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The transcriptional response to low temperature is weakly conserved across Enterobacteriales

ABSTRACT: The transcriptional response to low temperature is weakly conserved across Enterobacteriales

PROVIDER: PRJNA1111795 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR29034700_1.fastq.gz	Fastqsanger.gz
	SRR29034700_2.fastq.gz	Fastqsanger.gz
	SRR29034701_1.fastq.gz	Fastqsanger.gz
	SRR29034701_2.fastq.gz	Fastqsanger.gz
	SRR29034702_1.fastq.gz	Fastqsanger.gz

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The transcriptional response to low temperature is weakly conserved across Enterobacteriales

Project description:Bacteria respond to changes in their external environment like temperature by changing the transcription of their genes, but we know little about how these regulatory patterns evolve. We used RNA-seq to study the transcriptional response of a shift from 37°C to 15°C in wild-type Escherichia coli, Salmonella enterica, Citrobacter rodentium, Enterobacter cloacae, Klebsiella pneumoniae, and Serratia marcescens, as well as ∆rpoS strains of E. coli and S. enterica. We found that these species change the transcription of between 626 and 1057 genes in response to the temperature shift, but there are only 16 genes differentially expressed in wild-type strains of all six species. GO enrichment of regulated genes suggests many species-specific phenotypic responses to temperature changes, but terms involved in iron metabolism, central metabolism, and response to osmotic stress are implicated in at least half of the species. The alternative sigma factor RpoS regulates about 200 genes at 15°C in E. coli and S. enterica, with only 83 genes in common between the two species. Divergence in the RpoS-regulon between the two species is due to both species-specific genes in each genome as well as differences in regulation of shared genes. Overall, there is limited conservation of the response to low temperature generally, or the RpoS-regulated part of the response specifically, due both to some genes being species-specific, as well as the species-specific regulation of shared genes. Regulatory responses to a common stress evolve rapidly between closely related species.

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Project description:As a species mostly planted in tropical and subtropical regions, rice is sensitive to chilling temperature, especially at reproductive stage. However, the effect of low temperature on seed development has not been well characterized. The transcriptome of two rice cultivars Zhonghua11 and Hanfeng were analyzed to characterize the gene regulatory networks of rice seed during low temperature treatment.

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Project description:A collection of carbapenemase producing Enterobacteriales from an outbreak investigation Raw sequence reads

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Community of haloarchaea, enriched at low temperature

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low temperature (10 oC) microbial fuel cells

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Low temperature stress in cv. Dicktoo

Project description:In this study we used the Affymetrix Barley 1 GeneChip to investigate transcriptome responses of barley cv. Dicktoo to low temperature, including triplicated measurements of cold, freeze/thaw cycles and de-acclimation over 33 days. Keywords: stress response

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Responses of maize source leaf metabolism to low temperature, low nitrogen and low phosphorus stress

Project description:Abiotic stress causes disturbances in the cellular homeostasis. Re-adjustment of balance in carbon, nitrogen and phosphorus metabolism therefore plays a central role in stress adaptation. However, it is currently unknown which parts of the primary cell metabolism follow common patterns under different stress conditions and which represent specific responses. To address these questions, changes in transcriptome, metabolome and ionome were analyzed in maize source leaves from plants suffering low temperature, low nitrogen (N) and low phosphorus (P) stress. The selection of maize as study object provided data directly from an important crop species and the so far underexplored C4 metabolism. Growth retardation was comparable under all tested stress conditions. The only primary metabolic pathway responding similar to all stresses was nitrate assimilation, which was down-regulated. The largest group of commonly regulated transcripts followed the expression pattern: down under low temperature and low N, but up under low P. Several members of this transcript cluster could be connected to P metabolism and correlated negatively to different phosphate concentration in the leaf tissue. Accumulation of starch under low temperature and low N stress, but decrease in starch levels under low under low P conditions indicated that only low P treated leaves suffered carbon starvation. In conclusion, maize employs very different strategies for management of nitrogen and phosphorus metabolism under stress. While nitrate assimilation was regulated depending on demand by growth processes, phosphate concentrations changed depending on availability, thus building up reserves under excess conditions. Carbon and energy metabolism of the C4 maize leaves were particularly sensitive to P starvation.

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