Tevatia Rahul, Oyler George A
Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America.
Synaptic Research LLC, Baltimore, Maryland, United States of America.
PLoS One. 2018 Jan 2;13(1):e0190282. doi: 10.1371/journal.pone.0190282. eCollection 2018.
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.
损伤DNA结合蛋白1（DDB1）结合WD40（DWD）蛋白高度保守，参与众多发育和生理过程，如开花时间控制、光形态建成和非生物胁迫反应。绿色植物中该蛋白家族在植物和藻类中的系统发育是理解该家族在如此重要且多样的功能中出现的关键领域。我们旨在研究绿色植物中DWD的假定同源物，并更深入地掌握DWD的进化情况。公开可用基因组数据的进步使我们能够进行广泛的全基因组DWD检索。以注释的拟南芥DWD为参考，我们为所研究的光合自养生物生成并表征了一个全面的DWD数据库。此外，采用了一种通用的DWD分类系统（A至K型），该系统基于：（i）DWD基序的位置，（ii）DWD基序的数量，以及（iii）其他结构域的存在与否。约72 - 80%的DWD有一个DWD基序，而17 - 24%的DWD有两个，0.5 - 4.7%的DWD有三个DWD基序。拟南芥DWD的邻接法系统发育构建使我们能够将这些底物受体分为15组。尽管从微藻到高等陆地植物DWD的数量增加，但在整个绿色植物中DWD与WD40的比例保持恒定。DWD的扩展似乎是持续的DWD基因流动以及若干基因复制事件的结果。网络、系统发育和统计分析描绘了绿色植物中DWD的进化相关性。
