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Prediction of Mechanisms of Action of Antibacterial Compounds by Gene Expression Profiling. Bernd Hutter, 2004.We have generated a database of expression profiles carrying the transcriptional responses of the model organism Bacillus subtilis following treatment with 37 well-characterized antibacterial compounds of different classes . The database was used to build a predictor for the assignment of the mechanisms of action (MoAs) of antibacterial compounds by the use of support vector machines . This predictor was able to correctly classify the MoA class for most compounds tested . Furthermore, we provide evidence that the in vivo MoA of hexachlorophene does not match the MoA predicted from in vitro data, a situation frequently faced in drug discovery . A database of this kind may facilitate the prioritization of novel antibacterial entities in drug discovery programs . Potential applications and limitations are discussed . Atypical Processing in Domain III of 23S rRNA of Rhizobium leguminosarum ATCC 10004T at a Position Homologous to an rRNA Fragmentation Site in Protozoa. Franziska Klein, 2002.For still unknown reasons, the 23S rRNA of many  -Proteobacteria shows a unique fragmentation pattern compared to other bacteria . The 23S rRNA processing involves RNase III and additional, yet unidentified enzymes . The
-proteobacterium Rhizobium leguminosarum ATCC 10004T possesses two fragmentation sites in its 23S rRNA . The first one harbors an intervening sequence in helix 9 which is cleaved by RNase III . We demonstrate that the mature 5' end of the resulting 2.6-kb rRNA fragment is generated by additional removal of helix 10 . A fraction of the 2.6-kb rRNA is further processed in domain III, giving rise to two 1.3-kb rRNA fragments . We mapped the domain III fragmentation site and found it to be at a position which has only been reported for trypanosomatid protozoa . This fragmentation site is also unique in that it lacks an intervening sequence . We found that the simultaneous occurrence of 2.6-kb and 1.3-kb rRNA fragments is not due to interoperonal sequence differences but rather reflects slow processing . The different characteristics of the two fragmentation sites in the 23S rRNA suggest that they are processed by different mechanisms . Interestingly, the amount of 2.6-kb rRNA varies during culture growth . We observed a transient increase in the relative amount of 2.6-kb rRNA fragments during the first hours after inoculation, which points to changes in the ratio of rRNA synthesis rate to domain III processing rate during the growth of a culture .
A Polysaccharide Deacetylase Gene (pdaA) Is Required for Germination and for Production of Muramic  -Lactam Residues in the Spore Cortex of Bacillus subtilis.Tatsuya Fukushima, 2002.The predicted amino acid sequence of Bacillus subtilis yfjS (renamed pdaA) exhibits high similarity to those of several polysaccharide deacetylases . ß-Galactosidase fusion experiments and results of Northern hybridization with sporulation sigma mutants indicated that the pdaA gene is transcribed by E  G RNA polymerase . pdaA-deficient spores were bright by phase-contrast microscopy, and the spores were induced to germination on the addition of L-alanine . Germination-associated spore darkening, a slow and partial decrease in absorbance, and slightly lower dipicolinic acid release compared with that by the wild-type strain were observed . In particular, the release of hexosamine-containing materials was lacking in the pdaA mutant . Muropeptide analysis indicated that the pdaA-deficient spores completely lacked muramic
-lactam . A pdaA-gfp fusion protein constructed in strain 168 and pdaA-deficient strains indicated that the protein is localized in B . subtilis spores . The biosynthetic pathway of muramic
-lactam is discussed .
Identification of rhtX and fptX, Novel Genes Encoding Proteins That Show Homology and Function in the Utilization of the Siderophores Rhizobactin 1021 by Sinorhizobium meliloti and Pyochelin by Pseudomonas aeruginosa, Respectively. Páraic Ó Cuív, 2004.Rhizobactin 1021 is a hydroxymate siderophore produced by the soil bacterium Sinorhizobium meliloti 2011 . A regulon comprising rhtA, encoding the outer membrane receptor protein for the ferrisiderophore; the biosynthesis operon rhbABCDEF; and rhrA, the Ara-C-like regulator of the receptor and biosynthesis genes has been previously described . We report the discovery of a gene, located upstream of rhbA and named rhtX (for "rhizobactin transport"), which is required, in addition to rhtA, to confer the ability to utilize rhizobactin 1021 on a strain of S . meliloti that does not naturally utilize the siderophore . Rhizobactin 1021 is structurally similar to aerobactin, which is transported in Escherichia coli via the IutA outer membrane receptor and the FhuCDB inner membrane transport system . E . coli expressing iutA and fhuCDB was found to also transport rhizobactin 1021 . We demonstrated that RhtX alone could substitute for FhuCDB to transport rhizobactin 1021 in E . coli . RhtX shows similarity to a number of uncharacterized proteins which are encoded proximal to genes that are either known to be or predicted to be involved in iron acquisition . Among these is PA4218 of Pseudomonas aeruginosa, which is located close to the gene cluster that functions in pyochelin biosynthesis and outer membrane transport . PA4218 was mutated by allelic replacement, and the mutant was found to have a pyochelin utilization-defective phenotype . It is proposed that PA4218 be named fptX (for "ferripyochelin transport") . RhtX and FptX appear to be members of a novel family of permeases that function as single-subunit transporters of siderophores . Clade-Specific 16S Ribosomal DNA Oligonucleotides Reveal the Predominance of a Single Marine Synechococcus Clade throughout a Stratified Water Column in the Red Sea. Nicholas J. Fuller, 2003.
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