Multiple Pathways for Suppression of Mutants Affecting G1-Specific Transcription in Saccharomyces cerevisiae

In the budding yeast, Saccharomyces cerevisiae, control of cell proliferation is exerted primarily during G1 phase. The G1-specific transcription of several hundred genes, many with roles in early cell cycle events, requires the transcription factors SBF and MBF, each composed of Swi6 and a DNA-binding protein, Swi4 or Mbp1, respectively. Binding of these factors to promoters is essential but insufficient for robust transcription. Timely transcriptional activation requires Cln3/CDK activity. To identify potential targets for Cln3/CDK, we identified multicopy suppressors of the temperature sensitivity of new conditional alleles of SWI6. A bck2Δ background was used to render SWI6 essential. Seven multicopy suppressors of bck2Δ swi6-ts mutants were identified. Three genes, SWI4, RME1, and CLN2, were identified previously in related screens and shown to activate G1-specific expression of genes independent of CLN3 and SWI6. The other four genes, FBA1, RPL40a/UBI1, GIN4, and PAB1, act via apparently unrelated pathways downstream of SBF and MBF. Each depends upon CLN2, but not CLN1, for its suppressing activity. Together with additional characterization these findings indicate that multiple independent pathways are sufficient for proliferation in the absence of G1-specific transcriptional activators.

[1]  Kim Nasmyth,et al.  The role of SWI4 and SWI6 in the activity of G1 cyclins in yeast , 1991, Cell.

[2]  A. Sachs,et al.  Differential effects of aromatic and charged residue substitutions in the RNA binding domains of the yeast poly(A)-binding protein. , 1997, Journal of molecular biology.

[3]  A. Sachs,et al.  RNA Recognition Motif 2 of Yeast Pab1p Is Required for Its Functional Interaction with Eukaryotic Translation Initiation Factor 4G , 1998, Molecular and Cellular Biology.

[4]  Y Chen,et al.  The yeast Mcm1 protein is regulated posttranscriptionally by the flux of glycolysis , 1995, Molecular and cellular biology.

[5]  J. Caviston,et al.  The role of Cdc42p GTPase-activating proteins in assembly of the septin ring in yeast. , 2003, Molecular biology of the cell.

[6]  M. Snyder,et al.  Nim1-related kinases coordinate cell cycle progression with the organization of the peripheral cytoskeleton in yeast. , 1999, Genes & development.

[7]  R. Sikorski,et al.  A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. , 1989, Genetics.

[8]  K Nasmyth,et al.  CLB5 and CLB6, a new pair of B cyclins involved in DNA replication in Saccharomyces cerevisiae. , 1993, Genes & development.

[9]  David Botstein,et al.  Two differentially regulated mRNAs with different 5′ ends encode secreted and intracellular forms of yeast invertase , 1982, Cell.

[10]  E. Garí,et al.  The Cln3 cyclin is down‐regulated by translational repression and degradation during the G1 arrest caused by nitrogen deprivation in budding yeast , 1997, The EMBO journal.

[11]  Michael Primig,et al.  Anatomy of a transcription factor important for the Start of the cell cycle in Saccharomyces cerevisiae , 1992, Nature.

[12]  C. Ptak,et al.  Increased Ubiquitin Expression Suppresses the Cell Cycle Defect Associated with the Yeast Ubiquitin Conjugating Enzyme, CDC34 (UBC3) , 1995, The Journal of Biological Chemistry.

[13]  M. Tyers,et al.  The PCL2 (ORFD)-PHO85 cyclin-dependent kinase complex: a cell cycle regulator in yeast. , 1994, Science.

[14]  K. Nasmyth,et al.  A role for the transcription factors Mbp1 and Swi4 in progression from G1 to S phase. , 1993, Science.

[15]  L. Breeden,et al.  A novel Mcm1-dependent element in the SWI4, CLN3, CDC6, and CDC47 promoters activates M/G1-specific transcription. , 1997, Genes & development.

[16]  F. Cross,et al.  Genes that can bypass the CLN requirement for Saccharomyces cerevisiae cell cycle START. , 1994, Molecular and cellular biology.

