論文 - 鈴木　治夫

The recombination-cold region as an epidemiological marker of recombinogenic opportunistic pathogen Mycobacterium avium.

Yano H, Suzuki H, Maruyama F, Iwamoto T

BMC genomics （BMC Genomics）  20 （ 1 ） 752 2019年10月

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© 2019 The Author(s). Background: The rapid identification of lineage remains a challenge in the genotyping of clinical isolates of recombinogenic pathogens. The chromosome of Mycobacterium avium subsp. hominissuis (MAH), an agent of Mycobacterium avium complex (MAC) lung disease, is often mosaic and is composed of chromosomal segments originating from different lineages. This makes it difficult to infer the MAH lineage in a simple experimental set-up. To overcome this difficulty, we sought to identify chromosomal marker genes containing lineage-specific alleles by genome data mining. Results: We conducted genetic population structure analysis, phylogenetic analysis, and a survey of historical recombination using data from 125 global MAH isolates. Six MAH lineages (EA1, EA2, SC1, SC2, SC3, and SC4) were identified in the current dataset. One P-450 gene (locus-tag MAH-0788/MAV-0940) in the recombination-cold region was found to have multiple alleles that could discriminate five lineages. By combining the information about allele type from one additional gene, the six MAH lineages as well as other M. avium subspecies were distinguishable. A recombination-cold region of 116 kb contains an insertion hotspot and is flanked by a mammalian cell-entry protein operon where allelic variants have previously been reported to occur. Hence, we speculate that the acquisition of lineage-or strain-specific insertions has introduced homology breaks in the chromosome, thereby reducing the chance of interlineage recombination. Conclusions: The allele types of the newly identified marker genes can be used to predict major lineages of M. avium. The single nucleotide polymorphism typing approach targeting multiallelic loci in recombination-cold regions will facilitate the epidemiological study of MAC, and may also be useful for equivalent studies of other nontuberculous mycobacteria potentially carrying mosaic genomes.

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Large-scale Molecular Evolutionary Analysis Uncovers a Variety of Polynucleotide Kinase Clp1 Family Proteins in the Three Domains of Life.

Saito M, Sato A, Nagata S, Tamaki S, Tomita M, Suzuki H, Kanai A

Genome biology and evolution 2019年09月

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Genomic analysis of Pseudomonas sp. Strain SCT, an iodate-reducing bacterium isolated from marine sediment, reveals a possible use for bioremediation

Harada M., Ito K., Nakajima N., Yamamura S., Tomita M., Suzuki H., Amachi S.

G3: Genes, Genomes, Genetics （G3: Genes, Genomes, Genetics）  9 （ 5 ） 1321 - 1329 2019年05月

研究論文（学術雑誌）, 査読有り

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Copyright © 2019 Harada et al. Strain SCT is an iodate-reducing bacterium isolated from marine sediment in Kanagawa Prefecture, Japan. In this study, we determined the draft genome sequence of strain SCT and compared it to complete genome sequences of other closely related bacteria, including Pseudomonas stutzeri. A phylogeny inferred from concatenation of core genes revealed that strain SCT was closely related to marine isolates of P. stutzeri. Genes present in the SCT genome but absent from the other analyzed P. stutzeri genomes comprised clusters corresponding to putative prophage regions and possible operons. They included pil genes, which encode type IV pili for natural transformation; the mer operon, which encodes resistance systems for mercury; and the pst operon, which encodes a Pi-specific transport system for phosphate uptake. We found that strain SCT had more prophage-like genes than the other P. stutzeri strains and that the majority (70%) of them were SCT strain-specific. These genes, encoded on distinct prophage regions, may have been acquired after branching from a common ancestor following independent phage transfer events. Thus, the genome sequence of Pseudomonas sp. strain SCT can provide detailed insights into its metabolic potential and the evolution of genetic elements associated with its unique phenotype.

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Comparative genomics of Bacteria commonly identified in the built environment

Merino N., Zhang S., Tomita M., Suzuki H.

BMC Genomics （BMC Genomics）  20 （ 1 ） 92 2019年01月

研究論文（学術雑誌）, 査読有り

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© 2019 The Author(s). Background: The microbial community of the built environment (BE) can impact the lives of people and has been studied for a variety of indoor, outdoor, underground, and extreme locations. Thus far, these microorganisms have mainly been investigated by culture-based methods or amplicon sequencing. However, both methods have limitations, complicating multi-study comparisons and limiting the knowledge gained regarding in-situ microbial lifestyles. A greater understanding of BE microorganisms can be achieved through basic information derived from the complete genome. Here, we investigate the level of diversity and genomic features (genome size, GC content, replication strand skew, and codon usage bias) from complete genomes of bacteria commonly identified in the BE, providing a first step towards understanding these bacterial lifestyles. Results: Here, we selected bacterial genera commonly identified in the BE (or "Common BE genomes") and compared them against other prokaryotic genera ("Other genomes"). The "Common BE genomes" were identified in various climates and in indoor, outdoor, underground, or extreme built environments. The diversity level of the 16S rRNA varied greatly between genera. The genome size, GC content and GC skew strength of the "Common BE genomes" were statistically larger than those of the "Other genomes" but were not practically significant. In contrast, the strength of selected codon usage bias (S value) was statistically higher with a large effect size in the "Common BE genomes" compared to the "Other genomes." Conclusion: Of the four genomic features tested, the S value could play a more important role in understanding the lifestyles of bacteria living in the BE. This parameter could be indicative of bacterial growth rates, gene expression, and other factors, potentially affected by BE growth conditions (e.g., temperature, humidity, and nutrients). However, further experimental evidence, species-level BE studies, and classification by BE location is needed to define the relationship between genomic features and the lifestyles of BE bacteria more robustly.

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Reconsidering plasmid maintenance factors for computational plasmid design

Yano H., Shintani M., Tomita M., Suzuki H., Oshima T.

Computational and Structural Biotechnology Journal （Computational and Structural Biotechnology Journal）  17   70 - 81 2019年01月

研究論文（学術雑誌）, 査読有り

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© 2018 The Authors Plasmids are genetic parasites of microorganisms. The genomes of naturally occurring plasmids are expected to be polished via natural selection to achieve long-term persistence in the microbial cell population. However, plasmid genomes are extremely diverse, and the rules governing plasmid genomes are not fully understood. Therefore, computationally designing plasmid genomes optimized for model and nonmodel organisms remains challenging. Here, we summarize current knowledge of the plasmid genome organization and the factors that can affect plasmid persistence, with the aim of constructing synthetic plasmids for use in gram-negative bacteria. Then, we introduce publicly available resources, plasmid data, and bioinformatics tools that are useful for computational plasmid design.

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Identification of novel Legionella genes required for endosymbiosis in Paramecium based on comparative genome analysis with Holospora spp.

Watanabe K, Suzuki H, Nishida T, Mishima M, Tachibana M, Fujishima M, Shimizu T, Watarai M

FEMS microbiology ecology （FEMS microbiology ecology）  94 （ 11 ）  2018年11月

研究論文（学術雑誌）, 査読有り,  ISSN  0168-6496

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The relationship between Legionella and protist hosts has a huge impact when considering the infectious risk in humans because it facilitates the long-term replication and survival of Legionella in the environment. The ciliate Paramecium is considered to be a protist host for Legionella in natural environments, but the details of their endosymbiosis are largely unknown. In this study, we determined candidate Legionella pneumophila genes that are likely to be involved in the establishment of endosymbiosis in Paramecium caudatum by comparing the genomes of Legionella spp. and Holospora spp. that are obligate endosymbiotic bacteria in Paramecium spp. Among the candidate genes, each single deletion mutant for five genes (lpg0492, lpg0522, lpg0523, lpg2141 and lpg2398) failed to establish endosymbiosis in P. caudatum despite showing intracellular growth in human macrophages. The mutants exhibited no characteristic changes in terms of their morphology, multiplication rate or capacity for modulating the phagosomes in which they were contained, but their resistance to lysozyme decreased significantly. This study provides insights into novel factors required by L. pneumophila for endosymbiosis in P. caudatum, and suggests that endosymbiotic organisms within conspecific hosts may have shared genes related to effective endosymbiosis establishment.

