and 282.
The invention further provides an isolated nucleic acid encoding an 85C antigen oϊ Mycobacterium tuberculosis comprising at least one altered codon which is selected to increase expression of the 85C antigen in an Escherichia coli expression system, wherein the codon is selected from the codons consisting of positions 3, 4, 6, 17, 24, 30, 36, 39, 43, 64, 65, 66, 67, 71, 77, 85, 86, 101, 103, 106, 109, 118, 125, 126, 128, 148, 149, 150, 153, 162, 171, 198, 201, 206, 215, 216, 219, 224, 232, 241, 249, 252, 258, 260, 261, 263, 265, 272, 282, 286, 287, and 291.
The examples and strategy described herein for increasing the production of recombinant antigen 85 is not limited to E. coli but can be applied to other bacterial organisms, including Bacillus subtilis, Salmonella, humans and other mammals.
The invention therefore further provides an isolated nucleic acid encoding an 85 antigen of Mycobacterium tuberculosis comprising at least one altered codon which is selected to increase expression of the 85 antigen in a mammalian or mammalian-derived expression system.
The invention also provides an improved method of producing a Mycobacterium protein in a host cell comprising altering a codon of a nucleic acid encoding the Mycobacterium protein so that the codon of the altered nucleic acid is one preferred by the host and introducing the nucleic acid containing the altered codon into the host, whereby the host expresses the nucleic acid thereby producing the Mycobacterium protein.
The invention also provides an isolated nucleic acid encoding a protein of Mycobacterium comprising at least one altered codon which is designed to increase expression of the protein in an Escherichia coli expression system, wherein the codon is selected from the group consisting of AGG, AGA, ATA, CGA, CTA, CGG, CTT, CTC, GGG, and GGA.
Additional advantages of the invention will be set forth in part in the description which follows, and in part will be apparent from the description, or may be learned by practice of the invention. The advantages of the invention will be realized and attained by means of the elements and combinations particularly pointed out in the appended claims. It is to be understood that both the foregoing general description and the following detailed description are exemplary and explanatory only and are not restrictive of the invention, as claimed.
The accompanying figures, which are incorporated in and constitute a part of this specification, illustrate several embodiments of the invention and together with the description, serve to explain the principles of the invention.
Throughout this application, various publications are referenced. The disclosure of these publications in their entireties are hereby incorporated by reference into this application to more fully describe the state of the art to which this application pertains.
BRIEF DESCRIPTION OF THE DRAWINGS
Figure 1 shows a coomasie blue-stained polyacrylamide gel of recombinant antigen 85B recovered from 50 ml of broth containing E. coli transformed with wild-type and mutant 85B genes. Five one ml fractions were eluted off the nickel resin affinity column. As ten μl of each fraction were applied to a lane, the protein on the gel corresponds to that harvested from 0.5 ml of the original broth culture. Figure 2 shows a coomasie blue-stained PAGE gel of recombinant antigen 85 A recovered from E. coli containing the wild-type and mutant 85A genes. Lane numbers represent the fractions eluted off the nickel resin affinity column, and the protein on the gel corresponds to that harvested from 0.5 ml of the original broth culture.
DETAILED DESCRIPTION OF THE INVENTION
The present invention may be understood more readily by reference to the following detailed description of the preferred embodiments of the invention and the Example included therein and to the Figures and their previous and following description.
Before the present compounds and methods are disclosed and described, it is to be understood that this invention is not limited to specific nucleic acids, specific proteins, or specific methods, as such may, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only and is not intended to be limiting.
It must be noted that, as used in the specification and the appended claims, the singular forms "a," "an," and "the" include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to "a protein" includes multiple copies of the protein and can also include more than one particular species of molecule.
In one aspect, the invention relates to a compound comprising a nucleic acid encoding an 85 antigen oϊ Mycobacterium, wherein at least one codon of the nucleic acid encoding the 85 antigen is altered whereby expression of the 85 antigen in an expression system is increased over expression in the same expression system of a nucleic acid sequence having a wild-type codon at the same position as the altered codon. The term "altered" is used herein to describe changing the primary sequence of the nucleic acid from a particular codon to a synonymous codon. Because of the degeneracy of the genetic code, certain amino acids are designated by more than one nucleic acid triplet. The codon CGG, for example, is one of 6 possible codons coding for the amino acid arginine. This codon can be "altered" to one of the remaining five codons coding for arginine. The expression of the particular gene, therefore, can be maximized by determining which codons, when altered from their wild-type sequence to a synonymous codon, result in increased expression of the gene.
A "gene" refers to the entire portion of DNA that is involved in the synthesis of a particular protein. This includes a structural region including a coding region of the nucleic acid which begins at the 5' end of the translational start codon (usually ATG) and extends to the stop codon (TAG, TGA, or TAA) at the 3' end. The gene may also contain a promoter region which is usually located upstream of the start codon of the structural region, as well as other regulatory regions such as a transcriptional terminator.
Expression refers to the transcription and translation of a gene to yield the encoded protein, in particular a Mycobacterium protein. The synthetic nucleic acids of the present invention are expressed at a higher level in a particular expression system, E. coli for example, than the corresponding wild-type nucleic acids. One of ordinary skill in the art will appreciate that expression of nucleic acids containing altered codons in a particular expression system should be compared to the expression of the wild-type nucleic acids using the same regulatory sequences, the promoter for example, and the same type of host cells. It will also be apparent that analogous means of accessing the level of expression of the nucleic acids should also be used for any comparisons.
The structural region of the gene encoding a particular protein can be from one type of organism; a particular Mycobacterium for example. In one embodiment of the present invention, the Mycobacterium from which a nucleic acid encoding an 85 antigen is derived, wherein at least one codon of the nucleic acid encoding the 85 antigen is altered whereby expression of the 85 antigen in an expression system is increased over expression in the same expression system of a nucleic acid sequence having a wild-type codon at the same position as the altered codon can be Mycobacterium tuberculosis. Alternatively, the Mycobacterium can be Mycobacterium bovis. Alternatively, the Mycobacterium can be Mycobacterium africanum. Alternatively, the Mycobacterium can be Mycobacterium leprae. There are many other Mycobacterium species to which the present invention relates. These Mycobacterium species include Mycobacterium agr, Mycobacterium aichiense, Mycobacterium asiaticum, Mycobacterium aurum, Mycobacterium avium, Mycobacterium avium-intracellulare, Mycobacterium celatum, Mycobacterium chelonae, Mycobacterium chitae, Mycobacterium chlorophenolicum, Mycobacterium chlorophenolicus, Mycobacterium chubuense, Mycobacterium coηfluentis, Mycobacterium cookii, Mycobacterium diernhoferi, Mycobacterium duvalii, Mycobacterium fallax, Mycobacterium farcinogenes, Mycobacterium flavescens, ycobacterium fortuitum, Mycobacterium gadium, Mycobacterium gastri, Mycobacterium genavense, Mycobacterium geneveuse, Mycobacterium gilvum, Mycobacterium gordonae, Mycobacterium habana, Mycobacterium haemophilum, Mycobacterium hiberniae, Mycobacterium interjectum, Mycobacterium intermedium, Mycobacterium intracellulare, Mycobacterium kansaii, Mycobacterium kansasii, Mycobacterium komossense, Mycobacterium lufu, Mycobacterium malmoense, Mycobacterium marinum, Mycobacterium microti, Mycobacterium neoaurum, Mycobacterium nonchromogenicum, Mycobacterium obuense, Mycobacterium paratuberculosis, Mycobacterium phlei, Mycobacterium pulveris, Mycobacterium rhodesiae, Mycobacterium scrofulaceum, Mycobacterium senegalense, Mycobacterium shimoidei, Mycobacterium simiae, Mycobacterium smegmatis, Mycobacterium sphagni, Mycobacterium szulgai, Mycobacterium terrae, Mycobacterium thermoresistible, Mycobacterium triviale, Mycobacterium tuberculosis, Mycobacterium ulcerans, Mycobacterium vaccae, and Mycobacterium xenopi.
Alternatively, the structural region may comprise sequences from a plurality of organisms, such as different species oϊ Mycobacterium, or organisms of different genera, such as E. coli and Mycobacterium for example. One skilled in the art will appreciate where a protein from Mycobacterium is to be expressed in an organism other than a Mycobacterium, such as E. coli, one can substitute particular E. coli sequences such as a 5' untranslated region for the corresponding Mycobacterium sequences to design a nucleic acid for expression in E. coli. In this manner, for example, the expressed nucleic acid could contain a coding region corresponding to the Mycobacterium protein and a leader region containing an E. coli ribosome binding region.
The Mycobacterium sequence can be a monocistronic sequence or a polycistronic sequence. Where the Mycobacterium sequence is monocistronic, the leader and the trailer can be from Mycobacterium or another organism. Where the Mycobacterium sequence is polycistronic, in addition to the leader and the trailer being either from Mycobacterium or another organism, the intercistronic sequence can also be from either Mycobacterium or another organism.
The structural region can also be from more than one type oϊ Mycobacterium. For example, fusion proteins can be constructed using standard techniques such as gene cloning or gene synthesis to construct a nucleic acid encoding a hybrid protein. In this manner, one skilled in the art can design a nucleic acid encoding a hybrid 85 antigen which may be a hybrid between 85A and 85B antigens, a hybrid between 85B and 85C antigens, a hybrid between 85A and 85C antigens, or a hybrid between 85A, 85B, and 85C antigens.
The structural gene may also contain one or more modifications in sequences other than the protein coding regions which could affect the biological activity or the chemical structure of the expression product, the rate of expression or the manner of expression control. Such modifications include, but are not limited to, mutations, insertions, deletions and substitutions of one or more nucleotides.
