Large-Scale Analysis of Kinase Signaling in Yeast Pseudohyphal Development Identifies Regulation of Ribonucleoprotein Granules

Yeast pseudohyphal filamentation is a stress-responsive growth transition relevant to processes required for virulence in pathogenic fungi. Pseudohyphal growth is controlled through a regulatory network encompassing conserved MAPK (Ste20p, Ste11p, Ste7p, Kss1p, and Fus3p), protein kinase A (Tpk2p), Elm1p, and Snf1p kinase pathways; however, the scope of these pathways is not fully understood. Here, we implemented quantitative phosphoproteomics to identify each of these signaling networks, generating a kinase-dead mutant in filamentous S. cerevisiae and surveying for differential phosphorylation. By this approach, we identified 439 phosphoproteins dependent upon pseudohyphal growth kinases. We report novel phosphorylation sites in 543 peptides, including phosphorylated residues in Ras2p and Flo8p required for wild-type filamentous growth. Phosphoproteins in these kinase signaling networks were enriched for ribonucleoprotein (RNP) granule components, and we observe co-localization of Kss1p, Fus3p, Ste20p, and Tpk2p with the RNP component Igo1p. These kinases localize in puncta with GFP-visualized mRNA, and KSS1 is required for wild-type levels of mRNA localization in RNPs. Kss1p pathway activity is reduced in lsm1Δ/Δ and pat1Δ/Δ strains, and these genes encoding P-body proteins are epistatic to STE7. The P-body protein Dhh1p is also required for hyphal development in Candida albicans. Collectively, this study presents a wealth of data identifying the yeast phosphoproteome in pseudohyphal growth and regulatory interrelationships between pseudohyphal growth kinases and RNPs.

• Publication year

  2015

• Venue

  PLoS Genetics

• Publication date

  2015-10-01

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1371/journal.pgen.1005564PMID 26447709PMCID 4598065
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Dynamic phosphoproteomics reveals TORC1-dependent regulation of yeast nucleotide and amino acid biosynthesis

  2015cited by this paper
• Pooled Segregant Sequencing Reveals Genetic Determinants of Yeast Pseudohyphal Growth

  2014cited by this paper
• The Yeast Sks1p Kinase Signaling Network Regulates Pseudohyphal Growth and Glucose Response

  2014cited by this paper
• Phosphoproteomic analysis identifies proteins involved in transcription-coupled mRNA decay as targets of Snf1 signaling

  2014cited by this paper
• Protein Kinases Are Associated with Multiple, Distinct Cytoplasmic Granules in Quiescent Yeast Cells

  2014cited by this paper
• Towards Systematic Discovery of Signaling Networks in Budding Yeast Filamentous Growth Stress Response Using Interventional Phosphorylation Data

  2013cited by this paper
• Processing Body and Stress Granule Assembly Occur by Independent and Differentially Regulated Pathways in Saccharomyces cerevisiae

  2013cited by this paper
• Genetic Networks Inducing Invasive Growth in Saccharomyces cerevisiae Identified Through Systematic Genome-Wide Overexpression

  2013cited by this paper
• Global Analysis of Yeast mRNPs

  2012cited by this paper
• Global Gene Deletion Analysis Exploring Yeast Filamentous Growth

  2012cited by this paper
• A Large-Scale Complex Haploinsufficiency-Based Genetic Interaction Screen in Candida albicans: Analysis of the RAM Network during Morphogenesis

  2011cited by this paper
• Stress-specific composition, assembly and kinetics of stress granules in Saccharomyces cerevisiae

  2011cited by this paper
• Accumulation of P-bodies in Candida albicans under different stress and filamentous growth conditions.

  2011influential reference
• Conditionally controlling nuclear trafficking in yeast by chemical-induced protein dimerization

  2010cited by this paper
• Initiation of the TORC1-regulated G0 program requires Igo1/2, which license specific mRNAs to evade degradation via the 5'-3' mRNA decay pathway.

