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Archives of Microbiology (v.194, #3)
Expression of a polycistronic messenger RNA involved in antibiotic production in an rnc mutant of Streptomyces coelicolor by Marcha L. Gatewood; George H. Jones (pp. 147-155).
RNase III is a double strand specific endoribonuclease that is involved in the regulation of gene expression in bacteria. In Streptomyces coelicolor, an RNase III (rnc) null mutant manifests decreased ability to synthesize antibiotics, suggesting that RNase III globally regulates antibiotic production in that species. As RNase III is involved in the processing of ribosomal RNAs in S. coelicolor and other bacteria, an alternative explanation for the effects of the rnc mutation on antibiotic production would involve the formation of defective ribosomes in the absence of RNase III. Those ribosomes might be unable to translate the long polycistronic messenger RNAs known to be produced by operons containing genes for antibiotic production. To examine this possibility, we have constructed a reporter plasmid whose insert encodes an operon derived from the actinorhodin cluster of S. coelicolor. We show that an rnc null mutant of S. coelicolor is capable of translating the polycistronic message transcribed from the operon. We show further that RNA species with the mobilities expected for mature 16S and 23S ribosomal RNAs are produced in the rnc mutant even though the mutant contains higher levels of the 30S rRNA precursor than the wild-type strain.
Keywords: RNase III; Antibiotic; Streptomyces; Ribosome; Polycistronic mRNA
Crystal structure of the complex between 4-hydroxybutyrate CoA-transferase from Clostridium aminobutyricum and CoA by Sofia Macieira; Jin Zhang; Wolfgang Buckel; Albrecht Messerschmidt (pp. 157-166).
Clostridium aminobutyricum ferments 4-aminobutyrate (γ-aminobutyrate, GABA) to ammonia, acetate and butyrate via 4-hydroxybutyrate that is activated to the CoA-thioester catalyzed by 4-hydroxybutyrate CoA-transferase. Then, 4-hydroxybutyryl-CoA is dehydrated to crotonyl-CoA, which disproportionates to butyryl-CoA and acetyl-CoA. Cocrystallization of the CoA-transferase with the alternate substrate butyryl-CoA yielded crystals with non-covalently bound CoA and two water molecules at the active site. Most likely, butyryl-CoA reacted with the active site Glu238 to CoA and the mixed anhydride, which slowly hydrolyzed during crystallization. The structure of the CoA is similar but less stretched than that of the CoA-moiety of the covalent enzyme-CoA-thioester in 4-hydroxybutyrate CoA-transferase from Shewanella oneidensis. In contrast to the structures of the apo-enzyme and enzyme-CoA-thioester, the structure described here has a closed conformation, probably caused by a flip of the active site loop (residues 215–219). During turnover, the closed conformation may protect the anhydride intermediate from hydrolysis and CoA from dissociation from the enzyme. Hence, one catalytic cycle changes conformation of the enzyme four times: free enzyme—open conformation, CoA+ anhydride 1—closed, enzyme-CoA-thioester—open, CoA + anhydride-2—closed, free enzyme—open.
Keywords: Coenzyme A; Crystal structure; Enzyme complex
The genetic analysis of the flp locus of Actinobacillus pleuropneumoniae by Tingting Li; Zhuofei Xu; Tengfei Zhang; Lu Li; Huanchun Chen; Rui Zhou (pp. 167-176).
Actinobacillus pleuropneumoniae, one of the most important porcine respiratory pathogens, exhibits tight adherence to cell surfaces. The Flp pilus, which is assembled by the proteins encoded by the flp (fimbrial low-molecular-weight protein) operon, may play an important role in the bacterial adherence. In this study, the flp operons of twelve A. pleuropneumoniae serotype reference strains were sequenced and analyzed. The phenotypic diversity of fimbriae was observed using transmission electron microscopy, and the adherence ability was tested against a porcine lung epithelial cell line. The complete flp operon was identified in the reference strains of serotypes 1, 4, 5, 7, 12, and 13, consisting of 14 genes (flp1-flp2-tadV-rcpCAB-tadZABCDEFG). Fimbriae were observed protruding from the bacterial cell surfaces of these strains. In contrast, the flp promoter was absent in serotypes 2, 3, 6, 9, and 11, and the flp1 gene was truncated in serotypes 10 and 15. No pilus was observed on the surfaces of these strains. The piliated strains have higher efficiency of adhesion than the pilus-negative strains. Our data demonstrated that the Flp pili are involved in A. pleuropneumoniae adherence. The genetic diversity of the flp operons among different strains may contribute, at least in part, to the variation in virulence of Actinobacillus pleuropneumoniae.
