scholarly journals Genetic Interaction between RLM1 and F-box Motif Encoding gene SAF1 Contributes to Stress Response in Saccharomyces cerevisiae

2019 ◽  
Author(s):  
Meenu Sharma ◽  
V. Verma ◽  
Narendra K Bairwa
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Transcription Factor ◽  
Stress Response ◽  
Experimental Analysis ◽  
Genetic Interaction ◽  
Cellular Growth ◽  
Calcofluor White ◽  
Genome Database ◽  
Adenine Deaminase

AbstractStress response is mediated by transcription of stress responsive genes. F-box motif protein Saf1 involves in SCF-E3 ligase mediated degradation of the adenine deaminase, Aah1 upon nutrient stress. Four transcription regulators, BUR6, MED6, SPT10, SUA7, have been reported for SAF1 gene in genome database of Saccharomyces cerevisiae. Here in this study an in-silco analysis of gene expression and transcription factor databases was carried out to understand the regulation of SAF1 gene expression during stress for hypothesis generation and experimental analysis. The GEO profile database analysis showed increased expression of SAF1 gene when treated with clioquinol, pterostilbene, gentamicin, hypoxia, genotoxic, desiccation, and heat stress, in WT cells. SAF1 gene expression in stress conditions correlated positively whereas AAH1 expression negatively with RLM1 transcription factor, which was not reported earlier. Based on analysis of expression profile and regulatory association of SAF1 and RLM1, we hypothesized that inactivation of both the genes may contribute to stress tolerance. The experimental analysis with the double mutant, saf1Δrlm1Δ for cellular growth response to stress causing agents, showed tolerance to calcofluor white, SDS, and hydrogen peroxide. On the contrary, saf1Δrlm1Δ showed sensitivity to MMS, HU, DMSO, Nocodazole, Benomyl stress. Based on in-silico and experimental data we suggest that SAF1 and RLM1 both interact genetically in differential response to genotoxic and general stressors.

scholarly journals Genetic interaction between RLM1 and F-box motif encoding gene SAF1 contributes to stress response in Saccharomyces cerevisiae

2021 ◽  
Vol 43 (1) ◽  
Author(s):  
Meenu Sharma ◽  
V. Verma ◽  
Narendra K. Bairwa
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Transcription Factor ◽  
Stress Response ◽  
Stress Tolerance ◽  
Experimental Analysis ◽  
Genetic Interaction ◽  
Cellular Growth ◽  
Genome Database ◽  
Transcription Regulators ◽  
Adenine Deaminase

Abstract Background Stress response is mediated by the transcription of stress-responsive genes. The F-box motif protein Saf1p is involved in SCF-E3 ligase mediated degradation of the adenine deaminase, Aah1p upon nutrient stress. The four transcription regulators, BUR6, MED6, SPT10, SUA7, are listed for SAF1 in the genome database of Saccharomyces cerevisiae. Here in this study, we carried out an in-silico analysis of gene expression and transcription factor databases to understand the regulation of SAF1 expression during stress for hypothesis and experimental analysis. Result An analysis of the GEO profile database indicated an increase in SAF1 expression when cells were treated with stress agents such as Clioquinol, Pterostilbene, Gentamicin, Hypoxia, Genotoxic, desiccation, and heat. The increase in expression of SAF1 during stress conditions correlated positively with the expression of RLM1, encoding the Rlm1p transcription factor. The expression of AAH1 encoding Aah1p, a Saf1p substrate for ubiquitination, appeared to be negatively correlated with the expression of RLM1 as revealed by an analysis of the Yeastract expression database. Based on analysis of expression profile and regulatory association of SAF1 and RLM1, we hypothesized that inactivation of both the genes together may contribute to stress tolerance. The experimental analysis of cellular growth response of cells lacking both SAF1 and RLM1 to selected stress agents such as cell wall and osmo-stressors, by spot assay indicated stress tolerance phenotype similar to parental strain however sensitivity to genotoxic and microtubule depolymerizing stress agents. Conclusions Based on in-silico and experimental data we suggest that SAF1 and RLM1 both interact genetically in differential response to genotoxic and general stressors.