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Collaborative environmental DNA sampling from petal surfaces of flowering cherry Cerasus × yedoensis ‘Somei-yoshino’ across the Japanese archipelago

Ohta T., Kawashima T., Shinozaki N., Dobashi A., Hiraoka S., Hoshino T., Kanno K., Kataoka T., Kawashima S., Matsui M., Nemoto W., Nishijima S., Suganuma N., Suzuki H., Taguchi Y., Takenaka Y., Tanigawa Y., Tsuneyoshi M., Yoshitake K., Sato Y., Yamashita R., Arakawa K., Iwasaki W.

Journal of Plant Research （Journal of Plant Research）  131 （ 4 ） 709 - 717 2018年07月

研究論文（学術雑誌）, 査読有り,  ISSN  09189440

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© 2018, The Botanical Society of Japan and Springer Japan KK, part of Springer Nature. Recent studies have shown that environmental DNA is found almost everywhere. Flower petal surfaces are an attractive tissue to use for investigation of the dispersal of environmental DNA in nature as they are isolated from the external environment until the bud opens and only then can the petal surface accumulate environmental DNA. Here, we performed a crowdsourced experiment, the “Ohanami Project”, to obtain environmental DNA samples from petal surfaces of Cerasus × yedoensis ‘Somei-yoshino’ across the Japanese archipelago during spring 2015. C. × yedoensis is the most popular garden cherry species in Japan and clones of this cultivar bloom simultaneously every spring. Data collection spanned almost every prefecture and totaled 577 DNA samples from 149 collaborators. Preliminary amplicon-sequencing analysis showed the rapid attachment of environmental DNA onto the petal surfaces. Notably, we found DNA of other common plant species in samples obtained from a wide distribution; this DNA likely originated from the pollen of the Japanese cedar. Our analysis supports our belief that petal surfaces after blossoming are a promising target to reveal the dynamics of environmental DNA in nature. The success of our experiment also shows that crowdsourced environmental DNA analyses have considerable value in ecological studies.

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Focusing the diversity of Gardnerella vaginalis through the lens of ecotypes

Cornejo O., Hickey R., Suzuki H., Forney L.

Evolutionary Applications （Evolutionary Applications）  11 （ 3 ） 312 - 324 2018年03月

研究論文（学術雑誌）, 査読有り,  ISSN  17524563

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© 2017 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd Gardnerella vaginalis has long been associated with bacterial vaginosis, a condition that increases the risk of women to preterm birth, sexually transmitted infections, and other adverse sequelae. However, G. vaginalis is also commonly found in healthy asymptomatic women of all ages. This raises the question if genetic differences among strains might distinguish potentially pathogenic from commensal strains. To disentangle the diversity of G. vaginalis, we invoked the concept of ecotypes—lineages of genetically and ecologically distinct strains within a named species—to better understand their evolutionary history and identify functional characteristics. We compared the genomes of G. vaginalis to six species in the closely related Bifidobacterium genus and found that G. vaginalis has a large accessory genome relative to Bifidobacterium, including many unique genes possibly involved in metabolism, drug resistance, and virulence. We then performed a comparative genomic analysis of 35 strains of G. vaginalis to infer a phylogeny based on the combined analysis of the core genome, using nucleotide substitution models, and the accessory genome, using gene gain/loss models. With the inferred tree topology, we performed comparisons of functional gene content among lineages that diverged at varying depths in the phylogeny and found significant differences in the representation of genes putatively involved in pathogenicity. Our functional enrichment analysis suggests that some lineages of G. vaginalis may possess enhanced pathogenic capabilities, including genes involved in mucus degradation like sialidases, while others may be commensal strains, lacking many of these pathogenic capabilities. The combined phylogenetic evidence and functional enrichment analysis allowed us to identify distinct ecotypes that have evolved in G. vaginalis as the result of the differential gene gain/loss for specific functions, including the capability to cause disease. We finally discuss how this analysis framework could be used to gain insight into the etiology of bacterial vaginosis and improve diagnosis.

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Genomic Analysis of <i>Rhodococcus</i> sp. Br-6, a Bromate Reducing Bacterium Isolated From Soil in Chiba, Japan.

Ito K, Harada M, Nakajima N, Yamamura S, Tomita M, Suzuki H, Amachi S

Journal of genomics 6   122 - 126 2018年

研究論文（学術雑誌）, 査読有り

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Comparative genomic analysis of <i>Clostridium difficile</i> ribotype 027 strains including the newly sequenced strain NCKUH-21 isolated from a patient in Taiwan.

Suzuki H, Tomita M, Tsai PJ, Ko WC, Hung YP, Huang IH, Chen JW

Gut pathogens （Gut Pathogens）  9 （ 1 ） 70 2017年

研究論文（学術雑誌）, 査読有り

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© 2017 The Author(s). Background: Clostridium difficile is a Gram-positive anaerobe and the leading cause of antibiotic-associated diarrhea worldwide. The emergence of ribotype 027 (RT027) strains is associated with increased incidence of infection and mortality. To further understand the relationship between C. difficile NCKUH-21, a RT027 strain isolated from a patient in Taiwan, and other RT027 strains, we performed whole-genome shotgun sequencing on NCKUH-21 and comparative genomic analyses. Results: The genome size, G+C content, and gene number for the NCKUH-21 strain were determined to be similar to those for other C. difficile strains. The core genome phylogeny indicated that the five RT027 strains R20291, CD196, NCKUH-21, BI1, and 2007855 formed a clade. A pathogenicity locus, tcdR-tcdB-tcdE-orf-tcdA-tcdC, was conserved in the genome. A genomic region highly similar to the Clostridium phage $$\upvarphi$$ φ CD38-2 was present in the NCKUH-21 strain but absent in the other RT027 strains and designated as the prophage $$\upvarphi$$ φ NCKUH-21. The prophage $$\upvarphi$$ φ NCKUH-21 genes were significantly higher in G+C content than the other genes in the NCKUH-21 genome, indicating that the prophage does not match the base composition of the host genome. Conclusions: This is the first whole-genome analysis of a RT027 C. difficile strain isolated from Taiwan. Due to the high identity with $$\upvarphi$$ φ CD38-2, the prophage identified in the NCKUH-21 genome has the potential to regulate toxin production. These results provide important information for understanding the pathogenicity of RT027 C. difficile in Taiwan.

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Draft Genome Sequence of <i>Roseovarius</i> sp. A-2, an Iodide-Oxidizing Bacterium Isolated from Natural Gas Brine Water, Chiba, Japan.

Yuliana T, Nakajima N, Yamamura S, Tomita M, Suzuki H, Amachi S

Journal of genomics 5   51 - 53 2017年

研究論文（学術雑誌）, 査読有り

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Draft Genome Sequence of Arenibacter sp. Strain C-21, an Iodine-Accumulating Bacterium Isolated from Surface Marine Sediment.

Ito K, Nakajima N, Yamamura S, Tomita M, Suzuki H, Amachi S

Genome announcements （Genome Announcements）  4 （ 5 ）  2016年10月

研究論文（学術雑誌）, 査読有り

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© 2016 Ito et al. Arenibacter sp. strain C-21, isolated from surface marine sediment of Japan, accumulates iodine in the presence of glucose and iodide (I-). We report here the draft genome sequence of this strain to provide insight into the molecular mechanism underlying its iodine-accumulating ability.

