메뉴 건너뛰기




Volumn 5, Issue , 2014, Pages

Diverse and divergent protein post-translational modifications in two growth stages of a natural microbial community

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; CELLULAR APOPTOSIS SUSCEPTIBILITY PROTEIN; PROTEOME;

EID: 84904965551     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms5405     Document Type: Article
Times cited : (45)

References (60)
  • 1
    • 44449137093 scopus 로고    scopus 로고
    • The microbial engines that drive earth's biogeochemical cycles
    • DOI 10.1126/science.1153213
    • Falkowski, P. G., Fenchel, T. & Delong, E. F. The microbial engines that drive Earth's biogeochemical cycles. Science 320, 1034-1039 (2008). (Pubitemid 351929518)
    • (2008) Science , vol.320 , Issue.5879 , pp. 1034-1039
    • Falkowski, P.G.1    Fenchel, T.2    Delong, E.F.3
  • 3
    • 34547347640 scopus 로고    scopus 로고
    • Functional metaproteome analysis of protein extracts from contaminated soil and groundwater
    • DOI 10.1038/ismej.2007.39, PII ISMEJ200739
    • Benndorf, D., Balcke, G. U., Harms, H. & von Bergen, M. Functional metaproteome analysis of protein extracts from contaminated soil and groundwater. ISME J. 1, 224-234 (2007). (Pubitemid 47145293)
    • (2007) ISME Journal , vol.1 , Issue.3 , pp. 224-234
    • Benndorf, D.1    Balcke, G.U.2    Harms, H.3    Von Bergen, M.4
  • 4
    • 58049112263 scopus 로고    scopus 로고
    • Transport functions dominate the SAR11 metaproteome at low-nutrient extremes in the Sargasso Sea
    • Sowell, S. M. et al. Transport functions dominate the SAR11 metaproteome at low-nutrient extremes in the Sargasso Sea. ISME J. 3, 93-105 (2009).
    • (2009) ISME J. , vol.3 , pp. 93-105
    • Sowell, S.M.1
  • 5
    • 28044433451 scopus 로고    scopus 로고
    • Protein posttranslational modifications: The chemistry of proteome diversifications
    • DOI 10.1002/anie.200501023
    • Walsh, C. T., Garneau-Tsodikova, S. & Gatto, Jr G. J. Protein posttranslational modifications: the chemistry of proteome diversifications. Angew. Chem. Int. Ed. 44, 7342-7372 (2005). (Pubitemid 41689988)
    • (2005) Angewandte Chemie - International Edition , vol.44 , Issue.45 , pp. 7342-7372
    • Walsh, C.T.1    Garneau-Tsodikova, S.2    Gatto Jr., G.J.3
  • 7
    • 70349546862 scopus 로고    scopus 로고
    • Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution
    • Holt, L. J. et al. Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution. Science 325, 1682-1686 (2009).
    • (2009) Science , vol.325 , pp. 1682-1686
    • Holt, L.J.1
  • 8
    • 68949212379 scopus 로고    scopus 로고
    • Lysine acetylation targets protein complexes and co-regulates major cellular functions
    • Choudhary, C. et al. Lysine acetylation targets protein complexes and co-regulates major cellular functions. Science 325, 834-840 (2009).
    • (2009) Science , vol.325 , pp. 834-840
    • Choudhary, C.1
  • 9
    • 77149120797 scopus 로고    scopus 로고
    • Acetylation of metabolic enzymes coordinates carbon source utilization and metabolic flux
    • Wang, Q. et al. Acetylation of metabolic enzymes coordinates carbon source utilization and metabolic flux. Science 327, 1004-1007 (2010).
    • (2010) Science , vol.327 , pp. 1004-1007
    • Wang, Q.1
  • 10
    • 84863420067 scopus 로고    scopus 로고
    • Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium
    • van Noort, V. et al. Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium. Mol. Syst. Biol. 8, 571 (2012).
