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Evolutionary Mechanisms of Microbial Genomes 2012 International Journal of Evolutionary Biology Evolutionary Mechanisms of Microbial Genomes 2012 Guest Editors: Hiromi Nishida, Shinji Kondo, Hideaki Nojiri, Ken-ichi Noma, and Kenro Oshima Evolutionary Mechanisms of Microbial Genomes 2012 International Journal of Evolutionary Biology Evolutionary Mechanisms of Microbial Genomes 2012 Guest Editors: Hiromi Nishida, Shinji Kondo, Hideaki Nojiri, Ken-ichi Noma, and Kenro Oshima Copyright © 2012 Hindawi Publishing Corporation. All rights reserved. This is a special issue published in “International Journal of Evolutionary Biology.” All articles are open access articles distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Editorial Board Giacomo Bernardi, USA Kazuho Ikeo, Japan Jeffrey R. Powell, USA Terr y Burke, UK Yoh Iwasa, Japan Hudson Kern Reeve, USA Ignacio Doadrio, Spain Henrik J. Jensen, UK Y. Satta, Japan Simon Easteal, Australia Amitabh Joshi, India Koji Tamura, Japan Santiago F. Elena, Spain Hirohisa Kishino, Japan Yoshio Tateno, Japan Renato Fani, Italy A. Moya, Spain E. N. Trifonov, Israel Dmitry A. Filatov, UK G. Pesole, Italy Eske Willerslev, Denmark F. Gonza’lez-Candelas, Spain I. Popescu, USA Shozo Yokoyama, USA D. Graur, USA David Posada, Spain Contents Evolutionary Mechanisms of Microbial Genomes 2012, Hiromi Nishida, Shinji Kondo, Hideaki Nojiri, Ken-ichi Noma, and Kenro Oshima Volume 2012, Article ID 872768, 2 pages Phylogenetic Position of Aquificales Based on the Whole Genome Sequences of Six Aquificales Species, Kenro Oshima, Yoko Chiba, Yasuo Igarashi, Hiroyuki Arai, and Masaharu Ishii Volume 2012, Article ID 859264, 9 pages Detection of Horizontal Gene Transfers from Phylogenetic Comparisons, Victor Satler Pylro, Luciano de Souza Vespoli, Gabriela Frois Duarte, and Karla Suemy Clemente Yotoko Volume 2012, Article ID 813015, 7 pages Comparative Pathogenomics of Bacteria Causing Infectious Diseases in Fish, Ponnerassery S. Sudheesh, Aliya Al-Ghabshi, Nashwa Al-Mazrooei, and Saoud Al-Habsi Volume 2012, Article ID 457264, 16 pages Whole-Genome Profiling of a Novel Mutagenesis Technique Using Proofreading-Deficient DNA Polymerase δ, Yuh Shiwa, Sanae Fukushima-Tanaka, Ken Kasahara, Takayuki Horiuchi, and Hirofumi Yoshikawa Volume 2012, Article ID 860797, 8 pages Dispensabilities of Carbonic Anhydrase in Proteobacteria, Kenji Ueda, Hiromi Nishida, and Teruhiko Beppu Volume 2012, Article ID 324549, 5 pages Evolution of Lysine Biosynthesis in the Phylum Deinococcus-Thermus, Hiromi Nishida and Makoto Nishiyama Volume 2012, Article ID 745931, 6 pages Vehicles, Replicators, and Intercellular Movement of Genetic Information: Evolutionary Dissection of a Bacterial Cell, Matti Jalasvuori Volume 2012, Article ID 874153, 17 pages Comparative Analyses of Base Compositions, DNA Sizes, and Dinucleotide Frequency Profiles in Archaeal and Bacterial Chromosomes and Plasmids, Hiromi Nishida Volume 2012, Article ID 342482, 5 pages Comparative Analyses of Homocitrate Synthase Genes of Ascomycetous Yeasts, Hiromi Nishida Volume 2012, Article ID 254941, 4 pages Genome Signature Difference between Deinococcus radiodurans and Thermus thermophilus, Hiromi Nishida, Reina Abe, Taishi Nagayama, and Kentaro Yano Volume 2012, Article ID 6, 205274 pages Hindawi Publishing Corporation International Journal of Evolutionary Biology Volume 2012, Article ID 872768, 2 pages doi:10.1155/2012/872768 Editorial Evolutionary Mechanisms of Microbial Genomes 2012 Hiromi Nishida,1 Shinji Kondo,2 Hideaki Nojiri,3 Ken-ichi Noma,4 and Kenro Oshima5 1 Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan 2 Laboratory for Cellular Systems Modeling, RIKEN Research Center for Allergy and Immunology, Kanagawa 230-0045, Japan 3 Laboratory of Environmental Biochemistry, Biotechnology Research Center, The University of Tokyo, Tokyo 113-8657, Japan 4 Gene Expression and Regulation Program, The Wistar Institute, 3601 Spruce Street, Room 116, Philadelphia, PA 19104, USA 5 Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan Correspondence should be addressed to Hiromi Nishida, [email protected] Received 11 July 2012; Accepted 11 July 2012 Copyright © 2012 Hiromi Nishida et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. What is the driving force in the course of microbial genome of GC content and chromosome size in bacteria than in evolution? What is the mechanism for distinguishing self- archaea. genome from others? These fundamental questions