Role of bacterial peptidase f inferred by statistical analysis and further experimental validation

HFSP Journal

Volumn 2, Issue 1, 2008, Pages 29-41

  Kleine, Liliana Lopez ^a,b   Monnet, Véronique ^a   Pechoux, Christine ^c   Trubuil, Alain ^b  

^a CEMAGREF   (France)

^b UR341 National Agronomical Research Institute (INRA)   (France)

^c NRA Plateforme de microscopie électronique   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS); LACTOCOCCUS LACTIS;

EID: 72449120889     PISSN: 19552068     EISSN: 1955205X     Source Type: Journal    
DOI: 10.2976/1.2820377     Document Type: Article

References (52)

1. Aerts, S, Lambrechts, D, Maity, S, Van, Loo P, Coessens, B, De Smet, F, Tranchevent, LC, De Moor, B, Marynen, P, Hassan, B, Carmeliet, P, and Moreau, Y (2006). "Gene prioritization through genomic data fusion." Nat. Biotechnol. 34, 537-544.
2. Akesson, M, Förster, J, and Nielsen, J (2004). "Integration of gene expression data into genome-scale metabolic models." Metab.
3. Eng. 6, 285-293.
4. Atrih, A, Bacher, G, Allmaier, G, Williamson, MP, and Foster, SJ (1999). " Analysis of peptidoglycan structure from vegetative cells of Bacillis subtilis 168 and Role of PBR 5 in Peptidoglycan Maturation." J. Bacteriol. 181, 3956-3966.
5. Bendtsen, JD, Nielsen, H, von Heijne, G, and Brunak, S (2004) " Improved prediction of signal peptides: SignalP 3.0." J. Mol. Biol. 340, 783-795.
6. Blattner, FR, Plunkett, G, Bloch, CA, Perna, NT, Burland, V., Riley, M, Collado-Vides, J, Glasner, JD, Rode, CK, Mayhew, GF, Gregor, J, Davis, NW, Kirkpatrick, HA, Goeden, MA, Rose, DJ, Mau, B, and Shao, Y (1997) "The complete genome sequence of Escherichia coli K-12." Science 277, 1453-1474.
7. Bolotin, A, Wincker, P, Mauger, S, Jaillon, O, Malarme, K, Weissenbach, J, Ehrlich, SD, and Sorokin, A (2001). "The complete genomesequence of the lactic acid bacterium Lactococcus lactis." Genome Res.11, 731-753.
8. Borgwardt, KM, Gretton, A, Rasch, MJ, Kriegel, HP, Schölkopf, B, and Smola, AJ. (2006). "Integrating structured biological data by Kernel Maximum Mean Discrepancy." Bioinformatics 22, 49-57.
9. Chatel, JM, Langella, P, Adel-Patient, K, Commissaire, J, Wal, JM, and Corthier, G (2001). "Induction of mucosal immune response after intranasal or oral inoculation of mice with Lactococcus lactis producing bovine beta-lactoglobulin." Clin. Diagn. Lab Immunol. 8, 545-551.
10. Chen, L, Tai, PC, Briggs, MS, and Gierasch, LM (1987). "Protein translocation into Escherichia coli membrane vesicles is inhibited by functional synthetic signal peptides." Biol. Chem. 262, 1427-1429.
11. Chich, JF, David, O, Villers, F, Schaeffer, B, Lutomsli, D, and Huet, S (2007). "Statistics for proteomics: experimental design and 2-DEdifferential analysis." J. Chromatogr., B: Biomed. Appl. 849, 261-272.
12. Cocaign-Bousquet, M, Garrigues, C, Novak, L, Lindley, ND, and Loubiere, P (1995). "Rational development of a simple synthetic medium for the sustained growth of Lactococcus lactis." J. Appl. Bacteriol. 79, 108-116.
13. Conlin, CA, Trun, NJ, Silhavy, TJ, and Miller, CG (1992). "Escherichiacoli prlC Encodes an Endopeptidase and is homologous to the
14. Salmonella typhimurium opdA gene." J. Bacteriol. 174, 5881-5887.
15. Covert, MW, Knight, EM, Reed, JL, Herrgard,MJ, and Palsson, BO (2004). "Integrating high-throughput and computational data elucidates bacterial networks." Nature (London) 429, 92-96.
