luxS-Dependent Gene Regulation inEscherichia coliK-12 Revealed by Genomic Expression Profiling

Abstract

The bacterial quorum-sensing autoinducer 2 (AI-2) has received intense interest because the gene for its synthase, luxS, is common among a large number of bacterial species. We have identified luxS-controlled genes in Escherichia coli under two different growth conditions using DNA microarrays. Twenty-three genes were affected by luxS deletion in the presence of glucose, and 63 genes were influenced by luxS deletion in the absence of glucose. Minimal overlap among these gene sets suggests the role of luxS is condition dependent. Under the latter condition, the metE gene, the lsrACDBFG operon, and the flanking genes of the lsr operon (lsrR, lsrK, tam, and yneE) were among the most significantly induced genes by luxS. The E. coli lsr operon includes an additional gene, tam, encoding an S-adenosyl-L-methionine-dependent methyltransferase. Also, lsrR and lsrK belong to the same operon, lsrRK, which is positively regulated by the cyclic AMP receptor protein and negatively regulated by LsrR. lsrK is additionally transcribed by a promoter between lsrR and lsrK. Deletion of luxS was also shown to affect genes involved in methionine biosynthesis, methyl transfer reactions, iron uptake, and utilization of carbon. It was surprising, however, that so few genes were affected by luxS deletion in this E. coli K-12 strain under these conditions. Most of the highly induced genes are related to AI-2 production and transport. These data are consistent with the function of LuxS as an important metabolic enzyme but appear not to support the role of AI-2 as a true signal molecule for E. coli W3110 under the investigated conditions.

Escherichia coli transcription factor YncC (McbR) regulates colanic acid and biofilm formation by repressing expression of periplasmic protein YbiM (McbA)

“…Therefore, YncC binding of the promoter regions of the two most-induced genes in both glass wool and agar biofilm cells (ybiM and sfsA, Table 2), the two most-induced genes in glass wool biofilm cells (ybeL and uspF, Table 2), as well as with the one of the most repressed genes in glass wool biofilm cells (yebT, Table 3) was investigated using gel shift experiments. We were especially interested in ybiM and yebT since not only were they differentially expressed on yncC mutation but also both of them are regulated by AI-2 (DeLisa et al, 2001b;Wang et al, 2005). It was found that YncC binds to the promoter region of the ybiM gene (Figure 3a), but YncC did not bind under these conditions to the promoter regions of ybeL, sfsA, uspF and yebT (Figure 3b and data not shown).…”

LsrR-binding site recognition and regulatory characteristics in Escherichia coli AI-2 quorum sensing

“…LsrR has been revealed to be able to repress transcription from the lsrA and lsrR promoters, with deletion of lsrR resulting in maximal transcription of the lsr operon and the lsrR gene in S. typhimurium and E. coli [26,31]. Since LsrR contains a predicted HTH DNA-binding domain, it has been suggested to repress the transcription of the lsr operon and itself by directly binding to their promoters.…”

Proteome-wide Subcellular Topologies of E. coli Polypeptides Database (STEPdb)

“…The "basic" K-12 proteome comprises 3897 proteins (supplemental Table S4A). The transcripts encoding 3849 of these polypeptides (42)(43)(44)(45) as well as 3178 of these polypeptides have been detected in cells grown in LB broth (48,49).…”

“…transcribed at mRNA level) were considered to be all genes that have transcripts identified as "present" at either of four microarray datasets (42)(43)(44)(45)(46) or quantified in single cell analyses (44).…”