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Volumn 11, Issue 1, 2010, Pages

A proteogenomic update to Yersinia: Enhancing genome annotation

Author keywords

[No Author keywords available]

Indexed keywords

SIGNAL PEPTIDE; BACTERIAL PROTEIN;

EID: 77955212650     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-460     Document Type: Article
Times cited : (45)

References (29)
  • 1
    • 42049085804 scopus 로고    scopus 로고
    • Yersinia pestis
    • London, UK: Academic Press, Sussman M
    • Brubaker RR. Yersinia pestis. Molecular Medical Microbiology 2002, 3:2033-2058. London, UK: Academic Press, Sussman M.
    • (2002) Molecular Medical Microbiology , vol.3 , pp. 2033-2058
    • Brubaker, R.R.1
  • 4
    • 0035367127 scopus 로고    scopus 로고
    • Whole-genome analysis: annotations and updates
    • 10.1016/S0959-440X(00)00213-X, 11406390
    • Gaasterland T, Oprea M. Whole-genome analysis: annotations and updates. Curr Opin Struct Biol 2001, 11:377-381. 10.1016/S0959-440X(00)00213-X, 11406390.
    • (2001) Curr Opin Struct Biol , vol.11 , pp. 377-381
    • Gaasterland, T.1    Oprea, M.2
  • 5
    • 0036175276 scopus 로고    scopus 로고
    • The past, present and future of genome-wide re-annotation
    • COMMENT2001, 10.1186/gb-2002-3-2-comment2001, 139008, 11864365
    • Ouzounis CA, Karp PD. The past, present and future of genome-wide re-annotation. Genome Biol 2002, 3. COMMENT2001, 10.1186/gb-2002-3-2-comment2001, 139008, 11864365.
    • (2002) Genome Biol , vol.3
    • Ouzounis, C.A.1    Karp, P.D.2
  • 6
    • 0035150398 scopus 로고    scopus 로고
    • Use of mass spectrometry-derived data to annotate nucleotide and protein sequence databases
    • 10.1016/S0968-0004(00)01726-6, 11165518
    • Mann M, Pandey A. Use of mass spectrometry-derived data to annotate nucleotide and protein sequence databases. Trends Biochem Sci 2001, 26:54-61. 10.1016/S0968-0004(00)01726-6, 11165518.
    • (2001) Trends Biochem Sci , vol.26 , pp. 54-61
    • Mann, M.1    Pandey, A.2
  • 7
    • 44249084514 scopus 로고    scopus 로고
    • Proteogenomics: needs and roles to be filled by proteomics in genome annotation
    • 10.1093/bfgp/eln010, 18334489
    • Ansong C, Purvine SO, Adkins JN, Lipton MS, Smith RD. Proteogenomics: needs and roles to be filled by proteomics in genome annotation. Brief Funct Genomic Proteomic 2008, 7:50-62. 10.1093/bfgp/eln010, 18334489.
    • (2008) Brief Funct Genomic Proteomic , vol.7 , pp. 50-62
    • Ansong, C.1    Purvine, S.O.2    Adkins, J.N.3    Lipton, M.S.4    Smith, R.D.5
  • 8
    • 0030805979 scopus 로고    scopus 로고
    • Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12
    • 10.1002/elps.1150180807, 9298646
    • Link AJ, Robison K, Church GM. Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12. Electrophoresis 1997, 18:1259-313. 10.1002/elps.1150180807, 9298646.
    • (1997) Electrophoresis , vol.18 , pp. 1259-1313
    • Link, A.J.1    Robison, K.2    Church, G.M.3
  • 10
    • 0034868629 scopus 로고    scopus 로고
    • Proteomics reveals open reading frames in Mycobacterium tuberculosis H37Rv not predicted by genomics
    • 10.1128/IAI.69.9.5905-5907.2001, 98710, 11500470
    • Jungblut PR, Müller EC, Mattow J, Kaufmann SH. Proteomics reveals open reading frames in Mycobacterium tuberculosis H37Rv not predicted by genomics. Infect Immun 2001, 69:5905-5907. 10.1128/IAI.69.9.5905-5907.2001, 98710, 11500470.
    • (2001) Infect Immun , vol.69 , pp. 5905-5907
    • Jungblut, P.R.1    Müller, E.C.2    Mattow, J.3    Kaufmann, S.H.4
  • 12
    • 55749091105 scopus 로고    scopus 로고
    • Subproteomic tools to increase genome annotation complexity
    • 10.1002/pmic.200800226, 18814329
