메뉴 건너뛰기




Volumn 8, Issue 8, 2010, Pages 2223-2239

In-depth analysis of exoproteomes from marine bacteria by shotgun liquid chromatography-tandem mass spectrometry: The Ruegeria pomeroyi DSS-3 case-study

Author keywords

Environmental proteomics; Exoproteome; Marine bacteria; Proteogenomics; Toxins

Indexed keywords

ABC TRANSPORTER; EXOPROTEOME; PEPTIDE; PROTEIN; PROTEOME; TOXIN; TRYPSIN; UNCLASSIFIED DRUG;

EID: 77956401047     PISSN: None     EISSN: 16603397     Source Type: Journal    
DOI: 10.3390/md8082223     Document Type: Article
Times cited : (47)

References (56)
  • 3
    • 43949120140 scopus 로고    scopus 로고
    • Diversity, ecology, and genomics of the Roseobacter clade: A short overview
    • Brinkhoff, T.; Giebel, H.A.; Simon, M. Diversity, ecology, and genomics of the Roseobacter clade: a short overview. Arch. Microbiol. 2008, 189, 531-539.
    • (2008) Arch. Microbiol. , vol.189 , pp. 531-539
    • Brinkhoff, T.1    Giebel, H.A.2    Simon, M.3
  • 4
    • 33750371632 scopus 로고    scopus 로고
    • Environmental biology of the marine Roseobacter lineage
    • Wagner-Dobler, I.; Biebl, H. Environmental biology of the marine Roseobacter lineage. Annu. Rev. Microbiol. 2006, 60, 255-280.
    • (2006) Annu. Rev. Microbiol. , vol.60 , pp. 255-280
    • Wagner-Dobler, I.1    Biebl, H.2
  • 5
    • 34248231288 scopus 로고    scopus 로고
    • Taxonomic evaluation of the genera Ruegeria and Silicibacter: A proposal to transfer the genus Silicibacter Petursdottir and Kristjansson 1999 to the genus Ruegeria Uchino et al. 1999
    • Yi, H.; Lim, Y.W.; Chun, J. Taxonomic evaluation of the genera Ruegeria and Silicibacter: a proposal to transfer the genus Silicibacter Petursdottir and Kristjansson 1999 to the genus Ruegeria Uchino et al. 1999. Int. J. Syst. Evol. Microbiol. 2007, 57, 815-819.
    • (2007) Int. J. Syst. Evol. Microbiol. , vol.57 , pp. 815-819
    • Yi, H.1    Lim, Y.W.2    Chun, J.3
  • 8
    • 35148888991 scopus 로고    scopus 로고
    • Transcriptional response of Silicibacter pomeroyi DSS-3 to dimethylsulfoniopropionate (DMSP)
    • Burgmann, H.; Howard, E.C.; Ye, W.; Sun, F.; Sun, S.; Napierala, S.; Moran, M.A. Transcriptional response of Silicibacter pomeroyi DSS-3 to dimethylsulfoniopropionate (DMSP). Environ. Microbiol. 2007, 9, 2742-2755.
    • (2007) Environ. Microbiol. , vol.9 , pp. 2742-2755
    • Burgmann, H.1    Howard, E.C.2    Ye, W.3    Sun, F.4    Sun, S.5    Napierala, S.6    Moran, M.A.7
  • 11
    • 15944366553 scopus 로고    scopus 로고
    • Profiling the secretomes of plant pathogenic Proteobacteria
    • Preston, G.M.; Studholme, D.J.; Caldelari, I. Profiling the secretomes of plant pathogenic Proteobacteria. FEMS Microbiol. Rev. 2005, 29, 331-360.
    • (2005) FEMS Microbiol. Rev. , vol.29 , pp. 331-360
    • Preston, G.M.1    Studholme, D.J.2    Caldelari, I.3
  • 12
    • 63549137674 scopus 로고    scopus 로고
    • Secretion and subcellular localizations of bacterial proteins: A semantic awareness issue
    • Desvaux, M.; Hébraud, M.; Talon, R.; Henderson, I.R. Secretion and subcellular localizations of bacterial proteins: a semantic awareness issue. Trends Microbiol. 2009, 17, 139-145.
