Phosphoproteome of Cryptococcus neoformans.

UNLABELLED Cryptococcus neoformans is an encapsulated pathogenic yeast, which causes life threatening meningitis in immunocompromised individuals. C. neoformans var. grubii is the most prevalent and virulent form among the two varieties of C. neoformans - C. neoformans var. grubii and C. neoformans var. neoformans. The virulence of C. neoformans is mainly conferred by its capsule and melanin. cAMP dependent PKA-induced phosphorylation events are reported to be associated with the expression of these virulence traits, which highlights the importance of phosphoproteins in virulence and infection. Therefore, we performed global profiling of phosphoproteome of C. neoformans to enable a better understanding of molecular regulation of its virulence and pathogenesis. High resolution mass spectrometry of TiO2 enriched phosphopeptides from C. neoformans var. grubii grown in culture led to the identification of 1089 phosphopeptides derived from 648 proteins including about 45 kinases. Motif enrichment analysis revealed that most CDK family substrates were found to be phosphorylated. This indicates that cyclin-dependent kinases were among the active kinases in the pathogen in culture. These studies provide a framework for understanding virulence mechanisms in the context of signalling pathways in pathogenic yeast. This article is part of a Special Issue entitled: Trends in Microbial Proteomics. BIOLOGICAL SIGNIFICANCE C. neoformans is a pathogenic yeast responsible for cryptococcal meningitis. Melanin and polysaccharide capsule have been established as some of the key virulence factors that play a major role in the pathogenesis of C. neoformans. Recent studies have shown the role of kinase mediated signalling pathways in governing biosynthesis of these virulence factors. This study revealed 1540 phosphorylation sites in 648 proteins providing a comprehensive view of phosphoproteins in C. neoformans. This should serve as a useful resource to explore activated signalling pathways in C. neoformans and their association with its virulence and pathogenesis.

[1]  A. Mitchell,et al.  Interaction of Cryptococcus neoformans Rim101 and Protein Kinase A Regulates Capsule , 2010, PLoS pathogens.

[2]  S. Patel,et al.  The Casein Kinase I Protein Cck1 Regulates Multiple Signaling Pathways and Is Essential for Cell Integrity and Fungal Virulence in Cryptococcus neoformans , 2011, Eukaryotic Cell.

[3]  Y. Liu,et al.  The Sphingolipid Long-chain Base-Pkh1/2-Ypk1/2 Signaling Pathway Regulates Eisosome Assembly and Turnover* , 2008, Journal of Biological Chemistry.

[4]  J. Lodge,et al.  Role of Cryptococcus neoformans Rho1 GTPases in the PKC1 Signaling Pathway in Response to Thermal Stress , 2012, Eukaryotic Cell.

[5]  H. Bach,et al.  Protein kinase and phosphatase signaling in Mycobacterium tuberculosis physiology and pathogenesis. , 2010, Biochimica et biophysica acta.

[6]  Wendell A. Lim,et al.  Correction: Evolution of Phosphoregulation: Comparison of Phosphorylation Patterns across Yeast Species , 2009, PLoS Biology.

[7]  S. T. Cowan PRINCIPLES AND PRACTICE OF BACTERIAL TAXONOMY--A FORWARD LOOK. , 1965, Journal of general microbiology.

[8]  J. Deutscher,et al.  Analysis of the serine/threonine/tyrosine phosphoproteome of the pathogenic bacterium Listeria monocytogenes reveals phosphorylated proteins related to virulence , 2011, Proteomics.

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

[10]  O. H. Lowry,et al.  Protein measurement with the Folin phenol reagent. , 1951, The Journal of biological chemistry.

[11]  J. Kronstad,et al.  The cAMP/Protein Kinase A Pathway and Virulence in Cryptococcus neoformans , 2011, Mycobiology.

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

[13]  M. Helmer-Citterich,et al.  Adaptation of a 2D in-gel kinase assay to trace phosphotransferase activities in the human pathogen Leishmania donovani. , 2011, Journal of proteomics.

[14]  B. Kuster,et al.  Confident Phosphorylation Site Localization Using the Mascot Delta Score , 2010, Molecular & Cellular Proteomics.

[15]  P. R. Kraus,et al.  The Cryptococcus neoformans MAP kinase Mpk1 regulates cell integrity in response to antifungal drugs and loss of calcineurin function , 2003, Molecular microbiology.

[16]  Mami Okada,et al.  Plasmodium falciparum FIKK Kinase Members Target Distinct Components of the Erythrocyte Membrane , 2010, PloS one.

