Combinatorial control by the protein kinases PKA, PHO85 and SNF1 of transcriptional induction of the Saccharomyces cerevisiae GSY2 gene at the diauxic shift

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.

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

Microbiology ◽

10.1099/13500872-142-3-459 ◽

1996 ◽

Vol 142 (3) ◽

pp. 459-467 ◽

Cited By ~ 51

Author(s):

E. Boy-Marcotte ◽

D. Tadi ◽

M. Perrot ◽

H. Boucherie ◽

M. Jacquet

Keyword(s):

Gene Expression ◽

Saccharomyces Cerevisiae ◽

Diauxic Shift ◽

Camp Levels

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Expressed in the Yeast Saccharomyces cerevisiae, Human ERK5 Is a Client of the Hsp90 Chaperone That Complements Loss of the Slt2p (Mpk1p) Cell Integrity Stress-Activated Protein Kinase

Eukaryotic Cell ◽

10.1128/ec.00263-06 ◽

2006 ◽

Vol 5 (11) ◽

pp. 1914-1924 ◽

Cited By ~ 44

Author(s):

Andrew W. Truman ◽

Stefan H. Millson ◽

James M. Nuttall ◽

Victoria King ◽

Mehdi Mollapour ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Map Kinase ◽

Protein Kinases ◽

Strong Association ◽

Active Form ◽

Cell Integrity ◽

Binding Studies ◽

Hsp90 Inhibition ◽

Binding Surface ◽

Hsp90 Chaperone

ABSTRACT ERK5 is a mitogen-activated protein (MAP) kinase regulated in human cells by diverse mitogens and stresses but also suspected of mediating the effects of a number of oncogenes. Its expression in the slt2Δ Saccharomyces cerevisiae mutant rescued several of the phenotypes caused by the lack of Slt2p (Mpk1p) cell integrity MAP kinase. ERK5 is able to provide this cell integrity MAP kinase function in yeast, as it is activated by the cell integrity signaling cascade that normally activates Slt2p and, in its active form, able to stimulate at least one key Slt2p target (Rlm1p, the major transcriptional regulator of cell wall genes). In vitro ERK5 kinase activity was abolished by Hsp90 inhibition. ERK5 activity in vivo was also lost in a strain that expresses a mutant Hsp90 chaperone. Therefore, human ERK5 expressed in yeast is an Hsp90 client, despite the widely held belief that the protein kinases of the MAP kinase class are non-Hsp90-dependent activities. Two-hybrid and protein binding studies revealed that strong association of Hsp90 with ERK5 requires the dual phosphorylation of the TEY motif in the MAP kinase activation loop. These phosphorylations, at positions adjacent to the Hsp90-binding surface recently identified for a number of protein kinases, may cause a localized rearrangement of this MAP kinase region that leads to creation of the Hsp90-binding surface. Complementation of the slt2Δ yeast defect by ERK5 expression establishes a new tool with which to screen for novel agonists and antagonists of ERK5 signaling as well as for isolating mutant forms of ERK5.

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MKK1 and MKK2, which encode Saccharomyces cerevisiae mitogen-activated protein kinase-kinase homologs, function in the pathway mediated by protein kinase C

Molecular and Cellular Biology ◽

10.1128/mcb.13.5.3076-3083.1993 ◽

1993 ◽

Vol 13 (5) ◽

pp. 3076-3083

Author(s):

K Irie ◽

M Takase ◽

K S Lee ◽

D E Levin ◽

H Araki ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Protein Kinase C ◽

Protein Kinase ◽

Map Kinase ◽

Protein Kinases ◽

Cell Lysis ◽

Yeast Cells ◽

Temperature Sensitive ◽

Kinase C ◽

Mitogen Activated Protein

The PKC1 gene of Saccharomyces cerevisiae encodes a homolog of mammalian protein kinase C that is required for normal growth and division of yeast cells. We report here the isolation of the yeast MKK1 and MKK2 (for mitogen-activated protein [MAP] kinase-kinase) genes which, when overexpressed, suppress the cell lysis defect of a temperature-sensitive pkc1 mutant. The MKK genes encode protein kinases most similar to the STE7 product of S. cerevisiae, the byr1 product of Schizosaccharomyces pombe, and vertebrate MAP kinase-kinases. Deletion of either MKK gene alone did not cause any apparent phenotypic defects, but deletion of both MKK1 and MKK2 resulted in a temperature-sensitive cell lysis defect that was suppressed by osmotic stabilizers. This phenotypic defect is similar to that associated with deletion of the BCK1 gene, which is thought to function in the pathway mediated by PCK1. The BCK1 gene also encodes a predicted protein kinase. Overexpression of MKK1 suppressed the growth defect caused by deletion of BCK1, whereas an activated allele of BCK1 (BCK1-20) did not suppress the defect of the mkk1 mkk2 double disruption. Furthermore, overexpression of MPK1, which encodes a protein kinase closely related to vertebrate MAP kinases, suppressed the defect of the mkk1 mkk2 double mutant. These results suggest that MKK1 and MKK2 function in a signal transduction pathway involving the protein kinases encoded by PKC1, BCK1, and MPK1. Genetic epistasis experiments indicated that the site of action for MKK1 and MKK2 is between BCK1 and MPK1.