Keywords: Actinobacillus pleuropneumoniae ; The flp operon; Adherence and colonization; Flp pili; Reference strains
Antimicrobial factor from Bacillus amyloliquefaciens inhibits Paenibacillus larvae, the causative agent of American foulbrood by Lisianne Brittes Benitez; Renata Voltolini Velho; Amanda de Souza da Motta; Jéferson Segalin; Adriano Brandelli (pp. 177-185).
Bacillus amyloliquefaciens LBM 5006 produces an antimicrobial factor active against Paenibacillus larvae, a major honeybee pathogen. The antagonistic effect and the mode of action of the antimicrobial factor were investigated. The antibacterial activity was produced starting at mid-logarithmic growth phase, reaching its maximum during the stationary phase. Exposure of cell suspensions of P. larvae to this antimicrobial resulted in loss of cell viability and reduction in optical density associated with cell lysis. Scanning electron microscopy showed damaged cell envelope and loss of protoplasmic material. The antimicrobial factor was stable for up to 80°C, but it was sensitive to proteinase K and trypsin. Mass spectrometry analysis indicates that the antimicrobial activity is associated with iturin-like peptides. The antimicrobial factor from B. amyloliquefaciens LBM 5006 showed a bactericidal effect against P. larvae cells and spores. This is the first report on iturin activity against P. larvae. This antimicrobial presents potential for use in the control of American foulbrood disease.
Keywords: Antimicrobial peptide; Bacillus ; American foulbrood disease; Iturin
Phylogenetic assessment of culture collection strains of Thiobacillus thioparus, and definitive 16S rRNA gene sequences for T. thioparus, T. denitrificans, and Halothiobacillus neapolitanus by Rich Boden; David Cleland; Peter N. Green; Yoko Katayama; Yoshihito Uchino; J. Colin Murrell; Donovan P. Kelly (pp. 187-195).
The 16S rRNA gene sequences of 12 strains of Thiobacillus thioparus held by different culture collections have been compared. A definitive sequence for the reference type strain (Starkey; ATCC 8158T) was obtained. The sequences for four examples of the Starkey type strain were essentially identical, confirming their sustained identity after passage through different laboratories. One strain (NCIMB 8454) was reassigned as a strain of Halothiobacillus neapolitanus, and a second (NCIMB 8349) was a species of Thermithiobacillus. These two strains have been renamed in their catalog by the National Collection of Industrial and Marine Bacteria. The 16S rRNA gene sequence of the type strain of Halothiobacillus neapolitanus (NCIMB 8539T) was determined and used to confirm the identity of other culture collection strains of this species. The reference sequences for the type strains of Thiobacillus thioparus and Halothiobacillus neapolitanus have been added to the online List of Prokaryotic Names with Standing in Nomenclature. Comparison of the 16S rRNA gene sequences available for strains of Thiobacillus denitrificans indicated that the sequence for the type strain (NCIMB 9548T) should always be used as the reference sequence for new and existing isolates.
Keywords: Halothiobacillus neapolitanus ; Thermithiobacillus ; Thiobacillus X ; Thiobacillus thioparus ; Thiobacillus denitrificans ; Type strains
Variations in exopolysaccharide production by Rhizobium tropici by Ann K. Staudt; Lawrence G. Wolfe; Joshua D. Shrout (pp. 197-206).
Rhizobium tropici, a legume-symbiont soil bacterium, is known for its copious production of exopolysaccharide (EPS). Many aspects of this organism’s growth and EPS production, however, remain uncharacterized, including the influence of environment and culturing conditions upon EPS. Here, we demonstrate that R. tropici EPS chemical composition and yield differ when grown with different substrates in a defined minimal medium in batch culture. Exopolysaccharide was quantified from R. tropici grown using arabinose, glucose, sucrose, mannitol, fructose, or glutamate as a sole carbon source. All tested substrates produced plenteous amounts of exopolysaccharide material. Variations in pH and carbon-to-nitrogen (C/N) ratio also resulted in assorted cell growth and exopolysaccharide production differences. We found that optimizing the C/N ratio has a greater impact upon R. tropici EPS production than upon R. tropici growth. A maximum EPS yield of 4.08 g/L was realized under optimized conditions, which is large even in comparison with other known rhizobia. We provide evidence that the chemical composition of R. tropici EPS can vary with changes to the growth environment. The composition of glucose-grown EPS contained rhamnose-linked residues that were not present in arabinose-grown EPS.
