Abstract
The world of prokaryotes (bacteria and archaea) is much more diverse than that of eukaryotes. After glancing the diversity of prokaryotes, the basic structure of prokaryote genomes is discussed using Escherichia coli as an example, followed by discussions on GC content heterogeneity, horizontal gene transfer, codon usage, prokaryotic metagenomes, plasmids, and CRISPR-Cas system.
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References
Fox, G. E., Magrum, L. J., Balch, W. E., Wolfe, R. S., & Woese, C. R. (1977). Classification of methanogenic bacteria by 16S ribosomal RNA characterization. Proceedings of the National Academy of Sciences USA, 74, 4537–4541.
Woese, C. R., & Fox, G. E. (1977). Phylogenetic structure of the prokaryotic domain: The primary kingdoms. Proceedings of the National Academy of Sciences USA, 74, 5088–5090.
Woese, C. R., et al. (1990). Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya. Proceedings of the National Academy of Sciences USA, 87, 4576–4579.
Koga, Y. (2012). Archaea. In Encyclopedia of evolution (pp. 37–42). Tokyo: Kyoritsu Shuppan (in Japanese).
Parks, D. H., et al. (2017). Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life. Nature Microbiology, 2, 1533–1542.
Fukami-Kobayashi, K., Minezaki, Y., Tateno, Y., & Nishikawa, K. (2007). A tree of life based on protein domain organizations. Molecular Biology and Evolution, 24, 1181–1189.
Battistuzzi, F. U., Feijão, A., & Hedges, S. B. (2004). A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land. BMC Evolutionary Biology, 4, 44.
Battistuzzi, F. U., & Hedges, S. B. (2009). A major clade of Prokaryotes with ancient adaptations to life on land. Molecular Biology and Evolution, 26, 335–343.
Yokono, M., Satoh, S., & Tanaka, A. (2018). Comparative analyses of whole-genome protein sequences from multiple organisms. Scientific Reports, 8, 6800.
Maeda, A. H., Nishi, S., Ozeki, Y., Ohta, Y., Hatada, Y., & Kanaly, R. A. (2013). Draft genome sequence of Sphingobium sp. strain KK22, a high-molecular-weight polycyclic aromatic hydrocarbon-degrading bacterium isolated from cattle pasture soil. Genome Announcements, 1, e00911–e00913.
GenProtEC database (http://genprotec.mbl.edu/overview.html).
PEC database at http://www.shigen.nig.ac.jp/ecoli/pec/genes.jsp.
Blattner, F. R., et al. (1997). The complete genome sequence of Escherichia coli K-12. Science, 277, 1453–1462.
Mahillon, J., & Chandler, M. (1998). Insertion sequences. Microbiology and Molecular Biology Reviews, 62, 725–774.
Hayashi, T., et al. (2001). Complete genome sequence of enterohemorrhagic Escherichia coli O157: H7 and genomic comparison with a laboratory strain K-12. DNA Research, 8, 11–22.
Watanabe, H., Mori, H., Itoh, T., & Gojobori, T. (1997). Genome plasticity as a paradigm of eubacteria evolution. Journal of Molecular Evolution, 44(Suppl 1), S57–S64.
Fraser, C. M., et al. (1995). The minimal gene complement of Mycoplasma genitalium. Science, 270, 397–403.
Shigenobu, S., Watanabe, H., Hattori, M., Sakaki, Y., & Ishikawa, H. (2000). Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS. Nature, 407, 81–86.
Cole, S. T., et al. (2001). Massive gene decay in the leprosy bacillus. Nature, 409, 1007–1011.
Gregory, T. R., & DeSakke, R. (2005). Chapter 10: Comparative genomics in Prokaryotes. In T. R. Gregory (Ed.), The evolution of the genome. Burlington: Elsevier.
Ferdows, M. S., & Barbour, A. G. (1989). Megabase-sized linear DNA in the bacterium Borrelia burgdorferi, the Lyme disease agent. Proceedings of the National Academy of Sciences USA, 86, 5969–5973.
Omura, S., et al. (2001). Genome sequence of an industrial microorganism Streptomyces avermitilis: Deducing the ability of producing secondary metabolites. Proceedings of the National Academy of Sciences USA, 98, 12215–12220.
