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The ytkD (mutTA) Gene of Bacillus subtilis Encodes a Functional Antimutator 8-Oxo-(dGTP/GTP)ase and Is under Dual Control of Sigma A and Sigma F RNA Polymerases. Martha I. Ramírez, 2004.The regulation of expression of ytkD, a gene that encodes the first functional antimutator 8-oxo-dGTPase activity of B . subtilis, was studied here . A ytkD-lacZ fusion integrated into the ytkDlocus of wild-type B . subtilis 168 revealed that this gene isexpressed during both vegetative growth and early stages of sporulation . In agreement with this result, ytkD mRNAs were detected by both Northern blotting and reverse transcription-PCR during both developmental stages . These results suggested that ytkD is transcribed by the sequential action of RNA polymerases containing the sigma factors  A
and
F,
respectively . In agreement with this suggestion, the spore-associated
expression was almost completely abolished in a sigF genetic
background but not ina B . subtilis strain lacking a
functional sigG gene . Primerextension analysis mapped
transcriptional start sites on mRNAsamples isolated from vegetative
and early sporulating cellsof B . subtilis. Inspection of the
sequences lying upstream ofthe transcription start sites revealed
the existence of typical
A-
and
F-type
promoters . These results support the conclusion that ytkD
expression is subjected to dual regulation and suggestthat the
antimutator activity of YtkD is required not only duringvegetative
growth but also during the early sporulation stagesand/or
germination of B . subtilis. While ytkD expression obeyed
a dual pattern of temporal expression, specific stress induction
of the transcription of this gene does not appear to occur,
since neither oxidative damage [following either treatment with
paraquat or hydrogen peroxide] nor mitomycin C treatment or
B
general stress inducers [sodium chloride, ethanol, or heat]affected
the levels of the gene product produced.
Contribution of Aggregation-Promoting Factor to Maintenance of Cell Shape in Lactobacillus gasseri 4B2. Ivana Jankovic, 2003.Aggregation-promoting factor (APF) was originally described as a protein involved in the conjugation and autoaggregation of Lactobacillus gasseri 4B2, whose corresponding apf gene was cloned and sequenced . In this report, we identified and sequenced an additional apf gene located in the region upstream of the previously published one . Inactivation of both apf genes was unsuccessful, indicating that APF function may be essential for the cell . Overproduction of APF proteins caused drastic alteration in the cell shape of this strain . These cells were irregular, twisted, enlarged, and tightly bound in unbreakable clumps of chains . Down-regulation of APF synthesis was achieved by cloning of the apf2 promoter region on a high-copy-number plasmid, which recruited a putative apf activator . As a consequence, the shape of the corresponding recombinant cells was elongated (filamentous) and cell division sites were no longer visible . None of the induced changes in APF production levels was clearly correlated with modifications of the aggregation phenotype . This report shows, for the first time, that APF proteins are mainly critical for L. gasseri 4B2 cell shape maintenance . Colonial Differentiation in Streptomyces coelicolor Depends on Translation of a Specific Codon within the adpA Gene. Kien T. Nguyen, 2003.We identified adpA as an araC-like regulatory gene needed for colonial morphogenesis in Streptomyces coelicolor and showed that its activity depended on a unique TTA triplet corresponding to the leucyl-tRNA gene (bldA). These findings partially explained the dependence of aerial mycelium formation on a rare tRNA that is postulated to have developmental control functions . Molecular Diversity of Sulfate-Reducing Bacteria from Two Different Continental Margin Habitats. Xueduan Liu, 2003.This study examined the natural diversity and distributions of sulfate-reducing bacteria along a natural carbon gradient extending down the shelf-slope transition zone of the eastern Pacific continental margin . Dissimilatory (bi)sulfite reductase gene sequences (dsrAB) were PCR amplified and cloned from five different sampling sites, each at a discrete depth, from two different margin systems, one off the Pacific coast of Mexico and another off the coast of Washington State . A total of 1,762 clones were recovered and evaluated by restriction fragment length polymorphism (RFLP) analysis . The majority of the gene sequences recovered showed site and depth restricted distributions; however, a limited number of gene sequences were widely distributed within and between the margin systems . Cluster analysis identified 175 unique RFLP patterns, and nucleotide sequences were determined for corresponding clones . Several different continental margin DsrA sequences clustered with those from formally characterized taxa belonging to the delta subdivision of the class Proteobacteria (Desulfobulbus propionicus, Desulfosarcina variabilis) and the Bacillus-Clostridium (Desulfotomaculum putei) divisions, although the majority of the recovered sequences were phylogenetically divergent relative to all of the other DsrA sequences available for comparison . This study revealed extensive new genetic diversity among sulfate-reducing bacteria in continental margin sedimentary habitats, which appears to be tightly coupled to slope depth, specifically carbon bioavailability .
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