Unknown,Transcriptomics,Genomics,Proteomics

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Growth and gene expression changes in Pseudomonas alloputida KT2440 in response to light and heavy lanthanides

ABSTRACT: The effect of lanthanum concentration and the effect of different lanthanide elements on gene expression and growth was tested in P. alloputida KT2440. Gene expression analysis was based on high-throughput RNAseq starting from rRNA-depleted samples, followed by determining differentially expressed genes.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Pseudomonas putida

SUBMITTER: Carl-Eric Wegner

PROVIDER: E-MTAB-13102 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Disruptions of protein homeostasis in the endoplasmic reticulum (ER) elicit activation of the unfolded protein response (UPR), a translation- and transcription-coupled proteostatic stress response pathway. The primary translational control arm of the UPR is initiated by the PERK-dependent phosphorylation of eIF2Î±, leading to a large-scale reprogramming of translation and subsequent activation of an ATF4-mediated transcriptional program. It has remained challenging, however, to accurately evaluate the contribution of each component of the eIF2Î±/ATF4 pathway to the remodelling of transcription and translation. Here, we have used mouse embryonic fibroblasts containing either a knock-in of the non-phosphorylatable eIF2Î± S51A mutant or knock-out for ATF4 by ribosome profiling and mRNA-seq to define the specific contributions of eIF2Î± phosphoryation and ATF4 in controlling the translational and transcriptional components of the UPR. These studies show that the transcriptional and translational targets of each P-eIF2Î±, ATF4, and the other UPR gene expression programs overlapped extensively, leading to a core set of UPR genes whose robust expression in response to ER stress is driven by multiple mechanisms. The identification of other, more factor-specific targets illustrated the potential for functional specialization of the UPR. As the UPR progressed temporally, cells employed distinct combinations of transcriptional and translational mechanisms, initiated by different factors, to adapt to ongoing stress. These effects were accompanied by a buffering effect where changes in mRNA levels were coupled to opposing changes in ribosome loading, a property which makes cooperation between transcription and translation essential to confer robust protein expression. Translational analysis by ribosome profiling and mRNA-seq of PERK pathways mutants during the UPR. Mouse embryonic fibroblasts (MEFs) lacking components of the PERK pathway (eIF2a phosphorylation and ATF4) were subjected to ER stress and analyzed by ribosome profiling.

Dataset Information

Growth and gene expression changes in Pseudomonas alloputida KT2440 in response to light and heavy lanthanides

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