Analysis of cell envelope proteins

Handbook of Listeria Monocytogenes

Volumn , Issue , 2008, Pages 359-393

  Desvaux, Mickaël ^a   Hébraud, Michel ^a  

^a CEMAGREF   (France)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 63549123437     PISSN: None     EISSN: None     Source Type: Book    
DOI: None     Document Type: Chapter

References (270)

1. Woese, C.R., A new biology for a new century, Microbiol. Mol. Biol. Rev., 68, 173, 2004.
2. Shatalkin, A.I., Highest level of division in classification of organisms. 3. Monodermata and didermata, Zh. Obshch. Biol., 65, 195, 2004.
3. Danchin, A., The Delphic boat: What genomes tell us, Harvard University Press, Cambridge, MA, 2003.
4. Monod, J., Le hasard et la nécessité: Essai sur la philosophie naturelle de la biologie moderne, Éditions du Seuil, Paris, 1970.
5. Cavalier-Smith, T., Rooting the tree of life by transition analyses, Biol. Direct., 1, 19, 2006.
6. Cavalier-Smith, T., The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification, Int. J. Syst. Evol. Microbiol., 52, 7, 2002.
7. Gupta, R.S., The natural evolutionary relationships among prokaryotes, Crit. Rev. Microbiol., 26, 111, 2000.
8. Desvaux, M. et al., Protein cell surface display in Gram-positive bacteria: From single protein to macromolecular protein structure, FEMS Microbiol. Lett., 256, 1, 2006.
9. Garrity, G. M., Bergey’s manual of systematic bacteriology, 2nd ed., Springer, Berlin, 2001.
10. Woese, C.R., Bacterial evolution, Microbiol. Rev., 51, 221, 1987.
11. Snel, B., Huynen, M.A., and Dutilh, B.E., Genome trees and the nature of genome evolution, Annu. Rev. Microbiol., 59, 191, 2005.
12. Gupta, R.S. and Griffiths, E., Critical issues in bacterial phylogeny, Theor. Popul. Biol., 61, 423, 2002.
13. Mira, A. et al., Evolutionary relationships of Fusobacterium nucleatum based on phylogenetic analysis and comparative genomics, BMC Evol. Biol., 4, 50, 2004.
14. Botero, L.M. et al., Thermobaculum terrenum gen. nov., sp. nov.: A nonphototrophic Gram-positive thermophile representing an environmental clone group related to the Chloroflexi (green nonsulfur bacteria) and Thermomicrobia, Arch. Microbiol., 181, 269, 2004.
15. Roberts, A.J. and Wiedmann, M., Pathogen, host and environmental factors contributing to the pathogenesis of listeriosis, Cell Mol. Life Sci., 60, 904, 2003.
16. Vaneechoutte, M. et al., Comparison of PCR-based DNA fingerprinting techniques for the identification of Listeria species and their use for atypical Listeria isolates, Int. J. Syst. Bacteriol., 48, 127, 1998.
17. Hain, T., Steinweg, C., and Chakraborty, T., Comparative and functional genomics of Listeria spp., J. Biotechnol., 126, 37, 2006.
18. Nelson, K.E. et al., Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species, Nucl. Acids Res., 32, 2386, 2004.
19. Glaser, P. et al., Comparative genomics of Listeria species, Science, 294, 849, 2001.
20. Hain, T. et al., Whole-genome sequence of Listeria welshimeri reveals common steps in genome reduction with Listeria innocua as compared to Listeria monocytogenes, J. Bacteriol., 188, 7405, 2006.
21. Fraser, C.M. et al., The value of complete microbial genome sequencing (you get what you pay for), J. Bacteriol., 184, 6403, 2002.
22. Demchick, P. and Koch, A.L., The permeability of the wall fabric of Escherichia coli and Bacillus subtilis, J. Bacteriol., 178, 768, 1996.
23. Jeffery, C.J., Moonlighting proteins, Trends Biochem. Sci., 24, 8, 1999.
24. Schaumburg, J. et al., The cell wall subproteome of Listeria monocytogenes, Proteomics, 4, 2991, 2004.
25. Gupta, R.S., Protein phylogenies and signature sequences: A reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes, Microbiol. Mol. Biol. Rev., 62, 1435, 1998.
26. Henderson, I.R. et al., Type V protein secretion pathway: The autotransporter story, Microbiol. Mol. Biol. Rev., 68, 692, 2004.
27. Salmond, G.P. and Reeves, P.J., Membrane traffic wardens and protein secretion in Gram-negative bacteria, Trends Biochem. Sci., 18, 7, 1993.
28. Henderson, I.R. et al., Renaming protein secretion in the Gram-negative bacteria, Trends Microbiol., 8, 352, 2000.
29. Economou, A. et al., Secretion by numbers: Protein traffic in prokaryotes, Mol. Microbiol., 62, 308, 2006.
30. Tjalsma, H. et al., Signal peptide-dependent protein transport in Bacillus subtilis: A genome-based survey of the secretome, Microbiol. Mol. Biol. Rev., 64, 515, 2000.
31. Pallen, M.J., Chaudhuri, R.R., and Henderson, I.R., Genomic analysis of secretion systems, Curr. Opin. Microbiol., 6, 519, 2003.
32. Tjalsma, H. et al., Proteomics of protein secretion by Bacillus subtilis: Separating the “secrets” of the secretome, Microbiol. Mol. Biol. Rev., 68, 207, 2004.
33. Desvaux, M. et al., Genomic analysis of the protein secretion systems in Clostridium acetobutylicum ATCC824, Biochim. Biophys. Acta-Mol. Cell Res., 1745, 223, 2005.
34. Busch, W. and Saier, M.H., Jr., The transporter classification (TC) system, Crit. Rev. Biochem. Mol. Biol., 37, 287, 2002.
35. Ajouz, B. et al., Release of thioredoxin via the mechanosensitive channel MscL during osmotic downshock of Escherichia coli cells, J. Biol. Chem., 273, 26670, 1998.