scholarly journals Activating Transcription Factor 3 Is Integral to the Eukaryotic Initiation Factor 2 Kinase Stress Response

2004 ◽  
Vol 24 (3) ◽  
pp. 1365-1377 ◽  
Author(s):  
Hao-Yuan Jiang ◽  
Sheree A. Wek ◽  
Barbara C. McGrath ◽  
Dan Lu ◽  
Tsonwin Hai ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Amino Acid ◽  
Stress Response ◽  
Amino Acid Starvation ◽  
Initiation Factor ◽  
Activating Transcription Factor 3 ◽  
Eukaryotic Initiation Factor ◽  
Initiation Factor 2 ◽  
Activating Transcription Factor

ABSTRACT In response to environmental stress, cells induce a program of gene expression designed to remedy cellular damage or, alternatively, induce apoptosis. In this report, we explore the role of a family of protein kinases that phosphorylate eukaryotic initiation factor 2 (eIF2) in coordinating stress gene responses. We find that expression of activating transcription factor 3 (ATF3), a member of the ATF/CREB subfamily of basic-region leucine zipper (bZIP) proteins, is induced in response to endoplasmic reticulum (ER) stress or amino acid starvation by a mechanism requiring eIF2 kinases PEK (Perk or EIF2AK3) and GCN2 (EIF2AK4), respectively. Increased expression of ATF3 protein occurs early in response to stress by a mechanism requiring the related bZIP transcriptional regulator ATF4. ATF3 contributes to induction of the CHOP transcriptional factor in response to amino acid starvation, and loss of ATF3 function significantly lowers stress-induced expression of GADD34, an eIF2 protein phosphatase regulatory subunit implicated in feedback control of the eIF2 kinase stress response. Overexpression of ATF3 in mouse embryo fibroblasts partially bypasses the requirement for PEK for induction of GADD34 in response to ER stress, further supporting the idea that ATF3 functions directly or indirectly as a transcriptional activator of genes targeted by the eIF2 kinase stress pathway. These results indicate that ATF3 has an integral role in the coordinate gene expression induced by eIF2 kinases. Given that ATF3 is induced by a very large number of environmental insults, this study supports involvement of eIF2 kinases in the coordination of gene expression in response to a more diverse set of stress conditions than previously proposed.

Neighbourhoods in the yeast regulatory network in different physiological states

2020 ◽  
Author(s):  
Arthur M Lesk ◽  
Arun S Konagurthu
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Dna Damage ◽  
Transcription Factor ◽  
Stress Response ◽  
Local Structure ◽  
Regulatory Network ◽  
Diauxic Shift ◽  
Central Node ◽  
Similarities And Differences

Abstract Motivation The gene expression regulatory network in yeast controls the selective implementation of the information contained in the genome sequence. We seek to understand how, in different physiological states, the network reconfigures itself to produce a different proteome. Results This article analyses this reconfiguration, focussing on changes in the local structure of the network. In particular, we define, extract and compare the 1-neighbourhoods of each transcription factor, where a 1-neighbourhood of a node in a network is the minimal subgraph of the network containing all nodes connected to the central node by an edge. We report the similarities and differences in the topologies and connectivities of these neighbourhoods in five physiological states for which data are available: cell cycle, DNA damage, stress response, diauxic shift and sporulation. Based on our analysis, it seems apt to regard the components of the regulatory network as ‘software’, and the responses to changes in state, ‘reprogramming’.

Insights into Responses to Extreme Environmental Conditions in Humans from Studies on Saccharomyces cerevisiae

2015 ◽  
Vol 65 (6) ◽  
pp. 444
Author(s):  
Ramesh C. Meena ◽  
Amitabha Chakrabarti
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Stress Response ◽  
Gene Expression Data ◽  
Molecular Mechanisms ◽  
Multiple Stressors ◽  
Expression Data ◽  
Environmental Stress Response ◽  
Yeast Saccharomyces Cerevisiae ◽  
Pathways Analysis

