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Volumn 111, Issue 52, 2014, Pages E5633-E5642

Proteogenomic analysis and global discovery of posttranslational modifications in prokaryotes

Author keywords

Cyanobacteria; Photosynthesis; Post translational modifications; Proteogenomics; Synechococcus

Indexed keywords

PROTEOME; BACTERIAL PROTEIN;

EID: 84924325914     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1412722111     Document Type: Article
Times cited : (54)

References (45)
  • 2
    • 84901599553 scopus 로고    scopus 로고
    • A draft map of the human proteome
    • Kim MS, et al. (2014) A draft map of the human proteome. Nature 509(7502):575-581.
    • (2014) Nature , vol.509 , Issue.7502 , pp. 575-581
    • Kim, M.S.1
  • 3
    • 80555142954 scopus 로고    scopus 로고
    • A proteogenomic analysis of Anopheles gambiae using high-resolution Fourier transform mass spectrometry
    • Chaerkady R, et al. (2011) A proteogenomic analysis of Anopheles gambiae using high-resolution Fourier transform mass spectrometry. Genome Res 21(11):1872-1881.
    • (2011) Genome Res , vol.21 , Issue.11 , pp. 1872-1881
    • Chaerkady, R.1
  • 4
    • 84901611036 scopus 로고    scopus 로고
    • Mass-spectrometry-based draft of the human proteome
    • Wilhelm M, et al. (2014) Mass-spectrometry-based draft of the human proteome. Nature 509(7502):582-587.
    • (2014) Nature , vol.509 , Issue.7502 , pp. 582-587
    • Wilhelm, M.1
  • 5
    • 76449114765 scopus 로고    scopus 로고
    • High-coverage proteome analysis reveals the first insight of protein modification systems in the pathogenic spirochete Leptospira interrogans
    • Cao XJ, et al. (2010) High-coverage proteome analysis reveals the first insight of protein modification systems in the pathogenic spirochete Leptospira interrogans. Cell Res 20(2):197-210.
    • (2010) Cell Res , vol.20 , Issue.2 , pp. 197-210
    • Cao, X.J.1
  • 6
    • 34548452940 scopus 로고    scopus 로고
    • Whole proteome analysis of post-translational modifications: Applications of mass-spectrometry for proteogenomic annotation
    • Gupta N, et al. (2007) Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation. Genome Res 17(9):1362-1377.
    • (2007) Genome Res , vol.17 , Issue.9 , pp. 1362-1377
    • Gupta, N.1
  • 7
    • 84892876508 scopus 로고    scopus 로고
    • Beyond gene expression: The impact of protein post-translational modifications in bacteria
    • Cain JA, Solis N, Cordwell SJ (2014) Beyond gene expression: The impact of protein post-translational modifications in bacteria. J Proteomics 97:265-286.
    • (2014) J Proteomics , vol.97 , pp. 265-286
    • Cain, J.A.1    Solis, N.2    Cordwell, S.J.3
  • 8
    • 84890644637 scopus 로고    scopus 로고
    • Status of large-scale analysis of post-translational modifications by mass spectrometry
    • Olsen JV, Mann M (2013) Status of large-scale analysis of post-translational modifications by mass spectrometry. Mol Cell Proteomics 12(12):3444-3452.
    • (2013) Mol Cell Proteomics , vol.12 , Issue.12 , pp. 3444-3452
    • Olsen, J.V.1    Mann, M.2
  • 9
    • 77149158441 scopus 로고    scopus 로고
    • Unrestricted identification of modified proteins using MS/MS
    • Ahrné E, Müller M, Lisacek F (2010) Unrestricted identification of modified proteins using MS/MS. Proteomics 10(4):671-686.
    • (2010) Proteomics , vol.10 , Issue.4 , pp. 671-686
    • Ahrné, E.1    Müller, M.2    Lisacek, F.3
  • 10
    • 77951636862 scopus 로고    scopus 로고
    • Proteogenomics and systems biology: Quest for the ultimate missing parts
    • Armengaud J (2010) Proteogenomics and systems biology: Quest for the ultimate missing parts. Expert Rev Proteomics 7(1):65-77.
