Proteomics characterization of cytoplasmic and lipid-associated membrane proteins of human pathogen mycoplasma fermentans m64

PLoS ONE

Volumn 7, Issue 4, 2012, Pages

  Liu, Yi Chang ^a   Lin, I Hsuan ^a,b   Chung, Wei Jen ^a   Hu, Wensi S ^a   Ng, Wailap Victor ^a   Lu, Chi Yu ^a   Huang, Tsung Yen ^a   Shu, Hung Wei ^a   Hsiao, Kwang Jen ^c   Tsai, Shih Feng ^a,d   Chang, Chuan Hsiung ^a   Lin, Chao Hsiung ^a,c  

^a NATIONAL YANG MING UNIVERSITY   (Taiwan)

^b ACADEMIA SINICA   (Taiwan)

^c TAIPEI VETERANS GENERAL HOSPITAL   (Taiwan)

^d NATIONAL HEALTH RESEARCH INSTITUTES   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; LIPID ASSOCIATED MEMBRANE PROTEIN; LIPOPROTEIN; MEMBRANE PROTEIN; SIGNAL PEPTIDE; TRITON X 114; UNCLASSIFIED DRUG; LIPID LINKED PROTEIN; PROTEOME; VIRULENCE FACTOR;

AMPHOPHILICITY; ANIMAL CELL; ARTICLE; BACTERIAL STRAIN; BIOINFORMATICS; CHEMICAL PHENOMENA; CYTOPLASM; EXTRACTION; MACROPHAGE; MASS SPECTROMETRY; MYCOPLASMA FERMENTANS; NONHUMAN; OPEN READING FRAME; ORTHOLOGY; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEOMICS; TWO DIMENSIONAL GEL ELECTROPHORESIS; AMINO ACID SEQUENCE; ANIMAL; BACTERIAL GENOME; CELL LINE; GENETICS; GLYCOLYSIS; HUMAN; IMMUNOLOGY; METABOLISM; MOLECULAR GENETICS; MOUSE; PHYLOGENY; PROTEIN SECONDARY STRUCTURE; SEQUENCE HOMOLOGY;

AMINO ACID SEQUENCE; ANIMALS; BACTERIAL PROTEINS; CELL LINE; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; GENOME, BACTERIAL; GLYCOLYSIS; HUMANS; LIPID-LINKED PROTEINS; MACROPHAGES; MICE; MOLECULAR SEQUENCE ANNOTATION; MOLECULAR SEQUENCE DATA; MYCOPLASMA FERMENTANS; NF-KAPPA B; OPEN READING FRAMES; PHYLOGENY; PROTEIN STRUCTURE, SECONDARY; PROTEOME; PROTEOMICS; SEQUENCE HOMOLOGY, AMINO ACID; VIRULENCE FACTORS;

EID: 84859964338     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0035304     Document Type: Article

References (83)