    • (2009) Trends Microbiol. , vol.17 , pp. 139-145
    • Desvaux, M.1    Hébraud, M.2    Talon, R.3    Henderson, I.R.4
  • 13
    • 5644233706 scopus 로고    scopus 로고
    • The secretome of the plant pathogenic bacterium Erwinia chrysanthemi
    • DOI 10.1002/pmic.200300814
    • Kazemi-Pour, N.; Condemine, G.; Hugouvieux-Cotte-Pattat, N. The secretome of the plant pathogenic bacterium Erwinia chrysanthemi. Proteomics 2004, 4, 3177-3186. (Pubitemid 39372399)
    • (2004) Proteomics , vol.4 , Issue.10 , pp. 3177-3186
    • Kazemi-Pour, N.1    Condemine, G.2    Hugouvieux-Cotte-Pattat, N.3
  • 14
    • 77954718616 scopus 로고    scopus 로고
    • Expanding the known repertoire of virulence factors produced by Bacillus cereus through early secretome profiling in three redox conditions
    • doi:10.1074/mcp.M000027-MCP201
    • Clair, G.; Roussi, S.; Armengaud, J.; Duport, C. Expanding the known repertoire of virulence factors produced by Bacillus cereus through early secretome profiling in three redox conditions. Mol. Cell. Proteomics 2010, doi:10.1074/mcp.M000027-MCP201.
    • (2010) Mol. Cell. Proteomics
    • Clair, G.1    Roussi, S.2    Armengaud, J.3    Duport, C.4
  • 15
    • 25844455216 scopus 로고    scopus 로고
    • A comparative study of Bacillus cereus, Bacillus thuringiensis and Bacillus anthracis extracellular proteomes
    • Gohar, M.; Gilois, N.; Graveline, R.; Garreau, C.; Sanchis, V.; Lereclus, D. A comparative study of Bacillus cereus, Bacillus thuringiensis and Bacillus anthracis extracellular proteomes. Proteomics 2005, 5, 3696-3711.
    • (2005) Proteomics , vol.5 , pp. 3696-3711
    • Gohar, M.1    Gilois, N.2    Graveline, R.3    Garreau, C.4    Sanchis, V.5    Lereclus, D.6
  • 16
    • 0345354678 scopus 로고    scopus 로고
    • Detection of secreted peptides by using hypothesis-driven multistage mass spectrometry
    • Kalkum, M.; Lyon, G.J.; Chait, B.T. Detection of secreted peptides by using hypothesis-driven multistage mass spectrometry. Proc. Natl. Acad. Sci. USA 2003, 100, 2795-2800.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 2795-2800
    • Kalkum, M.1    Lyon, G.J.2    Chait, B.T.3
  • 17
    • 34447116519 scopus 로고    scopus 로고
    • Protein secretion and membrane insertion systems in gram-negative bacteria
    • Saier, M.H., Jr. Protein secretion and membrane insertion systems in gram-negative bacteria. J. Membr. Biol. 2006, 214, 75-90.
    • (2006) J. Membr. Biol. , vol.214 , pp. 75-90
    • Saier Jr., M.H.1
  • 18
    • 71549149451 scopus 로고    scopus 로고
    • A comprehensive assessment of N-terminal signal peptides prediction methods
    • Choo, K.H.; Tan, T.W.; Ranganathan, S. A comprehensive assessment of N-terminal signal peptides prediction methods. BMC Bioinformatics 2009, 10, S2.
    • (2009) BMC Bioinformatics , vol.10
    • Choo, K.H.1    Tan, T.W.2    Ranganathan, S.3
  • 20
    • 34248531753 scopus 로고    scopus 로고
    • Locating proteins in the cell using TargetP, SignalP and related tools
    • Emanuelsson, O.; Brunak, S.; von Heijne, G.; Nielsen, H. Locating proteins in the cell using TargetP, SignalP and related tools. Nat. Protoc. 2007, 2, 953-971.