remain Two papers are presented about horizontal gene transfer elusive although rigorous studies are underway by using in genome evolution. M. Jalasvuori in “Vehicles, replicators, comparative genomics. The special issue “Evolutionary mech- and intercellular movement of genetic information: Evolution- anisms of microbial genomes” has been launched in 2011 and ary dissection of a bacterial cell” discussed a hypothesis that presented 11 original papers. Here, this new version in 2012 any given biosphere comprising prokaryotic cell vehicles and presents 10 papers (one review and nine research articles). genetic replicators may naturally evolve toward possessing Two papers are presented in phylogenomics. K. Oshima horizontally moving replicators of various types. V. S. Pylro et al. revealed a close relationship of Aquificales to Ther- et al. described horizontal gene transfer events of the gene motogales based on the whole-genome comparison in “Phy- dszC involved in the cleavage of carbon-sulfur bonds in logenetic position of Aquificales based on the whole genome “Detection of horizontal gene transfers from phylogenetic sequences of six Aquificales species.” An extensive and elabo- comparisons.” rate review of fish pathogenic bacteria has been presented AnarticleaboutDNAmutationispresentedbyY.Shiwa by P. S. Sudheesh et al. in “Comparative pathogenomics of et al. in “Whole-genome profiling of a novel mutagenesis bacteria causing infectious diseases in fish.” technique using proofreading-deficient DNA polymerase δ.” Two papers are presented on subjects related to evolu- They compared mutations created by the chemical muta- tion of base composition in genomes. H. Nishida et al. in gen ethyl methanesulfonate (EMS) and the proofreading- “Genome signature difference between Deinococcus radiodu- deficient DNA polymerase δ and found that the mutations rans and Thermus thermophilus” observed distinct tetranu- created by the proofreading-deficient DNA polymerase δ cleotide frequencies between the genomes of D. radiodurans generated more diverse amino acid substitution patterns and T. thermophilus, potentially reflecting different evolu- than those by EMS. tionary backgrounds of the two species after divergence Three papers are presented on subjects related to from common ancestor. H. Nishida in “Comparative analyses metabolic pathway. H. Nishida in “Comparative analyses of of base compositions, DNA sizes, and dinucleotide frequency homocitrate synthase genes of ascomycetous yeasts”described profiles in archaeal and bacterial chromosomes and plasmids” gene duplications of the homocitrate synthase which have reported lower GC content (by up to ∼10%) of plasmids occurred multiple times during evolution of the ascomyce- compared to their host chromosomes and higher correlation tous yeasts. H. Nishida and M. Nishiyama in “Evolution 2 International Journal of Evolutionary Biology of lysine biosynthesis in the phylum Deinococcus-Thermus” reported that bacterial lysine biosynthesis genes of the common ancestor of the Deinococcus-Thermus phylum used the α-aminoadipate pathway instead of the diaminopimelate pathway. K. Ueda et al. in “Dispensabilities of carbonic anhydrase in Proteobacteria” analyzed the distribution of carbonic anhydrase (CA) in proteobacteria, compared CA- retaining and CA-deficient genomes, and found absence of coding sequence in some strains and frame shifts in others. In closing this introduction to the special issue, we would like to express our full appreciation to all the authors and reviewers for their enormous efforts that have made the timely completion of our assignment successful. We sincerely hope that this special issue will stimulate further the investigation of evolutionary mechanisms of microbial genomes. Hiromi Nishida Shinji Kondo Hideaki Nojiri Ken-ichi Noma Kenro Oshima Hindawi Publishing Corporation International Journal of Evolutionary Biology Volume 2012, Article ID 859264, 9 pages doi:10.1155/2012/859264 Research Article Phylogenetic Position of Aquificales Based on the Whole Genome Sequences of Six Aquificales Species Kenro Oshima,1 Yoko Chiba, 2 Yasuo Igarashi, 2 Hiroyuki Arai,2 and Masaharu Ishii2 1 Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan 2 Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan Correspondence should be addressed to Kenro Oshima, [email protected] Received 10 February 2012; Revised 17 April 2012; Accepted 18 April 2012 Academic Editor: Hiromi Nishida Copyright
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