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Nucleic Acids Res. Nov 15, 1996; 24(22): 4420–4449.
PMCID: PMC146264

Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae.

Abstract

The entire genome of the bacterium Mycoplasma pneumoniae M129 has been sequenced. It has a size of 816,394 base pairs with an average G+C content of 40.0 mol%. We predict 677 open reading frames (ORFs) and 39 genes coding for various RNA species. Of the predicted ORFs, 75.9% showed significant similarity to genes/proteins of other organisms while only 9.9% did not reveal any significant similarity to gene sequences in databases. This permitted us tentatively to assign a functional classification to a large number of ORFs and to deduce the biochemical and physiological properties of this bacterium. The reduction of the genome size of M. pneumoniae during its reductive evolution from ancestral bacteria can be explained by the loss of complete anabolic (e.g. no amino acid synthesis) and metabolic pathways. Therefore, M. pneumoniae depends in nature on an obligate parasitic lifestyle which requires the provision of exogenous essential metabolites. All the major classes of cellular processes and metabolic pathways are briefly described. For a number of activities/functions present in M. pneumoniae according to experimental evidence, the corresponding genes could not be identified by similarity search. For instance we failed to identify genes/proteins involved in motility, chemotaxis and management of oxidative stress.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • CHANOCK RM. Mycoplasma pneumoniae: proposed nomenclature for atypical pneumonia organism (Eaton agent). Science. 1963 May 10;140(3567):662–662. [PubMed]
  • Krause DC. Mycoplasma pneumoniae cytadherence: unravelling the tie that binds. Mol Microbiol. 1996 Apr;20(2):247–253. [PubMed]
  • Dybvig K. Mycoplasmal genetics. Annu Rev Microbiol. 1990;44:81–104. [PubMed]
  • Morowitz HJ. The completeness of molecular biology. Isr J Med Sci. 1984 Sep;20(9):750–753. [PubMed]
  • Razin S. Peculiar properties of mycoplasmas: the smallest self-replicating prokaryotes. FEMS Microbiol Lett. 1992 Dec 15;100(1-3):423–431. [PubMed]
  • Peterson SN, Hu PC, Bott KF, Hutchison CA., 3rd A survey of the Mycoplasma genitalium genome by using random sequencing. J Bacteriol. 1993 Dec;175(24):7918–7930. [PMC free article] [PubMed]
  • Fraser CM, Gocayne JD, White O, Adams MD, Clayton RA, Fleischmann RD, Bult CJ, Kerlavage AR, Sutton G, Kelley JM, et al. The minimal gene complement of Mycoplasma genitalium. Science. 1995 Oct 20;270(5235):397–403. [PubMed]
  • Hilbert H, Himmelreich R, Plagens H, Herrmann R. Sequence analysis of 56 kb from the genome of the bacterium Mycoplasma pneumoniae comprising the dnaA region, the atp operon and a cluster of ribosomal protein genes. Nucleic Acids Res. 1996 Feb 15;24(4):628–639. [PMC free article] [PubMed]
  • Bork P, Ouzounis C, Casari G, Schneider R, Sander C, Dolan M, Gilbert W, Gillevet PM. Exploring the Mycoplasma capricolum genome: a minimal cell reveals its physiology. Mol Microbiol. 1995 Jun;16(5):955–967. [PubMed]
  • Inamine JM, Loechel S, Hu PC. Analysis of the nucleotide sequence of the P1 operon of Mycoplasma pneumoniae. Gene. 1988 Dec 15;73(1):175–183. [PubMed]
  • Wenzel R, Herrmann R. Cloning of the complete Mycoplasma pneumoniae genome. Nucleic Acids Res. 1989 Sep 12;17(17):7029–7043. [PMC free article] [PubMed]
  • Su CJ, Chavoya A, Baseman JB. Regions of Mycoplasma pneumoniae cytadhesin P1 structural gene exist as multiple copies. Infect Immun. 1988 Dec;56(12):3157–3161. [PMC free article] [PubMed]
  • Almagor M, Yatziv S, Kahane I. Inhibition of host cell catalase by Mycoplasma pneumoniae: a possible mechanism for cell injury. Infect Immun. 1983 Jul;41(1):251–256. [PMC free article] [PubMed]
  • Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. [PMC free article] [PubMed]
