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Evolution of Protein Ductility in Duplicated Genes of Plants
Previous work has shown that ductile/intrinsically disordered proteins (IDPs) and residues (IDRs) are found in all unicellular and multicellular organisms, wherein they are essential for basic cellular functions and complement the function of rigid proteins. In addition, computational studies of div...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Frontiers Media S.A.
2018
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6109787/ https://www.ncbi.nlm.nih.gov/pubmed/30177944 http://dx.doi.org/10.3389/fpls.2018.01216 |
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author | Yruela, Inmaculada Contreras-Moreira, Bruno Dunker, A. Keith Niklas, Karl J. |
author_facet | Yruela, Inmaculada Contreras-Moreira, Bruno Dunker, A. Keith Niklas, Karl J. |
author_sort | Yruela, Inmaculada |
collection | PubMed |
description | Previous work has shown that ductile/intrinsically disordered proteins (IDPs) and residues (IDRs) are found in all unicellular and multicellular organisms, wherein they are essential for basic cellular functions and complement the function of rigid proteins. In addition, computational studies of diverse phylogenetic lineages have revealed: (1) that protein ductility increases in concert with organismic complexity, and (2) that distributions of IDPs and IDRs along the chromosomes of plant species are non-random and correlate with variations in the rates of the genetic recombination and chromosomal rearrangement. Here, we show that approximately 50% of aligned residues in paralogs across a spectrum of algae, bryophytes, monocots, and eudicots are IDRs and that a high proportion (ca. 60%) are in disordered segments greater than 30 residues. When three types of IDRs are distinguished (i.e., identical, similar and variable IDRs) we find that species with large numbers of chromosome and endoduplicated genes exhibit paralogous sequences with a higher frequency of identical IDRs, whereas species with small chromosomes numbers exhibit paralogous sequences with a higher frequency of similar and variable IDRs. These results are interpreted to indicate that genome duplication events influence the distribution of IDRs along protein sequences and likely favor the presence of identical IDRs (compared to similar IDRs or variable IDRs). We discuss the evolutionary implications of gene duplication events in the context of ductile/disordered residues and segments, their conservation, and their effects on functionality. |
format | Online Article Text |
id | pubmed-6109787 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-61097872018-09-03 Evolution of Protein Ductility in Duplicated Genes of Plants Yruela, Inmaculada Contreras-Moreira, Bruno Dunker, A. Keith Niklas, Karl J. Front Plant Sci Plant Science Previous work has shown that ductile/intrinsically disordered proteins (IDPs) and residues (IDRs) are found in all unicellular and multicellular organisms, wherein they are essential for basic cellular functions and complement the function of rigid proteins. In addition, computational studies of diverse phylogenetic lineages have revealed: (1) that protein ductility increases in concert with organismic complexity, and (2) that distributions of IDPs and IDRs along the chromosomes of plant species are non-random and correlate with variations in the rates of the genetic recombination and chromosomal rearrangement. Here, we show that approximately 50% of aligned residues in paralogs across a spectrum of algae, bryophytes, monocots, and eudicots are IDRs and that a high proportion (ca. 60%) are in disordered segments greater than 30 residues. When three types of IDRs are distinguished (i.e., identical, similar and variable IDRs) we find that species with large numbers of chromosome and endoduplicated genes exhibit paralogous sequences with a higher frequency of identical IDRs, whereas species with small chromosomes numbers exhibit paralogous sequences with a higher frequency of similar and variable IDRs. These results are interpreted to indicate that genome duplication events influence the distribution of IDRs along protein sequences and likely favor the presence of identical IDRs (compared to similar IDRs or variable IDRs). We discuss the evolutionary implications of gene duplication events in the context of ductile/disordered residues and segments, their conservation, and their effects on functionality. Frontiers Media S.A. 2018-08-20 /pmc/articles/PMC6109787/ /pubmed/30177944 http://dx.doi.org/10.3389/fpls.2018.01216 Text en Copyright © 2018 Yruela, Contreras-Moreira, Dunker and Niklas. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Plant Science Yruela, Inmaculada Contreras-Moreira, Bruno Dunker, A. Keith Niklas, Karl J. Evolution of Protein Ductility in Duplicated Genes of Plants |
title | Evolution of Protein Ductility in Duplicated Genes of Plants |
title_full | Evolution of Protein Ductility in Duplicated Genes of Plants |
title_fullStr | Evolution of Protein Ductility in Duplicated Genes of Plants |
title_full_unstemmed | Evolution of Protein Ductility in Duplicated Genes of Plants |
title_short | Evolution of Protein Ductility in Duplicated Genes of Plants |
title_sort | evolution of protein ductility in duplicated genes of plants |
topic | Plant Science |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6109787/ https://www.ncbi.nlm.nih.gov/pubmed/30177944 http://dx.doi.org/10.3389/fpls.2018.01216 |
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