The Possible Crystallization Process in the Origin of Bacteria, Archaea, Viruses, and Mobile Elements
We propose a hypothesis for the simultaneous emergence of bacteria, archaea, viruses, and mobile elements by sequential and concrete biochemical pathways. The emergence process can be considered analogous to crystallization, where genetic and biochemical systems stabilize as organisms evolve from th...
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2024-12-01
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| author | Akari Yoshimura Masayuki Seki |
| author_facet | Akari Yoshimura Masayuki Seki |
| author_sort | Akari Yoshimura |
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| description | We propose a hypothesis for the simultaneous emergence of bacteria, archaea, viruses, and mobile elements by sequential and concrete biochemical pathways. The emergence process can be considered analogous to crystallization, where genetic and biochemical systems stabilize as organisms evolve from their common ancestor, the LUCA, which was a non-free-living pool of single operon type genomes including double-stranded (ds) DNA at an ancient submarine alkaline vent. Each dsDNA operon was transcribed by different systems in σ, TFIIB, or TBP genomes. Double-stranded DNA operons can fuse and stabilize through the action of specific transcription systems, leading to differentiation between the Bacteria (σ genome) and Archaea (TBP genome) domains. Error catastrophe can be overcome by the parallel gain of DNA replication and DNA repair mechanisms in both genomes. Enlarged DNA enabled efficient local biochemical reactions. Both genomes independently recruited lipids to facilitate reactions by forming coacervates at the chamber of the vent. Bilayer lipid membrane formation, proto-cell formation with a permeable membrane, proto-cell division, and the evolution of membrane-associated biochemistry are presented in detail. Simultaneous crystallization of systems in non-free-living bacteria and non-free-living archaea triggered the co-crystallization of primitive viruses and mobile elements. An arms race between non-free-living cells and primitive viruses finally led to free-living cells with a cell wall and mature viruses. |
| format | Article |
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| institution | Kabale University |
| issn | 2079-7737 |
| language | English |
| publishDate | 2024-12-01 |
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| spelling | doaj-art-331e4bbaa2f145c78faea6de6f37638c2025-01-24T13:23:16ZengMDPI AGBiology2079-77372024-12-01141310.3390/biology14010003The Possible Crystallization Process in the Origin of Bacteria, Archaea, Viruses, and Mobile ElementsAkari Yoshimura0Masayuki Seki1Division of Biochemistry, Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, Sendai 981-8558, JapanDivision of Biochemistry, Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, Sendai 981-8558, JapanWe propose a hypothesis for the simultaneous emergence of bacteria, archaea, viruses, and mobile elements by sequential and concrete biochemical pathways. The emergence process can be considered analogous to crystallization, where genetic and biochemical systems stabilize as organisms evolve from their common ancestor, the LUCA, which was a non-free-living pool of single operon type genomes including double-stranded (ds) DNA at an ancient submarine alkaline vent. Each dsDNA operon was transcribed by different systems in σ, TFIIB, or TBP genomes. Double-stranded DNA operons can fuse and stabilize through the action of specific transcription systems, leading to differentiation between the Bacteria (σ genome) and Archaea (TBP genome) domains. Error catastrophe can be overcome by the parallel gain of DNA replication and DNA repair mechanisms in both genomes. Enlarged DNA enabled efficient local biochemical reactions. Both genomes independently recruited lipids to facilitate reactions by forming coacervates at the chamber of the vent. Bilayer lipid membrane formation, proto-cell formation with a permeable membrane, proto-cell division, and the evolution of membrane-associated biochemistry are presented in detail. Simultaneous crystallization of systems in non-free-living bacteria and non-free-living archaea triggered the co-crystallization of primitive viruses and mobile elements. An arms race between non-free-living cells and primitive viruses finally led to free-living cells with a cell wall and mature viruses.https://www.mdpi.com/2079-7737/14/1/3the last universal common ancestorsubmarine alkaline hydrothermal ventTBPσ-factorDNA polymeraserecombinase |
| spellingShingle | Akari Yoshimura Masayuki Seki The Possible Crystallization Process in the Origin of Bacteria, Archaea, Viruses, and Mobile Elements Biology the last universal common ancestor submarine alkaline hydrothermal vent TBP σ-factor DNA polymerase recombinase |
| title | The Possible Crystallization Process in the Origin of Bacteria, Archaea, Viruses, and Mobile Elements |
| title_full | The Possible Crystallization Process in the Origin of Bacteria, Archaea, Viruses, and Mobile Elements |
| title_fullStr | The Possible Crystallization Process in the Origin of Bacteria, Archaea, Viruses, and Mobile Elements |
| title_full_unstemmed | The Possible Crystallization Process in the Origin of Bacteria, Archaea, Viruses, and Mobile Elements |
| title_short | The Possible Crystallization Process in the Origin of Bacteria, Archaea, Viruses, and Mobile Elements |
| title_sort | possible crystallization process in the origin of bacteria archaea viruses and mobile elements |
| topic | the last universal common ancestor submarine alkaline hydrothermal vent TBP σ-factor DNA polymerase recombinase |
| url | https://www.mdpi.com/2079-7737/14/1/3 |
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