    • (2012) Mol. Syst. Biol. , vol.8 , pp. 571
    • Van Noort, V.1
  • 11
    • 84859222354 scopus 로고    scopus 로고
    • The methylproteome and the intracellular methylation network
    • Erce, M. A., Pang, C. N., Hart-Smith, G. & Wilkins, M. R. The methylproteome and the intracellular methylation network. Proteomics 12, 564-586 (2012).
    • (2012) Proteomics , vol.12 , pp. 564-586
    • Erce, M.A.1    Pang, C.N.2    Hart-Smith, G.3    Wilkins, M.R.4
  • 12
    • 84860176878 scopus 로고    scopus 로고
    • Endogenous protein S-Nitrosylation in E. Coli: Regulation by OxyR
    • Seth, D., Hausladen, A., Wang, Y. J. & Stamler, J. S. Endogenous protein S-Nitrosylation in E. coli: regulation by OxyR. Science 336, 470-473 (2012).
    • (2012) Science , vol.336 , pp. 470-473
    • Seth, D.1    Hausladen, A.2    Wang, Y.J.3    Stamler, J.S.4
  • 14
    • 84860349570 scopus 로고    scopus 로고
    • In vivo relevance of citrullinated proteins and the challenges in their detection
    • De Ceuleneer, M., Van Steendam, K., Dhaenens, M. & Deforce, D. In vivo relevance of citrullinated proteins and the challenges in their detection. Proteomics 12, 752-760 (2012).
    • (2012) Proteomics , vol.12 , pp. 752-760
    • De Ceuleneer, M.1    Van Steendam, K.2    Dhaenens, M.3    Deforce, D.4
  • 15
    • 84870014480 scopus 로고    scopus 로고
    • Comprehensive mass spectrometric mapping of the hydroxylated amino acid residues of the alpha1(V) collagen chain
    • Yang, C. et al. Comprehensive mass spectrometric mapping of the hydroxylated amino acid residues of the alpha1(V) collagen chain. J. Biol. Chem. 287, 40598-40610 (2012).
    • (2012) J. Biol. Chem. , vol.287 , pp. 40598-40610
    • Yang, C.1
  • 16
    • 79953175993 scopus 로고    scopus 로고
    • A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12
    • Strader, M. B. et al. A proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of Escherichia coli ribosomal protein S12. Mol. Cell. Proteomics 10, M110005199 (2011).
    • (2011) Mol. Cell. Proteomics , vol.10
    • Strader, M.B.1
  • 17
    • 77957875163 scopus 로고    scopus 로고
    • Moving from transcriptional to phosphoevolution: Generalizing regulatory evolution?
    • Moses, A. M. & Landry, C. R. Moving from transcriptional to phosphoevolution: generalizing regulatory evolution? Trends Genet. 26, 462-467 (2010).
    • (2010) Trends Genet , vol.26 , pp. 462-467
    • Moses, A.M.1    Landry, C.R.2
  • 18
    • 70349526350 scopus 로고    scopus 로고
    • Comparative analysis reveals conserved protein phosphorylation networks implicated in multiple diseases
    • Tan, C. S. et al. Comparative analysis reveals conserved protein phosphorylation networks implicated in multiple diseases. Sci. Signal. 2, ra39 (2009).
    • (2009) Sci. Signal. , vol.2
    • Tan, C.S.1
  • 19
    • 84864213113 scopus 로고    scopus 로고
    • Systematic functional prioritization of protein posttranslational modifications
    • Beltrao, P. et al. Systematic functional prioritization of protein posttranslational modifications. Cell 150, 413-425 (2012).
    • (2012) Cell , vol.150 , pp. 413-425
    • Beltrao, P.1
  • 20
    • 67649972198 scopus 로고    scopus 로고
    • Evolution of phosphoregulation: Comparison of phosphorylation patterns across yeast species
    • Beltrao, P. et al. Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast species. PLoS Biol. 7, e1000134 (2009).
