Spore formation by the bacterium Bacillus subtilis is an elaborate developmental process that is triggered by nutrient limitation. Here we report that cells that have entered the pathway to sporulate produce and export a killing factor and a signaling protein that act cooperatively to block sister cells from sporulating and to cause them to lyse. The sporulating cells feed on the nutrients thereby released, which allows them to keep growing rather than to complete morphogenesis. We propose that sporulation is a stress-response pathway of last resort and that B. subtilis delays a commitment to spore formation by cannibalizing its siblings.

We describe a three-protein signal-transduction pathway that governs immunity to a protein toxin involved in cannibalism by the spore-forming bacterium Bacillus subtilis. Cells of B. subtilis enter the pathway to sporulate under conditions of nutrient limitation but delay becoming committed to spore formation by killing nonsporulating siblings and feeding on the dead cells. Killing is mediated by the exported toxic protein SdpC. We report that extracellular SdpC induces the synthesis of an immunity protein, SdpI, that protects toxin-producing cells from being killed. SdpI, a polytopic membrane protein, is encoded by a two-gene operon under sporulation control that contains the gene for an autorepressor, SdpR. The autorepressor binds to and blocks the promoter for the operon. Evidence indicates that SdpI is also a signal-transduction protein that responds to the SdpC toxin by sequestering the SdpR autorepressor at the membrane. Sequestration relieves repression and stimulates synthesis of immunity protein.

The AcrAB-TolC multidrug efflux pump confers resistance to a wide variety of antibiotics and other compounds in Escherichia coli. Here we show that AcrZ (formerly named YbhT), a 49-amino-acid inner membrane protein, associates with the AcrAB-TolC complex. Copurification of AcrZ with AcrB, in the absence of both AcrA and TolC, two-hybrid assays and suppressor mutations indicate that this interaction occurs through the inner membrane protein AcrB. The highly conserved acrZ gene is coregulated with acrAB through induction by the MarA, Rob, and SoxS transcription regulators. In addition, mutants lacking AcrZ are sensitive to many, but not all, of the antibiotics transported by AcrAB-TolC. This differential antibiotic sensitivity suggests that AcrZ may enhance the ability of the AcrAB-TolC pump to export certain classes of substrates.multidrug resistance | resistance-nodulation-division | RND superfamily

More than 80 small regulatory RNAs (sRNAs) and 60 proteins of 16 to 50 amino acids (small proteins) are encoded in the Escherichia coli genome. The vast majority of the corresponding genes have no known function. We screened 125 DNA bar-coded mutants to identify novel cell envelope stress and acute acid shock phenotypes associated with deletions of genes coding for sRNAs and small proteins. Nine deletion mutants (ssrA, micA, ybaM, ryeF, yqcG, sroH, ybhT, yobF, and glmY) were sensitive to cell envelope stress and two were resistant (rybB and blr). Deletion mutants of genes coding for four small proteins (yqgB, mgrB, yobF, and yceO) were sensitive to acute acid stress. We confirmed each of these phenotypes in one-on-one competition assays against otherwise-wild-type lacZ mutant cells. A more detailed investigation of the SsrA phenotype suggests that ribosome release is critical for resistance to cell envelope stress. The bar-coded deletion collection we generated can be screened for sensitivity or resistance to virtually any stress condition.Small regulatory RNAs (sRNAs) play critical regulatory roles in all domains of life. Numerous approaches have been taken to discover sRNA-encoding genes in bacteria (reviewed in references 1 and 26), including bioinformatic searches for conservation as well as promoter and Rho-independent terminator sequences in intergenic regions. sRNAs have also been detected directly by sequencing or microarray analysis, often after size selection or coimmunoprecipitation with RNA-binding proteins. Approximately 80 sRNAs have been identified in Escherichia coli. A few sRNAs bind proteins to effect a cellular response, but the vast majority of sRNAs characterized to date act by base pairing with mRNAs (reviewed in reference 52

Historically, small proteins of less than 50 amino acids, in their final processed forms or genetically encoded as such, have been understudied. However, both serendipity and more recent focused efforts have led to the identification of a number of new small proteins in both Gramnegative and Gram-positive bacteria. Increasing evidence demonstrates that small proteins participate in a wide array of cellular processes and exhibit great diversity in their mechanisms of action, yet general principles of small protein function are emerging. This review highlights examples of small proteins that participate in cell signaling, act as antibiotics and toxins, and serve as structural proteins. We also describe additional roles for small proteins in altering membrane fluidity, acting as metal chaperones, and regulating the functions of larger proteins.