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Shk1, a homolog of the Saccharomyces cerevisiae Ste20 and mammalian p65PAK protein kinases, is a component of a Ras/Cdc42 signaling module in the fission yeast Schizosaccharomyces pombe.

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.92.13.6180 ◽

1995 ◽

Vol 92 (13) ◽

pp. 6180-6184 ◽

Cited By ~ 109

Author(s):

S. Marcus ◽

A. Polverino ◽

E. Chang ◽

D. Robbins ◽

M. H. Cobb ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Schizosaccharomyces Pombe ◽

Fission Yeast ◽

Protein Kinases

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Transcriptional activation upon pheromone stimulation mediated by a small domain of Saccharomyces cerevisiae Ste12p.

Molecular and Cellular Biology ◽

10.1128/mcb.17.11.6410 ◽

1997 ◽

Vol 17 (11) ◽

pp. 6410-6418 ◽

Cited By ~ 44

Author(s):

H Pi ◽

C T Chien ◽

S Fields

Keyword(s):

Saccharomyces Cerevisiae ◽

Map Kinase ◽

Transcriptional Activation ◽

Transcriptional Activity ◽

Activation Domain ◽

Yeast Saccharomyces Cerevisiae ◽

Activation Domains ◽

Hybrid Proteins ◽

High Level ◽

Transcriptional Induction

In the yeast Saccharomyces cerevisiae, Ste12p induces transcription of pheromone-responsive genes by binding to a DNA sequence designated the pheromone response element. We generated a series of hybrid proteins of Ste12p with the DNA-binding and activation domains of the transcriptional activator Gal4p to define a pheromone induction domain of Ste12p sufficient to mediate pheromone-induced transcription by these hybrid proteins. A minimal pheromone induction domain, delineated as residues 301 to 335 of Ste12p, is dependent on the pheromone mitogen-activated protein (MAP) kinase pathway for induction activity. Mutation of the three serine and threonine residues within the minimal pheromone induction domain did not affect transcriptional induction, indicating that the activity of this domain is not directly regulated by MAP kinase phosphorylation. By contrast, mutation of the two tyrosines or their preceding acidic residues led to a high level of transcriptional activity in the absence of pheromone and consequently to the loss of pheromone induction. This constitutively high activity was not affected by mutations in the MAP kinase cascade, suggesting that the function of the pheromone induction domain is normally repressed in the absence of pheromone. By two-hybrid analysis, this minimal domain interacts with two negative regulators, Dig1p and Dig2p (also designated Rst1p and Rst2p), and the interaction is abolished by mutation of the tyrosines. The pheromone induction domain itself has weak and inducible transcriptional activity, and its ability to potentiate transcription depends on the activity of an adjacent activation domain. These results suggest that the pheromone induction domain of Ste12p mediates transcriptional induction via a two-step process: the relief of repression and synergistic transcriptional activation with another activation domain.

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Adaptive Evolution of a Lactose-Consuming Saccharomyces cerevisiae Recombinant

Applied and Environmental Microbiology ◽

10.1128/aem.00186-08 ◽

2008 ◽

Vol 74 (6) ◽

pp. 1748-1756 ◽

Cited By ~ 59

Author(s):

Pedro M. R. Guimarães ◽

Jean François ◽

Jean Luc Parrou ◽

José A. Teixeira ◽

Lucília Domingues

Keyword(s):

