Check out our New Publishers' Select for Free Articles

Archives of Microbiology (v.189, #5)

Diverse endophytic nitrogen-fixing bacteria isolated from wild rice Oryza rufipogon and description of Phytobacter diazotrophicus gen. nov. sp. nov. by Guo Xia Zhang; Gui Xiang Peng; En Tao Wang; Hui Yan; Qing Hua Yuan; Wu Zhang; Xu Lou; Hui Wu; Zhi Yuan Tan (pp. 431-439).

Twenty-three nitrogen-fixing bacteria were isolated from surface-sterilized stems and roots of wild rice Oryza rufipogon. Four clusters were defined among these bacteria by SDS-PAGE protein patterns and further confirmed by IS-PCR finger-printing analysis. Phylogenetic analysis of 16S rRNA gene sequences showed that the representative strains LS 8 and LS 18 of cluster II formed a monophyletic group sharing 94.0–97.3% similarities with defined enterobacterial species within the genera Salmonella, Citrobacter, Pantoea, Klebsiella, and Enterobacter. DNA–DNA hybridization, physiological, biochemical tests, and cell morphology also revealed that these strains could be differentiated from the related enterobacterial species. Based upon these results, we propose Phytobacter diazotrophicus gen. nov., sp. nov. to the bacterial group represented by strains LS 8 and LS 18. The type strain is LS 8^T (=DSM 17806^T = LMG 23328^T = CGMCC 1.5339^T). The DNA G+C content of strain LS 8^T is 58.6 ± 0.5 mol%.

Keywords: Phytobacter diazotrophicus ; Diazotroph; Oryza rufipogon

Characterization of a 30S ribosomal subunit assembly intermediate found in Escherichia coli cells growing with neomycin or paromomycin by Cerrone Foster; W. Scott Champney (pp. 441-449).

Neomycin and paromomycin are aminoglycoside antibiotics that specifically stimulate the misreading of mRNA by binding to the decoding site of 16S rRNA in the 30S ribosomal subunit. Recent work has shown that both antibiotics also inhibit 30S subunit assembly in Escherichia coli and Staphylococcus aureus cells. This work describes the characteristics of an assembly intermediate produced in E. coli cells grown with neomycin or paromomycin. Antibiotic treatment stimulated the accumulation of a 30S assembly precursor with a sedimentation coefficient of 21S. The particle was able to bind radio-labeled antibiotics in vivo and in vitro. Hybridization experiments showed that the 21S precursor particle contained unprocessed 16S rRNA with both 5′ and 3′ extensions. Ten 30S ribosomal proteins were found in the precursor after inhibition by each drug. In addition, cell free reconstitution assays generated a 21S particle after incubation with either aminoglycoside. This work helps to define the features of the ribosome structure as a target for antimicrobial agents and may provide information needed for the design of more effective antibiotics.

Keywords: 30S subunit; Escherichia coli ; Aminoglycosides; Ribosome assembly

Transcriptional response of Desulfovibrio vulgaris Hildenborough to oxidative stress mimicking environmental conditions by Patrícia M. Pereira; Qiang He; António V. Xavier; Jizhong Zhou; Inês A. C. Pereira; Ricardo O. Louro (pp. 451-461).

Sulfate-reducing bacteria (SRB) are anaerobes readily found in oxic–anoxic interfaces. Multiple defense pathways against oxidative conditions were identified in these organisms and proposed to be differentially expressed under different concentrations of oxygen, contributing to their ability to survive oxic conditions. In this study, Desulfovibrio vulgaris Hildenborough cells were exposed to the highest concentration of oxygen that SRB are likely to encounter in natural habitats, and the global transcriptomic response was determined. Three hundred and seven genes were responsive, with cellular roles in energy metabolism, protein fate, cell envelope and regulatory functions, including multiple genes encoding heat shock proteins, peptidases and proteins with heat shock promoters. Of the oxygen reducing mechanisms of D. vulgaris only the periplasmic hydrogen-dependent mechanism was up-regulated, involving the [NiFeSe] hydrogenase, formate dehydrogenase(s) and the Hmc membrane complex. The oxidative defense response concentrated on damage repair by metal-free enzymes. These data, together with the down-regulation of the ferric uptake regulator operon, which restricts the availability of iron, and the lack of response of the peroxide-sensing regulator operon, suggest that a major effect of this oxygen stress is the inactivation and/or degradation of multiple metalloproteins present in D. vulgaris as a consequence of oxidative damage to their metal clusters.