The 85 antigen oϊ Mycobacterium comprises three different proteins; the 85A antigen, the 85B antigen, and the 85C antigen, which are set forth in the Sequence Listing as SEQ ID NO: 1 , SEQ ID NO: 2, and SEQ ID NO:3, respectfully. In another embodiment of the present invention, the nucleic acid sequence encoding an 85 antigen of Mycobacterium wherein at least one codon of the nucleic acid encoding the 85 antigen is altered whereby expression of the 85 antigen in an expression system is increased over expression in the same expression system of a nucleic acid sequence having a wild-type codon at the same position as the altered codon is selected from the group consisting of 85A antigen, 85B antigen, and 85C antigen.
In a presently preferred embodiment of the present invention, the compound comprising a nucleic acid encoding an 85 antigen oϊ Mycobacterium wherein at least one codon of the nucleic acid encoding the 85 antigen is altered whereby expression of the 85 antigen in an expression system is increased over expression in the same expression system of a nucleic acid having a wild-type codon at the same position as the altered codon comprises the nucleic acid encoding the 85A antigen and the altered codon is selected from the group consisting of positions 3, 113, 115, 117, and 119.
In another embodiment of the present invention, the nucleic acid comprises the nucleic acid encoding the 85B antigen and the altered codon is selected from the group consisting of positions 3, 5, 206, 207, 224, and 225.
In another embodiment of the present invention, the nucleic acid comprises the nucleic acid encoding the 85B antigen and the altered codon is selected from the group consisting of positions 3, 5, 113, 206, and 207.
In another embodiment of the present invention, the nucleic acid comprises the nucleic acid encoding the 85C antigen and the altered codon is selected from the group consisting of positions 3, 4, 6, 101, 103, 109, and 224.
In another embodiment of the present invention, the nucleic acid comprises the nucleic acid encoding the 85A antigen and the altered codon is selected from the group consisting of positions 3, 6, 15, 17, 24, 28, 33, 34, 39, 64, 67, 69, 76, 85, 107, 113, 115, 117, 119, 122, 123, 125, 126, 131, 134, 140, 144, 147, 150, 153, 155, 161, 195, 197, 198, 207, 217, 229, 234, 261, 271, 276, 280, 285, 286, 289, 290, and 292. In another embodiment of the present invention, the nucleic acid comprises the nucleic acid encoding the 85B antigen and the altered codon is selected from the group consisting of positions 3, 5, 8, 15, 30, 33, 34, 39, 64, 65, 67, 68, 69, 72, 74, 109, 113, 117, 125, 126, 130, 131, 135, 140, 150, 155, 158, 160, 161, 166, 182, 183, 184, 193, 194, 198, 201, 206, 207, 212, 219, 224, 225, 229, 249, 258, 261, 271, 280, and 282. In another embodiment of the present invention, the nucleic acid comprises the nucleic acid encoding the 85C antigen and the altered codon is selected from the group consisting of positions 3, 4, 6, 17, 24, 30, 36, 39, 43, 64, 65, 66, 67, 71, 77, 85, 86, 101, 103, 106, 109, 118, 125, 126, 128, 148, 149, 150, 153, 162, 171, 198, 201, 206, 215, 216, 219, 224, 232, 241, 249, 252, 258, 260, 261, 263, 265, 272, 282, 286, 287, and 291.
In another embodiment, the nucleic acid encodes a Mycobacterium tuberculosis or a. Mycobacterium bovis 85 A antigen and the nucleic acid comprises at least one altered codon selected from the group consisting of positions 3, 113, 115, 117, and 119. In another embodiment, the nucleic acid encodes a Mycobacterium tuberculosis or a Mycobacterium bovis 85A antigen and the nucleic acid comprises at least two altered codons selected from the group consisting of positions 3, 113, 115, 117, and 119. In another embodiment, the nucleic acid encodes a. Mycobacterium tuberculosis or a Mycobacterium bovis 85A antigen and the nucleic acid comprises at least three altered codons selected from the group consisting of positions 3, 113, 115, 117, and 119. In another embodiment, the nucleic acid encodes a Mycobacterium tuberculosis or a Mycobacterium bovis 85A antigen and the nucleic acid comprises at least four altered codons selected from the group consisting of positions 3, 113, 115, 117, and 119. In another embodiment, the nucleic acid encodes a Mycobacterium tuberculosis or a Mycobacterium bovis 85A antigen and the nucleic acid comprises five altered codons wherein the codons are at positions 3, 113, 115, 117, and 119. In another embodiment, the nucleic acid encodes a Mycobacterium tuberculosis or a Mycobacterium bovis 85B antigen and the nucleic acid comprises at least one altered codon selected from the group consisting of positions 3, 5, 206, 207, 224, and 225. In another embodiment, the nucleic acid encodes a Mycobacterium tuberculosis or a Mycobacterium bovis 85B antigen and the nucleic acid comprises at least two altered codons selected from the group consisting of positions 3, 5, 206, 207, 224, and 225. In another embodiment, the nucleic acid encodes a Mycobacterium tuberculosis or a Mycobacterium bovis 85B antigen and the nucleic acid comprises at least three altered codons selected from the group consisting of positions 3, 5, 206, 207, 224, and 225. In another embodiment, the nucleic acid encodes a Mycobacterium tuberculosis or a Mycobacterium bovis 85B antigen and the nucleic acid comprises at least four altered codons selected from the group consisting of positions 3, 5, 206, 207, 224, and 225. In another embodiment, the nucleic acid encodes a Mycobacterium tuberculosis or a Mycobacterium bovis 85B antigen and the nucleic acid comprises at least five altered codons selected from the group consisting of positions 3, 5, 206, 207, 224, and 225. In another embodiment, the nucleic acid encodes a Mycobacterium tuberculosis or a Mycobacterium bovis 85B antigen and the nucleic acid comprises six altered codons wherein the codons are at positions 3, 5, 206, 207, 224, and 225. In another embodiment, the nucleic acid encodes a Mycobacterium 85B antigen and the nucleic acid comprises at least one altered codon selected from the group consisting of positions 3, 5, 113, 206, and 207. In another embodiment, the nucleic acid encodes a Mycobacterium 85B antigen and the nucleic acid comprises at least two altered codons selected from the group consisting of positions 3, 5, 113, 206, and 207. In another embodiment, the nucleic acid encodes a Mycobacterium 85B antigen and the nucleic acid comprises at least three altered codons selected from the group consisting of positions 3, 5, 113, 206, and 207. In another embodiment, the nucleic acid encodes a Mycobacterium 85B antigen and the nucleic acid comprises at least four altered codons selected from the group consisting of positions 3, 5, 113, 206, and 207. In yet another embodiment, the nucleic acid encodes a Mycobacterium 85B antigen and the nucleic acid comprises five altered codons wherein the codons are at positions 3, 5, 113, 206, and 207.
One skilled in the art will recognize that the codon numbering used herein corresponds to the most favorable alignment of the 85 antigen genes. For example, the codon at position 26 in SEQ ID NO.1-5 is TTC and the codon at position 39 in these same sequences is CTC despite the fact that SEQ ID NO.3 is six nucleotides shorter than SEQ ID NO. 1, SEQ ID NO.2, SEQ ID NO.4, and SEQ ID NO.5 in this same region. The six nucleotides may therefore be represented in a sequence alignment as a six bas gap; however the above-discussed CTC codon in SEQ ID NO.3 aligns with the other sequences at their codon position 39 and is referenced herein as codon 39, not codon 37.
Alternatively, only specific amino acid codons oϊ a Mycobacterium protein are altered. Accordingly, the present invention provides an isolated nucleic acid encoding a protein oϊ Mycobacterium comprising at least one codon altered to increase expression of the nucleic acid wherein the codon is selected from the group consisting of AGG, AGA, ATA, CGA, CTA, CGG, CTT, CTC, GGG, and GGA.
Specifically, the codons AGG, CGG, CGA, and AGA in a Mycobacterium protein can be altered to CGT or CGC. Additionally, the codon ATA in a Mycobacterium protein can be altered to ATT or ATC. Additionally, the codons CTT, CTA, and CTC in a Mycobacterium protein can be altered to CTG. Additionally, the codon GGG and GGA in a Mycobacterium protein can be altered to GGT or GGC.
The nucleic acids encoding a Mycobacterium 85 antigen as described in the Example contained herein do not contain the arginine codon CGA. Accordingly, the present invention also specifically provides an isolated nucleic acid encoding an 85 antigen oϊ Mycobacterium comprising at least one codon altered to increase expression of the nucleic acid wherein the codon is selected from the group consisting of AGG, AGA, ATA, CTA, CGG, CTT, CTC, GGG, and GGA.
The wild-type nucleic acids encoding a Mycobacterium 85 A antigen, an 85B antigen, and an 85C antigen, have the specific nucleic acid sequences disclosed herein as SEQ ID NO: 1, SEQ ID NO:2, and SEQ ID NO:3, respectfully. Therefore these nucleic acids can be altered at specific codon locations rather than altered at specific codon sequences. Accordingly, the present invention provides an isolated nucleic acid encoding an 85 A protein oϊ Mycobacterium tuberculosis or Mycobacterium bovis comprising at least one codon altered to increase expression of the nucleic acid wherein the codon is selected from the codons consisting of positions 3, 6, 15, 17, 24, 28, 33, 34, 39, 64, 67, 69, 76, 85, 107, 113, 115, 117, 119, 122, 123, 125, 126, 131, 134, 140, 144, 147, 150, 153, 155, 161, 195, 197, 198, 207, 217, 229, 234, 261, 271, 276, 280, 285, 286, 289, 290, and 292.
Additionally, the present invention provides an isolated nucleic acid encoding an 85B antigen oϊ Mycobacterium tuberculosis ox Mycobacterium bovis comprising at least one codon altered to increase expression of the nucleic acid wherein the codon is selected from the codons consisting of positions 3, 5, 8, 15, 30, 33, 34, 39, 64, 65, 67, 68, 69, 72, 74, 109, 113, 117, 125, 126, 130, 131, 135, 140, 150, 155, 158, 160, 161, 166, 182, 183, 184, 193, 194, 198, 201, 206, 207, 212, 219, 224, 225, 229, 249, 258, 261, 271, 280, and 282.
