Functional divergence and origin of the DAG-like gene family in plants

Abstract The nuclear-encoded DAG-like (DAL) gene family plays critical roles in organelle C-to-U RNA editing in Arabidopsis thaliana. However, the origin, diversification and functional divergence of DAL genes remain unclear. Here, we analyzed the genomes of diverse plant species and found that: DAL...

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Autores principales:	Meijie Luo, Manjun Cai, Jianhua Zhang, Yurong Li, Ruyang Zhang, Wei Song, Ke Zhang, Hailin Xiao, Bing Yue, Yonglian Zheng, Yanxin Zhao, Jiuran Zhao, Fazhan Qiu
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/8a816fb041b5481581d1290df28b03d1
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spelling	oai:doaj.org-article:8a816fb041b5481581d1290df28b03d12021-12-02T11:40:43ZFunctional divergence and origin of the DAG-like gene family in plants10.1038/s41598-017-05961-22045-2322https://doaj.org/article/8a816fb041b5481581d1290df28b03d12017-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-05961-2https://doaj.org/toc/2045-2322Abstract The nuclear-encoded DAG-like (DAL) gene family plays critical roles in organelle C-to-U RNA editing in Arabidopsis thaliana. However, the origin, diversification and functional divergence of DAL genes remain unclear. Here, we analyzed the genomes of diverse plant species and found that: DAL genes are specific to spermatophytes, all DAL genes share a conserved gene structure and protein similarity with the inhibitor I9 domain of subtilisin genes found in ferns and mosses, suggesting that DAL genes likely arose from I9-containing proproteases via exon shuffling. Based on phylogenetic inference, DAL genes can be divided into five subfamilies, each composed of putatively orthologous and paralogous genes from different species, suggesting that all DAL genes originated from a common ancestor in early seed plants. Significant type I functional divergence was observed in 6 of 10 pairwise comparisons, indicating that shifting functional constraints have contributed to the evolution of DAL genes. This inference is supported by the finding that functionally divergent amino acids between subfamilies are predominantly located in the DAL domain, a critical part of the RNA editosome. Overall, these findings shed light on the origin of DAL genes in spermatophytes and outline functionally important residues involved in the complexity of the RNA editosome.Meijie LuoManjun CaiJianhua ZhangYurong LiRuyang ZhangWei SongKe ZhangHailin XiaoBing YueYonglian ZhengYanxin ZhaoJiuran ZhaoFazhan QiuNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-11 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Meijie Luo Manjun Cai Jianhua Zhang Yurong Li Ruyang Zhang Wei Song Ke Zhang Hailin Xiao Bing Yue Yonglian Zheng Yanxin Zhao Jiuran Zhao Fazhan Qiu Functional divergence and origin of the DAG-like gene family in plants
description	Abstract The nuclear-encoded DAG-like (DAL) gene family plays critical roles in organelle C-to-U RNA editing in Arabidopsis thaliana. However, the origin, diversification and functional divergence of DAL genes remain unclear. Here, we analyzed the genomes of diverse plant species and found that: DAL genes are specific to spermatophytes, all DAL genes share a conserved gene structure and protein similarity with the inhibitor I9 domain of subtilisin genes found in ferns and mosses, suggesting that DAL genes likely arose from I9-containing proproteases via exon shuffling. Based on phylogenetic inference, DAL genes can be divided into five subfamilies, each composed of putatively orthologous and paralogous genes from different species, suggesting that all DAL genes originated from a common ancestor in early seed plants. Significant type I functional divergence was observed in 6 of 10 pairwise comparisons, indicating that shifting functional constraints have contributed to the evolution of DAL genes. This inference is supported by the finding that functionally divergent amino acids between subfamilies are predominantly located in the DAL domain, a critical part of the RNA editosome. Overall, these findings shed light on the origin of DAL genes in spermatophytes and outline functionally important residues involved in the complexity of the RNA editosome.
format	article
author	Meijie Luo Manjun Cai Jianhua Zhang Yurong Li Ruyang Zhang Wei Song Ke Zhang Hailin Xiao Bing Yue Yonglian Zheng Yanxin Zhao Jiuran Zhao Fazhan Qiu
author_facet	Meijie Luo Manjun Cai Jianhua Zhang Yurong Li Ruyang Zhang Wei Song Ke Zhang Hailin Xiao Bing Yue Yonglian Zheng Yanxin Zhao Jiuran Zhao Fazhan Qiu
author_sort	Meijie Luo
title	Functional divergence and origin of the DAG-like gene family in plants
title_short	Functional divergence and origin of the DAG-like gene family in plants
title_full	Functional divergence and origin of the DAG-like gene family in plants
title_fullStr	Functional divergence and origin of the DAG-like gene family in plants
title_full_unstemmed	Functional divergence and origin of the DAG-like gene family in plants
title_sort	functional divergence and origin of the dag-like gene family in plants
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/8a816fb041b5481581d1290df28b03d1
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Functional divergence and origin of the DAG-like gene family in plants

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