1. Razin S, Yogev D, Naot Y, (1998) Molecular biology and pathogenicity of mycoplasmas. Microbiol Mol Biol Rev 62: 1094-1156.
2. Garnier M, Foissac X, Gaurivaud P, Laigret F, Renaudin J, et al. (2001) Mycoplasmas, plants, insect vectors: a matrimonial triangle. Comptes rendus de l'Academie des sciences Serie III, Sciences de la vie 324: 923-928.
3. Lo SC, Shih JW, Newton PB III, Wong DM, Hayes MM, et al. (1989) Virus-like infectious agent (VLIA) is a novel pathogenic mycoplasma: Mycoplasma incognitus. Am J Trop Med Hyg 41: 586-600.
4. Blanchard A, Montagnier L, (1994) AIDS-associated mycoplasmas. Annu Rev Microbiol 48: 687-712.
5. Shimizu T, Kida Y, Kuwano K, (2004) Lipid-associated membrane proteins of Mycoplasma fermentans and M. penetrans activate human immunodeficiency virus long-terminal repeats through Toll-like receptors. Immunology 113: 121-129.
6. Wright SH, (2011) Inflammatory arthritis. Advance for NPs & PAs 2: 29-30, 32.
7. Seya T, Matsumoto M, (2002) A lipoprotein family from Mycoplasma fermentans confers host immune activation through Toll-like receptor 2. Int J Biochem Cell Biol 34: 901-906.
8. Romero F, Moreno E, Ruiz-Bravo A, Jimenez-Valera M, (2004) In vivo immunomodulation by Mycoplasma fermentans membrane lipoprotein. Curr Microbiol 48: 237-239.
9. Rawadi G, (2000) Mycoplasma fermentans interaction with monocytes/macrophages: molecular basis. Microbes Infect 2: 955-964.
10. Shimizu T, Kida Y, Kuwano K, (2008) A triacylated lipoprotein from Mycoplasma genitalium activates NF-kappaB through Toll-like receptor 1 (TLR1) and TLR2. Infect Immun 76: 3672-3678.
11. McGowin CL, Ma L, Martin DH, Pyles RB, (2009) Mycoplasma genitalium-encoded MG309 activates NF-kappaB via Toll-like receptors 2 and 6 to elicit proinflammatory cytokine secretion from human genital epithelial cells. Infect Immun 77: 1175-1181.
12. Jungblut PR, (2001) Proteome analysis of bacterial pathogens. Microbes Infect 3: 831-840.
13. Ashton PD, Curwen RS, Wilson RA, (2001) Linking proteome and genome: how to identify parasite proteins. Trends Parasitol 17: 198-202.
14. Hu WS, Hayes MM, Wang RY, Shih JW, Lo SC, (1998) High-frequency DNA rearrangements in the chromosomes of clinically isolated Mycoplasma fermentans. Curr Microbiol 37: 1-5.
15. Shu H-W, Liu T-T, Chang H-Y, Liu Y-M, Wu K-M, et al. (2011) Genome sequence of the repetitive sequence rich Mycoplasma fermentans strain M64. J Bacteriol JB.05228-05211.
16. Gorg A, Obermaier C, Boguth G, Harder A, Scheibe B, et al. (2000) The current state of two-dimensional electrophoresis with immobilized pH gradients. Electrophoresis 21: 1037-1053.
17. Blum H, Beiers H, Gross HJ, (1987) Improved silver staining of plant proteins, RNA and DNA in polyacrylamide gels. Electrophoresis 8: 93-99.
18. Gharahdaghi F, Weinberg CR, Meagher DA, Imai BS, Mische SM, (1999) Mass spectrometric identification of proteins from silver-stained polyacrylamide gel: a method for the removal of silver ions to enhance sensitivity. Electrophoresis 20: 601-605.
19. Havlis J, Thomas H, Sebela M, Shevchenko A, (2003) Fast-response proteomics by accelerated in-gel digestion of proteins. Anal Chem 75: 1300-1306.
20. Bordier C, (1981) Phase separation of integral membrane proteins in Triton X-114 solution. J Biol Chem 256: 1604-1607.
21. Feng SH, Lo SC, (1994) Induced mouse spleen B-cell proliferation and secretion of immunoglobulin by lipid-associated membrane proteins of Mycoplasma fermentans incognitus and Mycoplasma penetrans. Infect Immun 62: 3916-3921.
