Proteome of Mycoplasma pneumoniae

Methods of Biochemical Analysis

Volumn 49, Issue , 2006, Pages 39-56

  Herrmann, Richard ^a   Ruppert, Thomas ^a  

^a UNIVERSITY OF HEIDELBERG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; DETERGENT; OCTOXINOL; PHOSPHOPROTEIN; PROTEOME; RNA; SIGNAL PEPTIDE;

BACTERIAL GENE; CHEMISTRY; GENETICS; METABOLISM; METHODOLOGY; MYCOPLASMA PNEUMONIAE; OPEN READING FRAME; PROTEIN PROCESSING; PROTEOMICS; REVIEW; TWO DIMENSIONAL GEL ELECTROPHORESIS;

BACTERIAL PROTEINS; DETERGENTS; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; GENES, BACTERIAL; MYCOPLASMA PNEUMONIAE; OCTOXYNOL; OPEN READING FRAMES; PHOSPHOPROTEINS; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEIN SORTING SIGNALS; PROTEOME; PROTEOMICS; RNA;

EID: 84872170281     PISSN: 00766941     EISSN: None     Source Type: Book Series    
DOI: None     Document Type: Review

References (71)

1. Biberfeld, G, and Biberfeld, P. (1970). Ultrastructural features of Mycoplasma pneumoniae. J. Bacteriol. 102:855-861.
2. Blattner, F. R., Plunkett, G., 3rd, Bloch, C. A., Perna, N. T., Burland, V., Riley, M., Collado-Vides, J., Glasner, J. D., Rode, C. K., Mayhew, G. F., Gregor, J., Davis, N. W., Kirkpatrick, H. A., Goeden, M. A., Rose, D. J., Mau, B., and Shao, Y. (1997). The complete genome sequence of Escherichia coli K-12. Science 277:1453-1474.
3. Blonder, J., Conrads, T. P., Yu, L. R., Terunuma, A., Janini, G. M., Issaq, H. J., Vogel, J. C., and Veenstra, T. D. (2004). A detergent-and cyanogen bromide-free method for integral membrane proteomics: Application to Halobacterium purple membranes and the human epidermal membrane proteome. Proteomics 4:31-45.
4. Braun, V., and Rehn, K. (1969). Chemical characterization, spacial distribution and function of a lipoprotein of the E. coli cell wall. Eur. J. Biochem. 10:426-438.
5. Calcutt, M. J., Kim, M. F., Karpas, A. B., Muhlradt, P. F., and Wise, K. S. (1999). Differential posttranslational processing confers intraspecies variation of a major surface lipoprotein and a macrophage-activating lipopeptide of Mycoplasma fermentans. Infect. Immun. 67:760-771.
6. Catrein, I., Herrmann, R., Bosserhoff, A., and Ruppert, T. (in press). Absence of the conserved bacterial SPaseI gene but experimental proof for a signal peptidase I activity in Mycoplasma pneumoniae. FEPS 272:2892-2900.
7. Chen, S., Jancrick, J., Yokota, H., Kim, R., and Kim, S. H. (2004). Crystal structure of a protein associated with cell division from Mycoplasma pneumoniae (GI: 13508053): A novel fold with a conserved sequence motif. Proteins 55:785-791.
8. Choi, I. G., Shin, D. H., Brandsen, J., Jancarik, J., Busso, D., Yokota, H., Kim, R., and Kim, S. H. (2003). Crystal structure of a stress inducible protein from Mycoplasma pneumoniae at 2.85 Å resolution. J. Struct. Funct. Genomics 4:31-34.
9. Cordwell, S. J., Basseal, D. J., and Humphery-Smith, I. (1997). Proteome analysis of Spiroplasma melliferum (A56) and protein characterisation across species boundaries. Electrophoresis 18:1335-1346.