  • Bairoch A, Boeckmann B. The SWISS-PROT protein sequence data bank. Nucleic Acids Res. 1991 Apr 25;19 (Suppl):2247–2249. [PMC free article] [PubMed]
  • Barker WC, George DG, Mewes HW, Pfeiffer F, Tsugita A. The PIR-International databases. Nucleic Acids Res. 1993 Jul 1;21(13):3089–3092. [PMC free article] [PubMed]
  • Pearson WR, Lipman DJ. Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A. 1988 Apr;85(8):2444–2448. [PMC free article] [PubMed]
  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403–410. [PubMed]
  • Bairoch A. PROSITE: a dictionary of sites and patterns in proteins. Nucleic Acids Res. 1992 May 11;20 (Suppl):2013–2018. [PMC free article] [PubMed]
  • Inamine JM, Ho KC, Loechel S, Hu PC. Evidence that UGA is read as a tryptophan codon rather than as a stop codon by Mycoplasma pneumoniae, Mycoplasma genitalium, and Mycoplasma gallisepticum. J Bacteriol. 1990 Jan;172(1):504–506. [PMC free article] [PubMed]
  • Nakai K, Kanehisa M. Expert system for predicting protein localization sites in gram-negative bacteria. Proteins. 1991;11(2):95–110. [PubMed]
  • Proft T, Herrmann R. Identification and characterization of hitherto unknown Mycoplasma pneumoniae proteins. Mol Microbiol. 1994 Jul;13(2):337–348. [PubMed]
  • Proft T, Hilbert H, Layh-Schmitt G, Herrmann R. The proline-rich P65 protein of Mycoplasma pneumoniae is a component of the Triton X-100-insoluble fraction and exhibits size polymorphism in the strains M129 and FH. J Bacteriol. 1995 Jun;177(12):3370–3378. [PMC free article] [PubMed]
  • Razin S, Jacobs E. Mycoplasma adhesion. J Gen Microbiol. 1992 Mar;138(3):407–422. [PubMed]
  • Ruland K, Wenzel R, Herrmann R. Analysis of three different repeated DNA elements present in the P1 operon of Mycoplasma pneumoniae: size, number and distribution on the genome. Nucleic Acids Res. 1990 Nov 11;18(21):6311–6317. [PMC free article] [PubMed]
  • Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty BA, Merrick JM, et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science. 1995 Jul 28;269(5223):496–512. [PubMed]
  • Riley M. Functions of the gene products of Escherichia coli. Microbiol Rev. 1993 Dec;57(4):862–952. [PMC free article] [PubMed]
  • Baker TA, Wickner SH. Genetics and enzymology of DNA replication in Escherichia coli. Annu Rev Genet. 1992;26:447–477. [PubMed]
  • Mills LB, Stanbridge EJ, Sedwick WD, Korn D. Purification and partial characterization of the principal deoxyribonucleic acid polymerase from Mycoplasmatales. J Bacteriol. 1977 Nov;132(2):641–649. [PMC free article] [PubMed]
  • Barnes MH, Tarantino PM, Jr, Spacciapoli P, Brown NC, Yu H, Dybvig K. DNA polymerase III of Mycoplasma pulmonis: isolation and characterization of the enzyme and its structural gene, polC. Mol Microbiol. 1994 Sep;13(5):843–854. [PubMed]
  • Koonin EV, Bork P. Ancient duplication of DNA polymerase inferred from analysis of complete bacterial genomes. Trends Biochem Sci. 1996 Apr;21(4):128–129. [PubMed]
  • Camerini-Otero RD, Hsieh P. Homologous recombination proteins in prokaryotes and eukaryotes. Annu Rev Genet. 1995;29:509–552. [PubMed]
  • Demple B, Harrison L. Repair of oxidative damage to DNA: enzymology and biology. Annu Rev Biochem. 1994;63:915–948. [PubMed]
  • Sancar A, Sancar GB. DNA repair enzymes. Annu Rev Biochem. 1988;57:29–67. [PubMed]
  • Haldenwang WG. The sigma factors of Bacillus subtilis. Microbiol Rev. 1995 Mar;59(1):1–30. [PMC free article] [PubMed]
  • Hyman HC, Gafny R, Glaser G, Razin S. Promoter of the Mycoplasma pneumoniae rRNA operon. J Bacteriol. 1988 Jul;170(7):3262–3268. [PMC free article] [PubMed]
  • Moran CP, Jr, Lang N, LeGrice SF, Lee G, Stephens M, Sonenshein AL, Pero J, Losick R. Nucleotide sequences that signal the initiation of transcription and translation in Bacillus subtilis. Mol Gen Genet. 1982;186(3):339–346. [PubMed]
  • Das A. Control of transcription termination by RNA-binding proteins. Annu Rev Biochem. 1993;62:893–930. [PubMed]