22. Fu SL, Hsu YH, Lee PY, Hou WC, Hung LC, et al. (2006) Dioscorin isolated from Dioscorea alata activates TLR4-signaling pathways and induces cytokine expression in macrophages. Biochem Biophys Res Commun 339: 137-144.
23. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
24. Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M, (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res 32: D277-280.
25. Strittmatter A, (2010) Mycoplasma fermentans JER chromosome, complete genome.
26. Matsuda K, Irikura D, (2009) (2009) Mycoplasma fermentans PG18 DNA, nearly complete genome.
27. Krogh A, Larsson B, von Heijne G, Sonnhammer EL, (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305: 567-580.
28. Juncker AS, Willenbrock H, Von Heijne G, Brunak S, Nielsen H, et al. (2003) Prediction of lipoprotein signal peptides in Gram-negative bacteria. Protein Sci 12: 1652-1662.
29. NCBI Protein database. Available: http://www.ncbi.nlm.nih.gov/protein. Accessed 2012 Mar 17.
30. Sweredoski MJ, Baldi P, (2009) COBEpro: a novel system for predicting continuous B-cell epitopes. Protein Eng Des Sel 22: 113-120.
31. Magnan CN, Zeller M, Kayala MA, Vigil A, Randall A, et al. (2010) High-throughput prediction of protein antigenicity using protein microarray data. Bioinformatics 26: 2936-2943.
32. von Mering C, Jensen LJ, Kuhn M, Chaffron S, Doerks T, et al. (2007) STRING 7-recent developments in the integration and prediction of protein interactions. Nucleic Acids Res 35: D358-362.
33. Katoh K, Toh H, (2008) Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform 9: 286-298.
34. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Mol Biol Evol.
35. Ferrer-Navarro M, Gomez A, Yanes O, Planell R, Aviles FX, et al. (2006) Proteome of the bacterium Mycoplasma penetrans. J Proteome Res 5: 688-694.
36. Wasinger VC, Pollack JD, Humphery-Smith I, (2000) The proteome of Mycoplasma genitalium. Chaps-soluble component. Eur J Biochem 267: 1571-1582.
37. Regula JT, Ueberle B, Boguth G, Gorg A, Schnolzer M, et al. (2000) Towards a two-dimensional proteome map of Mycoplasma pneumoniae. Electrophoresis 21: 3765-3780.
38. Hutchison CA, Peterson SN, Gill SR, Cline RT, White O, et al. (1999) Global transposon mutagenesis and a minimal Mycoplasma genome. Science 286: 2165-2169.
39. Woese CR, Maniloff J, Zablen LB, (1980) Phylogenetic analysis of the mycoplasmas. Proceedings of the National Academy of Sciences of the United States of America 77: 494-498.
40. Weisburg WG, Tully JG, Rose DL, Petzel JP, Oyaizu H, et al. (1989) A phylogenetic analysis of the mycoplasmas: basis for their classification. Journal of bacteriology 171: 6455-6467.
41. Vasconcelos AT, Ferreira HB, Bizarro CV, Bonatto SL, Carvalho MO, et al. (2005) Swine and poultry pathogens: the complete genome sequences of two strains of Mycoplasma hyopneumoniae and a strain of Mycoplasma synoviae. Journal of bacteriology 187: 5568-5577.
42. Sirand-Pugnet P, Lartigue C, Marenda M, Jacob D, Barre A, et al. (2007) Being pathogenic, plastic, and sexual while living with a nearly minimal bacterial genome. PLoS Genet 3: e75.
43. Carvalho FM, Fonseca MM, Batistuzzo De Medeiros S, Scortecci KC, Blaha CA, et al. (2005) DNA repair in reduced genome: the Mycoplasma model. Gene 360: 111-119.
44. Fuchs TM, Deppisch H, Scarlato V, Gross R, (1996) A new gene locus of Bordetella pertussis defines a novel family of prokaryotic transcriptional accessory proteins. J Bacteriol 178: 4445-4452.