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Draft Genome Sequences of 37 Salmonella enterica Strains Isolated from Poultry Sources in Nigeria.

Useh NM, Ngbede EO, Akange N, Thomas M, Foley A, Keena MC, Nelson E, Christopher-Hennings J, Tomita M, Suzuki H, Scaria J

Genome announcements （Genome Announcements）  4 （ 3 ）  2016年05月

研究論文（学術雑誌）, 査読有り

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© 2016 Useh et al. Here, we report the availability of draft genomes of several Salmonella serotypes, isolated from poultry sources from Nigeria. These genomes will help to further understand the biological diversity of S. enterica and will serve as references in microbial trace-back studies to improve food safety.

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Draft Genome Sequence of Caedibacter varicaedens, a Kappa Killer Endosymbiont Bacterium of the Ciliate Paramecium biaurelia.

Suzuki H, Dapper AL, Jackson CE, Lee H, Pejaver V, Doak TG, Lynch M, Preer JR Jr

Genome announcements （Genome Announcements）  3 （ 6 ）  2015年11月

研究論文（学術雑誌）, 査読有り

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© 2015 Suzuki et al. Caedibacter varicaedens is a kappa killer endosymbiont bacterium of the ciliate Paramecium biaurelia. Here, we present the draft genome sequence of C. varicaedens.

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Analysis of amino acid and codon usage in Paramecium bursaria.

Dohra H, Fujishima M, Suzuki H

FEBS letters （FEBS Letters）  589 （ 20 Pt B ） 3113 - 8 2015年10月

研究論文（学術雑誌）, 査読有り,  ISSN  0014-5793

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© 2015 Federation of European Biochemical Societies. The ciliate Paramecium bursaria harbors the green-alga Chlorella symbionts. We reassembled the P. bursaria transcriptome to minimize falsely fused transcripts, and investigated amino acid and codon usage using the transcriptome data. Surface proteins preferentially use smaller amino acid residues like cysteine. Unusual synonymous codon and amino acid usage in highly expressed genes can reflect a balance between translational selection and other factors. A correlation of gene expression level with synonymous codon or amino acid usage is emphasized in genes down-regulated in symbiont-bearing cells compared to symbiont-free cells. Our results imply that the selection is associated with P. bursaria-Chlorella symbiosis.

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Comparative genomic and phenomic analysis of Clostridium difficile and Clostridium sordellii, two related pathogens with differing host tissue preference.

Scaria J, Suzuki H, Ptak CP, Chen JW, Zhu Y, Guo XK, Chang YF

BMC genomics （BMC Genomics）  16 （ 1 ） 448 2015年06月

研究論文（学術雑誌）, 査読有り

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© 2015 Scaria et al. Background: Clostridium difficile and C. sordellii are two anaerobic, spore forming, gram positive pathogens with a broad host range and the ability to cause lethal infections. Despite strong similarities between the two Clostridial strains, differences in their host tissue preference place C. difficile infections in the gastrointestinal tract and C. sordellii infections in soft tissues. Results: In this study, to improve our understanding of C. sordellii and C. difficile virulence and pathogenesis, we have performed a comparative genomic and phenomic analysis of the two. The global phenomes of C. difficile and C. sordellii were compared using Biolog Phenotype microarrays. When compared to C. difficile, C. sordellii was found to better utilize more complex sources of carbon and nitrogen, including peptides. Phenotype microarray comparison also revealed that C. sordellii was better able to grow in acidic pH conditions. Using next generation sequencing technology, we determined the draft genome of C. sordellii strain 8483 and performed comparative genome analysis with C. difficile and other Clostridial genomes. Comparative genome analysis revealed the presence of several enzymes, including the urease gene cluster, specific to the C. sordellii genome that confer the ability of expanded peptide utilization and survival in acidic pH. Conclusions: The identified phenotypes of C. sordellii might be important in causing wound and vaginal infections respectively. Proteins involved in the metabolic differences between C. sordellii and C. difficile should be targets for further studies aimed at understanding C. difficile and C. sordellii infection site specificity and pathogenesis.

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Draft Genome Sequences of Five Legionella pneumophila Strains Isolated from Environmental Water Samples.

Watanabe K, Suzuki H, Nakao R, Shimizu T, Watarai M

Genome announcements （Genome Announcements）  3 （ 3 ）  2015年05月

研究論文（学術雑誌）, 査読有り

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© 2015 Watanabe et al. Legionella pneumophila is the causative agent of legionellosis. Here, we report the draft genome sequences of five L. pneumophila strains, Bnt314, Ofk308, Twr292, Ymg289, and Ymt294, isolated from environmental water samples. Comparative analyses of these genomes may reveal the survival mechanisms and virulence of L. pneumophila in the natural environment.

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Draft Genome Sequence of Anaeromyxobacter sp. Strain PSR-1, an Arsenate-Respiring Bacterium Isolated from Arsenic-Contaminated Soil.

Tonomura M, Ehara A, Suzuki H, Amachi S

Genome announcements （Genome Announcements）  3 （ 3 ）  2015年05月

研究論文（学術雑誌）, 査読有り

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© 2015 Tonomura et al. Here, we report a draft genome sequence of Anaeromyxobacter sp. strain PSR-1, an arsenate-respiring bacterium isolated from arsenic-contaminated soil. It contained three distinct arsenic resistance gene clusters (ars operons), while no respiratory arsenate reductase gene (arr) was identified.

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Draft Genome Sequence of Pseudomonas sp. nov. H2.

Loftie-Eaton W, Suzuki H, Bashford K, Heuer H, Stragier P, De Vos P, Settles ML, Top EM

Genome announcements （Genome Announcements）  3 （ 2 ）  2015年04月

研究論文（学術雑誌）, 査読有り

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© 2015 Loftie-Eaton et al. We report the draft genome sequence of Pseudomonas sp. nov. H2, isolated from creek sediment in Moscow, ID, USA. The strain is most closely related to Pseudomonas putida. However, it has a slightly smaller genome that appears to have been impacted by horizontal gene transfer and poorly maintains IncP-1 plasmids.

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Draft Genome Sequence of Geobacter sp. Strain OR-1, an Arsenate-Respiring Bacterium Isolated from Japanese Paddy Soil.

Ehara A, Suzuki H, Amachi S

Genome announcements （Genome Announcements）  3 （ 1 ）  2015年01月

研究論文（学術雑誌）, 査読有り

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© 2015 Ehara et al. Here, we report a draft genome sequence of Geobacter sp. strain OR-1, an arsenate-respiring bacterium isolated from Japanese paddy soil. It contained two distinct arsenic islands, one including genes for a respiratory arsenate reductase (Arr) as well as for arsenic resistance (arsD-arsA-acr3-arsR-arrA-arrB) and the second containing only genes for arsenic resistance.

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Inflammation-associated adherent-invasive Escherichia coli are enriched in pathways for use of propanediol and iron and M-cell translocation.