  • Hecker M, Schumann W, Völker U. Heat-shock and general stress response in Bacillus subtilis. Mol Microbiol. 1996 Feb;19(3):417–428. [PubMed]
  • Parkinson JS. Signal transduction schemes of bacteria. Cell. 1993 Jun 4;73(5):857–871. [PubMed]
  • Simoneau P, Li CM, Loechel S, Wenzel R, Herrmann R, Hu PC. Codon reading scheme in Mycoplasma pneumoniae revealed by the analysis of the complete set of tRNA genes. Nucleic Acids Res. 1993 Oct 25;21(21):4967–4974. [PMC free article] [PubMed]
  • Breton R, Watson D, Yaguchi M, Lapointe J. Glutamyl-tRNA synthetases of Bacillus subtilis 168T and of Bacillus stearothermophilus. Cloning and sequencing of the gltX genes and comparison with other aminoacyl-tRNA synthetases. J Biol Chem. 1990 Oct 25;265(30):18248–18255. [PubMed]
  • Shine J, Dalgarno L. The 3'-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites. Proc Natl Acad Sci U S A. 1974 Apr;71(4):1342–1346. [PMC free article] [PubMed]
  • Shapiro L. Protein localization and asymmetry in the bacterial cell. Cell. 1993 Jun 4;73(5):841–855. [PubMed]
  • Proft T, Hilbert H, Plagens H, Herrmann R. The P200 protein of Mycoplasma pneumoniae shows common features with the cytadherence-associated proteins HMW1 and HMW3. Gene. 1996 May 24;171(1):79–82. [PubMed]
  • Kahane I, Tucker S, Leith DK, Morrison-Plummer J, Baseman JB. Detection of the major adhesin P1 in triton shells of virulent Mycoplasma pneumoniae. Infect Immun. 1985 Dec;50(3):944–946. [PMC free article] [PubMed]
  • Su CJ, Chavoya A, Dallo SF, Baseman JB. Sequence divergency of the cytadhesin gene of Mycoplasma pneumoniae. Infect Immun. 1990 Aug;58(8):2669–2674. [PMC free article] [PubMed]
  • Ruland K, Himmelreich R, Herrmann R. Sequence divergence in the ORF6 gene of Mycoplasma pneumonia. J Bacteriol. 1994 Sep;176(17):5202–5209. [PMC free article] [PubMed]
  • Vicente M, Errington J. Structure, function and controls in microbial division. Mol Microbiol. 1996 Apr;20(1):1–7. [PubMed]
  • Sankaran K, Gupta SD, Wu HC. Modification of bacterial lipoproteins. Methods Enzymol. 1995;250:683–697. [PubMed]
  • Gilson E, Alloing G, Schmidt T, Claverys JP, Dudler R, Hofnung M. Evidence for high affinity binding-protein dependent transport systems in gram-positive bacteria and in Mycoplasma. EMBO J. 1988 Dec 1;7(12):3971–3974. [PMC free article] [PubMed]
  • Citti C, Wise KS. Mycoplasma hyorhinis vlp gene transcription: critical role in phase variation and expression of surface lipoproteins. Mol Microbiol. 1995 Nov;18(4):649–660. [PubMed]
  • Higgins CF. ABC transporters: from microorganisms to man. Annu Rev Cell Biol. 1992;8:67–113. [PubMed]
  • Postma PW, Lengeler JW, Jacobson GR. Phosphoenolpyruvate:carbohydrate phosphotransferase systems of bacteria. Microbiol Rev. 1993 Sep;57(3):543–594. [PMC free article] [PubMed]
  • Fath MJ, Kolter R. ABC transporters: bacterial exporters. Microbiol Rev. 1993 Dec;57(4):995–1017. [PMC free article] [PubMed]
  • Schatz G, Dobberstein B. Common principles of protein translocation across membranes. Science. 1996 Mar 15;271(5255):1519–1526. [PubMed]
  • Plackett P, Marmion BP, Shaw EJ, Lemcke RM. Immunochemical analysis of Mycoplasma pneumoniae. 3. Separation and chemical identification of serologically active lipids. Aust J Exp Biol Med Sci. 1969 Apr;47(2):171–195. [PubMed]
  • Matic I, Rayssiguier C, Radman M. Interspecies gene exchange in bacteria: the role of SOS and mismatch repair systems in evolution of species. Cell. 1995 Feb 10;80(3):507–515. [PubMed]
  • Atkins JF, Gesteland RF. A case for trans translation. Nature. 1996 Feb 29;379(6568):769–771. [PubMed]
  • Rottem S, Adar L, Gross Z, Ne'eman Z, Davis PJ. Incorporation and modification of exogenous phosphatidylcholines by mycoplasmas. J Bacteriol. 1986 Jul;167(1):299–304. [PMC free article] [PubMed]

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