    • (2010) Expert Rev Proteomics , vol.7 , Issue.1 , pp. 65-77
    • Armengaud, J.1
  • 11
    • 83755181765 scopus 로고    scopus 로고
    • The tricarboxylic acid cycle in cyanobacteria
    • Zhang S, Bryant DA (2011) The tricarboxylic acid cycle in cyanobacteria. Science 334(6062):1551-1553.
    • (2011) Science , vol.334 , Issue.6062 , pp. 1551-1553
    • Zhang, S.1    Bryant, D.A.2
  • 12
    • 33645216333 scopus 로고    scopus 로고
    • Niche partitioning among Prochlorococcus ecotypes along ocean-scale environmental gradients
    • Johnson ZI, et al. (2006) Niche partitioning among Prochlorococcus ecotypes along ocean-scale environmental gradients. Science 311(5768):1737-1740.
    • (2006) Science , vol.311 , Issue.5768 , pp. 1737-1740
    • Johnson, Z.I.1
  • 13
    • 84873082993 scopus 로고    scopus 로고
    • From cyanobacteria to plants: Conservation of PII functions during plastid evolution
    • Chellamuthu VR, Alva V, Forchhammer K (2013) From cyanobacteria to plants: Conservation of PII functions during plastid evolution. Planta 237(2):451-462.
    • (2013) Planta , vol.237 , Issue.2 , pp. 451-462
    • Chellamuthu, V.R.1    Alva, V.2    Forchhammer, K.3
  • 14
    • 84867640438 scopus 로고    scopus 로고
    • Bioengineering of carbon fixation, biofuels, and biochemicals in cyanobacteria and plants
    • Rosgaard L, de Porcellinis AJ, Jacobsen JH, Frigaard NU, Sakuragi Y (2012) Bioengineering of carbon fixation, biofuels, and biochemicals in cyanobacteria and plants. J Biotechnol 162(1):134-147.
    • (2012) J Biotechnol , vol.162 , Issue.1 , pp. 134-147
    • Rosgaard, L.1    De Porcellinis, A.J.2    Jacobsen, J.H.3    Frigaard, N.U.4    Sakuragi, Y.5
  • 15
    • 84855497373 scopus 로고    scopus 로고
    • Solar hydrogen-producing bionanodevice outperforms natural photosynthesis
    • Lubner CE, et al. (2011) Solar hydrogen-producing bionanodevice outperforms natural photosynthesis. Proc Natl Acad Sci USA 108(52):20988-20991.
    • (2011) Proc Natl Acad Sci USA , vol.108 , Issue.52 , pp. 20988-20991
    • Lubner, C.E.1
  • 17
    • 84859771858 scopus 로고    scopus 로고
    • Transcription profiling of the model cyanobacterium Synechococcus sp. Strain PCC 7002 by Next-Gen (SOLiD™) sequencing of cDNA
    • Ludwig M, Bryant DA (2011) Transcription profiling of the model cyanobacterium Synechococcus sp. strain PCC 7002 by Next-Gen (SOLiD™) sequencing of cDNA. Front Microbiol 2:41.
    • (2011) Front Microbiol , vol.2 , pp. 41
    • Ludwig, M.1    Bryant, D.A.2
  • 18
    • 84872373339 scopus 로고    scopus 로고
    • Acclimation of the global transcriptome of the cyanobacterium Synechococcus sp. strain PCC 7002 to nutrient limitations and different nitrogen sources
    • Ludwig M, Bryant DA (2012) Acclimation of the global transcriptome of the cyanobacterium Synechococcus sp. strain PCC 7002 to nutrient limitations and different nitrogen sources. Front Microbiol 3:145.