  2010influential reference
• Environmental and Genetic Determinants of Colony Morphology in Yeast

  2010cited by this paper
• Dcp2 phosphorylation by Ste20 modulates stress granule assembly and mRNA decay in Saccharomyces cerevisiae

  2010cited by this paper
• A Profile of Differentially Abundant Proteins at the Yeast Cell Periphery during Pseudohyphal Growth*

  2010cited by this paper
• Phosphoproteomic Analysis Reveals Interconnected System-Wide Responses to Perturbations of Kinases and Phosphatases in Yeast

  2010cited by this paper
• Analyzing P-bodies and stress granules in Saccharomyces cerevisiae.

  2010influential reference
• Shedding of the mucin-like flocculin Flo11p reveals a new aspect of fungal adhesion regulation.

  2010cited by this paper
• Eukaryotic stress granules: the ins and outs of translation.

  2009cited by this paper
• A practical guide to the MaxQuant computational platform for SILAC-based quantitative proteomics

  2009cited by this paper
• Unconventional Genomic Architecture in the Budding Yeast Saccharomyces cerevisiae Masks the Nested Antisense Gene NAG1

  2008cited by this paper
• Analysis of the yeast kinome reveals a network of regulated protein localization during filamentous growth.

  2008cited by this paper
• Large-scale analysis of yeast filamentous growth by systematic gene disruption and overexpression.

  2008cited by this paper
• P bodies promote stress granule assembly in Saccharomyces cerevisiae

  2008cited by this paper
• An Interrelationship Between Autophagy and Filamentous Growth in Budding Yeast

  2007cited by this paper
• Morphogenesis in Candida albicans.

  2007cited by this paper
• Organelle DB: an updated resource of eukaryotic protein localization and function

  2006influential reference
• Translation-independent inhibition of mRNA deadenylation during stress in Saccharomyces cerevisiae.

  2006cited by this paper
• Target hub proteins serve as master regulators of development in yeast.

  2006cited by this paper
• Quantitative Phosphoproteomics Applied to the Yeast Pheromone Signaling Pathway*S

  2005cited by this paper
• Mss11p Is a Central Element of the Regulatory Network That Controls FLO11 Expression and Invasive Growth in Saccharomyces cerevisiae

  2005cited by this paper
• Global analysis of protein phosphorylation in yeast

  2005cited by this paper
• Stress granules and processing bodies are dynamically linked sites of mRNP remodeling

  2005cited by this paper
• Processing bodies require RNA for assembly and contain nontranslating mRNAs.

  2005cited by this paper
• Inhibition of 5' to 3' mRNA degradation under stress conditions in Saccharomyces cerevisiae: from GCN4 to MET16.

  2004cited by this paper
• Pheromone-dependent destruction of the Tec1 transcription factor is required for MAP kinase signaling specificity in yeast.

  2004cited by this paper
• A signaling mucin at the head of the Cdc42- and MAPK-dependent filamentous growth pathway in yeast.

  2004cited by this paper
• Persistent Activation by Constitutive Ste7 Promotes Kss1-Mediated Invasive Growth but Fails To Support Fus3-Dependent Mating in Yeast

  2004influential reference
• The distinct morphogenic states of Candida albicans.

  2004cited by this paper
• Engineered Control of Cell Morphology In Vivo Reveals Distinct Roles for Yeast and Filamentous Forms of Candida albicans during Infection

  2003cited by this paper
• Snf1 Kinases with Different β-Subunit Isoforms Play Distinct Roles in Regulating Haploid Invasive Growth

  2003cited by this paper
• Elm1p is one of three upstream kinases for the Saccharomyces cerevisiae SNF1 complex.

  2003cited by this paper
• Decapping and Decay of Messenger RNA Occur in Cytoplasmic Processing Bodies

  2003influential reference
• Candida albicans: A molecular revolution built on lessons from budding yeast

  2002cited by this paper
• Snf1 Protein Kinase and the Repressors Nrg1 and Nrg2 Regulate FLO11, Haploid Invasive Growth, and Diploid Pseudohyphal Differentiation

  2002cited by this paper
• Stable Isotope Labeling by Amino Acids in Cell Culture, SILAC, as a Simple and Accurate Approach to Expression Proteomics*

  2002influential reference
• Control of pseudohyphae formation in Saccharomyces cerevisiae.

  2001cited by this paper
• A filamentous growth response mediated by the yeast mating pathway.

