Multisite Phosphorylation of the Guanine Nucleotide Exchange Factor Cdc24 during Yeast Cell Polarization

Background Cell polarization is essential for processes such as cell migration and asymmetric cell division. A common regulator of cell polarization in most eukaryotic cells is the conserved Rho GTPase, Cdc42. In budding yeast, Cdc42 is activated by a single guanine nucleotide exchange factor, Cdc24. The mechanistic details of Cdc24 activation at the onset of yeast cell polarization are unclear. Previous studies have suggested an important role for phosphorylation of Cdc24, which may regulate activity or function of the protein, representing a key step in the symmetry breaking process. Methodology/Principal Findings Here, we directly ask whether multisite phosphorylation of Cdc24 plays a role in its regulation. We identify through mass spectrometry analysis over thirty putative in vivo phosphorylation sites. We first focus on sites matching consensus sequences for cyclin-dependent and p21-activated kinases, two kinase families that have been previously shown to phosphorylate Cdc24. Through site-directed mutagenesis, yeast genetics, and light and fluorescence microscopy, we show that nonphosphorylatable mutations of these consensus sites do not lead to any detectable consequences on growth rate, morphology, kinetics of polarization, or localization of the mutant protein. We do, however, observe a change in the mobility shift of mutant Cdc24 proteins on SDS-PAGE, suggesting that we have indeed perturbed its phosphorylation. Finally, we show that mutation of all identified phosphorylation sites does not cause observable defects in growth rate or morphology. Conclusions/Significance We conclude that lack of phosphorylation on Cdc24 has no overt functional consequences in budding yeast. Yeast cell polarization may be more tightly regulated by inactivation of Cdc42 by GTPase activating proteins or by alternative methods of Cdc24 regulation, such as conformational changes or oligomerization.

[1]  A. Bretscher,et al.  Polarization of cell growth in yeast. I. Establishment and maintenance of polarity states. , 2000, Journal of cell science.

[2]  Bruce Stillman,et al.  Cold Spring Harbor Laboratory , 1995, Current Biology.

[3]  C. Monnig,et al.  Determinants for substrate phosphorylation by p21-activated protein kinase (gamma-PAK). , 1997, Biochemistry.

[4]  Michael B. Yaffe,et al.  Scansite 2.0: proteome-wide prediction of cell signaling interactions using short sequence motifs , 2003, Nucleic Acids Res..

[5]  B. Séraphin,et al.  The tandem affinity purification (TAP) method: a general procedure of protein complex purification. , 2001, Methods.

[6]  K. Murata,et al.  Transformation of intact yeast cells treated with alkali cations. , 1984, Journal of bacteriology.

[7]  Tony Pawson,et al.  Multisite phosphorylation of a CDK inhibitor sets a threshold for the onset of DNA replication , 2001, Nature.

[8]  P. Laurent-Puig [Cell polarity]. , 1990, Gastroenterologie clinique et biologique.

[9]  J. Pringle,et al.  Use of a screen for synthetic lethal and multicopy suppressee mutants to identify two new genes involved in morphogenesis in Saccharomyces cerevisiae , 1991, Molecular and cellular biology.

[10]  J. Pringle,et al.  CDC42 and CDC43, two additional genes involved in budding and the establishment of cell polarity in the yeast Saccharomyces cerevisiae , 1990, The Journal of cell biology.

[11]  C. Der,et al.  GEF means go: turning on RHO GTPases with guanine nucleotide-exchange factors , 2005, Nature Reviews Molecular Cell Biology.

[12]  M. Mann,et al.  Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics. , 2003, Analytical chemistry.

[13]  E. O’Shea,et al.  Global analysis of protein expression in yeast , 2003, Nature.

[14]  Aljoscha Nern,et al.  Nucleocytoplasmic Shuttling of the Cdc42p Exchange Factor Cdc24p , 2000, The Journal of cell biology.

[15]  I. Herskowitz,et al.  Two active states of the Ras-related Bud1/Rsr1 protein bind to different effectors to determine yeast cell polarity. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[16]  K. Toenjes,et al.  Separate membrane targeting and anchoring domains function in the localization of the S. cerevisiae Cdc24p guanine nucleotide exchange factor , 2004, Current Genetics.

[17]  Matthias Peter,et al.  The nucleotide exchange factor Cdc24p may be regulated by auto‐inhibition , 2004, The EMBO journal.

[18]  E. O’Shea,et al.  Global analysis of protein localization in budding yeast , 2003, Nature.

[19]  Matthias Peter,et al.  Nuclear sequestration of the exchange factor Cdc24 by Far1 regulates cell polarity during yeast mating , 2000, Nature Cell Biology.

[20]  P. Philippsen,et al.  Additional modules for versatile and economical PCR‐based gene deletion and modification in Saccharomyces cerevisiae , 1998, Yeast.

[21]  M. Mann,et al.  Quantitative Phosphoproteomics Applied to the Yeast Pheromone Signaling Pathway*S , 2005, Molecular & Cellular Proteomics.

[22]  Brendan K Faherty,et al.  Optimization and Use of Peptide Mass Measurement Accuracy in Shotgun Proteomics*S , 2006, Molecular & Cellular Proteomics.

[23]  Xin-Yun Huang,et al.  Structural Basis for Relief of Autoinhibition of the Dbl Homology Domain of Proto-Oncogene Vav by Tyrosine Phosphorylation , 2000, Cell.

