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Archives of Microbiology (v.194, #2)
Comparative in silico analysis of chemotaxis system of Campylobacter fetus by Dina Fahmy; Christopher J. Day; Victoria Korolik (pp. 57-63).
Chemoreceptor and chemotaxis signal transduction cascade genes of C. fetus subsp. fetus 82-40 show high level of similarity to that in C. jejuni and appears to include sixteen diverse transducer-like protein (tlp) genes that appear similar to nine of the twelve tlp genes in the C. jejuni NCTC 11168 with a percent identity ranging from 15 to 50%. Sixteen putative C. fetus 82-40 tlp genes belong to three classes: A, B, and C, as well as an aerotaxis gene, based on their predicted structure. C. fetus subsp. fetus 82-40 chemoreceptor and chemotaxis signal transduction pathway genes have close phylogenetic relationship of chemotaxis genes between Campylobacteraceae and Helicobacteraceae.
Keywords: Chemotaxis; Chemosensory receptors; Campylobacter fetus
Corynebacterium glutamicum RNase E/G-type endoribonuclease encoded by NCgl2281 is involved in the 5′ maturation of 5S rRNA by Tomoya Maeda; Masaaki Wachi (pp. 65-73).
Corynebacterium glutamicum has one RNase E/G ortholog and one RNase J ortholog but no RNase Y. We previously reported that the C. glutamicum NCgl2281 gene encoding the RNase E/G ortholog complemented the rng::cat mutation in Escherichia coli but not the rne-1 mutation. In this study, we constructed an NCgl2281 knockout mutant and found that the mutant cells accumulated 5S rRNA precursor molecules. The processing of 16S and 23S rRNA, tRNA, and tmRNA was normal. Primer extension analysis revealed that the RNase E/G ortholog cleaved at the −1 site of the 5′ end of 5S rRNA. However, 3′ maturation was essentially unaffected. These findings showed that C. glutamicum NCgl2281 endoribonuclease is involved in the 5′ maturation of 5S rRNA. This is the first report showing the physiological function of the RNase E/G ortholog in bacteria having one RNase E/G and one RNase J but no RNase Y.
Keywords: RNase E; RNase G; rRNA maturation; Corynebacterium glutamicum
Genetic analysis of MA4079, an aldehyde dehydrogenase homolog, in Methanosarcina acetivorans by Michael Kliefoth; Julian D. Langer; Nicole Matschiavelli; Ellen Oelgeschläger; Michael Rother (pp. 75-85).
When Methanosarcina acetivorans grows on carbon monoxide (CO), it synthesizes high levels of a protein, MA4079, homologous to aldehyde dehydrogenases. To investigate the role of MA4079 in M. acetivorans, mutants lacking the encoding gene were generated and phenotypically analyzed. Loss of MA4079 had no effect on methylotrophic growth but led to complete abrogation of methylotrophic growth in the presence of even small amounts of CO, which indicated the mutant’s inability to acclimate to the presence of this toxic gas. Prolonged incubation with CO allowed the isolation of a strain in which the effect of MA4079 deletion is suppressed. The strain, designated Mu3, tolerated the presence of high CO partial pressures even better than the wild type. Immunological analysis using antisera against MA4079 suggested that it is not abundant in M. acetivorans. Comparison of proteins differentially abundant in Mu3 and the wild type revealed an elevated level of methyl-coenzyme M reductase and a decreased level of one isoform of carbon monoxide dehydrogenase/acetyl-coenzyme A synthase, which suggests that pleiotropic mutation(s) compensating for the loss of MA4079 affected catabolism. The data presented point toward a role of MA4079 to enable M. acetivorans to properly acclimate to CO.
Keywords: Methanosarcina acetivorans ; Carbon monoxide; Acclimation; Aldehyde dehydrogenase; Sensing; Regulation
Sinorhizobium fredii HH103 does not strictly require KPS and/or EPS to nodulate Glycyrrhiza uralensis, an indeterminate nodule-forming legume by Isabel Margaret-Oliver; Wang Lei; Maribel Parada; Miguel A. Rodríguez-Carvajal; Juan C. Crespo-Rivas; Ángeles Hidalgo; Antonio Gil-Serrano; Javier Moreno; Dulce N. Rodríguez-Navarro; Ana Buendía-Clavería; Javier Ollero; José E. Ruiz-Sainz; José M. Vinardell (pp. 87-102).