  2001cited by this paper
• Xbp1-Mediated Repression of CLB Gene Expression Contributes to the Modifications of Yeast Cell Morphology and Cell Cycle Seen during Nitrogen-Limited Growth

  2001cited by this paper
• Analysis of yeast protein kinases using protein chips

  2000cited by this paper
• High-throughput methods for the large-scale analysis of gene function by transposon tagging.

  2000cited by this paper
• A Sm‐like protein complex that participates in mRNA degradation

  2000cited by this paper
• Glucose starvation induces a drastic reduction in the rates of both transcription and degradation of mRNA in yeast.

  2000cited by this paper
• Pre-mRNA processing factors are required for nuclear export.

  2000cited by this paper
• Glucose depletion causes haploid invasive growth in yeast.

  2000cited by this paper
• Characterization of alcohol-induced filamentous growth in Saccharomyces cerevisiae.

  2000cited by this paper
• Interplay of intrinsic and extrinsic signals in yeast differentiation.

  2000cited by this paper
• Characterization of Fus3 localization: active Fus3 localizes in complexes of varying size and specific activity.

  1999cited by this paper
• Effectors of a developmental mitogen-activated protein kinase cascade revealed by expression signatures of signaling mutants.

  1999cited by this paper
• Regulation of G2/M progression by the STE mitogen-activated protein kinase pathway in budding yeast filamentous growth.

  1999cited by this paper
• Cyclic AMP-Dependent Protein Kinase Regulates Pseudohyphal Differentiation in Saccharomyces cerevisiae

  1999cited by this paper
• MAP kinase and cAMP filamentation signaling pathways converge on the unusually large promoter of the yeast FLO11 gene

  1999cited by this paper
• Dimorphism and virulence in Candida albicans.

  1998cited by this paper
• Repression of yeast Ste12 transcription factor by direct binding of unphosphorylated Kss1 MAPK and its regulation by the Ste7 MEK.

  1998influential reference
• The three yeast A kinases have specific signaling functions in pseudohyphal growth.

  1998cited by this paper
• Additional modules for versatile and economical PCR‐based gene deletion and modification in Saccharomyces cerevisiae

  1998cited by this paper
• Nonfilamentous C. albicans mutants are avirulent.

  1997cited by this paper
• Control of filament formation in Candida albicans by the transcriptional repressor TUP1.

  1997cited by this paper
• Combinatorial Control Required for the Specificity of Yeast MAPK Signaling

  1997cited by this paper
• Coordination of the mating and cell integrity mitogen-activated protein kinase pathways in Saccharomyces cerevisiae

  1997cited by this paper
• MAP kinases with distinct inhibitory functions impart signaling specificity during yeast differentiation.

  1997cited by this paper
• Molecular cloning and analysis of the dominant flocculation gene FLO8 from Saccharomyces cerevisiae.

  1996cited by this paper
• Two novel targets of the MAP kinase Kss1 are negative regulators of invasive growth in the yeast Saccharomyces cerevisiae.

  1996influential reference
• FLO11, a yeast gene related to the STA genes, encodes a novel cell surface flocculin

  1996cited by this paper
• Muc1, a mucin-like protein that is regulated by Mss10, is critical for pseudohyphal differentiation in yeast.

  1996cited by this paper
• 'Fusel' alcohols induce hyphal-like extensions and pseudohyphal formation in yeasts.

  1996cited by this paper
• Molecular cloning and analysis of the dominant flocculation gene

  1996cited by this paper
• Ras2 signals via the Cdc42/Ste20/mitogen-activated protein kinase module to induce filamentous growth in Saccharomyces cerevisiae.

  1996cited by this paper
• Phosphorylation and localization of Kss1, a MAP kinase of the Saccharomyces cerevisiae pheromone response pathway.

  1995cited by this paper
• Elements of the yeast pheromone response pathway required for filamentous growth of diploids.

  1993cited by this paper
• Unipolar cell divisions in the yeast S. cerevisiae lead to filamentous growth: regulation by starvation and RAS.

  1992cited by this paper
• FUS3 represses CLN1 and CLN2 and in concert with KSS1 promotes signal transduction.

  1991cited by this paper
• Three different genes in S. cerevisiae encode the catalytic subunits of the cAMP-dependent protein kinase.