    • (2009) PLoS Biol , vol.7
    • Beltrao, P.1
  • 21
    • 79960797509 scopus 로고    scopus 로고
    • Proteome-wide mapping of the Drosophila acetylome demonstrates a high degree of conservation of lysine acetylation
    • Weinert, B. T. et al. Proteome-wide mapping of the Drosophila acetylome demonstrates a high degree of conservation of lysine acetylation. Sci. Signal. 4, ra48 (2011).
    • (2011) Sci. Signal. , vol.4
    • Weinert, B.T.1
  • 22
    • 54549123613 scopus 로고    scopus 로고
    • Comparative phosphoproteomics reveals evolutionary and functional conservation of phosphorylation across eukaryotes
    • Boekhorst, J., van Breukelen, B., Heck, Jr. A. & Snel, B. Comparative phosphoproteomics reveals evolutionary and functional conservation of phosphorylation across eukaryotes. Genome Biol. 9, R144 (2008).
    • (2008) Genome Biol , vol.9
    • Boekhorst, J.1    Van Breukelen, B.2    Heck Jr., A.3    Snel, B.4
  • 24
    • 77349126360 scopus 로고    scopus 로고
    • Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities
    • USA
    • Denef, V. J. et al. Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities. Proc. Natl. Acad. Sci. USA 107, 2383-2390 (2010).
    • (2010) Proc. Natl. Acad. Sci. , vol.107 , pp. 2383-2390
    • Denef, V.J.1
  • 25
    • 84860160394 scopus 로고    scopus 로고
    • In situ evolutionary rate measurements show ecological success of recently emerged bacterial hybrids
    • Denef, V. J. & Banfield, J. F. In situ evolutionary rate measurements show ecological success of recently emerged bacterial hybrids. Science 336, 462-466 (2012).
    • (2012) Science , vol.336 , pp. 462-466
    • Denef, V.J.1    Banfield, J.F.2
  • 26
    • 84879613791 scopus 로고    scopus 로고
    • Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation
    • Swaney, D. L. et al. Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation. Nat. Methods 10, 676-682 (2013).
    • (2013) Nat. Methods , vol.10 , pp. 676-682
    • Swaney, D.L.1
  • 27
    • 84879637572 scopus 로고    scopus 로고
    • Integrated proteomic analysis of post-translational modifications by serial enrichment
    • Mertins, P. et al. Integrated proteomic analysis of post-translational modifications by serial enrichment. Nat. Methods 10, 634-637 (2013).
    • (2013) Nat. Methods , vol.10 , pp. 634-637
    • Mertins, P.1
  • 28
    • 79960979428 scopus 로고    scopus 로고
    • A large-scale method to measure absolute protein phosphorylation stoichiometries
    • Wu, R. et al. A large-scale method to measure absolute protein phosphorylation stoichiometries. Nat. Methods 8, 677-683 (2011).
    • (2011) Nat. Methods , vol.8 , pp. 677-683
    • Wu, R.1
  • 29
    • 77951644400 scopus 로고    scopus 로고
    • Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis
    • Olsen, J. V. et al. Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. Sci. Signal. 3, ra3 (2010).
    • (2010) Sci. Signal. , vol.3
    • Olsen, J.V.1
  • 30
    • 34548336772 scopus 로고    scopus 로고
    • Higher-energy C-trap dissociation for peptide modification analysis
    • DOI 10.1038/nmeth1060, PII NMETH1060
    • Olsen, J. V. et al. Higher-energy C-trap dissociation for peptide modification analysis. Nat. Methods 4, 709-712 (2007). (Pubitemid 47338163)
    • (2007) Nature Methods , vol.4 , Issue.9 , pp. 709-712
    • Olsen, J.V.1    Macek, B.2    Lange, O.3    Makarov, A.4    Horning, S.5    Mann, M.6
  • 31
    • 84881014876 scopus 로고    scopus 로고
    • Sipros/ProRata: A versatile informatics system for quantitative community proteomics
    • Wang, Y., Ahn, T. H., Li, Z. & Pan, C. Sipros/ProRata: a versatile informatics system for quantitative community proteomics. Bioinformatics 29, 2064-2065 (2013).