Even further, the present invention provides an isolated nucleic acid encoding an
85C antigen oϊ Mycobacterium tuberculosis or Mycobacterium bovis comprising at least one codon altered to increase expression of the nucleic acid wherein the codon is selected from the codons consisting of positions 3, 4, 6, 17, 24, 30, 36, 39, 43, 64, 65, 66, 67, 71, 77, 85, 86, 101, 103, 106, 109, 118, 125, 126, 128, 148, 149, 150, 153, 162, 171, 198, 201, 206, 215, 216, 219, 224, 232, 241, 249, 252, 258, 260, 261, 263, 265, 272, 282, 286, 287, and 291.
Where the expression system is not based on E. coli, the codons altered to increase expression of a nucleic acid encoding a Mycobacterium protein can also differ. Accordingly, the present invention provides an isolated nucleic acid encoding a protein oϊ Mycobacterium comprising at least one codon altered to increase expression of the nucleic acid in a mammalian or mammalian-derived expression system wherein the codon is selected from the group consisting of GCG, CGT, CGA, GGT, ATA, TTA, CTA, TTG, CTT, CCG, TCG, AGT, TCA, TCT, ACG, GTA, and GTT. Specifically, the codon GCG in a Mycobacterium protein can be altered to GCC, GCT, or GCA. Additionally, the codons CGT and CGA in a Mycobacterium protein can be altered to AGG, AGA, CGG, or CGC. Additionally, the codon GGT in a Mycobacterium protein can be altered to GGC, GGA, or GGG. Additionally, the codon ATA in a Mycobacterium protein can be altered to ATT or ATC. Additionally, the codons TTA, CTA, TTG, and CTT in a Mycobacterium protein can be altered to CTG or CTC. Additionally, the codon CCG in a Mycobacterium protein can be altered to CCC, CCT, or CCA. Additionally, the codons TCG, AGT, TCA, and TCT in a Mycobacterium protein can be altered to AGC or TCC. Additionally, the codon ACG in a Mycobacterium protein can be altered to ACC, ACA, or ACT. Additionally, the codons GTA and GTT in a Mycobacterium protein can be altered to GTG or GTC.
In a specific embodiment, the present invention also provides an isolated nucleic acid encoding an 85 A protein oϊ Mycobacterium tuberculosis or Mycobacterium bovis comprising at least one codon altered to increase expression of the nucleic acid in a mammalian or mammalian-derived expression system wherein the codon is selected from the codons consisting of positions 4, 6, 7, 14, 15, 16, 17, 20, 28, 29, 30, 33, 44, 56, 57, 64, 67, 71, 73, 76, 91, 106, 124, 125, 126, 130, 131, 132, 134, 136, 146, 148, 150, 153, 158, 160, 167, 169, 182, 186, 187, 193, 195, 216, 217, 220, 225, 247, 257, 260, 261, 269, 283, 285, and 291.
In another specific embodiment, the present invention also provides an isolated nucleic acid encoding an 85B protein oϊ Mycobacterium tuberculosis or Mycobacterium bovis comprising at least one codon altered to increase expression of the nucleic acid in a mammalian or mammalian-derived expression system wherein the codon is selected from the codons consisting of positions 4, 7, 14, 15, 16, 17, 24, 29, 33, 35, 36, 56, 57, 64, 67, 68, 71, 85, 88, 106, 109, 125, 126, 130, 131, 135, 148, 150, 156, 167, 169, 173, 181, 183, 184, 186, 194, 207, 209, 216, 219, 221, 224, 229, 233, 234, 243, 247, 257, 261, 276, 280, 281, and 282. In yet another specific embodiment, the present invention also provides an isolated nucleic acid encoding an 85C protein oϊ Mycobacterium tuberculosis or Mycobacterium bovis comprising at least one codon altered to increase expression of the nucleic acid in a mammalian or mammalian-derived expression system wherein the codon is selected from the codons consisting of positions 2, 5, 6, 16, 17, 31, 35, 41, 56, 64, 66, 67, 77, 86, 101, 109, 117, 121, 122, 124, 125, 126, 128, 130, 132, 137, 140, 144, 147, 148, 149, 150, 155, 161, 162, 167, 171, 173, 181, 182, 186, 195, 212, 224, 225, 226, 245, 248, 257, 263, 285, 288, 293, and 294.
One skilled in the art will appreciate that there are numerous techniques available by which one can obtain a nucleic acid sequence encoding an 85 antigen of Mycobacterium wherein at least one codon of the nucleic acid encoding the 85 antigen is altered whereby expression of the 85 antigen in an expression system is increased over expression in the same expression system of a nucleic acid sequence having a wild-type codon at the same position as the altered codon. One method of obtaining the nucleic acid is by constructing the nucleic acid by synthesizing a recombinant DNA molecule. For example, oligonucleotide synthesis procedures are routine in the art and oligonucleotides coding for a particular protein or regulatory region are readily obtainable through automated DNA synthesis. A nucleic acid for one strand of a double-stranded molecule can be synthesized and hybridized to its complementary strand. One can design these oligonucleotides such that the resulting double-stranded molecule has either internal restriction sites or appropriate 5' or 3' overhangs at the termini for cloning into an appropriate vector. Double-stranded molecules coding for relatively large proteins or regulatory regions can be synthesized by first constructing several different double-stranded molecules that code for particular regions of the protein or regulatory region, followed by ligating these DNA molecules together. For example, Cunningham, et al, "Receptor and Antibody Epitopes in Human Growth Hormone Identified by Homolog-Scanning Mutagenesis," Science, Vol. 243, pp. 1330- 1336 (1989), have constructed a synthetic gene encoding the human growth hormone gene by first constructing overlapping and complementary synthetic oligonucleotides and ligating these fragments together. See also, Ferretti, et al, Proc. Nat. Acad. Sci. 82:599-603 (1986), wherein synthesis of a 1057 base pair synthetic bovine rhodopsin gene from synthetic oligonucleotides is disclosed. Once the appropriate DNA molecule is synthesized, this DNA can be cloned downstream of an appropriate promoter. Techniques such as this are routine in the art and are well documented.
An example of another method of obtaining a nucleic acid encoding an 85 antigen oϊ Mycobacterium wherein at least one codon of the nucleic acid encoding the 85 antigen is altered whereby expression of the 85 antigen in an expression system is increased over expression in the same expression system of a nucleic acid sequence having a wild-type codon at the same position as the altered codon is to isolate the corresponding wild-type nucleic acid from the organism in which it is found and clone it in an appropriate vector. For example, a DNA or cDNA library can be constructed and screened for the presence of the nucleic acid of interest. Methods of constructing and screening such libraries are well known in the art and kits for performing the construction and screening steps are commercially available (for example, Stratagene Cloning Systems, La Jolla, CA). Once isolated, the nucleic acid can be directly cloned into an appropriate vector, or if necessary, be modified to facilitate the subsequent cloning steps. Such modification steps are routine, an example of which is the addition of oligonucleotide linkers which contain restriction sites to the termini of the nucleic acid. General methods are set forth in Sambrook et al., "Molecular Cloning, a
Laboratory Manual," Cold Spring Harbor Laboratory Press (1989). Once isolated, one can alter selected codons using standard laboratory techniques, PCR for example.
Yet another example of a method of obtaining a nucleic acid encoding an 85 antigen oϊ Mycobacterium wherein at least one codon of the nucleic acid encoding the 85 antigen is altered whereby expression of the 85 antigen in an expression system is increased over expression in the same expression system of a nucleic acid sequence having a wild-type codon at the same position as the altered codon is to amplify the corresponding wild-type nucleic acid from the nucleic acids found within a host organism containing the wild-type nucleic acid and clone the amplified nucleic acid in an appropriate vector. One skilled in the art will appreciate that the amplification step may be combined with a mutation step, using primers not completely homologous to the target nucleic acid for example, to simultaneously amplify the nucleic acid and alter specific positions of the nucleic acid. An example of this method of constructing a nucleic acid sequence encoding an 85 antigen oϊ Mycobacterium wherein at least one codon of the nucleic acid encoding the 85 antigen is altered is contained and described in the Example contained herein, where the wild-type nucleic acids were previously available, but the desired mutant nucleic acids were generated from this wild-type template using PCR.
The nucleic acid sequence encoding an 85 antigen oϊ Mycobacterium wherein at least one codon of the nucleic acid encoding the 85 antigen is altered whereby expression of the 85 antigen in an expression system is increased over expression in the same expression system of a nucleic acid sequence having a wild-type codon at the same position as the altered codon may be introduced into a host cell for expression of that nucleic acid by any number of methods that are familiar to one skilled in the art. For example, DNA may be introduced into a host by calcium chloride transformation of the host, by protoplast transformation, by prokaryotic transduction, electroporation, or via the use of phage vectors. (Sambrook et al.) Other methods more commonly used for other hosts include calcium phosphate transfection, liposome delivery, DEAE-dextran mediated transfection, lipofectin-mediated transfection, injection, or viral vectors.
One skilled in the art will also appreciate that any number of host cells may be used for expressing the nucleic acids of the present invention. For example, and as described in the Example contained herein, E. coli may be used as the host expression system. Other hosts can alternatively be used for the expression system for the nucleic acids and methods of the present invention. For example, other bacterial hosts such as Bacillus can be used as the host for expressing the nucleic acid. Other hosts may also be used as the expression host. For example, yeast hosts, plant hosts, mammalian hosts, insect hosts, and other various viral hosts may be used. These types of host expression systems are well known in the art. For an example of a plant expression, see U.S. Patent No. 5,380,831, where a synthetic insecticidal gene was constructed, cloned into a plant expression vector, and introduced into plant cells where the gene was expressed and the subsequent protein produced. The expression system used to express the nucleic acids of the present invention can comprise a human or human-derived expression system.