  1987cited by this paper
• Cloning and characterization of BCY1, a locus encoding a regulatory subunit of the cyclic AMP-dependent protein kinase in Saccharomyces cerevisiae

  1987cited by this paper
• Morphogenesis in Candida albicans.

  1985cited by this paper
• Multiplicity of the amino acid permeases in Saccharomyces cerevisiae. IV. Evidence for a general amino acid permease.

  1966cited by this paper
• Multiplicity of the amino acid permeases in Saccharomyces cerevisiae. II. Evidence for a specific lysine-transporting system.

  1966cited by this paper

• Roles of P-body factors in Candida albicans filamentation and stress response

  2025influential citation
• Roles of P-body factors in Candida albicans filamentation and stress response

  2025influential citation
• The RNA binding protein Pub1 inhibits TORC1 activity in Saccharomyces cerevisiae

  2024cites this paper
• Current insight into the role of mRNA decay pathways in fungal pathogenesis.

  2024cites this paper
• The yeast AMP-activated protein kinase Snf1 phosphorylates the inositol polyphosphate kinase Kcs1

  2024cites this paper
• Transcriptional analysis of the dimorphic fungus Umbilicaria muehlenbergii reveals the molecular mechanism of phenotypic transition

  2023cites this paper
• A Protein–Protein Interaction Analysis Suggests a Wide Range of New Functions for the p21-Activated Kinase (PAK) Ste20

  2023cites this paper
• The NPR/Hal family of protein kinases in yeasts: biological role, phylogeny and regulation under environmental challenges

  2022cites this paper
• Fus3 and Tpk2 protein kinases regulate the phosphorylation-dependent functions of RNA helicase Dhh1 in yeast mating and Ste12 protein expression

  2022cites this paper
• Post-transcriptional and translational control of the morphology and virulence in human fungal pathogens.

  2021cites this paper
• The Complex Genetic Basis and Multilayered Regulatory Control of Yeast Pseudohyphal Growth.

  2021cites this paper
• The intersection between stress responses and inositol pyrophosphates in Saccharomyces cerevisiae

  2020cites this paper
• Roles of Dhh1 RNA helicase in yeast filamentous growth: Analysis of N-terminal phosphorylation residues and ATPase domains

  2020influential citation
• Functional association of Loc1 and Puf6 with RNA helicase Dhh1 in translational regulation of Saccharomyces cerevisiae Ste12

  2019cites this paper
• Anuj Kumar

  2019cites this paper
• Rewired cellular signaling coordinates sugar and hypoxic responses for anaerobic xylose fermentation in yeast

  2019cites this paper
• A Stress-Responsive Signaling Network Regulating Pseudohyphal Growth and Ribonucleoprotein Granule Abundance in Saccharomyces cerevisiae

  2019cites this paper
• The 5′ Untranslated Region of the EFG1 Transcript Promotes Its Translation To Regulate Hyphal Morphogenesis in Candida albicans

  2018cites this paper
• Inositol polyphosphates regulate and predict yeast pseudohyphal growth phenotypes

  2018cites this paper
• Integration of protein phosphorylation, acetylation, and methylation data sets to outline lung cancer signaling networks

  2018cites this paper
• Messengers for morphogenesis: inositol polyphosphate signaling and yeast pseudohyphal growth

  2018cites this paper
• Granules of translation factor mRNAs and their potential role in the localisation of the translation machinery to regions of polarised growth

  2017cites this paper
• Light-sensing via hydrogen peroxide and a peroxiredoxin

  2017cites this paper
• Insights regarding fungal phosphoproteomic analysis.

  2017cites this paper
• Analysis of Kinase Signaling Pathways Regulating Filamentous Developmentin Saccharomyces cerevisiae and Candida albicans

  2017influential citation
• Global regulatory roles of the cAMP/PKA pathway revealed by phenotypic, transcriptomic and phosphoproteomic analyses in a null mutant of the PKA catalytic subunit in Candida albicans

  2017cites this paper
• Post‐transcriptional gene regulation in the biology and virulence of Candida albicans

  2016cites this paper
• Control of Candida albicans morphology and pathogenicity by post-transcriptional mechanisms

  2016cites this paper