Categorization of Phosphorylation Site Behavior during the Diauxic Shift in Saccharomyces cerevisiae

2021 ◽  
Author(s):  
Brandon M. Gassaway ◽  
Joao A. Paulo ◽  
Steven P. Gygi
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Phosphorylation Site ◽  
Diauxic Shift

scholarly journals Global mapping of protein–metabolite interactions in Saccharomyces cerevisiae reveals that Ser-Leu dipeptide regulates phosphoglycerate kinase activity

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Marcin Luzarowski ◽  
Rubén Vicente ◽  
Andrei Kiselev ◽  
Mateusz Wagner ◽  
Dennis Schlossarek ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Small Molecules ◽  
Phosphoglycerate Kinase ◽  
Glycolytic Enzyme ◽  
Diauxic Shift ◽  
Cellular Processes ◽  
Targeted Analysis ◽  
Global Mapping ◽  
Biochemical Approach ◽  
User Friendly

AbstractProtein–metabolite interactions are of crucial importance for all cellular processes but remain understudied. Here, we applied a biochemical approach named PROMIS, to address the complexity of the protein–small molecule interactome in the model yeast Saccharomyces cerevisiae. By doing so, we provide a unique dataset, which can be queried for interactions between 74 small molecules and 3982 proteins using a user-friendly interface available at https://promis.mpimp-golm.mpg.de/yeastpmi/. By interpolating PROMIS with the list of predicted protein–metabolite interactions, we provided experimental validation for 225 binding events. Remarkably, of the 74 small molecules co-eluting with proteins, 36 were proteogenic dipeptides. Targeted analysis of a representative dipeptide, Ser-Leu, revealed numerous protein interactors comprising chaperones, proteasomal subunits, and metabolic enzymes. We could further demonstrate that Ser-Leu binding increases activity of a glycolytic enzyme phosphoglycerate kinase (Pgk1). Consistent with the binding analysis, Ser-Leu supplementation leads to the acute metabolic changes and delays timing of a diauxic shift. Supported by the dipeptide accumulation analysis our work attests to the role of Ser-Leu as a metabolic regulator at the interface of protein degradation and central metabolism.

scholarly journals High cAMP Levels Antagonize the Reprogramming of Gene Expression that Occurs at the Diauxic Shift in Saccharomyces Cerevisiae

Microbiology ◽  
1996 ◽  
Vol 142 (3) ◽  
pp. 459-467 ◽  
Author(s):  
E. Boy-Marcotte ◽  
D. Tadi ◽  
M. Perrot ◽  
H. Boucherie ◽  
M. Jacquet
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Diauxic Shift ◽  
Camp Levels

scholarly journals Multiple phosphorylated forms of the Saccharomyces cerevisiae Mcm1 protein include an isoform induced in response to high salt concentrations.

1997 ◽  
Vol 17 (2) ◽  
pp. 819-832 ◽  
Author(s):  
M H Kuo ◽  
E T Nadeau ◽  
E J Grayhack
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Signal Transduction ◽  
Osmotic Stress ◽  
Target Genes ◽  
Serum Response Factor ◽  
Phosphorylation Site ◽  
High Salt ◽  
Salt Medium ◽  
Membrane Function

The Saccharomyces cerevisiae Mcm1 protein is an essential multifunctional transcription factor which is highly homologous to human serum response factor. Mcm1 protein acts on a large number of distinctly regulated genes: haploid cell-type-specific genes, G2-cell-cycle-regulated genes, pheromone-induced genes, arginine metabolic genes, and genes important for cell wall and cell membrane function. We show here that Mcm1 protein is phosphorylated in vivo. Several (more than eight) isoforms of Mcm1 protein, resolved by isoelectric focusing, are present in vivo; two major phosphorylation sites lie in the N-terminal 17 amino acids immediately adjacent to the conserved MADS box DNA-binding domain. The implications of multiple species of Mcm1, particularly the notion that a unique Mcm1 isoform could be required for regulation of a specific set of Mcm1's target genes, are discussed. We also show here that Mcm1 plays an important role in the response to stress caused by NaCl. G. Yu, R. J. Deschenes, and J. S. Fassler (J. Biol. Chem. 270:8739-8743, 1995) showed that Mcm1 function is affected by mutations in the SLN1 gene, a signal transduction component implicated in the response to osmotic stress. We find that mcm1 mutations can confer either reduced or enhanced survival on high-salt medium; deletion of the N terminus or mutation in the primary phosphorylation site results in impaired growth on high-salt medium. Furthermore, Mcm1 protein is a target of a signal transduction system responsive to osmotic stress: a new isoform of Mcm1 is induced by NaCl or KCl; this result establishes that Mcm1 itself is regulated.

scholarly journals Changes in gene expression in the Ras/adenylate cyclase system of Saccharomyces cerevisiae: correlation with cAMP levels and growth arrest.