In addition to various hosts that may be used to express the nucleic acids of the present invention, there are also various vectors that may be used to express a nucleic acid by the particular host. For example, there are numerous E. coli vectors that are available for expressing nucleic acids. One example of an E. coli vector used for expressing a nucleic acid wherein at least one codon of the nucleic acid encoding the 85 antigen is altered whereby expression of the 85 antigen in the E. coli expression system is increased over expression in the same E. coli expression system of a nucleic acid sequence having a wild-type codon at the same position as the altered codon is the vector pTrcHisB.
One skilled in the art will recognize that various vectors have more or less applicability depending on the particular host. One example of a particular technique for introducing nucleic acids into a particular host is the use of retroviral vector systems which can package a recombinant retroviral genome. (See e.g., Pastan et al. "A retrovirus carrying an MDR1 cDNA confers multidrug resistance and polarized expression of P-glycoprotein in MDCK cells." Proc. Nat. Acad. Sci. 85:4486 (1988) and Miller et al "Redesign of retrovirus packaging cell lines to avoid recombination leading to helper virus production." Mol. Cell Biol. 6:2895 (1986)). The produced recombinant retrovirus can then be used to infect and thereby deliver to the infected cells a nucleic acid sequence encoding an 85 antigen oϊ Mycobacterium wherein at least one codon of the nucleic acid encoding the 85 antigen is altered to increase expression of the 85 antigen. The exact method of introducing the altered nucleic acid into mammalian cells is, of course, not limited to the use of retroviral vectors. Other techniques are widely available for this procedure including the use of adenoviral vectors (Mitani et al. "Transduction of human bone marrow by adenoviral vector." Human Gene Therapy 5:941-948 (1994)), adenoassociated viral vectors (Goodman et al. "Recombinant adenoassociated virus-mediated gene transfer into hematopoietic progenitor cells." Blood 84:1492-1500 (1994)), lentiviral vectors (Naidini et al. "In vivo gene delivery and stable transduction of nondividing cells by a lentiviral vector." Science 272:263-267 (1996)), pseudotyped retroviral vectors (Agrawal et al. "Cell-cycle kinetics and VSV-G pseudotyped retrovirus mediated gene transfer in blood-derived CD34+ cells." Exp. Hematol. 24:738-747 (1996)), and physical transfection techniques (Schwarzenberger et al. "Targeted gene transfer to human hematopoietic progenitor cell lines through the c-ldt receptor. " Blood 87:472-478 (1996)). This invention can be used in conjunction with any of these or other commonly used gene transfer methods.
The various vectors and hosts used to express the nucleic acids of the present invention may be used to express the nucleic acids in culture. For example, a vector comprising a nucleic acid provided by the present invention may be introduced into a tissue culture cell line, such as COS cells, and expressed whereby the nucleic acid is expressed in culture.
Alternatively, various vectors and hosts used to express the nucleic acids of the present invention may be used to express the nucleic acids in vivo. For example, a vector comprising a nucleic acid provided by the present invention may be introduced into cells of the eukaryotic host which is being administered a nucleic acid provided by the present invention to provide a polypeptide for purposes of eliciting an immune response by the host. The nucleic acids provided by the present invention may, therefore, be used as templates for the production of proteins which may be used to vaccinate a subject against Mycobacterium infection since the primary sequences of the polypeptides encoded by the nucleic acids provided by the present invention are identical to the corresponding wild-type Mycobacterium polypeptides. One skilled in the art will recognize there are also various techniques for introducing the nucleic acids comprising the nucleic acids provided by the present invention into host cells in vivo, such as, but not limited to, liposome delivery and "naked DNA" techniques.
In another embodiment, the present invention also provides a Mycobacterium
85B antigen wherein at least 20mg of this protein are produced per liter of cell culture using an expression system described herein. Thus, a composition comprising at least 20mg oϊ a Mycobacterium antigen obtained per liter of the cell culture is provided. Furthermore, similar high expression levels oϊ the Mycobacterium 85A antigen and the Mycobacterium 85C antigen using an expression systems described herein are provided. Similar compositions of 85A and 85C antigens are also provided.
The proteins provided by the present invention may also be used to treat an existing Mycobacterial infection, to provide a vaccine, as well as provide a Mycobacterium protein that can be used as a therapeutic. Additionally, the proteins may be reintroduced into a Mycobacterium which may be used as a whole organism vaccine or therapeutic.
Further, various vectors and hosts used to express the nucleic acids of the present invention may be used to express the nucleic acids ex vivo. For example, a vector comprising a nucleic acid provided by the present invention may be introduced into cells of the host which have, previous to the introduction of the nucleic acid, been removed from the host. The cells of the host comprising those cells containing the introduced nucleic acid can then be used to express the nucleic acid and therefore produce the polypeptide in culture, or the cells of the host comprising those cells containing the introduced nucleic acid can then be reintroduced into the host and thereby used to express the nucleic acid and therefore produce the polypeptide in vivo.
One skilled in the art will appreciate that the codons selected to be altered to increase the expression of the nucleic acid relative to the wild-type nucleic acid will vary depending on which expression system is used to express the nucleic acid. For example, the codon preference for E. coli is different than the codon preference for mammals. Therefore one can design a nucleic acid with an altered codon(s) for expression in one expression system which may be different from a nucleic acid with an altered codon(s) in a different expression system while both nucleic acids encode the same polypeptide.
In another aspect, therefore, the invention relates to a method of producing a
Mycobacterium protein in a host cell comprising altering a codon of a nucleic acid encoding the Mycobacterium protein so that the altered codon of the nucleic acid is one preferred by the host and introducing the nucleic acid containing the altered codon into the host, whereby the host expresses the nucleic acid thereby producing the Mycobacterium protein.
The nucleic acid encoding a Mycobacterium protein in which a codon is altered to be one preferred by the host may comprise any Mycobacterium nucleic acid encoding any Mycobacterium protein. In a presently preferred embodiment of the invention, the nucleic acid used in the improved method of producing a Mycobacterium protein encodes an 85 antigen oϊ Mycobacterium selected from the group consisting of 85 A antigen, 85B antigen, and 85C antigen.
In another aspect of the present invention, the nucleic acid used in the improved method of producing a Mycobacterium protein encodes an 85 antigen which is a hybrid 85 antigen selected from the group consisting of an 85A/85B hybrid, an 85A/85C hybrid, an 85B/85C hybrid, and an 85/A/85B/85C hybrid.
In the improved method of producing a Mycobacterium protein in a host cell comprising altering a codon of a nucleic acid encoding the Mycobacterium protein, the particular Mycobacterium is selected from the group consisting oϊ Mycobacterium tuberculosis, Mycobacterium bovis, Mycobacterium africanum, and Mycobacterium leprae. Therefore the improved method described herein may be used to produce different Mycobacterium proteins for various applications. For example, a Mycobacterium protein derived from Mycobacterium tuberculosis may be used to elicit an immune response from a subject. This particular utility therefore may be directed toward immunizing a subject from subsequent infection by Mycobacterium tuberculosis. Alternatively, a nucleic acid from Mycobacterium leprae may be used in the improved method to produce a protein encoded by that nucleic acid for a similar use. Additionally, a nucleic acid from Mycobacterium bovis may be used in the improved method to produce a protein encoded by that nucleic acid to elicit an immune response from a bovine subject and a human subject. One skilled in the art will recognize that there is a wide range of cross-reactivity between different Mycobacterium species such that an antigen from one species can be used to elicit an immune response in a subject that is infected with a different species of Mycobacterium. For example, an 85 antigen from Mycobacterium bovis can be used to elicit an immune response in a human subject. Other organisms that can be infected by Mycobacterium species, and therefore can be administered proteins provided by the present invention, include but are not limited to elephants, buffalo, goats, bovine, sheep, camels, pigs, horses, cats, dogs, birds, asses, mules, monkeys, and a large assortment of rodents. (Thoen CO. "Tuberculosis in wild and domestic mammals" pp. 157-162. In: Bloom BR (ed.), Tuberculosis: Pathogenesis, Protection, and Control, ASM Press, Washington, DC. 1994).
The nucleic acid oϊ Mycobacterium used in the method described herein can encode any number of proteins. For example, the nucleic acid can encode a Mycobacterium virulence factor, or a gene or genes involved in cellular metabolism or cellular biosynthesis. The following list is a partial list of other genes of tuberculosis orM. bovis that may be altered to increase expression of those nucleic acids:
M. tuberculosislbovis gene for: GenoBase identifiers: MtrA (mtrA gene) MT01971
MtrB (mtrB gene) MT 14909
10 k antigen MT 10KA01 , MT 1 OKAG
RNA polymerase beta subunit C (rpoC gene) MT11452
RNA polymerase beta subunit B (rpoB gene) MT 12205 14 kDa antigen MT14KA
65 kDa heat-shock protein MT 17957
32 kDa protein MT32KD, MT32KPI1
34 K protein MT34KAA
35 kDa protein MT35KD A 38 K protein MT38K
3-dehydroquinate synthase and 3-dehydroquinase MT3DEHQ antigen 84 MTAG84 antigen 88 MTAG88
L-alanine dehydrogenase MTALADH
19 kDa antigen MTANT19 aroA MTARO
AT 103 gene for tuberculin-related peptide MTAT103
ATI OS gene MTAT10S at9s gene MTAT9S biotin carboxyl carrier protein MTBCARBCP diaminopimelate decarboxylase (lysA) MTCAPDC heat-shock protein genes (dnaK, grpE, and dnaJ) MTDNAGRP, MTDNAJ esatό (early secreted antigen of tuberculosis) MTESAT6 dihydrofolate reductase MTFOLA groE gene for KCS and 10-kDa products MTGROEOP DNA gyrase A and B subunits MTGYRAB mce gene MTMCE
MPT70 protein MTMPT70
MPT40 protein and phospholipase C MTMTP40, MTMTP40A mycocerosic acid synthase MTMYACSYN antigen B MTPABA
DNA polymerase MTPOLA re DNA MTREGX
MPT64 MTRNAMPT ribosomal protein S12 MTRPS12A ribonucleotide reductase Rl subunit MTRSOR
65 kDa antigen (cell wall protein a) MTTCWPA thymidilate synthase MTTHYA elongation factor TU MTTUF orotidine-5'-monophosphate decarboxylase (uraA) MB072 20 kD antigen protein MB19KD alcohol dehydrogenase MBADH ornithine carbamoyltransferase MBARGF meso-diaminopimelate biosynthetic pathway (dapB) MBDAPB immunogenic protein MPB57 MBMPB57, MBBPB57A antigen MPB70 MBMPBAA ribosomal protein L7/L 12 MBRPLL ribosomal protein S12 and S7 MBRPS127X putative host cell receptor binding protein S46909
30S ribosomal protein S65565
The protein produced by the method described herein can be used in a number of other applications as well. The proteins can also be used as reagents in applications such as immunodiagnostic assays, for example to detect the presence of
Figure imgf000029_0001
antigens. The proteins can also be used in therapeutic applications, such as to generate antibodies to the protein which can be administered to a subject infected with an organism whose genome encodes the protein.