Keywords: Exopolysaccharide; EPS; Rhizobia
Identification and characterization of novel esterases from a deep-sea sediment metagenome by Xiawei Jiang; Xuewei Xu; Yingyi Huo; Yuehong Wu; Xufen Zhu; Xinqi Zhang; Min Wu (pp. 207-214).
A deep-sea sediment metagenomic library was constructed and screened for lipolytic enzymes by activity-based approach. Nine novel lipolytic enzymes were identified, and the amino acid sequences shared 56% to 84% identity to other lipolytic enzymes in the database. Phylogenetic analysis showed that these enzymes belonged to family IV lipolytic enzymes. One of the lipolytic enzymes, Est6, was successfully cloned and expressed in Escherichia coli Rosetta in a soluble form. The recombinant protein was purified by Ni-nitrilotriacetic affinity chromatography column and characterized using p-nitrophenyl esters with various chain lengths. The est6 gene consisted of 909 bp that encoded 302 amino acid residues. Est6 was most similar to a lipolytic enzyme from uncultured bacterium (ACL67845, 61% identity) isolated from the South China Sea marine sediment metagenome. The characterization of Est6 revealed that it was a cold-active esterase and exhibited the highest activity toward p-nitrophenyl butyrate (C4) at 20°C and pH 7.5.
Keywords: Deep-sea sediment; Metagenomic library; Family IV lipolytic enzymes; Cold-active
Bacillus berkeleyi sp. nov., isolated from the sea urchin Strongylocentrotus intermedius by Olga I. Nedashkovskaya; Stefanie Van Trappen; Galina M. Frolova; Paul De Vos (pp. 215-221).
A bacterial strain, designated KMM 6244T, was isolated from the sea urchin Strongylocentrotus intermedius and subjected to a polyphasic taxonomic investigation. The bacterium was found to be heterotrophic, aerobic, non-motile and spore-forming. Comparative phylogenetic analysis based on 16S rRNA gene sequencing placed the marine isolate in the genus Bacillus. The nearest neighbor of strain KMM 6244T was Bacillus decolorationis LMG 19507T with a 16S rRNA gene sequence similarity of 98.0%. Sequence similarities with the other recognized Bacillus species were less than 96.0%. The results of the DNA–DNA hybridization experiments revealed a low relatedness (37%) of the novel isolate with the type strain of B. decolorationis LMG 19507T. Strain KMM 6244T grew at 4–45°C and with 0–12% NaCl. It produced catalase and oxidase and hydrolyzed aesculin, casein, gelatin and DNA. The predominant fatty acids were anteiso-C15:0, iso-C15:0, anteiso-C17:0, C15:0, iso-C16:0 and iso-C14:0. The DNA G + C content was 39.4 mol%. A combination of phylogenetic, genotypic and phenotypic data clearly indicated that strain KMM 6244T represents a novel species in the genus Bacillus, for which the name Bacillus berkeleyi sp. nov. is proposed. The type strain is KMM 6244T (KCTC 12718T = LMG 26357T).
Keywords: Bacillus berkeleyi ; Aerobic marine spore-forming bacteria; Phylogeny; Taxonomy
Most probable number quantification of hypophosphite and phosphite oxidizing bacteria in natural aquatic and terrestrial environments by Brandee L. Stone; Andrea K. White (pp. 223-228).
Concentrations of hypophosphite and phosphite oxidizing bacteria were found to be high, relative to bacterial concentrations growing on phosphate, in sediment and soil during winter and summer seasons from 12 common terrestrial and aquatic sites using a most probable number method. The percent of total culturable bacterial concentrations that could use these reduced phosphorus compounds as a sole source of phosphorus were as follows: hypophosphite, 7–100%; phosphite, 10–67%; aminoethylphosphonate, 34–270%. The average MPN/g (±SEM) was as follows: phosphate, 6.19 × 106 (±2.40 × 106); hypophosphite, 2.61 × 106 (±1.35 × 106) phosphite, 1.91 × 106 (±1.02 × 106); aminoethylphosphonate, 3.90 × 106 (± 1.95 × 106). Relatively high concentrations of reduced phosphorus oxidizing bacteria were found in both pristine sites and sites with urban and agricultural disturbance. Concentrations of reduced phosphorus oxidizing bacteria in anoxic sediments and soil were equivalent. Our data indicate that reduced phosphorus oxidizing bacteria are abundant in the environment and provide strong evidence for the importance of bacterial P oxidation in nature.
Keywords: Reduced phosphorus oxidation; Phosphorus cycle; Nutrient cycling; Hypophosphite; Phosphite; Microbial metabolism