36. Kachlany, S.C. et al., Nonspecific adherence by Actinobacillus actinomycetemcomitans requires genes widespread in Bacteria and Archaea, J. Bacteriol., 182, 6169, 2000.
37. Desvaux, M. and Hébraud, M., The protein secretion systems in Listeria: Inside-out bacterial virulence, FEMS Microbiol. Rev., 30, 774, 2006.
38. Desvaux, M. et al., The general secretory pathway: A general misnomer? Trends Microbiol., 12, 306, 2004.
39. Cao, T.B. and Saier, M.H., Jr., The general protein secretory pathway: Phylogenetic analyses leading to evolutionary conclusions, Biochim. Biophys. Acta-Biomembr., 1609, 115, 2003.
40. Valent, Q.A. et al., The Escherichia coli SRP and SecB targeting pathways converge at the translocon, EMBO J., 17, 2504, 1998.
41. Van Wely, K.H.M. et al., Translocation of proteins across the cell envelope of Gram-positive bacteria, FEMS Microbiol. Rev., 25, 437, 2001.
42. de Keyzer, J., van der Does, C., and Driessen, A.J., The bacterial translocase: A dynamic protein channel complex, Cell Mol. Life Sci., 60, 2034, 2003.
43. Economou, A. et al., SecA membrane cycling at SecYEG is driven by distinct ATP binding and hydrolysis events and is regulated by SecD and SecF, Cell, 83, 1171, 1995.
44. Lenz, L.L. and Portnoy, D.A., Identification of a second Listeria secA gene associated with protein secretion and the rough phenotype, Mol. Microbiol., 45, 1043, 2002.
45. Bensing, B.A. and Sullam, P.M., An accessory sec locus of Streptococcus gordonii is required for export of the surface protein GspB and for normal levels of binding to human platelets, Mol. Microbiol., 44, 1081, 2002.
46. Lenz, L.L. et al., SecA2-dependent secretion of autolytic enzymes promotes Listeria monocytogenes pathogenesis, Proc. Natl. Acad. Sci. USA, 100, 12432, 2003.
47. Dramsi, S. et al., FbpA, a novel multifunctional Listeria monocytogenes virulence factor, Mol. Microbiol., 53, 639, 2004.
48. Froderberg, L. et al., Versatility of inner membrane protein biogenesis in Escherichia coli, Mol. Microbiol., 47, 1015, 2003.
49. Tjalsma, H., Bron, S., and van Dijl, J.M., Complementary impact of paralogous Oxa1-like proteins of Bacillus subtilis on post-translocational stages in protein secretion, J. Biol. Chem., 278, 15622, 2003.
50. Madden, J.C., Ruiz, N., and Caparon, M., Cytolysin-mediated translocation (CMT): A functional equivalent of Type III secretion in Gram-positive bacteria, Cell, 104, 143, 2001.
51. Desvaux, M. et al., Type III secretion: What’s in a name? Trends Microbiol., 14, 157, 2006.
52. Bonnemain, C. et al., Differential roles of multiple signal peptidases in the virulence of Listeria monocytogenes, Mol. Microbiol., 51, 1251, 2004.
53. Raynaud, C. and Charbit, A., Regulation of expression of type I signal peptidases in Listeria monocytogenes, Microbiology, 151, 3769, 2005.
54. Reglier-Poupet, H. et al., Maturation of lipoproteins by type II signal peptidase is required for phagosomal escape of Listeria monocytogenes, J. Biol. Chem., 278, 49469, 2003.
55. Navarre, W.W. and Schneewind, O., Surface proteins of Gram-positive bacteria and mechanisms of their targeting to the cell wall envelope, Microbiol. Mol. Biol. Rev., 63, 174, 1999.
56. Mazmanian, S.K., Ton-That, H., and Schneewind, O., Sortase-catalyzed anchoring of surface proteins to the cell wall of Staphylococcus aureus, Mol. Microbiol., 40, 1049, 2001.
57. Dramsi, S., Trieu-Cuot, P., and Bierne, H., Sorting sortases: A nomenclature proposal for the various sortases of Gram-positive bacteria, Res. Microbiol., 156, 289, 2005.
58. Pucciarelli, M.G. et al., Identification of substrates of the Listeria monocytogenes sortases A and B by a nongel proteomic analysis, Proteomics, 5, 4808, 2005.
59. Bierne, H. et al., Inactivation of the srtA gene in Listeria monocytogenes inhibits anchoring of surface proteins and affects virulence, Mol. Microbiol., 43, 869, 2002.
60. Lee, S.G., Pancholi, V., and Fischetti, V.A., Characterization of unique glycosylated anchor endopeptidase that cleaves the LPXTG sequence motif of cell surface proteins of Gram-positive bacteria, J. Biol. Chem., 277, 46912, 2002.
61. Lee, S.G. and Fischetti, V.A., Purification and characterization of LPXTGase from Staphylococcus aureus: The amino acid composition mirrors that found in the peptidoglycan, J. Bacteriol., 188, 389, 2006.
62. Kleinkauf, H. and von Dohren, H., The nonribosomal peptide biosynthetic system-On the origins of structural diversity of peptides, cyclopeptides and related compounds, Antonie Van Leeuwenhoek, 67, 229, 1995.
63. Fekkes, P. and Driessen, A.J., Protein targeting to the bacterial cytoplasmic membrane, Microbiol. Mol. Biol. Rev., 63, 161, 1999.
64. von Heijne, G., A new method for predicting signal sequence cleavage sites, Nucleic Acids Res., 14, 4683, 1986.
65. Menne, K.M., Hermjakob, H., and Apweiler, R., A comparison of signal sequence prediction methods using a test set of signal peptides, Bioinformatics, 16, 741, 2000.
66. Nielsen, H. et al., Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites, Protein Eng., 10, 1, 1997.
67. Bendtsen, J.D. et al., Improved prediction of signal peptides: SignalP 3.0, J. Mol. Biol., 340, 783, 2004.
68. Zhang, Z. and Henzel, W.J., Signal peptide prediction based on analysis of experimentally verified cleavage sites, Protein Sci., 13, 2819, 2004.
