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

doi:10.1098/rsob.210190

IOCAS-IR > 实验海洋生物学重点实验室

	tRNA copy number and codon usage in the sea cucumber genome provide insights into adaptive translation for saponin biosynthesis
	Liu, Chengzhang 1,2,3; Yuan, Jianbo 1,2,3; Zhang, Xiaojun 1,2,3; Jin, Songjun 1,2,3; Li, Fuhua 1,2,3; Xiang, Jianhai1,2,3
	2021-11-10
发表期刊	OPEN BIOLOGY
卷号	11 期号:11 页码:16
通讯作者	Zhang, Xiaojun(xjzhang@qdio.ac.cn) ; Li, Fuhua(fhli@qdio.ac.cn)
摘要	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 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.
关键词	tRNA adaptive translation saponin biosynthesis cytochrome P450 UDP-glycosyltransferases
DOI	10.1098/rsob.210190
收录类别	SCI
语种	英语
资助项目	National Natural Science Foundation of China[31772885] ; National Natural Science Foundation of China[31972782] ; National Natural Science Foundation of China[41876167] ; National Key R&D Programme of China[2018YFD0900103] ; Strategic Priority Research Programme of the Chinese Academy of Sciences[XDA24030105] ; Senior User Project of RV KEXUE[KEXUE2018G19]
WOS研究方向	Biochemistry & Molecular Biology
WOS类目	Biochemistry & Molecular Biology
WOS记录号	WOS:000716335100002
出版者	ROYAL SOC
引用统计	被引频次：1[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.qdio.ac.cn/handle/337002/177174
专题	实验海洋生物学重点实验室
通讯作者	Zhang, Xiaojun; Li, Fuhua
作者单位	1.Chinese Acad Sci, Ctr Ocean Megasci, Inst Oceanol, CAS, Qingdao 266071, Peoples R China 2.Chinese Acad Sci, Ctr Ocean Megasci, Inst Oceanol, Shandong Prov Key Lab Expt Marine Biol, Qingdao 266071, Peoples R China 3.Lab Marine Biol & Biotechnol, Qingdao Natl Lab Marine Sci & Technol, Qingdao 266237, Peoples R China
第一作者单位	中国科学院海洋大科学研究中心
通讯作者单位	中国科学院海洋大科学研究中心
推荐引用方式 GB/T 7714	Liu, Chengzhang,Yuan, Jianbo,Zhang, Xiaojun,et al. tRNA copy number and codon usage in the sea cucumber genome provide insights into adaptive translation for saponin biosynthesis[J]. OPEN BIOLOGY,2021,11(11):16.
APA	Liu, Chengzhang,Yuan, Jianbo,Zhang, Xiaojun,Jin, Songjun,Li, Fuhua,&Xiang, Jianhai.(2021).tRNA copy number and codon usage in the sea cucumber genome provide insights into adaptive translation for saponin biosynthesis.OPEN BIOLOGY,11(11),16.
MLA	Liu, Chengzhang,et al."tRNA copy number and codon usage in the sea cucumber genome provide insights into adaptive translation for saponin biosynthesis".OPEN BIOLOGY 11.11(2021):16.

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