    • (2012) Front Microbiol , vol.3 , pp. 145
    • Ludwig, M.1    Bryant, D.A.2
  • 19
    • 80855128254 scopus 로고    scopus 로고
    • Deep proteome and transcriptome mapping of a human cancer cell line
    • Nagaraj N, et al. (2011) Deep proteome and transcriptome mapping of a human cancer cell line. Mol Syst Biol 7:548.
    • (2011) Mol Syst Biol , vol.7 , pp. 548
    • Nagaraj, N.1
  • 20
    • 84891816492 scopus 로고    scopus 로고
    • Systematic analyses of the transcriptome, translatome, and proteome provide a global view and potential strategy for the C-HPP
    • Chang C, et al. (2014) Systematic analyses of the transcriptome, translatome, and proteome provide a global view and potential strategy for the C-HPP. J Proteome Res 13(1):38-49.
    • (2014) J Proteome Res , vol.13 , Issue.1 , pp. 38-49
    • Chang, C.1
  • 21
    • 84875931748 scopus 로고    scopus 로고
    • Proteogenomic analysis of human colon carcinoma cell lines LIM1215, LIM1899, and LIM2405
    • Fanayan S, et al. (2013) Proteogenomic analysis of human colon carcinoma cell lines LIM1215, LIM1899, and LIM2405. J Proteome Res 12(4):1732-1742.
    • (2013) J Proteome Res , vol.12 , Issue.4 , pp. 1732-1742
    • Fanayan, S.1
  • 22
    • 79956322553 scopus 로고    scopus 로고
    • Global quantification of mammalian gene expression control
    • Schwanhäusser B, et al. (2011) Global quantification of mammalian gene expression control. Nature 473(7347):337-342.
    • (2011) Nature , vol.473 , Issue.7347 , pp. 337-342
    • Schwanhäusser, B.1
  • 23
    • 84879879014 scopus 로고    scopus 로고
    • Variation and genetic control of protein abundance in humans
    • Wu L, et al. (2013) Variation and genetic control of protein abundance in humans. Nature 499(7456):79-82.
    • (2013) Nature , vol.499 , Issue.7456 , pp. 79-82
    • Wu, L.1
  • 24
    • 84867158880 scopus 로고    scopus 로고
    • A proteogenomic survey of the Medicago truncatula genome
    • Volkening JD, et al. (2012) A proteogenomic survey of the Medicago truncatula genome. Mol Cell Proteomics 11(10):933-944.
    • (2012) Mol Cell Proteomics , vol.11 , Issue.10 , pp. 933-944
    • Volkening, J.D.1
  • 25
    • 84894619287 scopus 로고    scopus 로고
    • HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics
    • Branca RM, et al. (2014) HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics. Nat Methods 11(1):59-62.
    • (2014) Nat Methods , vol.11 , Issue.1 , pp. 59-62
    • Branca, R.M.1
  • 26
    • 36549015654 scopus 로고    scopus 로고
    • Mass spectrometry-based prokaryote gene annotation
    • Ishino Y, Okada H, Ikeuchi M, Taniguchi H (2007) Mass spectrometry-based prokaryote gene annotation. Proteomics 7(22):4053-4065.
    • (2007) Proteomics , vol.7 , Issue.22 , pp. 4053-4065
    • Ishino, Y.1    Okada, H.2    Ikeuchi, M.3    Taniguchi, H.4
  • 27
    • 0036137327 scopus 로고    scopus 로고
    • A probabilistic method for identifying start codons in bacterial genomes
    • Suzek BE, Ermolaeva MD, Schreiber M, Salzberg SL (2001) A probabilistic method for identifying start codons in bacterial genomes. Bioinformatics 17(12):1123-1130.
    • (2001) Bioinformatics , vol.17 , Issue.12 , pp. 1123-1130
    • Suzek, B.E.1    Ermolaeva, M.D.2    Schreiber, M.3    Salzberg, S.L.4
  • 28
    • 80052036518 scopus 로고    scopus 로고
    • Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium
    • Ansong C, et al. (2011) Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium. BMC Genomics 12:433.
