Sulfur and Nitrogen Limitation in Escherichia coli K-12: Specific Homeostatic Responses

Abstract

We determined global transcriptional responses of Escherichia coli K-12 to sulfur (S)-or nitrogen (N)-limited growth in adapted batch cultures and cultures subjected to nutrient shifts. Using two limitations helped to distinguish between nutrient-specific changes in mRNA levels and common changes related to the growth rate. Both homeostatic and slow growth responses were amplified upon shifts. This made detection of these responses more reliable and increased the number of genes that were differentially expressed. We analyzed microarray data in several ways: by determining expression changes after use of a statistical normalization algorithm, by hierarchical and k-means clustering, and by visual inspection of aligned genome images. Using these tools, we confirmed known homeostatic responses to global S limitation, which are controlled by the activators CysB and Cbl, and found that S limitation propagated into methionine metabolism, synthesis of FeS clusters, and oxidative stress. In addition, we identified several open reading frames likely to respond specifically to S availability. As predicted from the fact that the ddp operon is activated by NtrC, synthesis of cross-links between diaminopimelate residues in the murein layer was increased under N-limiting conditions, as was the proportion of tripeptides. Both of these effects may allow increased scavenging of N from the dipeptide D-alanine-D-alanine, the substrate of the Ddp system.

Sizing up metatranscriptomics

“…Similar arguments can be made regarding the assumption that protein abundance is a reliable proxy for cellular rates, as post-translational regulation of protein activity and concentration of substrate both strongly affect catalysis rates. For instance, expression of bacterial enzymes can be constitutive and therefore unlinked to environmental signals (for example, proteorhodopsin in marine Flavobacteria and SAR11, and DMSP lyases in marine roseobacters; Curson et al, 2008;Riedel et al, 2010;Steindler et al, 2011); induced proteins may outlive the resources they were synthesized to exploit (for example, in microscale substrate patches or plumes that dissipate in within minutes; Stocker et al, 2008); and proteins expressed in response to a scarcity may actually be most abundant when reaction rates are lowest (for example, ammonium or phosphate transporters during nutrient starvation; Gyaneshwar et al, 2005;Sowell et al, 2009). Even for pure cultures growing under laboratory conditions, systems biology-based analyses typically show that protein levels cannot be readily correlated with metabolic flux (Ovacik and Androulakis, 2008).…”

Lessons from Escherichia coli genes similarly regulated in response to nitrogen and sulfur limitation

“…To determine responses of a wild-type strain, we compared its transcriptional profiles under nutrient-limiting and -excess conditions and under conditions of rapid transition between the two, magnifying transcriptional responses (2). Homeostatic responses to N or S limitation entail increased assimilation of preferred N or S sources, respectively, and scavenging of alternative N or S sources from the medium (1,3). Common responses to N and S limitation apparently occur as a consequence of slow growth.…”

“…W e have previously explored global responses of Escherichia coli K12 to limitation for the nutrients nitrogen (N) or sulfur (S) on glass-slide DNA microarrays (1). To determine responses of a wild-type strain, we compared its transcriptional profiles under nutrient-limiting and -excess conditions and under conditions of rapid transition between the two, magnifying transcriptional responses (2).…”

Increased sulfate uptake by E. coli overexpressing the SLC26-related SulP protein Rv1739c from Mycobacterium tuberculosis

“…Moreover, PA1647 mRNA was increased 6-fold by growth of the cystic fibrosis P. aeruginosa isolate E601 on (sulfate-rich) mucin in sulfate-free conditions (Tralau et al 2007). Sulfate starvation experiments revealed no upregulation of the ychM gene in E. coli (Gyaneshwar et al 2005 ) or of any SulP gene product in B. subtilis (Auger et al 2002), but have not been published for M. tb. Nonetheless, the P. aeruginosa data provide evidence for a role of a Rv1739c-related polypeptide in the sulfur assimilation response, and suggest a direct or supporting role in sulfate transport function.…”

“…Thus, CysA-mediated sulfate uptake in E. coli is strongly regulated by cell density in rich medium. This density-dependence may in part reflect sulfate depletion from the medium, since sulfate starvation of E. coli altered expression of the genes encoding the ABC sulfate permease subunits (Gyaneshwar et al 2005).…”