Evolution of protein ductility in duplicated genes of plants

Inmaculada Yruela, Bruno Contreras-Moreira, A. Dunker, Karl J. Niklas

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

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.

Original languageEnglish (US)
Article number1216
JournalFrontiers in Plant Science
Volume9
DOIs
StatePublished - Aug 20 2018

Fingerprint

algae
genes
proteins
chromosomes
genetic recombination
gene duplication
Liliopsida
chromosome number
complement
amino acid sequences
genome
phylogeny
organisms
Bryophyta

Keywords

  • Genome duplication
  • IDPs
  • Paralogs
  • Plants
  • Polyploidy
  • Protein disorder
  • Protein ductility

ASJC Scopus subject areas

  • Plant Science

Cite this

Evolution of protein ductility in duplicated genes of plants. / Yruela, Inmaculada; Contreras-Moreira, Bruno; Dunker, A.; Niklas, Karl J.

In: Frontiers in Plant Science, Vol. 9, 1216, 20.08.2018.

Research output: Contribution to journalArticle

Yruela, Inmaculada ; Contreras-Moreira, Bruno ; Dunker, A. ; Niklas, Karl J. / Evolution of protein ductility in duplicated genes of plants. In: Frontiers in Plant Science. 2018 ; Vol. 9.
@article{d62479601180487d8724361bd064b0ff,
title = "Evolution of protein ductility in duplicated genes of plants",
abstract = "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.",
keywords = "Genome duplication, IDPs, Paralogs, Plants, Polyploidy, Protein disorder, Protein ductility",
author = "Inmaculada Yruela and Bruno Contreras-Moreira and A. Dunker and Niklas, {Karl J.}",
year = "2018",
month = "8",
day = "20",
doi = "10.3389/fpls.2018.01216",
language = "English (US)",
volume = "9",
journal = "Frontiers in Plant Science",
issn = "1664-462X",
publisher = "Frontiers Media S. A.",

}

TY - JOUR

T1 - Evolution of protein ductility in duplicated genes of plants

AU - Yruela, Inmaculada

AU - Contreras-Moreira, Bruno

AU - Dunker, A.

AU - Niklas, Karl J.

PY - 2018/8/20

Y1 - 2018/8/20

N2 - 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.

AB - 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.

KW - Genome duplication

KW - IDPs

KW - Paralogs

KW - Plants

KW - Polyploidy

KW - Protein disorder

KW - Protein ductility

UR - http://www.scopus.com/inward/record.url?scp=85054546403&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85054546403&partnerID=8YFLogxK

U2 - 10.3389/fpls.2018.01216

DO - 10.3389/fpls.2018.01216

M3 - Article

AN - SCOPUS:85054546403

VL - 9

JO - Frontiers in Plant Science

JF - Frontiers in Plant Science

SN - 1664-462X

M1 - 1216

ER -