Biomedical subjects

Akira Hiraishi

Publications and source records attributed to Akira Hiraishi.

At least 19 recordsLinked to original sources

PubMed2006

Characterization of extracellular RNAs produced by the marine photosynthetic bacterium Rhodovulum sulfidophilum.

The marine photosynthetic bacterium Rhodovulum sulfidophilum produces extracellular nucleic acids that are involved in its flocculation. These were found to be produced concomitantly with cell growth. The RNA fraction of these extracellular nucleic acids was subjected to cDNA analysis by applying a micro RNA cloning method and found to contain mainly fully mature-sized tRNAs and fragments of 16S and 23S rRNAs. Analyses of modified bases and genes of the RNAs revealed no structural difference between the intracellular and extracellular RNAs. This is the first report of structural analyses of bacterial extracellular RNAs.

Base Sequence↗

PubMed2006

Sphingosinicella microcystinivorans gen. nov., sp. nov., a microcystin-degrading bacterium.

Three strains of bacteria that degrade the cyanobacterial hepatotoxin microcystin, Y2T, MDB2 and MDB3, were isolated from a eutrophic lake, Lake Suwa, and the Tenryu River, Japan, and characterized. These strains were aerobic and chemo-organotrophic and their cells were Gram-negative, non-spore-forming rods, motile by means of single polar flagella. Yellow-pigmented colonies were formed on nutrient agar media. The strains assimilated only citrate among the organic compounds tested as carbon sources. The G+C content of genomic DNA ranged from 63.6 to 63.7 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the new isolates formed a tight cluster within the family Sphingomonadaceae but were clearly separate from established genera of this family, e.g. Sphingomonas, Sphingobium, Novosphingobium and Sphingopyxis; sequence similarities between the new isolates and type strains from established genera ranged from 90.9 to 94.9 %. Chemotaxonomic and phenotypic data supported the conclusion that these strains were members of the family Sphingomonadaceae. The major components of the cellular fatty acids were 18 : 1omega7c (36-41 %) and 16 : 1omega7c (33-36 %). Hydroxy fatty acids were mainly 2-OH 14 : 0 (11-13 %), and 3-OH fatty acids were absent. Glycosphingolipids were detected. Ubiquinone-10 and homospermidine were present as the major quinine and polyamine, respectively. Thus, it is proposed that the three strains represent a new genus and species of the family Sphingomonadaceae with the name Sphingosinicella microcystinivorans gen. nov., sp. nov. The type strain is Y2T (= KCTC 12019T = JCM 13185T).

Bacterial Toxins↗

PubMed2006

Characterization of phototrophic purple nonsulfur bacteria forming colored microbial mats in a swine wastewater ditch.

The community structure of pink-colored microbial mats naturally occurring in a swine wastewater ditch was studied by culture-independent biomarker and molecular methods as well as by conventional cultivation methods. The wastewater in the ditch contained acetate and propionate as the major carbon nutrients. Thin-section electron microscopy revealed that the microbial mats were dominated by rod-shaped cells containing intracytoplasmic membranes of the lamellar type. Smaller numbers of oval cells with vesicular internal membranes were also found. Spectroscopic analyses of the cell extract from the biomats showed the presence of bacteriochlorophyll a and carotenoids of the spirilloxanthin series. Ubiquinone-10 was detected as the major quinone. A clone library of the photosynthetic gene, pufM, constructed from the bulk DNA of the biomats showed that all of the clones were derived from members of the genera Rhodobacter and Rhodopseudomonas. The dominant phototrophic bacteria from the microbial mats were isolated by cultivation methods and identified as being of the genera Rhodobacter and Rhodopseudomonas by studying 16S rRNA and pufM gene sequence information. Experiments of oxygen uptake with lower fatty acids revealed that the freshly collected microbial mats and the Rhodopseudomonas isolates had a wider spectrum of carbon utilization and a higher affinity for acetate than did the Rhodobacter isolates. These results demonstrate that the microbial mats were dominated by the purple nonsulfur bacteria of the genera Rhodobacter and Rhodopseudomonas, and the bioavailability of lower fatty acids in wastewater is a key factor allowing the formation of visible microbial mats with these phototrophs.