    • (2011) BMC Genomics , vol.12 , pp. 433
    • Ansong, C.1
  • 29
    • 0036015649 scopus 로고    scopus 로고
    • Expression of the Escherichia coli pcnB gene is translationally limited using an inefficient start codon: A second chromosomal example of translation initiated at AUU
    • Binns N, Masters M (2002) Expression of the Escherichia coli pcnB gene is translationally limited using an inefficient start codon: A second chromosomal example of translation initiated at AUU. Mol Microbiol 44(5):1287-1298.
    • (2002) Mol Microbiol , vol.44 , Issue.5 , pp. 1287-1298
    • Binns, N.1    Masters, M.2
  • 30
    • 13544262685 scopus 로고    scopus 로고
    • Genome-wide prediction of stop codon readthrough during translation in the yeast Saccharomyces cerevisiae
    • Williams I, Richardson J, Starkey A, Stansfield I (2004) Genome-wide prediction of stop codon readthrough during translation in the yeast Saccharomyces cerevisiae. Nucleic Acids Res 32(22):6605-6616.
    • (2004) Nucleic Acids Res , vol.32 , Issue.22 , pp. 6605-6616
    • Williams, I.1    Richardson, J.2    Starkey, A.3    Stansfield, I.4
  • 31
    • 80055001959 scopus 로고    scopus 로고
    • Evidence of abundant stop codon readthrough in Drosophila and other metazoa
    • Jungreis I, et al. (2011) Evidence of abundant stop codon readthrough in Drosophila and other metazoa. Genome Res 21(12):2096-2113.
    • (2011) Genome Res , vol.21 , Issue.12 , pp. 2096-2113
    • Jungreis, I.1
  • 32
    • 84875459298 scopus 로고    scopus 로고
    • Heterologous stop codon readthrough of metazoan readthrough candidates in yeast
    • Chan CS, Jungreis I, Kellis M (2013) Heterologous stop codon readthrough of metazoan readthrough candidates in yeast. PLoS ONE 8(3):e59450.
    • (2013) PLoS ONE , vol.8 , Issue.3 , pp. e59450
    • Chan, C.S.1    Jungreis, I.2    Kellis, M.3
  • 33
    • 0037165964 scopus 로고    scopus 로고
    • A new UAG-encoded residue in the structure of a methanogen methyltransferase
    • Hao B, et al. (2002) A new UAG-encoded residue in the structure of a methanogen methyltransferase. Science 296(5572):1462-1466.
    • (2002) Science , vol.296 , Issue.5572 , pp. 1462-1466
    • Hao, B.1
  • 34
    • 0037166006 scopus 로고    scopus 로고
    • Pyrrolysine encoded by UAG in Archaea: Charging of a UAG-decoding specialized tRNA
    • Srinivasan G, James CM, Krzycki JA (2002) Pyrrolysine encoded by UAG in Archaea: Charging of a UAG-decoding specialized tRNA. Science 296(5572):1459-1462.
    • (2002) Science , vol.296 , Issue.5572 , pp. 1459-1462
    • Srinivasan, G.1    James, C.M.2    Krzycki, J.A.3
  • 35
    • 84875887558 scopus 로고    scopus 로고
    • How many signal peptides are there in bacteria?
    • Ivankov DN, et al. (2013) How many signal peptides are there in bacteria? Environ Microbiol 15(4):983-990.
    • (2013) Environ Microbiol , vol.15 , Issue.4 , pp. 983-990
    • Ivankov, D.N.1
  • 36
    • 2942578482 scopus 로고    scopus 로고
    • Peptide signal molecules and bacteriocins in Gram-negative bacteria: A genome-wide in silico screening for peptides containing a double-glycine leader sequence and their cognate transporters
    • Dirix G, et al. (2004) Peptide signal molecules and bacteriocins in Gram-negative bacteria: A genome-wide in silico screening for peptides containing a double-glycine leader sequence and their cognate transporters. Peptides 25(9):1425-1440.
