Yoshihiko Sako

Kyoto University, Kioto, Kyōto, Japan

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Publications (120)276.06 Total impact

  • [Show abstract] [Hide abstract]
    ABSTRACT: Carbon monoxide dehydrogenase-I (CODH-I) from the CO-utilizing bacterium Carboxydothermus hydrogenoformans are expected to be utilized as a part of reproducible carbon dioxide photoreduction system. However, the over-expression system for CODH-I remains to be constructed. CODH-I constitutes a hydrogenase/CODH gene cluster including a gene encoding a Ni-insertion accessory protein, CooC (cooC3). Through co-expression of CooC3, we found an over-expression system with higher activity. The Rec-CODH-I with the co-expression exhibits 8060 U/mg which was approximately threefold than that without co-expression (2270 U/mg). In addition, co-expression resulted in Ni(2+) content increase; the amount of Ni atoms of Rec-CODH-I was approximately thrice than that without co-expression.
    Bioscience Biotechnology and Biochemistry 04/2014; 78(4):582-7. · 1.27 Impact Factor
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    ABSTRACT: Bacteriophages rapidly diversify their genes through co-evolution with their hosts. We hypothesize that gene diversification of phages leads to locality in phages genome. To test this hypothesis, we investigated the genetic diversity and composition of Microcystis cyanophages using 104 sequences of Ma-LMM01-type cyanophages from two geographically distant sampling sites. The intergenetic region between the ribonucleotide reductase genes nrdA and nrdB was used as the genetic marker. This region contains the host-derived auxiliary metabolic genes nblA, an unknown function gene g04, and RNA ligase gene g03. The sequences obtained were conserved in the Ma-LMM01 gene order and contents. Although the genetic diversity of the sequences was high, it varied by gene. The genetic diversity of nblA was the lowest, suggesting that nblA is a highly significant gene that does not allow mutation. In contrast, g03 sequences had many point mutations. RNA ligase is involved in the counter-host's phage defense mechanism, suggesting that phage defense also plays an important role for rapid gene diversification. The maximum parsimony network and phylogenic analysis showed the sequences from the two sampling sites were distinct. These findings suggest Ma-LMM01-type phages rapidly diversify their genomes through co-evolution with hosts in each location and eventually provided locality of their genomes.
    Archives of Microbiology 03/2014; · 1.91 Impact Factor
  • Sotaro Kuno, Yoshihiko Sako, Takashi Yoshida
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    ABSTRACT: Clustered regularly interspaced short palindromic repeat (CRISPR) confers adaptive immunity against phages via sequence fragments (spacers) derived from mobile genetic elements (MGEs), thus serving as a memory of the past host-phage co-evolution. To understand co-evolutionary dynamics in natural settings, we examined CRISPR diversity in 94 isolates of Microcystis aeruginosa from a small eutrophic pond. Fifty-two isolates possessed the CRISPR and were classified into 22 different CRISPR-related genotypes, suggesting stable coexistence of multiple genotypes with different phage susceptibility. Seven CRISPR-related genotypes showed variation of spacers at the leader-end of the CRISPR, indicating active spacer addition from MGEs. An abundant phylotype (based on internal transcribed spacer (ITS) of rRNA gene) contained different CRISPR spacer genotypes with the same CRISPR-associated cas2 gene. These data suggest that selective phage infection and possibly plasmid transfer may contribute to maintenance of multiple genotypes of M. aeruginosa and rapid co-evolution within a host-phage combination may be driven by increased contact frequency. Forty-two isolates lacked detectable CRISPR loci. Relative abundance of the CRISPR-lacking genotypes in the population suggests that the CRISPR loss may be selected for enhanced genetic exchange.