69. Hiller, K. et al., PrediSi: Prediction of signal peptides and their cleavage positions, Nucleic Acids Res., 32, W375, 2004.
70. Gomi, M., Sonoyama, M., and Mitaku, S., High performance system for signal peptide prediction: SOSUIsignal, Chem-Bio Info. J., 4, 142, 2004.
71. Käll, L., Krogh, A., and Sonnhammer, E.L., A combined transmembrane topology and signal peptide prediction method, J. Mol. Biol., 338, 1027, 2004.
72. Cai, Y.D., Lin, S.L., and Chou, K.C., Support vector machines for prediction of protein signal sequences and their cleavage sites, Peptides, 24, 159, 2003.
73. Gardy, J.L. et al., PSORT-B: Improving protein subcellular localization prediction for Gram-negative bacteria, Nucleic Acids Res., 31, 3613, 2003.
74. Gardy, J.L. et al., PSORTb v.2.0: Expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis, Bioinformatics, 21, 617, 2005.
75. Altschul, S.F. et al., Basic local alignment search tool, J. Mol. Biol., 215, 403, 1990.
76. Choo, K.H., Tan, T.W., and Ranganathan, S., SPdb-A signal peptide database, BMC Bioinformatics, 6, 249, 2005.
77. Reinhardt, A. and Hubbard, T., Using neural networks for prediction of the subcellular location of proteins, Nucleic Acids Res., 26, 2230, 1998.
78. Hua, S. and Sun, Z., Support vector machine approach for protein subcellular localization prediction, Bioinformatics, 17, 721, 2001.
79. Yu, C.S., Lin, C.J., and Hwang, J.K., Predicting subcellular localization of proteins for Gram-negative bacteria by support vector machines based on n-peptide compositions, Protein Sci., 13, 1402, 2004.
80. Yu, C.S. et al., Prediction of protein subcellular localization, Proteins, 64, 643, 2006.
81. Nair, R. and Rost, B., Mimicking cellular sorting improves prediction of subcellular localization, J. Mol. Biol., 348, 85, 2005.
82. Dönnes, P. and Höglund, A., Predicting protein subcellular localization: Past, present, and future, Geno. Prot. Bioinfo., 2, 209, 2004.
83. Lu, Z. et al., Predicting subcellular localization of proteins using machine-learned classifiers, Bioinformatics, 20, 547, 2004.
84. Gardy, J.L. and Brinkman, F.S., Methods for predicting bacterial protein subcellular localization, Nat. Rev. Microbiol., 4, 741, 2006.
85. Shen, H.B. and Chou, K.C., Gpos-PLoc: An ensemble classifier for predicting subcellular localization of Gram-positive bacterial proteins, Protein Eng. Des. Sel., 20, 39, 2007.
86. Guo, T. et al., DBSubLoc: Database of protein subcellular localization, Nucleic Acids Res., 32, D122, 2004.
87. Rey, S. et al., PSORTdb: A protein subcellular localization database for bacteria, Nucleic Acids Res., 33, D164, 2005.
88. Lu, P. et al., PA-GOSUB: A searchable database of model organism protein sequences with their predicted gene ontology molecular function and subcellular localization, Nucleic Acids Res., 33, D147, 2005.
89. Billion, A. et al., Augur-A computational pipeline for whole genome microbial surface protein prediction and classification, Bioinformatics, 22, 2819, 2006.
90. Trost, M. et al., Comparative proteome analysis of secretory proteins from pathogenic and nonpathogenic Listeria species, Proteomics, 5, 1544, 2005.
91. Berks, B.C., Palmer, T., and Sargent, F., Protein targeting by the bacterial twin-arginine translocation (Tat) pathway, Curr. Opin. Microbiol., 8, 174, 2005.
92. Müller, M., Twin-arginine-specific protein export in Escherichia coli, Res. Microbiol., 156, 131, 2005.
93. Lee, P.A., Tullman-Ercek, D., and Georgiou, G., The bacterial twin-arginine translocation pathway, Annu. Rev. Microbiol., 60, 373, 2006.
94. Mori, H. and Cline, K., Post-translational protein translocation into thylakoids by the Sec and {increment}pH-dependent pathways, Biochim. Biophys. Acta-Mol. Cell Res., 1541, 80, 2001.
95. Bruser, T. and Sanders, C., An alternative model of the twin arginine translocation system, Microbiol. Res., 158, 7, 2003.
96. Sargent, F., Berks, B.C., and Palmer, T., Pathfinders and trailblazers: A prokaryotic targeting system for transport of folded proteins, FEMS Microbiol. Lett., 254, 198, 2006.
97. Alami, M. et al., Differential interactions between a twin-arginine signal peptide and its translocase in Escherichia coli, Mol. Cell, 12, 937, 2003.
98. Gohlke, U. et al., The TatA component of the twin-arginine protein transport system forms channel complexes of variable diameter, Proc. Natl. Acad. Sci. USA, 102, 10482, 2005.
99. Dilks, K. et al., Prokaryotic utilization of the twin-arginine translocation pathway: A genomic survey, J. Bacteriol., 185, 1478, 2003.
100. Rose, R.W. et al., Adaptation of protein secretion to extremely high-salt conditions by extensive use of the twin-arginine translocation pathway, Mol. Microbiol., 45, 943, 2002.
101. Bendtsen, J.D. et al., Prediction of twin-arginine signal peptides, BMC Bioinformatics, 6, 167, 2005.
102. Yen, M.R. et al., Sequence and phylogenetic analyses of the twin-arginine targeting (Tat) protein export system, Arch. Microbiol., 177, 441, 2002.
103. Ize, B., Gerard, F., and Wu, L.F., In vivo assessment of the Tat signal peptide specificity in Escherichia coli, Arch. Microbiol., 178, 548, 2002.
104. Ignatova, Z. et al., Unusual signal peptide directs penicillin amidase from Escherichia coli to the Tat translocation machinery, Biochem. Biophys. Res. Commun., 291, 146, 2002.