[24]  R. Arkowitz,et al.  Oligomerization Regulates the Localization of Cdc24, the Cdc42 Activator in Saccharomyces cerevisiae* , 2008, Journal of Biological Chemistry.

[25]  J. Wootton,et al.  Analysis of compositionally biased regions in sequence databases. , 1996, Methods in enzymology.

[26]  Daniel J. Lew,et al.  Symmetry-Breaking Polarization Driven by a Cdc42p GEF-PAK Complex , 2008, Current Biology.

[27]  Matthias Peter,et al.  Phosphorylation of Bem2p and Bem3p may contribute to local activation of Cdc42p at bud emergence , 2007, The EMBO journal.

[28]  J. Moskow,et al.  Assembly of Scaffold-mediated Complexes Containing Cdc42p, the Exchange Factor Cdc24p, and the Effector Cla4p Required for Cell Cycle-regulated Phosphorylation of Cdc24p* , 2001, The Journal of Biological Chemistry.

[29]  Anupama E. Gururaj,et al.  p21-activated kinase signaling in breast cancer , 2004, Breast Cancer Research.

[30]  Mike Tyers,et al.  A Mechanism for Cell-Cycle Regulation of MAP Kinase Signaling in a Yeast Differentiation Pathway , 2007, Cell.

[31]  L. Hartwell Genetic control of the cell division cycle in yeast. IV. Genes controlling bud emergence and cytokinesis. , 1971, Experimental cell research.

[32]  Daniel Figeys,et al.  Activation of the Cdc42p GTPase by cyclin‐dependent protein kinases in budding yeast , 2007, The EMBO journal.

[33]  J. Yates,et al.  Protein identification at the low femtomole level from silver-stained gels using a new fritless electrospray interface for liquid chromatography-microspray and nanospray mass spectrometry. , 1998, Analytical biochemistry.

[34]  M. Peter,et al.  Phosphorylation of the Cdc42 exchange factor Cdc24 by the PAK-like kinase Cla4 may regulate polarized growth in yeast. , 2000, Molecular cell.

[35]  A. Adams,et al.  Methods in yeast genetics : a Cold Spring Harbor Laboratory course manual , 1998 .

[36]  John C. Wootton,et al.  Non-globular Domains in Protein Sequences: Automated Segmentation Using Complexity Measures , 1994, Comput. Chem..

[37]  Zhenbiao Yang,et al.  RHO Gtpases and the Actin Cytoskeleton , 2000 .

[38]  James E. Ferrell,et al.  Tuning Bulk Electrostatics to Regulate Protein Function , 2007, Cell.

[39]  A. Shevchenko,et al.  Femtomole sequencing of proteins from polyacrylamide gels by nano-electrospray mass spectrometry , 1996, Nature.

[40]  J. Yates,et al.  An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database , 1994, Journal of the American Society for Mass Spectrometry.

[41]  Douglas I. Johnson Cdc42: An Essential Rho-Type GTPase Controlling Eukaryotic Cell Polarity , 1999, Microbiology and Molecular Biology Reviews.

[42]  Amy S. Gladfelter,et al.  Scaffold-mediated symmetry breaking by Cdc42p , 2003, Nature Cell Biology.

[43]  Kay Hofmann,et al.  A positive feedback loop stabilizes the guanine‐nucleotide exchange factor Cdc24 at sites of polarization , 2002, The EMBO journal.

[44]  Steven P. Gygi,et al.  Cdk1 coordinates cell-surface growth with the cell cycle , 2007, Nature Cell Biology.

[45]  S. Etienne-Manneville,et al.  Cdc42 - the centre of polarity , 2004, Journal of Cell Science.

[46]  Y. Anraku,et al.  A DBL-homologous region of the yeast CLS4/CDC24 gene product is important for Ca(2+)-modulated bud assembly. , 1991, Biochemical and biophysical research communications.

[47]  J. Pringle,et al.  Multicopy suppression of the cdc24 budding defect in yeast by CDC42 and three newly identified genes including the ras-related gene RSR1. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[48]  N. Blom,et al.  Sequence and structure-based prediction of eukaryotic protein phosphorylation sites. , 1999, Journal of molecular biology.

[49]  Jason Moffat,et al.  Late-G1 cyclin–CDK activity is essential for control of cell morphogenesis in budding yeast , 2004, Nature Cell Biology.

[50]  J. Pringle Staining of bud scars and other cell wall chitin with calcofluor. , 1991, Methods in enzymology.

[51]  E. Bi,et al.  Central Roles of Small GTPases in the Development of Cell Polarity in Yeast and Beyond , 2007, Microbiology and Molecular Biology Reviews.

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

[53]  S. Morales,et al.  Analysis of cell-cycle specific localization of the Rdi1p RhoGDI and the structural determinants required for Cdc42p membrane localization and clustering at sites of polarized growth , 2004, Current Genetics.

[54]  Thomas Schmidt,et al.  Robust cell polarity is a dynamic state established by coupling transport and GTPase signaling , 2004, The Journal of cell biology.

[55]  J. Chant,et al.  A mechanism of Bud1p GTPase action suggested by mutational analysis and immunolocalization , 1996, Current Biology.

[56]  K. Toenjes,et al.  The guanine-nucleotide-exchange factor Cdc24p is targeted to the nucleus and polarized growth sites , 1999, Current Biology.

[57]  B. Séraphin,et al.  A generic protein purification method for protein complex characterization and proteome exploration , 1999, Nature Biotechnology.