16. Dev, IK, and Ray, PH (1990). "Signal peptidases and signal peptidehydrolases." J. Bioenerg. Biomembr. 22, 271-290.
17. Emr, SD, and Bassford, PJ (1982). "Localization and processing of outer membrane and periplasmic proteins in Escherichia coli strains harboring export-specific suppressor mutations." Biol. Chem. 257, 5852-5860.
18. Emr, SD, and Silhavy, TJ (1980). "Mutations affecting localization ofEscherichia coli outer membrane protein, the bacteriophage λ receptor." J. Mol. Biol. 141, 63-90.
19. EPAPS Document No. E-HJFOA5-2-002801 for supplemental material. This document can be reached through a direct link in the online article's HTML reference section via the EPAPS homepage (http://www.aip.org/pubservs/epaps.html).
20. Gitton, C, Meyrand, M, Wang, J, Caron, C, Trubuil, A, Guillot, A, and Mistou, MY (2005). "Proteomic signature of Lactococcus lactis NCDO763 cultivated in milk." Appl. Environ. Microbiol. 71, 7152-7163.
21. Glauner, B (1988). "Separation and quantification of muropeptides with high-performance liquid chromatography." Anal. Biochem. 172, 451-464.
22. Guedon, E, Serror, P, Ehrlich, SD, Renault, P, and Delorme, C (2001). "Pleiotropic transcriptional repressor CodY senses the intracellular pool of branched-chain amino acids in Lactococcus lactis." Med. Mundi 40, 1227-1239.
23. Guillot, A, Gitton, C, Anglade, P, and Mistou, MY (2003). "Proteomic analysis of Lactococcus lactis, a lactic acid bacterium." Proteomics 3, 337-354.
24. Gyaneshwar, P, Paliy, O, McAuliffe, J, Popham, DL, Jordan, MI, and Kustu, S (2005). "Sulphur and nitrogen limitation in Escherichia coli K12, specific homeostatic responses." J. Bacteriol. 187, 1074-1090.
25. Ho, Y, Gruhler, A, Heilbut, A, Bader, GD, Moore, L, Adams, SL, Millar, A, Taylor, P, Bennett, K, and Boutilier, K (2002). "Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry." Nature (London) 415, 180-183.
26. Hoffman, CS, and Winston, F (1987). "A ten-minute DNA preparation from yeast efficiently releases autonomous plasmids for transformation of Escherichia coli." Gene 57, 267-272.
27. Ichihara, S, Beppu, N, and Mizushima, S (1984). "Protease IV, a cytoplasmic membrane protein of Escherichia coli, has signal peptide peptidase activity." Biol. Chem. 259, 9853-9857.
28. Ito, T, Chiba, T, Ozawa, R, Yoshida, M, Hattori, M, and Sakaki, Y (2001). "A comprehensive two-hybrid analysis to explore the yeast protein interactome." Proc. Natl. Acad. Sci. U.S.A. 98, 4569-4574.
29. Kanamaru, K, Stephenson, S, and Perego, M (2002). "Overexpression of the PepF oligopeptidase inhibits sporulation initiation in Bacillus subtilis." J. Bacteriol. 184, 43-50.
30. Kanehisa, M, Goto, S, Kawashima, S, and Nakaya, A (2002). "The KEGG databases at GenomeNet." Nucleic Acids Res. 30, 42-46.
31. Kondor, RI, and Lafferty, J (2002). "Diffusion kernels on graphs and other discrete input spaces." International Conference for Machine Learning pp. 315-322.
32. Kavanaugh, JS, Thoendel, M, and Horswill, AR (2007). "A role for type I signal peptidase in Staphylococcus aureus quorum sensing." Mol. Microbiol. 65, 780-798.
33. de Magalhães, JP, Costa, J, and Toussaint, O (2005). " HAGR: the Human Aging Genomic Resources. " Nucleic Acids Res. 33, Database issue D537-D543.
34. Monnet, V, Nardi, M, Chopin, A, Chopin, MC, and Gripon, JC (1994). " Biochemical and genetic characterization of PepF an oligoendopeptidase from Lactococcus lactis." J. Biol. Chem. 269, 32070-32076.
