Complete genome and proteome of Acholeplasma laidlawii

Journal of Bacteriology

Volumn 193, Issue 18, 2011, Pages 4943-4953

  Lazarev, V N ^a,e   Levitskii, S A ^a,e   Basovskii, Y I ^a   Chukin, M M ^a   Akopian, T A ^a   Vereshchagin, V V ^a   Kostrjukova, E S ^a   Kovaleva, G Y ^b   Kazanov, M D ^b   Malko, D B ^c   Vitreschak, A G ^b   Sernova, N V ^b   Gelfand, M S ^b,d   Demina, I A ^a   Serebryakova, M V ^a   Galyamina, M A ^a   Vtyurin, N N ^a   Rogov, S I ^a   Alexeev, D G ^a   Ladygina, V G ^a   Govorun, V M ^a,e   more..

^a FEDERAL RESEARCH AND CLINICAL CENTER OF PHYSICAL CHEMICAL MEDICINE OF FEDERAL MEDICAL BIOLOGICAL AGENCY   (Russian Federation)

^b INSTITUTE FOR INFORMATION TRANSMISSION PROBLEMS   (Russian Federation)

^c VAVILOV INSTITUTE OF GENERAL GENETICS   (Russian Federation)

^d MOSCOW STATE UNIVERSITY   (Russian Federation)

^e KURCHATOV INSTITUTE   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; ADENOSINE TRIPHOSPHATASE; AMINO ACID; BACTERIAL PROTEIN; CARBOHYDRATE; CAROTENOID; CARRIER PROTEIN; CATION TRANSPORT PROTEIN; CELL MEMBRANE PROTEIN; CYTOSINE; DNA DIRECTED RNA POLYMERASE; GLYCEROLIPID; GLYCEROPHOSPHOLIPID; GUANOSINE; INTEGRAL MEMBRANE PROTEIN; LINOLEIC ACID; METHIONINE TRANSFER RNA; NUCLEOTIDE; OLEIC ACID; PALMITIC ACID; PHENYLALANINE TRANSFER RNA; PROTEOME; PROTON COUPLED THIAMINE TRANSPORTER; SATURATED FATTY ACID; SERINE TRANSFER RNA; SPHINGOLIPID; STEARIC ACID; T BOX TRANSCRIPTION FACTOR; THREONINE TRANSFER RNA; UNCLASSIFIED DRUG; URIDINE;

ACHOLEPLASMA LAIDLAWII; ACYLATION; ARTICLE; BACTERIAL CHROMOSOME; BACTERIAL GENOME; BACTERIAL METABOLISM; CARBOHYDRATE METABOLISM; CELL FUNCTION; CELLULAR STRESS RESPONSE; COMPLETE GENOME SEQUENCE; DNA REPAIR; FATTY ACID SYNTHESIS; GENE EXPRESSION REGULATION; GENETIC CODE; GENOME ANALYSIS; LIPID METABOLISM; MUTAGENESIS; NONHUMAN; NUCLEOTIDE METABOLISM; NUCLEOTIDE SEQUENCE; PHYTOPLASMA; PREDICTION; PRIORITY JOURNAL; PROTEIN PHOSPHORYLATION; PROTEIN PROCESSING; PROTEOMICS; REGULATORY RNA SEQUENCE; REGULATORY SEQUENCE; RIBOSWITCH; SIGNAL TRANSDUCTION; STOP CODON; VITAMIN METABOLISM;

ACHOLEPLASMA LAIDLAWII; BACTERIAL PROTEINS; BASE COMPOSITION; DNA, BACTERIAL; DNA, CIRCULAR; GENE EXPRESSION PROFILING; GENOME, BACTERIAL; MOLECULAR SEQUENCE DATA; PROTEOME; SEQUENCE ANALYSIS, DNA;

ACHOLEPLASMA; ACHOLEPLASMA LAIDLAWII; ACHOLEPLASMATACEAE; ACHOLEPLASMATALES; MOLLICUTES;

EID: 80052520529     PISSN: 00219193     EISSN: 10985530     Source Type: Journal    
DOI: 10.1128/JB.05059-11     Document Type: Article

References (65)

1. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
2. Bai, X., et al. 2006. Living with genome instability: the adaptation of phytoplasmas to diverse environments of their insect and plant hosts. J. Bacteriol. 188:3682-3696.
3. Bairoch, A., and R. Apweiler. 2000. The SWISSPROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res. 28:45-48.
4. Benders, G. A., et al. 2010. Cloning whole bacterial genomes in yeast. Nucleic Acids Res. 38:2558-2569.
5. Bugg, T. D., and P. E. Brandish. 1994. From peptidoglycan to glycoproteins: common features of lipid-linked oligosaccharide biosynthesis. FEMS Microbiol. Lett. 119:255-262.
6. Chambaud, I., et al. 2001. The complete genome sequence of the murine respiratory pathogen Mycoplasma pulmonis. Nucleic Acids Res. 29:2145-2153.
7. Chou, H. H., and M. H. Holmes. 2001. DNA sequence quality trimming and vector removal. Bioinformatics 17:1093-1104.
8. Colman, S. D., P. C. Hu, W. Litaker, and K. F. Bott. 1990. A physical map of the Mycoplasma genitalium genome. Mol. Microbiol. 4:683-687.
9. Craig, R., and R. C. Beavis. 2003. A method for reducing the time required to match protein sequences with tandem mass spectra. Rapid Commun. Mass Spectrom. 17:2310-2316.
10. Dandekar, T., et al. 2000. Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames. Nucleic Acids Res. 28:3278-3288.
11. Edwards, J. C., D. Chapman, and W. A. Cramp. 1983. Radiation studies of Acholeplasma laidlawii: the role of membrane composition. Int. J. Radiat. Biol. Relat. Stud. Phys. Chem. Med. 44:405-412.
12. Ewing, B., L. Hillier, M. C. Wendl, and P. Green. 1998. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8:175-185.
13. Fraser, C. M., et al. 1995. The minimal gene complement of Mycoplasma genitalium. Science 270:397-403.
14. Ghai, R., T. Hain, and T. Chakraborty. 2004. GenomeViz: visualizing microbial genomes. BMC Bioinformatics 5:198.
15. Gibson, D. G., et al. 2008. Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science 319:1215-1220.
16. Guell, M., et al. 2009. Transcriptome complexity in a genome-reduced bacterium. Science 326:1268-1271.
17. Halbedel, S., C. Hames, and J. Stulke. 2007. Regulation of carbon metabolism in the mollicutes and its relation to virulence. J. Mol. Microbiol. Biotechnol. 12:147-154.
18. Jaffe, J. D., H. C. Berg, and G. M. Church. 2004. Proteogenomic mapping as a complementary method to perform genome annotation. Proteomics 4:59-77.
19. Jaffe, J. D., et al. 2004. The complete genome and proteome of Mycoplasma mobile. Genome Res. 14:1447-1461.
20. Jan, G., C. Fontenelle, M. Le Henaff, and H. Wroblewski. 1995. Acylation and immunological properties of Mycoplasma gallisepticum membrane proteins. Res. Microbiol. 146:739-750.
21. Jensen, O. N., M. Wilm, A. Shevchenko, and M. Mann. 1999. Sample preparation methods for mass spectrometric peptide mapping directly from 2-DE gels. Methods Mol. Biol. 112:513-530.
22. Kim, J. N., A. Roth, and R. R. Breaker. 2007. Guanine riboswitch variants from Mesoplasma florum selectively recognize 2'-deoxyguanosine. Proc. Natl. Acad. Sci. U. S. A. 104:16092-16097.
23. Krogh, A., B. Larsson, G. von Heijne, and E. L. Sonnhammer. 2001. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305:567-580.
24. Kuhner, S., et al. 2009. Proteome organization in a genome-reduced bacterium. Science 326:1235-1240.
25. Laemmli, U. K. 1970. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227:680-685.
26. Laidlaw, P. P., and W. J. Elford. 1936. A new group of filterable organisms. Proc. R. Soc. Lond. Ser. B Biol. Sci. 120:292-303.
27. Lowe, T. M., and S. R. Eddy. 1997. tRNAscan-SE: a program for improved detection of tRNA genes in genomic sequence. Nucleic Acids Res. 25:955-964.
28. Reference deleted.
29. Macek, B., et al. 2007. The serine/threonine/tyrosine phosphoproteome of the model bacterium Bacillus subtilis. Mol. Cell. Proteomics 6:697-707.
30. Mandal, M., and R. R. Breaker. 2004. Gene regulation by riboswitches. Nat. Rev. Mol. Cell Biol. 5:451-463.
31. Maniloff, J., and H. J. Morowitz. 1972. Cell biology of the mycoplasmas. Bacteriol. Rev. 36:263-290.
32. McCoy, R. E., et al. 1989. Plant diseases associated with mycoplasma-like organisms, p. 545-560. In R. Whitcomb and J. G. Tully (ed.), The mycoplasmas. Academic Press Inc., San Diego, CA.
33. McElhaney, R. N. 1984. The structure and function of the Acholeplasma laidlawii plasma membrane. Biochim. Biophys. Acta 779:1-42.
34. McLean, M. J., K. H. Wolfe, and K. M. Devine. 1998. Base composition skews, replication orientation, and gene orientation in 12 prokaryote genomes. J. Mol. Evol. 47:691-696.