    • (2007) Nat. Protoc. , vol.2 , pp. 953-971
    • Emanuelsson, O.1    Brunak, S.2    Von Heijne, G.3    Nielsen, H.4
  • 21
    • 77952040946 scopus 로고    scopus 로고
    • Computational Prediction and Experimental Validation of Signal Peptide Cleavages in the Extracellular Proteome of a Natural Microbial Community
    • Erickson, B.K.; Mueller, R.; Verberkmoes, N.C.; Shah, M.; Singer, S.W.; Thelen, M.; Banfield, J.F.; Hettich, R.L. Computational Prediction and Experimental Validation of Signal Peptide Cleavages in the Extracellular Proteome of a Natural Microbial Community. J. Proteome Res. 2010, 9, 2148-2159.
    • (2010) J. Proteome Res. , vol.9 , pp. 2148-2159
    • Erickson, B.K.1    Mueller, R.2    Verberkmoes, N.C.3    Shah, M.4    Singer, S.W.5    Thelen, M.6    Banfield, J.F.7    Hettich, R.L.8
  • 22
    • 69949116837 scopus 로고    scopus 로고
    • Evaluation of signal peptide prediction algorithms for identification of mycobacterial signal peptides using sequence data from proteomic methods
    • Leversen, N.A.; de Souza, G.A.; Malen, H.; Prasad, S.; Jonassen, I.; Wiker, H.G. Evaluation of signal peptide prediction algorithms for identification of mycobacterial signal peptides using sequence data from proteomic methods. Microbiology 2009, 155, 2375-2383.
    • (2009) Microbiology , vol.155 , pp. 2375-2383
    • Leversen, N.A.1    De Souza, G.A.2    Malen, H.3    Prasad, S.4    Jonassen, I.5    Wiker, H.G.6
  • 23
    • 42549137778 scopus 로고    scopus 로고
    • LocateP: Genome-scale subcellular-location predictor for bacterial proteins
    • Zhou, M.; Boekhorst, J.; Francke, C.; Siezen, R. LocateP: Genome-scale subcellular-location predictor for bacterial proteins. BMC Bioinformatics 2008, 9, 173.
    • (2008) BMC Bioinformatics , vol.9 , pp. 173
    • Zhou, M.1    Boekhorst, J.2    Francke, C.3    Siezen, R.4
  • 24
    • 42949143130 scopus 로고    scopus 로고
    • Application of proteomics in biotechnology - Microbial proteomics
    • Josic, D.; Kovac, S. Application of proteomics in biotechnology - microbial proteomics. Biotechnol. J. 2008, 3, 496-509.
    • (2008) Biotechnol. J. , vol.3 , pp. 496-509
    • Josic, D.1    Kovac, S.2
  • 25
    • 63849104493 scopus 로고    scopus 로고
    • Environmental proteomics: A paradigm shift in characterizing microbial activities at the molecular level
    • Keller, M.; Hettich, R. Environmental proteomics: a paradigm shift in characterizing microbial activities at the molecular level. Microbiol. Mol. Biol. Rev. 2009, 73, 62-70.
    • (2009) Microbiol. Mol. Biol. Rev. , vol.73 , pp. 62-70
    • Keller, M.1    Hettich, R.2
  • 26
    • 77149152780 scopus 로고    scopus 로고
    • Environmental proteomics: Analysis of structure and function of microbial communities
    • Schneider, T.; Riedel, K. Environmental proteomics: analysis of structure and function of microbial communities. Proteomics 2010, 10, 785-798.
    • (2010) Proteomics , vol.10 , pp. 785-798
    • Schneider, T.1    Riedel, K.2
  • 27
    • 77951636862 scopus 로고    scopus 로고
    • Proteogenomics and systems biology: Quest for the ultimate missing parts
    • Armengaud, J. Proteogenomics and systems biology: quest for the ultimate missing parts. Expert Rev. Proteomics 2010, 7, 65-77.
    • (2010) Expert Rev. Proteomics , vol.7 , pp. 65-77
    • Armengaud, J.1
  • 28
    • 67649229164 scopus 로고    scopus 로고
    • Insight into the core and variant exoproteomes of Listeria monocytogenes species by comparative subproteomic analysis
    • Dumas, E.; Desvaux, M.; Chambon, C.; Hébraud, M. Insight into the core and variant exoproteomes of Listeria monocytogenes species by comparative subproteomic analysis. Proteomics 2009, 9, 3136-3155.