    • (2013) Bioinformatics , vol.29 , pp. 2064-2065
    • Wang, Y.1    Ahn, T.H.2    Li, Z.3    Pan, C.4
  • 32
    • 79953305843 scopus 로고    scopus 로고
    • Quantitative tracking of isotope flows in proteomes of microbial communities
    • Pan, C. et al. Quantitative tracking of isotope flows in proteomes of microbial communities. Mol. Cell. Proteomics 10, M110.006049 (2011).
    • (2011) Mol. Cell. Proteomics , vol.10
    • Pan, C.1
  • 33
    • 77953272819 scopus 로고    scopus 로고
    • Ecological distribution and population physiology defined by proteomics in a natural microbial community
    • Mueller, R. S. et al. Ecological distribution and population physiology defined by proteomics in a natural microbial community. Mol. Syst. Biol. 6, 374 (2010).
    • (2010) Mol. Syst. Biol. , vol.6 , pp. 374
    • Mueller, R.S.1
  • 34
    • 33847630405 scopus 로고    scopus 로고
    • Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry
    • DOI 10.1038/nmeth1019, PII NMETH1019
    • Elias, J. E. & Gygi, S. P. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat. Methods 4, 207-214 (2007). (Pubitemid 46358868)
    • (2007) Nature Methods , vol.4 , Issue.3 , pp. 207-214
    • Elias, J.E.1    Gygi, S.P.2
  • 35
    • 84879654317 scopus 로고    scopus 로고
    • A large synthetic peptide and phosphopeptide reference library for mass spectrometry-based proteomics
    • Marx, H. et al. A large synthetic peptide and phosphopeptide reference library for mass spectrometry-based proteomics. Nat. Biotechnol. 31, 557-564 (2013).
    • (2013) Nat. Biotechnol. , vol.31 , pp. 557-564
    • Marx, H.1
  • 36
    • 84879401680 scopus 로고    scopus 로고
    • Global dynamics of the Escherichia coli proteome and phosphoproteome during growth in minimal medium
    • Soares, N. C., Spat, P., Krug, K. & Macek, B. Global dynamics of the Escherichia coli proteome and phosphoproteome during growth in minimal medium. J. Proteome Res. 12, 2611-2621 (2013).
    • (2013) J. Proteome Res. , vol.12 , pp. 2611-2621
    • Soares, N.C.1    Spat, P.2    Krug, K.3    MacEk, B.4
  • 37
    • 84873343462 scopus 로고    scopus 로고
    • Comprehensive profiling of protein lysine acetylation in Escherichia coli
    • Zhang, K., Zheng, S., Yang, J. S., Chen, Y. & Cheng, Z. Comprehensive profiling of protein lysine acetylation in Escherichia coli. J. Proteome Res. 12, 844-851 (2013).
    • (2013) J. Proteome Res. , vol.12 , pp. 844-851
    • Zhang, K.1    Zheng, S.2    Yang, J.S.3    Chen, Y.4    Cheng, Z.5
  • 38
    • 79961036057 scopus 로고    scopus 로고
    • Proteome changes in the initial bacterial colonist during ecological succession in an acid mine drainage biofilm community
    • Mueller, R. S. et al. Proteome changes in the initial bacterial colonist during ecological succession in an acid mine drainage biofilm community. Environ. Microbiol. 13, 2279-2292 (2011).