35. Myers, G. S., et al. 2006. Skewed genomic variability in strains of the toxigenic bacterial pathogen, Clostridium perfringens. Genome Res. 16:1031-040.
36. Neverov, A. D., M. Gelfand, and A. A. Mironov. 2003. GipsyGene: a statisticsbased gene recognizer for fungal genomes. Biophysics (Moscow) 48:71-75.
37. Oshima, K., et al. 2004. Reductive evolution suggested from the complete genome sequence of a plant-pathogenic phytoplasma. Nat. Genet. 36:27-29.
38. Overbeek, R., M. Fonstein, M. D'Souza, G. D. Pusch, and N. Maltsev. 1999. The use of gene clusters to infer functional coupling. Proc. Natl. Acad. Sci. U. S. A. 96:2896-2901.
39. Pollack, J. D., V. V. Tryon, and K. D. Beaman. 1983. The metabolic pathways of Acholeplasma and Mycoplasma: an overview. Yale J. Biol. Med. 56:709-716.
40. Pop, M., D. S. Kosack, and S. L. Salzberg. 2004. Hierarchical scaffolding with Bambus. Genome Res. 14:149-159.
41. Razin, S. 1978. The mycoplasmas. Microbiol. Rev. 42:414-470.
42. Razin, S. 1962. Nucleic acid precursor requirements of Mycoplasma laidlawii. J. Gen. Microbiol. 28:243-250.
43. Razin, S., D. Yogev, and Y. Naot. 1998. Molecular biology and pathogenicity of mycoplasmas. Microbiol. Mol. Biol. Rev. 62:1094-1156.
44. Rocha, E. P., A. Danchin, and A. Viari. 1999. Translation in Bacillus subtilis: roles and trends of initiation and termination, insights from a genome analysis. Nucleic Acids Res. 27:3567-3576.
45. Rottem, S. 2002. Sterols and acylated proteins in mycoplasmas. Biochem. Biophys. Res. Commun. 292:1289-1292.
46. Rutherford, K., et al. 2000. Artemis: sequence visualization and annotation. Bioinformatics 16:944-945.
47. Saito, Y., J. R. Silvius, and N. McElhaney. 1977. Membrane lipid biosynthesis in Acholeplasma laidlawii B: de novo biosynthesis of saturated fatty acids by growing cells. J. Bacteriol. 132:497-504.
48. Salzberg, S. L., A. L. Delcher, S. Kasif, and O. White. 1998. Microbial gene identification using interpolated Markov models. Nucleic Acids Res. 26:544-548.
49. Sasaki, Y., et al. 2002. The complete genomic sequence of Mycoplasma penetrans, an intracellular bacterial pathogen in humans. Nucleic Acids Res. 30:5293-5300.
50. Serebryakova, M. V., et al. 2011. The acylation state of surface lipoproteins of mollicute Acholeplasma laidlawii. J. Biol. Chem. 286:22769-22776.
51. Sernova, N. V., and M. S. Gelfand. 2008. Identification of replication origins in prokaryotic genomes. Brief. Bioinform. 9:376-391.
52. Shevchenko, A., M. Wilm, O. Vorm, and M. Mann. 1996. Mass spectrometric sequencing of proteins from silver-stained polyacrylamide gels. Anal. Chem. 68:850-858.
53. Smith, P. F. 1984. Lipoglycans from mycoplasmas. Crit. Rev. Microbiol. 11:157-186.
54. Stormo, G. D., T. D. Schneider, and L. M. Gold. 1982. Characterization of translational initiation sites in E. coli. Nucleic Acids Res. 10:2971-2996.
55. Su, H. C., C. A. Hutchison III, and M. C. Giddings. 2007. Mapping phosphoproteins in Mycoplasma genitalium and Mycoplasma pneumoniae. BMC Microbiol. 7:63.
56. Sutton, G., O. White, M. Adams, and A. Kerlavage. 1995. TIGR Assembler: a new tool for assembling large shotgun sequencing projects. Genome Sci. Technol. 1:9-19.
57. Tatusov, R. L., E. V. Koonin, and D. J. Lipman. 1997. A genomic perspective on protein families. Science 278:631-637.
58. Thomas, J. M., D. Horspool, G. Brown, V. Tcherepanov, and C. Upton. 2007. GraphDNA: a Java program for graphical display of DNA composition analyses. BMC Bioinformatics 8:21.
59. Tusnady, G. E., and I. Simon. 2001. The HMMTOP transmembrane topology prediction server. Bioinformatics 17:849-850.
60. Vasconcelos, A. T., et al. 2005. Swine and poultry pathogens: the complete genome sequences of two strains of Mycoplasma hyopneumoniae and a strain of Mycoplasma synoviae. J. Bacteriol. 187:5568-5577.
61. Reference deleted
62. Vitreschak, A. G., and M. A. M. S. Gelfand. 2001. RNApattern program: searching for RNA secondary structure by the pattern rule, p. 623-625. Abstr. 3rd Int. Conf. Complex Syst. NECSI, Samara, Russia.
63. Vitreschak, A. G., D. A. Rodionov, A. A. Mironov, and M. S. Gelfand. 2004. Riboswitches: the oldest mechanism for the regulation of gene expression? Trends Genet. 20:44-50.
64. Westberg, J., et al. 2004. The genome sequence of Mycoplasma mycoides subsp. mycoides SC type strain PG1T, the causative agent of contagious bovine pleuropneumonia (CBPP). Genome Res. 14:221-227.
65. Worliczek, H. L., P. Kampfer, R. Rosengarten, B. J. Tindall, and H. J. Busse. 2007. Polar lipid and fatty acid profiles-re-vitalizing old approaches as a modern tool for the classification of mycoplasmas? Syst. Appl. Microbiol. 30:355-370.