45. He X, Thornton J, Carmicle-Davis S, McDaniel LS, (2006) Tex, a putative transcriptional accessory factor, is involved in pathogen fitness in Streptococcus pneumoniae. Microb Pathog 41: 199-206.
46. Johnson SJ, Close D, Robinson H, Vallet-Gely I, Dove SL, et al. (2008) Crystal structure and RNA binding of the Tex protein from Pseudomonas aeruginosa. J Mol Biol 377: 1460-1473.
47. Ansai T, Yu W, Urnowey S, Barik S, Takehara T, (2003) Construction of a pepO gene-deficient mutant of Porphyromonas gingivalis: potential role of endopeptidase O in the invasion of host cells. Oral Microbiol Immunol 18: 398-400.
48. Razin S, (1978) The mycoplasmas. Microbiol Rev 42: 414-470.
49. Mitchell A, Finch LR, (1977) Pathways of nucleotide biosynthesis in Mycoplasma mycoides subsp. mycoides. J Bacteriol 130: 1047-1054.
50. Wang L, Westberg J, Bolske G, Eriksson S, (2001) Novel deoxynucleoside-phosphorylating enzymes in mycoplasmas: evidence for efficient utilization of deoxynucleosides. Mol Microbiol 42: 1065-1073.
51. Pollack JD, Myers MA, Dandekar T, Herrmann R, (2002) Suspected utility of enzymes with multiple activities in the small genome Mycoplasma species: the replacement of the missing "household" nucleoside diphosphate kinase gene and activity by glycolytic kinases. OMICS 6: 247-258.
52. Bizarro CV, Schuck DC, (2007) Purine and pyrimidine nucleotide metabolism in Mollicutes. Genetics and Molecular Biology 30: 190-201.
53. Olson LD, Renshaw CA, Rottem S, Boal JH, (1993) Arginine utilization by Mycoplasma fermentans is not regulated by glucose metabolism: a 13C-NMR study. FEMS Microbiol Lett 108: 47-52.
54. Tola S, Crobeddu S, Chessa G, Uzzau S, Idini G, et al. (2001) Sequence, cloning, expression and characterisation of the 81-kDa surface membrane protein (P80) of Mycoplasma agalactiae. FEMS Microbiol Lett 202: 45-50.
55. Kitzerow A, Henrich B, (2001) The cytosolic HinT protein of Mycoplasma hominis interacts with two membrane proteins. Mol Microbiol 41: 279-287.
56. Hopfe M, Hoffmann R, Henrich B, (2004) P80, the HinT interacting membrane protein, is a secreted antigen of Mycoplasma hominis. BMC Microbiol 4: 46.
57. Lenz LL, Dere B, Bevan MJ, (1996) Identification of an H2-M3-restricted Listeria epitope: implications for antigen presentation by M3. Immunity 5: 63-72.
58. Theiss P, Karpas A, Wise KS, (1996) Antigenic topology of the P29 surface lipoprotein of Mycoplasma fermentans: differential display of epitopes results in high-frequency phase variation. Infect Immun 64: 1800-1809.
59. Leigh SA, Wise KS, (2002) Identification and functional mapping of the Mycoplasma fermentans P29 adhesin. Infect Immun 70: 4925-4935.
60. Hopfe M, Henrich B, (2008) OppA, the ecto-ATPase of Mycoplasma hominis induces ATP release and cell death in HeLa cells. BMC Microbiol 8: 55.
61. Dudler R, Schmidhauser C, Parish RW, Wettenhall RE, Schmidt T, (1988) A mycoplasma high-affinity transport system and the in vitro invasiveness of mouse sarcoma cells. Embo J 7: 3963-3970.
62. Chang AH, Parsonnet J, (2010) Role of bacteria in oncogenesis. Clinical Microbiology Reviews 23: 837-857.
63. Sippel KH, Robbins AH, Reutzel R, Boehlein SK, Namiki K, et al. (2009) Structural insights into the extracytoplasmic thiamine-binding lipoprotein p37 of Mycoplasma hyorhinis. J Bacteriol 191: 2585-2592.
64. Lu T, (2008) (2009) Characterization and strain distribution of multicopy allelic variants of the M. fermentans membrane lipoprotein gene.
