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Title: Evolution of DDB1-binding WD40 (DWD) in the viridiplantae

Abstract

Damaged DNA Binding 1 (DDB1)—binding WD40 (DWD) proteins are highly conserved and involved in a plethora of developmental and physiological processes such as flowering time control, photomorphogenesis, and abiotic stress responses. The phylogeny of this family of proteins in plants and algae of viridiplante is a critical area to understand the emergence of this family in such important and diverse functions. We aimed to investigate the putative homologs of DWD in the viridiplante and establish a deeper DWD evolutionary grasp. The advancement in publicly available genomic data allowed us to perform an extensive genome-wide DWD retrieval. Using annotated Arabidopsis thaliana DWDs as the reference, we generated and characterized a comprehensive DWD database for the studied photoautotrophs. Further, a generic DWD classification system (Type A to K), based on (i) position of DWD motifs, (ii) number of DWD motifs, and (iii) presence/absence of other domains, was adopted. About 72–80% DWDs have one DWD motif, whereas 17–24% DWDs have two and 0.5–4.7% DWDs have three DWD motifs. Neighbor-joining phylogenetic construction of A. thaliana DWDs facilitated us to tune these substrate receptors into 15 groups. Though the DWD count increases from microalgae to higher land plants, the ratio of DWD to WD40 remainedmore » constant throughout the viridiplante. The DWD expansion appeared to be the consequence of consistent DWD genetic flow accompanied by several gene duplication events. The network, phylogenetic, and statistical analysis delineated DWD evolutionary relevance in the viridiplante.« less

Authors:
ORCiD logo [1];  [2];  [3]
  1. Johns Hopkins Univ., Baltimore, MD (United States). Dept. of Chemical and Biomolecular Engineering
  2. Johns Hopkins Univ., Baltimore, MD (United States). Dept. of Chemical and Biomolecular Engineering; Synaptic Research LLC, Baltimore, MD (United States)
  3. National Taiwan Univ., Taipei (Taiwan)
Publication Date:
Research Org.:
Univ. of California, San Diego, CA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1499885
Grant/Contract Number:  
EE0003373
Resource Type:
Accepted Manuscript
Journal Name:
PLoS ONE
Additional Journal Information:
Journal Volume: 13; Journal Issue: 1; Journal ID: ISSN 1932-6203
Publisher:
Public Library of Science
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Tevatia, Rahul, Oyler, George A., and Chang, Ing-Feng. Evolution of DDB1-binding WD40 (DWD) in the viridiplantae. United States: N. p., 2018. Web. doi:10.1371/journal.pone.0190282.
Tevatia, Rahul, Oyler, George A., & Chang, Ing-Feng. Evolution of DDB1-binding WD40 (DWD) in the viridiplantae. United States. doi:10.1371/journal.pone.0190282.
Tevatia, Rahul, Oyler, George A., and Chang, Ing-Feng. Tue . "Evolution of DDB1-binding WD40 (DWD) in the viridiplantae". United States. doi:10.1371/journal.pone.0190282. https://www.osti.gov/servlets/purl/1499885.
@article{osti_1499885,
title = {Evolution of DDB1-binding WD40 (DWD) in the viridiplantae},
author = {Tevatia, Rahul and Oyler, George A. and Chang, Ing-Feng},
abstractNote = {Damaged DNA Binding 1 (DDB1)—binding WD40 (DWD) proteins are highly conserved and involved in a plethora of developmental and physiological processes such as flowering time control, photomorphogenesis, and abiotic stress responses. The phylogeny of this family of proteins in plants and algae of viridiplante is a critical area to understand the emergence of this family in such important and diverse functions. We aimed to investigate the putative homologs of DWD in the viridiplante and establish a deeper DWD evolutionary grasp. The advancement in publicly available genomic data allowed us to perform an extensive genome-wide DWD retrieval. Using annotated Arabidopsis thaliana DWDs as the reference, we generated and characterized a comprehensive DWD database for the studied photoautotrophs. Further, a generic DWD classification system (Type A to K), based on (i) position of DWD motifs, (ii) number of DWD motifs, and (iii) presence/absence of other domains, was adopted. About 72–80% DWDs have one DWD motif, whereas 17–24% DWDs have two and 0.5–4.7% DWDs have three DWD motifs. Neighbor-joining phylogenetic construction of A. thaliana DWDs facilitated us to tune these substrate receptors into 15 groups. Though the DWD count increases from microalgae to higher land plants, the ratio of DWD to WD40 remained constant throughout the viridiplante. The DWD expansion appeared to be the consequence of consistent DWD genetic flow accompanied by several gene duplication events. The network, phylogenetic, and statistical analysis delineated DWD evolutionary relevance in the viridiplante.},
doi = {10.1371/journal.pone.0190282},
journal = {PLoS ONE},
number = 1,
volume = 13,
place = {United States},
year = {2018},
month = {1}
}

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