Acetic Acid↗

PubMed2005

Nocardioides aromaticivorans sp. nov., a dibenzofuran-degrading bacterium isolated from dioxin-polluted environments.

Seven strains of dibenzofuran (DF)-degrading bacteria isolated from dioxin-polluted environments were characterized. These isolates were able to grow with dibenzofuran as the sole carbon and energy source. During the growth with dibenzofuran, they produced a soluble yellow metabolite that exhibited a unique pH-dependent shift of absorption maxima. Dibenzo-p-dioxin and biphenyl were also degraded with pigment production. The isolates were strictly aerobic and chemoorganotrophic and had gram-positive, nonmotile, rod-shaped cells. Chemotaxonomic analyses showed that cells contained L,L-diaminopimeric acid in the peptidoglycan, branched-chain fatty acids as major fatty acids, and menaquinone MK-8(H4) as the sole respiratory quinone. The G + C content of the DNA of the isolates ranged from 72.0 to 72.4 mol%. The 16S rRNA gene sequences of the isolates were very similar to each other (> or = 99.8%). The phylogenetic analysis showed that the isolates formed a cluster with species of the genus Nocardioides with Nocardioides simplex and Nocardioides nitrophenolicus as their nearest neighbors. DNA-DNA hybridization studies showed that the isolates showed a hybridization level of less than 55% to any tested species of the genus Nocardioides. Based on these data, Nocardioides aromaticivorans sp. nov. is proposed for the new DF-degrading isolates. The type strain is strain H-1 (IAM 14992, JCM 11674, DSM 15131).

Actinomycetales↗

PubMed2005

Chryseobacterium shigense sp. nov., a yellow-pigmented, aerobic bacterium isolated from a lactic acid beverage.

A yellow-pigmented bacterium designated strain GUM-Kaji(T) was isolated from a lactic acid beverage. The strain had Gram-negative, non-motile, rod-shaped cells. It was strictly aerobic and chemo-organotrophic and grew at 5-30 degrees C and at pH 5-8. The major components of the non-polar and 3-hydroxy fatty acids were C15:0 iso and 3-OH-C17:0 iso, respectively. Menaquinone MK-6 was detected as the sole quinone. 16S rRNA gene sequence comparisons revealed that strain GUM-Kaji(T) is affiliated to the genus Chryseobacterium, with Chryseobacterium joostei as its phylogenetic neighbour, but there were low levels of similarity (<96%) to any established species of the genus. The G+C content of the genomic DNA was 36.6 mol%. The novel bacterium differed from any known species of Chryseobacterium in terms of a number of phenotypic properties. Thus, the name Chryseobacterium shigense sp. nov. is proposed for this novel bacterium. The type strain is strain GUM-Kaji(T) (=BAMY 1001(T)=NCIMB 14047(T)=DSM 17126(T)).

Aerobiosis↗

PubMed2005

Unique kinetic properties of phenol-degrading variovorax strains responsible for efficient trichloroethylene degradation in a chemostat enrichment culture.

