Genome-Wide Identification and Transcriptional Analysis of Arabidopsis DUF506 Gene Family

The Domain of unknown function 506 (DUF506) family, which belongs to the PD-(D/E)XK nuclease superfamily, has not been functionally characterized. In this study, 266 DUF506 domain-containing genes were identified from algae, mosses, and land plants showing their...

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Autor principal:	Sheng Ying
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	abiotic stress arabidopsis domain of unknown function (DUF) domain-structure evolutionary analysis expression profiling Biology (General) QH301-705.5 Chemistry QD1-999
Acceso en línea:	https://doaj.org/article/f664558ae6494dfc9ca76b42db1e4ec9
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spelling	oai:doaj.org-article:f664558ae6494dfc9ca76b42db1e4ec92021-11-11T16:54:27ZGenome-Wide Identification and Transcriptional Analysis of Arabidopsis <i>DUF506</i> Gene Family10.3390/ijms2221114421422-00671661-6596https://doaj.org/article/f664558ae6494dfc9ca76b42db1e4ec92021-10-01T00:00:00Zhttps://www.mdpi.com/1422-0067/22/21/11442https://doaj.org/toc/1661-6596https://doaj.org/toc/1422-0067The Domain of unknown function 506 (<i>DUF506</i>) family, which belongs to the PD-(D/E)XK nuclease superfamily, has not been functionally characterized. In this study, 266 <i>DUF506</i> domain-containing genes were identified from algae, mosses, and land plants showing their wide occurrence in photosynthetic organisms. Bioinformatics analysis identified 211 high-confidence <i>DUF506</i> genes across 17 representative land plant species. Phylogenetic modeling classified three groups of plant <i>DUF506</i> genes that suggested functional preservation among the groups based on conserved gene structure and motifs. Gene duplication and Ka/Ks evolutionary rates revealed that <i>DUF506</i> genes are under purifying positive selection pressure. Subcellular protein localization analysis revealed that <i>DUF506</i> proteins were present in different organelles. Transcript analyses showed that 13 of the Arabidopsis <i>DUF506</i> genes are ubiquitously expressed in various tissues and respond to different abiotic stresses and ABA treatment. Protein-protein interaction network analysis using the STRING-DB, AtPIN (<i>Arabidopsis thaliana</i> Protein Interaction Network), and AI-1 (Arabidopsis Interactome-1) tools indicated that AtDUF506s potentially interact with iron-deficiency response proteins, salt-inducible transcription factors, or calcium sensors (calmodulins), implying that <i>DUF506</i> genes have distinct biological functions including responses to environmental stimuli, nutrient-deficiencies, and participate in Ca(2+) signaling. Current results provide insightful information regarding the molecular features of the <i>DUF506</i> family in plants, to support further functional characterizations.Sheng YingMDPI AGarticleabiotic stressarabidopsisdomain of unknown function (DUF)domain-structureevolutionary analysisexpression profilingBiology (General)QH301-705.5ChemistryQD1-999ENInternational Journal of Molecular Sciences, Vol 22, Iss 11442, p 11442 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	abiotic stress arabidopsis domain of unknown function (DUF) domain-structure evolutionary analysis expression profiling Biology (General) QH301-705.5 Chemistry QD1-999
spellingShingle	abiotic stress arabidopsis domain of unknown function (DUF) domain-structure evolutionary analysis expression profiling Biology (General) QH301-705.5 Chemistry QD1-999 Sheng Ying Genome-Wide Identification and Transcriptional Analysis of Arabidopsis <i>DUF506</i> Gene Family
description	The Domain of unknown function 506 (<i>DUF506</i>) family, which belongs to the PD-(D/E)XK nuclease superfamily, has not been functionally characterized. In this study, 266 <i>DUF506</i> domain-containing genes were identified from algae, mosses, and land plants showing their wide occurrence in photosynthetic organisms. Bioinformatics analysis identified 211 high-confidence <i>DUF506</i> genes across 17 representative land plant species. Phylogenetic modeling classified three groups of plant <i>DUF506</i> genes that suggested functional preservation among the groups based on conserved gene structure and motifs. Gene duplication and Ka/Ks evolutionary rates revealed that <i>DUF506</i> genes are under purifying positive selection pressure. Subcellular protein localization analysis revealed that <i>DUF506</i> proteins were present in different organelles. Transcript analyses showed that 13 of the Arabidopsis <i>DUF506</i> genes are ubiquitously expressed in various tissues and respond to different abiotic stresses and ABA treatment. Protein-protein interaction network analysis using the STRING-DB, AtPIN (<i>Arabidopsis thaliana</i> Protein Interaction Network), and AI-1 (Arabidopsis Interactome-1) tools indicated that AtDUF506s potentially interact with iron-deficiency response proteins, salt-inducible transcription factors, or calcium sensors (calmodulins), implying that <i>DUF506</i> genes have distinct biological functions including responses to environmental stimuli, nutrient-deficiencies, and participate in Ca(2+) signaling. Current results provide insightful information regarding the molecular features of the <i>DUF506</i> family in plants, to support further functional characterizations.
format	article
author	Sheng Ying
author_facet	Sheng Ying
author_sort	Sheng Ying
title	Genome-Wide Identification and Transcriptional Analysis of Arabidopsis <i>DUF506</i> Gene Family
title_short	Genome-Wide Identification and Transcriptional Analysis of Arabidopsis <i>DUF506</i> Gene Family
title_full	Genome-Wide Identification and Transcriptional Analysis of Arabidopsis <i>DUF506</i> Gene Family
title_fullStr	Genome-Wide Identification and Transcriptional Analysis of Arabidopsis <i>DUF506</i> Gene Family
title_full_unstemmed	Genome-Wide Identification and Transcriptional Analysis of Arabidopsis <i>DUF506</i> Gene Family
title_sort	genome-wide identification and transcriptional analysis of arabidopsis <i>duf506</i> gene family
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/f664558ae6494dfc9ca76b42db1e4ec9
work_keys_str_mv	AT shengying genomewideidentificationandtranscriptionalanalysisofarabidopsisiduf506igenefamily
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Genome-Wide Identification and Transcriptional Analysis of Arabidopsis <i>DUF506</i> Gene Family

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