Dogan B, Suzuki H, Herlekar D, Sartor RB, Campbell BJ, Roberts CL, Stewart K, Scherl EJ, Araz Y, Bitar PP, Lefébure T, Chandler B, Schukken YH, Stanhope MJ, Simpson KW

Inflammatory bowel diseases （Inflammatory Bowel Diseases）  20 （ 11 ） 1919 - 32 2014年11月

研究論文（学術雑誌）, 査読有り,  ISSN  1078-0998

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Copyright © 2014 Crohn's & Colitis Foundation of America, Inc. Background: Perturbations of the intestinal microbiome, termed dysbiosis, are linked to intestinal inflammation. Isolation of adherent-invasive Escherichia coli (AIEC) from intestines of patients with Crohn's disease (CD), dogs with granulomatous colitis, and mice with acute ileitis suggests these bacteria share pathoadaptive virulence factors that promote inflammation. Methods: To identify genes associated with AIEC, we sequenced the genomes of phylogenetically diverse AIEC strains isolated from people with CD (4), dogs with granulomatous colitis (2), and mice with ileitis (2) and 1 non-AIEC strain from CD ileum and compared them with 38 genome sequences of E. coli and Shigella. We then determined the prevalence of AIEC-associated genes in 49 E. coli strains from patients with CD and controls and correlated genotype with invasion of intestinal epithelial cells, persistence within macrophages, AIEC pathotype, and growth in standardized conditions. Results: Genes encoding propanediol utilization (pdu operon) and iron acquisition (yersiniabactin, chu operon) were overrepresented in AIEC relative to nonpathogenic E. coli. PduC (propanediol dehydratase) was enriched in CD-derived AIEC, correlated with increased cellular invasion, and persistence in vitro and was increasingly expressed in fucose-containing media. Growth of AIEC required iron, and the presence of chuA (heme acquisition) correlated with persistence in macrophages. CD-associated AIEC with lpfA154 (long polar fimbriae) demonstrated increased invasion of epithelial cells and translocation across M cells. Conclusions: Our findings provide novel insights into the genetic basis of the AIEC pathotype, supporting the concept that AIEC are equipped to exploit and promote intestinal inflammation and reveal potential targets for intervention against AIEC and inflammation-associated dysbiosis.

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Draft genome sequences of three Holospora species (Holospora obtusa, Holospora undulata, and Holospora elegans), endonuclear symbiotic bacteria of the ciliate Paramecium caudatum.

Dohra H, Tanaka K, Suzuki T, Fujishima M, Suzuki H

FEMS microbiology letters （FEMS Microbiology Letters）  359 （ 1 ） 16 - 8 2014年10月

研究論文（学術雑誌）, 査読有り,  ISSN  0378-1097

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© 2014 Federation of European Microbiological Societies. We present draft genome sequences of three Holospora species, hosted by the ciliate Paramecium caudatum; that is, the macronucleus-specific H. obtusa and the micronucleus-specific H. undulata and H. elegans. We investigate functions of orthologous core genes conserved across the three Holospora species, which may be essential for the infection and survival in the host nucleus.

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Draft genome sequence of strain q-1, an iodide-oxidizing alphaproteobacterium isolated from natural gas brine water.

Ehara A, Suzuki H, Kanesaki Y, Yoshikawa H, Amachi S

Genome announcements （Genome Announcements）  2 （ 4 ）  2014年07月

研究論文（学術雑誌）, 査読有り

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© 2014 Ehara et al. Here we report the draft genome sequence of strain Q-1, an iodide (I-)-oxidizing heterotrophic bacterium in the class Alphaproteobacteria isolated from natural gas brine water. The genome sequence contained a multicopper oxidase gene probably responsible for iodide oxidation. A photosynthetic gene cluster was found but genes for carbon-fixation were absent.

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Draft genome sequence of Gluconobacter thailandicus NBRC 3257.

Matsutani M, Suzuki H, Yakushi T, Matsushita K

Standards in genomic sciences （Standards in Genomic Sciences）  9 （ 3 ） 614 - 23 2014年06月

研究論文（学術雑誌）, 査読有り

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Gluconobacter thailandicus strain NBRC 3257, isolated from downy cherry (Prunus tomentosa), is a strict aerobic rod-shaped Gram-negative bacterium. Here, we report the features of this organism, together with the draft genome sequence and annotation. The draft genome sequence is composed of 107 contigs for 3,446,046 bp with 56.17% G+C content and contains 3,360 protein-coding genes and 54 RNA genes.

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Comparative functional genomics of Lactobacillus spp. reveals possible mechanisms for specialization of vaginal lactobacilli to their environment.

Mendes-Soares H, Suzuki H, Hickey RJ, Forney LJ

Journal of bacteriology （Journal of Bacteriology）  196 （ 7 ） 1458 - 70 2014年04月

研究論文（学術雑誌）, 査読有り,  ISSN  0021-9193

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Lactobacilli are found in a wide variety of habitats. Four species, Lactobacillus crispatus, L. gasseri, L. iners, and L. jensenii, are common and abundant in the human vagina and absent from other habitats. These may be adapted to the vagina and possess characteristics enabling them to thrive in that environment. Furthermore, stable codominance of multiple Lactobacillus species in a single community is infrequently observed. Thus, it is possible that individual vaginal Lactobacillus species possess unique characteristics that confer to them host-specific competitive advantages. We performed comparative functional genomic analyses of representatives of 25 species of Lactobacillus, searching for habitat-specific traits in the genomes of the vaginal lactobacilli. We found that the genomes of the vaginal species were significantly smaller and had significantly lower GC content than those of the nonvaginal species. No protein families were found to be specific to the vaginal species analyzed, but some were either overor underrepresented relative to nonvaginal species. We also found that within the vaginal species, each genome coded for species- specific protein families. Our results suggest that even though the vaginal species show no general signatures of adaptation to the vaginal environment, each species has specific and perhaps unique ways of interacting with its environment, be it the host or other microbes in the community. These findings will serve as a foundation for further exploring the role of lactobacilli in the ecological dynamics of vaginal microbial communities and their ultimate impact on host health. © 2014, American Society for Microbiology.

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Comparison of gene expression of Paramecium bursaria with and without Chlorella variabilis symbionts.

Kodama Y, Suzuki H, Dohra H, Sugii M, Kitazume T, Yamaguchi K, Shigenobu S, Fujishima M

BMC genomics （BMC Genomics）  15 （ 1 ） 183 2014年03月

研究論文（学術雑誌）, 査読有り

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Background: The ciliate Paramecium bursaria harbors several hundred cells of the green-alga Chlorella sp. in their cytoplasm. Irrespective of the mutual relation between P. bursaria and the symbiotic algae, both cells retain the ability to grow without the partner. They can easily reestablish endosymbiosis when put in contact with each other. Consequently, P. bursaria is an excellent model for studying cell-cell interaction and the evolution of eukaryotic cells through secondary endosymbiosis between different protists. Despite the importance of this organism, no genomic resources have been identified for P. bursaria to date. This investigation compared gene expressions through RNA-Seq analysis and de novo transcriptome assembly of symbiont-free and symbiont-bearing host cells.Results: To expedite the process of gene discovery related to the endosymbiosis, we have undertaken Illumina deep sequencing of mRNAs prepared from symbiont-bearing and symbiont-free P. bursaria cells. We assembled the reads de novo to build the transcriptome. Sequencing using Illumina HiSeq2000 platform yielded 232.3 million paired-end sequence reads. Clean reads filtered from the raw reads were assembled into 68,175 contig sequences. Of these, 10,557 representative sequences were retained after removing Chlorella sequences and lowly expressed sequences. Nearly 90% of these transcript sequences were annotated by similarity search against protein databases. We identified differentially expressed genes in the symbiont-bearing P. bursaria cells relative to the symbiont-free cells, including heat shock 70 kDa protein and glutathione S-transferase.Conclusions: This is the first reported comprehensive sequence resource of Paramecium - Chlorella endosymbiosis. Results provide some keys for the elucidation of secondary endosymbiosis in P. bursaria. We identified P. bursaria genes that are differentially expressed in symbiont-bearing and symbiont-free conditions. © 2014 Kodama et al.; licensee BioMed Central Ltd.

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Characterization of the heart transcriptome of the white shark (Carcharodon carcharias).

