Bacterial Phosphoproteomic Analysis Reveals the Correlation Between Protein Phosphorylation and Bacterial Pathogenicity

Increasing evidence shows that protein phosphorylation on serine, threonine and tyrosine residues is a major regulatory post-translational modification in the bacteria. This review focuses on the implications of bacterial phosphoproteome in bacterial pathogenicity and highlights recent development of methods in phosphoproteomics and the connectivity of the phosphorylation networks. Recent technical developments in the high accuracy mass spectrometry have dramatically transformed proteomics and made it possible the characterization of a few exhaustive site-specific bacterial phosphoproteomes. The high abundance of tyrosine phosphorylations in a few bacterial phosphoproteomes suggests their roles in the pathogenicity, especially in the case of pathogen–host interactions; the high abundance of multi-phosphorylation sites in bacterial phosphoprotein is a compensation of the relatively small phosphorylation size and an indicator of the delicate regulation of protein functions.

[1]  L. Iakoucheva,et al.  The importance of intrinsic disorder for protein phosphorylation. , 2004, Nucleic acids research.

[2]  George M. Church,et al.  Extensive phosphorylation with overlapping specificity by Mycobacterium tuberculosis serine/threonine protein kinases , 2010, Proceedings of the National Academy of Sciences.

[3]  A. Labigne,et al.  Helicobacter pylori hspA‐hspB heat‐shock gene cluster: nucleotide sequence, expression, putative function and immunogenicity , 1994, Molecular microbiology.

[4]  J. Wojcik,et al.  The protein–protein interaction map of Helicobacter pylori , 2001, Nature.

[5]  A. Goldberg,et al.  Heat shock-induced phosphorylation of GroEL alters its binding and dissociation from unfolded proteins. , 1994, The Journal of biological chemistry.

[6]  Qing‐Yu He,et al.  Application of immobilized metal affinity chromatography in proteomics , 2005, Expert review of proteomics.

[7]  Ke Wang,et al.  PSORT-B: improving protein subcellular localization prediction for Gram-negative bacteria , 2003, Nucleic Acids Res..

[8]  R. Morona,et al.  Attachment of capsular polysaccharide to the cell wall of Streptococcus pneumoniae type 2 is required for invasive disease. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[9]  H. Zou,et al.  Immobilized Zirconium Ion Affinity Chromatography for Specific Enrichment of Phosphopeptides in Phosphoproteome Analysis*S , 2007, Molecular & Cellular Proteomics.

[10]  H. Haraguchi,et al.  Metallomics: An integrated biometal science , 2009 .

[11]  R. Aebersold,et al.  A systematic approach to the analysis of protein phosphorylation , 2001, Nature Biotechnology.

[12]  Ayako Endo,et al.  Identification of in Vivo Substrates of the Chaperonin GroEL from Bacillus subtilis , 2007, Bioscience, biotechnology, and biochemistry.

[13]  P. Kennelly,et al.  The serine, threonine, and/or tyrosine-specific protein kinases and protein phosphatases of prokaryotic organisms: a family portrait. , 1998, FEMS microbiology reviews.

[14]  A. Cozzone,et al.  Analysis of the protein-kinase activity of Escherichia coli cells. , 1979, Biochemical and biophysical research communications.

[15]  R. Morona,et al.  Tyrosine phosphorylation of CpsD negatively regulates capsular polysaccharide biosynthesis in Streptococcus pneumoniae , 2000, Molecular microbiology.

[16]  B. Finlay,et al.  Enteropathogenic E. coli (EPEC) Transfers Its Receptor for Intimate Adherence into Mammalian Cells , 1997, Cell.

[17]  T. Hackstadt,et al.  A chlamydial type III translocated protein is tyrosine-phosphorylated at the site of entry and associated with recruitment of actin. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[18]  B. Marshall,et al.  UNIDENTIFIED CURVED BACILLI IN THE STOMACH OF PATIENTS WITH GASTRITIS AND PEPTIC ULCERATION , 1984, The Lancet.

[19]  M. Mann,et al.  The Ser/Thr/Tyr phosphoproteome of Lactococcus lactis IL1403 reveals multiply phosphorylated proteins , 2008, Proteomics.

[20]  Alain J. Cozzone,et al.  Identification of the idiosyncratic bacterial protein tyrosine kinase (BY-kinase) family signature , 2008, Bioinform..

