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In Silico and Transcriptional Analysis of Carbohydrate Uptake Systems of Streptomyces coelicolor A3(2). Ralph Bertram, 2004.Streptomyces coelicolor is the prototype for the investigation of antibiotic-producing and differentiating actinomycetes . Assoil bacteria, streptomycetes can metabolize a wide varietyof carbon sources and are hence vested with various specificpermeases . Their activity and regulation substantially determinethe nutritional state of the cell and, therefore, influencemorphogenesis and antibiotic production . We have surveyed thegenome of S . coelicolor A3[2] to provide a thorough descriptionof the carbohydrate uptake systems . Among 81 ATP-binding cassette[ABC] permeases that are present in the genome, we found 45to encode a putative solute binding protein, an essential featurefor carbohydrate permease function . Similarity analysis allowedthe prediction of putative ABC systems for transport of cellobioseand cellotriose, alpha-glucosides, lactose, maltose, maltodextrins,ribose, sugar alcohols, xylose, and ß-xylosides . Anovel putative bifunctional protein composed of a substratebinding and a membrane-spanning moiety is likely to account for ribose or ribonucleoside uptake . Glucose may be incorporated by a proton-driven symporter of the major facilitator superfamily while a putative sodium-dependent permease of the solute-sodium symporter family may mediate uptake of galactose and a facilitator protein of the major intrinsic protein family may internalize glycerol . Of the predicted gene clusters, reverse transcriptasePCRs showed active gene expression in 8 of 11 systems . Togetherwith the previously surveyed permeases of the phosphotransferasesystem that accounts for the uptake of fructose and N-acetylglucosamine, the genome of S . coelicolor encodes at least 53 potential carbohydrate uptake systems. TtgV Bound to a Complex Operator Site Represses Transcription of the Promoter for the Multidrug and Solvent Extrusion TtgGHI Pump. María-Eugenia Guazzaroni, 2004.The TtgGHI efflux pump of Pseudomonas putida extrudes a variety of antibiotics and solvents . We show that the ttgGHI operon is transcribed in vitro and in vivo from a single promoter and not from two overlapping promoters as previously proposed . The expression of this promoter is controlled by the TtgV repressor, whose operator expands through four helical turns that overlap the –10 region of the promoter . We also show that TtgV is released from its operator on binding of effectors such as aliphatic alcohols . Mutational analysis of the ttgGHI promoter revealed that substitutions at –13, –12, and –8 yielded promoters that were unable to drive transcription whereas certain mutations at –9, –11, and –6 to –3 increased expression in vivo . The cause of the increased expression was either a decrease in the affinity of the TtgV protein for its operator or an increase in the affinity of RNA polymerase for the mutant promoters . Biogeography of the Purple Nonsulfur Bacterium Rhodopseudomonas palustris. Yasuhiro Oda, 2003.The biogeography of the purple nonsulfur bacterium Rhodopseudomonas palustris on a local scale was investigated . Thirty clones of phototrophic bacteria were isolated from each of five unevenly spaced sampling locations in freshwater marsh sediments along a linear 10-m transect, and a total of 150 clones were characterized by BOX-PCR genomic DNA fingerprinting . Cluster analysis of 150 genomic fingerprints yielded 26 distinct genotypes, and 106 clones constituted four major genotypes that were repeatedly isolated . Representatives of these four major genotypes were tentatively identified as R . palustris based on phylogentic analyses of 16S rRNA gene sequences . The differences in the genomic fingerprint patterns among the four major genotypes were accompanied by differences in phenotypic characteristics . These phenotypic differences included differences in the kinetics of carbon source use, suggesting that there may be functional differences with possible ecological significance among these clonal linages . Morisita-Horn similarity coefficients (CMH), which were used to compare the numbers of common genotypes found at pairs of sampling locations, showed that there was substantial similarity between locations that were 1 cm apart (CMH,  0.95) but there was almost no similarity between locations that were
9 m apart (CMH,
 0.25) . These calculations showed there was a gradual decrease in similarity among the five locations as a function of distance and that clones of R . palustris were lognormally distributed along the linear 10-m transect . These data indicate that natural populations of R . palustris are assemblages of genetically distinct ecotypes and that the distribution of each ecotype is patchy .
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