Richards VP, Suzuki H, Stanhope MJ, Shivji MS

BMC genomics （BMC Genomics）  14 （ 1 ） 697 2013年10月

研究論文（学術雑誌）, 査読有り

　概要を見る

Background: The white shark (Carcharodon carcharias) is a globally distributed,apex predator possessing physical, physiological, and behavioral traits thathave garnered it significant public attention. In addition to interest inthe genetic basis of its form and function, as a representative of theoldest extant jawed vertebrate lineage, white sharks are also ofconservation concern due to their small population size and threat fromoverfishing. Despite this, surprisingly little is known about the biology ofwhite sharks, and genomic resources are unavailable. To address thisdeficit, we combined Roche-454 and Illumina sequencing technologies tocharacterize the first transciptome of any tissue for this species. Results: From white shark heart cDNA we generated 665,399 Roche 454 reads (medianlength 387-bp) that were assembled into 141,626 contigs (mean length503-bp). We also generated 78,566,588 Illumina reads, which we aligned tothe 454 contigs producing 105,014 454/Illumina consensus sequences. Tothese, we added 3,432 non-singleton 454 contigs. By comparing thesesequences to the UniProtKB/Swiss-Prot database we were able to annotate21,019 translated open reading frames (ORFs) of ≥ 20 amino acids. Ofthese, 19,277 were additionally assigned Gene Ontology (GO) functionalannotations. While acknowledging the limitations of our single tissuetranscriptome, Fisher tests showed the white shark transcriptome to besignificantly enriched for numerous metabolic GO terms compared to the zebrafish and human transcriptomes, with white shark showing more similarity tohuman than to zebra fish (i.e. fewer terms were significantly different). Wealso compared the transcriptome to other available elasmobranch sequences,for signatures of positive selection and identified several genes ofputative adaptive significance on the white shark lineage. The white sharktranscriptome also contained 8,404 microsatellites (dinucleotide,trinucleotide, or tetranucleotide motifs ≥ five perfect repeats).Detailed characterization of these microsatellites showed that ORFs withtrinucleotide repeats, were significantly enriched for transcriptionregulatory roles and that trinucleotide frequency within ORFs was lower thanfor a wide range of taxonomic groups including other vertebrates.Conclusion: The white shark heart transcriptome represents a valuable resource for futureelasmobranch functional and comparative genomic studies, as well as forpopulation and other biological studies vital for effective conservation ofthis globally vulnerable species. © 2013 Richards et al.; licensee BioMed Central Ltd.

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Draft Genome Sequence of Holospora undulata Strain HU1, a Micronucleus-Specific Symbiont of the Ciliate Paramecium caudatum.

Dohra H, Suzuki H, Suzuki T, Tanaka K, Fujishima M

Genome announcements （Genome Announcements）  1 （ 4 ）  2013年08月

研究論文（学術雑誌）, 査読有り

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© 2013 Dohra et al. Holospora undulata is a micronucleus-specific symbiont of the ciliate Paramecium caudatum. We report here the draft genome sequence of H. undulata strain HU1. This genome information will contribute to the study of symbiosis between H. undulata and the host P. caudatum.

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Complete Genome Sequence of the Porcine Strain Brachyspira pilosicoli P43/6/78(T.).

Lin C, den Bakker HC, Suzuki H, Lefébure T, Ponnala L, Sun Q, Stanhope MJ, Wiedmann M, Duhamel GE

Genome announcements （Genome Announcements）  1 （ 1 ）  2013年01月

研究論文（学術雑誌）, 査読有り

　概要を見る

© 2013 Lin et al. Reported herein is the complete genome sequence of Brachyspira pilosicoli strain P43/6/78T, isolated from a pig with clinical disease. This sequence will aid in the study of genome-wide comparison among Brachyspira species.

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Functional bias of positively selected genes in Streptococcus genomes.

Suzuki H, Stanhope MJ

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases （Infection, Genetics and Evolution）  12 （ 2 ） 274 - 7 2012年03月

研究論文（学術雑誌）, 査読有り,  ISSN  1567-1348

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Rates of nonsynonymous substitution (dN) significantly higher than rates of synonymous substitution (dS) have been used as evidence of positive selection for the fixation of advantageous point mutations. It has been suggested that positive selection contributes to the evolution of virulence factors and certain functional categories in bacterial pathogens. The genus Streptococcus contains a number of important human and agricultural pathogens. Here we assessed positive selection across 13 Streptococcus species, and their relationship with virulence factors and functional categories. We found that known virulence genes were subject to positive selection pressure as much as other genes. After false discovery rate correction for multiple comparisons, no functional categories were significantly over- or under-represented in positively selected genes relative to other genes. Our results suggest that within the genus Streptococcus positive selection based on dN/dS ratios is not distributed with bias across biological functions. © 2012.

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Comparative genomic analysis of the genus Staphylococcus including Staphylococcus aureus and its newly described sister species Staphylococcus simiae.

Suzuki H, Lefébure T, Bitar PP, Stanhope MJ

BMC genomics （BMC Genomics）  13 （ 1 ） 38 2012年01月

研究論文（学術雑誌）, 査読有り

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Background: Staphylococcus belongs to the Gram-positive low G + C content group of the Firmicutes division of bacteria. Staphylococcus aureus is an important human and veterinary pathogen that causes a broad spectrum of diseases, and has developed important multidrug resistant forms such as methicillin-resistant S. aureus (MRSA). Staphylococcus simiae was isolated from South American squirrel monkeys in 2000, and is a coagulase-negative bacterium, closely related, and possibly the sister group, to S. aureus. Comparative genomic analyses of closely related bacteria with different phenotypes can provide information relevant to understanding adaptation to host environment and mechanisms of pathogenicity.Results: We determined a Roche/454 draft genome sequence for S. simiae and included it in comparative genomic analyses with 11 other Staphylococcus species including S. aureus. A genome based phylogeny of the genus confirms that S. simiae is the sister group to S. aureus and indicates that the most basal Staphylococcus lineage is Staphylococcus pseudintermedius, followed by Staphylococcus carnosus. Given the primary niche of these two latter taxa, compared to the other species in the genus, this phylogeny suggests that human adaptation evolved after the split of S. carnosus. The two coagulase-positive species (S. aureus and S. pseudintermedius) are not phylogenetically closest but share many virulence factors exclusively, suggesting that these genes were acquired by horizontal transfer. Enrichment in genes related to mobile elements such as prophage in S. aureus relative to S. simiae suggests that pathogenesis in the S. aureus group has developed by gene gain through horizontal transfer, after the split of S. aureus and S. simiae from their common ancestor.Conclusions: Comparative genomic analyses across 12 Staphylococcus species provide hypotheses about lineages in which human adaptation has taken place and contributions of horizontal transfer in pathogenesis. © 2012 Suzuki et al; licensee BioMed Central Ltd.

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Comparative genomic analysis of the Streptococcus dysgalactiae species group: gene content, molecular adaptation, and promoter evolution.

Suzuki H, Lefébure T, Hubisz MJ, Pavinski Bitar P, Lang P, Siepel A, Stanhope MJ

Genome biology and evolution （Genome Biology and Evolution）  3 （ 1 ） 168 - 85 2011年

研究論文（学術雑誌）, 査読有り

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Comparative genomics of closely related bacterial species with different pathogenesis and host preference can provide a means of identifying the specifics of adaptive differences. Streptococcus dysgalactiae (SD) is comprised of two subspecies: S. dysgalactiae subsp. equisimilis is both a human commensal organism and a human pathogen, and S. dysgalactiae subsp. dysgalactiae is strictly an animal pathogen. Here, we present complete genome sequences for both taxa, with analyses involving other species of Streptococcus but focusing on adaptation in the SD species group. We found little evidence for enrichment in biochemical categories of genes carried by each SD strain, however, differences in the virulence gene repertoire were apparent. Some of the differences could be ascribed to prophage and integrative conjugative elements. We identified approximately 9% of the nonrecombinant core genome to be under positive selection, some of which involved known virulence factors in other bacteria. Analyses of proteomes by pooling data across genes, by biochemical category, clade, or branch, provided evidence for increased rates of evolution in several gene categories, as well as external branches of the tree. Promoters were primarily evolving under purifying selection but with certain categories of genes evolving faster. Many of these fast-evolving categories were the same as those associated with rapid evolution in proteins. Overall, these results suggest that adaptation to changing environments and new hosts in the SD species group has involved the acquisition of key virulence genes along with selection of orthologous protein-coding loci and operon promoters. © 2011 The Author(s).