[21]  Hanno Steen,et al.  Analysis of protein phosphorylation using mass spectrometry: deciphering the phosphoproteome. , 2002, Trends in biotechnology.

[22]  D. Petranovic,et al.  Insights from site-specific phosphoproteomics in bacteria. , 2008, Biochimica et biophysica acta.

[23]  L. Brill,et al.  Automated immobilized metal affinity chromatography/nano-liquid chromatography/electrospray ionization mass spectrometry platform for profiling protein phosphorylation sites. , 2005, Rapid communications in mass spectrometry : RCM.

[24]  Jörg Stülke,et al.  The Phosphoproteome of the Minimal Bacterium Mycoplasma pneumoniae , 2010, Molecular & Cellular Proteomics.

[25]  Joseph Schlessinger,et al.  Signal transduction by receptors with tyrosine kinase activity , 1990, Cell.

[26]  S. Mande,et al.  Facilitated Oligomerization of Mycobacterial GroEL: Evidence for Phosphorylation-Mediated Oligomerization , 2009, Journal of bacteriology.

[27]  S. Souchelnytskyi,et al.  Efficient enrichment of intact phosphorylated proteins by modified immobilized metal‐affinity chromatography , 2005, Proteomics.

[28]  M. Mann,et al.  Stable isotope labeling by amino acids in cell culture (SILAC) applied to quantitative proteomics of Bacillus subtilis. , 2010, Journal of proteome research.

[29]  Ivan Mijakovic,et al.  Protein phosphorylation in bacterial signal transduction. , 2011, Biochimica et biophysica acta.

[30]  P. Cohen,et al.  The regulation of protein function by multisite phosphorylation--a 25 year update. , 2000, Trends in biochemical sciences.

[31]  P. Cohen,et al.  The origins of protein phosphorylation , 2002, Nature Cell Biology.

[32]  M. Bott,et al.  Towards a phosphoproteome map of Corynebacterium glutamicum , 2003, Proteomics.

[33]  C. Schaab Analysis of phosphoproteomics data. , 2011, Methods in molecular biology.

[34]  S. Mazmanian,et al.  The love–hate relationship between bacterial polysaccharides and the host immune system , 2006, Nature Reviews Immunology.

[35]  P. Roepstorff,et al.  Highly Selective Enrichment of Phosphorylated Peptides from Peptide Mixtures Using Titanium Dioxide Microcolumns* , 2005, Molecular & Cellular Proteomics.

[36]  J. Porath,et al.  Isolation of phosphoproteins by immobilized metal (Fe3+) affinity chromatography. , 1986, Analytical biochemistry.

[37]  H. Reeves,et al.  Phosphorylation of Isocitrate dehydrogenase of Escherichia coli. , 1979, Science.

[38]  M. Tomita,et al.  Ser/Thr/Tyr phosphoproteome analysis of pathogenic and non‐pathogenic Pseudomonas species , 2009, Proteomics.

[39]  M. Hecker,et al.  Highly phosphorylated bacterial proteins , 2004, Proteomics.

[40]  Qing‐Yu He,et al.  Phosphoproteomic analysis reveals the multiple roles of phosphorylation in pathogenic bacterium Streptococcus pneumoniae. , 2010, Journal of proteome research.

[41]  Jörg Bernhardt,et al.  Dynamics of protein phosphorylation on Ser/Thr/Tyr in Bacillus subtilis , 2007, Proteomics.

[42]  Ivan Mijakovic,et al.  NetPhosBac – A predictor for Ser/Thr phosphorylation sites in bacterial proteins , 2009, Proteomics.

[43]  A. Heck,et al.  Selective isolation at the femtomole level of phosphopeptides from proteolytic digests using 2D-NanoLC-ESI-MS/MS and titanium oxide precolumns. , 2004, Analytical chemistry.

[44]  L. Johnson The regulation of protein phosphorylation. , 2009, Biochemical Society transactions.

[45]  S. Moss,et al.  Helicobacter pylori virulence factors in gastric carcinogenesis. , 2009, Cancer letters.

[46]  Forest M White,et al.  Quantitative phosphoproteomics by mass spectrometry: Past, present, and future , 2008, Proteomics.

[47]  C. Whitfield Biosynthesis and assembly of capsular polysaccharides in Escherichia coli. , 2006, Annual review of biochemistry.

[48]  M. Blaser Ecology of Helicobacter pylori in the human stomach. , 1997, The Journal of clinical investigation.