    • (2011) Environ. Microbiol. , vol.13 , pp. 2279-2292
    • Mueller, R.S.1
  • 39
    • 67649576309 scopus 로고    scopus 로고
    • Community genomic and proteomic analyses of chemoautotrophic iron-oxidizing 'Leptospirillum rubarum' (Group II) and 'Leptospirillum ferrodiazotrophum' (Group III) bacteria in acid mine drainage biofilms
    • Goltsman, D. S. et al. Community genomic and proteomic analyses of chemoautotrophic iron-oxidizing 'Leptospirillum rubarum' (Group II) and 'Leptospirillum ferrodiazotrophum' (Group III) bacteria in acid mine drainage biofilms. Appl. Environ. Microbiol. 75, 4599-4615 (2009).
    • (2009) Appl. Environ. Microbiol. , vol.75 , pp. 4599-4615
    • Goltsman, D.S.1
  • 41
    • 44449133775 scopus 로고    scopus 로고
    • Virus population dynamics and acquired virus resistance in natural microbial communities
    • DOI 10.1126/science.1157358
    • Andersson, A. F. & Banfield, J. F. Virus population dynamics and acquired virus resistance in natural microbial communities. Science 320, 1047-1050 (2008). (Pubitemid 351929541)
    • (2008) Science , vol.320 , Issue.5879 , pp. 1047-1050
    • Andersson, A.F.1    Banfield, J.F.2
  • 43
    • 10044252242 scopus 로고    scopus 로고
    • Making sense of it all: Bacterial chemotaxis
    • DOI 10.1038/nrm1524
    • Wadhams, G. H. & Armitage, J. P. Making sense of it all: bacterial chemotaxis. Nat. Rev. Mol. Cell Biol. 5, 1024-1037 (2004). (Pubitemid 39611538)
    • (2004) Nature Reviews Molecular Cell Biology , vol.5 , Issue.12 , pp. 1024-1037
    • Wadhams, G.H.1    Armitage, J.P.2
  • 44
    • 59849106371 scopus 로고    scopus 로고
    • Protein promiscuity and its implications for biotechnology
    • Nobeli, I., Favia, A. D. & Thornton, J. M. Protein promiscuity and its implications for biotechnology. Nat. Biotechnol. 27, 157-167 (2009).
    • (2009) Nat. Biotechnol. , vol.27 , pp. 157-167
    • Nobeli, I.1    Favia, A.D.2    Thornton, J.M.3
  • 46
    • 65549086559 scopus 로고    scopus 로고
    • A yeast hybrid provides insight into the evolution of gene expression regulation
    • Tirosh, I., Reikhav, S., Levy, A. A. & Barkai, N. A yeast hybrid provides insight into the evolution of gene expression regulation. Science 324, 659-662 (2009).
    • (2009) Science , vol.324 , pp. 659-662
    • Tirosh, I.1    Reikhav, S.2    Levy, A.A.3    Barkai, N.4
  • 47
    • 84870875533 scopus 로고    scopus 로고
    • Coupling a detergent lysis/cleanup methodology with intact protein fractionation for enhanced proteome characterization
    • Sharma, R. et al. Coupling a detergent lysis/cleanup methodology with intact protein fractionation for enhanced proteome characterization. J. Proteome Res. 11, 6008-6018 (2012).
    • (2012) J. Proteome Res. , vol.11 , pp. 6008-6018
    • Sharma, R.1
  • 48
    • 67349266694 scopus 로고    scopus 로고
    • Universal sample preparation method for proteome analysis
    • Wisniewski, J. R., Zougman, A., Nagaraj, N. & Mann, M. Universal sample preparation method for proteome analysis. Nat. Methods 6, 359-362 (2009).
    • (2009) Nat. Methods , vol.6 , pp. 359-362
    • Wisniewski, J.R.1    Zougman, A.2    Nagaraj, N.3    Mann, M.4
  • 49
    • 0035106351 scopus 로고    scopus 로고
    • Large-scale analysis of the yeast proteome by multidimensional protein identification technology
    • DOI 10.1038/85686
    • Washburn, M. P., Wolters, D. & Yates, 3rd J. R. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat. Biotechnol. 19, 242-247 (2001). (Pubitemid 32220565)
    • (2001) Nature Biotechnology , vol.19 , Issue.3 , pp. 242-247
    • Washburn, M.P.1    Wolters, D.2    Yates, J.R.3
  • 50
    • 0037447834 scopus 로고    scopus 로고
    • Microbial communities in acid mine drainage
    • Baker B.J.Banfield J.F.