The following example is put forth so as to provide those of ordinary skill in the art with a complete disclosure and description of how the attenuated prokaryotes claimed herein are made and evaluated, and demonstrates the methods of the present invention, and is intended to be purely exemplary of the invention and is not intended to limit the scope of what the inventors regard as their invention. Efforts have been made to ensure accuracy with respect to numbers (e.g., amounts, temperature, etc.) but some errors and deviations should be accounted for. Unless indicated otherwise, parts are parts by weight, temperature is in °C and pressure is at or near atmospheric.
EXAMPLE
Mutations to the wild-type antigen 85 genes that increase recombinant antigen 85 production in E. coli:
Using the known published gene sequences for the three 85 antigen proteins of
Mycobacterium tuberculosis (85 A (SEQ ID NO: l), 85B (SEQ ID NO:2), and 85C (SEQ ID NO:3)), oligonucleotide primers were constructed and used to amplify via the polymerase chain reaction (PCR) each of the three wild-type 85 antigen genes individually. The 5' oligonucleotides contained an EcoRI endonuclease restriction site, while the 3' oligonucleotides contained a BamW. restriction site to facilitate subsequent cloning. After successful PCR amplification of the individual genes, the PCR products were cleaved with BamHΪ and EcoRI and cloned into the BamHl and EcόRl sites of the plasmid pBCSK+ (Stratagene, La Jolla CA), and then transformed into E. coli strain DH5α. Plasmid DNA was isolated from these transformants.
The expression plasmid pTrcHisB (Invitrogen) contains the trp and lac promoter upstream to the multiple cloning site and a sequence that encodes an N-terminal fusion peptide. This sequence also codes for an ATG initiation codon, six histidine residues in series that function as a metal binding domain in the translated protein, and an enterokinase cleavage recognition site. This expression plasmid was digested with BamHl and EcoRI, which have single restriction sites in the multiple cloning site of pTrcHisB and the 85 antigen genes then individually ligated in-frame between these sites. Each recombinant expression plasmid therefore contained a powerful promoter followed by an initiation codon, the six histidines, the enterokinase cleavage site, one of the three individual 85 antigen genes, and a stop codon. Six such plasmids were constructed, one for each of the following proteins: BCG 85A, BCG 85C, M. tuberculosis H37Rv 85 A, M. tuberculosis H37Rv 85B, and tuberculosis H37Rv 85C.
These recombinant plasmids were then transformed into the E. coli strain Top 10, (Invitrogen). The transformed strains were grown to mid-log phase, and expression was induced by the addition of IPTG (isopropylthio-β-D-galactoside). After allowing the cultures to grow an additional 1-5 hours, the cells were harvested by centrifugation. Proteins were extracted using either a denaturing protocol using guanidine and urea, or a non-denaturing protocol using phosphate buffers while repeatedly freezing, thawing, and sonicating the pellet suspension and the extraction solution then placed on a nickel resin column. In the denaturing protocol, the column was repeatedly washed with an increasingly acidic urea/phosphate solution to gradually remove unwanted proteins. The recombinant 85 antigen was then eluted by further lowering the pH. In the non- denaturing protocol, the column was repeatedly washed with phosphate buffer. Proteins were then eluted from the nickel resin column by increasing concentrations of imidazole, which displaces the histidine from the nickel column.
Although each of the three wild-type 85 antigen genes was expressed in E. coli using the pTrcHisB vector, we observed antigen-specific differences in the amounts of recombinant protein recovered. Specifically, comparisons of the recovery of the recombinant 85 antigens when each was harvested on the same day under the same growth conditions showed differential expression with: recombinant antigen 85A, about 16 mg/liter; recombinant antigen 85B, only 0.5 mg per liter; and recombinant antigen 85C, about 7 mg/liter. These differences were present despite the fact that 85A, 85B, and 85C are highly homologous, and the similarity of the growth curves of the E. coli strains producing each antigen made it unlikely that the poor expression of 85B could be attributed it to a toxic effect on E. coli that was not exhibited by the antigens 85A and 85C. Furthermore, as each of the genes had been cloned downstream of the same E. coli promoter (i.e. Ire), the transcription of each should be comparable. We therefore theorized that the difference in production might be attributable to the efficiency with which each mRNA was translated.
Construction of a mutant 85B gene
As a first test of this hypothesis, we identified a region of the 85B gene containing two adjacent unpreferred codons, i.e., CGG-CTA at codon positions 206- 207 of the antigen 85B gene sequence. CGG encodes for arginine (R) and CTA encodes for leucine (L). CGG is a nonpreferred codon that is used by E. coli only 10% of the time that arginine is encoded. In contrast, CGT (CGU) and CGC are preferred codons for arginine, encoding for 37% and 38% of E. coli arginine respectively.
Similarly, CTA is an unpreferred codon for leucine, encoding for only 4% of __. coli leucine. Other codons for leucine are CTG, CTT, CTC, TTG, and TTA which encode for 50%), 11%), 10%, 12%, and 13% of E. coli leucine respectively. We decided first to change the codons CCG-CTA into CGT-CTG. Whereas this substitution in the nucleotide sequence of the gene does not alter the amino acid sequence of the protein, it might enhance the production of recombinant 85B in E. coli. We also changed the preceding ACC codon into ACG to add a Mlul endonuclease restriction site while still encoding for the amino acid threonine. This added restriction site produced a rapid means to screen for transformants that contain the desired mutations. In summary, nucleotides ACC-CCG-CTA (amino acids 205-207) were changed to ACG-CGT-CTG.
Site-directed mutagenesis was performed using PCR. The DNA template for the PCR reaction was the previously described 85B gene in the pTrcHisB expression vector. The names and sequences of the primers were as follows:
[a] 85B L211: GATGGATCCA-T(1)TC-TCC-CGG-CCG-GGG-CTG-CCG- GTC (SEQ ID NO.6). This primer encodes for a BamHl restriction site followed by the first 24 nucleotides (8 codons; nucleotides 1-24) corresponding to the mature exoenzyme form of the 85B antigen. Nucleotide #1 is numbered.
[b] 85B R626 mut: AAC-CCA-CAG-ACG-CGT-GTT-GTT-TGC-GAC-CAG- CTT-GGG-GAT- CTG (SEQ ID NO.7). This is an antisense primer encoding for nucleotides number 627 through 586, but containing the mutations noted above to produce the desired codon changes and to introduce the Mlul restriction site. Nucleotides 621, 618, and 615 were changed to produce the mutant 85B antigen gene and are underlined.
[c] 85B L612 mut: A(613)CG-CGT-CTG-TGG-GTT-TAT-TGC-GGG-AAC-
GGC-ACC- CCG (SEQ ID NO.8). This is a sense primer from nucleotide 613 through 648 that also contains the mutations noted above to produce the desired codon changes and to introduce theλ_7./I restriction site. Nucleotides 615, 618, and 621 were changed to produce the mutant 85B antigen gene and are underlined. [d] 85B R102: GATGAATTC-TCA-GCC-GGC-GCC-TAA-CGA-ACT-CTG- CAG (SEQ ID NO.9). This is an antisense primer containing an EcoRI restriction site followed by a stop codon and the last 24 nucleotides of the 85B gene.
Primers 85B L211 and 85B R626 mut were used to amplify the first 627 nucleotides of the portion of the 85B gene that encodes the mature exoenzyme form of the antigen (corresponding to nucleotides 1 through 627 as numbered in SEQ ID NO:2). The product of this PCR contained the nucleotide substitutions at bases 615, 618, and 621. Primers 85B L612 mut and 85B R102 were used to amplify the nucleotides from base 613 to the end of the 85B gene. Again, this PCR product contained the nucleotide changes at bases 615, 618, and 621. These two PCR products contained 15 bases of overlap (bases 613 through 627). This area of overlap allowed the two products to actually function as primers for each other. PCR was repeated using the two original PCR products along with primers 85B L211 and 85B R102. The product of this PCR was a full length fragment which contained the nucleotide changes at bases 615, 618, and 621. This PCR product was ligated into the BamHl and EcoRI restriction sites of plasmid pTrcHisB, and transformed into the E. coli strain TOP 10. The bacterial cells were grown to an OD600 of 0.6, induced with ImM isopropylthio-β-D-galactoside (IPTG), and harvested after 5 hours of growth. A 50 ml culture produced approximately 1.4 mg of recombinant antigen 85B, which is equivalent to 27 mg per liter. A polyacrylamide gel comparing the protein harvested from transformants carrying the wild-type and the mutated antigen 85B genes in pTrcHisB expression plasmids is shown in Figure 1.
This data demonstrates the increased production of the recombinant antigen 85B by approximately 50-fold by changing only three codons in the wild-type gene without altering the amino acid sequence of the recombinant protein. Further experiments also tested additional altered codons in the 85B antigen gene at positions 3, 5, 224, and 225, which even further increased expression of this gene.
