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Transcriptomic and genomic identification of spliceosomal genes from Euglena gracilis : Identification of Euglena gracilis spliceosomal genes

Diverse splicing types in nuclear and chloroplast genes of protist Euglena gracilis have been recognized for decades. However, the splicing machinery responsible for processing nuclear precursor messenger RNA introns, including trans-splicing of the 5′ terminal outron and spliced leader (SL) RNA, re...

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Autores principales: Gao, Pingwei, Zhong, Yujie, Sun, Chengfu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10679874/
https://www.ncbi.nlm.nih.gov/pubmed/37705346
http://dx.doi.org/10.3724/abbs.2023143
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author Gao, Pingwei
Zhong, Yujie
Sun, Chengfu
author_facet Gao, Pingwei
Zhong, Yujie
Sun, Chengfu
author_sort Gao, Pingwei
collection PubMed
description Diverse splicing types in nuclear and chloroplast genes of protist Euglena gracilis have been recognized for decades. However, the splicing machinery responsible for processing nuclear precursor messenger RNA introns, including trans-splicing of the 5′ terminal outron and spliced leader (SL) RNA, remains elusive. Here, we identify 166 spliceosomal protein genes and two snRNA genes from E. gracilis by performing bioinformatics analysis from a combination of next-generation and full-length transcriptomic RNA sequencing (RNAseq) data as well as draft genomic data. With the spliceosomal proteins we identified in hand, the insensitivity of E. gracilis to some splicing modulators is revealed at the sequence level. The prevalence of SL RNA-mediated trans-splicing is estimated to be more than 70% from our full-length RNAseq data. Finally, the splicing proteomes between E. gracilis and its three evolutionary cousins within the same Excavata group are compared. In conclusion, our study characterizes the spliceosomal components in E. gracilis and provides the molecular basis for further exploration of underlying splicing mechanisms.
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spelling pubmed-106798742023-09-13 Transcriptomic and genomic identification of spliceosomal genes from Euglena gracilis : Identification of Euglena gracilis spliceosomal genes Gao, Pingwei Zhong, Yujie Sun, Chengfu Acta Biochim Biophys Sin (Shanghai) Research Article Diverse splicing types in nuclear and chloroplast genes of protist Euglena gracilis have been recognized for decades. However, the splicing machinery responsible for processing nuclear precursor messenger RNA introns, including trans-splicing of the 5′ terminal outron and spliced leader (SL) RNA, remains elusive. Here, we identify 166 spliceosomal protein genes and two snRNA genes from E. gracilis by performing bioinformatics analysis from a combination of next-generation and full-length transcriptomic RNA sequencing (RNAseq) data as well as draft genomic data. With the spliceosomal proteins we identified in hand, the insensitivity of E. gracilis to some splicing modulators is revealed at the sequence level. The prevalence of SL RNA-mediated trans-splicing is estimated to be more than 70% from our full-length RNAseq data. Finally, the splicing proteomes between E. gracilis and its three evolutionary cousins within the same Excavata group are compared. In conclusion, our study characterizes the spliceosomal components in E. gracilis and provides the molecular basis for further exploration of underlying splicing mechanisms. Oxford University Press 2023-09-13 /pmc/articles/PMC10679874/ /pubmed/37705346 http://dx.doi.org/10.3724/abbs.2023143 Text en © The Author(s) 2021. 0 https://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Research Article
Gao, Pingwei
Zhong, Yujie
Sun, Chengfu
Transcriptomic and genomic identification of spliceosomal genes from Euglena gracilis : Identification of Euglena gracilis spliceosomal genes
title Transcriptomic and genomic identification of spliceosomal genes from Euglena gracilis : Identification of Euglena gracilis spliceosomal genes
title_full Transcriptomic and genomic identification of spliceosomal genes from Euglena gracilis : Identification of Euglena gracilis spliceosomal genes
title_fullStr Transcriptomic and genomic identification of spliceosomal genes from Euglena gracilis : Identification of Euglena gracilis spliceosomal genes
title_full_unstemmed Transcriptomic and genomic identification of spliceosomal genes from Euglena gracilis : Identification of Euglena gracilis spliceosomal genes
title_short Transcriptomic and genomic identification of spliceosomal genes from Euglena gracilis : Identification of Euglena gracilis spliceosomal genes
title_sort transcriptomic and genomic identification of spliceosomal genes from euglena gracilis : identification of euglena gracilis spliceosomal genes
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10679874/
https://www.ncbi.nlm.nih.gov/pubmed/37705346
http://dx.doi.org/10.3724/abbs.2023143
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