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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 wide occurrence in photosynthetic org...

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Autor principal: Ying, Sheng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8583954/
https://www.ncbi.nlm.nih.gov/pubmed/34768874
http://dx.doi.org/10.3390/ijms222111442
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author Ying, Sheng
author_facet Ying, Sheng
author_sort Ying, Sheng
collection PubMed
description 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 wide occurrence in photosynthetic organisms. Bioinformatics analysis identified 211 high-confidence DUF506 genes across 17 representative land plant species. Phylogenetic modeling classified three groups of plant DUF506 genes that suggested functional preservation among the groups based on conserved gene structure and motifs. Gene duplication and Ka/Ks evolutionary rates revealed that DUF506 genes are under purifying positive selection pressure. Subcellular protein localization analysis revealed that DUF506 proteins were present in different organelles. Transcript analyses showed that 13 of the Arabidopsis DUF506 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 (Arabidopsis thaliana 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 DUF506 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 DUF506 family in plants, to support further functional characterizations.
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spelling pubmed-85839542021-11-12 Genome-Wide Identification and Transcriptional Analysis of Arabidopsis DUF506 Gene Family Ying, Sheng Int J Mol Sci Article 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 wide occurrence in photosynthetic organisms. Bioinformatics analysis identified 211 high-confidence DUF506 genes across 17 representative land plant species. Phylogenetic modeling classified three groups of plant DUF506 genes that suggested functional preservation among the groups based on conserved gene structure and motifs. Gene duplication and Ka/Ks evolutionary rates revealed that DUF506 genes are under purifying positive selection pressure. Subcellular protein localization analysis revealed that DUF506 proteins were present in different organelles. Transcript analyses showed that 13 of the Arabidopsis DUF506 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 (Arabidopsis thaliana 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 DUF506 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 DUF506 family in plants, to support further functional characterizations. MDPI 2021-10-23 /pmc/articles/PMC8583954/ /pubmed/34768874 http://dx.doi.org/10.3390/ijms222111442 Text en © 2021 by the author. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Ying, Sheng
Genome-Wide Identification and Transcriptional Analysis of Arabidopsis DUF506 Gene Family
title Genome-Wide Identification and Transcriptional Analysis of Arabidopsis DUF506 Gene Family
title_full Genome-Wide Identification and Transcriptional Analysis of Arabidopsis DUF506 Gene Family
title_fullStr Genome-Wide Identification and Transcriptional Analysis of Arabidopsis DUF506 Gene Family
title_full_unstemmed Genome-Wide Identification and Transcriptional Analysis of Arabidopsis DUF506 Gene Family
title_short Genome-Wide Identification and Transcriptional Analysis of Arabidopsis DUF506 Gene Family
title_sort genome-wide identification and transcriptional analysis of arabidopsis duf506 gene family
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8583954/
https://www.ncbi.nlm.nih.gov/pubmed/34768874
http://dx.doi.org/10.3390/ijms222111442
work_keys_str_mv AT yingsheng genomewideidentificationandtranscriptionalanalysisofarabidopsisduf506genefamily