Keywords: Oxidative stress; Desulfovibrio ; Genomics; Metalloproteins; Fur; PerR; Thioredoxin; Hmc

Biosynthesis of rubradirin as an ansamycin antibiotic from Streptomyces achromogenes var. rubradiris NRRL3061 by Chun-Gyu Kim; Janardan Lamichhane; Kwang-Il Song; Van D. Nguyen; Dong-Hee Kim; Tae-Sung Jeong; Sung-Ho Kang; Kyoung-Wook Kim; Jyoti Maharjan; Young-Soo Hong; Jae Seon Kang; Jin-Cheol Yoo; Jung-Joon Lee; Tae-Jin Oh; Kwangkyoung Liou; Jae Kyung Sohng (pp. 463-473).

The four overlapping cosmids from the rubradirin producer, Streptomyces achromogenes var rubradiris NRRL 3061, have 58 ORFs within a 105.6 kb fragment. These ORFs harbored essential genes responsible for the formation and attachment of four distinct moieties, along with the genes associated with regulatory, resistance, and transport functions. The PKS (rubA) and glycosyltransferase (rubG2) genes were disrupted in order to demonstrate a complete elimination of rubradirin production. The rubradirin biosynthetic pathway was proposed based on the putative functions of the gene products, the functional identification of sugar genes, and the mutant strains.

Keywords: Ansamycin; Biosynthesis; Polyketide synthase; Rubradirin; Rubranitrose; Streptomyces

Quorum sensing by N-acylhomoserine lactones is not required for Aeromonas hydrophila during growth with organic particles in lake water microcosms by Katharina Styp von Rekowski; Melanie Hempel; Bodo Philipp (pp. 475-482).

It was investigated whether quorum sensing (QS) mediated by N-acylhomoserine lactones (AHLs) was important for heterotrophic bacteria from the littoral zone of the oligotrophic Lake Constance for growth with organic particles. More than 900 colonies from lake water microcosms with artificial organic aggregates consisting of autoclaved unicellular algae embedded in agarose beads were screened for AHL-production. AHL-producing bacteria of the genus Aeromonas enriched in the microcosms but AHLs could not be detected in any microcosm. To test for a potential function of AHL-mediated QS, growth experiments with the wild type and an AHL-deficient mutant of Aeromonas hydrophila in lake water microcosms were performed. Growth of both strains did not differ in single cultures and showed no mutual influence in co-cultures. In co-cultures with a competitor bacterium belonging to the Cytophaga–Flavobacterium group, growth of both A. hydrophila strains was reduced while growth of the competitor bacterium was not affected. Exogenous AHL-addition did not influence growth of the Aeromonas strains in any microcosm experiment. These results showed that AHL-mediated QS was not required for A. hydrophila during colonization and degradation of organic particles in lake water microcosms, suggesting that cell–cell signalling of heterotrophic bacteria in oligotrophic waters relies on novel signal molecules.

Keywords: Aeromonas ; Biofilm; N-Acylhomoserine lactones; Oligotrophic lakes; Quorum sensing

Structural analysis of cell wall mannan of Candida sojae, a new yeast species isolated from defatted soybean flakes by Hiroko Oyamada; Yukiko Ogawa; Nobuyuki Shibata; Yoshio Okawa; Shigeo Suzuki; Hidemitsu Kobayashi (pp. 483-490).

