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Networks of function and shared ancestry provide insights into diversification of histone fold domain in the plant kingdom

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Title Networks of function and shared ancestry provide insights into diversification of histone fold domain in the plant kingdom
 
Creator Kumar, Amish
Yadav, Gitanjali
 
Subject Histone fold motif
Plant kingdom
Co-expression networks
Gene regulatory networks
Protein-protein interaction networks
 
Description Accepted date: 25 November 2019
The Histone Fold Motif (HFM) of core histone proteins is one of the most highly conserved signature motifs in living organisms. Despite significant variation in sequence over millions of years of evolution, the HFM retains a distinctive structural fold that has diversified into several non-histone protein families. We have identified over 4000 HFM containing proteins in plants that are not histones, raising the question of why the family has expanded so considerably in the plant kingdom. We find that a majority of non-histone HFMs are playing regulatory roles, and that they are distributed widely within and across taxonomic groups. In this work we explore the relationships between the HFM of non-histones and that of their ancestral core histone forerunners, using a network approach. Networks of core histones and non-histone counterparts were superimposed with additional layers of complexity, like functional annotations, sub cellular locations, taxonomy and shared ancestry. HFM networks of model plants rice and Arabidopsis were investigated in terms of gene expression, interactions with other proteins as well as regulatory potential, to gain insights into diversification events during evolution that are not immediately evident from phylogenetic trees or raw data alone. Taken together, the networks elucidate diverse paths of evolution of the histone fold motif, leading to sub-functionalization and neo-functionalization of the HFM.
GY concieved the idea and AK planned and executed the work. This work was funded by the DBT-BTISNET and DST-SERB grant, AK obtained fellowship grant from UGC-CSIR and NIPGR. GY is funded by the DBT-Cambridge Lectureship and the GCRF TIGR2ESS Grant ID [BB/P027970/1TIGR2ESS]. Authors thank Director, NIPGR for support.
 
Date 2020-07-28T11:07:36Z
2020-07-28T11:07:36Z
2020
 
Type Book chapter
 
Identifier In: Cherifi H, Gaito S, Mendes JF, Moro E, Rocha LM (eds), Complex Networks and Their Applications VIII, COMPLEX NETWORKS 2019. Studies in Computational Intelligence, vol 882. Springer, Cham, pp 789-801
978-3-030-36683-4
1860-9503
https://doi.org/10.1007/978-3-030-36683-4_63
https://link.springer.com/chapter/10.1007/978-3-030-36683-4_63
http://223.31.159.10:8080/jspui/handle/123456789/1080
 
Language en_US
 
Format application/pdf
 
Publisher Springer Nature Publishing AG