<p>The versatility of the yeast experimental model has aided in innumerable ways in the understanding of fundamental cellular functions and has also contributed towards the elucidation of molecular mechanisms underlying several pathological conditions in humans. Genome-wide expression, functional, localization and interaction studies on the yeast Saccharomyces cerevisiae exposed to various stressors have made profound contributions towards the understanding of stress response pathways. Analysis of gene expression data from S. cerevisiae cells indicate that the expression of a common set of genes is altered upon exposure to all the stress conditions examined. This common response to multiple stressors is known as the Environmental stress response. Knowledge gained from studies on the yeast model has now become helpful in understanding stress response pathways and associated disease conditions in humans. Cross-species microarray experiments and analysis of data with ever improving computational methods has led to a better comparison of gene expression data between diverse organisms that include yeast and humans.</p>

scholarly journals Absence of Replication fork associated factor CTF4 and F-box motif Encoding Gene SAF1 leads to reduction in Cell Size and Stress Tolerance Phenotype in S. cerevisiae

2019 ◽  
Author(s):  
Meenu Sharma ◽  
Samar Singh ◽  
V. Verma ◽  
Narendra K Bairwa
Keyword(s):  
Cell Size ◽  
Replication Fork ◽  
Genetic Interaction ◽  
Dna Helicase ◽  
Calcofluor White ◽  
Gene Deletions ◽  
Replication Checkpoint ◽  
Rich Media ◽  
Size Growth ◽  
Adenine Deaminase

AbstractChromosome transmission fidelity factor, Ctf4 in S. cerevisiae associates with replication fork and helps in the sister chromatid cohesion. At the replication fork, Ctf4 links DNA helicase with the DNA polymerase. The absence of Ctf4 invokes replication checkpoint in the cells. The Saf1 of S.cerevisiae interacts with Skp1 of SCF-E3 ligase though F box-motif and ubiquitinates the adenine deaminase Aah1 during phase transition due to nutrient stress. The genetic interaction between the CTF4 and SAF1 has not been studied. Here we report genetic interaction between CTF4 and SAF1 which impacts the growth fitness and response to stress. The single and double gene deletions of SAF1 and CTF4 were constructed in the BY4741 genetic background. The strains were tested for growth on rich media and media containing stress causing agents. The saf1Δctf4Δ cells with reduced cell size showed the fastest growth phenotype on YPD medium when compared with the saf1Δ, ctf4Δ, and WT. The saf1Δctf4Δ cells also showed the tolerance to MMS, NaCl, Glycerol, SDS, Calcofluor white, H2O2, DMSO, Benomyl, and Nocodazole when compared with the saf1Δ, ctf4Δ, and WT cells. However, saf1Δctf4Δ cells showed the sensitivity to HU when compared with WT and saf1Δ. Based on these observations we suggest that SAF1 and CTF4 interact genetically to regulate the cell size, growth and stress response.

Hsp104 expression and morphological changes associated with disinfectants in saccharomyces cerevisiae: environmental bioassay using stress response

1998 ◽  
Vol 38 (7) ◽  
pp. 237-243 ◽  
Author(s):  
K. Fujita ◽  
H. Iwahashi ◽  
R. Kawai ◽  
Y. Komatsu
Keyword(s):  
Gene Expression ◽  
Saccharomyces Cerevisiae ◽  
Stress Response ◽  
Stress Proteins ◽  
Morphological Changes ◽  
Chemical Stress ◽  
Lacz Gene ◽  
Galactosidase Activity ◽  
Hybrid Gene ◽  
Sublethal Concentrations

On exposure of Saccharomyces cerevisiae to sublethal concentrations of disinfectants such as TPN, Thiuram, Captan and Oxine-copper; 70-, 90-kDa proteins and heat-shock protein Hsp104 were induced without morphological changes. Considering these stress proteins as critical signs, we can determine how cells are damaged by pesticides under sublethal conditions. Furthermore, Hsp104-lacZ hybrid gene (a lacZ gene put under control of Hsp104 promoter) in S. cerevisiae was sensitively expressed in the presence of sublethal concentrations of these disinfectants by measuring the relative β-galactosidase activity. It follows that not only monitoring the growth phase or the induction of synthesized proteins but also detecting the level of gene expression shows the chemical stress response rapidly, conveniently and reproducibly. We conclude that the use of a yeast strain with a stress reporter gene is a novel and simple bioassay relative to human health and to the ecosystem in general.

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