Ontology highlight
ABSTRACT:
PROVIDER: PRJNA615685 | ENA |
REPOSITORIES: ENA
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Project description:The extreme radiation resistance of Deinococcus bacteria requires the radiation-stimulated cleavage of protein DdrO by a specific metalloprotease called IrrE. DdrO is the repressor of a predicted radiation/desiccation response (RDR) regulon, composed of radiation-induced genes having a conserved DNA motif (RDRM) in their promoter regions. Here, we showed that addition of zinc ions to purified apo-IrrE, and short exposure of Deinococcus cells to zinc ions, resulted in cleavage of DdrO in vitro and in vivo, respectively. Binding of IrrE to RDRM-containing DNA or interaction of IrrE with DNA-bound DdrO was not observed. The data are in line with IrrE being a zinc peptidase, and indicate that increased zinc availability, caused by oxidative stress, triggers the in vivo cleavage of DdrO unbound to DNA. Transcriptomics and proteomics of Deinococcus deserti confirmed the IrrE-dependent regulation of predicted RDR regulon genes and also revealed additional members of this regulon. Comparative analysis showed that the RDR regulon is largely well conserved in Deinococcus species, but also showed diversity in the regulon composition. Notably, several RDR genes with an important role in radiation resistance in Deinococcus radiodurans, for example pprA, are not conserved in some other radiation-resistant Deinococcus species.
2017-04-03 | GSE95658 | GEO
Project description:Cellular tolerance toward furfural is a complex phenotype involved many genes, and hard to be improved by manipulating individual genes. We previously established exogenous global regulator IrrE mutants that confer Escherichia coli with significantly enhanced tolerance to furfural stress. In order to elucidate the mechanism for enhancement of furfural tolerance in the mutants and to identify new genes and pathways that can be possible targets for engineering of furfural tolerance, we carried out comparative transcriptomic with the representative strains F1-37 and WT (harboring the furfural-tolerant mutant F1-37 of IrrE and the wild type IrrE, respectively). The data from transcriptome analyses were deposited here.
2012-01-28 | GSE35100 | GEO
Project description:Cellular tolerance toward furfural is a complex phenotype involved many genes, and hard to be improved by manipulating individual genes. We previously established exogenous global regulator IrrE mutants that confer Escherichia coli with significantly enhanced tolerance to furfural stress. In order to elucidate the mechanism for enhancement of furfural tolerance in the mutants and to identify new genes and pathways that can be possible targets for engineering of furfural tolerance, we carried out comparative transcriptomic with the representative strains F1-37 and WT (harboring the furfural-tolerant mutant F1-37 of IrrE and the wild type IrrE, respectively). The data from transcriptome analyses were deposited here. Cells of furfural-tolerant mutant F1-37 and wild-type strain WT were grown in LB medium supplemented with furfural, and the cells were harvested in the exponential phase. The samples for both of these two strains were prepared in triplicate with biological replicates.
2012-01-28 | E-GEOD-35100 | biostudies-arrayexpress
Project description:Cellular tolerance toward ethanol is a complex phenotype involved many genes, and hard to be improved by manipulating individual genes. We previously established exogenous global regulator IrrE mutants that confer Escherichia coli with significantly enhanced tolerance to stresses, including ethanol. In order to elucidate the mechanism for enhancement of ethanol tolerance in the mutants and to identify new genes and pathways that can be possible targets for engineering of ethanol tolerance, we carried out comparative transcriptomic and proteomic analyses with the representative strains E1 and E0 (harboring the ethanol-tolerant mutant E1 of IrrE and the wild type IrrE, respectively). The data from transcriptome analyses were deposited here.
2012-05-01 | GSE30441 | GEO
Project description:IrrE is a unique gene in Deinococcus, which is the switch of DNA repair and celluar surival network. Expressing IrrE enhanced the salt tolence in E. coli. To understand the effect of IrrE to E. coli during salt shock, we constructed the IrrE-expressing plasmid pMG1-IrrE. And pMG1 is the empty vector used as a control. The GroESL promoter was amplified from D. radiodurans R1 genomic DNA by PCR with proper primers. The PCR product was ligated into the T-cloning site of T-vector pMD18T, generating the plasmid pMG1.
2010-07-29 | GSE17465 | GEO
Project description:Welan gum is mainly produced by Sphingomonas sp. ATCC 31555 and has broad applications in industry such as that in cement production. Both carbon and nitrogen sources are essential for welan production. However, how nitrogen sources affect the metabolism and gene transcription of welan remains elusive. Here, we used next-generation sequencing RNA-seq to analyze the transcriptome of Sphingomonas sp. ATCC 31555 in the presence of inorganic or organic nitrogen sources. Enriched gene expression and pathway analysis suggest that organic nitrogen sources significantly enhanced the expression of genes in central metabolic pathways of Sphingomonas sp. ATCC 31555 and those critical for welan synthesis compared to that observed using inorganic nitrogen sources. The present study improves our understanding of the molecular mechanism underlying the use of nitrogen in welan synthesis in Sphingomonas sp., as well as provides an important transcriptome resource for Sphingomonas sp. in relation to nitrogen sources.
2016-03-25 | GSE79497 | GEO
Project description:Cellular tolerance toward ethanol is a complex phenotype involved many genes, and hard to be improved by manipulating individual genes. We previously established exogenous global regulator IrrE mutants that confer Escherichia coli with significantly enhanced tolerance to stresses, including ethanol. In order to elucidate the mechanism for enhancement of ethanol tolerance in the mutants and to identify new genes and pathways that can be possible targets for engineering of ethanol tolerance, we carried out comparative transcriptomic and proteomic analyses with the representative strains E1 and E0 (harboring the ethanol-tolerant mutant E1 of IrrE and the wild type IrrE, respectively). The data from transcriptome analyses were deposited here. Cells of ethanol-tolerant mutant E1 and wild-type strain E0 were grown in 1.5% ethanol, and the samples for both of these two strains were prepared in triplicate with biological replicates
2012-04-30 | E-GEOD-30441 | biostudies-arrayexpress
Project description:IrrE is a unique gene in Deinococcus, which is the switch of DNA repair and celluar surival network. Expressing IrrE enhanced the salt tolence in E. coli. To understand the effect of IrrE to E. coli during salt shock, we constructed the IrrE-expressing plasmid pMG1-IrrE. And pMG1 is the empty vector used as a control. The GroESL promoter was amplified from D. radiodurans R1 genomic DNA by PCR with proper primers. The PCR product was ligated into the T-cloning site of T-vector pMD18T, generating the plasmid pMG1. RNA extracted from cells of E. coli K-12 JM109 cells with pMG1 after 4 h of growth to OD 600 achieve 0.4, or cells with pMG1 after 1mol/L NaCl shock for 10 min (and 60 min) when their OD600 achieved 0.4. RNA extracted from cells of E. coli K-12 JM109 cells with pMG1-IrrE after 4 h of growth to OD 600 achieve 0.4, or cells with pMG1-IrrE after 1mol/L NaCl shock for 10 min (and 60 min)when their OD600 achieved 0.4. pMG1 and pMG1-IrrE datasets normalized separately.
2010-07-29 | E-GEOD-17465 | biostudies-arrayexpress