Gene expression analysis of E. coli strains provides insights into the role of gene regulation in diversification
- 24 October 2014
- journal article
- Published by Oxford University Press (OUP) in The ISME Journal
- Vol. 9 (5), 1130-1140
- https://doi.org/10.1038/ismej.2014.204
Abstract
Escherichia coli spans a genetic continuum from enteric strains to several phylogenetically distinct, atypical lineages that are rare in humans, but more common in extra-intestinal environments. To investigate the link between gene regulation, phylogeny and diversification in this species, we analyzed global gene expression profiles of four strains representing distinct evolutionary lineages, including a well-studied laboratory strain, a typical commensal (enteric) strain and two environmental strains. RNA-Seq was employed to compare the whole transcriptomes of strains grown under batch, chemostat and starvation conditions. Highly differentially expressed genes showed a significantly lower nucleotide sequence identity compared with other genes, indicating that gene regulation and coding sequence conservation are directly connected. Overall, distances between the strains based on gene expression profiles were largely dependent on the culture condition and did not reflect phylogenetic relatedness. Expression differences of commonly shared genes (all four strains) and E. coli core genes were consistently smaller between strains characterized by more similar primary habitats. For instance, environmental strains exhibited increased expression of stress defense genes under carbon-limited growth and entered a more pronounced survival-like phenotype during starvation compared with other strains, which stayed more alert for substrate scavenging and catabolism during no-growth conditions. Since those environmental strains show similar genetic distance to each other and to the other two strains, these findings cannot be simply attributed to genetic relatedness but suggest physiological adaptations. Our study provides new insights into ecologically relevant gene-expression and underscores the role of (differential) gene regulation for the diversification of the model bacterial species.Keywords
This publication has 37 references indexed in Scilit:
- How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes?BMC Genomics, 2012
- Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial speciesProceedings of the National Academy of Sciences of the United States of America, 2011
- Differential expression analysis for sequence count dataGenome Biology, 2010
- Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAsBMC Genomics, 2009
- Cryptic Lineages of the Genus EscherichiaApplied and Environmental Microbiology, 2009
- Comparative systems biology across an evolutionary gradient within the Shewanella genusProceedings of the National Academy of Sciences of the United States of America, 2009
- Structure and Complexity of a Bacterial TranscriptomeJournal of Bacteriology, 2009
- Ultrafast and memory-efficient alignment of short DNA sequences to the human genomeGenome Biology, 2009
- THE LOCI OF EVOLUTION: HOW PREDICTABLE IS GENETIC EVOLUTION?Evolution, 2008
- The bacterial species definition in the genomic eraPhilosophical Transactions B, 2006