Project description:Loss of nutrient supply elicits alterations of the SUMO proteome and sumoylation is crucial to various cellular processes including transcription. However, the physiological significance of sumoylation of transcriptional regulators is unclear. To begin clarifying this, we mapped the SUMO proteome under nitrogen-limiting conditions in Saccharomyces cerevisiae. Interestingly, several RNA polymerase III (RNAPIII) components are major SUMO targets under normal growth conditions, including Rpc53, Rpc82, and Ret1, and nutrient starvation results in rapid desumoylation of these proteins. These findings are supported by ChIP-seq experiments that show that SUMO is highly enriched at tDNA genes. Furthermore, RNA-seq experiments revealed that preventing sumoylation results in significantly decreased tRNA transcription. TORC1 inhibition resulted in the same effect, and our data indicate that the SUMO and TORC1 pathways are both required for robust tDNA expression. Importantly, tRNA transcription was strongly reduced in cells expressing a non-sumoylatable Rpc82-4KR mutant, which correlated with a misassembled RNAPIII transcriptional complex. Our data suggest that in addition to TORC1 activity, sumoylation of RNAPIII is key to reaching full translational capacity under optimal growth conditions.
Project description:This model was reconstructed from single-nucleus RNA-seq (snRNA-seq) data of human postmortem brain and curated using published metabolomics data from human iPSC-derived neurons and cerebrospinal fluid (CSF), together with gene expression data from the Human Protein Atlas. It more accurately simulates human neuronal metabolic flux in neurodegenerative conditions such as Alzheimer's disease (AD).
Project description:We performed transcriptome (RNA-seq) analyses for Campylobacter jejuni 11168 wild-type (WT) and Cj1608 deletion mutant (ΔCj1608::aphA-3) under oxidative stress and optimal microaerobic growth conditions. The expression of 231 genes was affected by oxidative stress in stressed wild-type cells (WTS) compared to non-stressed cells (WT). A comparison of genes expressed in the ΔCj1608 and WT strains under optimal growth conditions revealed 380 differently expressed genes. Moreover, transcriptional changes and overall final protein levels correlated across multiple genes. The data were validated through RT-qPCR and phenotype experiments for selected processes.
Project description:We performed transcriptome (RNA-seq) analyses for Arcobacter butzleri RM4018 wild-type (WT) and Abu0127 deletion mutant (ΔAbu0127::aphA-3) under oxidative stress and optimal microaerobic growth conditions. The expression of 290 genes was affected by oxidative stress in stressed wild-type cells (WTS) compared to non-stressed cells (WT). A comparison of genes expressed in the ΔAbu0127 and WT strains under optimal growth conditions revealed 779 differently expressed genes. Moreover, transcriptional changes and overall final protein levels correlated across multiple genes. The data were validated through RT-qPCR and phenotype experiments for selected processes.
Project description:We performed transcriptome (RNA-seq) analyses for Helicobacter pylori N6 wild-type (WT) and HP1021 deletion mutant (ΔHP1021::aphA-3) under oxidative stress and optimal microaerobic growth conditions. The expression of 411 genes was affected by oxidative stress in stressed wild-type cells (WTS) compared to non-stressed cells (WT). Interestingly, ΔHP1021 did not respond to oxidative stress. A comparison of genes expressed in the ΔHP1021 and WT strains under optimal growth conditions revealed 191 differently expressed genes. Moreover, transcriptional changes and overall final protein levels correlated across multiple genes. The data were validated through RT-qPCR and phenotype experiments for selected processes.