Sueoka, N. (1962). On the genetic basis of variation and heterogeneity of DNA base composition. Proceedings of the National Academy of Sciences USA, 48, 582–592.
Moran, N. A. (2002). Microbial minimalism: Genome reduction in bacterial pathogens. Cell, 108, 583–586.
Rocha, E. P. C., & Danchin, A. (2002). Base composition bias might result from competition for metabolic resources. Trends in Genetics, 18, 291–294.
Saitou, N. (2007). Introduction to genome evolution studies. Tokyo: Kyoritsu Shuppan. (in Japanese).
Karlin, S., & Ladunga, I. (1994). Comparisons of eukaryotic genome sequences. Proceedings of the National Academy of Sciences USA, 91, 12832–12836.
Karlin, S., & Mrazek, J. (1997). Compositional differences within and between eukaryotic genomes. Proceedings of the National Academy of Sciences of the United States of America, 94, 10227–10232.
Karlin, S., Mrazek, J., & Campbell, A. (1997). Compositional biases of bacterial genomes and evolutionary implications. Journal of Bacteriology, 179, 3899–3913.
Karlin, S. (2005). Statistical signals in bioinformatics. Proceedings of the National Academy of Sciences USA, 102, 13355–13362.
Nakashima, H., Nishikawa, K., & Ooi, T. (1997). Differences in dinucleotide frequencies of human, yeast, and Escherichia coli genes. DNA Research, 4, 185–192.
Nakashima, H., Ota, M., Nishikawa, K., & Ooi, T. (1998). Genes from nine genomes are separated into their organisms in the dinucleotide composition space. DNA Research, 5, 251–259.
Kohonen, T. (1990). The self-organizing map. Proceedings of the IEEE, 78, 1464–1480.
Abe, T., Kanaya, S., Kinouchi, M., Ichiba, Y., Kozuki, T., & Ikemura, T. (2003). Informatics for unveiling hidden genome signatures. Genome Research, 13, 693–702.
Snel, B., Bork, P., & Huynen, M. A. (1999). Genome phylogeny based on gene content. Nature Genetics, 21, 108–110.
Tekaia, F., Lazcano, A., & Dujon, B. (1999). The genomic tree as revealed from whole proteome comparisons. Genome Research, 9, 550–557.
Fitz-Gibbon, S. T., & House, C. H. (1999). Whole genome-based phylogenetic analysis of free living microorganisms. Nucleic Acids Research, 27, 4218–4222.
Bansal, A. K., & Meyer, T. E. (2002). Evolutionary analysis by whole-genome comparisons. Journal of Bacteriology, 184, 2260–2272.
Gupta, R. S. (1998). Protein phylogenies and signature sequences: A reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes. Microbiology and Molecular Biology Reviews, 62, 1435–1491.
Gupta, R. S. (2001). The branching order and phylogenetic placement of species from completed bacterial genomes, based on conserved indels found in various proteins. International Microbiology, 4, 187–202.
Dandekar, T., Snel, B., Huynen, M., & Bork, P. (1998). Conservation of gene order: A fingerprint of proteins that physically interact. Trends in Biochemical Sciences, 23, 324–328.
Huynen, M. A., & Bork, P. (1998). Measuring genome evolution. Proceedings of the National Academy of Sciences USA, 95, 5849–5856.
Kunisawa, T. (2001). Gene arrangements and phylogeny in the class Proteobacteria. Journal of Theoretical Biology, 213, 9–19.
Suyama, M., & Bork, P. (2001). Evolution of prokaryotic gene order: Genome rearrangements in closely related species. Trends in Genetics, 17, 10–13.
Pride, D. T., Meinersmann, R. J., Wassenaar, T. M., & Blaser, M. J. (2003). Evolutionary implications of microbial genome tetranucleotide frequency biases. Genome Research, 13, 145–155.
Takahashi, M., Kryukov, K., & Saitou, N. (2009). Estimation of bacterial species phylogeny through oligonucleotide frequency distances. Genomics, 93, 525–533.
Rzhetsky, A., & Nei, M. (1992). A simple method for estimating and testing minimum-evolution trees. Molecular Biology and Evolution, 9, 945–967.
Koonin, E. V. (2011). The Logic of chance. Upper Saddle River: Pearson Education.