Saccharomyces Cerevisiae ◽

Copy Number ◽

Cheese Whey ◽

Kluyveromyces Lactis ◽

Strain Improvement ◽

Attractive Alternative ◽

Evolutionary Engineering ◽

Serial Transfer ◽

Lactose Fermentation ◽

Transcriptional Induction

ABSTRACT The construction of Saccharomyces cerevisiae strains that ferment lactose has biotechnological interest, particularly for cheese whey fermentation. A flocculent lactose-consuming S. cerevisiae recombinant expressing the LAC12 (lactose permease) and LAC4 (β-galactosidase) genes of Kluyveromyces lactis was constructed previously but showed poor efficiency in lactose fermentation. This strain was therefore subjected to an evolutionary engineering process (serial transfer and dilution in lactose medium), which yielded an evolved recombinant strain that consumed lactose twofold faster, producing 30% more ethanol than the original recombinant. We identified two molecular events that targeted the LAC construct in the evolved strain: a 1,593-bp deletion in the intergenic region (promoter) between LAC4 and LAC12 and a decrease of the plasmid copy number by about 10-fold compared to that in the original recombinant. The results suggest that the intact promoter was unable to mediate the induction of the transcription of LAC4 and LAC12 by lactose in the original recombinant and that the deletion established the transcriptional induction of both genes in the evolved strain. We propose that the tuning of the expression of the heterologous LAC genes in the evolved recombinant was accomplished by the interplay between the decreased copy number of both genes and the different levels of transcriptional induction for LAC4 and LAC12 resulting from the changed promoter structure. Nevertheless, our results do not exclude other possible mutations that may have contributed to the improved lactose fermentation phenotype. This study illustrates the usefulness of simple evolutionary engineering approaches in strain improvement. The evolved strain efficiently fermented threefold-concentrated cheese whey, providing an attractive alternative for the fermentation of lactose-based media.

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Septin-Associated Protein Kinases in the Yeast Saccharomyces cerevisiae

Frontiers in Cell and Developmental Biology ◽

10.3389/fcell.2016.00119 ◽

2016 ◽

Vol 4 ◽

Cited By ~ 6

Author(s):

Adam M. Perez ◽

Gregory C. Finnigan ◽

Françoise M. Roelants ◽

Jeremy Thorner

Keyword(s):

Saccharomyces Cerevisiae ◽

Protein Kinases ◽

Yeast Saccharomyces Cerevisiae

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Amino acid changes in Xrs2p, Dun1p, and Rfa2p that remove the preferred targets of the ATM family of protein kinases do not affect DNA repair or telomere length in Saccharomyces cerevisiae

DNA Repair ◽

10.1016/s1568-7864(03)00115-0 ◽

2003 ◽

Vol 2 (9) ◽

pp. 1041-1064 ◽

Cited By ~ 38

Author(s):

Julia C. Mallory ◽

Vladimir I. Bashkirov ◽

Kelly M. Trujillo ◽

Jachen A. Solinger ◽

Margaret Dominska ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Dna Repair ◽

Amino Acid ◽

Telomere Length ◽

Protein Kinases

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Alteration of the Protein Kinase Binding Domain Enhances Function of the Saccharomyces cerevisiae Molecular Chaperone Cdc37

Eukaryotic Cell ◽

10.1128/ec.00165-07 ◽

2007 ◽

Vol 6 (8) ◽

pp. 1363-1372 ◽

Cited By ~ 5

Author(s):

Min Ren ◽

Arti Santhanam ◽

Paul Lee ◽

Avrom Caplan ◽

Stephen Garrett

Keyword(s):

Saccharomyces Cerevisiae ◽

Protein Kinase ◽

Protein Kinases ◽

Molecular Chaperone ◽

Binding Domain ◽

Growth Defect ◽

Temperature Sensitive ◽

Physical Interaction ◽

General Function ◽

Amino Terminal

ABSTRACT Cdc37 is a molecular chaperone that has a general function in the biogenesis of protein kinases. We identified mutations within the putative “protein kinase binding domain” of Cdc37 that alleviate the conditional growth defect of a strain containing a temperature-sensitive allele, tpk2(Ts), of the cyclic AMP-dependent protein kinase (PKA). These dominant mutations alleviate the temperature-sensitive growth defect by elevating PKA activity, as judged by their effects on PKA-regulated processes, localization and phosphorylation of the PKA effector Msn2, as well as in vitro PKA activity. Although the tpk2(Ts) growth defect is also alleviated by Cdc37 overproduction, the CDC37 dominant mutants contain wild-type Cdc37 protein levels. In addition, Saccharomyces cerevisiae Ste11 protein kinase has an elevated physical interaction with the altered Cdc37 protein. These results implicate specific amino-terminal residues in the interaction between Cdc37 and client protein kinases and provide further genetic and biochemical support for a model in which Cdc37 functions as a molecular chaperone for protein kinases.

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