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Genome-Wide Identification and Expression Analysis of Pseudouridine Synthase Family in Arabidopsis and Maize

Pseudouridine (Ψ), the isomer of uridine (U), is the most abundant type of RNA modification, which is crucial for gene regulation in various cellular processes. Pseudouridine synthases (PUSs) are the key enzymes for the U-to-Ψ conversion. However, little is known about the genome-wide features and b...

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Autores principales: Xie, Yuting, Gu, Yeting, Shi, Guangping, He, Jianliang, Hu, Wenjing, Zhang, Zhonghui
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8910892/
https://www.ncbi.nlm.nih.gov/pubmed/35269820
http://dx.doi.org/10.3390/ijms23052680
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author Xie, Yuting
Gu, Yeting
Shi, Guangping
He, Jianliang
Hu, Wenjing
Zhang, Zhonghui
author_facet Xie, Yuting
Gu, Yeting
Shi, Guangping
He, Jianliang
Hu, Wenjing
Zhang, Zhonghui
author_sort Xie, Yuting
collection PubMed
description Pseudouridine (Ψ), the isomer of uridine (U), is the most abundant type of RNA modification, which is crucial for gene regulation in various cellular processes. Pseudouridine synthases (PUSs) are the key enzymes for the U-to-Ψ conversion. However, little is known about the genome-wide features and biological function of plant PUSs. In this study, we identified 20 AtPUSs and 22 ZmPUSs from Arabidopsis and maize (Zea mays), respectively. Our phylogenetic analysis indicated that both AtPUSs and ZmPUSs could be clustered into six known subfamilies: RluA, RsuA, TruA, TruB, PUS10, and TruD. RluA subfamily is the largest subfamily in both Arabidopsis and maize. It’s noteworthy that except the canonical XXHRLD-type RluAs, another three conserved RluA variants, including XXNRLD-, XXHQID-, and XXHRLG-type were also identified in those key nodes of vascular plants. Subcellular localization analysis of representative AtPUSs and ZmPUSs in each subfamily revealed that PUS proteins were localized in different organelles including nucleus, cytoplasm and chloroplasts. Transcriptional expression analysis indicated that AtPUSs and ZmPUSs were differentially expressed in various tissues and diversely responsive to abiotic stresses, especially suggesting their potential roles in response to heat and salt stresses. All these results would facilitate the functional identification of these pseudouridylation in the future.
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spelling pubmed-89108922022-03-11 Genome-Wide Identification and Expression Analysis of Pseudouridine Synthase Family in Arabidopsis and Maize Xie, Yuting Gu, Yeting Shi, Guangping He, Jianliang Hu, Wenjing Zhang, Zhonghui Int J Mol Sci Article Pseudouridine (Ψ), the isomer of uridine (U), is the most abundant type of RNA modification, which is crucial for gene regulation in various cellular processes. Pseudouridine synthases (PUSs) are the key enzymes for the U-to-Ψ conversion. However, little is known about the genome-wide features and biological function of plant PUSs. In this study, we identified 20 AtPUSs and 22 ZmPUSs from Arabidopsis and maize (Zea mays), respectively. Our phylogenetic analysis indicated that both AtPUSs and ZmPUSs could be clustered into six known subfamilies: RluA, RsuA, TruA, TruB, PUS10, and TruD. RluA subfamily is the largest subfamily in both Arabidopsis and maize. It’s noteworthy that except the canonical XXHRLD-type RluAs, another three conserved RluA variants, including XXNRLD-, XXHQID-, and XXHRLG-type were also identified in those key nodes of vascular plants. Subcellular localization analysis of representative AtPUSs and ZmPUSs in each subfamily revealed that PUS proteins were localized in different organelles including nucleus, cytoplasm and chloroplasts. Transcriptional expression analysis indicated that AtPUSs and ZmPUSs were differentially expressed in various tissues and diversely responsive to abiotic stresses, especially suggesting their potential roles in response to heat and salt stresses. All these results would facilitate the functional identification of these pseudouridylation in the future. MDPI 2022-02-28 /pmc/articles/PMC8910892/ /pubmed/35269820 http://dx.doi.org/10.3390/ijms23052680 Text en © 2022 by the authors. 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
Xie, Yuting
Gu, Yeting
Shi, Guangping
He, Jianliang
Hu, Wenjing
Zhang, Zhonghui
Genome-Wide Identification and Expression Analysis of Pseudouridine Synthase Family in Arabidopsis and Maize
title Genome-Wide Identification and Expression Analysis of Pseudouridine Synthase Family in Arabidopsis and Maize
title_full Genome-Wide Identification and Expression Analysis of Pseudouridine Synthase Family in Arabidopsis and Maize
title_fullStr Genome-Wide Identification and Expression Analysis of Pseudouridine Synthase Family in Arabidopsis and Maize
title_full_unstemmed Genome-Wide Identification and Expression Analysis of Pseudouridine Synthase Family in Arabidopsis and Maize
title_short Genome-Wide Identification and Expression Analysis of Pseudouridine Synthase Family in Arabidopsis and Maize
title_sort genome-wide identification and expression analysis of pseudouridine synthase family in arabidopsis and maize
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8910892/
https://www.ncbi.nlm.nih.gov/pubmed/35269820
http://dx.doi.org/10.3390/ijms23052680
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