Transcriptional repression by Tup1–Ssn6This paper is one of a selection of papers published in this Special Issue, entitled 27th International West Coast Chromatin and Chromosome Conference, and has undergone the Journal's usual peer review process.

Malavé, Tania M.; Dent, Sharon Y.R.

doi:10.1139/o06-073

Cited by 107 publications

(78 citation statements)

References 63 publications

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“…In S. cerevisiae, the homolog of RCO-1, Tup1, forms a complex with Ssn6 to repress gene expression (30,31). To examine whether the Neurospora Ssn6 homolog RCM-1 (NCU06842) has a similar role, we generated a RCM-1 antibody and used it to purify RCM-1 from Neurospora by immunoprecipitation.…”

Section: Resultsmentioning

confidence: 99%

“…Thus, RCM-1 may recruit RCO-1 to the chromatin, which may explain the lack of detectable RCO-1/chromatin association by ChIP assays at the frq locus. However, neither RCO-1/Tup1 nor RCM-1/Ssn6 has a known DNA binding domain, and thus they may interact with DNA through another partner capable of binding to specific DNA sequences (30,31). The identity of such a factor (indicated as TF in Fig.…”

Section: Discussionmentioning

confidence: 99%

“…However, we recently discovered that frq transcription can occur in a WC-independent manner, and the suppression of the WC-independent frq transcription by RCO-1 is essential for circadian clock function (29). The homolog of RCO-1 in Saccharomyces cerevisiae is Tup1, a component of the Tup1-Ssn6 complex that represses gene expression (30,31). Even though our previous results suggest that RCO-1 regulates the chromatin status at the frq locus, RCO-1 does not appear to be associated with the frq locus.…”

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confidence: 99%

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Role for Protein Kinase A in the Neurospora Circadian Clock by Regulating White Collar-Independent frequency Transcription through Phosphorylation of RCM-1

Liu

et al. 2015

Molecular and Cellular Biology

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Rhythmic activation and repression of clock gene expression is essential for the eukaryotic circadian clock functions. In the Neurospora circadian oscillator, the transcription of the frequency (frq) gene is periodically activated by the White Collar (WC) complex and suppressed by the FRQ-FRH complex. We previously showed that there is WC-independent frq transcription and its repression is required for circadian gene expression. How WC-independent frq transcription is regulated is not known. We show here that elevated protein kinase A (PKA) activity results in WC-independent frq transcription and the loss of clock function. We identified RCM-1 as the protein partner of RCO-1 and an essential component of the clock through its role in suppressing WCindependent frq transcription. RCM-1 is a phosphoprotein and is a substrate of PKA in vivo and in vitro. Mutation of the PKAdependent phosphorylation sites on RCM-1 results in WC-independent transcription of frq and impaired clock function. Furthermore, we showed that RCM-1 is associated with the chromatin at the frq locus, a process that is inhibited by PKA. Together, our results demonstrate that PKA regulates frq transcription by inhibiting RCM-1 activity through RCM-1 phosphorylation. Circadian clocks allow prokaryotic and eukaryotic organisms to regulate their daily molecular, cellular, behavioral, and physiological activities. The eukaryotic circadian clocks are composed of autoregulatory negative-feedback loops, including positive and negative elements that form the core circadian oscillators (1-6). Rhythmic transcriptional activation of the negative elements by the positive elements and rhythmic repression of positive elements by the negative elements are thought to be the main molecular basis for the generation of endogenous rhythmicity in eukaryotic clock systems. In addition to regulation at the transcriptional level, posttranslational modification of clock proteins by phosphorylation plays essential roles in clock functions (7-10).In the filamentous fungus Neurospora crassa, the core circadian negative feedback loop is composed of the positive elements, White Collar 1 (WC-1) and White Collar 2 (WC-2), and the negative elements, FREQUENCY (FRQ) and its partner FRQ-interacting RNA helicase (FRH) (2,3,11,12). WC-1 and WC-2, two Per-Arnt-Sim (PAS) domain-containing transcription factors, form the WC heterodimeric complex that binds to the Clock (C)-box of frq promoter to activate frq transcription (13-18). On the other hand, FRQ and FRH form the FFC complex to inhibit frq transcription by suppressing the activity of the WC complex by promoting WC phosphorylation (19)(20)(21)(22)(23)(24). FRQ is progressively phosphorylated over time before its degradation through the ubiquitin-proteasome pathway mediated by FWD-1 (21, 25-28). Genetic analyses show that the FRQ-dependent phosphorylation of WC-1 and WC-2 that suppresses White Collar complex (WCC) activity is mostly mediated by CKI and CKII (21).WC complex was long thought to be the only transcriptional activator o...