    Microbiology 02/2014; · 3.06 Impact Factor
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    ABSTRACT: The cyanobacterium, Microcystis aeruginosa, contains a large number of defense genes ( Makarova et al., 2011); thus, it is a good model to study the co-evolution of phage and bacteria. Here, we isolated and characterized two phage-resistant M. aeruginosa mutants that came from a phage intermediate-sensitive culture. To determine the mutation conferring resistance, a protein expression pattern analysis was performed comparing phage-sensitive and -resistant sub-strains using SDS-PAGE. There were no apparent differences in expression patterns in the soluble fraction; however, a ∼90 kDa protein in the hydrophobic fraction from the phage-sensitive sub-strain was observed. Using a successive thermal asymmetric interlaced-PCR, the entire sequence encoding the protein, assigned ISP90, as well as its neighboring regions (ca. 7.8 kb) was determined. ISP90 contained no conserved domains and was predicted to be a membrane-associated protein. No mutations were detected in the nucleotide sequences coding ISP90 and diversification of ISP90 regions within this species were observed. Diversification of ISP90 regions within this species suggests a possible genomic island that may be subjected to selective pressures from phages. The ISP90 sequence involving phage resistance/sensitivity contributes to the understanding of co-evolution between M. aeruginosa and phages.
    Harmful Algae 01/2014; 34:69–75. · 2.90 Impact Factor
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    ABSTRACT: Nitric oxide reductase (NOR) catalyzes the reduction of nitric oxide to generate nitrous oxide. We recently reported on the crystal structure of a quinol-dependent NOR (qNOR) from Geobacillus stearothermophilus [Y. Matsumoto, T. Tosha, A.V. Pisliakov, T. Hino, H. Sugimoto, S. Nagano, Y. Sugita and Y. Shiro, Nat. Struct. Mol. Biol. 19 (2012) 238–246], and suggested that a water channel from the cytoplasm, which is not observed in cytochrome c-dependent NOR (cNOR), functions as a pathway transferring catalytic protons. Here, we further investigated the functional and structural properties of qNOR, and compared the findings with those for cNOR. The pH optimum for the enzymatic reaction of qNOR was in the alkaline range, whereas Pseudomonas aeruginosa cNOR showed a higher activity at an acidic pH. The considerably slower reduction rate, and a correlation of the pH dependence for enzymatic activity and the reduction rate suggest that the reduction process is the rate-determining step for the NO reduction by qNOR, while the reduction rate for cNOR was very fast and therefore is unlikely to be the rate-determining step. A close examination of the heme/non-heme iron binuclear center by resonance Raman spectroscopy indicated that qNOR has a more polar environment at the binuclear center compared with cNOR. It is plausible that a water channel enhances the accessibility of the active site to solvent water, creating more polar environment in qNOR. This structural feature could control certain properties of the active site, such as redox potential, which could explain the different catalytic properties of the two NORs. This article is part of a Special Issue entitled: 18th European Bioenergetic Conference.
    Biochimica et Biophysica Acta 01/2014; · 4.66 Impact Factor
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    ABSTRACT: Nitric oxide reductase (NOR) catalyzes the generation of nitrous oxide (N2 O) via the reductive coupling of two nitric oxide (NO) molecules at a heme/non-heme Fe center. We report herein on the structures of the reduced and ligand-bound forms of cytochrome c-dependent NOR (cNOR) from Pseudomonas aeruginosa at a resolution of 2.3-2.7 Å, to elucidate structure-function relationships in NOR, and compare them to those of cytochrome c oxidase (CCO) that is evolutionarily related to NOR. Comprehensive crystallographic refinement of the CO-bound form of cNOR suggested that a total of four atoms can be accommodated at the binuclear center. Consistent with this, binding of bulky acetaldoxime (CH3 -CH=N-OH) to the binuclear center of cNOR was confirmed by the structural analysis. Active site reduction and ligand binding in cNOR induced only ~0.5 Å increase in the heme/non-heme Fe distance, but no significant structural change in the protein. The highly localized structural change is consistent with the lack of proton-pumping activity in cNOR, because redox-coupled conformational changes are thought to be crucial for proton pumping in CCO. It also permits the rapid decomposition of cytotoxic NO in denitrification. In addition, the shorter heme/non-heme Fe distance even in the bulky ligand-bound form of cNOR (~4.5 Å) than the heme/Cu distance in CCO (~5 Å) suggests the ability of NOR to maintain two NO molecules within a short distance in the confined space of the active site, thereby facilitating N-N coupling to produce a hyponitrite intermediate for the generation of N2 O. © Proteins 2013;. © 2013 Wiley Periodicals, Inc.
