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.
NADH is an endogenous autofluorescent regulatory metabolite detected in the nuclear regions of live cells which when analysed for the bound and free form can aid in determining a cell's metabolic status and molecular activity. Detecting the spectral differences of free and bound NADH in live cells is currently limited due to the very small differences in emission. The Spectral Phasor technique enables not only examination of small shifts in spectral emissions but also provides the spatial location of spectrally different components in live cells without any prior knowledge of the species. The phasor representation enables direct comparison of either optical sections (i.e. different focal planes) of one cell or multiple cells for global analysis.Here we describe the use of Spectral Phasors to spatially map NADH's spectral emission in the nucleus of live cells under normal culture conditions and those stimulated into the early stages of differentiation. A comparison of undifferentiated cells and those stimulated to differentiate demonstrate differing spatial distributions of emission spectra associated with NADH. Undifferentiated cells displayed shorter emissions cantered in the nucleus, while longer wavelengths were localised around the perinuclear boarder. Cells stimulated into the early stages of differentiation displayed a redirection of the shorter emissions to regional clustering predominately in one area close to the nuclear/cytoplasmic boarder, while the longer wavelengths were localised throughout the remainder of the nucleus. Here we show the application of the Spectral Phasor technique to identify discrete wavelength shifts associated with endogenous NADH autofluorescence in the nucleus, and observed changes in their spatial distribution in live cells during the early stages of differentiation.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.