    • Baker, B. J. & Banfield, J. F. Microbial communities in acid mine drainage. FEMS Microbiol. Ecol. 44, 139-152 (2003).
    • (2003) FEMS Microbiol. Ecol. , vol.44 , pp. 139-152
  • 51
    • 27644555055 scopus 로고    scopus 로고
    • Interpretation of shotgun proteomic data: The protein inference problem
    • DOI 10.1074/mcp.R500012-MCP200
    • Nesvizhskii, A. I. & Aebersold, R. Interpretation of shotgun proteomic data: the protein inference problem. Mol. Cell. Proteomics 4, 1419-1440 (2005). (Pubitemid 41555469)
    • (2005) Molecular and Cellular Proteomics , vol.4 , Issue.10 , pp. 1419-1440
    • Nesvizhskii, A.I.1    Aebersold, R.2
  • 52
    • 79953212975 scopus 로고    scopus 로고
    • Confident phosphorylation site localization using the mascot delta score
    • Savitski, M. M. et al. Confident phosphorylation site localization using the Mascot Delta Score. Mol. Cell. Proteomics 10, M110.003830 (2011).
    • (2011) Mol. Cell. Proteomics , vol.10
    • Savitski, M.M.1
  • 55
    • 0034201441 scopus 로고    scopus 로고
    • EMBOSS: The European molecular biology open software suite
    • Rice, P., Longden, I. & Bleasby, A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 16, 276-277 (2000).
    • (2000) Trends Genet , vol.16 , pp. 276-277
    • Rice, P.1    Longden, I.2    Bleasby, A.3
  • 56
    • 4344571581 scopus 로고    scopus 로고
    • Rank products: A simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments
    • DOI 10.1016/j.febslet.2004.07.055, PII S0014579304009354
    • Breitling, R., Armengaud, P., Amtmann, A. & Herzyk, P. Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments. FEBS Lett. 573, 83-92 (2004). (Pubitemid 39141040)
    • (2004) FEBS Letters , vol.573 , Issue.1-3 , pp. 83-92
    • Breitling, R.1    Armengaud, P.2    Amtmann, A.3    Herzyk, P.4
  • 57
    • 77951234057 scopus 로고    scopus 로고
    • MUFOLD: A new solution for protein 3D structure prediction
    • Zhang, J. et al. MUFOLD: a new solution for protein 3D structure prediction. Proteins 78, 1137-1152 (2010).
    • (2010) Proteins , vol.78 , pp. 1137-1152
    • Zhang, J.1
  • 58
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch, W. & Sander, C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22, 2577-2637 (1983).
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 59
    • 0023645203 scopus 로고
    • Interior and surface of monomeric proteins
    • Miller, S., Janin, J., Lesk, A. M. & Chothia, C. Interior and surface of monomeric proteins. J. Mol. Biol. 196, 641-656 (1987).
    • (1987) J. Mol. Biol. , vol.196 , pp. 641-656
    • Miller, S.1    Janin, J.2    Lesk, A.M.3    Chothia, C.4
  • 60
    • 20144377620 scopus 로고    scopus 로고
    • Prediction of solvent accessibility and sites of deleterious mutations from protein sequence
    • DOI 10.1093/nar/gki633
    • Chen, H. & Zhou, H.-X. Prediction of solvent accessibility and sites of deleterious mutations from protein sequence. Nucleic Acids Res. 33, 3193-3199 (2005). (Pubitemid 41194463)
    • (2005) Nucleic Acids Research , vol.33 , Issue.10 , pp. 3193-3199
    • Chen, H.1    Zhou, H.-X.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.