105. Robinson, C. and Bolhuis, A., Tat-dependent protein targeting in prokaryotes and chloroplasts, Biochim. Biophys. Acta-Mol. Cell Res., 1694, 135, 2004.
106. Peabody, C.R. et al., Type II protein secretion and its relationship to bacterial Type 4 pili and archaeal flagella, Microbiology, 149, 3051, 2003.
107. Chung, Y.S. and Dubnau, D., All seven comG open reading frames are required for DNA binding during transformation of competent Bacillus subtilis, J. Bacteriol., 180, 41, 1998.
108. Claverys, J.P. and Martin, B., Bacterial “competence” genes: Signatures of active transformation, or only remnants? Trends Microbiol., 11, 161, 2003.
109. Chen, I. and Dubnau, D., DNA uptake during bacterial transformation, Nat. Rev. Microbiol., 2, 241, 2004.
110. Dubnau, D., Binding and transport of transforming DNA by Bacillus subtilis: The role of Type-4 pilinlike proteins-A review, Gene, 192, 191, 1997.
111. Filloux, A., The underlying mechanisms of Type II protein secretion, Biochim. Biophys. Acta, 1694, 163, 2004.
112. Chung, Y.S. and Dubnau, D., ComC is required for the processing and translocation of comGC, a pilinlike competence protein of Bacillus subtilis, Mol. Microbiol., 15, 543, 1995.
113. LaPointe, C.F. and Taylor, R.K., The type 4 prepilin peptidases comprise a novel family of aspartic acid proteases, J. Biol. Chem., 275, 1502, 2000.
114. Chen, I., Provvedi, R., and Dubnau, D., A macromolecular complex formed by a pilin-like protein in competent Bacillus subtilis, J. Biol. Chem., 281, 21720, 2006.
115. de Castro, E. et al., ScanProsite: Detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins, Nucleic Acids Res., 34, W362, 2006.
116. Peel, M., Donachie, W., and Shaw, A., Temperature-dependent expression of flagella of Listeria monocytogenes studied by electron microscopy, SDS-PAGE and western blotting, J. Gen. Microbiol., 134, 2171, 1988.
117. Way, S.S. et al., Characterization of flagellin expression and its role in Listeria monocytogenes infection and immunity, Cell Microbiol., 6, 235, 2004.
118. Sanchez-Campillo, M. et al., Modulation of DNA topology by flaR, a new gene from Listeria monocytogenes, Mol. Microbiol., 18, 801, 1995.
119. Michel, E. et al., Characterization of a large motility gene cluster containing the cheR, motAB genes of Listeria monocytogenes and evidence that PrfA down-regulates motility genes, FEMS Microbiol. Lett., 169, 341, 1998.
120. Knudsen, G.M., Olsen, J.E., and Dons, L., Characterization of DegU, a response regulator in Listeria monocytogenes, involved in regulation of motility and contributes to virulence, FEMS Microbiol. Lett., 240, 171, 2004.
121. Grundling, A. et al., Listeria monocytogenes regulates flagellar motility gene expression through MogR, a transcriptional repressor required for virulence, Proc. Natl. Acad. Sci. USA, 101, 12318, 2004.
122. Shen, A. et al., A bifunctional O-GlcNAc transferase governs flagellar motility through antirepression, Genes Dev., 20, 3283, 2006.
123. Schirm, M. et al., Flagellin from Listeria monocytogenes is glycosylated with β-O-linked N-acetylglucosamine, J. Bacteriol., 186, 6721, 2004.
124. Lemon, K.P., Higgins, D.E., and Kolter, R., Flagellar motility is critical for Listeria monocytogenes biofilm formation, J. Bacteriol., 189, 4418, 2007.
125. O’Neil, H.S. and Marquis, H., Listeria monocytogenes flagella are used for motility, not as adhesins, to increase host cell invasion, Infect. Immun., 74, 6675, 2006.
126. Popowska, M., Analysis of the peptidoglycan hydrolases of Listeria monocytogenes: Multiple enzymes with multiple functions, Pol. J. Microbiol., 53, 29, 2004.
127. Popowska, M. and Markiewicz, Z., Murein-hydrolyzing activity of flagellin FlaA of Listeria monocytogenes, Pol. J. Microbiol., 53, 237, 2004.
128. Macnab, R.M., How bacteria assemble flagella, Annu. Rev. Microbiol., 57, 77, 2003.
129. Aizawa, S.I., Bacterial flagella and Type III secretion systems, FEMS Microbiol. Lett., 202, 157, 2001.
130. Journet, L., Hughes, K.T., and Cornelis, G.R., Type III secretion: A secretory pathway serving both motility and virulence, Mol. Membr. Biol. 22, 41, 2005.
131. Macnab, R.M., Type III flagellar protein export and flagellar assembly, Biochim. Biophys. Acta-Mol. Cell Res., 1694, 207, 2004.
132. Minamino, T. and Namba, K., Self-assembly and Type III protein export of the bacterial flagellum, J. Mol. Microbiol. Biotechnol., 7, 5, 2004.
133. Troisfontaines, P. and Cornelis, G.R., Type III secretion: More systems than you think, Physiology (Bethesda), 20, 326, 2005.
134. Young, G.M., Schmiel, D.H., and Miller, V.L., A new pathway for the secretion of virulence factors by bacteria, the flagellar export apparatus functions as a protein-secretion system, Proc. Natl. Acad. Sci. USA, 96, 6456, 1999.
135. Cornelis, G.R., The Type III secretion injectisome, Nat. Rev. Microbiol., 4, 811, 2006.
136. Ghelardi, E. et al., Requirement of flhA for swarming differentiation, flagellin export, and secretion of virulence-associated proteins in Bacillus thuringensis, J. Bacteriol., 184, 6424, 2002.
137. Wang, I.N., Smith, D.L., and Young, R., Holins: The protein clocks of bacteriophage infections, Annu. Rev. Microbiol., 54, 799, 2000.