    Proteins Structure Function and Bioinformatics 12/2013; · 3.34 Impact Factor
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    ABSTRACT: Physicochemical characteristics and archaeal and bacterial community structures in an iron-rich coastal hydrothermal field, where the temperature of the most active hot spot reaches above 100 ー C, were investigated to obtain fundamental information on microbes inhabiting a coastal hydrothermal field. The environmental settings of the coastal hydrothermal field were similar in some degree to those of deep-sea hydrothermal environments because of its emission of H2, CO2, and sulfide from the bottom of the hot spot. The results of clone analyses based on the 16S rRNA gene led us to speculate the presence of a chemo-synthetic microbial ecosystem, where chemolithoautotrophic thermophiles, primarily the bacterial order Aquificales, function as primary producers using H2 or sulfur compounds as their energy source and CO2 as their carbon source, and the organic compounds synthesized by them support the growth of chemoheterotrophic thermophiles, such as members of the order Thermales and the family Desulfurococcaceae. In addition, the dominance of members of the bacterial genus Herbaspirillum in the high temperature bottom layer led us to speculate the temporal formation of mesophilic zones where they can also function as primary producing or nitrogen-fixing bacteria.
    Microbes and Environments 11/2013; · 2.44 Impact Factor
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    ABSTRACT: A unique [Ni-Fe-S] cluster (C-cluster) constitutes the active center of Ni-containing carbon monoxide dehydrogenases (CODHs). His(261), which coordinates one of the Fe atoms with Cys(295), is suggested to be the only residue required for Ni coordination in the C-cluster. To evaluate the role of Cys(295), we constructed CODH-II variants. Ala substitution for the Cys(295) substitution resulted in the decrease of Ni content and didn't result in major change of Fe content. In addition, the substitution had no effect on the ability to assemble a full complement of [Fe-S] clusters. This strongly suggests Cys(295) indirectly and His(261) together affect Ni-coordination in the C-cluster.
    Biochemical and Biophysical Research Communications 10/2013; · 2.28 Impact Factor
  • Takashi Daifuku, Takashi Yoshida, Yoshihiko Sako
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    ABSTRACT: Aeropyrum spp are aerobic, heterotrophic, and hyperthermophilic marine archaea. There are two closely related Aeropyrum species, Aeropyrum camini and Aeropyrum pernix, which are isolated from geographically distinct locations. Recently, we compared their genome sequences to determine their genomic variation. They possess highly conserved small genomes, reflecting their close relationship. The entire genome similarity may result from their survival strategies in adapting to extreme environmental conditions. Meanwhile, synteny disruptions were observed in some regions including clustered regularly interspaced short palindromic repeats elements. Further, the largest portion of their non-orthologous genes were genes in the two proviral regions of A. pernix (Aeropyrum pernix spindle-shaped virus 1 and Aeropyrum pernix ovoid virus 1) or ORFans considered to be derived from viruses. Our data shows that genomic diversification of Aeropyrum spp may be substantially induced by viruses. This suggests that Aeropyrum spp may have a large pan-genome that can be extended by viruses, while each of the species shares a highly conserved small genome specializing for extreme environments.
    Mobile genetic elements. 09/2013; 3(5):e26833.