    • (2004) Peptides , vol.25 , Issue.9 , pp. 1425-1440
    • Dirix, G.1
  • 37
    • 80053345905 scopus 로고    scopus 로고
    • SignalP 4.0: Discriminating signal peptides from transmembrane regions
    • Petersen TN, Brunak S, von Heijne G, Nielsen H (2011) SignalP 4.0: Discriminating signal peptides from transmembrane regions. Nat Methods 8(10):785-786.
    • (2011) Nat Methods , vol.8 , Issue.10 , pp. 785-786
    • Petersen, T.N.1    Brunak, S.2    Von Heijne, G.3    Nielsen, H.4
  • 38
    • 3242878999 scopus 로고    scopus 로고
    • PrediSi: Prediction of signal peptides and their cleavage positions
    • Hiller K, Grote A, Scheer M, Munch R, Jahn D (2004) PrediSi: Prediction of signal peptides and their cleavage positions. Nucleic Acids Res 32(Web Server issue): W375-W379.
    • (2004) Nucleic Acids Res , vol.32 , Issue.WEB SERVER ISSUE , pp. W375-W379
    • Hiller, K.1    Grote, A.2    Scheer, M.3    Munch, R.4    Jahn, D.5
  • 39
    • 84875959292 scopus 로고    scopus 로고
    • Global phosphoproteomic analysis reveals diverse functions of serine/threonine/tyrosine phosphorylation in the model cyanobacterium Synechococcus sp. Strain PCC 7002
    • Yang MK, et al. (2013) Global phosphoproteomic analysis reveals diverse functions of serine/threonine/tyrosine phosphorylation in the model cyanobacterium Synechococcus sp. strain PCC 7002. J Proteome Res 12(4):1909-1923.
    • (2013) J Proteome Res , vol.12 , Issue.4 , pp. 1909-1923
    • Yang, M.K.1
  • 40
    • 84859877187 scopus 로고    scopus 로고
    • Fast multi-blind modification search through tandem mass spectrometry
    • M111.010199
    • Na S, Bandeira N, Paek E (2012) Fast multi-blind modification search through tandem mass spectrometry. Mol Cell Proteomics 11(4):M111.010199.
    • (2012) Mol Cell Proteomics , vol.11 , Issue.4
    • Na, S.1    Bandeira, N.2    Paek, E.3
  • 41
    • 57449099865 scopus 로고    scopus 로고
    • MaxQuant enables high peptide identification rates, individualized p.P.B.-range mass accuracies and proteome-wide protein quantification
    • Cox J, Mann M (2008) MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 26(12):1367-1372.
    • (2008) Nat Biotechnol , vol.26 , Issue.12 , pp. 1367-1372
    • Cox, J.1    Mann, M.2
  • 42
    • 80052942443 scopus 로고    scopus 로고
    • Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification
    • Tan M, et al. (2011) Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification. Cell 146(6):1016-1028.
    • (2011) Cell , vol.146 , Issue.6 , pp. 1016-1028
    • Tan, M.1
  • 43
    • 78650516004 scopus 로고    scopus 로고
    • Identification of lysine succinylation as a new post-translational modification
    • Zhang Z, et al. (2011) Identification of lysine succinylation as a new post-translational modification. Nat Chem Biol 7(1):58-63.
    • (2011) Nat Chem Biol , vol.7 , Issue.1 , pp. 58-63
    • Zhang, Z.1
  • 44
    • 33644876912 scopus 로고    scopus 로고
    • The PeptideAtlas project
    • Desiere F, et al. (2006) The PeptideAtlas project. Nucleic Acids Res 34(Database issue): D655-D658.
    • (2006) Nucleic Acids Res , vol.34 , Issue.DATABASE ISSUE , pp. D655-D658
    • Desiere, F.1
  • 45
    • 69649109364 scopus 로고    scopus 로고
    • Circos: An information aesthetic for comparative genomics
    • Krzywinski M, et al. (2009) Circos: An information aesthetic for comparative genomics. Genome Res 19(9):1639-1645.
    • (2009) Genome Res , vol.19 , Issue.9 , pp. 1639-1645
    • Krzywinski, M.1


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