10. Cordwell, S. J., Wilkins, M. R., Cerpa-Poljak, A., Gooley, A. A., Duncan, M., Williams, K. L., and Humphery-Smith, I. (1995). Cross-species identification of proteins separated by two-dimensional gel electrophoresis using matrix-assisted laser desorption ionisation/time-of-flight mass spectrometry and amino acid composition. Electrophoresis 16:438-443.
11. Dandekar, T., Huynen, M., Regula, J. T., Ueberle, B., Zimmermann, C. U., Andrade, M., Doerks, T., Sanchez-Pulido, L., Snel, B., Suyama, M., Yuan, Y. P., Herrmann, R., and Bork, P. (2000). Reannotating the Mycoplasma pneumoniae genome sequence: Adding value, function and reading frames. Nucleic Acids Res. 28:3278-3288.
12. Dirksen, L. B., Krebes, K. A., and Krause, D. C. (1994). Phosphorylation of cytadherence-accessory proteins in Mycoplasma pneumoniae. J. Bacteriol. 176:7499-7505.
13. Dumke, R., Catrein, I., Pirkl, E., Herrmann, R., and Jacobs, E. (2003). Subtyping of Mycoplasma pneumoniae isolates based on extended genome sequencing and on expression profiles. Int. J. Med. Microbiol. 292:513-525.
14. Edman, M., Jarhede, T., Sjostrom, M., and Wieslander, A. (1999). Different sequence patterns in signal peptides from mycoplasmas, other gram-positive bacteria, and Escherichia coli: A multivariate data analysis. Proteins 35:195-205.
15. Ferrer-Navarro, M., Gomez, A., Yanes, O., Planell, R., Aviles, F. X., Pinol, J., Perez Pons, J. A., and Querol, E. (2006). Proteome of the bacterium Mycoplasma penetrans. J Proteome Res 5:688-694.
16. Fraser, C. M., Gocayne, J. D., White, O., Adams, M. D., Clayton, R. A., Fleischmann, R. D., Bult, C. J., Kerlavage, A. R., Sutton, G., Kelley, J. M., Fritchman, R. D., Weidman, J. F., Small, K. V., Sandusky, M., Fuhrmann, J., Nguyen, D., Utterback, T. R., Saudek, D. M., Phillips, C. A., Merric, J. M., Tomb, J. F., Dougherty, B. A., Bott, K. F., Hu P. C., Lucier, T. S., Peterson, S. N., Smith, H. O., Hutchison, C. A. 3rd, and Venter, J. C. (1995). The minimal gene complement of Mycoplasma genitalium. Science 270:397-403.
17. Froehlich, J. E., Wilkerson, C. G., Ray, W. K., McAndrew, R. S., Osteryoung, K. W., Gage, D. A., and Phinney, B. S. (2003). Proteomic study of the Arabidopsis thaliana chloroplastic envelope membrane utilizing alternatives to traditional two-dimensional electrophoresis. J. Proteome Res. 2:413-425.
18. Göbel, U., Speth, V., and Bredt, W. (1981). Filamentous structures in adherent Mycoplasma pneumoniae cells treated with nonionic detergents. J. Cell. Biol. 91:537-543.
19. Grigoriev, I. V., and Choi, I. G. (2002). Target selection for structural genomics: A single genome approach. Omics 6:349-362.
20. Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F., Gelb, M. H., and Aebersold, R. (1999). Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 17:994-999.
21. Han, D. K., Eng, J., Zhou, H., and Aebersold, R. (2001). Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry. Nat. Biotechnol. 19:946-951.
22. Hasselbring, B. M., Jordan, J. L., and Krause, D. C. (2005). Mutant analysis reveals a specific requirement for protein P30 in Mycoplasma pneumoniae gliding motility. J Bacteriol 187:6281-6289.
23. Hegermann, J., Herrmann, R., and Mayer, F. (2002). Cytoskeletal elements in the bacterium Mycoplasma pneumoniae. Naturwissenschaften 89:453-458.
