Viva Origino
Online ISSN : 1346-6933
Print ISSN : 0910-4003
Volume 32, Issue 2
Displaying 1-5 of 5 articles from this issue
  • Kunio Kawamura, Fumitaka Okamoto, Noriko Okuda
    2004 Volume 32 Issue 2 Pages 68-80
    Published: 2004
    Released on J-STAGE: January 29, 2022
    JOURNAL FREE ACCESS

      The condensation reaction of oligonucleotides was investigated to develop a prebiotic model reaction for the formation of oligonucleotides which can be examined under hydrothermal conditions. The reaction behavior of (1) the condensation of 12-mer oligonucleotide (5’-pGGGCCCCCCGGrG, 5’-pGGGCCCGGGCCrC), (2) the condensation of oligoguanylate (5’-pGGGGGrG, 5’-pGGGGGGGrG) in the absence and presence of a oligocytidylate template, (3) the condensation of mix-hexanucleotide including guanine and cytosine (5’-pGGGCCrC,5’-pGCGCGrC,5’-pGCCCGrG) in the absence and presence of several 12-mer oligonucleotides, was investigated at 0 – 25℃. In these systems, it was expected that the dimerization of the starting oligonucleotides would be enhanced using 12-mer oligonucleotides or in the presence of a template oligonucleotide. However, the cyclization of oligonucleotides proceeded as the main process and the dimerization was not efficient. The rates of the cyclization of 12-mer oligonucleotides were not much different from those of hexanucleotides determined in previous studies. The rate of cyclization of 5’-pGGGGGrG or 5’-pGGGGGGGrG was somewhat affected with a oligocytidylate template. Although the cyclization of mixhexanucleotides was not much affected by the presence of 5’-GGGCCCCCCGGG or 5’-GGGCCCGGGCCC,the condensation of mix-hexanucleotides did not proceed in the presence of 5’-GCGCGCGCGCGC or 5’-GCCCGGGCCCGG. These resultes indicate that cyclization of short oligonucleotides have readily proceeded even in the presence of template oligonucleotides so that the accumulation of RNA would not be efficient through the dimerization of short oligonucleotides. Conclusively, the reactions tested in this study are not suitable for the elongation model of oligonucleotide which acts under hydrothermal conditions

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  • Shin Miyakawa
    2004 Volume 32 Issue 2 Pages 81-95
    Published: 2004
    Released on J-STAGE: January 29, 2022
    JOURNAL FREE ACCESS

      It remains uncertain whether life originated in a hot environment or a cold environment, although many studies have been done from several different perspectives. The theory of the hot origin of life is based on the presence of hyperthermophiles near the root of the phylogenetic tree, the discovery of unique environments for life surrounding hydrothermal vents, the greenhouse effect of a dense CO2 atmosphere, and the isotopic fluctuation of oxygen. However, bioorganic molecules are rather unstable at high temperatures. Here, I review previous studies concerning the hot and cold origins of life and re-assess which is more plausible.

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  • Yonosuke Maki, Kazutoshi Ogawa, Akira Shimizu
    2004 Volume 32 Issue 2 Pages 96-108
    Published: 2004
    Released on J-STAGE: January 29, 2022
    JOURNAL FREE ACCESS

      During a period of not so far after the origins of life on earth, symbiotic microbial cooperation in some way must has started. Kato and Shimizu proposed a name of “pristine ecosystem” to such the symbiotic cooperation (microbial interaction), because it could be positioned at origins of ecosystem. However, the scene of structure and function of the cooperation has not become evident. Sulfur-turf is filamentous microbial mat growing in hot spring effluents, and the filament of the mat consists of a few sulfur-oxidizing bacteria (large sausage-shaped and small curved), sulfur particles, and cellulose as a matrix substance. Here, we took up sulfur-turf as a model of pristine symbiotic cooperation, and discussed a possibility of the correlation of filament structure, specially emphasized the roll of cellulose-core, with three steps of a series of sulfur-oxidizing reaction; hydrogen sulfide to sulfate via elemental sulfur and thiosulfate. Sulfide oxidation probably proceeds at the outside of the filament or of the mat by sausage-shaped bacteria and resulting elemental sulfur. As both of elemental sulfur and cellulose are hydrophobic, sulfur particles may be concentrated around cellulose-core of the filament where microaerophilic conditions are prevailed, and is oxidized to thiosulfate by sausage-shaped bacteria or by curved bacteria. Thiosulfate decreases pH value around the cellulose-core and is oxidized to sulfate. The significance of cellulose as matrix substance in the steps of sulfur-oxidation should be emphasized. Pristine symbiotic cooperation may have started in microbial mats as syntrophic, namely as a style of substrate chain and in a manner of exosymbiotic relation.

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  • Hiroyuki YAMAMOTO
    2004 Volume 32 Issue 2 Pages 109-117
    Published: 2004
    Released on J-STAGE: January 29, 2022
    JOURNAL FREE ACCESS

      The rRNA-gene phylogeny of modern life revealed possible evolutionary history of microorganisms, and suggested their ancestral organism came from thermal environments. If the assumption which raised from the gene sequences indicates right direction of life evolution, it must correspond with geological clues, such as the evidences of fossil and biomaker, and the paleoecological studies. Multidisciplinary collaboration with geologists, meteologist and microbiologists recently disclose the Archean life history from the oldest sedimentary rocks and the molecular records within gene sequences. The knowledge may be still fragmentally, and some of them remains under discussion. The hypothetical history of microbial ecosystem written in this article opens after the first Earth’s biosphere established by ancestral microorganism.

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  • Hiroshi Xavier CHIURA
    2004 Volume 32 Issue 2 Pages 118-137
    Published: 2004
    Released on J-STAGE: January 29, 2022
    JOURNAL FREE ACCESS

      As whole-genome sequencing projects advance, it is becoming clear that gene exchange among organisms of the microbial consortia is constitutive. On average, 2.6 prophages per specie have been found in free-living bacteria, and between 3% and 10% of various bacterial genomes’ DNA are composed of prophages. Based upon data, it has been suggested that Escherichia coli and Salmonella separated ca 100 million years ago. Although the rRNA operon is highly conserved, E. coli has an extremely variable genome size ranging from 4.5 to 5.5 Mb, of which ca 10% consists of acquired genes as the result of horizontal gene transfer. The genome of the E. coli strain O157 Sakai has a large amount of strain-specific DNA (1.44 Mb), and contains 18 prophages or prophage remnants accounting for ca 50% of the strain-specific sequences. Moreover, six large chromosome segments, which seem to represent prophage-like genetic elements, are found in O157. Thus, phage genes are an integral part of O157 genome, indicating that virus-mediated high frequency horizontal gene transfer played a predominant role in the emergence of this strain. Direct evidence of such horizontal gene transfer is provided by prophages or prophage remnant sequences in O157 as well as in other strains.

      The case of E. coli is an example of how viruses might have influenced evolutionary diversification and speciation. Therefore, it is clear that virus-mediated horizontal gene transfer would have had much more impact in the environment than previously considered. The discovery of non-specific gene transfer mediators, especially in thermal environments, is evidence that such particles might be widespread, contributing to evolutionary diversification and speciation. Viruses may have evolved to sustain ‘selfish’ genes for their coats, and consequently underwent restriction of specific host range. “Transduction” may have major effects on the genetic structure and evolution of the global population of bacteria and other organisms in the natural environment. “Broad-host range gene transporters” conserved in the environment could be descendants of an ancestral “gene transfer apparatus” that likely provided the main role of conserving genetic resources and distributing novel genes to microbial communities in early evolutionary history.

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