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Predicting plasmid promiscuity based on genomic signature.

Suzuki H, Yano H, Brown CJ, Top EM

Journal of bacteriology （Journal of Bacteriology）  192 （ 22 ） 6045 - 55 2010年11月

研究論文（学術雑誌）, 査読有り,  ISSN  0021-9193

　概要を見る

Despite the important contribution of self-transmissible plasmids to bacterial evolution, little is understood about the range of hosts in which these plasmids have evolved. Our goal was to infer this so-called evolutionary host range. The nucleotide composition, or genomic signature, of plasmids is often similar to that of the chromosome of their current host, suggesting that plasmids acquire their hosts' signature over time. Therefore, we examined whether the evolutionary host range of plasmids could be inferred by comparing their trinucleotide composition to that of all completely sequenced bacterial chromosomes. The diversity of candidate hosts was determined using taxonomic classification and genetic distance. The method was first tested using plasmids from six incompatibility (Inc) groups whose host ranges are generally thought to be narrow (IncF, IncH, and IncI) or broad (IncN, IncP, and IncW) and then applied to other plasmid groups. The evolutionary host range was found to be broad for IncP plasmids, narrow for IncF and IncI plasmids, and intermediate for IncH and IncN plasmids, which corresponds with their known host range. The IncW plasmids as well as several plasmids from the IncA/C, IncP, IncQ, IncU, and PromA groups have signatures that were not similar to any of the chromosomal signatures, raising the hypothesis that these plasmids have not been ameliorated in any host due to their promiscuous nature. The inferred evolutionary host range of IncA/C, IncP-9, and IncL/M plasmids requires further investigation. In this era of high-throughput sequencing, this genomic signature method is a useful tool for predicting the host range of novel mobile elements. Copyright © 2010, American Society for Microbiology. All Rights Reserved.

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Comparative genomics of pAKD4, the prototype IncP-1delta plasmid with a complete backbone.

Sen D, Yano H, Suzuki H, Król JE, Rogers L, Brown CJ, Top EM

Plasmid （Plasmid）  63 （ 2 ） 98 - 107 2010年03月

研究論文（学術雑誌）, 査読有り,  ISSN  0147-619X

　概要を見る

Plasmids of the incompatibility group IncP-1 are important agents of horizontal gene transfer and contribute to the spread of antibiotic resistance and xenobiotic degradation within bacterial communities. Even though some prototype plasmids have been studied in much detail, the diversity of this plasmid group was still greatly underestimated until recently, as only two of the five currently known divergent sub-groups had been described. To further improve our insight into the diversity and evolutionary history of this family of broad-host-range plasmids, we compared the complete nucleotide sequence of a new IncP-1δ plasmid pAKD4 to the genomes of other IncP-1 plasmids. Plasmid pAKD4 was previously isolated by exogenous plasmid isolation from an agricultural soil in Norway. Its 56,803. bp nucleotide sequence shows high similarity in gene sequence and gene order to both plasmids pEST4011 and pIJB1, the only other IncP-1δ plasmids sequenced so far. While all three plasmids have a typical IncP-1 backbone comprising replication, transfer, and stable inheritance/control genes, the low sequence similarity in some regions and presence/absence of some backbone genes compared to other IncP-1 plasmids cluster them in a divergent sub-group. Therefore this study validates the presence of a real IncP-1δ clade with multiple plasmids. Moreover, since both pEST4011 and pIJB1 are missing a portion of their transfer genes, pAKD4 represents the first completely sequenced self-transferable plasmid with a complete IncP-1δ backbone. We therefore propose it to be the prototype IncP-1δ plasmid. © 2009 Elsevier Inc.

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The vaginal bacterial communities of Japanese women resemble those of women in other racial groups.

Zhou X, Hansmann MA, Davis CC, Suzuki H, Brown CJ, Schütte U, Pierson JD, Forney LJ

FEMS immunology and medical microbiology （FEMS Immunology and Medical Microbiology）  58 （ 2 ） 169 - 81 2010年03月

研究論文（学術雑誌）, 査読有り,  ISSN  0928-8244

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To determine whether different racial groups shared common types of vaginal microbiota, we characterized the composition and structure of vaginal bacterial communities in asymptomatic and apparently healthy Japanese women in Tokyo, Japan, and compared them with those of White and Black women from North America. The composition of vaginal communities was compared based on community profiles of terminal restriction fragments of 16S rRNA genes and phylogenetic analysis of cloned 16S rRNA gene sequences of the numerically dominant bacterial populations. The types of vaginal communities found in Japanese women were similar to those of Black and White women. As with White and Black women, most vaginal communities were dominated by lactobacilli, and only four species of Lactobacillus (Lactobacillus iners, Lactobacillus crispatus, Lactobacillus jensenii, and Lactobacillus gasseri) were commonly found. Communities dominated by multiple species of lactobacilli were common in Japanese and White women, but rare in Black women. The incidence, in Japanese women, of vaginal communities with several non-Lactobacillus species at moderately high frequencies was intermediate between Black women and White women. The limited number of community types found among women in different ethnic groups suggests that host genetic factors, including the innate and adaptive immune systems, may be more important in determining the species composition of vaginal bacterial communities than are cultural and behavioral differences. © 2009 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

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Evolutionary dynamics of complete Campylobacter pan-genomes and the bacterial species concept.

Lefébure T, Bitar PD, Suzuki H, Stanhope MJ

Genome biology and evolution （Genome Biology and Evolution）  2 （ 1 ） 646 - 55 2010年

研究論文（学術雑誌）, 査読有り

　概要を見る

Defining bacterial species and understanding the relative cohesiveness of different components of their genomes remains a fundamental problem in microbiology. Bacterial species tend to be comprised of both a set of core and dispensable genes, with the sum of these two components forming the species pan-genome. The role of the core and dispensable genes in defining bacterial species and the question of whether pan-genomes are finite or infinite remain unclear. Here we demonstrate, through the analysis of 96 genome sequences derived from two closely related sympatric sister species of pathogenic bacteria (Campylobacter coli and C. jejuni), that their pan-genome is indeed finite and that there are unique and cohesive features to each of their genomes defining their genomic identity. The two species have a similar pan-genome size; however, C. coli has acquired a larger core genome and each species has evolved a number of species-specific core genes, possibly reflecting different adaptive strategies. Genome-wide assessment of the level of lateral gene transfer within and between the two sister species, as well as within the core and non-core genes, demonstrates a resistance to interspecies recombination in the core genome of the two species and therefore provides persuasive support for the core genome hypothesis for bacterial species. © The Author(s) 2010.

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Quantitative analysis of replication-related mutation and selection pressures in bacterial chromosomes and plasmids using generalised GC skew index.