1993 ◽  
Vol 4 (7) ◽  
pp. 757-765 ◽  
Author(s):  
M Russell ◽  
J Bradshaw-Rouse ◽  
D Markwardt ◽  
W Heideman
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Adenylate Cyclase ◽  
Oxidative Metabolism ◽  
Growth Arrest ◽  
Intracellular Camp ◽  
Adenylate Cyclase System ◽  
Diauxic Shift ◽  
Yeast Saccharomyces Cerevisiae ◽  
Camp Levels

Levels of cyclic 3',5'-cyclic monophosphate (cAMP) play an important role in the decision to enter the mitotic cycle in the yeast, Saccharomyces cerevisiae. In addition to growth arrest at stationary phase, S. cerevisiae transiently arrest growth as they shift from fermentative to oxidative metabolism (the diauxic shift). Experiments examining the role of cAMP in growth arrest at the diauxic shift show the following: 1) yeast lower cAMP levels as they exhaust their glucose supply and shift to oxidative metabolism of ethanol, 2) a reduction in cAMP is essential for traversing the diauxic shift, 3) the decrease in adenylate cyclase activity is associated with a decrease in the expression of CYR1 and CDC25, two positive regulators of cAMP levels and an increase in the expression of IRA1 and IRA2, two negative regulators of intracellular cAMP, 4) mutants carrying disruptions in IRA1 and IRA2 were unable to arrest cell division at the diauxic shift and were unable to progress into the oxidative phase of growth. These results indicate that changes cAMP levels are important in regulation of growth arrest at the diauxic shift and that changes in gene expression plays a role in the regulation of the Ras/adenylate cyclase system.

scholarly journals A Protein Interaction Map of the Mitotic Spindle

2007 ◽  
Vol 18 (10) ◽  
pp. 3800-3809 ◽  
Author(s):  
Jonathan Wong ◽  
Yuko Nakajima ◽  
Stefan Westermann ◽  
Ching Shang ◽  
Jung-seog Kang ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Protein Interactions ◽  
Mitotic Spindle ◽  
Phosphorylation Site ◽  
Protein Functions ◽  
Regulation Mechanisms ◽  
Novel Interactions ◽  
Interaction Map ◽  
Spindle Function ◽  
Two Hybrid

The mitotic spindle consists of a complex network of proteins that segregates chromosomes in eukaryotes. To strengthen our understanding of the molecular composition, organization, and regulation of the mitotic spindle, we performed a system-wide two-hybrid screen on 94 proteins implicated in spindle function in Saccharomyces cerevisiae. We report 604 predominantly novel interactions that were detected in multiple screens, involving 303 distinct prey proteins. We uncovered a pattern of extensive interactions between spindle proteins reflecting the intricate organization of the spindle. Furthermore, we observed novel connections between kinetochore complexes and chromatin-modifying proteins and used phosphorylation site mutants of NDC80/TID3 to gain insights into possible phospho-regulation mechanisms. We also present analyses of She1p, a novel spindle protein that interacts with the Dam1 kinetochore/spindle complex. The wealth of protein interactions presented here highlights the extent to which mitotic spindle protein functions and regulation are integrated with each other and with other cellular activities.

Dominant mutations in a gene encoding a putative protein kinase (BCK1) bypass the requirement for a Saccharomyces cerevisiae protein kinase C homolog

1992 ◽  
Vol 12 (1) ◽  
pp. 172-182
Author(s):  
K S Lee ◽  
D E Levin
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Protein Kinase C ◽  
Protein Kinase ◽  
Catalytic Domain ◽  
Phosphorylation Site ◽  
Cell Lysis ◽  
Amino Acid Identity ◽  
Temperature Sensitive ◽  
Stabilizing Agents ◽  
Kinase C

The PKC1 gene of Saccharomyces cerevisiae encodes a homolog of mammalian protein kinase C that is required for yeast cell growth and division. To identify additional components of the pathway in which PKC1 functions, we isolated extragenic suppressors of a pkc1 deletion mutant. All of the suppressor mutations were dominant for suppressor function and defined a single locus, which was designated BCK1 (for bypass of C kinase). A molecular clone of one suppressor allele, BCK1-20, was isolated on a centromere-containing plasmid through its ability to rescue a conditional pkc1 mutant. The BCK1 gene possesses a 4.4-kb uninterrupted open reading frame predicted to encode a 163-kDa protein kinase. The BCK1 gene product is not closely related to any known protein kinase, sharing only 45% amino acid identity with its closest known relative (the STE11-encoded protein kinase) through a region restricted to its putative C-terminal catalytic domain. Deletion of BCK1 resulted in a temperature-sensitive cell lysis defect, which was suppressed by osmotic stabilizing agents. Because pkc1 mutants also display a cell lysis defect, we suggest that PKC1 and BCK1 may normally function within the same pathway. Suppressor alleles of BCK1 differed from the wild-type gene in a region surrounding a potential PKC phosphorylation site immediately upstream of the predicted catalytic domain. This region may serve as a hinge between domains whose interaction is regulated by PKC1.