Construction of the mutant 85A gene The following codon changes were made in the 85A gene: [1] CGT (arginine) was substituted for CGG (arginine) in codon 3 (nucleotides 7-9); [2] CGT (arginine) was substituted for AGG (arginine) in codon 113 (nucleotides 337-339); [3] GTT (valine) was substituted for GTC (valine) in codon 115 (nucleotides 343-345); [4] CCG (proline) was substituted for CCC (proline) in codon 117 (nucleotides 349-351); and [5] GGT (glycine) was substituted for GGA (glycine) in codon 119 (nucleotides 355- 357). These substitutions increased the yield of 85A from about 15 to greater than 60 mg per liter of culture.
Site-directed mutagenesis was again performed using PCR. The template for the
PCR was the 85A gene (SEQ ID NO:l) amplified from M tuberculosis strain H37Rv and cloned into the pTrcHisB expression vector. The names and sequences of the primers are as follows:
[a] 85AL mut 2: GATGGATCCA-T(1)TT-TCC-CGT-CCG-GGC-TTG-CCG-
GTG-GAG (SEQ ID NO.10). This primer encodes for a BamHl restriction site followed by the first 27 nucleotides (9 codons) of the mature secreted 85 A protein. It includes the mutation noted above to produce the desired change in codon 3. Nucleotide #1 is numbered.
[b] 85AR 360 m t: ACC-GGT-CGG-CTT-AAC-GTG-ACG-GTT-GGC-CTG- CAG-CCA-CCC (SEQ ID NO.1 1). This antisense primer encodes for nucleotides number 357-319 and contains the mutations noted above to produce the desired changes in codons 113, 115, 117, and 119. Nucleotides 337, 339, 345, 351, and 357 were changed to produce the desired mutant 85A antigen gene and are underlined.
[c] 85AL mut 339: C(337)GT-CAC-GTT-AAG-CCG-ACC-GGT-AGC- GCC-GTC-GTC-GGT-CTT (SEQ ID NO.12). This sense primer encodes for nucleotides number 337-375 and contains the mutations noted above to produce the desired changes in codons 113, 115, 1 17, and 119. Nucleotides 337, 339, 345, 351, and 357 were changed to produce the desired mutant 85 A antigen gene and are underlined. [d] 85AR 100: GATGAATTC-CTA-GGC-GCC-CTG-CGG-CGG-GCC-CGG (SEQ ID NO.13). This is an antisense primer containing an EcoRl restriction site followed by the stop codon and the last 7 codons (numbers 288-295) of the 85A gene.
Using the pTrcHisB plasmid containing the 85 A gene from tuberculosis strain H37Rv as the template, the primers 85 A L mut2 and 85AR360 mut were used to amplify the first 357 bases of the mutant 85A gene. The primers 85AL mut 339 and 85AR 100 were used to amplify the last 548 bases of the mutant 85A gene. These two products were purified on a low-melt agarose gel. A final PCR was then preformed using these two PCR products with the primers 85AL mut 339 and 85AR 100. The product from this PCR was the desired 85A mutant gene. This product was digested with BamHl and EcoRI, and ligated into pTrcHisB. This plasmid was transformed into the Top 10 strain of E. coli. Expression was induced with IPTG and the recombinant antigen 85 A protein was harvested and purified as previously described. A polyacrylamide gel comparing the protein harvested from transformants carrying the wild-type (15-20 mg per liter) and the mutated (> 60 mg per liter) antigen 85A genes in pTrcHisB expression plasmids is shown in Figure 2.
In summary, in the examples given above, we have shown the profound effect on recombinant antigen production of replacing adjacent CGG-CTA codons in the 85B gene. We also have shown that the replacement of a CGG, ATA, and other codons in the antigen 85 A gene similarly has a marked effect on antigen production. Based on the results of these experiments, altering codons at positions 3, 4, 6, 101, 103, 109, and 224 of the 85C antigen gene oϊ Mycobacterium tuberculosis should also result in increased yields of that antigen. The methods and experiments described herein can readily be applied to the 85 antigen genes oϊ Mycobacterium bovis, such as 85A (SEQ ID NO.4) and 85B (SEQ ID NO.5).
Codons which may have the greatest adverse effect on the production of recombinant proteins in E. coli include AGG, AGA, ATA, CGA, CTA, CGG, CTT, CTC, GGG, and GGA. Except for CGA, each of these codons is found in one or more of the antigen 85 genes. The replacement of these codons should result in an increased yield of recombinant antigen 85 when the genes are expressed in E. coli.
SEQUENCE LISTING
(1) GENERAL INFORMATION:
(i) APPLICANT: Vanderbilt University
(ii) TITLE OF INVENTION: SYNTHETIC GENES FOR RECOMBINANT MYCOBACTERIUM PROTEINS
(iii) NUMBER OF SEQUENCES: 13
(iv) CORRESPONDENCE ADDRESS:
(A) ADDRESSEE: Vanderbilt University
(B) STREET: 305 Kirkland Hall
(C) CITY: Nashville
(D) STATE: Tennessee
(E) COUNTRY: USA
(F) ZIP: 37240
(v) COMPUTER READABLE FORM:
(A) MEDIUM TYPE: Floppy disk
(B) COMPUTER: IBM PC compatible
(C) OPERATING SYSTEM: PC-DOS/MS-DOS
(D) SOFTWARE: Patentln Release #1.0, Version #1.30
(vi) CURRENT APPLICATION DATA:
(A) APPLICATION NUMBER: TO BE ASSIGNED
(B) FILING DATE: HEREWITH
(C) CLASSIFICATION:
(vii) PRIOR APPLICATION DATA:
(A) APPLICATION NUMBER: US 08/797,301
(B) FILING DATE: 07-FEB-1997
(C) CLASSIFICATION:
(viii) ATTORNEY/AGENT INFORMATION:
(A) NAME: SPRATT, Gwendolyn D.
(B) REGISTRATION NUMBER: 36,016
(C) REFERENCE/DOCKET NUMBER: 22000.0055/P
(2) INFORMATION FOR SEQ ID NO : 1 :
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 885 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS : double
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: DNA (genomic)
(xi) SEQUENCE DESCRIPTION: SEQ ID NO : 1 :
TTTTCCCGGC CGGGCTTGCC GGTGGAGTAC CTGCAGGTGC CGTCGCCGTC GATGGGCCGT 60
GACATCAAGG TCCAATTCCA AAGTGGTGGT GCCAACTCGC CCGCCCTGTA CCTGCTCGAC 120
GGCCTGCGCG CGCAGGACGA CTTCAGCGGC TGGGACATCA ACACCCCGGC GTTCGAGTGG 180
TACGACCAGT CGGGCCTGTC GGTGGTCATG CCGGTGGGTG GCCAGTCAAG CTTCTACTCC 240
GACTGGTACC AGCCCGCCTG CGGCAAGGCC GGTTGCCAGA CTTACAAGTG GGAGACCTTC 300
CTGACCAGCG AGCTGCCGGG GTGGCTGCAG GCCAACAGGC ACGTCAAGCC CACCGGAAGC 360 GCCGTCGTCG GTCTTTCGAT GGCTGCTTCT TCGGCGCTGA CGCTGGCGAT CTATCACCCC 420
CAGCAGTTCG TCTACGCGGG AGCGATGTCG GGCCTGTTGG ACCCCTCCCA GGCGATGGGT 480
CCCACCCTGA TCGGCCTGGC GATGGGTGAC GCTGGCGGCT ACAAGGCCTC CGACATGTGG 540
GGCCCGAAGG AGGACCCGGC GTGGCAGCGC AACGACCCGC TGTTGAACGT CGGGAAGCTG 600
ATCGCCAACA ACACCCGCGT CTGGGTGTAC TGCGGCAACG GCAAGCCGTC GGATCTGGGT 660
GGCAACAACC TGCCGGCCAA GTTCCTCGAG GGCTTCGTGC GGACCAGCAA CATCAAGTTC 720
CAAGACGCCT ACAACGCCGG TGGCGGCCAC AACGGCGTGT TCGACTTCCC GGACAGCGGT 780
ACGCACAGCT GGGAGTACTG GGGCGCGCAG CTCAACGCTA TGAAGCCCGA CCTGCAACGG 840
CACTGGGTGC CACGCCCAAC ACCGGGCCCG CCGCAGGGCG CCTAG 885
(2) INFORMATION FOR SEQ ID NO : 2 :
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 858 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS : double
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: DNA (genomic)
(xi) SEQUENCE DESCRIPTION: SEQ ID NO : 2 :
TTCTCCCGGC CGGGGCTGCC GGTCGAGTAC CTGCAGGTGC CGTCGCCGTC GATGGGCCGC 60
GACATCAAGG TTCAGTTCCA GAGCGGTGGG AACAACTCAC CTGCGGTTTA TCTGCTCGAC 120
GGCCTGCGCG CCCAAGACGA CTACAACGGC TGGGATATCA ACACCCCGGC GTTCGAGTGG 180
TACTACCAGT CGGGACTGTC GATAGTCATG CCGGTCGGCG GGCAGTCCAG CTTCTACAGC 240
GACTGGTACA GCCCGGCCTG CGGTAAGGCT GGCTGCCAGA CTTACAAGTG GGAAACCTTC 300
CTGACCAGCG AGCTGCCGCA ATGGTTGTCC GCCAACAGGG CCGTGAAGCC CACCGGCAGC 360
GCTGCAATCG GCTTGTCGAT GGCCGGCTCG TCGGCAATGA TCTTGGCCGC CTACCACCCC 420