The Sinorhizobium fredii HH103 rkp-1 region, which is involved in capsular polysaccharide (KPS) biosynthesis, is constituted by the rkpU, rkpAGHIJ, and kpsF3 genes. Two mutants in this region affecting the rkpA (SVQ536) and rkpI (SVQ538) genes were constructed. Polyacrylamide gel electrophoresis and 1H-NMR analyses did not detect KPS in these mutants. RT-PCR experiments indicated that, most probably, the rkpAGHI genes are cotranscribed. Glycine max cultivars (cvs.) Williams and Peking inoculated with mutants SVQ536 and SVQ538 showed reduced nodulation and symptoms of nitrogen starvation. Many pseudonodules were also formed on the American cv. Williams but not on the Asiatic cv. Peking, suggesting that in the determinate nodule-forming S. fredii-soybean symbiosis, bacterial KPS might be involved in determining cultivar-strain specificity. S. fredii HH103 mutants unable to produce KPS or exopolysaccharide (EPS) also showed reduced symbiotic capacity with Glycyrrhiza uralensis, an indeterminate nodule-forming legume. A HH103 exoA-rkpH double mutant unable to produce KPS and EPS was still able to form some nitrogen-fixing nodules on G. uralensis. Thus, here we describe for the first time a Sinorhizobium mutant strain, which produces neither KPS nor EPS is able to induce the formation of functional nodules in an indeterminate nodule-forming legume.
Keywords: Sinorhizobium fredii ; rkp-1 region; KPS mutants; Glycine max ; Glycyrrhiza uralensis
Aquimarina salinaria sp. nov., a novel algicidal bacterium isolated from a saltpan by Wen-Ming Chen; Fu-Sian Sheu; Shih-Yi Sheu (pp. 103-112).
A bacterial strain designated antisso-27T, previously isolated from saltpan in Taiwan while screening for bacteria for algicidal activity, was characterized using the polyphasic taxonomic approach. Strain antisso-27T was Gram-negative, aerobic, brownish yellow colored, rod-shaped, non-flagellated and non-gliding. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain antisso-27T belonged to the genus Aquimarina within the family Flavobacteriaceae with relatively low sequence similarities of 94.0–96.6% to other valid Aquimarina spp. It contained iso-C17:0 3-OH, iso-C15:0, iso-C16:0, iso-C15:1 and iso-C15:0 3-OH as the main fatty acids and contained a menaquinone with six isoprene units (MK-6) as the major isoprenoid quinone. Major polar lipids were phosphatidylethanolamine, diphosphatidylglycerol, an uncharacterized aminolipid and five uncharacterized phospholipids. Strain antisso-27T employed direct mode of algicidal lysis to Chlorella vulgaris strain 211-31; nevertheless, it released an algicidal substance against M. aeruginosa strain MTY01. This is the first study that the Aquimarina species possesses both direct and indirect algicidal activities. On the basis of the phylogenetic and phenotypic data, strain antisso-27T should be classified as representing a novel species, for which the name A. salinaria sp. nov. is proposed. The type strain is A. salinaria antisso-27T (= BCRC 80080T = LMG 25375T).
Keywords: Aquimarina salinaria ; Algicidal activity; Polyphasic taxonomy; Phylogeny
Poseidonocella pacifica gen. nov., sp. nov. and Poseidonocella sedimentorum sp. nov., novel alphaproteobacteria from the shallow sandy sediments of the Sea of Japan by Lyudmila A. Romanenko; Naoto Tanaka; Vasily I. Svetashev; Nataliya I. Kalinovskaya (pp. 113-121).
