Abstract
Adaptive mechanisms that facilitate intestinal colonization by the human microbiota, including Escherichia coli, may be better understood by analyzing the physiology and gene expression of bacteria in low-oxygen environments. We used high-throughput transcriptomics and proteomics to compare the expression profiles of E. coli grown under aerobic versus microaerobic conditions. Clustering of high-abundance transcripts under microaerobiosis highlighted genes controlling acid-stress adaptation (gadAXW, gadAB, hdeAB-yhiD and hdeD operons), cell adhesion/biofilm formation (pgaABCD and csgDEFG operons), electron transport (cydAB), oligopeptide transport (oppABCDF), and anaerobic respiration/fermentation (hyaABCDEF and hycABCDEFGHI operons). In contrast, downregulated genes were involved in iron transport (fhuABCD, feoABC and fepA-entD operons), iron-sulfur cluster assembly (iscRSUA and sufABCDSE operons), aerobic respiration (sdhDAB and sucABCDSE operons), and de novo nucleotide synthesis (nrdHIEF). Additionally, quantitative proteomics showed that the products (proteins) of these high- or low-abundance transcripts were expressed consistently. Our findings highlight interrelationships among energy production, carbon metabolism, and iron homeostasis. Moreover, we have identified and validated a subset of differentially expressed noncoding small RNAs (i.e., CsrC, RyhB, RprA and GcvB), and we discuss their regulatory functions during microaerobic growth. Collectively, we reveal key changes in gene expression at the transcriptional and post-transcriptional levels that sustain E. coli growth when oxygen levels are low.
Highlights
Escherichia coli is a Gram-negative commensal bacterium that commonly inhabits the intestines of humans and other animals under microaerobic or anaerobic conditions
ArcA belongs to the two-component ArcAB system, which functions as a microaerobic redox regulator, whereas FNR is known for its major regulatory role in the transition from aerobic to anaerobic growth through the activation of genes involved in anaerobic metabolism and repression of genes involved in aerobic metabolism
Samples of purified RNA were used for the RNA deep-sequencing analyses, and the same batches of RNA were used for Northern blot validation
Summary
Escherichia coli is a Gram-negative commensal bacterium that commonly inhabits the intestines of humans and other animals under microaerobic or anaerobic conditions. Previous studies have shown that E. coli growth at different concentrations of oxygen involves substantial reprogramming of the gene expression controlled by several transcription factors, such as ArcA and FNR, which together enable E. coli to adapt to and survive under altered oxygen availabilities [1–7]. Our understanding of microaerobic/anaerobic growth and adaptation remains limited due to the lack of an integrated overview of the transcriptional and post-transcriptional events involved in these processes. These missing links in the regulatory network are critical for gaining in-depth insights into the mechanisms and gene expression patterns that define the physiology, reproduction, and growth of bacteria (both commensal and pathogenic) in the intestine and other deep tissues
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