CAGCAGTTCA TCTACGCCGG CTCGCTGTCG GCCCTGCTGG ACCCCTCTCA GGGGATGGGG 480
CCTAGCCTGA TCGGCCTCGC GATGGGTGAC GCCGGCGGTT ACAAGGCCGC AGACATGTGG 540
GGTCCCTCGA GTGACCCGGC ATGGGAGCGC AACGACCCTA CGCAGCAGAT CCCCAAGCTG 600
GTCGCAAACA ACACCCGGCT ATGGGTTTAT TGCGGGAACG GCACCCCGAA CGAGTTGGGC 660
GGTGCCAACA TACCCGCCGA GTTCTTGGAG AACTTCGTTC GTAGCAGCAA CCTGAAGTTC 720
CAGGATGCGT ACAACGCCGC GGGCGGGCAC AACGCCGTGT TCAACTTCCC GCCCAACGGC 780
ACGCACAGCT GGGAGTACTG GGGCGCTCAG CTCAACGCCA TGAAGGGTGA CCTGCAGAGT 840
TCGTTAGGCG CCGGCTGA 858
(2) INFORMATION FOR SEQ ID NO : 3 :
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 885 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: DNA (genomic)
(xi) SEQUENCE DESCRIPTION: SEQ ID NO : 3
TTCTCTAGGC CCGGTCTTCC AGTGGAATAT CTGCAGGTGC CATCCGCGTC GATGGGCCGC 60
GACATCAAGG TCCAGTTCCA GGGCGGCGGA CCGCACGCGG TCTACCTGCT CGACGGTCTG 120
CGGGCCCAGG ATGACTACAA CGGCTGGGAC ATCAACACCC CGGCCTTCGA GGAGTACTAC 180
CAGTCAGGGT TGTCGGTGAT CATGCCCGTG GGCGGCCAAT CCAGTTTCTA CACCGACTGG 240
TATCAGCCCT CGCAGAGCAA CGGCCAGAAC TACACCTACA AGTGGGAGAC CTTCCTTACC 300
AGAGAGATGC CCGCCTGGCT ACAGGCCAAC AAGGGCGTGT CCCCGACAGG CAACGCGGCG 360
GTGGGTCTTT CGATGTCGGG CGGTTCCGCG CTGATCCTGG CCGCGTACTA CCCGCAGCAG 420 TTCCCGTACG CCGCGTCGTT GTCGGGCTTC CTCAACCCGT CCGAGGGCTG GTGGCCGACG 480
CTGATCGGCC TGGCGATGAA CGACTCGGGC GGTTACAACG CCAACAGCAT GTGGGGTCCG 540
TCCAGCGACC CGGCCTGGAA GCGCAACGAC CCAATGGTTC AGATTCCCCG CCTGGTCGCC 600
AACAACACCC GGATCTGGGT GTACTGCGGT AACGGCACAC CCAGCGACCT CGGCGGCGAC 660
AACATACCGG CGAAGTTCCT GGAAGGCCTC ACCCTGCGCA CCAACCAGAC CTTCCGGGAC 720
ACCTACGCGG CCGACGGTGG ACGCAACGGG GTGTTTAACT TCCCGCCCAA CGGAACACAC 780
TCGTGGCCCT ACTGGAACGA GCAGCTGGTC GCCATGAAGG CCGATATCCA GCATGTGCTC 840
AACGGCGCGA CACCCCCGGC CGCCCCTGCT GCGCCGGCCG CCTGA 885
(2) INFORMATION FOR SEQ ID NO:4:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 888 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: DNA (genomic)
(xi) SEQUENCE DESCRIPTION: SEQ ID NO : 4 :
TTTTCCCGGC CGGGCTTGCC GGTGGAGTAC CTGCAGGTGC CGTCGCCGTC GATGGGCCGT 60
GACATCAAGG TCCAATTCCA AAGTGGTGGT GCCAACTCGC CCGCCCTGTA CCTGCTCGAC 120
GGCCTGCGCG CGCAGGACGA CTTCAGCGGC TGGGACATCA ACACCCCGGC GTTCGAGTGG 180
TACGACCAGT CGGGCCTGTC GGTGGTCATG CCGGTGGGTG GCCAGTCAAG CTTCTACTCC 240
GACTGGTACC AGCCCGCCTG CGGCAAGGCC GGTTGCCAGA CTTACAAGTG GGAGACCTTC 300
CTGACCAGCG AGCTGCCGGG GTGGCTGCAG GCCAACAGGC ACGTCAAGCC CACCGGAAGC 360
GCCGTCGTCG GTCTTTCGAT GGCTGCTTCT TCGGCGCTGA CGCTGGCGAT CTATCACCCC 420
CAGCAGTTCG TCTACGCGGG AGCGATGTCG GGCCTGTTGG ACCCCTCCCA GGCGATGGGT 480
CCCACCCTGA TCGGCCTGGC GATGGGTGAC GCTGGCGGCT ACAAGGCCTC CGACATGTGG 540
GGCCCGAAGG AGGACCCGGC GTGGCAGCGC AACGACCCGC TGTTGAACGT CGGGAAGCTG 600
ATCGCCAACA ACACCCGCGT CTGGGTGTAC TGCGGCAACG GCAAGCCGTC GGATCTGGGT 660
GGCAACAACC TGCCGGCCAA GTTCCTCGAG GGCTTCGTGC GGACCAGCAA CATCAAGTTC 720
CAAGACGCCT ACAACGCCGG TGGCGGCCAC AACGGCGTGT TCGACTTCCC GGACAGCGGT 780
ACGCACAGCT GGGAGTACTG GGGGGCGCAG CTCAACGCTA TGAAGCCCGA CCTGCAACGG 840
GCACTGGGTG CCACGCCCAA CACCGGGCCC GCGCCCCAGG GCGCCTAG 888
(2) INFORMATION FOR SEQ ID NO : 5 :
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 858 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: DNA (genomic)
(xi) SEQUENCE DESCRIPTION: SEQ ID NO : 5 :
TTCTCCCGGC CGGGGCTGCC GGTCGAGTAC CTGCAGGTGC CGTCGCCGTC GATGGGCCGC 60
GACATCAAGG TTCAGTTCCA GAGCGGTGGG AACAACTCAC CTGCGGTTTA TCTGCTCGAC 120
GGCCTGCGCG CCCAAGACGA CTACAACGGC TGGGATATCA ACACCCCGGC CTTCGAGGAG 180
TACTACCAGT CAGGGTTGTC GGTGATCATG CCGGTCGGCG GGCAGTCCAG CTTCTACAGC 240
GACTGGTACA GCCCGGCCTG CGGTAAGGCT GGCTGCCAGA CTTACAAGTG GGAAACCCTC 300
CTGACCAGCG AGCTGCCGCA ATGGTTGTCC GCCAACAGGG CCGTGAAGCC CACCGGCAGC 360
GCTGCAATCG GCTTGTCGAT GGCCGGCTCG TCGGCAATGA TCTTGGCCGC CTACCACCCC 420
CAGCAGTTCA TCTACGCCGG CTCGCTGTCG GCCCTGCTGG ACCCCTCTCA GGGGATGGGG 480 CCTAGCCTGA TCGGCCTCGC GATGGGTGAC GCCGGCGGTT ACAAGGCCGC AGACATGTGG 540
GGTCCCTCGA GTGACCCGGC ATGGGAGCGC AACGACCCTA CGCAGCAGAT CCCCAAGCTG 600
GTCGCAAACA ACACCCGGCT ATGGGTTTAT TGCGGGAACG GCACCCCGAA CGAGTTGGGC 660
GGTGCCAACA TACCCGCCGA GTTCTTGGAG AACTTCGTTC GTAGCAGCAA CCTGAAGTTC 720
CAGGATGCGT ACAACGCCGC GGGCGGGCAC AACGCCGTGT TCAACTTCCC GCCCAACGGC 780
ACGCACAGCT GGGAGTACTG GGGCGCTCAG CTCAACGCCA TGAAGGGTGA CCTGCAGAGT 840
TCGTTAGGCG CCGGCTGA 858
(2) INFORMATION FOR SEQ ID NO : 6 :
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 34 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: single
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: DNA (oligonucleotide)
(xi) SEQUENCE DESCRIPTION: SEQ ID NO : 6 :
GATGGATCCA TTCTCCCGGC CGGGGCTGCC GGTC 34
(2) INFORMATION FOR SEQ ID NO : 7 :
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 42 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: single
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: DNA (oligonucleotide)
(xi) SEQUENCE DESCRIPTION: SEQ ID NO : 7 :
AACCCACAGA CGCGTGTTGT TTGCGACCAG CTTGGGGATC TG 42
(2) INFORMATION FOR SEQ ID NO : 8 :
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 36 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: single
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: DNA (oligonucleotide)
(xi) SEQUENCE DESCRIPTION: SEQ ID NO : 8 :
ACGCGTCTGT GGGTTTATTG CGGGAACGGC ACCCCG 36
(2) INFORMATION FOR SEQ ID NO : 9 :
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 36 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: single
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: DNA (oligonucleotide) (xi) SEQUENCE DESCRIPTION: SEQ ID NO : 9 :
GATGAATTCT CAGCCGGCGC CTAACGAACT CTGCAG 36
(2) INFORMATION FOR SEQ ID NO: 10: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 37 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: single
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: DNA (oligonucleotide)
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 10:
GATGGATCCA TTTTCCCGTC CGGGCTTGCC GGTGGAG 37
(2) INFORMATION FOR SEQ ID NO : 11 : (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 39 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: single
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: DNA (oligonucleotide)
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 11:
ACCGGTCGGC TTAACGTGAC GGTTGGCCTG CAGCCACCC 39
(2) INFORMATION FOR SEQ ID NO:12: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 39 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: single
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: DNA (oligonucleotide)
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 12:
CGTCACGTTA AGCCGACCGG TAGCGCCGTC GTCGGTCTT 39
(2) INFORMATION FOR SEQ ID NO: 13: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 33 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: single
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: DNA (oligonucleotide) (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 13: GATGAATTCC TAGGCGCCCT GCGGCGGGCC CGG 33

Claims

What is claimed is:
1. A compound comprising a nucleic acid encoding an 85 antigen of Mycobacterium, wherein at least one codon of the nucleic acid encoding the 85 antigen is altered whereby expression of the 85 antigen in an expression system is increased over expression in the same expression system of a nucleic acid having a wild-type codon at the same position as the altered codon.