138. Bayles, K.W., Are the molecular strategies that control apoptosis conserved in bacteria? Trends Microbiol., 11, 306, 2003.
139. Young, R. and Blasi, U., Holins: Form and function in bacteriophage lysis, FEMS Microbiol. Rev., 17, 191, 1995.
140. Bernhardt, T.G. et al., Breaking free: “Protein antibiotics” and phage lysis, Res. Microbiol., 153, 493, 2002.
141. Loessner, M.J., Bacteriophage endolysins-Current state of research and applications, Curr. Opin. Microbiol., 8, 480, 2005.
142. Ziedaite, G. et al., The holin protein of bacteriophage PRD1 forms a pore for small-molecule and endolysin translocation, J. Bacteriol., 187, 5397, 2005.
143. Bläsi, U. and Young, R., Two beginnings for a single purpose: The dual-start holins in the regulation of phage lysis, Mol. Microbiol., 21, 675, 1996.
144. Groicher, K.H. et al., The Staphylococcus aureus lrgAB operon modulates murein hydrolase activity and penicillin tolerance, J. Bacteriol., 182, 1794, 2000.
145. Rice, K.C. et al., The Staphylococcus aureus cidAB operon: Evaluation of its role in regulation of murein hydrolase activity and penicillin tolerance, J. Bacteriol., 185, 2635, 2003.
146. Saier, M.H., Jr., Tran, C.V., and Barabote, R.D., TC-DB: The transporter classification database for membrane transport protein analyses and information, Nucleic Acids Res., 34, D181-D186, 2006.
147. Young, R., Bacteriophage holins: Deadly diversity, J. Mol. Microbiol. Biotechnol., 4, 21, 2002.
148. Ramanculov, E. and Young, R., Functional analysis of the phage T4 holin in a lambda context, Mol. Genet. Genomics, 265, 345, 2001.
149. Loessner, M.J. et al., Complete nucleotide sequence, molecular analysis and genome structure of bacteriophage A118 of Listeria monocytogenes: Implications for phage evolution, Mol. Microbiol., 35, 324, 2000.
150. Vukov, N. et al., Functional regulation of the Listeria monocytogenes bacteriophage A118 holin by an intragenic inhibitor lacking the first transmembrane domain, Mol. Microbiol., 48, 173, 2003.
151. Loessner, M.J., Wendlinger, G., and Scherer, S., Heterogeneous endolysins in Listeria monocytogenes bacteriophages: A new class of enzymes and evidence for conserved holin genes within the siphoviral lysis cassettes, Mol. Microbiol., 16, 1231, 1995.
152. Tan, K.S., Wee, B.Y., and Song, K.P., Evidence for holin function of tcdE gene in the pathogenicity of Clostridium difficile, J. Med. Microbiol., 50, 613, 2001.
153. Mukherjee, K. et al., Proteins released during high toxin production in Clostridium difficile, Microbiology, 148, 2245, 2002.
154. Pallen, M.J., The ESAT-6/WXG100 superfamily- and a new Gram-positive secretion system? Trends Microbiol., 10, 209, 2002.
155. Converse, S.E. and Cox, J.S., A protein secretion pathway critical for Mycobacterium tuberculosis virulence is conserved and functional in Mycobacterium smegmatis, J. Bacteriol., 187, 1238, 2005.
156. Champion, P.A. et al., C-terminal signal sequence promotes virulence factor secretion in Mycobacterium tuberculosis, Science, 313, 1632, 2006.
157. Stanley, S.A. et al., Acute infection and macrophage subversion by Mycobacterium tuberculosis require a specialized secretion system, Proc. Natl. Acad. Sci. USA, 100, 13001, 2003.
158. Okkels, L.M. and Andersen, P., Protein-protein interactions of proteins from the ESAT-6 family of Mycobacterium tuberculosis, J. Bacteriol., 186, 2487, 2004.
159. Renshaw, P.S. et al., Conclusive evidence that the major T-cell antigens of the Mycobacterium tuberculosis complex ESAT-6 and CFP-10 form a tight, 1:1 complex and characterization of the structural properties of ESAT-6, CFP-10, and the ESAT-6*CFP-10 complex. Implications for pathogenesis and virulence, J. Biol. Chem., 277, 21598, 2002.
160. Burts, M.L. et al., EsxA and EsxB are secreted by an ESAT-6-like system that is required for the pathogenesis of Staphylococcus aureus infections, Proc. Natl. Acad. Sci. USA, 102, 1169, 2005.
161. Guinn, K.M. et al., Individual RD1-region genes are required for export of ESAT-6/CFP-10 and for virulence of Mycobacterium tuberculosis, Mol. Microbiol., 51, 359, 2004.
162. Brodin, P. et al., ESAT-6 proteins: Protective antigens and virulence factors? Trends Microbiol., 12, 500, 2004.
163. Way, S.S. and Wilson, C.B., The Mycobacterium tuberculosis ESAT-6 homologue in Listeria monocytogenes is dispensable for growth in vitro and in vivo, Infect. Immun., 73, 6151, 2005.
164. Shockman, G.D. and Barrett, J.F., Structure, function, and assembly of cell walls of Gram-positive bacteria, Annu. Rev. Microbiol., 37, 501, 1983.
165. Archibald, A.R., Structure and assembly of the cell wall in Bacillus subtilis, Biochem. Soc. Trans., 13, 990, 1985.
166. Schäffer, C. and Messner, P., The structure of secondary cell wall polymers: How Gram-positive bacteria stick their cell walls together, Microbiology, 151, 643, 2005.
167. Sára, M. and Sleytr, U.B., S-Layer proteins, J. Bacteriol., 182, 859, 2000.
168. Klein, C. et al., The membrane proteome of Halobacterium salinarum, Proteomics, 5, 180, 2005.
169. Harris, M.A. et al., The Gene Ontology (GO) database and informatics resource, Nucleic Acids Res., 32, D258, 2004.
170. Samuelson, J.C. et al., YidC mediates membrane protein insertion in bacteria, Nature, 406, 637, 2000.
171. Luirink, J. et al., Biogenesis of inner membrane proteins in Escherichia coli, Annu. Rev. Microbiol., 59, 329, 2005.