Sawada, H., Suzuki, F., Matsuda, I., & Saitou, N. (1999). Phylogenetic analysis of Pseudomonas syringe pathovar suggests the horizontal gene transfer of argK and the evolutionary stability of hrp gene cluster. Journal of Molecular Evolution, 49, 627–644.
Heinrichs, D. E., Yethon, J. A., & Whitfield, C. (1998). Molecular basis for structural diversity in the core regions of the lipopolysaccharides of Escherichia coli and Salmonella enterica. Molecular Microbiology, 30, 221–232.
Nakamura, Y., Itoh, T., Matsuda, H., & Gojobori, T. (2004). Biased biological functions of horizontally transferred genes in prokaryotic genomes. Nature Genetics, 36, 760–766.
Abby, S. S., Tannier, E., Gouy, M., & Daubin, V. (2012). Lateral gene transfer as a support for the tree of life. Proceedings of the National Academy of Sciences USA, 109, 4962–4967.
Doolittle, W. (1999). Phylogenetic classification and the universal tree. Science, 284, 2124–2129.
Saitou, N. (2004). Genome and evolution. Tokyo: Shinyosha. (in Japanese).
Ikemura, T. (1981). Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: A proposal for a synonymous codon choice that is optimal for the E. coli translational system. Journal of Molecular Biology, 151, 389–409.
Ikemura, T. (1982). Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes. Differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting transfer RNAs. Journal of Molecular Biology, 158, 573–597.
Ikemura, T. (1985). Codon usage and tRNA content in unicellular and multicellular organisms. Molecular Biology and Evolution, 2, 13–34.
Sharp, P. M., & Li, W. H. (1987). The rate of synonymous substitution in enterobacterial genes is inversely related to codon usage bias. Molecular Biology and Evolution, 4, 222–230.
Kanaya, S., Yamada, Y., Kinouchi, M., Kudo, Y., & Ikemura, T. (2001). Codon usage and tRNA genes in eukaryotes: Correlation of codon usage diversity with translation efficiency and with CG-dinucleotide usage as assessed by multivariate analysis. Journal of Molecular Evolution, 53, 290–298.
Nakamura, Y., Gojobori, T., & Ikemura, T. (2000). Codon usage tabulated from international DNA sequence databases: Status for the year 2000. Nucleic Acids Research, 28, 292.
Athey, J., et al. (2017) A new and updated resource for codon usage tables.
Venter, J. C., et al. (2004). Environmental genome shotgun sequencing of the Sargasso Sea. Science, 304, 66–74.
Abe, T., Sugawara, T., Kanaya, S., & Ikemura, T. (2005). Novel phylogenetic studies of genomic sequence fragments derived from uncultured microbe mixtures in environmental and clinical samples. DNA Research, 12, 281–290.
Rusch, D. B., et al. (2007). The Sorcerer II global ocean sampling expedition: Northwest Atlantic through Eastern Tropical Pacific. PLoS Biology, 5, e77.
Yooseph, S., et al. (2007). The Sorcerer II global ocean sampling expedition: Expanding the universe of protein families. PLoS Biology, 5, e16.
Kurokawa, K., et al. (2007). Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Research, 14, 169–181.
Yatsunenko, T., et al. (2012). Human gut microbiome viewed across age and geography. Nature, 486, 222–227.
Craig, R., & Millan, A. S. (2015). Microbial evolution: towards resolving the plasmid paradox. Current Biology, 25, R753–R773.
Shintani, M., et al. (2015). Genomics of microbial plasmids: classification and identification based on replication and transfer systems and host taxonomy. Frontiers in Microbiology, 6, 242.
Esser, K., et al. (1986). Plasmids of Eukaryotes. Berlin: Springer.
Harrison, E., & Brockhurst, M. A. (2012). Plasmid-mediated horizontal gene transfer is a coevolutionary process. Trends in Microbiology, 20, 262–267.
Bier, E., et al. (2018). Advances in engineering the fly genome with the CRISPR-Cas system. Genetics, 208, 1–18.
Ishino, Y., Shinagawa, H., Makino, K., Amemura, M., & Nakata, A. (1987). Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product. Journal of Bacteriology, 169, 5429–5433.
Jansen, R., et al. (2002). Identification of genes that are associated with DNA repeats in prokaryotes. Molecular Microbiology, 43, 1565–1575.