[17]  D. Botstein,et al.  Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF , 2001, Nature.

[18]  L. Johnston,et al.  Rme1, a negative regulator of meiosis, is also a positive activator of G1 cyclin gene expression. , 1995, The EMBO journal.

[19]  M Aldea,et al.  Whi3 binds the mRNA of the G1 cyclin CLN3 to modulate cell fate in budding yeast. , 2001, Genes & development.

[20]  K. Nasmyth.  Regulating the HO endonuclease in yeast. , 1993, Current opinion in genetics & development.

[21]  I. Herskowitz,et al.  Cell cycle control by a complex of the cyclin HCS26 (PCL1) and the kinase PHO85. , 1994, Science.

[22]  D. Lew,et al.  Cdc28 tyrosine phosphorylation and the morphogenesis checkpoint in budding yeast. , 1996, Molecular biology of the cell.

[23]  R. Roeder,et al.  S Phase Activation of the Histone H2B Promoter by OCA-S, a Coactivator Complex that Contains GAPDH as a Key Component , 2003, Cell.

[24]  K. Arndt,et al.  Activation of CLN1 and CLN2 G1 cyclin gene expression by BCK2 , 1995, Molecular and cellular biology.

[25]  F. Cross,et al.  Cla4p, a Saccharomyces cerevisiae Cdc42p-activated kinase involved in cytokinesis, is activated at mitosis , 1997, Molecular and cellular biology.

[26]  B. Futcher,et al.  Relationship between the function and the location of G1 cyclins in S. cerevisiae. , 2001, Journal of cell science.

[27]  B. Futcher,et al.  Isolation and characterization of WHI3, a size-control gene of Saccharomyces cerevisiae. , 2001, Genetics.

[28]  L. Breeden,et al.  The MSN1 and NHP6A genes suppress SWI6 defects in Saccharomyces cerevisiae. , 1999, Genetics.

[29]  M. Kirschner,et al.  Properties of Saccharomyces cerevisiae wee1 and its differential regulation of p34CDC28 in response to G1 and G2 cyclins. , 1993, The EMBO journal.

[30]  Kim Nasmyth,et al.  Positive feedback in the activation of Gl cyclins in yeast , 1991, Nature.

[31]  L. Breeden,et al.  Cell cycle-regulated phosphorylation of Swi6 controls its nuclear localization. , 1995, Molecular biology of the cell.

[32]  Frederick R. Cross,et al.  Distinct Subcellular Localization Patterns Contribute to Functional Specificity of the Cln2 and Cln3 Cyclins of Saccharomyces cerevisiae , 2000, Molecular and Cellular Biology.

[33]  S. Elledge,et al.  Human CPR (cell cycle progression restoration) genes impart a Far- phenotype on yeast cells. , 1997, Genetics.

[34]  R. W. Davis,et al.  High-frequency transformation of yeast: autonomous replication of hybrid DNA molecules. , 1979, Proceedings of the National Academy of Sciences of the United States of America.

[35]  R. D. Gietz,et al.  New yeast-Escherichia coli shuttle vectors constructed with in vitro mutagenized yeast genes lacking six-base pair restriction sites. , 1988, Gene.

[36]  Brenda J. Andrews,et al.  Transcriptional activation of CLN1, CLN2, and a putative new G1 cyclin (HCS26) by SWI4, a positive regulator of G1-specific transcription , 1991, Cell.

[37]  Mike Tyers,et al.  Cdc53 Targets Phosphorylated G1 Cyclins for Degradation by the Ubiquitin Proteolytic Pathway , 1996, Cell.

[38]  L. Dirick,et al.  Roles and regulation of Cln‐Cdc28 kinases at the start of the cell cycle of Saccharomyces cerevisiae. , 1995, The EMBO journal.

[39]  F. Cross,et al.  A potential positive feedback loop controlling CLN1 and CLN2 gene expression at the start of the yeast cell cycle , 1991, Cell.

[40]  K Nasmyth,et al.  growth and for cytokinesis in budding yeast. Ste20-like protein kinases are required for normal localization of cell , 2007 .