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

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Role for Protein Kinase A in the Neurospora Circadian Clock by Regulating White Collar-Independent frequency Transcription through Phosphorylation of RCM-1

Liu

et al. 2015

Molecular and Cellular Biology

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“…The complex is composed of four molecules of Tup1 and one molecule of Cyc8 (17). Tup1-Cyc8 is implicated in the repression of over 300 genes, including genes that are cell type-specific, glucose repressible, DNA damage inducible, or involved in flocculation or the hypoxic response (18,19). Our results strongly suggest that the inability of wild-type S. cerevisiae to assimilate mannitol can be attributed to the repressive functions of the Tup1-Cyc8 corepressor.…”

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confidence: 76%

Acquisition of the Ability To Assimilate Mannitol by Saccharomyces cerevisiae through Dysfunction of the General Corepressor Tup1-Cyc8

Chujo

Yoshida

Ota

et al. 2015

Appl Environ Microbiol

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Saccharomyces cerevisiae normally cannot assimilate mannitol, a promising brown macroalgal carbon source for bioethanol production. The molecular basis of this inability remains unknown. We found that cells capable of assimilating mannitol arose spontaneously from wild-type S. cerevisiae during prolonged culture in mannitol-containing medium. Based on microarray data, complementation analysis, and cell growth data, we demonstrated that acquisition of mannitol-assimilating ability was due to spontaneous mutations in the genes encoding Tup1 or Cyc8, which constitute a general corepressor complex that regulates many kinds of genes. We also showed that an S. cerevisiae strain carrying a mutant allele of CYC8 exhibited superior salt tolerance relative to other ethanologenic microorganisms; this characteristic would be highly beneficial for the production of bioethanol from marine biomass. Thus, we succeeded in conferring the ability to assimilate mannitol on S. cerevisiae through dysfunction of Tup1-Cyc8, facilitating production of ethanol from mannitol. Macroalgae, consisting of green, red, and brown algae, are promising sources of biofuels for several reasons: (i) macroalgae are more productive than land crops; (ii) arable land is not required for algal cultivation, obviating the necessity for irrigation, fertilizer, etc.; and (iii) macroalgae contain no lignin (1-4). Both red and brown algae contain high levels of carbohydrates, and a method for producing biofuel from these carbohydrates would be of tremendous economic and environmental benefit.Brown macroalgae contain up to 33% (wt/wt [dry weight]) mannitol, which is the sugar alcohol corresponding to mannose and a promising carbon source for bioethanol production (1, 5, 6). Although some bacteria, such as Escherichia coli and Zymobacter palmae, can assimilate mannitol, i.e., utilize mannitol and produce ethanol (6, 7), bacteria are generally sensitive to ethanol, as well as, several other growth-inhibitory compounds. Z. palmae and E. coli KO11 can produce ca. 1.3% (wt/vol) and 2.6% (wt/vol) ethanol from 3.8% (wt/vol) and 9.0% (wt/vol) mannitol, respectively; however, both strains are sensitive to 5% (wt/vol) ethanol (8,9). Yeast is currently considered to have several advantages over ethanologenic bacteria, including high tolerance to ethanol and inhibitory compounds (10). Several yeast strains, such as Pichia angophorae and Saccharomyces paradoxus NBRC0259-3, can produce ethanol from mannitol (8, 11). However, compared to the well-characterized model organism Saccharomyces cerevisiae, the host-vector systems of these yeasts are not well equipped, and their genetics and physiologies are poorly defined.Mannitol dehydrogenase is the key enzyme that catalyzes the pyridine nucleotide-dependent oxidation of D-mannitol to Dfructose (12). Despite the existence of genes encoding putative homologs of mannitol dehydrogenase (YEL070W and YNR073C), S. cerevisiae strains, including the S288C reference strain, are unable to assimilate mannitol for growth; a few exceptions exi...