A chemostat enrichment of soil bacteria growing on phenol as the sole carbon source has been shown to exhibit quite high trichloroethylene (TCE)-degrading activities. To identify the bacterial populations responsible for the high TCE-degrading activity, a multidisciplinary survey of the chemostat enrichment was conducted by employing molecular-ecological and culture-dependent approaches. Three chemostat enrichment cultures were newly developed under different phenol-loading conditions (0.25, 0.75, and 1.25 g liter(-1) day(-1)) in this study, and the TCE-degrading activities of the enrichments were measured. Among them, the enrichment at 0.75 g liter(-1) day(-1) (enrichment 0.75) expressed the highest activity. Denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA gene fragments detected a Variovorax ribotype as the strongest band in enrichment 0.75; however, it was not a major ribotype in the other samples. Bacteria were isolated from enrichment 0.75 by direct plating, and their 16S rRNA genes and genes encoding the largest subunit of phenol hydroxylase (LmPHs) were analyzed. Among the bacteria isolated, several strains were affiliated with the genus Variovorax and were shown to have high-affinity-type LmPHs. The LmPH of the Variovorax strains was also detected as the major genotype in enrichment 0.75. Kinetic analyses of phenol and TCE degradation revealed, however, that these strains exhibited quite low affinity for phenol compared to other phenol-degrading bacteria, while they showed quite high specific TCE-degrading activities and relatively high affinity for TCE. Owing to these unique kinetic traits, the Variovorax strains can obviate competitive inhibition of TCE degradation by the primary substrate of the catabolic enzyme (i.e., phenol), contributing to the high TCE-degrading activity of the chemostat enrichments. On the basis of physiological information, mechanisms accounting for the way the Variovorax population overgrew the chemostat enrichment are discussed.

Amino Acid Sequence↗

PubMed2005

Phylogenetic characterization of a polychlorinated-dioxin- dechlorinating microbial community by use of microcosm studies.

Microcosms capable of reductive dechlorination of polychlorinated dibenzo-p-dioxins/dibenzofurans (PCDD/Fs) were constructed in glass bottles by seeding them with a polluted river sediment and incubating them anaerobically with an organic medium. All of the PCDD/F congeners detected were equally reduced without the accumulation of significant amounts of less-chlorinated congeners as the intermediate or end products. Alternatively, large amounts of catechol and salicylic acid were produced in the upper aqueous phase. Thus, the dechlorination of PCDD/Fs and the oxidative degradation of the dechlorinated products seemed to take place simultaneously in the microcosm. Denaturing gel gradient electrophoresis and clone library analyses of PCR-amplified 16S rRNA genes from the microcosm showed that members of the phyla Firmicutes, Proteobacteria, and Bacteroidetes predominated. A significant number of Chloroflexi clones were also detected. Quantitative real-time PCR with specific primer sets showed that the 16S rRNA genes of a putative dechlorinator, "Dehalococcoides," and its relatives accounted for 0.1% of the total rRNA gene copies of the microcosm. Most of the clones thus obtained formed a cluster distinct from the typical "Dehalococcoides" group. Quinone profiling indicated that ubiquinones accounted for 18 to 25% of the total quinone content, suggesting the coexistence and activity of ubiquinone-containing aerobic bacteria. These results suggest that the apparent complete dechlorination of PCDD/Fs found in the microcosm was due to a combination of the dechlorinating activity of the "Dehalococcoides"-like organisms and the oxidative degradation of the dechlorinated products by aerobic bacteria with aromatic hydrocarbon dioxygenases.

Anaerobiosis↗

PubMed2005

Anaerobic degradation of aromatic compounds by magnetospirillum strains: isolation and degradation genes.

Four Magnetospirillum strains degrading toluene, phenol, benzoate, and other aromatic compounds under anaerobic conditions were isolated from denitrifying enrichment cultures. One of the isolates, toluene-degrading strain TS-6, contained genes that are homologous to those encoding benzylsuccinate synthase (Bss) and benzoyl-CoA reductase (Bcr), two key enzymes of anaerobic toluene and benzoate degradation respectively in known denitrifying bacteria. Transcription of the genes was confirmed. It was controlled by growth substrates and oxygen conditions, but bcr genes were unexpectedly expressed in aerobic cells grown on benzoate. It was confirmed that the genus Magnetospirillum represents the third genus of denitrifying bacteria capable of degrading aromatic compounds under anaerobic conditions, besides the genera Thauera and Azoarcus.

