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Comparative study of lysine acetylation in Vesicomyidae clam Archivesica marissinica and the manila clam Ruditapes philippinarum: adaptation mechanisms in cold seep environments

文献类型：期刊论文

作者Kong, Xue2,3; Wang, Wei2,3; Chen, Sunan2,3; