Growth of Biological Complexity from Prokaryotes to Hominids Reflected in the Human Genome

The growth of complexity in evolution is a most intriguing phenomenon. Using gene phylostratigraphy, we showed this growth (as reflected in regulatory mechanisms) in the human genome, tracing the path from prokaryotes to hominids. Generally, the different regulatory gene families expanded at differe...

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Autores principales:	Alexander E. Vinogradov, Olga V. Anatskaya
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	evolution of complexity gene phylostratigraphy transcription factors epigenetic factors nervous system cancer Biology (General) QH301-705.5 Chemistry QD1-999
Acceso en línea:	https://doaj.org/article/46712b7e376a4ebebe89102be5294416
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spelling	oai:doaj.org-article:46712b7e376a4ebebe89102be52944162021-11-11T17:06:52ZGrowth of Biological Complexity from Prokaryotes to Hominids Reflected in the Human Genome10.3390/ijms2221116401422-00671661-6596https://doaj.org/article/46712b7e376a4ebebe89102be52944162021-10-01T00:00:00Zhttps://www.mdpi.com/1422-0067/22/21/11640https://doaj.org/toc/1661-6596https://doaj.org/toc/1422-0067The growth of complexity in evolution is a most intriguing phenomenon. Using gene phylostratigraphy, we showed this growth (as reflected in regulatory mechanisms) in the human genome, tracing the path from prokaryotes to hominids. Generally, the different regulatory gene families expanded at different times, yet only up to the Euteleostomi (bony vertebrates). The only exception was the expansion of transcription factors (TF) in placentals; however, we argue that this was not related to increase in general complexity. Surprisingly, although TF originated in the Prokaryota while chromatin appeared only in the Eukaryota, the expansion of epigenetic factors predated the expansion of TF. Signaling receptors, tumor suppressors, oncogenes, and aging- and disease-associated genes (indicating vulnerabilities in terms of complex organization and strongly enrichment in regulatory genes) also expanded only up to the Euteleostomi. The complexity-related gene properties (protein size, number of alternative splicing mRNA, length of untranslated mRNA, number of biological processes per gene, number of disordered regions in a protein, and density of TF–TF interactions) rose in multicellular organisms and declined after the Euteleostomi, and possibly earlier. At the same time, the speed of protein sequence evolution sharply increased in the genes that originated after the Euteleostomi. Thus, several lines of evidence indicate that molecular mechanisms of complexity growth were changing with time, and in the phyletic lineage leading to humans, the most salient shift occurred after the basic vertebrate body plan was fixed with bony skeleton. The obtained results can be useful for evolutionary medicine.Alexander E. VinogradovOlga V. AnatskayaMDPI AGarticleevolution of complexitygene phylostratigraphytranscription factorsepigenetic factorsnervous systemcancerBiology (General)QH301-705.5ChemistryQD1-999ENInternational Journal of Molecular Sciences, Vol 22, Iss 11640, p 11640 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	evolution of complexity gene phylostratigraphy transcription factors epigenetic factors nervous system cancer Biology (General) QH301-705.5 Chemistry QD1-999
spellingShingle	evolution of complexity gene phylostratigraphy transcription factors epigenetic factors nervous system cancer Biology (General) QH301-705.5 Chemistry QD1-999 Alexander E. Vinogradov Olga V. Anatskaya Growth of Biological Complexity from Prokaryotes to Hominids Reflected in the Human Genome
description	The growth of complexity in evolution is a most intriguing phenomenon. Using gene phylostratigraphy, we showed this growth (as reflected in regulatory mechanisms) in the human genome, tracing the path from prokaryotes to hominids. Generally, the different regulatory gene families expanded at different times, yet only up to the Euteleostomi (bony vertebrates). The only exception was the expansion of transcription factors (TF) in placentals; however, we argue that this was not related to increase in general complexity. Surprisingly, although TF originated in the Prokaryota while chromatin appeared only in the Eukaryota, the expansion of epigenetic factors predated the expansion of TF. Signaling receptors, tumor suppressors, oncogenes, and aging- and disease-associated genes (indicating vulnerabilities in terms of complex organization and strongly enrichment in regulatory genes) also expanded only up to the Euteleostomi. The complexity-related gene properties (protein size, number of alternative splicing mRNA, length of untranslated mRNA, number of biological processes per gene, number of disordered regions in a protein, and density of TF–TF interactions) rose in multicellular organisms and declined after the Euteleostomi, and possibly earlier. At the same time, the speed of protein sequence evolution sharply increased in the genes that originated after the Euteleostomi. Thus, several lines of evidence indicate that molecular mechanisms of complexity growth were changing with time, and in the phyletic lineage leading to humans, the most salient shift occurred after the basic vertebrate body plan was fixed with bony skeleton. The obtained results can be useful for evolutionary medicine.
format	article
author	Alexander E. Vinogradov Olga V. Anatskaya
author_facet	Alexander E. Vinogradov Olga V. Anatskaya
author_sort	Alexander E. Vinogradov
title	Growth of Biological Complexity from Prokaryotes to Hominids Reflected in the Human Genome
title_short	Growth of Biological Complexity from Prokaryotes to Hominids Reflected in the Human Genome
title_full	Growth of Biological Complexity from Prokaryotes to Hominids Reflected in the Human Genome
title_fullStr	Growth of Biological Complexity from Prokaryotes to Hominids Reflected in the Human Genome
title_full_unstemmed	Growth of Biological Complexity from Prokaryotes to Hominids Reflected in the Human Genome
title_sort	growth of biological complexity from prokaryotes to hominids reflected in the human genome
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/46712b7e376a4ebebe89102be5294416
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Growth of Biological Complexity from Prokaryotes to Hominids Reflected in the Human Genome

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