    • Wei C, Peng J, Xiong Z, Yang J, Wang J, Jin Q. Subproteomic tools to increase genome annotation complexity. Proteomics 2008, 8:4209-4213. 10.1002/pmic.200800226, 18814329.
    • (2008) Proteomics , vol.8 , pp. 4209-4213
    • Wei, C.1    Peng, J.2    Xiong, Z.3    Yang, J.4    Wang, J.5    Jin, Q.6
  • 13
    • 33744980249 scopus 로고    scopus 로고
    • Complete genome sequence of Yersinia pestis strains Antiqua and Nepal516: evidence of gene reduction in an emerging pathogen
    • 10.1128/JB.00124-06, 1482938, 16740952
    • Chain PS, Hu P, Malfatti SA, Radnedge L, Larimer F, Vergez LM, Worsham P, Chu MC, Andersen GL. Complete genome sequence of Yersinia pestis strains Antiqua and Nepal516: evidence of gene reduction in an emerging pathogen. J Bacteriol 2006, 188:4453-4463. 10.1128/JB.00124-06, 1482938, 16740952.
    • (2006) J Bacteriol , vol.188 , pp. 4453-4463
    • Chain, P.S.1    Hu, P.2    Malfatti, S.A.3    Radnedge, L.4    Larimer, F.5    Vergez, L.M.6    Worsham, P.7    Chu, M.C.8    Andersen, G.L.9
  • 14
    • 42049103631 scopus 로고    scopus 로고
    • Characterizing the dynamic nature of the Yersinia pestis periplasmic proteome in response to nutrient exhaustion and temperature change
    • 10.1002/pmic.200700923, 18383009
    • Pieper R, Huang ST, Clark DJ, Robinson JM, Parmar PP, Alami H, Bunai CL, Perry RD, Fleischmann RD, Peterson SN. Characterizing the dynamic nature of the Yersinia pestis periplasmic proteome in response to nutrient exhaustion and temperature change. Proteomics 2008, 8:1442-1458. 10.1002/pmic.200700923, 18383009.
    • (2008) Proteomics , vol.8 , pp. 1442-1458
    • Pieper, R.1    Huang, S.T.2    Clark, D.J.3    Robinson, J.M.4    Parmar, P.P.5    Alami, H.6    Bunai, C.L.7    Perry, R.D.8    Fleischmann, R.D.9    Peterson, S.N.10
  • 15
    • 0020338446 scopus 로고
    • Sequence of a 1.26-kb DNA fragment containing the structural gene for E.coli initiation factor IF3: presence of an AUU initiator codon
    • 553041, 6325158
    • Sacerdot C, Fayat G, Dessen P, Springer M, Plumbridge JA, Grunberg-Manago M, Blanquet S. Sequence of a 1.26-kb DNA fragment containing the structural gene for E.coli initiation factor IF3: presence of an AUU initiator codon. EMBO J 1982, 1:311-315. 553041, 6325158.
    • (1982) EMBO J , vol.1 , pp. 311-315
    • Sacerdot, C.1    Fayat, G.2    Dessen, P.3    Springer, M.4    Plumbridge, J.A.5    Grunberg-Manago, M.6    Blanquet, S.7
  • 16
    • 34548452940 scopus 로고    scopus 로고
    • Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation
    • 10.1101/gr.6427907, 1950905, 17690205
    • Gupta N, Tanner S, Jaitly N, Adkins JN, Lipton M, Edwards R, Romine M, Osterman A, Bafna V, Smith RD, Pevzner PA. Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation. Genome Res 2007, 17:1362-1377. 10.1101/gr.6427907, 1950905, 17690205.
    • (2007) Genome Res , vol.17 , pp. 1362-1377
    • Gupta, N.1    Tanner, S.2    Jaitly, N.3    Adkins, J.N.4    Lipton, M.5    Edwards, R.6    Romine, M.7    Osterman, A.8    Bafna, V.9    Smith, R.D.10    Pevzner, P.A.11
  • 17
    • 0020638192 scopus 로고
    • A putative signal peptide recognition site and sequence in eukaryotic and prokaryotic signal peptides
    • 10.1016/S0022-2836(83)80341-6, 6345794
    • Perlman D, Halvorson HO. A putative signal peptide recognition site and sequence in eukaryotic and prokaryotic signal peptides. J Mol Biol 1983, 167:391-409. 10.1016/S0022-2836(83)80341-6, 6345794.
    • (1983) J Mol Biol , vol.167 , pp. 391-409
    • Perlman, D.1    Halvorson, H.O.2
  • 19
    • 34147162107 scopus 로고    scopus 로고
    • Genome re-annotation: a wiki solution?
    • 10.1186/gb-2007-8-6-r102, 1839116, 17274839