Anaerobiosis↗

PubMed2004

Phylogenetic distribution of unusual triheme to tetraheme cytochrome subunit in the reaction center complex of purple photosynthetic bacteria.

To understand the evolutionary relationship between triheme and tetraheme cytochrome subunits in the reaction center complex, genes located downstream of that coding for the M subunit of the reaction center complex (pufM) were amplified by PCR and analyzed in six established and two unidentified species of the genus Rhodovulum and five species of the genus Rhodobacter. All the Rhodovulum species tested had the pufC gene coding for the reaction-center-bound cytochrome subunit, while all the Rhodobacter species were found to have the pufX gene at the corresponding position. Analyses of the amino acid sequences of the pufC gene products showed that the cytochrome subunits of all the Rhodovulum species have three heme-binding-motifs and lack a methionine residue probably working as the sixth axial-ligand to one of the three hemes. Phylogenetic relationships among Rhodovulum species based on the pufC gene products were basically consistent with those based on 16S rRNA sequences, suggesting that the basic characteristics of the triheme cytochrome subunit have been conserved during the evolutionary process of the Rhodovulum species.

Journal Article↗

PubMed2004

Extracellular RNAs produced by a marine photosynthetic bacterium Rhodovulum sulfidophilum.

A marine photosynthetic bacterium Rhodovulum sulfidophilum secretes nucleic acids. Previously we have shown that these extracellular nucleic acids are a mixture of double-strand DNAs and single-strand RNAs. Here, we have more closely analyzed the RNA fraction of these extracellular nucleic acids. We determined the sequences of secreted RNAs. They have same sequences with parts of Rhodovulum sulfidophilum DSM 2351 16SrRNA or parts of ribosomal RNA operon of related species. Some of them were tRNAs. Interestingly, these tRNAs were mature tRNAs that had mature sizes, mature 5'-ends as well as 3'-CCA sequences. Additionally, we have found that these sequences were coded on genome, as expected. All of the secreted RNAs we detected may be parts of intracellular RNAs.

Electrophoresis, Polyacrylamide Gel↗

PubMed2004

Aerobic and anaerobic toluene degradation by a newly isolated denitrifying bacterium, Thauera sp. strain DNT-1.

A newly isolated denitrifying bacterium, Thauera sp. strain DNT-1, grew on toluene as the sole carbon and energy source under both aerobic and anaerobic conditions. When this strain was cultivated under oxygen-limiting conditions with nitrate, first toluene was degraded as oxygen was consumed, while later toluene was degraded as nitrate was reduced. Biochemical observations indicated that initial degradation of toluene occurred through a dioxygenase-mediated pathway and the benzylsuccinate pathway under aerobic and denitrifying conditions, respectively. Homologous genes for toluene dioxygenase (tod) and benzylsuccinate synthase (bss), which are the key enzymes in aerobic and anaerobic toluene degradation, respectively, were cloned from genomic DNA of strain DNT-1. The results of Northern blot analyses and real-time quantitative reverse transcriptase PCR suggested that transcription of both sets of genes was induced by toluene. In addition, the tod genes were induced under aerobic conditions, whereas the bss genes were induced under both aerobic and anaerobic conditions. On the basis of these results, it is concluded that strain DNT-1 modulates the expression of two different initial pathways of toluene degradation according to the availability of oxygen in the environment.

Aerobiosis↗

PubMed2004

Rare bacterium of new genus isolated with prolonged enrichment culture.