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    ABSTRACT: The increasing number of genome sequences for archaea and bacteria show their adaptation to different environmental conditions at the genomic level. Aeropyrum spp. are aerobic and hyperthermophilic archaea. Aeropyrum camini was isolated from a deep-sea hydrothermal vent, and Aeropyrum pernix was isolated from a coastal solfataric vent. To investigate the adaptation strategy in each habitat, we compared the genomes of the two species. Shared genome features were small genome size, high GC content, and a large portion of orthologous genes (86-88%). The genomes also showed high synteny. These shared features may have been derived from the small number of mobile genetic elements and the lack of a RecBCD system, a recombinational enzyme complex. In addition, the specialized physiology (aerobic and hyperthermophilic) of Aeropyrum spp. may also contribute to the entire genome similarity. Despite having stable genomes, interference of synteny occurred with two proviruses, A. pernix spindle-shaped virus 1 (APSV1) and A. pernix ovoid virus 1 (APOV1), and clustered regularly interspaced short palindromic repeats (CRISPR) elements. Spacer sequences derived from the A. camini CRISPR showed significant match with proto-spacers of the two proviruses infecting A. pernix, indicating A. camini interacted with viruses closely related to APSV1 and APOV1. Further, a significant fraction of the non-orthologous genes (41-45%) were proviral genes or ORFans probably originating from viruses. Although the genomes of A. camini and A. pernix were conserved, we observed non-synteny that was primarily attributed to virus-related elements. Our findings indicated the genomic diversification of Aeropyrum spp. are substantially caused by viruses.
    Applied and Environmental Microbiology 07/2013; · 3.95 Impact Factor
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    ABSTRACT: Elongation factor-1alpha (EF-1alpha) and elongation factor-like (EFL) proteins are functionally homologous to one another, and are core components of the eukaryotic translation machinery. The patchy distribution of the two elongation factor types across global eukaryotic phylogeny is suggestive of a 'differential loss' hypothesis that assumes that EF-1alpha and EFL were present in the most recent common ancestor of eukaryotes followed by independent differential losses of one of the two factors in the descendant lineages. To date, however, just one diatom and one fungus have been found to have both EF-1alpha and EFL (dual-EF-containing species). In this study, we characterized 35 new EF-1alpha/EFL sequences from phylogenetically diverse eukaryotes. In so doing we identified 11 previously unreported dual-EF-containing species from diverse eukaryote groups including the Stramenopiles, Apusomonadida, Goniomonadida, and Fungi. Phylogenetic analyses suggested vertical inheritance of both genes in each of the dual-EF lineages. In the dual-EF-containing species we identified, the EF-1alpha genes appeared to be highly divergent in sequence and suppressed at the transcriptional level compared to the co-occurring EFL genes. According to the known EF-1alpha/EFL distribution, the differential loss process should have occurred independently in diverse eukaryotic lineages, and more dual-EF-containing species remain unidentified. We predict that dual-EF-containing species retain the divergent EF-1alpha homologues only for a sub-set of the original functions. As the dual-EF-containing species are distantly related to each other, we propose that independent re-modelling of EF-1alpha function took place in multiple branches in the tree of eukaryotes.
    BMC Evolutionary Biology 06/2013; 13(1):131. · 3.29 Impact Factor
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    ABSTRACT: In bacteria, 70S ribosomes (consisting of 30S and 50S subunits) dimerize to form 100S ribosomes, which were first discovered in Escherichia coli. Ribosome modulation factor (RMF) and hibernation promoting factor (HPF) mediate this dimerization in stationary phase. The 100S ribosome is translationally inactive, but it dissociates into two translationally active 70S ribosomes after transfer from starvation to fresh medium. Therefore, the 100S ribosome is called the 'hibernating ribosome'. The gene encoding RMF is found widely throughout the Gammaproteobacteria class, but is not present in any other bacteria. In this study, 100S ribosome formation in six species of Gammaproteobacteria and eight species belonging to other bacterial classes was compared. There were several marked differences between the two groups: (i) Formation of 100S ribosomes was mediated by RMF and short HPF in Gammaproteobacteria species, similar to E. coli, whereas it was mediated only by long HPF in the other bacterial species; (ii) RMF/short HPF-mediated 100S ribosome formation occurred specifically in stationary phase, whereas long HPF-mediated 100S ribosome formation occurred in all growth phases; and (iii) 100S ribosomes formed by long HPF were much more stable than those formed by RMF and short HPF.