    • (2009) Proteomics , vol.9 , pp. 3136-3155
    • Dumas, E.1    Desvaux, M.2    Chambon, C.3    Hébraud, M.4
  • 31
    • 70350465145 scopus 로고    scopus 로고
    • Proteomic analysis of the secretome of human umbilical vein endothelial cells using a combination of free-flow electrophoresis and nanoflow LC-MS/MS
    • Tunica, D.; Yin, X.; Sidibe, A.; Stegemann, C.; Nissum, M.; Zeng, L.; Brunet, M.; Mayr, M. Proteomic analysis of the secretome of human umbilical vein endothelial cells using a combination of free-flow electrophoresis and nanoflow LC-MS/MS. Proteomics 2009, 9, 4991-4996.
    • (2009) Proteomics , vol.9 , pp. 4991-4996
    • Tunica, D.1    Yin, X.2    Sidibe, A.3    Stegemann, C.4    Nissum, M.5    Zeng, L.6    Brunet, M.7    Mayr, M.8
  • 32
    • 33947588089 scopus 로고    scopus 로고
    • Profiling the secretome of the marine bacterium Pseudoalteromonas tunicata using amine-specific isobaric tagging (iTRAQ)
    • DOI 10.1021/pr060416x
    • Evans, F.F.; Raftery, M.J.; Egan, S.; Kjelleberg, S. Profiling the secretome of the marine bacterium Pseudoalteromonas tunicata using amine-specific isobaric tagging (iTRAQ). J. Proteome Res. 2007, 6, 967-975. (Pubitemid 46480461)
    • (2007) Journal of Proteome Research , vol.6 , Issue.3 , pp. 967-975
    • Evans, F.F.1    Raftery, M.J.2    Egan, S.3    Kjelleberg, S.4
  • 33
    • 3242731195 scopus 로고    scopus 로고
    • A model for random sampling and estimation of relative protein abundance in shotgun proteomics
    • Liu, H.; Sadygov, R.G.; Yates, J.R., III. A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem. 2004, 76, 4193-4201.
    • (2004) Anal. Chem. , vol.76 , pp. 4193-4201
    • Liu, H.1    Sadygov, R.G.2    Yates III, J.R.3
  • 34
    • 38649095599 scopus 로고    scopus 로고
    • An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data
    • DOI 10.1021/pr700758r
    • Mueller, L.N.; Brusniak, M.-Y.; Mani, D.R.; Aebersold, R. An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data. J. Proteome Res. 2008, 7, 51-61. (Pubitemid 351171115)
    • (2008) Journal of Proteome Research , vol.7 , Issue.1 , pp. 51-61
    • Mueller, L.N.1    Brusniak, M.-Y.2    Mani, D.R.3    Aebersold, R.4
  • 35
    • 0033981139 scopus 로고    scopus 로고
    • Characterization of PaxA and its operon: A cohemolytic RTX toxin determinant from pathogenic Pasteurella aerogenes
    • Kuhnert, P.; Heyberger-Meyer, B.; Nicolet, J.; Frey, J. Characterization of PaxA and its operon: a cohemolytic RTX toxin determinant from pathogenic Pasteurella aerogenes. Infect. Immun. 2000, 68, 6-12.
    • (2000) Infect. Immun. , vol.68 , pp. 6-12
    • Kuhnert, P.1    Heyberger-Meyer, B.2    Nicolet, J.3    Frey, J.4
  • 37
    • 66349116973 scopus 로고    scopus 로고
    • A perfect genome annotation is within reach with the proteomics and genomics alliance
    • Armengaud, J. A perfect genome annotation is within reach with the proteomics and genomics alliance. Curr. Opin. Microbiol. 2009, 12, 292-300.
    • (2009) Curr. Opin. Microbiol. , vol.12 , pp. 292-300
    • Armengaud, J.1
  • 38
    • 0032127904 scopus 로고    scopus 로고
    • N-terminal processing: The methionine aminopeptidase and N alpha-acetyl transferase families
    • Bradshaw, R.A.; Brickey, W.W.; Walker, K.W. N-terminal processing: the methionine aminopeptidase and N alpha-acetyl transferase families. Trends Biochem. Sci. 1998, 23, 263-267.