Dynamic change in microbial flora was monitored with an oxygen electrode. The 1st phase microorganisms, which first grew well in LB medium, were followed by the 2nd phase microorganisms, which supposedly assimilated microbial cells of the 1st phase and their metabolites. In a similar way, a change in microbial flora was observed from the 1st phase to the 4th phase in 84 hr. Based on this observation, prolonged enrichment culture was done for as long as two months to increase the ratio of existence of rare microorganisms. From these culture liquids, four slow-growing bacteria (provisionally named Shinshu-ah1, -ah2, -ah3, and -ah4), which formed scarcely visible small colonies, were isolated. Sequence analysis of their 16S rDNA showed that Shinshu-ah1 had 97% homology with Bradyrhizobium japonicum and uncultured alpha proteobacterium clone blaii 16, Shinshu-ah2 91% with Rasbo bacterium, Alpha proteobacterium 34619, Bradyrhizobium genosp. P, Afipia felis and an unidentified bacterium, Shinshu-ah3 99% with Methylobacterium mesophilicum, and Shinshu-ah4 95% with Agromyces ramosus DSM 43045. Phylogenetic study indicated that Shinshu-ah2 had a possibility to form a new family, Shinshu-ah1 a new genus, and Shinshu-ah4 a new species.

Afipia↗

PubMed2003

Complex II from phototrophic purple bacterium Rhodoferax fermentans displays rhodoquinol-fumarate reductase activity.

It has long been accepted that bacterial quinol-fumarate reductase (QFR) generally uses a low-redox-potential naphthoquinone, menaquinone (MK), as the electron donor, whereas mitochondrial QFR from facultative and anaerobic eukaryotes uses a low-redox-potential benzoquinone, rhodoquinone (RQ), as the substrate. In the present study, we purified novel complex II from the RQ-containing phototrophic purple bacterium, Rhodoferax fermentans that exhibited high rhodoquinol-fumarate reductase activity in addition to succinate-ubiquinone reductase activity. SDS/PAGE indicated that the purified R. fermentans complex II comprises four subunits of 64.0, 28.6, 18.7 and 17.5 kDa and contains 1.3 nmol heme per mg protein. Phylogenetic analysis and comparison of the deduced amino acid sequences of R. fermentans complex II with pro/eukaryotic complex II indicate that the structure and the evolutional origins of R. fermentans complex II are closer to bacterial SQR than to mitochondrial rhodoquinol-fumarate reductase. The results strongly indicate that R. fermentans complex II and mitochondrial QFR might have evolved independently, although they both utilize RQ for fumarate reduction.

Amino Acid Sequence↗

PubMed2003

Microbial community dynamics during start-up operation of flowerpot-using fed-batch reactors for composting of household biowaste.

Microbial community changes during start-up operation of flowerpot-using fed-batch reactors for composting of household biowaste were studied by quinone profiling, rRNA-targeted fluorescence in situ hybridization (FISH) and cultivation methods. Total and plate counts of bacteria and quinone contents in the reactors increased sharply with time during the start-up period. These increase patterns had two phases; the first increase occurred during 3-4 weeks from the start of waste loading and the second increase was found during the subsequent 4 weeks. The microbial biomass was temporally reduced between the two succession phases. Ubiquinones predominated at the beginning of operation but decreased sharply with time, whereas partially saturated menaquinones became predominant at the fully acclimated stage. These data indicated that the major constituents of microbial populations changed from ubiquinone-containing Proteobacteria to Actinobacteria during the period of operation. Neighbour-joining dendrograms constructed based on the quinone profile data suggested that at least one month is required to establish a stable community structure with the Actinobacteria predominating. The characteristic population shift in the start-up process was also demonstrated by FISH probing and 16S rDNA sequence comparisons of bacterial strains isolated.

Actinobacteria↗

PubMed2003

Enhygromyxa salina gen. nov., sp. nov., a slightly halophilic myxobacterium isolated from the coastal areas of Japan.