65. Calcutt MJ, Lewis MS, Wise KS, (2002) Molecular genetic analysis of ICEF, an integrative conjugal element that is present as a repetitive sequence in the chromosome of Mycoplasma fermentans PG18. J Bacteriol 184: 6929-6941.
66. Calcutt MJ, Kim MF, Karpas AB, Muhlradt PF, Wise KS, (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.
67. Theiss P, Wise KS, (1997) Localized frameshift mutation generates selective, high-frequency phase variation of a surface lipoprotein encoded by a mycoplasma ABC transporter operon. J Bacteriol 179: 4013-4022.
68. Sharma A, Sojar HT, Glurich I, Honma K, Kuramitsu HK, et al. (1998) Cloning, expression, and sequencing of a cell surface antigen containing a leucine-rich repeat motif from Bacteroides forsythus ATCC 43037. Infect Immun 66: 5703-5710.
69. Catrein I, Herrmann R, (2011) The proteome of Mycoplasma pneumoniae, a supposedly "simple" cell. Proteomics 11: 3614-3632.
70. Regula JT, Boguth G, Gorg A, Hegermann J, Mayer F, et al. (2001) Defining the mycoplasma 'cytoskeleton': the protein composition of the Triton X-100 insoluble fraction of the bacterium Mycoplasma pneumoniae determined by 2-D gel electrophoresis and mass spectrometry. Microbiology 147: 1045-1057.
71. Ueberle B, Frank R, Herrmann R, (2002) The proteome of the bacterium Mycoplasma pneumoniae: comparing predicted open reading frames to identified gene products. Proteomics 2: 754-764.
72. Jaffe JD, Berg HC, Church GM, (2004) Proteogenomic mapping as a complementary method to perform genome annotation. Proteomics 4: 59-77.
73. Kuhner S, van Noort V, Betts MJ, Leo-Macias A, Batisse C, et al. (2009) Proteome organization in a genome-reduced bacterium. Science 326: 1235-1240.
74. Gorg A, Weiss W, Dunn MJ, (2004) Current two-dimensional electrophoresis technology for proteomics. Proteomics 4: 3665-3685.
75. Herrmann R, Reiner B, (1998) Mycoplasma pneumoniae and Mycoplasma genitalium: a comparison of two closely related bacterial species. Curr Opin Microbiol 1: 572-579.
76. Yus E, Maier T, Michalodimitrakis K, van Noort V, Yamada T, et al. (2009) Impact of genome reduction on bacterial metabolism and its regulation. Science 326: 1263-1268.
77. Jaffe JD, Stange-Thomann N, Smith C, DeCaprio D, Fisher S, et al. (2004) The complete genome and proteome of Mycoplasma mobile. Genome Research 14: 1447-1461.
78. Fisunov GY, Alexeev DG, Bazaleev NA, Ladygina VG, Galyamina MA, et al. (2011) Core proteome of the minimal cell: comparative proteomics of three mollicute species. PloS one 6: e21964.
79. Nouvel LX, Sirand-Pugnet P, Marenda MS, Sagne E, Barbe V, et al. (2010) Comparative genomic and proteomic analyses of two Mycoplasma agalactiae strains: clues to the macro- and micro-events that are shaping mycoplasma diversity. BMC Genomics 11: 86.
80. Cacciotto C, Addis MF, Pagnozzi D, Chessa B, Coradduzza E, et al. (2010) The liposoluble proteome of Mycoplasma agalactiae: an insight into the minimal protein complement of a bacterial membrane. BMC Microbiol 10: 225.
81. Pinto PM, Chemale G, de Castro LA, Costa AP, Kich JD, et al. (2007) Proteomic survey of the pathogenic Mycoplasma hyopneumoniae strain 7448 and identification of novel post-translationally modified and antigenic proteins. Vet Microbiol 121: 83-93.
82. Pinto PM, Klein CS, Zaha A, Ferreira HB, (2009) Comparative proteomic analysis of pathogenic and non-pathogenic strains from the swine pathogen Mycoplasma hyopneumoniae. Proteome Sci 7: 45.
83. Menegatti AC, Tavares CP, Vernal J, Klein CS, Huergo L, et al. (2010) First partial proteome of the poultry pathogen Mycoplasma synoviae. Vet Microbiol 145: 134-141.