24. Hilbert, H., Himmelreich, R., Plagens, H., and Herrmann, R. (1996). 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. 24:628-639.
25. Himmelreich, R., Hilbert, H., Plagens, H., Pirkl, E., Li, B. C., and Herrmann, R. (1996). Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae. Nucleic Acids Res. 24:4420-4449.
26. Hutchison, C., Peterson, S., Gill, S., Cline, R., White, O., Fraser, C., Smith, H., and Venter, J. (1999). Global transposon mutagenesis and a minimal Mycoplasma genome. Science 286:2165-2169.
27. Inukai, M., Takeuchi, M., Shimizu, K., and Arai, M. (1978). Mechanism of action of globomycin. J. Antibiot. (Tokyo) 31:1203-1205.
28. Jacobs, E. (1991). Mycoplasma pneumoniae virulence factors and the immune response. Rev. Med. Microbiol. 2:83-90.
29. Jacobs, E., Fuchte, K., and Bredt, W. (1987). Amino acid sequence and antigenicity of the aminoterminus of the 168 kDa adherence protein of Mycoplasma pneumoniae. J. Gen. Microbiol. 133(Pt. 8):2233-2236.
30. Jaffe, J. D., Berg, H. C., and Church, G. M. (2004a). Proteogenomic mapping as a complementary method to perform genome annotation. Proteomics 4:59-77.
31. Jaffe, J. D., Stange-Thomann, N., Smith, C., DeCaprio, D., Fisher, S., Butler, J., Calvo, S., Elkins, T., FitzGerald, M. G., Hafez, N., Kodira, C. D., Major, J., Wang, S., Wilkinson, J., Nicol, R., Nusbaum, C., Birren, B., Berg, H. C., and Church, G. M. (2004b). The complete genome and proteome of Mycoplasma mobile. Genome Res. 14:1447-1461.
32. Kim, S. H., Shin, D. H., Liu, J., Oganesyan, V., Chen, S., Xu, Q. S., Kim, J. S., Das, D., Schulze-Gahmen, U., Holbrook, S. R., Holbrook, E. L., Martinez, B. A., Oganesyan, N., DeGiovanni, A., Lou, Y., Henriquez, M., Huang, C., Jancarik, J., Pufan, R., Choi, I. G., Chandonia, J. M., Hou, J., Gold, B., Yokota, H., Brenner, S. E., Adams, P. D., and Kim, R. (2005). Structural genomics of minimal organisms and protein fold space. J Struct Funct Genomics 6:63-70.
33. Kirchhoff, H. (1992). Motility. In J. Maniloff (Ed.), Mycoplasmas. Molecular Biology and Pathogenesis. American Society for Microbiology, Washington, D.C., pp. 289-306.
34. Kirchhoff, H., and Rosengarten, R. (1984). Isolation of a motile mycoplasma from fish. J. Gen. Microbiol. 130(Pt. 9):2439-2445.
35. Krause, D. C., and Balish, M. F. (2004). Cellular engineering in a minimal microbe: Structure and assembly of the terminal organelle of Mycoplasma pneumoniae. Mol. Microbiol. 51:917-924.
36. Krebes, K. A., Dirksen, L. B., and Krause, D. C. (1995). Phosphorylation of Mycoplasma pneumoniae cytadherence-accessory proteins in cell extracts. J. Bacteriol. 177:4571-4574.
37. Kunst, F., Ogasawara, N., Moszer, I., Albertini, A. M., Alloni, G., Azevedo, V., Bertero, M. G., Bessieres, P., Bolotin, A., Borchert, S., Borriss, R., Boursier, L., Brans, A., Braun, M., Brignell, S. C., Bron, S., Brouillet, S., Bruschi, C. V., Caldwell, B., Capuano, V., Carter, N. M., Choi, S. K., Codani, J. J., Connerton, I. F., Danchin, A., and et al. (1997). The complete genome sequence of the gram-positive bacterium Bacillus subtilis [see comments]. Nature 390:249-256.
38. Meng, K. E., and Pfister, R. M. (1980). Intracellular structures of Mycoplasma pneumoniae revealed after membrane removal. J. Bacteriol. 144:390-399.