[17]  Steven P Gygi,et al.  Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry , 2007, Nature Methods.

[18]  Zhou Songyang,et al.  Use of an oriented peptide library to determine the optimal substrates of protein kinases , 1994, Current Biology.

[19]  Edward L. Huttlin,et al.  Evaluation of HCD- and CID-type Fragmentation Within Their Respective Detection Platforms For Murine Phosphoproteomics* , 2011, Molecular & Cellular Proteomics.

[20]  K. Kwon-Chung,et al.  Encapsulation and melanin formation as indicators of virulence in Cryptococcus neoformans , 1986, Infection and immunity.

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

[22]  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.

[23]  J. Thorner,et al.  Pkh1 and Pkh2 differentially phosphorylate and activate Ypk1 and Ykr2 and define protein kinase modules required for maintenance of cell wall integrity. , 2002, Molecular biology of the cell.

[24]  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.

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

[26]  Kumaran Kandasamy,et al.  Evaluation of several MS/MS search algorithms for analysis of spectra derived from electron transfer dissociation experiments. , 2009, Analytical chemistry.

[27]  K. Wannemuehler,et al.  Estimation of the current global burden of cryptococcal meningitis among persons living with HIV/AIDS , 2009, AIDS.

[28]  B. Monsarrat,et al.  Functional characterization of the Mycobacterium tuberculosis serine/threonine kinase PknJ. , 2010, Microbiology.

[29]  Joseph Heitman,et al.  G protein-coupled receptor Gpr4 senses amino acids and activates the cAMP-PKA pathway in Cryptococcus neoformans. , 2005, Molecular biology of the cell.

[30]  P. R. Kraus,et al.  Identification of Cryptococcus neoformans Temperature-Regulated Genes with a Genomic-DNA Microarray , 2004, Eukaryotic Cell.

[31]  J. A. Spicer,et al.  Activation of a PAK-MEK signalling pathway in malaria parasite-infected erythrocytes , 2011, Cellular microbiology.

[32]  S. Gygi,et al.  An iterative statistical approach to the identification of protein phosphorylation motifs from large-scale data sets , 2005, Nature Biotechnology.

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

[34]  James E. Ferrell,et al.  Mechanisms of specificity in protein phosphorylation , 2007, Nature Reviews Molecular Cell Biology.

[35]  J. Heitman,et al.  Specialization of the HOG pathway and its impact on differentiation and virulence of Cryptococcus neoformans. , 2005, Molecular biology of the cell.

[36]  J. Heitman,et al.  A unique fungal two-component system regulates stress responses, drug sensitivity, sexual development, and virulence of Cryptococcus neoformans. , 2006, Molecular biology of the cell.

[37]  K. Kwon-Chung,et al.  Involvement of PDK1, PKC and TOR signalling pathways in basal fluconazole tolerance in Cryptococcus neoformans , 2012, Molecular microbiology.

[38]  T. Köcher,et al.  Universal and confident phosphorylation site localization using phosphoRS. , 2011, Journal of proteome research.

[39]  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.

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

[41]  T. Myers,et al.  A Novel Specificity Protein 1 (SP1)-like Gene Regulating Protein Kinase C-1 (Pkc1)-dependent Cell Wall Integrity and Virulence Factors in Cryptococcus neoformans* , 2011, The Journal of Biological Chemistry.

[42]  S. Gygi,et al.  Phosphoproteome analysis of fission yeast. , 2008, Journal of proteome research.

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

[44]  J. Heitman,et al.  Mating-Type-Specific and Nonspecific PAK Kinases Play Shared and Divergent Roles in Cryptococcus neoformans , 2002, Eukaryotic Cell.

[45]  W. Lim,et al.  Evolution of Phosphoregulation: Comparison of Phosphorylation Patterns across Yeast Species , 2009, PLoS biology.

[46]  K. Takeo,et al.  The single Cdk1-G1 cyclin of Cryptococcus neoformans is not essential for cell cycle progression, but plays important roles in the proper commitment to DNA synthesis and bud emergence in this yeast. , 2010, FEMS yeast research.

[47]  M. Mann,et al.  Feasibility of large-scale phosphoproteomics with higher energy collisional dissociation fragmentation. , 2010, Journal of proteome research.

[48]  B. Kemp,et al.  Protein kinase recognition sequence motifs. , 1990, Trends in biochemical sciences.

[49]  M. Robles,et al.  University of Birmingham High throughput functional annotation and data mining with the Blast2GO suite , 2022 .