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Biological meaning of “habitable zone” in nucleotide composition space
Organisms generally display two contrasting properties: large biodiversity and a uniform state of “life”. In this study, we focused on the question of how genome sequences describe “life” where a large number of biomolecules are harmonized. We analyzed the whole genome sequence of 2664 organisms, pa...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
The Biophysical Society of Japan (BSJ)
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5992858/ https://www.ncbi.nlm.nih.gov/pubmed/29892513 http://dx.doi.org/10.2142/biophysico.15.0_75 |
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author | Mitaku, Shigeki Sawada, Ryusuke |
author_facet | Mitaku, Shigeki Sawada, Ryusuke |
author_sort | Mitaku, Shigeki |
collection | PubMed |
description | Organisms generally display two contrasting properties: large biodiversity and a uniform state of “life”. In this study, we focused on the question of how genome sequences describe “life” where a large number of biomolecules are harmonized. We analyzed the whole genome sequence of 2664 organisms, paying attention to the nucleotide composition which is an intensive parameter from the genome sequence. The results showed that all organisms were plotted in narrow regions of the nucleotide composition space of the first and second letters of the codon. Since all genome sequences overlap irrespective of the living environment, it can be called a “habitable zone”. The habitable zone deviates by 500 times the standard deviation from the nucleotide composition expected from the random sequence, indicating that unexpectedly rare sequences are realized. Furthermore, we found that the habitable zones at the first and second letters of the codon serve as the background mechanisms for the functional network of biological systems. The habitable zone at the second letter of the codon controls the formation of transmembrane regions and the habitable zone at the first letter controls the formation of molecular recognition unit. These analyses showed that the habitable zone of the nucleotide composition space and the exquisite arrangement of amino acids in the codon table are conjugated to form biological systems. Finally, we discussed the evolution of the higher order of genome sequences. |
format | Online Article Text |
id | pubmed-5992858 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | The Biophysical Society of Japan (BSJ) |
record_format | MEDLINE/PubMed |
spelling | pubmed-59928582018-06-11 Biological meaning of “habitable zone” in nucleotide composition space Mitaku, Shigeki Sawada, Ryusuke Biophys Physicobiol Hypothesis and Perspective Organisms generally display two contrasting properties: large biodiversity and a uniform state of “life”. In this study, we focused on the question of how genome sequences describe “life” where a large number of biomolecules are harmonized. We analyzed the whole genome sequence of 2664 organisms, paying attention to the nucleotide composition which is an intensive parameter from the genome sequence. The results showed that all organisms were plotted in narrow regions of the nucleotide composition space of the first and second letters of the codon. Since all genome sequences overlap irrespective of the living environment, it can be called a “habitable zone”. The habitable zone deviates by 500 times the standard deviation from the nucleotide composition expected from the random sequence, indicating that unexpectedly rare sequences are realized. Furthermore, we found that the habitable zones at the first and second letters of the codon serve as the background mechanisms for the functional network of biological systems. The habitable zone at the second letter of the codon controls the formation of transmembrane regions and the habitable zone at the first letter controls the formation of molecular recognition unit. These analyses showed that the habitable zone of the nucleotide composition space and the exquisite arrangement of amino acids in the codon table are conjugated to form biological systems. Finally, we discussed the evolution of the higher order of genome sequences. The Biophysical Society of Japan (BSJ) 2018-04-21 /pmc/articles/PMC5992858/ /pubmed/29892513 http://dx.doi.org/10.2142/biophysico.15.0_75 Text en 2018 © The Biophysical Society of Japan This article is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. To view a copy of this license, visit https://creativecommons.org/licenses/by-nc-sa/4.0/. |
spellingShingle | Hypothesis and Perspective Mitaku, Shigeki Sawada, Ryusuke Biological meaning of “habitable zone” in nucleotide composition space |
title | Biological meaning of “habitable zone” in nucleotide composition space |
title_full | Biological meaning of “habitable zone” in nucleotide composition space |
title_fullStr | Biological meaning of “habitable zone” in nucleotide composition space |
title_full_unstemmed | Biological meaning of “habitable zone” in nucleotide composition space |
title_short | Biological meaning of “habitable zone” in nucleotide composition space |
title_sort | biological meaning of “habitable zone” in nucleotide composition space |
topic | Hypothesis and Perspective |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5992858/ https://www.ncbi.nlm.nih.gov/pubmed/29892513 http://dx.doi.org/10.2142/biophysico.15.0_75 |
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