We investigated the structural and immunochemical characteristics of cell wall mannan obtained from Candida sojae JCM 1644, which is a new yeast species isolated from defatted soybean flakes. The results of a slide-agglutination test and of an enzyme-linked immunosorbent assay using anti-factor sera to the pathogenic Candida species indicated that the cells and the C. sojae mannan were cross-reactive to the specific anti-factor sera against Candida albicans serotype A (FAb 6) and Candida guilliermondii (FAb 9). Two-dimensional homonuclear Hartmann–Hahn analysis indicated that the mannan consisted of various linked oligomannosyl side chains containing α-1,2-, α-1,3-, α-1,6- and β-1,2-linked mannose residues. However, although the determinants of antigenic factors 6 and 9 could be not found in this mannan, branched side chains, Manβ1-2Manα1-3[Manα1-6]Manα1-(2Manα1-)n2Man and a linear α-1,6-linked polymannosyl backbone, which are cross-reacted by FAbs 6 and 9, respectively, were identified. The mannan was subjected to acetolysis in order to determine the polymerization length of the α-1,2-linked oligomannosyl residue in the side chains. The result of ¹H-nuclear magnetic resonance analysis of the released oligosaccharides showed that the remarkable regularity in the length of α-1,2-linked oligomannosyl side chains, which were previously found in mannans of other Candida species, is not observed in this mannan.

Keywords: Antigenic factor; Candida sojae ; Cell wall mannan; Nuclear magnetic resonance; Polysaccharide antigen

Characterization of a new organization of the plantaricin locus in the inducible bacteriocin-producing Lactobacillus plantarum J23 of grape must origin by Beatriz Rojo-Bezares; Yolanda Sáenz; Laura Navarro; Rufino Jiménez-Díaz; Myriam Zarazaga; Fernanda Ruiz-Larrea; Carmen Torres (pp. 491-499).

Lactobacillus plantarum J23 was previously characterized as a bacteriocin-producer-strain when it was cocultured with other lactic acid bacteria. In this work, the genetic organization of the pln locus in the J23 strain was studied and compared with those of previously described L. plantarum C11, WCFS1 and NC8 strains. A new organization of the plantaricin locus was detected in the J23 strain. The sequenced fragment (20,266 bp) comprised plnJLR, plnMNOP, plnEFI, plnGHSTUVWXY, and plNC8IF-plNC8HK-plnD operons, as well as a new region that includes three new orfs (GenBank accession number DQ323671). When the J23 pln gene sequences were compared with those included in the GenBank database, the identity of the putative encoded proteins was in the range 67.1–100%. The regulatory system and the repertoire of putative bacteriocins of the J23 pln locus presented important differences with respect to the ones of C11, WCFS1 and NC8, such as the absence of plnK and the presence of a larger plnJ gene than the previously described for the other L. plantarum strains. The pln locus in L. plantarum strains seems to be a mosaic-like structure with different modules and reorganizations that presents highly conserved regions related to transport and bacteriocin maturation and variable regions related to regulation and bacteriocin production.

Keywords: Lactobacillus plantarum ; Bacteriocin; Plantaricin; Inducible activity; pln locus

The LuxR family members GdmRI and GdmRII are positive regulators of geldanamycin biosynthesis in Streptomyces hygroscopicus 17997 by Weiqing He; Jian Lei; Yuying Liu; Yiguang Wang (pp. 501-510).

The recent sequencing of the DNA region of the geldanamycin post-polyketide synthase (PKS) modification gene clusters revealed the presence of two regulatory genes: gdmRI (2,907 bp) and gdmRII (2,766 bp). The deduced products of gdmRI and gdmRII (968 and 921 amino acid residues, respectively) were identified as homologues of the LuxR transcriptional regulatory proteins. Inactivation by gene replacement of gdmRI or gdmRII in the Streptomyces hygroscopicus 17997 genome resulted in a complete loss of geldanamycin production. Complementation by a plasmid carrying gdmRI or gdmRII restored geldanamycin production, suggesting that the products of these two regulatory genes are positive regulators that are required for geldanamycin biosynthesis. The gdmRI transcript was detected in the ΔgdmRII mutant, and the gdmRII was detected in the ΔgdmRI mutant, indicating that the two genes are transcribed independently and do not regulate each other. Time course of gene expression analysis by RT-PCR of the geldanamycin biosynthetic genes showed that the transcription of gdmRI and gdmRII correlates with that of genes involved in polyketide biosynthesis, but not with the post-PKS modification gene gdmN, whose transcription is initiated earlier. gdmRI or gdmRII gene disruptants did not transcribe the polyketide biosynthetic related genes pks, gdmF, and gdnA-O-P, but did trancribe gdmN. These results demonstrated that gdmRI and gdmRII are pathway-specific positive regulators that control the polyketide biosynthetic genes in geldanamycin biosynthsis, but not the post-PKS modification gene, gdmN.