39. Merzbacher, M., Detsch, C., Hillen, W., and Stulke, J. (2004). Mycoplasma pneumoniae HPr kinase/phosphorylase. Eur. J. Biochem. 271:367-374.
40. Mitulovic, G., Stingl, C., Smoluch, M., Swart, R., Chervet, J. P., Steinmacher, I., Gerner, C., and Mechtler, K. (2004). Automated, on-line two-dimensional nano liquid chromatography tandem mass spectrometry for rapid analysis of complex protein digests. Proteomics 4:2545-2557.
41. Muhlradt, P. F. (2002). Immunomodulation by mycoplasmas: Artifacts, facts and active molecules. In S. Razin and R. Herrmann (Eds.), Molecular Biology and Pathogenicity of Mycoplasmas, New York: Kluwer Academic/Plenum, pp. 445-472.
42. Muhlradt, P. F., Meyer, H., and Jansen, R. (1996). Identification of S-(2,3-dihydroxypropyl)cystein in a macrophage-activating lipopeptide from Mycoplasma fermentans. Biochemistry 35:7781-7786.
43. Muhlradt, P. F., Kiess, M., Meyer, H., Sussmuth, R., and Jung, G. (1997). Isolation, structure elucidation, and synthesis of a macrophage stimulatory lipopeptide from Mycoplasma fermentans acting at picomolar concentration. J. Exp. Med. 185:1951-1958.
44. Nielsen, H., Engelbrecht, J., Brunak, S., and von Heijne, G. (1997). Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng. 10:1-6.
45. Ong, S. E., Kratchmarova, I., and Mann, M. (2003). Properties of 13C-substituted arginine in stable isotope labeling by amino acids in cell culture (SILAC). J. Proteome Res. 2:173-181.
46. Paetzel, M., Karla, A., Strynadka, N. C., and Dalbey, R. E. (2002). Signal peptidases. Chem. Rev. 102:4549-4580.
47. Peng, J., Elias, J. E., Thoreen, C. C., Licklider, L. J., and Gygi, S. P. (2003). Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: The yeast proteome. J. Proteome Res. 2:43-50.
48. Pyrowolakis, G., Hofmann, D., and Herrmann, R. (1998). The subunit b of the F0F1-type ATPase of the bacterium Mycoplasma pneumoniae is a lipoprotein. J. Biol. Chem. 273:24792-24796.
49. Radestock, U., and Bredt, W. (1977). Motility of Mycoplasma pneumoniae. J. Bacteriol. 129:1495-1501.
50. Razin, S., Yogev, D., and Naot, Y. (1998). Molecular biology and pathogenicity of mycoplasmas. Microbiol. Mol. Biol. Rev. 62:1094-1156.
51. Regula, J. T., Ueberle, B., Boguth, G., Görg, A., Schnölzer, M., Herrmann, R., and Frank, R. (2000). Towards a two-dimensional proteome map of Mycoplasma pneumoniae. Electrophoresis 21:3765-3780.
52. Regula, J. T., Boguth, G., Görg, A., Hegermann, J., Mayer, F., Frank, R., and Herrmann, R. (2001). Defining the mycoplasma " cytoskeleton": The protein composition of the Triton X-100 insoluble fraction of the bacterium Mycoplasma pneumoniae determined by two-dimensional gel electrophoresis and mass spectrometry. Microbiology 147:1045-1057.
53. Saleh, M. T., Fillon, M., Brennan, P. J., and Belisle, J. T. (2001). Identification of putative exported/secreted proteins in prokaryotic proteomes. Gene 269:195-204.
54. Sankaran, K., and Wu, H. C. (1994). Lipid modification of bacterial prolipoprotein. Transfer of diacylglyceryl moiety from phosphatidylglycerol. J. Biol. Chem. 269:19701-19706.
