The <i>WTM</i> Genes in Budding Yeast Amplify Expression of the Stress-Inducible Gene <i>RNR3</i>

Tringe, Susannah G.; Willis, Jason; Liberatore, Katie L.; Ruby, Stephanie W.

doi:10.1534/genetics.106.062042

Cited by 7 publications

(5 citation statements)

References 64 publications

(102 reference statements)

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“…For example, we find that the Wtm1 and Wtm2 proteins translocate out of the nucleus into the cytoplasm in response to MMS, as does Rnr4 (Figure 5D and E). Wtm proteins are involved in nuclear anchoring of the RNR small-subunits (54–57), with one study previously implicating the Wtm proteins in the control of RNR transcription (58). It appears that controlling the subcellular localization of the Wtm proteins may provide an additional mode of RNR regulation.…”

Section: Resultsmentioning

confidence: 99%

Genome-wide single-cell-level screen for protein abundance and localization changes in response to DNA damage in S. cerevisiae

Mazumder

Pesudo

McRee

et al. 2013

Nucleic Acids Research

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An effective response to DNA damaging agents involves modulating numerous facets of cellular homeostasis in addition to DNA repair and cell-cycle checkpoint pathways. Fluorescence microscopy-based imaging offers the opportunity to simultaneously interrogate changes in both protein level and subcellular localization in response to DNA damaging agents at the single-cell level. We report here results from screening the yeast Green Fluorescent Protein (GFP)-fusion library to investigate global cellular protein reorganization on exposure to the alkylating agent methyl methanesulfonate (MMS). Broad groups of induced, repressed, nucleus- and cytoplasm-enriched proteins were identified. Gene Ontology and interactome analyses revealed the underlying cellular processes. Transcription factor (TF) analysis identified principal regulators of the response, and targets of all major stress-responsive TFs were enriched amongst the induced proteins. An unexpected partitioning of biological function according to the number of TFs targeting individual genes was revealed. Finally, differential modulation of ribosomal proteins depending on methyl methanesulfonate dose was shown to correlate with cell growth and with the translocation of the Sfp1 TF. We conclude that cellular responses can navigate different routes according to the extent of damage, relying on both expression and localization changes of specific proteins.

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Section: Resultsmentioning

confidence: 99%

Genome-wide single-cell-level screen for protein abundance and localization changes in response to DNA damage in S. cerevisiae

Mazumder

Pesudo

McRee

et al. 2013

Nucleic Acids Research

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“…More regulatory factors were found to be involved in the transcriptional regulation of RNR genes. Wtm1 and Wtm2 have been reported to modulate the expression of RNR3 (Tringe et al , 2006). Moderate overexpression of both genes or high‐level expression of WTM2 alone upregulates RNR3‐lacZ in the absence of DNA damage.…”

Section: Mechanisms Of Transcriptional Regulation Of Yeast Genes In Rmentioning

confidence: 99%

“…Wtm2 was found to associate directly with the RNR3 promoter, and the association correlates with its ability to increase constitutive RNR3 expression. It remains unknown how Wtm2 increases RNR3 transcription, although some observations hint that Wtm2 might enhance RNR3 transcription by participating in chromatin remodeling (Tringe et al , 2006). Furthermore, Wtm1 associates with and anchors the Rnr2/Rnr4 complex in the nucleus in untreated cells.…”

Section: Mechanisms Of Transcriptional Regulation Of Yeast Genes In Rmentioning

confidence: 99%

DNA damage-induced gene expression inSaccharomyces cerevisiae

Pastushok

Xiao

2008

FEMS Microbiol Rev

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After exposure to DNA-damaging agents, both prokaryotic and eukaryotic cells activate stress responses that result in specific alterations in patterns of gene expression. Bacteria such as Escherichia coli possess both lesion-specific responses as well as an SOS response to general DNA damage, and the molecular mechanisms of these responses are well studied. Mechanisms of DNA damage response in lower eukaryotes such as Saccharomyces cerevisiae are apparently different from those in bacteria. It becomes clear that many DNA damage-inducible genes are coregulated by the cell-cycle checkpoint, a signal transduction cascade that coordinates replication, repair, transcription and cell-cycle progression. On the other hand, among several well-characterized yeast DNA damage-inducible genes, their effectors and mechanisms of transcriptional regulation are rather different. This review attempts to summarize the current state of knowledge on the molecular mechanisms of DNA damage-induced transcriptional regulation in this model lower eukaryotic microorganism.