172. Dalbey, R.E. and Kuhn, A., YidC family members are involved in the membrane insertion, lateral integration, folding, and assembly of membrane proteins, J. Cell Biol., 166, 769, 2004.
173. Van Bloois, E. et al., Distinct requirements for translocation of the N-tail and C-tail of the Escherichia coli inner membrane protein CyoA, J. Biol. Chem., 281, 10002, 2006.
174. Van der Laan, M., Nouwen, N.P., and Driessen, A.J., YidC-An evolutionary conserved device for the assembly of energy-transducing membrane protein complexes, Curr. Opin. Microbiol., 8, 182, 2005.
175. de Gier, J.W. and Luirink, J., The ribosome and YidC. New insights into the biogenesis of Escherichia coli inner membrane proteins, EMBO Rep., 4, 939, 2003.
176. Dalbey, R.E. and Chen, M., Sec-translocase mediated membrane protein biogenesis, Biochim. Biophys. Acta-Mol. Cell Res., 1694, 37, 2004.
177. von Heijne, G., Membrane-protein topology, Nat. Rev. Mol. Cell Biol., 7, 909, 2006.
178. White, S.H. and von Heijne, G., The machinery of membrane protein assembly, Curr. Opin. Struct. Biol., 14, 397, 2004.
179. Goder, V. and Spiess, M., Topogenesis of membrane proteins: determinants and dynamics, FEBS Lett, 504, 87, 2001.
180. Kocks, C. et al., L. monocytogenes-induced actin assembly requires the actA gene product, a surface protein, Cell, 68, 521, 1992.
181. Borezee, E. et al., SvpA, a novel surface virulence-associated protein required for intracellular survival of Listeria monocytogenes, Microbiology, 147, 2913, 2001.
182. Cabanes, D. et al., Surface proteins and the pathogenic potential of Listeria monocytogenes, Trends Microbiol., 10, 238, 2002.
183. Froderberg, L. et al., Targeting and translocation of two lipoproteins in Escherichia coli via the SRP/Sec/YidC pathway, J. Biol. Chem., 279, 31026, 2004.
184. Tjalsma, H. et al., The role of lipoprotein processing by signal peptidase II in the Gram-positive eubacterium Bacillus subtilis. Signal peptidase II is required for the efficient secretion of α-amylase, a nonlipoprotein, J. Biol. Chem., 274, 1698, 1999.
185. Hayashi, S. and Wu, H.C., Lipoproteins in bacteria, J. Bioenerg. Biomembr., 22, 451, 1990.
186. Baumgärtner, M. et al., Inactivation of Lgt allows systematic characterization of lipoproteins from Listeria monocytogenes, J. Bacteriol., 189, 313, 2007.
187. Sankaran, K. and Wu, H.C., Lipid modification of bacterial prolipoprotein. Transfer of diacylglyceryl moiety from phosphatidylglycerol, J. Biol. Chem., 269, 19701, 1994.
188. Garcia-Del Portillo, F. and Cossart, P., An important step in Listeria lipoprotein research, J. Bacteriol., 189, 294, 2007.
189. Hulo, N. et al., The PROSITE database, Nucleic Acids Res., 34, D227, 2006.
190. Sutcliffe, I. and Harrington, D.J., Pattern searches for the identification of putative lipoprotein genes in Gram-positive bacterial genomes, Microbiology, 148, 2065, 2002.
191. Babu, M.M. and Sankaran, K., DOLOP-database of bacterial lipoproteins, Bioinformatics, 18, 641, 2002.
192. Juncker, A.S. et al., Prediction of lipoprotein signal peptides in Gram-negative bacteria, Protein Sci., 12, 1652, 2003.
193. Fariselli, P., Finocchiaro, G., and Casadio, R., SPEPlip: The detection of signal peptide and lipoprotein cleavage sites, Bioinformatics, 19, 2498, 2003.
194. Taylor, P.D. et al., LipPred: A Web server for accurate prediction of lipoprotein signal sequences and cleavage sites, Bioinformation, 1, 335, 2006.
195. Sutcliffe, I.C. and Russell, R.R., Lipoproteins of Gram-positive bacteria, J. Bacteriol., 177, 1123, 1995.
196. + T cell-stimulating antigen of pathogenic bacteria by expression cloning, J. Exp. Med., 182, 1751, 1995.
197. Ko, R. and Smith, L.T., Identification of an ATP-driven, osmoregulated glycine betaine transport system in Listeria monocytogenes, Appl. Environ. Microbiol., 65, 4040, 1199.
198. Fraser, K.R. et al., Identification and characterization of an ATP binding cassette L-carnitine transporter in Listeria monocytogenes, Appl. Environ. Microbiol., 66, 4696, 2000.
199. Borezee, E., Pellegrini, E., and Berche, P., OppA of Listeria monocytogenes, an oligopeptide-binding protein required for bacterial growth at low temperature and involved in intracellular survival, Infect. Immun., 68, 7069, 2000.
200. Reglier-Poupet, H. et al., Identification of LpeA, a PsaA-like membrane protein that promotes cell entry by Listeria monocytogenes, Infect. Immun., 71, 474, 2003.
201. Gal, L. et al., CelG from Clostridium cellulolyticum: A multidomain endoglucanase acting efficiently on crystalline cellulose, J. Bacteriol., 179, 6595, 1997.
202. Gaudin, C. et al., CelE, a multidomain cellulase from Clostridium cellulolyticum: A key enzyme in the cellulosome? J. Bacteriol., 182, 1910, 2000.
203. Brinster, S., Furlan, S., and Serror, P., C-terminal WXL domain mediates cell wall binding in Enterococcus faecalis and other Gram-positive bacteria, J. Bacteriol., 189, 1244, 2007.
