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.
Overall design: This experiment measured the how six species of bacteria responded to a shift in tempterature from 37°C to 15°C. Bacteria were growing exponentially at 37°C in LB media, then shifted to 15°C for 3 hours. 4 replicates are present for each strain for each of the two temperatures.
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