Arakawa K, Suzuki H, Tomita M

BMC genomics （BMC Genomics）  10   640 2009年12月

研究論文（学術雑誌）, 査読有り

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Background: Due to their bi-directional replication machinery starting from a single finite origin, bacterial genomes show characteristic nucleotide compositional bias between the two replichores, which can be visualised through GC skew or (C-G)/(C+G). Although this polarisation is used for computational prediction of replication origins in many bacterial genomes, the degree of GC skew visibility varies widely among different species, necessitating a quantitative measurement of GC skew strength in order to provide confidence measures for GC skew-based predictions of replication origins.Results: Here we discuss a quantitative index for the measurement of GC skew strength, named the generalised GC skew index (gGCSI), which is applicable to genomes of any length, including bacterial chromosomes and plasmids. We demonstrate that gGCSI is independent of the window size and can thus be used to compare genomes with different sizes, such as bacterial chromosomes and plasmids. It can suggest the existence of different replication mechanisms in archaea and of rolling-circle replication in plasmids. Correlation of gGCSI values between plasmids and their corresponding host chromosomes suggests that within the same strain, these replicons have reproduced using the same replication machinery and thus exhibit similar strengths of replication strand skew.Conclusions: gGCSI can be applied to genomes of any length and thus allows comparative study of replication-related mutation and selection pressures in genomes of different lengths such as bacterial chromosomes and plasmids. Using gGCSI, we showed that replication-related mutation or selection pressure is similar for replicons with similar machinery. © 2009 Arakawa et al; licensee BioMed Central Ltd.

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Plasmids captured in C. metallidurans CH34: defining the PromA family of broad-host-range plasmids.

Van der Auwera GA, Król JE, Suzuki H, Foster B, Van Houdt R, Brown CJ, Mergeay M, Top EM

Antonie van Leeuwenhoek （Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology）  96 （ 2 ） 193 - 204 2009年08月

研究論文（学術雑誌）, 査読有り,  ISSN  0003-6072

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The self-transmissible, broad-host-range (BHR) plasmid pMOL98 was previously isolated from polluted soil using a triparental plasmid capture approach and shown to possess a replicon similar to that of the BHR plasmids pSB102 and pIPO2. Here, complete sequence analysis and comparative genomics reveal that the 55.5 kb nucleotide sequence of pMOL98 shows extensive sequence similarity and synteny with the BHR plasmid family that now includes pIPO2, pSB102, pTER331, and pMRAD02. They share a plasmid backbone comprising replication, partitioning and conjugative transfer functions. Comparison of the variable accessory regions of these plasmids shows that the majority of natural transposons, as well as the mini-transposon used to mark the plasmids, are inserted in the parA locus. The transposon unique to pMOL98 appears to have inserted from the chromosome of the recipient strain used in the plasmid capture procedure. This demonstrates the necessity for careful screening of plasmids and host chromosomes to avoid mis-interpretation of plasmid genome content. The presence of very similar BHR plasmids with different accessory genes in geographically distinct locations suggests an important role in horizontal gene exchange and bacterial adaptation for this recently defined plasmid group, which we propose to name "PromA". © Springer Science+Business Media B.V. 2009.

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Measure of synonymous codon usage diversity among genes in bacteria.

Suzuki H, Saito R, Tomita M

BMC bioinformatics （BMC Bioinformatics）  10   167 2009年06月

研究論文（学術雑誌）, 査読有り

　概要を見る

Background: In many bacteria, intragenomic diversity in synonymous codon usage among genes has been reported. However, no quantitative attempt has been made to compare the diversity levels among different genomes. Here, we introduce a mean dissimilarity-based index (Dmean) for quantifying the level of diversity in synonymous codon usage among all genes within a genome. Results: The application of Dmean to 268 bacterial genomes shows that in bacteria with extremely biased genomic G+C compositions there is little diversity in synonymous codon usage among genes. Furthermore, our findings contradict previous reports. For example, a low level of diversity in codon usage among genes has been reported for Helicobacter pylori, but based on Dmean, the diversity level of this species is higher than those of more than half of bacteria tested here. The discrepancies between our findings and previous reports are probably due to differences in the methods used for measuring codon usage diversity. Conclusion: We recommend that Dmean be used to measure the diversity level of codon usage among genes. This measure can be applied to other compositional features such as amino acid usage and dinucleotide relative abundance as a genomic signature. © 2009 Suzuki et al; licensee BioMed Central Ltd.

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Using Mahalanobis distance to compare genomic signatures between bacterial plasmids and chromosomes.

Suzuki H, Sota M, Brown CJ, Top EM

Nucleic acids research （Nucleic Acids Research）  36 （ 22 ） e147 2008年12月

研究論文（学術雑誌）, 査読有り,  ISSN  0305-1048

　概要を見る

Plasmids are ubiquitous mobile elements that serve as a pool of many host beneficial traits such as antibiotic resistance in bacterial communities. To understand the importance of plasmids in horizontal gene transfer, we need to gain insight into the 'evolutionary history' of these plasmids, i.e. the range of hosts in which they have evolved. Since extensive data support the proposal that foreign DNA acquires the host's nucleotide composition during long-term residence, comparison of nucleotide composition of plasmids and chromosomes could shed light on a plasmid's evolutionary history. The average absolute dinucleotide relative abundance difference, termed δ-distance, has been commonly used to measure differences in dinucleotide composition, or 'genomic signature', between bacterial chromosomes and plasmids. Here, we introduce the Mahalanobis distance, which takes into account the variance-covariance structure of the chromosome signatures. We demonstrate that the Mahalanobis distance is better than the δ-distance at measuring genomic signature differences between plasmids and chromosomes of potential hosts. We illustrate the usefulness of this metric for proposing candidate long-term hosts for plasmids, focusing on the virulence plasmids pXO1 from Bacillus anthracis, and pO157 from Escherichia coli O157:H7, as well as the broad host range multi-drug resistance plasmid pB10 from an unknown host. © 2008 The Author(s).

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Comparison of correspondence analysis methods for synonymous codon usage in bacteria.

Suzuki H, Brown CJ, Forney LJ, Top EM

DNA research : an international journal for rapid publication of reports on genes and genomes （DNA Research）  15 （ 6 ） 357 - 65 2008年12月

研究論文（学術雑誌）, 査読有り,  ISSN  1340-2838

　概要を見る

Synonymous codon usage varies both between organisms and among genes within a genome, and arises due to differences in G + C content, replication strand skew, or gene expression levels. Correspondence analysis (CA) is widely used to identify major sources of variation in synonymous codon usage among genes and provides a way to identify horizontally transferred or highly expressed genes. Four methods of CA have been developed based on three kinds of input data: absolute codon frequency, relative codon frequency, and relative synonymous codon usage (RSCU) as well as within-group CA (WCA). Although different CA methods have been used in the past, no comprehensive comparative study has been performed to evaluate their effectiveness. Here, the four CA methods were evaluated by applying them to 241 bacterial genome sequences. The results indicate that WCA is more effective than the other three methods in generating axes that reflect variations in synonymous codon usage. Furthermore, WCA reveals sources that were previously unnoticed in some genomes; e.g. synonymous codon usage related to replication strand skew was detected in Rickettsia prowazekii. Though CA based on RSCU is widely used, our evaluation indicates that this method does not perform as well as WCA.

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Modelling the spatial dynamics of plasmid transfer and persistence.

Krone SM, Lu R, Fox R, Suzuki H, Top EM

Microbiology (Reading, England) （Microbiology）  153 （ Pt 8 ） 2803 - 16 2007年08月

研究論文（学術雑誌）, 査読有り,  ISSN  1350-0872

　概要を見る

Bacterial plasmids are extra-chromosomal genetic elements that code for a wide variety of phenotypes in their bacterial hosts and are maintained in bacterial communities through both vertical and horizontal transfer. Current mathematical models of plasmid-bacteria dynamics, based almost exclusively on mass-action differential equations that describe these interactions in completely mixed environments, fail to adequately explain phenomena such as the long-term persistence of plasmids in natural and clinical bacterial communities. This failure is, at least in part, due to the absence of any spatial structure in these models, whereas most bacterial populations are spatially structured in microcolonies and biofilms. To help bridge the gap between theoretical predictions and observed patterns of plasmid spread and persistence, an individual-based lattice model (interacting particle system) that provides a predictive framework for understanding the dynamics of plasmid-bacteria interactions in spatially structured populations is presented here. To assess the accuracy and flexibility of the model, a series of experiments that monitored plasmid loss and horizontal transfer of the IncP-1β plasmid pB10:: rfp in Escherichia coli K12 and other bacterial populations grown on agar surfaces were performed. The model-based visual patterns of plasmid loss and spread, as well as quantitative predictions of the effects of different initial parental strain densities and incubation time on densities of transconjugants formed on a 2D grid, were in agreement with this and previously published empirical data. These results include features of spatially structured populations that are not predicted by mass-action differential equation models. © 2007 SGM.

