Regulation of transcription elongation in response to osmostress

Silva, Andréa; Cavero, Santiago; Begley, Victoria; Solé, Carme; Böttcher, René; Posas, Francesc; Nadal, Eulàlia de

doi:10.1371/journal.pgen.1007090

Cited by 20 publications

(21 citation statements)

References 51 publications

(80 reference statements)

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“…This study and previous stress tolerance investigations have identified several dozen to several hundred significant gene expression changes after stress exposure in budding yeasts 13,[16][17][18]28 . Despite analysis of stress-responsive genes in several robust species, rational engineering of robust strains remains difficult.…”

Section: Discussionsupporting

confidence: 60%

“…These results suggest that several genes from different gene families may contribute additively to robustness and/or that stress genes may exist as duplicates, as is the case for antifreeze protein genes in artic yeasts 15 . Thus, researchers have employed systems biology to characterize the transcriptome and/or proteome-wide stress-induced changes 13,14,[16][17][18] . These approaches have identified biological processes that exhibit altered expression in response to stress exposure, which build upon and relate to extensive previous research into gene functions (e.g.…”

Section: Introductionmentioning

confidence: 99%

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Stress-Induced Expression is Enriched for Evolutionarily Young Genes in Diverse Budding Yeasts

Doughty

Domenzain

Millán-Oropeza

et al. 2019

Preprint

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AbstractThe Saccharomycotina subphylum (budding yeasts) spans more than 400 million years of evolution and includes species that thrive in many of Earth’s harsh environments. Characterizing species that grow in harsh conditions could enable the design of more robust yeast strains for biotechnology. However, tolerance to stressful conditions is a multifactorial response, which is difficult to understand since many of the genes involved are as yet uncharacterized. In this work, three divergent yeast species were grown under multiple stressful conditions to identify stress-induced genes. For each condition, duplicated and non-conserved genes were significantly enriched for stress responsiveness compared to single-copy conserved genes. To understand this further, we developed a sorting method that considers evolutionary origin and duplication timing to assign an evolutionary age to each gene. Subsequent analysis of the sets of genes that changed expression revealed a relationship between stress-induced genes and the youngest gene set, regardless of the species or stress in question. These young genes are rarely essential for growth and evolve rapidly, which may facilitate their functionalization for stress tolerance and may explain their stress-induced expression. These findings show that systems-level analyses that consider gene age can expedite the identification of stress tolerance genes.

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Section: Discussionsupporting

confidence: 60%

Section: Introductionmentioning

confidence: 99%

Stress-Induced Expression is Enriched for Evolutionarily Young Genes in Diverse Budding Yeasts

Doughty

Domenzain

Millán-Oropeza

et al. 2019

Preprint

View full text Add to dashboard Cite

show abstract

“…This study and previous stress tolerance investigations have identified dozens to hundreds of significant gene expression changes after stress exposure in budding yeasts 13,[16][17][18]28 . Despite analysis of such stress-responsive genes in multiple species, rational engineering to further enhance robustness of industrial yeast strains remains difficult.…”

Section: Discussionsupporting

confidence: 52%

“…These results suggest that multiple genes from different gene families may contribute additively to robustness and/or that stress genes may exist as duplicates, as is the case for antifreeze protein genes in artic yeasts 15 . Thus, researchers have employed systems biology to characterize the transcriptome and/or proteome-wide stressinduced changes 13,14,[16][17][18] . These approaches have identified biological processes that exhibit altered expression in response to stress exposure, which builds upon and relates to previous research into gene functions (e.g., GO term enrichment analysis).…”

mentioning

confidence: 99%

Stress-induced expression is enriched for evolutionarily young genes in diverse budding yeasts

et al. 2020

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The Saccharomycotina subphylum (budding yeasts) spans 400 million years of evolution and includes species that thrive in diverse environments. To study niche-adaptation, we identify changes in gene expression in three divergent yeasts grown in the presence of various stressors. Duplicated and non-conserved genes are significantly more likely to respond to stress than genes that are conserved as single-copy orthologs. Next, we develop a sorting method that considers evolutionary origin and duplication timing to assign an evolutionary age to each gene. Subsequent analysis reveals that genes that emerged in recent evolutionary time are enriched amongst stress-responsive genes for each species. This gene expression pattern suggests that budding yeasts share a stress adaptation mechanism, whereby selective pressure leads to functionalization of young genes to improve growth in adverse conditions. Further characterization of young genes from species that thrive in harsh environments can inform the design of more robust strains for biotechnology.

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“…Shaping the Transcriptional Landscape through MAPK Signaling DOI: http://dx.doi.org /10.5772/intechopen.80634 Moreover, Hog1 phosphorylates the Spt4 elongation factor to regulate RNA Pol II processivity to stimulate elongation efficiency at stress-responsive genes [55]. As happens during initiation, Hog1 recruits other protein complexes with specific enzymatic activities such as deubiquitinase (Ubp3) to ensure the proper production of stress-responsive genes [50].…”

Section: Transcription Elongationmentioning

confidence: 99%

Shaping the Transcriptional Landscape through MAPK Signaling

Nadal-Ribelles¹,

Solé²,

Martínez-Cebrián³

et al. 2019

Gene Expression and Control

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A change in the transcriptional landscape is an equilibrium-breaking event important for many biological processes. Mitogen-activated protein kinase (MAPK) signaling pathways are dedicated to sensing extracellular cues and are highly conserved across eukaryotes. Modulation of gene expression in response to the extracellular environment is one of the main mechanisms by which MAPK regulates proteome homeostasis to orchestrate adaptive responses that determine cell fate. A massive body of knowledge generated from population and single-cell analyses has led to an understanding of how MAPK pathways operate. MAPKs have thus emerged as fundamental transcriptome regulators that function through a multilayered control of gene expression, a process often deregulated in disease, which therefore provides an attractive target for therapeutic strategies. Here, we summarize the current understanding of the mechanisms underlying MAPK-mediated gene expression in organisms ranging from yeast to mammals.

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Regulation of transcription elongation in response to osmostress

Cited by 20 publications

References 51 publications

Stress-Induced Expression is Enriched for Evolutionarily Young Genes in Diverse Budding Yeasts

Stress-Induced Expression is Enriched for Evolutionarily Young Genes in Diverse Budding Yeasts

Stress-induced expression is enriched for evolutionarily young genes in diverse budding yeasts

Shaping the Transcriptional Landscape through MAPK Signaling

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