Bacterial Phosphoproteomic Analysis Reveals the Correlation Between Protein Phosphorylation and Bacterial Pathogenicity
Tài liệu tham khảo
Cohen, 2000, The regulation of protein function by multisite phosphorylation—a 25 year update, Trends Biochem. Sci., 25, 596, 10.1016/S0968-0004(00)01712-6
Ninfa, 2010, Use of two-component signal transduction systems in the construction of synthetic genetic networks, Curr. Opin. Microbiol., 13, 240, 10.1016/j.mib.2010.01.003
Johnson, 2009, The regulation of protein phosphorylation, Biochem. Soc. Trans., 37, 627, 10.1042/BST0370627
Mann, 2002, Analysis of protein phosphorylation using mass spectrometry: deciphering the phosphoproteome, Trends Biotechnol., 20, 261, 10.1016/S0167-7799(02)01944-3
Ge, 2009, Metallomics: an integrated biometal science, Sci. China Ser. B-Chem., 52, 2055, 10.1007/s11426-009-0144-6
Paradela, 2008, Advances in the analysis of protein phosphorylation, J. Proteome Res., 7, 1809, 10.1021/pr7006544
Li, 2007, Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae, J. Proteome Res., 6, 1190, 10.1021/pr060559j
Manai, 1979, Analysis of the protein-kinase activity of Escherichia coli cells, Biochem. Biophys. Res. Commun., 91, 819, 10.1016/0006-291X(79)91953-3
Garnak, 1979, Phosphorylation of Isocitrate dehydrogenase of Escherichia coli, Science, 203, 1111, 10.1126/science.34215
Jers, 2008, Phosphoproteomics in bacteria: towards a systemic understanding of bacterial phosphorylation networks, Expert Rev. Proteomics, 5, 619, 10.1586/14789450.5.4.619
Soufi, 2008, Insights from site-specific phosphoproteomics in bacteria, Biochim. Biophys. Acta, 1784, 186, 10.1016/j.bbapap.2007.07.018
Bendt, 2003, Towards a phosphoproteome map of Corynebacterium glutamicum, Proteomics, 3, 1637, 10.1002/pmic.200300494
Voisin, 2007, The cytoplasmic phosphoproteome of the Gram-negative bacterium Campylobacter jejuni: evidence for modification by unidentified protein kinases, Proteomics, 7, 4338, 10.1002/pmic.200700483
Eymann, 2007, Dynamics of protein phosphorylation on Ser/Thr/Tyr in Bacillus subtilis, Proteomics, 7, 3509, 10.1002/pmic.200700232
Levine, 2006, Analysis of the dynamic Bacillus subtilis Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes, Proteomics, 6, 2157, 10.1002/pmic.200500352
Macek, 2007, The serine/threonine/tyrosine phosphoproteome of the model bacterium Bacillus subtilis, Mol. Cell. Proteomics, 6, 697, 10.1074/mcp.M600464-MCP200
Macek, 2008, Phosphoproteome analysis of E. coli reveals evolutionary conservation of bacterial Ser/Thr/Tyr phosphorylation, Mol. Cell. Proteomics, 7, 299, 10.1074/mcp.M700311-MCP200
Soufi, 2008, The Ser/Thr/Tyr phosphoproteome of Lactococcus lactis IL1403 reveals multiply phosphorylated proteins, Proteomics, 8, 3486, 10.1002/pmic.200800069
Sun, 2010, Phosphoproteomic analysis reveals the multiple roles of phosphorylation in pathogenic bacterium Streptococcus pneumoniae, J. Proteome Res., 9, 275, 10.1021/pr900612v
Lin, 2009, Phosphoproteomics of Klebsiella pneumoniae NTUH-K2044 reveals a tight link between tyrosine phosphorylation and virulence, Mol. Cell. Proteomics, 8, 2613, 10.1074/mcp.M900276-MCP200
Schmidl, 2010, The phosphoproteome of the minimal bacterium Mycoplasma pneumoniae: analysis of the complete known Ser/Thr kinome suggests the existence of novel kinases, Mol. Cell. Proteomics, 9, 1228, 10.1074/mcp.M900267-MCP200
Ravichandran, 2009, Ser/Thr/Tyr phosphoproteome analysis of pathogenic and non-pathogenic Pseudomonas species, Proteomics, 9, 2764, 10.1002/pmic.200800655
Prisic, 2010, Extensive phosphorylation with overlapping specificity by Mycobacterium tuberculosis serine/threonine protein kinases, Proc. Natl. Acad. Sci. USA, 107, 7521, 10.1073/pnas.0913482107
Parker, 2010, Analysis of the phosphoproteome of the multicellular bacterium Streptomyces coelicolor A3(2) by protein/peptide fractionation, phosphopeptide enrichment and high-accuracy mass spectrometry, Proteomics, 10, 2486, 10.1002/pmic.201000090