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Proteome-wide prediction of novel DNA/RNA-binding proteins using amino acid composition and periodicity in the hyperthermophilic archaeon Pyrococcus furiosus.

Fujishima K, Komasa M, Kitamura S, Suzuki H, Tomita M, Kanai A

DNA research : an international journal for rapid publication of reports on genes and genomes （DNA Research）  14 （ 3 ） 91 - 102 2007年06月

研究論文（学術雑誌）, 査読有り,  ISSN  1340-2838

　概要を見る

Proteins play a critical role in complex biological systems, yet about half of the proteins in publicly available databases are annotated as functionally unknown. Proteome-wide functional classification using bioinformatics approaches thus is becoming an important method for revealing unknown protein functions. Using the hyperthermophilic archaeon Pyrococcus furiosus as a model species, we used the support vector machine (SVM) method to discriminate DNA/RNA-binding proteins from proteins with other functions, using amino acid composition and periodicities as feature vectors. We defined this value as the composition score (CO) and periodicity score (PD). The P. furiosus proteins were classified into three classes (I-III) on the basis of the two-dimensional correlation analysis of CO score and PD score. As a result, approximately 87 of the functionally known proteins categorized as class I proteins (CO score + PD score > 0.6) were found to be DNA/RNA-binding proteins. Applying the two-dimensional correlation analysis to the 994 hypothetical proteins in P. furiosus, a total of 151 proteins were predicted to be novel DNA/RNA-binding protein candidates. DNA/RNA-binding activities of randomly chosen hypothetical proteins were experimentally verified. Six out of seven candidate proteins in class I possessed DNA/RNA-binding activities, supporting the efficacy of our method. © The Author 2007. Kazusa DNA Research Institute.

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Region-specific insertion of transposons in combination with selection for high plasmid transferability and stability accounts for the structural similarity of IncP-1 plasmids.

Sota M, Tsuda M, Yano H, Suzuki H, Forney LJ, Top EM

Journal of bacteriology （Journal of Bacteriology）  189 （ 8 ） 3091 - 8 2007年04月

研究論文（学術雑誌）, 査読有り,  ISSN  0021-9193

　概要を見る

The overall architecture of IncP-1 plasmids is very conserved in that the accessory genes are typically located in one or two specific regions: between oriV and trfA and between the tra and trb operons. Various hypotheses have been formulated to explain this, but none have been tested experimentally. We investigated whether this structural similarity is due to region-specific transposition alone or also is reliant on selection for plasmids with insertions limited to these two regions. We first examined the transposition of Tn21Km into IncP-1β plasmid pBP136 and found that most Tn21Km insertions (67%) were located around oriV. A similar experiment using the oriV region of IncP-1β plasmid pUO1 confirmed these results. We then tested the transferability, stability, and fitness cost of different pBP136 derivatives to determine if impairment of these key plasmid characters explained the conserved plasmid architecture. Most of the pBP136 derivatives with insertions in transfer genes were no longer transferable. The plasmids with insertions in the oriV-trfA and tra-trb regions were more stable than other plasmid variants, and one of these also showed a significantly lower fitness cost. In addition, our detailed sequence analysis of IncP-1 plasmids showed that Tn402/5053-like transposons are situated predominantly between the tra and trb operons and close to the putative resolution site for the ParA resolvase, a potential hot spot for those transposons. Our study presents the first empirical evidence that region-specific insertion of transposons in combination with selection for transferable and stable plasmids explains the structural similarity of IncP-1 plasmids. Copyright © 2007, American Society for Microbiology. All Rights Reserved.

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Variation in the correlation of G + C composition with synonymous codon usage bias among bacteria.

Suzuki H, Saito R, Tomita M

EURASIP journal on bioinformatics & systems biology （Eurasip Journal on Bioinformatics and Systems Biology）  2007   61374 2007年

研究論文（学術雑誌）, 査読有り,  ISSN  1687-4145

　概要を見る

G + C composition at the third codon position (GC3) is widely reported to be correlated with synonymous codon usage bias. However, no quantitative attempt has been made to compare the extent of this correlation among different genomes. Here, we applied Shannon entropy from information theory to measure the degree of GC3 bias and that of synonymous codon usage bias of each gene. The strength of the correlation of GC3 with synonymous codon usage bias, quantified by a correlation coefficient, varied widely among bacterial genomes, ranging from -0.07 to 0.95. Previous analyses suggesting that the relationship between GC3 and synonymous codon usage bias is independent of species are thus inconsistent with the more detailed analyses obtained here for individual species.

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A problem in multivariate analysis of codon usage data and a possible solution.

Suzuki H, Saito R, Tomita M

FEBS letters （FEBS Letters）  579 （ 28 ） 6499 - 504 2005年11月

研究論文（学術雑誌）, 査読有り,  ISSN  0014-5793

　概要を見る

Multivariate analyses are often used to identify major trends of variation in synonymous codon usage among genes. These analyses need to be performed on properly normalized codon usage data to avoid biases masking this synonymous variation, i.e., gene length, amino acid usage, and codon degeneracy; however, previous studies have failed to do so. In this paper, we demonstrate that the use of alternative normalized data (called 'relative adaptiveness' in the literature) can avoid all these biases and furthermore, can identify more trends of variation among genes, including GC-ending codon usage, GT-ending codon usage, and gene expression level. © 2005 Published by Elsevier B.V. on behalf of the Federation of European Biochemical Societies.

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A comprehensive software suite for the analysis of cDNAs.

Arakawa K, Suzuki H, Fujishima K, Fujimoto K, Ueda S, Matsui M, Tomita M

Genomics, proteomics & bioinformatics （Genomics, Proteomics and Bioinformatics）  3 （ 3 ） 179 - 88 2005年08月

研究論文（学術雑誌）, 査読有り,  ISSN  1672-0229

　概要を見る

We have developed a comprehensive software suite for bioinformatics research of cDNAs; it is aimed at rapid characterization of the features of genes and the proteins they code. Methods implemented include the detection of translation initiation and termination signals, statistical analysis of codon usage, comparative study of amino acid composition, comparative modeling of the structures of product proteins, prediction of alternative splice forms, and metabolic pathway reconstruction.

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The 'weighted sum of relative entropy': a new index for synonymous codon usage bias.

Suzuki H, Saito R, Tomita M

Gene （Gene）  335 （ 1-2 ） 19 - 23 2004年06月

研究論文（学術雑誌）, 査読有り,  ISSN  0378-1119

　概要を見る

Shannon entropy from information theory has been applied to estimate the degree of deviation from equal usage of synonymous codons; however, previous attempts have failed to take into account all three aspects of amino acid usage, i.e. (i) the number of distinct amino acids, (ii) their relative frequencies, and (iii) their degree of codon degeneracy. A new index taking into account all of these aspects is proposed. The index, designated as the 'weighted sum of relative entropy' (Ew), is defined as the sum of the relative entropy of each amino acid weighted by its relative frequency in the sequence. In this paper, we demonstrate that Ew allows us to avoid some amino acid usage biases and can yield results contradictory to those obtained by previous methods. © 2004 Elsevier B.V. All rights reserved.

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