Six isolates of novel marine myxobacteria, designated strains SHK-1T, SMK-1-1, SMK-1-3, SMK-10, SKK-2, and SMP-6, were obtained from various coastal samples (mud, sands and algae) collected around Japan. All of the isolates had Gram-negative rod-shaped cells, motile by gliding and grew aerobically. They showed bacteriolytic action, fruiting body formation, and NaCl requirement for growth with an optimum concentration of 1.0-2.0% (w/v). In addition, divalent cationic components of seawater, such as Mg2+ or Ca2+, were also needed for growth. The major respiratory quinone was MK-7. The G+C content of genomic DNA ranged from 65.6 to 67.4 mol% (by HPLC). The isolates shared almost identical 16S rDNA sequences, and clustered with a recently described marine myxobacterium, Plesiocystis pacifica, as their closest relative on a phylogenetic tree (95.9-96.0% similarity). Physiological and chemotaxonomic differences between the new strains and strains of the genus Plesiocystis justify the proposal of a new genus. Therefore, we propose to classify the six isolates into a new taxon of marine myxobacteria with the name, Enhygromyxa salina gen. nov., sp. nov. The type strain is SHK-1(T) (JCM 11769(T) = DSM 15217(T) = AJ 110011(T)).

Bacterial Typing Techniques↗

PubMed2003

Study on DNA precipitation with a cationic polymer PAC (poly aluminuim chloride).

We studied on the interactions between DNA and polyaluminuimchloride (PAC) by ultraviolet spectroscopy and electron microscopy to understand the interaction between negative-charged macromolecules and PAC. Sodium ion seems to have only weak effect on the manner of DNA/PAC complex. However, acetate and phosphate anions competed against phosphate in DNA for interaction with PAC. It seems that negative macromolecule in a water system may be similar behavior with DNA under PAC.

Aluminum Chloride↗

PubMed2003

Extracellular DNA and RNA produced by a marine photosynthetic bacterium Rhodovulum sulfidophilum.

A marine photosynthetic bacterium Rhodovulum sulfidophilum secretes nucleic acids that are involved in flocculating ability. These extracellular nucleic acids have not been well characterized. Here, we have analyzed these nucleic acids and revealed that the extracellular nucleic acids are a mixture of double-stranded DNAs and single-stranded RNAs. The DNAs have sizes of more than 30 kbp and at least a part of these DNAs is probably an amplified portion of genomic DNA. The RNAs seems to be tRNA like molecules from size estimation.

DNA, Bacterial↗

PubMed2003

Plesiocystis pacifica gen. nov., sp. nov., a marine myxobacterium that contains dihydrogenated menaquinone, isolated from the Pacific coasts of Japan.

Two strains of a novel myxobacterium (designated SIR-1T and SHI-1) were isolated from Japanese coasts located in the Pacific subtropical zone. Cells of both strains were Gram-negative, rod-shaped and motile by gliding. The strains were chemoheterotrophic and strictly aerobic. They had the common characteristics associated with myxobacteria, such as bacteriolytic action and fruiting-body formation. The characteristic feature of the strains was a NaCl growth requirement with an optimum concentration of 2.0-3.0 % (w/v), comparable to that of sea water. In addition, other cationic components of sea water, such as Mg2+, Ca2+ and K+, were needed for growth. The major respiratory quinone was MK-8(H2). The cellular fatty acid profile was characterized by the predominance of iso-C15:0. Characteristic fatty acids anteiso-C16:0 and anteiso-C17:0, and a long-chain polyunsaturated fatty acid (C20:4), were also detected. The G + C content of the genomic DNA of strains SIR-1T and SHI-1 was between 69.3 and 70.0 mol% (as determined by HPLC). Strains SIR-1T and SHI-1 shared almost identical 16S rDNA sequences, and clustered with the genus Nannocystis as their closest relative upon phylogenetic analysis. However, the phylogenetic distance between the novel strains and the genus Nannocystis was large enough to warrant their different generic allocation. This finding was supported by significant phenotypic differences between the novel strains and Nannocystis. Thus, strains SIR-1T and SHI-1 represent a novel genus and species, for which the names Plesiocystis and Plesiocystis pacifica, respectively, are proposed. The type strain of the species is SIR-1T (=JCM 11591T =DSM 14875T =AJ 13960T).

Base Composition↗