Ge, 2011, Phosphoproteome analysis of the pathogenic bacterium Helicobacter pylori reveals over-representation of tyrosine phosphorylation and multiply phosphorylated proteins, Proteomics, 11, 1449, 10.1002/pmic.201000649
Ubersax, 2007, Mechanisms of specificity in protein phosphorylation, Nat. Rev. Mol. Cell Biol., 8, 530, 10.1038/nrm2203
Kobir, 2011, Protein phosphorylation in bacterial signal transduction, Biochim. Biophys. Acta, 1810, 989, 10.1016/j.bbagen.2011.01.006
Soufi, 2010, Stable isotope labeling by amino acids in cell culture (SILAC) applied to quantitative proteomics of Bacillus subtilis, J. Proteome Res., 9, 3638, 10.1021/pr100150w
Manning, 2002, The protein kinase complement of the human genome, Science, 298, 1912, 10.1126/science.1075762
Cohen, 2002, The origins of protein phosphorylation, Nat. Cell Biol., 4, E127, 10.1038/ncb0502-e127
Miller, 2009, NetPhosBac—a predictor for Ser/Thr phosphorylation sites in bacterial proteins, Proteomics, 9, 116, 10.1002/pmic.200800285
Iakoucheva, 2004, The importance of intrinsic disorder for protein phosphorylation, Nucleic Acids Res., 32, 1037, 10.1093/nar/gkh253
Pandey, 2000, Analysis of receptor signaling pathways by mass spectrometry: identification of vav-2 as a substrate of the epidermal and platelet–derived growth factor receptors, Proc. Natl. Acad. Sci. USA, 97, 179, 10.1073/pnas.97.1.179
Andersson, 1986, Isolation of phosphoproteins by immobilized metal (Fe3+) affinity chromatography, Anal. Biochem., 154, 250, 10.1016/0003-2697(86)90523-3
Sun, 2005, Application of immobilized metal affinity chromatography in proteomics, Expert Rev. Proteomics, 2, 649, 10.1586/14789450.2.5.649
Oda, 2001, Enrichment analysis of phosphorylated proteins as a tool for probing the phosphoproteome, Nat. Biotechnol., 19, 379, 10.1038/86783
Zhou, 2001, A systematic approach to the analysis of protein phosphorylation, Nat. Biotechnol., 19, 375, 10.1038/86777
Beausoleil, 2004, Large-scale characterization of HeLa cell nuclear phosphoproteins, Proc. Natl. Acad. Sci. USA, 101, 12130, 10.1073/pnas.0404720101
Nita-Lazar, 2008, Quantitative phosphoproteomics by mass spectrometry: past, present, and future, Proteomics, 8, 4433, 10.1002/pmic.200800231
Dubrovska, 2005, Efficient enrichment of intact phosphorylated proteins by modified immobilized metal-affinity chromatography, Proteomics, 5, 4678, 10.1002/pmic.200500002
Feng, 2007, Immobilized zirconium ion affinity chromatography for specific enrichment of phosphopeptides in phosphoproteome analysis, Mol. Cell. Proteomics, 6, 1656, 10.1074/mcp.T600071-MCP200
Ficarro, 2002, Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae, Nat. Biotechnol., 20, 301, 10.1038/nbt0302-301
Larsen, 2005, Highly selective enrichment of phosphorylated peptides from peptide mixtures using titanium dioxide microcolumns, Mol. Cell. Proteomics, 4, 873, 10.1074/mcp.T500007-MCP200
Collins, 2007, Analysis of protein phosphorylation on a proteome-scale, Proteomics, 7, 2751, 10.1002/pmic.200700145
Syka, 2004, Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry, Proc. Natl. Acad. Sci. USA, 101, 9528, 10.1073/pnas.0402700101
Pinkse, 2004, Selective isolation at the femtomole level of phosphopeptides from proteolytic digests using 2D-NanoLC-ESI-MS/MS and titanium oxide precolumns, Anal. Chem., 76, 3935, 10.1021/ac0498617
Ficarro, 2005, Automated immobilized metal affinity chromatography/nano-liquid chromatography/electrospray ionization mass spectrometry platform for profiling protein phosphorylation sites, Rapid Commun. Mass Spectrom., 19, 57, 10.1002/rcm.1746
Conesa, 2005, Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research, Bioinformatics, 21, 3674, 10.1093/bioinformatics/bti610
Gardy, 2003, PSORT-B: improving protein subcellular localization prediction for Gram-negative bacteria, Nucleic Acids Res., 31, 3613, 10.1093/nar/gkg602
Schaab, 2011, Analysis of phosphoproteomics data, Methods Mol. Biol., 696, 41, 10.1007/978-1-60761-987-1_3
Marshall, 1984, Unidentified curved bacilli in the stomach of patients with gastritis and peptic ulceration, Lancet, 323, 1311, 10.1016/S0140-6736(84)91816-6
