Comparative transcriptome analysis of Shewanella MR-1 under oxic vs. suboxic conditions

To understand how cell physiological state affects mRNA translation, we used the bacterium Shewanella oneidensis MR-1 grown under steady state conditions at either 20% or 8.5% O2. Using a combination of quantitative proteomics and RNA-Seq, we generated high-confidence data on >1000 mRNA and protein pairs. By using a steady state model, we found that differences in protein–mRNA ratios were primarily due to differences in the translational efficiency of specific genes. When oxygen levels were lowered, 28% of the proteins showed at least a 2-fold change in expression. Transcription levels were significantly altered for 26% of the protein changes; translational efficiency was significantly altered for 46% and a combination of both was responsible for the remaining 28%. Changes in translational efficiency were significantly correlated with the codon usage pattern of the genes and measurable tRNA pools changed in response to altered O2 levels. Our results suggest that changes in the translational efficiency of proteins, in part due to altered tRNA pools, is a major determinant of regulated alterations in protein expression levels in bacteria. For further details, see the resulting publication and its supplemental material: Taylor, R. C. et al., "Changes in translational efficiency is a dominant regulatory mechanism in the environmental response of bacteria", Integrative Biology, 2013, 5, 1393. DOI: 10.1039/c3ib40120k Overall design: mRNA profiles of Shewanella MR-1 were generated by sequencing on SOLID sequencers under high (20%) or low (8.5%) oxygen, with primary sample comparison pair in triplicate, other samples in duplicate.