Barrangou, R., et al. (2007). CRISPR provides acquired resistance against viruses in prokaryotes. Science, 315, 1709–1712.
Koonin, E. V., Makarova, K. S., & Zhang, F. (2017). Diversity, classification and evolution of CRISPR-Cas systems. Current Opinion in Microbiology, 37, 67–78. Falush, D., et al. (2003). Traces of human migrations in Helicobacter pylori populations. Science, 299, 1582–1585.
Koonin, E. V., & Wolf, Y. I. (2016). Just how Lamarckian is CRISPR-Cas immunity: The continuum of evolvability mechanisms. Biology Direct, 11, 9.
Lamark, J.-B. (1809). Zoological philosophy, or exposition with regard to the natural history of animals (in French).
Falush, D., et al. (2003). Traces of human migrations in Helicobacter pylori populations. Science, 299, 1582–1585.
Suzuki, R., Shiota, S., & Yamaoka, Y. (2012). Molecular epidemiology, population genetics, and pathogenic role of Helicobacter pylori. Infection, Genetics and Evolution, 12, 203–213.
Kryukov, K., & Saitou, N. (2010). MISHIMA – A new method for high speed multiple alignment of nucleotide sequences of bacterial genome scale data. BMC Bioinformatics, 11, 142.
Kawai, M., Furuta, Y., Yahara, K., Tsuru, T., Oshima, K., Handa, N., et al. (2011). Evolution in an oncogenic bacterial species with extreme genome plasticity: Helicobacter pylori East Asian genomes. BMC Microbiology, 11, 104.
Thorell, K., et al. (2017). Rapid evolution of distinct Helicobacter pylori subpopulations in the Americas. PLoS Genetics, 13, e1006730.
Subsomwong, P., et al. (2017). Helicobacter pylori virulence genes of minor ethnic groups in North Thailand. Gut Pathogens, 9, 56.
Shapiro, B. J., Friedman, J., Cordero, O. X., Preheim, S. P., Timberlake, S. C., Szabo, G., et al. (2012). Population genomics of early events in the ecological differentiation of bacteria. Science, 336, 48–51.
Shapiro, B. J. (2018). What microbial population genomics has taught us about speciation. In: Population Genomics. Springer, Cham.
Mori, H., et al. (1997). Post-sequencing genome analysis of Escherichia coli. Tanpakushitsu-Kakusan-Koso, 46, 1977–1985. (in Japanese).
Yura, T., Mori, H., Nagai, H., Nagata, T., Ishihama, A., Fujita, N., et al. (1992). Systematic sequencing of the Escherichia coli genome: Analysis of the 0–2.4 min region. Nucleic Acids Research, 20, 3305–3308.
Fujita, N., Mori, H., Yura, T., & Ishihama, A. (1994). Systematic sequencing of the Escherichia coli genome: Analysis of the 2.4–4.1 min (110,917–193,643 bp) region. Nucleic Acids Research, 22, 1637–1639.
Oshima, T., et al. (1996). A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 12.7–28.0 min region on the linkage map. DNA Research, 3, 137–155.
Aiba, H., et al. (1996). A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 28.0–40.1 min region on the linkage map. DNA Research, 3, 363–377.
Itoh, T., et al. (1996). A 460-kb DNA sequence of the Escherichia coli K-12 genome corresponding to the 40.1–50.0 min region on the linkage map. DNA Research, 3, 379–392.
Yamamoto, Y., et al. (1997). Construction of a contiguous 874-kb sequence of the Escherichia coli – K12 genome corresponding to 50.0–68.8 min on the linkage map and analysis of its sequence features. DNA Research, 4, 91–113.
Fleischmann, R. D., et al. (1995). Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science, 269, 496–512.
http://en.wikipedia.org/wiki/Richard_Friedrich_Johannes_Pfeiffer.
Sanger, F., Coulson, A. R., Barrell, B. G., Smith, A. J. H., & Roe, B. A. (1980). Cloning in single-stranded bacteriophage as an aid to rapid DNA sequencing. Journal of Molecular Biology, 143, 161–178.
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Saitou, N. (2018). Prokaryote Genomes. In: Introduction to Evolutionary Genomics. Computational Biology, vol 17. Springer, Cham. https://doi.org/10.1007/978-3-319-92642-1_8
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DOI: https://doi.org/10.1007/978-3-319-92642-1_8
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