2. The compound of claim 1, wherein the Mycobacterium is selected from the group consisting oϊ Mycobacterium tuberculosis, Mycobacterium bovis, Mycobacterium africanum, and Mycobacterium leprae.
3. The compound of claim 1, wherein the nucleic acid encodes 85 A antigen and the altered codon is selected from the group consisting of positions 3, 113, 115, 117, and 119.
4. The compound of claim 1, wherein the nucleic acid encodes 85B antigen and the altered codon is selected from the group consisting of positions 3,
5, 206, 207, 224, and 225.
5. The compound of claim 1, wherein the nucleic acid encodes 85C antigen and the altered codon is selected from the group consisting of positions 3, 4, 6, 101, 103, 109, and 224.
6. The compound of claim 1, wherein the nucleic acid encodes 85 A antigen and the altered codon is selected from the group consisting of positions 3,
6, 15, 17, 24, 28, 33, 34, 39, 64, 67, 69, 76, 85, 107, 113, 115, 117, 119, 122, 123, 125, 126, 131, 134, 140, 144, 147, 150, 153, 155, 161, 195, 197, 198, 207, 217, 229, 234, 261, 271, 276, 280, 285, 286, 289, 290, and 292.
7. The compound of claim 1, wherein the nucleic acid encodes 85B antigen and the altered codon is selected from the group consisting of positions 3, 5, 8, 15, 30, 33, 34, 39, 64, 65, 67, 68, 69, 72, 74, 109, 113, 117, 125, 126, 130, 131, 135, 140, 150, 155, 158, 160, 161, 166, 182, 183, 184, 193, 194, 198, 201, 206, 207, 212, 219, 224, 225, 229, 249, 258, 261, 271, 280, and 282.
8. The compound of claim 1, wherein the nucleic acid encodes 85C antigen and the altered codon is selected from the group consisting of positions 3, 4, 6, 17, 24, 30, 36, 39, 43, 64, 65, 66, 67, 71, 77, 85, 86, 101, 103, 106, 109, 118, 125, 126, 128, 148, 149, 150, 153, 162, 171, 198, 201, 206, 215, 216, 219, 224, 232, 241, 249, 252, 258, 260, 261, 263, 265, 272, 282, 286, 287, and 291.
9. The compound of claim 1, wherein the altered nucleic acid is introduced into cells and expressed by the cells in culture.
10. The compound of claim 1, wherein the altered nucleic acid is introduced into cells and expressed by the cells in vivo.
11. The compound of claim 1, wherein the altered nucleic acid is introduced into cells and expressed by the cells ex vivo.
12. The compound of claim 1, wherein the expression system is selected from the group consisting of a bacterial expression system, a yeast expression system, a plant expression system, a mammalian expression system, an insect expression system, and a viral expression systems.
13. The compound of claim 1, wherein the expression system is an Escherichia coli expression system.
14. The compound of claim 1, wherein the 85 antigen oϊ Mycobacterium encoded by the nucleic acid is a hybrid 85 antigen selected from the group consisting of an 85A 85B hybrid, an 85A/85C hybrid, an 85B/85C hybrid, and an 85/A/85B/85C hybrid.
15. The compound of claim 6, wherein the nucleic acid encodes a Mycobacterium tuberculosis or a Mycobacterium bovis 85 A antigen and wherein the nucleic acid comprises at least one altered codon selected from the group consisting of positions 3, 113, 115, 117, and 119.
16. The compound of claim 6, wherein the nucleic acid encodes a Mycobacterium tuberculosis or a Mycobacterium bovis 85A antigen and wherein the nucleic acid comprises at least two altered codons selected from the group consisting of positions 3, 113, 115, 117, and 119.
17. The compound of claim 6, wherein the nucleic acid encodes a Mycobacterium tuberculosis or a Mycobacterium bovis 85 A antigen and wherein the nucleic acid comprises at least three altered codon selected from the group consisting of positions 3, 113, 115, 117, and 119.
18. The compound of claim 6, wherein the nucleic acid encodes a Mycobacterium tuberculosis or a Mycobacterium bovis 85 A antigen and wherein the nucleic acid comprises at least four altered codon selected from the group consisting of positions 3, 1 13, 115, 117, and 119.
19. The compound of claim 6, wherein the nucleic acid encodes a Mycobacterium tuberculosis or a Mycobacterium bovis 85 A antigen and wherein the nucleic acid comprises five altered codons at positions 3, 113, 115, 117, and 119.
20. The compound of claim 7, wherein the nucleic acid encodes a Mycobacterium tuberculosis or a Mycobacterium bovis 85B antigen and wherein the nucleic acid comprises at least one altered codon selected from the group consisting of positions 3, 5, 206, 207, 224, and 225.
21. The compound of claim 7, wherein the nucleic acid encodes a Mycobacterium tuberculosis or a Mycobacterium bovis 85B antigen and wherein the nucleic acid comprises at least two altered codons selected from the group consisting of positions 3, 5, 206, 207, 224, and 225.
22. The compound of claim 7, wherein the nucleic acid encodes a Mycobacterium tuberculosis or a Mycobacterium bovis 85B antigen and wherein the nucleic acid comprises at least three altered codons selected from the group consisting of positions 3, 5, 206, 207, 224, and 225.
23. The compound of claim 7, wherein the nucleic acid encodes a Mycobacterium tuberculosis or a Mycobacterium bovis 85B antigen and wherein the nucleic acid comprises at least four altered codons selected from the group consisting of positions 3, 5, 206, 207, 224, and 225.
24. The compound of claim 7, wherein the nucleic acid encodes a Mycobacterium tuberculosis or a Mycobacterium bovis 85B antigen and wherein the nucleic acid comprises at least five altered codons selected from the group consisting of positions 3, 5, 206, 207, 224, and 225.
25. The compound of claim 7, wherein the nucleic acid encodes a Mycobacterium tuberculosis or a Mycobacterium bovis 85B antigen and wherein the nucleic acid comprises six altered codons at positions 3, 5, 206, 207, 224, and 225.
26. An isolated nucleic acid encoding a protein oϊ Mycobacterium comprising at least one codon altered to increase expression of the nucleic acid, wherein the codon is selected from the group consisting of AGG, AGA, ATA, CGA, CTA, CGG, CTT, CTC, GGG, and GGA.
27. An isolated nucleic acid encoding an 85 antigen oϊ Mycobacterium comprising at least one codon altered to increase expression of the nucleic acid, wherein the codon is selected from the group consisting of AGG, AGA, ATA, CTA, CGG, CTT, CTC, GGG, and GGA.
28. An isolated nucleic acid encoding an 85A protein oϊ Mycobacterium tuberculosis or Mycobacterium bovis comprising at least one codon altered to increase expression of the nucleic acid, wherein the codon is selected from the codons consisting of positions 3, 6, 15, 17, 24, 28, 33, 34, 39, 64, 67, 69, 76, 85, 107, 113, 115, 117, 119, 122, 123, 125, 126, 131, 134, 140, 144, 147, 150, 153, 155, 161, 195, 197, 198, 207, 217, 229, 234, 261, 271, 276, 280, 285, 286, 289, 290, and 292.
29. An isolated nucleic acid encoding an 85B antigen oϊ Mycobacterium tuberculosis or Mycobacterium bovis comprising at least one codon altered to increase expression of the nucleic acid, wherein the codon is selected from the codons consisting of positions 3, 5, 8, 15, 30, 33, 34, 39, 64, 65, 67, 68, 69, 72, 74, 109, 113, 117, 125, 126, 130, 131, 135, 140, 150, 155, 158, 160, 161, 166, 182, 183, 184, 193, 194, 198, 201, 206, 207, 212, 219, 224, 225, 229, 249, 258, 261, 271, 280, and 282.
30. An isolated nucleic acid encoding an 85C antigen oϊ Mycobacterium tuberculosis or Mycobacterium bovis comprising at least one codon altered to increase expression of the nucleic acid, wherein the codon is selected from the codons consisting of positions 3, 4, 6, 17, 24, 30, 36, 39, 43, 64, 65, 66, 67, 71, 77, 85, 86, 101, 103, 106, 109, 118, 125, 126, 128, 148, 149, 150, 153, 162, 171, 198, 201, 206, 215, 216, 219, 224, 232, 241, 249, 252, 258, 260, 261, 263, 265, 272, 282, 286, 287, and 291.
31. An improved method of producing a Mycobacterium protein in a host cell comprising:
a. altering a codon of a nucleic acid encoding the Mycobacterium protein so that the altered codon of the nucleic acid is one preferred by the host;
b. introducing the nucleic acid containing the altered codon into the host, whereby the host expresses the nucleic acid thereby producing the Mycobacterium protein.
32. The method of claim 31 , wherein the nucleic acid encodes an 85 antigen of Mycobacterium selected from the group consisting of 85A antigen, 85B antigen, and 85C antigen.
33. The method of claim 31, wherein the nucleic acid encodes an 85 antigen of Mycobacterium which is a hybrid 85 antigen selected from the group consisting of an 85A/85B hybrid, an 85A/85C hybrid, an 85B/85C hybrid, and an 85/A 85B/85C hybrid.
34. The method of claim 31 , wherein the Mycobacterium is selected from the group consisting oϊ Mycobacterium tuberculosis, Mycobacterium bovis, Mycobacterium africanum, and Mycobacterium leprae.
35. The method of claim 31, wherein the altered nucleic acid is expressed in culture.
36. The method of claim 31, wherein the altered nucleic acid is expressed in vivo.
37. The method of claim 31, wherein the altered nucleic acid is expressed ex vivo.
PCT/US1998/002341 1997-02-07 1998-02-06 Synthetic genes for recombinant mycobacterium proteins WO1998035029A1 (en)

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