Functional divergence and origin of the DAG-like gene family in plants
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...
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| Published in | Scientific reports Vol. 7; no. 1; pp. 5688 - 11 |
|---|---|
| Main Authors | , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
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London
Nature Publishing Group UK
18.07.2017
Nature Publishing Group Nature Portfolio |
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| 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. |
|---|---|
| AbstractList | 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.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. 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. 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. 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. |
| ArticleNumber | 5688 |
| Author | Zhang, Ke Cai, Manjun Zhao, Jiuran Zhao, Yanxin Qiu, Fazhan Zhang, Ruyang Zhang, Jianhua Xiao, Hailin Song, Wei Luo, Meijie Zheng, Yonglian Li, Yurong Yue, Bing |
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| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/28720816$$D View this record in MEDLINE/PubMed |
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| SSID | ssj0000529419 |
| Score | 2.2698717 |
| Snippet | The nuclear-encoded
DAG-like
(
DAL
) gene family plays critical roles in organelle C-to-U RNA editing in
Arabidopsis thaliana
. However, the origin,... The nuclear-encoded DAG-like (DAL) gene family plays critical roles in organelle C-to-U RNA editing in Arabidopsis thaliana. However, the origin,... 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,... |
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| SourceType | Open Website Open Access Repository Aggregation Database Index Database Enrichment Source Publisher |
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| SubjectTerms | 38/22 38/77 38/90 45/47 631/181/735 631/208/8 631/449/2669 Amino acids Evolutionary genetics Ferns Genes Genomes Humanities and Social Sciences multidisciplinary Phylogeny Plant species Protein structure RNA editing Science Science (multidisciplinary) Subtilisin |
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| Title | Functional divergence and origin of the DAG-like gene family in plants |
| URI | https://link.springer.com/article/10.1038/s41598-017-05961-2 https://www.ncbi.nlm.nih.gov/pubmed/28720816 https://www.proquest.com/docview/1956120023 https://www.proquest.com/docview/1920395013 https://pubmed.ncbi.nlm.nih.gov/PMC5515838 https://doaj.org/article/8a816fb041b5481581d1290df28b03d1 |
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