35. Nardi, M, Renault, P, and Monnet, V (1997). " Duplication of the PepF gene and shuffling of DNA fragments on the lactose plasmid of Lactococcus lactis." J. Bacteriol. 179, 4164-4171.
36. Noirot, P, and Noirot-Gros, MF (2004). " Protein interaction networks in bacteria." Curr. Opin. Microbiol. 7, 505-512.
37. Novak, P, Ray, PH, and Dev, IK (1982). " Localization and purification of two enzymes from Escherichia coli capable of hydrolyzing a signal peptide." Biol. Chem. 261, 420-427.
38. Piuri, M, Sanchez-Rivas, C, and Ruzal, SM (2005). " Cell wall modifications during osmotic stress in Lactobacillus casei." J. Appl.Microbiol. 98, 84-95.
39. Qi, Y, Klein-Seetharam, J, and Bar-Joseph, Z (2005). " Random forest similarity for protein-protein interaction prediction from multiple sources." Biocomputing: Proc. Pacific Symposium 10, Hawaii.
40. Renault, P, Corthier, G, Goupil, N, Delorme, C, and Ehrlich, SD (1996). " Plasmid vectors for Gram-positive bacteria switching from high to low copy number." Gene 183, 175-182.
41. de Ruyter, PG. G. A, Kuipers, OP, Beerthuyzen, MM., van Alen- Boerrigter, I, and de Vos, WM (1996). " Functional analysis of promoters in the nisin gene cluster of Lactococcus lactis." J. Bacteriol. 178, 3434-3439.
42. Sambrook, J, and Russel, DW (2001). Molecular cloning: a laboratory manual, Cold Spring Harbor Laboratory Press
43. Schölkopf, B, Tsuda, K, and Vert, JP (2004). Kernel Methods in Computational Biology, MIT Press, Cambridge, MA.
44. Shin, JJ, Bryksin, AV, Godfrey, HP, and Cabello, FC (2004). " Localization of BmpA on the exposed outer membrane of Borrelia burgdorferi by monospecific anti-recombinant BmpA rabbit antibodies." Infect. Immun. 72, 2280-2287.
45. Siezen, RJ, Renckens, B, van Swam, I, Peters, S., van Kranenburg, R, and de Vos, WM (2005). " Complete sequence of four plasmids of Lactococcus lactis subsp cremoris SK11 reveal extensive adaptation to the dairy environment." Appl. Environ. Microbiol. 71, 8371-8382.
46. Tisljar, U, Knight, CG, and Barrett, AJ (1990). " An alternative quenched flourescence substrate for Pz-peptidase." Anal. Biochem. 186, 112-115.
47. Tjalsma, H, Bolhius, A, Jongbloed, JDH, Bron, S, and van Dijl, JM (2000). " Signal peptide-dependent protein transport in Bacillus subtilis: a genome-based survey of the secretome." Microbiol. Mol. Biol. Rev. 64, 515-547.
48. Werhli, A, and Husmeier, D (2007). " Reconstructing gene regulatory networks with Bayesian networks by combining expression data with multiple sources of prior knowledge." Stat. Appl. Genetics Mol. Biol. 6, Issue 1, Article 15.
49. Wicker, W, Moore, K, Dibb, N, Geissert, D, and Rice, M (1987). " Inhibition of purified Escherichia coli leader peptidase by the leader (signal) peptide of bacteriophage M13 procoat." J. Bacteriol. 169, 3821-3822.
50. Yamanishi, Y, Vert, JP, Nakaya, A, and Kaneisha, M (2003). " Extraction of correlated clusters from multiple genomic data by generalized kernel canonical correlation analysis." Bioinformatics 19 Suppl. 1, i323-i330.
51. Yamanishi, Y, Vert, JP, and Kanehisa, M (2004). " Protein network inference from multiple genomic data: a supervised approach." Bioinformatics 20, Suppl. 1, i363-i370.
52. Yamanishi, Y, and Vert, JP (2007). " Kernel Matrix Regression, Cornell University Library." (submitted: http://arxivorg/abs/q-bio/0702054v1).