55. Sasaki, Y., Ishikawa, J., Yamashita, A., Oshima, K., Kenri, T., Furuya, K., Yoshino, C., Horino, A., Shiba, T., Sasaki, T., and Hattori, M. (2002). The complete genomic sequence of Mycoplasma penetrans, an intracellular bacterial pathogen in humans. Nucleic Acids Res 30:5293-5300.
56. Sperker, B., Hu, P., and Herrmann, R. (1991). Identification of gene products of the P1 operon of Mycoplasma pneumoniae. Mol. Microbiol. 5:299-306.
57. Steinhauer, K., Jepp, T., Hillen, W., and Stulke, J. (2002). A novel mode of control of Mycoplasma pneumoniae HPr kinase/phosphatase activity reflects its parasitic lifestyle. Microbiology 148:3277-3284.
58. Stevens, M. K., and Krause, D. C. (1991). Localization of the Mycoplasma pneumoniae cytadherence-accessory proteins HMW1 and HMW4 in the cytoskeletonlike Triton shell. J. Bacteriol. 173:1041-1050.
59. Su, C. J., Tryon, V. V., and Baseman, J. B. (1987). Cloning and sequence analysis of cytadhesin P1 gene from Mycoplasma pneumoniae. Infect. Immun. 55:3023-3029.
60. Tatusov, R. L., Koonin, E. V., and Lipman, D. J. (1997). A genomic perspective on protein families. Science 278:631-637.
61. Tatusov, R. L., Fedorova, N. D., Jackson, J. D., Jacobs, A. R., Kiryutin, B., Koonin, E. V., Krylov, D. M., Mazumder, R., Mekhedov, S. L., Nikolskaya, A. N., Rao, B. S., Smirnov, S., Sverdlov, A. V., Vasudevan, S., Wolf, Y. I., Yin, J. J., and Natale, D. A. (2003). The COG database: An updated version includes eukaryotes. BMC Bioinformatics 4:41.
62. Taylor-Robinson, D. (1996). Infections due to species of Mycoplasma and Ureaplasma: An update. Clin. Infect. Dis. 23:671-682; quiz 683-674.
63. Tokunaga, M., Tokunaga, H., and Wu, H. C. (1982). Post-translational modification and processing of Escherichia coli prolipoprotein in vitro. Proc. Natl. Acad. Sci. USA 79:2255-2259.
64. Ueberle, B., Frank, R., and Herrmann, R. (2002). The proteome of the bacterium Mycoplasma pneumoniae: Comparing predicted open reading frames to identified gene products. Proteomics 2:754-764.
65. Uenoyama, A., and Miyata, M. (2005). Identification of a 123-kilodalton protein (Gli123) involved in machinery for gliding motility of Mycoplasma mobile. J Bacteriol 187:5578-5584.
66. Waites, K. B., and Talkington, D. F. (2004). Mycoplasma pneumoniae and its role as a human pathogen. Clin. Microbiol. Rev. 17:697-728.
67. Washburn, M. P., Wolters, D., and Yates, J. R., 3rd (2001). Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 19:242-247.
68. Wasinger, V. C., Pollack, J. D., and Humphery-Smith, I. (2000). The proteome of Mycoplasma genitalium. Chaps-soluble component. Eur. J. Biochem. 267:1571-1582.
69. Wildgruber, R., Reil, G., Drews, O., Parlar, H., and Gorg, A. (2002). Web-based two-dimensional database of Saccharomyces cerevisiae proteins using immobilized pH gradients from pH 6 to pH 12 and matrix-assisted laser desorption/ionization time of flight mass spectrometry. Proteomics 2:727-732.
70. Wolters, D. A., Washburn, M. P., and Yates, J. R., 3rd (2001). An automated multidimensional protein identification technology for shotgun proteomics. Anal. Chem. 73:5683-5690.
71. Wu, C. C., MacCoss, M. J., Howell, K. E., and Yates, J. R., 3rd (2003). A method for the comprehensive proteomic analysis of membrane proteins. Nat. Biotechnol. 21:532-538.