[49]  A. Ninfa,et al.  Use of two-component signal transduction systems in the construction of synthetic genetic networks. , 2010, Current opinion in microbiology.

[50]  K. Khoo,et al.  Phosphoproteomics of Klebsiella pneumoniae NTUH-K2044 Reveals a Tight Link between Tyrosine Phosphorylation and Virulence* , 2009, Molecular & Cellular Proteomics.

[51]  S. Foote,et al.  The cytoplasmic phosphoproteome of the Gram‐negative bacterium Campylobacter jejuni: Evidence for modification by unidentified protein kinases , 2007, Proteomics.

[52]  B. Chait,et al.  Enrichment analysis of phosphorylated proteins as a tool for probing the phosphoproteome , 2001, Nature Biotechnology.

[53]  Christoph Dehio,et al.  A bipartite signal mediates the transfer of type IV secretion substrates of Bartonella henselae into human cells. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[54]  Juan Pablo Albar,et al.  Advances in the analysis of protein phosphorylation. , 2008, Journal of proteome research.

[55]  A. Cozzone Bacterial tyrosine kinases: novel targets for antibacterial therapy? , 2009, Trends in microbiology.

[56]  Ivan Mijakovic,et al.  The Serine/Threonine/Tyrosine Phosphoproteome of the Model Bacterium Bacillus subtilis*S , 2007, Molecular & Cellular Proteomics.

[57]  M. Bibb,et al.  Analysis of the phosphoproteome of the multicellular bacterium Streptomyces coelicolor A3(2) by protein/peptide fractionation, phosphopeptide enrichment and high‐accuracy mass spectrometry , 2010, Proteomics.

[58]  J. Ferrell,et al.  Mechanisms of specificity in protein phosphorylation , 2007, Nature Reviews Molecular Cell Biology.

[59]  T. Hunter,et al.  The Protein Kinase Complement of the Human Genome , 2002, Science.

[60]  Scott A Gerber,et al.  Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae. , 2007, Journal of proteome research.

[61]  M. Mann,et al.  Analysis of receptor signaling pathways by mass spectrometry: identification of vav-2 as a substrate of the epidermal and platelet-derived growth factor receptors. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[62]  Protein kinase activity in Helicobacter pylori. , 1999, FEMS microbiology letters.

[63]  M. Collins,et al.  Analysis of protein phosphorylation on a proteome‐scale , 2007, Proteomics.

[64]  Qing‐Yu He,et al.  Phosphoproteome analysis of the pathogenic bacterium Helicobacter pylori reveals over‐representation of tyrosine phosphorylation and multiply phosphorylated proteins , 2011, Proteomics.

[65]  M. Hatakeyama Oncogenic mechanisms of the Helicobacter pylori CagA protein , 2004, Nature Reviews Cancer.

[66]  Steven P Gygi,et al.  Large-scale characterization of HeLa cell nuclear phosphoproteins. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[67]  J. Deutscher,et al.  Phosphoproteomics in bacteria: towards a systemic understanding of bacterial phosphorylation networks , 2008, Expert review of proteomics.

[68]  S. Falkow,et al.  Altered states: involvement of phosphorylated CagA in the induction of host cellular growth changes by Helicobacter pylori. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[69]  L. Kremer,et al.  Division and cell envelope regulation by Ser/Thr phosphorylation: Mycobacterium shows the way , 2010, Molecular microbiology.

[70]  Jérôme Garin,et al.  Analysis of the dynamic Bacillus subtilis Ser/Thr/Tyr phosphoproteome implicated in a wide variety of cellular processes , 2006, Proteomics.

[71]  Juan Miguel García-Gómez,et al.  BIOINFORMATICS APPLICATIONS NOTE Sequence analysis Manipulation of FASTQ data with Galaxy , 2005 .

[72]  C. Proud,et al.  Eukaryotic initiation factor 2B: identification of multiple phosphorylation sites in the ϵ‐subunit and their functions in vivo , 2001, The EMBO journal.

[73]  J. Shabanowitz,et al.  Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae , 2002, Nature Biotechnology.

[74]  J. Shabanowitz,et al.  Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[75]  Ivan Mijakovic,et al.  MATERIALS AND METHODS , 1981, Green Corrosion Inhibitors: Reviews and Applications.

[76]  Ivan Mijakovic,et al.  Tyrosine phosphorylation: an emerging regulatory device of bacterial physiology. , 2007, Trends in biochemical sciences.