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“…This mutation causes YRR1 to produce new interaction sites for three genes, namely, WTM2 , PUP1 , and ALE1 . WTM2 encodes a transcriptional regulator that regulates meiosis and the expression of nucleotide reductase, which can respond to DNA replication pressure ( Pemberton and Blobel, 1997 ; Tringe et al, 2006 ), PUP1 encodes the 20S proteasome subunit ( Haffter and Fox, 1991 ), and ALE1 encodes lysophospholipid acylase ( Riekhof et al, 2007 ). However, these three genes did not show differential expression at the transcriptional level, and the biological significance of this is not clear.…”

Section: Resultsmentioning

confidence: 99%

Capture Hi-C reveals the influence on dynamic three-dimensional chromosome organization perturbed by genetic variation or vanillin stress in Saccharomyces cerevisiae

et al. 2022

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Studying the mechanisms of resistance to vanillin in microorganisms, which is derived from lignin and blocks a major pathway of DNA double-strand break repair in yeast, will benefit the design of robust cell factories that produce biofuels and chemicals using lignocellulosic materials. A high vanillin-tolerant Saccharomyces cerevisiae strain EMV-8 carrying site mutations compared to its parent strain NAN-27 was selected for the analyses. The dynamics of the chromatin structure of eukaryotic cells play a critical role in transcription and the regulation of gene expression and thus the phenotype. Consequently, Hi-C and transcriptome analyses were conducted in EMV-8 and NAN-27 in the log phase with or without vanillin stress to determine the effects of mutations and vanillin disturbance on the dynamics of three-dimensional chromosome organization and the influence of the organization on the transcriptome. The outcomes indicated that the chromosome interaction pattern disturbed by vanillin stress or genetic mutations in the log phase was similar to that in mouse cells. The short chromosomes contact the short chromosomes, and the long chromosomes contact the long chromosomes. In response to vanillin stress, the boundaries of the topologically associating domain (TAD) in the vanillin-tolerant strain EMV-8 were more stable than those in its parent strain NAN-27. The motifs of SFL1, STB3, and NHP6A/B were enriched at TAD boundaries in both EMV-8 and NAN-27 with or without vanillin, indicating that these four genes were probably related to TAD formation. The Indel mutation of YRR1, whose absence was confirmed to benefit vanillin tolerance in EMV-8, caused two new interaction sites that contained three genes, WTM2, PUP1, and ALE1, whose overexpression did not affect vanillin resistance in yeast. Overall, our results revealed that in the log phase, genetic mutations and vanillin disturbance have a negligible effect on three-dimensional chromosome organization, and the reformation or disappearance of TAD boundaries did not show an association with gene expression, which provides an example for studying yeast chromatin structure during stress tolerance using Hi-C technology.

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The WTM Genes in Budding Yeast Amplify Expression of the Stress-Inducible Gene RNR3

Cited by 7 publications

References 64 publications

Genome-wide single-cell-level screen for protein abundance and localization changes in response to DNA damage in S. cerevisiae

Genome-wide single-cell-level screen for protein abundance and localization changes in response to DNA damage in S. cerevisiae

DNA damage-induced gene expression inSaccharomyces cerevisiae

Capture Hi-C reveals the influence on dynamic three-dimensional chromosome organization perturbed by genetic variation or vanillin stress in Saccharomyces cerevisiae

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