    Genes to Cells 05/2013; · 2.73 Impact Factor
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    ABSTRACT: A hydrogenogenic, carboxydotrophic marine bacterium strain KKC1(T) was isolated from a sediment core sample taken from a submerged marine caldera. Cells were non-motile 1.0-3.0 μm straight rods and Gram negative often observed with round endospores. Growth range was 55-68 °C, pH 5.2-9.3, and 0.8-14% (w/v) salinity. Optimum growth occurred at 65 °C, pH 7.0-7.5, and 2.4% salinity with a doubling time of 3.7 h. The isolate grew chemolithotrophically producing H2 from carbon monoxide (CO) oxidation with reduction of various electron acceptors, e.g., sulfite, thiosulfate, fumarate, ferric iron, and AQDS. KKC1(T) grew heterotrophically on pyruvate, lactate, fumarate, glucose, fructose, and mannose with thiosulfate as an electron acceptor. When grown mixotrophically on CO and pyruvate, C16:0 comprised almost half of the total cellular fatty acids. The G + C content was 50.6 mol%. The 16S rRNA gene sequence of KKC1(T) was most closely related to members of the genus Moorella with similarity ranging 91-89%. Based on physiological and phylogenetic novelty of the isolate, we propose the isolate as a new genus and species with the name Calderihabitans maritimus gen. nov., sp. nov.; the type strain is KKC1(T) (=DSM 26464(T) =NBRC 109353(T)).
    INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 04/2013; · 2.11 Impact Factor
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    Shigeko Kimura, Yoshihiko Sako, Takashi Yoshida
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    ABSTRACT: Viruses influence the abundance of host populations through virus-mediated host cell lysis. Viruses contribute to the generation and maintenance of host diversity, which also results in viral diversity throughout their co-evolution. Here, to determine the phage gene diversification throughout co-evolution of host and phage in a natural environment, we investigated the genetic diversity and temporal changes in Microcystis cyanophage populations using a total of 810 sequences of the Ma-LMM01-type cyanophage tail sheath gene (g91) from 2006 to 2011 in a natural pond. The sequences obtained were highly diverse and assigned to 419 different genotypes (GT1-GT419) clustered at 100% nucleotide sequence similarity. A maximum parsimony network showed the genotypes were largely divided into three sequence groups, which were dominated by major genotypes (more than 24 sequences: GT2, GT53, and GT163 in group I; GT25 in group II; and GT1 in group III). These major genotypes co-existed and oscillated throughout the sampling periods, suggesting the Microcystis-cyanophage co-evolution was partly driven by a negative frequency-dependent selection. Meanwhile, the high viral genetic diversity observed was derived from a large number of the variants of each major and moderately-frequent genotype (including 7 to 18 sequences: GT7, GT26, GT56, GT149, and GT182 in group I; GT152 in group II) (1-2 nucleotide substitutions). The variants almost always co-occurred with their origins. This manner of variant emergence suggests increased contact frequency with a host-phage population promotes rapid co-evolution in an arms race.
    Applied and Environmental Microbiology 02/2013; · 3.95 Impact Factor
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    ABSTRACT: A novel thermophilic, chemoheterotrophic, Gram-negative, multicellular filamentous bacterium, designated strain 110S(T), was isolated from an iron-rich coastal hydrothermal field in Japan. The isolate is facultatively aerobic and chemoheterotrophic. Phylogenetic analysis using 16S rRNA gene sequence nested strain 110S(T) in a novel class-level clone cluster of the phylum Chloroflexi. The isolate grew by dissimilatory iron- and nitrate-reduction under anaerobic conditions, which was the first report for these abilities in the phylum Chloroflexi. The novel isolate was capable of dissimilatory iron- and nitrate-reduction. The organism was capable of growth on oxygen, ferric iron, and nitrate as a possible electron acceptor, has a wide range of growth temperatures, and tolerates higher NaCl concentrations for growth compared to the other isolates in the phylum. Using phenotypic and phylogenetic data, strain 110S(T) (=JCM 17282(T) =NBRC 107679(T)=DSM 23922(T)=KCTC 23289(T) =ATCC BAA-2145(T)) is proposed as the type strain of a novel species in the new genus, Ardenticatena maritimus gen. nov., sp. nov. In addition, as strain 110S(T) apparently constitutes a new class of the phylum Chloroflexi with other related uncultivated clone sequences, we propose Ardenticatenia classis nov. and the subordinate taxa Ardenticatenales ord. nov. and Ardenticatenaceae fam. nov.
    INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY 02/2013; · 2.11 Impact Factor
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    ABSTRACT: Ma-LMM01 is a lytic phage infecting the toxic cyanobacterium Microcystis aeruginosa. We have investigated the transcription dynamics of host genes during phage infection using quantitative reverse transcriptase-PCR. No significant shutdown of host transcription occurred. There was no change in the transcript levels of the psbA genes [photosystem II D1 (PSII D1)], but the transcript levels of the stress response genes and the alternative σ factor gene sigB were upregulated. The transcript levels of the Calvin cycle genes and pentose phosphate pathway genes did not change or only slightly decreased, suggesting that sufficient amounts of NADPH and nucleic acid were available without redirection of the carbon flux. These results suggest that Ma-LMM01 infection induces protection of the host’s photosynthetic apparatus, conserves the host’s PSII through phycobilisome degradation using its own NblA and provides protection to the photosystem using host stress response genes. This protection of the host’s photosystem without extensive genetic manipulation may have some benefits for viruses infecting cyanobacteria that inhabit surface waters and may also be advantageous for Ma-LMM01 to avoid the host defense systems.
    Fisheries Science 01/2013; · 0.90 Impact Factor
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    ABSTRACT: The diversity of cyanobacteria and diazotrophs in the Japan Sea was investigated by analyzing sequences of cyanobacterial 16S rRNA genes and nitrogen fixation genes (nifH) from seawater sampled at depths ranging from the surface to 100 m at two stations. Of the 107 cyanobacterial 16S rRNA gene sequences obtained, 97 and three sequences were assigned to Synechococcus sub-cluster 5.1 and Prochlorococcus HL (II), respectively. Unlike other oceanic regions, at our two sampling stations the composition ratio of the sequences assignable to Synechococcus sub-cluster 5.3 was relatively high (8 %). No sequences of diazotrophic cyanobacteria were found in the cyanobacterial 16S rRNA genes. In the nifH clone library (36 sequences), ten sequences were identified as a UCYN-A group of diazotrophic cyanobacteria; the other 26 sequences (72 %) were assigned to proteobacteria. These results suggest that heterotrophic bacteria, including UCYN-A, dominate the diazotrophic community in the Japan Sea. Our study reveals the dominance of Synechococcus in cyanobacterial community and (photo)heterotrophic diazotrophs in the diazotrophic community in the Japan Sea, suggesting its unique characteristics.
    Fisheries Science 09/2012; 78(6):1293-1300. · 0.90 Impact Factor
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    ABSTRACT: Known viruses build their particles using a restricted number of redundant structural solutions. Here, we describe the Aeropyrum coil-shaped virus (ACV), of the hyperthermophilic archaeon Aeropyrum pernix, with a virion architecture not previously observed in the viral world. The nonenveloped, hollow, cylindrical virion is formed from a coiling fiber, which consists of two intertwining halves of a single circular nucleoprotein. The virus ACV is also exceptional for its genomic properties. It is the only virus with a single-stranded (ss) DNA genome among the known hyperthermophilic archaeal viruses. Moreover, the size of its circular genome, 24,893 nt, is double that of the largest known ssDNA genome, suggesting an efficient solution for keeping ssDNA intact at 90-95 °C, the optimal temperature range of A. pernix growth. The genome content of ACV is in line with its unique morphology and confirms that ACV is not closely related to any known virus.