204. Popowska, M. and Markiewicz, Z., Classes and functions of Listeria monocytogenes surface proteins, Pol. J. Microbiol., 53, 75, 2004.
205. Altschul, S.F. et al., Gapped BLAST and PSI-BLAST: A new generation of protein database search programs, Nucleic Acids Res., 25, 3389, 1997.
206. Eddy, S.R., Hidden Markov models, Curr. Opin. Struct. Biol., 6, 361, 1996.
207. Mulder, N.J. et al., New developments in the InterPro database, Nucleic Acids Res., 35, D224, 2007.
208. Bateman, A. et al., The Pfam protein families database, Nucleic Acids Res., 32, D138, 2004.
209. Schultz, J. et al., SMART, a simple modular architecture research tool: Identification of signaling domains, Proc. Natl. Acad. Sci. USA, 95, 5857, 1998.
210. Selengut, J.D. et al., TIGRFAMs and genome properties: Tools for the assignment of molecular function and biological process in prokaryotic genomes, Nucleic Acids Res., 35, D260, 2007.
211. Wilson, D. et al., The SUPERFAMILY database in 2007: Families and functions, Nucleic Acids Res., 35, D308, 2007.
212. Pallen, M.J. et al., An embarrassment of sortase-A richness of substrates? Trends Microbiol., 9, 97, 2001.
213. Marraffini, L.A., Dedent, A.C., and Schneewind, O., Sortases and the art of anchoring proteins to the envelopes of Gram-positive bacteria, Microbiol. Mol. Biol. Rev., 70, 192, 2006.
214. Paterson, G.K. and Mitchell, T.J., The biology of Gram-positive sortase enzymes, Trends Microbiol., 12, 89, 2004.
215. Ton-That, H., Marraffini, L.A., and Schneewind, O., Protein sorting to the cell wall envelope of Grampositive bacteria, Biochim. Biophys. Acta-Mol. Cell Res., 1694, 269, 2004.
216. Bierne, H. et al., Sortase B, a new class of sortase in Listeria monocytogenes, J. Bacteriol., 186, 1972, 2004.
217. Garandeau, C. et al., The sortase SrtA of Listeria monocytogenes is involved in processing of internalin and in virulence, Infect. Immun., 70, 1382, 2002.
218. Steen, A. et al., Cell wall attachment of a widely distributed peptidoglycan binding domain is hindered by cell wall constituents, J. Biol. Chem., 278, 23874, 2003.
219. Dussurget, O., Pizarro-Cerda, J., and Cossart, P., Molecular determinants of Listeria monocytogenes virulence, Annu. Rev. Microbiol., 58, 587, 2004.
220. Gaillard, J.L. et al., Entry of L. monocytogenes into cells is mediated by internalin, a repeat protein reminiscent of surface antigens from Gram-positive cocci, Cell, 65, 1127, 1991.
221. Braun, L. et al., InlB: An invasion protein of Listeria monocytogenes with a novel type of surface association, Mol. Microbiol., 25, 285, 1997.
222. Jonquieres, R. et al., Interaction between the protein InlB of Listeria monocytogenes and lipoteichoic acid: A novel mechanism of protein association at the surface of Gram-positive bacteria, Mol. Microbiol., 34, 902, 1999.
223. Marino, M. et al., GW domains of the Listeria monocytogenes invasion protein InlB are SH3-like and mediate binding to host ligands, EMBO J., 21, 5623, 2002.
224. Milohanic, E. et al., Transcriptome analysis of Listeria monocytogenes identifies three groups of genes differently regulated by PrfA, Mol. Microbiol., 47, 1613, 2003.
225. Siezen, R. et al., Lactobacillus plantarum gene clusters encoding putative cell-surface protein complexes for carbohydrate utilization are conserved in specific Gram-positive bacteria, BMC Genomics, 7, 126, 2006.
226. Nölling, J. et al., Genome sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum, J. Bacteriol., 183, 4823, 2001.
227. Baba, T. and Schneewind, O., Target cell specificity of a bacteriocin molecule: A C-terminal signal directs lysostaphin to the cell wall of Staphylococcus aureus, EMBO J., 15, 4789, 1996.
228. Anantharaman, V. and Aravind, L., Evolutionary history, structural features and biochemical diversity of the NlpC/P60 superfamily of enzymes, Genome Biol., 4, R11, 2003.
229. Scott, J.R. and Barnett, T.C., Surface proteins of Gram-positive bacteria and how they get there, Annu. Rev. Microbiol., 60, 397, 2006.
230. Bendtsen, J.D. et al., Nonclassical protein secretion in bacteria, BMC Microbiol., 5, 58, 2005.
231. Guiral, S. et al., Competence-programmed predation of noncompetent cells in the human pathogen Streptococcus pneumoniae: Genetic requirements, Proc. Natl. Acad. Sci. USA, 102, 8710, 2005.
232. Bergmann, S., Rohde, M., and Hammerschmidt, S., Glyceraldehyde-3-phosphate dehydrogenase of Streptococcus pneumoniae is a surface-displayed plasminogen-binding protein, Infect. Immun., 72, 2416, 2004.
233. Klose, J., Protein mapping by combined isoelectric focusing and electrophoresis of mouse tissues. A novel approach to testing for induced point mutations in mammals, Humangenetik, 26, 231, 1975.
234. O’Farrell, P.H., High resolution two-dimensional electrophoresis of proteins, J. Biol. Chem., 250, 4007, 1975.
235. Scheele, G.A., Two-dimensional gel analysis of soluble proteins. Characterization of guinea pig exocrine pancreatic proteins, J. Biol. Chem., 250, 5375, 1975.
236. VanBogelen, R.A. et al., The gene-protein database of Escherichia coli: Edition 5, Electrophoresis, 13, 1014, 1992.
237. Pasquali, C. et al., Two-dimensional gel electrophoresis of Escherichia coli homogenates: The Escherichia coli SWISS-2DPAGE database, Electrophoresis, 17, 547, 1996.
