Combined Transcriptomic and Proteomic Profiling of under Microaerobic versus Aerobic Conditions: The Multifaceted Roles of Noncoding Small RNAs and Oxygen-Dependent Sensing in Global Gene Expression Control.

Adaptive mechanisms that facilitate intestinal colonization by the human microbiota, including , 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 grown under aerobic versus microaerobic conditions. Clustering of high-abundance transcripts under microaerobiosis highlighted genes controlling acid-stress adaptation (, , and operons), cell adhesion/biofilm formation ( and operons), electron transport (), oligopeptide transport (), and anaerobic respiration/fermentation ( and operons). In contrast, downregulated genes were involved in iron transport (, and operons), iron-sulfur cluster assembly ( and operons), aerobic respiration ( and operons), and de novo nucleotide synthesis (). 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 growth when oxygen levels are low.