    • (1998) Trends Biochem. Sci. , vol.23 , pp. 263-267
    • Bradshaw, R.A.1    Brickey, W.W.2    Walker, K.W.3
  • 40
    • 0037413729 scopus 로고    scopus 로고
    • Control of protein life-span by N-terminal methionine excision
    • DOI 10.1093/emboj/cdg007
    • Giglione, C.; Vallon, O.; Meinnel, T. Control of protein life-span by N-terminal methionine excision. EMBO J. 2003, 22, 13-23. (Pubitemid 36091265)
    • (2003) EMBO Journal , vol.22 , Issue.1 , pp. 13-23
    • Giglione, C.1    Vallon, O.2    Meinnel, T.3
  • 41
    • 2942733563 scopus 로고    scopus 로고
    • New knowledge from old: In silico discovery of novel protein domains in Streptomyces coelicolor
    • Yeats, C.; Bentley, S.; Bateman, A. New knowledge from old: in silico discovery of novel protein domains in Streptomyces coelicolor. BMC Microbiol. 2003, 3, 3.
    • (2003) BMC Microbiol. , vol.3 , pp. 3
    • Yeats, C.1    Bentley, S.2    Bateman, A.3
  • 43
    • 46249086291 scopus 로고    scopus 로고
    • Identification and characterization of a repeat-in-toxin gene cluster in Vibrio anguillarum
    • Li, L.; Rock, J.L.; Nelson, D.R. Identification and characterization of a repeat-in-toxin gene cluster in Vibrio anguillarum. Infect. Immun. 2008, 76, 2620-2632.
    • (2008) Infect. Immun. , vol.76 , pp. 2620-2632
    • Li, L.1    Rock, J.L.2    Nelson, D.R.3
  • 45
    • 66149153084 scopus 로고    scopus 로고
    • Identification and characterization of hemolysin-like proteins similar to RTX toxin in Pasteurella pneumotropica
    • Sasaki, H.; Kawamoto, E.; Tanaka, Y.; Sawada, T.; Kunita, S.; Yagami, K.-i. Identification and characterization of hemolysin-like proteins similar to RTX toxin in Pasteurella pneumotropica. J. Bacteriol. 2009, 191, 3698-3705.
    • (2009) J. Bacteriol. , vol.191 , pp. 3698-3705
    • Sasaki, H.1    Kawamoto, E.2    Tanaka, Y.3    Sawada, T.4    Kunita, S.5    Yagami, K.-I.6
  • 47
    • 0036084146 scopus 로고    scopus 로고
    • InBase: The intein database
    • Perler, F.B. InBase: the intein database. Nucleic Acids Res. 2002, 30, 383-384.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 383-384
    • Perler, F.B.1
  • 54
    • 67650770057 scopus 로고    scopus 로고
    • A toolbox for validation of mass spectrometry peptides identification and generation of database: IRMa
    • Dupierris, V.; Masselon, C.; Court, M.; Kieffer-Jaquinod, S.; Bruley, C. A toolbox for validation of mass spectrometry peptides identification and generation of database: IRMa. Bioinformatics 2009, 25, 1980-1981.
    • (2009) Bioinformatics , vol.25 , pp. 1980-1981
    • Dupierris, V.1    Masselon, C.2    Court, M.3    Kieffer-Jaquinod, S.4    Bruley, C.5
  • 56
    • 70350488795 scopus 로고    scopus 로고
    • Horizontal gene transfer of the secretome drives the evolution of bacterial cooperation and virulence
    • Nogueira, T.; Rankin, D.J.; Touchon, M.; Taddei, F.; Brown, S.P.; Rocha, E.P.C. Horizontal gene transfer of the secretome drives the evolution of bacterial cooperation and virulence. Curr. Biol. 2009, 19, 1683-1691.
    • (2009) Curr. Biol. , vol.19 , pp. 1683-1691
    • Nogueira, T.1    Rankin, D.J.2    Touchon, M.3    Taddei, F.4    Brown, S.P.5    Rocha, E.P.C.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.