    • Salzberg SL. Genome re-annotation: a wiki solution?. Genome Biol 2007, 8:102. 10.1186/gb-2007-8-6-r102, 1839116, 17274839.
    • (2007) Genome Biol , vol.8 , pp. 102
    • Salzberg, S.L.1
  • 21
    • 58549101102 scopus 로고    scopus 로고
    • Discovery and revision of Arabidopsis genes by proteogenomics
    • 10.1073/pnas.0811066106, 2605632, 19098097
    • Castellana NE, Payne SH, Shen Z, Stanke M, Bafna V, Briggs SP. Discovery and revision of Arabidopsis genes by proteogenomics. Proc Natl Acad Sci USA 2008, 105:21034-21038. 10.1073/pnas.0811066106, 2605632, 19098097.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 21034-21038
    • Castellana, N.E.1    Payne, S.H.2    Shen, Z.3    Stanke, M.4    Bafna, V.5    Briggs, S.P.6
  • 22
    • 62249186821 scopus 로고    scopus 로고
    • Temperature and growth phase influence the outer-membrane proteome and the expression of a type VI secretion system in Yersinia pestis
    • 10.1099/mic.0.022160-0, 19202098
    • Pieper R, Huang ST, Robinson JM, Clark DJ, Alami H, Parmar PP, Perry RD, Fleischmann RD, Peterson SN. Temperature and growth phase influence the outer-membrane proteome and the expression of a type VI secretion system in Yersinia pestis. Microbiology 2009, 155:498-512. 10.1099/mic.0.022160-0, 19202098.
    • (2009) Microbiology , vol.155 , pp. 498-512
    • Pieper, R.1    Huang, S.T.2    Robinson, J.M.3    Clark, D.J.4    Alami, H.5    Parmar, P.P.6    Perry, R.D.7    Fleischmann, R.D.8    Peterson, S.N.9
  • 24
    • 33847630405 scopus 로고    scopus 로고
    • Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry
    • 10.1038/nmeth1019, 17327847
    • Elias JE, Gygi SP. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat Methods 2007, 4:207-214. 10.1038/nmeth1019, 17327847.
    • (2007) Nat Methods , vol.4 , pp. 207-214
    • Elias, J.E.1    Gygi, S.P.2
  • 25
    • 27544511899 scopus 로고    scopus 로고
    • InsPecT: identification of posttranslationally modified peptides from tandem mass spectra
    • 10.1021/ac050102d, 16013882
    • Tanner S, Shu H, Frank A, Wang LC, Zandi E, Mumby M, Pevzner PA, Bafna V. InsPecT: identification of posttranslationally modified peptides from tandem mass spectra. Anal Chem 2005, 77:4626-4639. 10.1021/ac050102d, 16013882.
    • (2005) Anal Chem , vol.77 , pp. 4626-4639
    • Tanner, S.1    Shu, H.2    Frank, A.3    Wang, L.C.4    Zandi, E.5    Mumby, M.6    Pevzner, P.A.7    Bafna, V.8
  • 26
    • 66749129629 scopus 로고    scopus 로고
    • A ranking-based scoring function for peptide-spectrum matches
    • 10.1021/pr800678b, 2692183, 19231891
    • Frank AM. A ranking-based scoring function for peptide-spectrum matches. J Proteome Res 2009, 8:2241-2252. 10.1021/pr800678b, 2692183, 19231891.
    • (2009) J Proteome Res , vol.8 , pp. 2241-2252
    • Frank, A.M.1
  • 28
    • 3042521098 scopus 로고    scopus 로고
    • Improved prediction of signal peptides: SignalP 3.0
    • 10.1016/j.jmb.2004.05.028, 15223320
    • Bendtsen JD, Nielsen H, von Heijne G, Brunak S. Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 2004, 340:783-795. 10.1016/j.jmb.2004.05.028, 15223320.
    • (2004) J Mol Biol , vol.340 , pp. 783-795
    • Bendtsen, J.D.1    Nielsen, H.2    von Heijne, G.3    Brunak, S.4
  • 29
    • 41449117976 scopus 로고    scopus 로고
    • Sybil: methods and software for multiple genome comparison and visualization
    • full_text, 18314579
    • Crabtree J, Angiuoli SV, Wortman JR, White OR. Sybil: methods and software for multiple genome comparison and visualization. Methods Mol Biol 2007, 408:93-108. full_text, 18314579.
    • (2007) Methods Mol Biol , vol.408 , pp. 93-108
    • Crabtree, J.1    Angiuoli, S.V.2    Wortman, J.R.3    White, O.R.4


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