The transcriptional response to low temperature is weakly conserved across theEnterobacteriaceae

Abstract

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-typeEscherichia coli, Salmonella enterica, Citrobacter rodentium, Enterobacter cloacae, Klebsiella pneumoniae,andSerratia marcescens, as well as ΔrpoSstrains ofE. coliandS. 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 differentially expressed genes in common among the 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 between 37°C and 15°C in bothE. coliandS. 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 the 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.ImportanceWe studied how different species of bacteria change the expression of their genes in response to a change in temperature. We found that the six species in this study change the level of expression of many of their genes in response to a shift from human body temperature (37°C) to a temperature that might be found out of doors (15°C). Surprisingly, there are very few genes that change expression in all six species. This was due to each species possessing many unique genes that no other species has and due to many genes that are present in the genome of each species changing expression in only one species. This study is important to the field because it illustrates that closely related species can share many genes but not use those genes in the same way in response to the same environmental change.