Institutional Repository of Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences
| tRNA copy number and codon usage in the sea cucumber genome provide insights into adaptive translation for saponin biosynthesis | |
Liu, Chengzhang1,2,3; Yuan, Jianbo1,2,3; Zhang, Xiaojun1,2,3; Jin, Songjun1,2,3; Li, Fuhua1,2,3; Xiang, Jianhai1,2,3
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| 2021-11-10 | |
| Source Publication | OPEN BIOLOGY
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| Volume | 11Issue:11Pages:16 |
| Corresponding Author | Zhang, Xiaojun(xjzhang@qdio.ac.cn) ; Li, Fuhua(fhli@qdio.ac.cn) |
| Abstract | 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. |
| Keyword | tRNA adaptive translation saponin biosynthesis cytochrome P450 UDP-glycosyltransferases |
| DOI | 10.1098/rsob.210190 |
| Indexed By | SCI |
| Language | 英语 |
| Funding Project | 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 Research Area | Biochemistry & Molecular Biology |
| WOS Subject | Biochemistry & Molecular Biology |
| WOS ID | WOS:000716335100002 |
| Publisher | ROYAL SOC |
| Citation statistics | |
| Document Type | 期刊论文 |
| Identifier | http://ir.qdio.ac.cn/handle/337002/177174 |
| Collection | 实验海洋生物学重点实验室 |
| Corresponding Author | Zhang, Xiaojun; Li, Fuhua |
| Affiliation | 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 |
| First Author Affilication | Center for Ocean Mega-Science, Chinese Academy of Sciences |
| Corresponding Author Affilication | Center for Ocean Mega-Science, Chinese Academy of Sciences |
| Recommended Citation 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. |
| Files in This Item: | ||||||
| File Name/Size | DocType | Version | Access | License | ||
| rsob.210190.pdf（8509KB） | 期刊论文 | 出版稿 | 限制开放 | CC BY-NC-SA | View | |
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