tRNA copy number and codon usage in the sea cucumber genome provide insights into adaptive translation for saponin biosynthesis

Genomic tRNA copy numbers determine cytoplasmic tRNA abundances, which in turn influence translation efficiency, but the underlying mechanism is not well understood. Using the sea cucumber Apostichopus japonicus as a model, we combined genomic sequence, transcriptome expression and ecological food r...

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Autores principales:	Chengzhang Liu, Jianbo Yuan, Xiaojun Zhang, Songjun Jin, Fuhua Li, Jianhai Xiang
Formato:	article
Lenguaje:	EN
Publicado:	The Royal Society 2021
Materias:	tRNA adaptive translation saponin biosynthesis cytochrome P450 UDP-glycosyltransferases Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/2a2d9b052d644fbe90d43adbe26ca91a
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spelling	oai:doaj.org-article:2a2d9b052d644fbe90d43adbe26ca91a2021-11-17T08:06:15ZtRNA copy number and codon usage in the sea cucumber genome provide insights into adaptive translation for saponin biosynthesis10.1098/rsob.2101902046-2441https://doaj.org/article/2a2d9b052d644fbe90d43adbe26ca91a2021-11-01T00:00:00Zhttps://royalsocietypublishing.org/doi/10.1098/rsob.210190https://doaj.org/toc/2046-2441Genomic tRNA copy numbers determine cytoplasmic tRNA abundances, which in turn influence translation efficiency, but the underlying mechanism is not well understood. Using the sea cucumber Apostichopus japonicus as a model, we combined genomic sequence, transcriptome expression and ecological food resource data to study its codon usage adaptation. The results showed that, unlike intragenic non-coding RNAs, transfer RNAs (tRNAs) tended to be transcribed independently. This may be attributed to their specific Pol III promoters that lack transcriptional regulation, which may underlie the correlation between genomic copy number and cytoplasmic abundance of tRNAs. Moreover, codon usage optimization was mostly restrained by a gene's amino acid sequence, which might be a compromise between functionality and translation efficiency. Genes for stress responses were highly optimized for most echinoderms, while enzymes for saponin biosynthesis (LAS, CYPs and UGTs) were especially optimized in sea cucumbers, which might promote saponin synthesis as a defence strategy. The genomic tRNA content of A. japonicus was positively correlated with amino acid content in its natural food particles, which should promote its efficiency in protein synthesis. We propose that coevolution between genomic tRNA content and codon usage of sea cucumbers facilitates their saponin synthesis and survival using food resources with low nutrient content.Chengzhang LiuJianbo YuanXiaojun ZhangSongjun JinFuhua LiJianhai XiangThe Royal SocietyarticletRNAadaptive translationsaponin biosynthesiscytochrome P450UDP-glycosyltransferasesBiology (General)QH301-705.5ENOpen Biology, Vol 11, Iss 11 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	tRNA adaptive translation saponin biosynthesis cytochrome P450 UDP-glycosyltransferases Biology (General) QH301-705.5
spellingShingle	tRNA adaptive translation saponin biosynthesis cytochrome P450 UDP-glycosyltransferases Biology (General) QH301-705.5 Chengzhang Liu Jianbo Yuan Xiaojun Zhang Songjun Jin Fuhua Li Jianhai Xiang tRNA copy number and codon usage in the sea cucumber genome provide insights into adaptive translation for saponin biosynthesis
description	Genomic tRNA copy numbers determine cytoplasmic tRNA abundances, which in turn influence translation efficiency, but the underlying mechanism is not well understood. Using the sea cucumber Apostichopus japonicus as a model, we combined genomic sequence, transcriptome expression and ecological food resource data to study its codon usage adaptation. The results showed that, unlike intragenic non-coding RNAs, transfer RNAs (tRNAs) tended to be transcribed independently. This may be attributed to their specific Pol III promoters that lack transcriptional regulation, which may underlie the correlation between genomic copy number and cytoplasmic abundance of tRNAs. Moreover, codon usage optimization was mostly restrained by a gene's amino acid sequence, which might be a compromise between functionality and translation efficiency. Genes for stress responses were highly optimized for most echinoderms, while enzymes for saponin biosynthesis (LAS, CYPs and UGTs) were especially optimized in sea cucumbers, which might promote saponin synthesis as a defence strategy. The genomic tRNA content of A. japonicus was positively correlated with amino acid content in its natural food particles, which should promote its efficiency in protein synthesis. We propose that coevolution between genomic tRNA content and codon usage of sea cucumbers facilitates their saponin synthesis and survival using food resources with low nutrient content.
format	article
author	Chengzhang Liu Jianbo Yuan Xiaojun Zhang Songjun Jin Fuhua Li Jianhai Xiang
author_facet	Chengzhang Liu Jianbo Yuan Xiaojun Zhang Songjun Jin Fuhua Li Jianhai Xiang
author_sort	Chengzhang Liu
title	tRNA copy number and codon usage in the sea cucumber genome provide insights into adaptive translation for saponin biosynthesis
title_short	tRNA copy number and codon usage in the sea cucumber genome provide insights into adaptive translation for saponin biosynthesis
title_full	tRNA copy number and codon usage in the sea cucumber genome provide insights into adaptive translation for saponin biosynthesis
title_fullStr	tRNA copy number and codon usage in the sea cucumber genome provide insights into adaptive translation for saponin biosynthesis
title_full_unstemmed	tRNA copy number and codon usage in the sea cucumber genome provide insights into adaptive translation for saponin biosynthesis
title_sort	trna copy number and codon usage in the sea cucumber genome provide insights into adaptive translation for saponin biosynthesis
publisher	The Royal Society
publishDate	2021
url	https://doaj.org/article/2a2d9b052d644fbe90d43adbe26ca91a
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tRNA copy number and codon usage in the sea cucumber genome provide insights into adaptive translation for saponin biosynthesis

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