Blaser, 1997, Ecology of Helicobacter pylori in the human stomach, J. Clin. Invest., 100, 759, 10.1172/JCI119588
Hatakeyama, 2004, Oncogenic mechanisms of the Helicobacter pylori CagA protein, Nat. Rev. Cancer, 4, 688, 10.1038/nrc1433
Wen, 2009, Helicobacter pylori virulence factors in gastric carcinogenesis, Cancer Lett., 282, 1, 10.1016/j.canlet.2008.11.016
Shi, 1998, The serine, threonine, and/or tyrosine-specific protein kinases and protein phosphatases of prokaryotic organisms: a family portrait, FEMS Microbiol. Rev., 22, 229, 10.1111/j.1574-6976.1998.tb00369.x
Grangeasse, 1999, Protein kinase activity in Helicobacter pylori, FEMS Microbiol. Lett., 176, 327, 10.1111/j.1574-6968.1999.tb13679.x
Ullrich, 1990, Signal transduction by receptors with tyrosine kinase activity, Cell, 61, 203, 10.1016/0092-8674(90)90801-K
Kenny, 1997, Enteropathogenic E. coli (EPEC) transfers its receptor for intimate adherence into mammalian cells, Cell, 91, 511, 10.1016/S0092-8674(00)80437-7
Segal, 1999, Altered states: involvement of phosphorylated CagA in the induction of host cellular growth changes by Helicobacter pylori, Proc. Natl. Acad. Sci. USA, 96, 14559, 10.1073/pnas.96.25.14559
Clifton, 2004, A chlamydial type III translocated protein is tyrosine-phosphorylated at the site of entry and associated with recruitment of actin, Proc. Natl. Acad. Sci. USA, 101, 10166, 10.1073/pnas.0402829101
Schulein, 2005, A bipartite signal mediates the transfer of type IV secretion substrates of Bartonella henselae into human cells, Proc. Natl. Acad. Sci. USA, 102, 856, 10.1073/pnas.0406796102
Cozzone, 2009, Bacterial tyrosine kinases: novel targets for antibacterial therapy?, Trends Microbiol., 17, 536, 10.1016/j.tim.2009.09.005
Molle, V. and Kremer, L. Division and cell envelope regulation by Ser/Thr phosphorylation: Mycobacterium shows the way. Mol. Microbiol. 75: 1064–1077.
Mazmanian, 2006, The love-hate relationship between bacterial polysaccharides and the host immune system, Nat. Rev. Immunol., 6, 849, 10.1038/nri1956
Grangeasse, 2007, Tyrosine phosphorylation: an emerging regulatory device of bacterial physiology, Trends Biochem. Sci., 32, 86, 10.1016/j.tibs.2006.12.004
Jadeau, 2008, Identification of the idiosyncratic bacterial protein tyrosine kinase (BY-kinase) family signature, Bioinformatics, 24, 2427, 10.1093/bioinformatics/btn462
Whitfield, 2006, Biosynthesis and assembly of capsular polysaccharides in Escherichia coli, Annu. Rev. Biochem., 75, 39, 10.1146/annurev.biochem.75.103004.142545
Morona, 2000, Tyrosine phosphorylation of CpsD negatively regulates capsular polysaccharide biosynthesis in Streptococcus pneumoniae, Mol. Microbiol., 35, 1431, 10.1046/j.1365-2958.2000.01808.x
Morona, 2006, Attachment of capsular polysaccharide to the cell wall of Streptococcus pneumoniae type 2 is required for invasive disease, Proc. Natl. Acad. Sci. USA, 103, 8505, 10.1073/pnas.0602148103
Wang, 2001, Eukaryotic initiation factor 2B: identification of multiple phosphorylation sites in the epsilon-subunit and their functions in vivo, EMBO J., 20, 4349, 10.1093/emboj/20.16.4349
Rosen, 2004, Highly phosphorylated bacterial proteins, Proteomics, 4, 3068, 10.1002/pmic.200400890
Endo, 2007, Identification of in vivo substrates of the chaperonin GroEL from Bacillus subtilis, Biosci. Biotechnol. Biochem., 71, 1073, 10.1271/bbb.60640
Suerbaum, 1994, Helicobacter pylori hspA-hspB heat-shock gene cluster: nucleotide sequence, expression, putative function and immunogenicity, Mol. Microbiol., 14, 959, 10.1111/j.1365-2958.1994.tb01331.x
Sherman, 1994, Heat shock-induced phosphorylation of GroEL alters its binding and dissociation from unfolded proteins, J. Biol. Chem., 269, 31479, 10.1016/S0021-9258(18)31719-8
Kumar, 2009, Facilitated oligomerization of mycobacterial GroEL: evidence for phosphorylation-mediated oligomerization, J. Bacteriol., 191, 6525, 10.1128/JB.00652-09
Rain, 2001, The protein-protein interaction map of Helicobacter pylori, Nature, 409, 211, 10.1038/35051615