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“…Transcriptional activators and repressors bind to cis-acting elements to activate and repress transcription, respectively, by affecting the chromatin structure and regulating RNA polymerase II accumulation in the promoter region (5-7). These transcriptional regulators also interact with coactivators and corepressors to regulate gene expression (8,9). The Tup family transcriptional corepressors are conserved between yeast and humans and regulate gene expression during the stress response and cellular differentiation (10,11).…”

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confidence: 99%

Antagonistic Controls of Chromatin and mRNA Start Site Selection by Tup Family Corepressors and the CCAAT-Binding Factor

Asada

Takemata

Hoffman

et al. 2015

Molecular and Cellular Biology

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The Tup family corepressors contribute to critical cellular responses, such as the stress response and differentiation, presumably by inducing repressive chromatin, though the precise repression mechanism remains to be elucidated. E ukaryotic chromosomal DNA is packaged in a highly organized and condensed chromatin structure. Many DNA-associated reactions, including DNA damage repair, replication, recombination, and transcription, are regulated by the chromatin structure (1, 2). The chromatin structure is modulated by two distinct classes of regulators, histone modification enzymes and ATP-dependent chromatin remodeling factors (3, 4). Such regulatory components are recruited by two types of cis-acting regulatory factors, transcriptional activators and repressors. Transcriptional activators and repressors bind to cis-acting elements to activate and repress transcription, respectively, by affecting the chromatin structure and regulating RNA polymerase II accumulation in the promoter region (5-7). These transcriptional regulators also interact with coactivators and corepressors to regulate gene expression (8, 9). The Tup family transcriptional corepressors are conserved between yeast and humans and regulate gene expression during the stress response and cellular differentiation (10, 11). Saccharomyces cerevisiae Tup1 represses some genes regulated by cell type, glucose, oxidative stress, DNA damage, and other cellular stress responses (12, 13). Tup1 represses the expression of genes via distinct mechanisms: by establishing a repressive chromatin structure around the target gene promoter, by recruiting histone deacetylases, and by directly interfering with the general transcription machinery (14-18). Two Tup1 orthologs in Schizosaccharomyces pombe, Tup11 and Tup12 (Tup11/12), regulate multiple stress-responsive genes, including the fbp1 ϩ and cta3 ϩ genes, to provide stress specificity (19,20). However, the precise molecular mechanisms of Tup1 family proteins in gene repression have not been fully uncovered.The fbp1 ϩ gene encodes fructose-1,6-bisphosphatase and is robustly induced upon glucose starvation (21,22). fbp1 ϩ expression is strictly repressed by Tup11/12 and activated by the transcriptional activators Atf1, Rst2, and Php5 (23-26). Atf1, a bZIP protein, is regulated through phosphorylation by the mitogen-activated protein kinase pathway (27-29), while Rst2, a C 2 H 2 Zn finger-type protein, is under the regulation of the protein kinase A pathway (23, 30). Php5, a component of the S. pombe CCAATbinding factor (CBF; also known as NF-Y) that possesses a histone hold domain, forms a complex with Php2/Php3 and contributes to cyc1 ϩ transcription (31, 32). In addition, two cis-acting elements required for fbp1 ϩ transcription have been identified (33). Upstream activation sequence 1 (UAS1) contains a cyclic AMP response element (CRE) and is the binding site for Atf1 and its binding partner, Pcr1 (34), while UAS2 resembles the S. cerevisiae stress response element (STRE) and serves as the binding site for Rst2 (...

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Transcriptional repression by Tup1–Ssn6This paper is one of a selection of papers published in this Special Issue, entitled 27th International West Coast Chromatin and Chromosome Conference, and has undergone the Journal's usual peer review process.

Cited by 107 publications

References 63 publications

Role for Protein Kinase A in the Neurospora Circadian Clock by Regulating White Collar-Independent frequency Transcription through Phosphorylation of RCM-1

Role for Protein Kinase A in the Neurospora Circadian Clock by Regulating White Collar-Independent frequency Transcription through Phosphorylation of RCM-1

Acquisition of the Ability To Assimilate Mannitol by Saccharomyces cerevisiae through Dysfunction of the General Corepressor Tup1-Cyc8

Antagonistic Controls of Chromatin and mRNA Start Site Selection by Tup Family Corepressors and the CCAAT-Binding Factor

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