    Proceedings of the National Academy of Sciences 07/2012; 109(33):13386-91. · 9.81 Impact Factor
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    ABSTRACT: Viruses play important roles in regulating the abundance, clonal diversity, and composition of their host populations. To assess their impact on the host populations, it is essential to understand the dynamics of virus infections in the natural environment. Cyanophages often carry host-like genes, including photosynthesis genes, which maintain host photosynthesis. This implies a diurnal pattern of cyanophage infection depending on photosynthesis. Here we investigated the infection pattern of Microcystis cyanophage by following the abundances of the Ma-LMM01-type phage tail sheath gene g91 and its transcript in a natural population. The relative g91 mRNA abundance within host cells showed a peak during the daylight hours and was lowest around midnight. The phage g91 DNA copy numbers in host cell fractions, which are predicted to indicate phage replication, increased in the afternoon, followed by an increase in the free-phage fractions. In all fractions, at least 1 of 71 g91 genotypes was observed (in tested host cell, free-phage, and RNA fractions), indicating that the replication cycle of the cyanophage (i.e., injection, transcription, replication, and release of progeny phages) was occurring. Thus, Microcystis cyanophage infection occurs in a diel cycle, which may depend on the light cycle. Additionally, our data show that the abundance of mature cyanophage produced within host cells was 1 to 2 orders of magnitude greater than that of released phages, suggesting that phage production may be higher than previously reported.
    Applied and Environmental Microbiology 06/2012; 78(16):5805-11. · 3.95 Impact Factor
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    ABSTRACT: Clustered regularly interspaced short palindromic repeats (CRISPR) confer sequence-dependent, adaptive resistance in prokaryotes against viruses and plasmids via incorporation of short sequences, called spacers, derived from foreign genetic elements. CRISPR loci are thus considered to provide records of past infections. To describe the host-parasite (i.e., cyanophages and plasmids) interactions involving the bloom-forming freshwater cyanobacterium Microcystis aeruginosa, we investigated CRISPR in four M. aeruginosa strains and in two previously sequenced genomes. The number of spacers in each locus was larger than the average among prokaryotes. All spacers were strain specific, except for a string of 11 spacers shared in two closely related strains, suggesting diversification of the loci. Using CRISPR repeat-based PCR, 24 CRISPR genotypes were identified in a natural cyanobacterial community. Among 995 unique spacers obtained, only 10 sequences showed similarity to M. aeruginosa phage Ma-LMM01. Of these, six spacers showed only silent or conservative nucleotide mutations compared to Ma-LMM01 sequences, suggesting a strategy by the cyanophage to avert CRISPR immunity dependent on nucleotide identity. These results imply that host-phage interactions can be divided into M. aeruginosa-cyanophage combinations rather than pandemics of population-wide infectious cyanophages. Spacer similarity also showed frequent exposure of M. aeruginosa to small cryptic plasmids that were observed only in a few strains. Thus, the diversification of CRISPR implies that M. aeruginosa has been challenged by diverse communities (almost entirely uncharacterized) of cyanophages and plasmids.
    Applied and Environmental Microbiology 05/2012; 78(15):5353-60. · 3.95 Impact Factor

Publication Stats

2k Citations
276.06 Total Impact Points

Institutions

  • 1997–2014
    • Kyoto University
      • • Graduate School of Agriculture / Faculty of Agriculture
      • • Division of Applied Biosciences
      Kioto, Kyōto, Japan
  • 2012
    • Kyoto Sangyo University
      • Faculty of Life Sciences
      Kioto, Kyōto, Japan
  • 2010–2011
    • Institut Pasteur
      • Department of Microbiology
      Lutetia Parisorum, Île-de-France, France
  • 2006
    • University of Alaska Fairbanks
      • Global Undersea Research Unit (GURU)
      Fairbanks, Alaska, United States
  • 2003–2006
    • Japan Agency for Marine-Earth Science Technology
      • Institute of Biogeosciences
      Йокосука, Kanagawa, Japan
  • 2005
    • Korea Research Institute of Bioscience and Biotechnology KRIBB
      • Environmental Biotechnology Laboratory
      Ansan, Gyeonggi, South Korea
    • The University of Shiga Prefecture
      • Department of Ecosystem Studies
      Hikone, Shiga-ken, Japan