238. Folio, P. et al., Two-dimensional electrophoresis database of Listeria monocytogenes EGDe proteome and proteomic analysis of mid-log and stationary growth phase cells, Proteomics, 4, 3187, 2004.
239. Cordwell, S.J., Technologies for bacterial surface proteomics, Curr. Opin. Microbiol., 9, 320, 2006.
240. Santoni, V., Molloy, M., and Rabilloud, T., Membrane proteins and proteomics: Un amour impossible? Electrophoresis, 21, 1054, 2000.
241. Santoni, V. et al., Membrane proteomics: use of additive main effects with multiplicative interaction model to classify plasma membrane proteins according to their solubility and electrophoretic properties, Electrophoresis, 21, 3329, 2000.
242. Mastro, R. and Hall, M., Protein delipidation and precipitation by tri-n-butylphosphate, acetone, and methanol treatment for isoelectric focusing and two-dimensional gel electrophoresis, Anal. Biochem., 273, 313, 1999.
243. Deshusses, J.M. et al., Exploitation of specific properties of trifluoroethanol for extraction and separation of membrane proteins, Proteomics, 3, 1418, 2003.
244. Planchon, S. et al., Proteomic analysis of cell envelope from Staphylococcus xylosus C2a, a coagulasenegative Staphylococcus, J. Proteome Res., 6, 3566, 2007.
245. Kotiranta, A. et al., Surface structure, hydrophobicity, phagocytosis, and adherence to matrix proteins of Bacillus cereus cells with and without the crystalline surface protein layer, Infect. Immun., 66, 4895, 1998.
246. Tresse, O. et al., Comparative evaluation of adhesion, surface properties, and surface protein composition of Listeria monocytogenes strains after cultivation at constant pH of 5 and 7, J. Appl. Microbiol., 101, 53, 2006.
247. Calvo, E. et al., Analysis of the Listeria cell wall proteome by two-dimensional nanoliquid chromatography coupled to mass spectrometry, Proteomics, 5, 433, 2005.
248. Ren, Q., Kang, K.H., and Paulsen, I.T., TransportDB: A relational database of cellular membrane transport systems, Nucl. Acids Res., 32, D284, 2004.
249. Hofmann, K. and Stoffel, W., PROFILEGRAPH: An interactive graphical tool for protein sequence analysis, Comput. Appl. Biosci., 8, 331, 1992.
250. Claros, M.G. and von Heijne, G., TopPred II: An improved software for membrane protein structure predictions, Comput. Appl. Biosci., 10, 685, 1994.
251. Rost, B. et al., Transmembrane helices predicted at 95% accuracy, Protein Sci., 4, 521, 1995.
252. Csero, M. et al., Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: The dense alignment surface method, Protein Eng., 10, 673, 1997.
253. Persson, B. and Argos, P., Prediction of membrane protein topology utilizing multiple sequence alignments, J. Protein Chem., 16, 453, 1997.
254. Kihara, D., Shimizu, T., and Kanehisa, M., Prediction of membrane proteins based on classification of transmembrane segments, Protein Eng., 11, 961, 1998.
255. Sonnhammer, E.L., von Heijne, G., and Krogh, A., A hidden Markov model for predicting transmembrane helices in protein sequences. Proc. Int. Conf. Intell. Syst. Mol. Biol., 6, 175, 1998.
256. Hirokawa, T., Boon-chieng, S., and Mitaku, S., SOSUI: Classification and secondary structure prediction system for membrane proteins, Bioinformatics, 14, 378, 1998.
257. Pasquier, C. and Hamodrakas, S.J., An hierarchical artificial neural network system for the classification of transmembrane proteins, Protein Eng., 12, 631, 1999.
258. Pilpel, Y., Ben-Tal, N., and Lancet, D., kPROT: A knowledge-based scale for the propensity of residue orientation in transmembrane segments. Application to membrane protein structure prediction, J. Mol. Biol., 294, 921, 1999.
259. Senes, A., Gerstein, M., and Engelman, D.M., Statistical analysis of amino acid patterns in transmembrane helices: The GxxxG motif occurs frequently and in association with beta-branched residues at neighboring positions, J. Mol. Biol., 296, 921, 2000.
260. Tusnady, G.E. and Simon, I., The HMMTOP transmembrane topology prediction server, Bioinformatics, 17, 849, 2001.
261. Deber, C.M. et al., TM Finder: A prediction program for transmembrane protein segments using a combination of hydrophobicity and nonpolar phase helicity scales, Protein Sci., 10, 212, 2001.
262. Cserzo, M. et al., On filtering false positive transmembrane protein predictions, Protein Eng., 15, 745, 2002.
263. Juretic, D., Zoranic, L., and Zucic, D., Basic charge clusters and predictions of membrane protein topology, J. Chem. Inf. Comput. Sci., 42, 620, 2002.
264. Zhou, H. et al., Web-based toolkits for topology prediction of transmembrane helical proteins, fold recognition, structure and binding scoring, folding-kinetics analysis and comparative analysis of domain combinations, Nucleic Acids Res., 33, W193, 2005.
265. Taylor, P.D., Attwood, T.K., and Flower, D.R., BPROMPT: A consensus server for membrane protein prediction, Nucleic Acids Res., 31, 3698, 2003.
266. Yuan, Z., Mattick, J.S., and Teasdale, R.D., SVMtm: Support vector machines to predict transmembrane segments, J. Comput. Chem., 25, 632, 2004.
267. Arai, M. et al., ConPred II: A consensus prediction method for obtaining transmembrane topology models with high reliability, Nucleic Acids Res., 32, W390, 2004.
268. Bagos, P.G., Liakopoulos, T.D., and Hamodrakas, S.J., Algorithms for incorporating prior topological information in HMMs: Application to transmembrane proteins, BMC Bioinform., 7, 189, 2006.
269. Cao, B. et al., Enhanced recognition of protein transmembrane domains with prediction-based structural profiles, Bioinformatics, 22, 303, 2006.
270. Jones, T.D., Improving the accuracy of transmembrane protein topology prediction using evolutionary information, Bioinformatics, 23, 538, 2007.