[41]  A. Sachs,et al.  The yeast poly(A)‐binding protein Pab1p stimulates in vitro poly(A)‐dependent and cap‐dependent translation by distinct mechanisms , 1999, The EMBO journal.

[42]  K. Nasmyth,et al.  Ordered Recruitment of Transcription and Chromatin Remodeling Factors to a Cell Cycle– and Developmentally Regulated Promoter , 2016, Cell.

[43]  Laura L. Newcomb,et al.  Glucose Regulation of Saccharomyces cerevisiae Cell Cycle Genes , 2003, Eukaryotic Cell.

[44]  Curt Wittenberg,et al.  An essential G1 function for cyclin-like proteins in yeast , 1989, Cell.

[45]  A. Sachs,et al.  Decapping of stabilized, polyadenylated mRNA in yeast pab1 mutants , 1999, Yeast.

[46]  M. Winey,et al.  Yeast Eap1p, an eIF4E-associated protein, has a separate function involving genetic stability , 2000, Current Biology.

[47]  A. Sachs,et al.  A common function for mRNA 5' and 3' ends in translation initiation in yeast. , 1995, Genes & development.

[48]  C. Wittenberg,et al.  Cell cycle-dependent transcription of CLN2 is conferred by multiple distinct cis-acting regulatory elements , 1994, Molecular and cellular biology.

[49]  R. Parker,et al.  A rapid method for localized mutagenesis of yeast genes , 1992, Yeast.

[50]  Ronald W. Davis,et al.  A genome-wide transcriptional analysis of the mitotic cell cycle. , 1998, Molecular cell.

[51]  D. Stillman,et al.  The Swi5 activator recruits the Mediator complex to the HO promoter without RNA polymerase II. , 2001, Genes & development.

[52]  M. Polymenis,et al.  Coupling of cell division to cell growth by translational control of the G1 cyclin CLN3 in yeast. , 1997, Genes & development.

[53]  K Nasmyth,et al.  Cdk1 triggers association of RNA polymerase to cell cycle promoters only after recruitment of the mediator by SBF. , 2001, Molecular cell.

[54]  L. Breeden,et al.  Start-specific transcription in yeast. , 1996, Current topics in microbiology and immunology.

[55]  L. Moore,et al.  Mutational analysis of a DNA sequence involved in linking gene expression to the cell cycle. , 1992, Biochemistry and cell biology = Biochimie et biologie cellulaire.

[56]  Michael Ruogu Zhang,et al.  Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. , 1998, Molecular biology of the cell.

[57]  B. Futcher,et al.  Comparison of the Saccharomyces cerevisiae G1 cyclins: Cln3 may be an upstream activator of Cln1, Cln2 and other cyclins. , 1993, The EMBO journal.

[58]  L. Breeden,et al.  Analysis of the SWI4/SWI6 protein complex, which directs G1/S-specific transcription in Saccharomyces cerevisiae , 1993, Molecular and cellular biology.

[59]  B. Futcher,et al.  Genetic analysis of the shared role of CLN3 and BCK2 at the G(1)-S transition in Saccharomyces cerevisiae. , 1999, Genetics.

[60]  M. Hentze,et al.  Starting at the Beginning, Middle, and End: Translation Initiation in Eukaryotes , 1997, Cell.

[61]  Bruce Futcher,et al.  The G1 Cyclin Cln3 Promotes Cell Cycle Entry via the Transcription Factor Swi6 , 2002, Molecular and Cellular Biology.

[62]  C. Wittenberg,et al.  CLN3, not positive feedback, determines the timing of CLN2 transcription in cycling cells. , 1995, Genes & development.

[63]  M. Longtine,et al.  Role of the Yeast Gin4p Protein Kinase in Septin Assembly and the Relationship between Septin Assembly and Septin Function , 1998, The Journal of cell biology.

[64]  Laura L. Newcomb,et al.  Regulation of Gene Expression by Glucose inSaccharomyces cerevisiae: a Role for ADA2and ADA3/NGG1 , 1999, Journal of bacteriology.

[65]  Curt Wittenberg,et al.  Cln3 Activates G1-Specific Transcription via Phosphorylation of the SBF Bound Repressor Whi5 , 2004, Cell.