The taxonomic study of two Gram-negative, aerobic, non-pigmented bacteria KMM 9010T and KMM 9023T isolated from a sandy sediment sample collected from the Sea of Japan seashore was performed. On the basis of the nearly complete 16S rRNA gene sequences, strains KMM 9010T and KMM 9023T clustered with the Roseobacter lineage (class Alphaproteobacteria) forming a distinct phylogenetic line adjacent to the genus Donghicola. Novel strains shared the highest sequence similarity of 96.4% to each other and lower than 96.1% similarities to other validly named genera of the class Alphaproteobacteria. In both strains, ubiquinone Q-10 was found to be the major respiratory quinone; phosphatidylcholine, phosphatidylglycerol, diphosphatidylglycerol, phosphatidic acid, and an unknown aminolipid were the major polar lipids and C18:1ω7c and 11-methyl C18:1ω7c were predominant fatty acids. The DNA G+C content was 60.5 mol% (KMM 9010T) and 65.4 mol% (KMM 9023T). Based on phenotypic properties and phylogenetic evidence, strains KMM 9010T and KMM 9023T should be classified as two novel species in a new genus, Poseidonocella gen. nov., with Poseidonocella pacifica sp. nov., the type species with the type strain KMM 9010T (= NRIC 0794T = JCM 17310T), and Poseidonocella sedimentorum sp. nov. as the second species with the type strain KMM 9023T (= NRIC 0796T = JCM 17311T).
Keywords: Class Alphaproteobacteria ; Poseidonocella gen. nov.; Poseidonocella pacifica sp. nov.; Poseidonocella sedimentorum sp. nov.; Phenotype; Phylogeny; Marine sediments
Puf operon sequences and inferred structures of light-harvesting complexes of three closely related Chromatiaceae exhibiting different absorption characteristics by Ovidiu Rücker; Anne Köhler; Beate Behammer; Katja Sichau; Jörg Overmann (pp. 123-134).
Whole cells of the purple sulfur bacterium strain 970 exhibit an unusual absorption peak at 963 nm. Its closest relatives, Thiorhodovibrio (Trv.) winogradskyi DSM6702T and strain 06511 display a bacteriochlorophyll (BChl) a absorption peak at 867 nm that is characteristic for most light-harvesting complexes 1 (LHC1) of proteobacteria. The puf operons encoding the LHC1 and reaction center proteins were amplified, cloned, and sequenced, and for the Trv. winogradskyi, strains show the common pufBALMC gene arrangement, whereas strain 970 contains a second pufBA copy downstream of pufC. Only pufB 1 A 1 is transcribed, and the corresponding mRNA fragment had an increased stability. Alignments of the deduced protein sequences showed that the LHC1 polypeptides are closely related to those of Thermochromatium (Tch.) tepidum. A deletion between αHis0 and αTrp+11, thought to be responsible for the redshifted Q y absorption in Tch. tepidum, was also detected in strain 970 and Trv. winogradskyi, whereas αLys+12 is replaced by histidine only in strain 970. Based on our structural modeling, the side chain of this αHis is predicted to be in close proximity to the BChl a, suggesting that it exerts a modulating effect on the spectral properties of the highly unusual LHC1 complex of strain 970.
Keywords: Anoxygenic photosynthesis; Photosynthesis genes; Puf genes; Light-harvesting complex; 3-D modeling; Chromatiaceae ; Purple sulfur bacteria
What is an autotroph? by Vijayasarathy Srinivasan; Harold J. Morowitz; Harald Huber (pp. 135-140).
The concept of autotrophy depends on the growth media for pure cultures supplying a single one carbon source for anabolism. Secondary carbon compounds added to the medium as chelators and/or vitamins confuse the meaning. This note suggests a clarification of definition suitable for contemporary biochemical studies of true autotrophs.
Keywords: Autotroph; Absolute autotroph; Growth media; Carbon fixation; Vitamin; EDTA; Chelator; Trace element; Transition metal; Biogenesis
A new class of adenylate kinase in methanogens is related to uridylate kinase by Laura L. Grochowski; Kaitlin Censky; Huimin Xu; Robert H. White (pp. 141-145).
The protein derived from the Methanocaldococcus jannaschii MJ0458 gene is annotated as a δ-1-pyrroline 5-carboxylate synthetase and is predicted to be related to aspartokinase and uridylate kinase. Analysis of the predicted protein sequence indicated that it is a unique kinase with few similarities to either uridylate or adenylate kinase. Here, we report that the MJ0458 gene product is a second type of archaeal adenylate kinase, AdkB. This enzyme is different from the established archaeal-specific adenylate kinase in both sequence and predicted tertiary structure.
Keywords: Archaea; Adenylate kinase; Uridylate kinase