Keywords: Geldanamycin biosynthesis; Positive regulator; Lux R family members

Two closely related pathways of nicotine catabolism in Arthrobacter nicotinovorans and Nocardioides sp. strain JS614 by Petra Ganas; Paula Sachelaru; Marius Mihasan; Gabor L. Igloi; Roderich Brandsch (pp. 511-517).

A virtually identical nicotine catabolic pathway including the heterotrimeric molybdenum enzyme nicotine and 6-hydroxy-pseudo-oxynicotine dehydrogenase, 6-hydroxy-l-nicotine oxidase, 2,6-dihydroxy-pseudo-oxynicotine hydrolase, and 2,6-dihydroxypyridine hydroxylase have been identified in A. nicotinovorans and Nocardioides sp. JS614. Enzymes catalyzing the same reactions and similar protein antigens were detected in the extracts of the two microorganisms. Nicotine blue and methylamine, two end products of nicotine catabolism were detected in the growth medium of both bacterial species. Nicotine catabolic genes are clustered on pAO1 in A. nicotinovorans, but located chromosomally in Nocardioides sp. JS614.

Keywords: Nicotine catabolism; Arthrobacter nicotinovorans ; Nocardioides sp. JS614; Catabolic plasmid pAO1; Horizontal gene transfer

Azospirillum brasilense Sp7 produces an outer-membrane lectin that specifically binds to surface-exposed extracellular polysaccharide produced by the bacterium by Paola Mora; Federico Rosconi; Laura Franco Fraguas; Susana Castro-Sowinski (pp. 519-524).

Azospirillum sp promotes the growth of many important crop plants. We demonstrated lectin binding activity in outer-membrane protein extracts of A. brasilense Sp7 by hemagglutination assays. The lectin specifically recognised the exopolysaccharide (EPS) produced by aggregated cells. Affinity chromatography using EPS-Sepharose was used to identify a 67 kDa outer-membrane lectin (OML) that recognised a binding region in the extracellular polysaccharide. Results show the specific recognition and binding between EPS and OML. The potential relationship between cell-to-cell aggregation and the OML–EPS interaction is discussed.

Keywords: Azospirillum ; Lectin; Extracellular polysaccharide

Exopolysaccharide biosynthesis is important for Mesorhizobium tianshanense: plant host interaction by Peng Wang; Zengtao Zhong; Jing Zhou; Tao Cai; Jun Zhu (pp. 525-530).

Mesorhizobium tianshanense is a nitrogen-fixing bacterium that can establish symbiotic associations with Glycyrrhiza uralensis in the form of root nodules. Nodule formation in rhizobia often requires various secreted carbohydrates. To investigate exopolysaccharide (EPS) production and function in M. tianshanense, we performed a genome-wide screen using transposon mutagenesis to identify genes involved in EPS production. We identified seven mutants that produced significantly lower amounts of EPS as well as a two-component sensor kinase/response regulator system that is involved in the activation of EPS synthesis. EPS mutants formed significantly less biofilm and displayed severely reduced nodulation capacity than wild type bacteria, suggesting that EPS synthesis can play important roles in the symbiosis process.

Keywords: Mesorhizobium tianshanense ; Exopolysaccharide production; Biofilms; Nodulation

Sections

Personal tools

Archives of Microbiology (v.189, #5)

Sections

Personal tools

Local resources

Archives of Microbiology (v.189, #5)