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Phylogenetic Analysis of Polyketide Synthase I Domains from Soil Metagenomic Libraries Allows Selection of Promising Clones. Aurélien Ginolhac, 2004.The metagenomic approach provides direct access to diverse unexplored genomes, especially from uncultivated bacteria in a given environment . This diversity can conceal many new biosynthetic pathways . Type I polyketide synthases (PKSI) are modular enzymes involved in the biosynthesis of many natural products of industrial interest . Among the PKSI domains, the ketosynthase domain (KS) was used to screen a large soil metagenomic library containing more than 100,000 clones to detect those containing PKS genes . Over 60,000 clones were screened, and 139 clones containing KS domains were detected . A 700-bp fragment of the KS domain was sequenced for 40 of 139 randomly chosen clones . None of the 40 protein sequences were identical to those found in public databases, and nucleic sequences were not redundant . Phylogenetic analyses were performed on the protein sequences of three metagenomic clones to select the clones which one can predict to produce new compounds . Two PKS-positive clones do not belong to any of the 23 published PKSI included in the analysis, encouraging further analyses on these two clones identified by the selection process . Transcription of the SsrAB Regulon Is Repressed by Alkaline pH and Is Independent of PhoPQ and Magnesium Concentration. Edward A. Miao, 2002.The Salmonella pathogenicity island 2 (SPI-2) type III secretion system is expressed by intracellular bacteria and translocates effector proteins across the vacuolar membrane . Signals sensed by Salmonella enterica serovar Typhimurium in the intracellular compartment activate SPI-2 gene expression through the two-component regulatory system SsrAB . The effects of environmental and genetic signals on expression of the SsrAB-regulated gene sspH2 were examined . SsrAB-dependent activation of sspH2 was detected in the presence of both low and moderate concentrations of magnesium or calcium and at acidic and neutral pHs . The levels of expression were comparable to those detected in bacteria recovered from cultured macrophages . The induction in media at alkaline pHs (pH 7.5 and 8.0) was greatly reduced compared to the induction observed at pH 7.0 or at a lower pH, suggesting that alkaline pH represses SsrAB activation . In addition, the PhoPQ two-component system, which is also activated intracellularly, was not required for activation of SsrAB . The Escherichia coli mazEF Suicide Module Mediates Thymineless Death. Boaz Sat, 2003.In 1954, Cohen and Barner discovered that a thymine auxotrophic (thyA) mutant of Escherichia coli undergoes cell death in response to thymine starvation . This phenomenon, called thymineless death (TLD), has also been found in many other organisms, including prokaryotes and eukaryotes . Though TLD has been studied intensively, its molecular mechanism has not yet been explained . Previously we reported on the E . coli mazEF system, a regulatable chromosomal suicide module that can be triggered by various stress conditions . MazF is a stable toxin, and MazE is an unstable antitoxin . Here, we show that cell death that is mediated by the mazEF module can also be activated by thymine starvation . We found that TLD depends on E . coli mazEF and that under thymine starvation, the activity of the mazEF promoter P2 is significantly reduced . Our results, which describe thymine starvation as a trigger for a built-in death program, have implications for programmed cell death in both prokaryotes and eukaryotes .
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