scholarly journals A Role for Checkpoint Kinase-Dependent Rad26 Phosphorylation in Transcription-Coupled DNA Repair in Saccharomyces cerevisiae

2009 ◽  
Vol 30 (2) ◽  
pp. 436-446 ◽  
Author(s):  
Michael Taschner ◽  
Michelle Harreman ◽  
Yumin Teng ◽  
Hefin Gill ◽  
Roy Anindya ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Dna Damage ◽  
Protein Synthesis ◽  
Excision Repair ◽  
Phosphorylation Site ◽  
Coupling Factor ◽  
Direct Role ◽  
Checkpoint Kinases ◽  
Nucleotide Excision ◽  
New Protein

ABSTRACT Upon DNA damage, eukaryotic cells activate a conserved signal transduction cascade known as the DNA damage checkpoint (DDC). We investigated the influence of DDC kinases on nucleotide excision repair (NER) in Saccharomyces cerevisiae and found that repair of both strands of an active gene is affected by Mec1 but not by the downstream checkpoint kinases, Rad53 and Chk1. Repair of the nontranscribed strand (by global genome repair) requires new protein synthesis, possibly reflecting the involvement of Mec1 in the activation of repair genes. In contrast, repair of the transcribed strand by transcription-coupled NER (TC-NER) occurs in the absence of new protein synthesis, and DNA damage results in Mec1-dependent but Rad53-, Chk1-, Tel1-, and Dun1-independent phosphorylation of the TC-NER factor Rad26, a member of the Swi/Snf group of ATP-dependent translocases and yeast homologue of Cockayne syndrome B. Mutation of the Rad26 phosphorylation site results in a decrease in the rate of TC-NER, pointing to direct activation of Rad26 by Mec1 kinase. These findings establish a direct role for Mec1 kinase in transcription-coupled repair, at least partly via phosphorylation of Rad26, the main transcription-repair coupling factor.

scholarly journals Translational Accuracy during Exponential, Postdiauxic, and Stationary Growth Phases in Saccharomyces cerevisiae

2004 ◽  
Vol 3 (2) ◽  
pp. 331-338 ◽  
Author(s):  
Guillaume Stahl ◽  
Samia N. Ben Salem ◽  
Lifeng Chen ◽  
Bing Zhao ◽  
Philip J. Farabaugh
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Slow Growth ◽  
Genetic Data ◽  
Diauxic Shift ◽  
Growth Phases ◽  
Stationary Growth ◽  
Strong Reduction ◽  
Translation Elongation ◽  
Translational Machinery ◽  
Translational Accuracy

ABSTRACT When the yeast Saccharomyces cerevisiae shifts from rapid growth on glucose to slow growth on ethanol, it undergoes profound changes in cellular metabolism, including the destruction of most of the translational machinery. We have examined the effect of this metabolic change, termed the diauxic shift, on the frequency of translational errors. Recoding sites are mRNA sequences that increase the frequency of translational errors, providing a convenient reporter of translational accuracy. We found that the diauxic shift causes no overall change in translational accuracy but does cause a strong reduction in the frequency of one type of programmed error: Ty +1 frameshifting. Genetic data suggest that this effect may be due to changes in the relative amounts of tRNA participating in translation elongation. We discuss possible implications for expression strategies that use recoding.

scholarly journals Rad53 Checkpoint Kinase Phosphorylation Site Preference Identified in the Swi6 Protein of Saccharomyces cerevisiae

2003 ◽  
Vol 23 (10) ◽  
pp. 3405-3416 ◽  
Author(s):  
Julia M. Sidorova ◽  
Linda L. Breeden
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Dna Damage ◽  
Phosphorylation Site ◽  
Site Preference ◽  
Phosphorylation Sites ◽  
Checkpoint Kinase ◽  
Checkpoint Signaling ◽  
And Function

ABSTRACT Rad53 of Saccharomyces cerevisiae is a checkpoint kinase whose structure and function are conserved among eukaryotes. When a cell detects damaged DNA, Rad53 activity is dramatically increased, which ultimately leads to changes in DNA replication, repair, and cell division. Despite its central role in checkpoint signaling, little is known about Rad53 substrates or substrate specificity. A number of proteins are implicated as Rad53 substrates; however, the evidence remains indirect. Previously, we have provided evidence that Swi6, a subunit of the Swi4/Swi6 late-G1-specific transcriptional activator, is a substrate of Rad53 in the G1/S DNA damage checkpoint. In the present study we identify Rad53 phosphorylation sites in Swi6 in vitro and demonstrate that at least one of them is targeted by Rad53 in vivo. Mutations in these phosphorylation sites in Swi6 shorten but do not eliminate the Rad53-dependent delay of the G1-to-S transition after DNA damage. We derive a consensus for Rad53 site preference at positions −2 and +2 (−2/+2) and identify its potential substrates in the yeast proteome. Finally, we present evidence that one of these candidates, the cohesin complex subunit Scc1 undergoes DNA damage-dependent phosphorylation, which is in part dependent on Rad53.

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