Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Herbaspirillum seropedicae A01 mutant grown on three nitrogen conditions: Ammonium limiting, Ammonium shock and Nitrate shock

ABSTRACT: H. seropedicae A01 mutant grown on three different nitrogen conditions: nitrogen limiting, ammonium shock and nitrate shock.

INSTRUMENT(S): Ion Torrent Proton

ORGANISM(S): Herbaspirillum seropedicae

SUBMITTER: Paloma Bonato

PROVIDER: E-MTAB-8268 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:High-temperature stress is a critical environmental parameter for all organisms and induces a cellular heat shock response, characterized by an upregulation of heat shock proteins. For Crenarchaeota, it is unknown how this response is regulated, given the lack of conservation of known prokaryotic or eukaryotic heat shock-regulating transcription factors and how cellular processes are affected. To this end, we studied the heat shock response of the thermoacidophilic Sulfolobus acidocaldarius, thriving in volcanic hot springs at 75°C, upon shift to 86°C, at the transcriptome and proteome level. By pulse-labeling of neosynthesized RNA and proteins upon heat shock, we show a drastic reduction of the cell’s major transcriptional activity immediately after shift and neosynthesis of certain abundant (heat shock) proteins, including the thermosome. By combining RNA-sequencing and mass spectrometry, we show that RNA levels of half of the genes are affected immediately after temperature shift and that reprogramming of the protein landscape takes at least one hour and changes are more subtle. Correlation analysis provides evidence that considerable post-transcriptional and post-translational regulation is occurring upon heat shock. Functional enrichment analysis indicates that nearly all biological processes are affected by heat shock. An overall downregulation is observed for transcription, translation, DNA replication and cell division. However, quality control of translation and of the protein landscape is increased. Many DNA repair pathways are differentially expressed, accompanied with an increase in a DNA import system. Furthermore, expression of DNA topoisomerases is investigated, coinciding with a significant differential expression of nucleoid-associated proteins. Based on these findings and considering the absence of a conserved DNA-binding motif, we propose that regulation of the heat shock response in Sulfolobales is most likely not established by a classical transcription factor, but is rather caused by changes in chromosome organization or established at the post-transcriptional level.

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Herbaspirillum seropedicae A01 mutant grown on three nitrogen conditions: Ammonium limiting, Ammonium shock and Nitrate shock

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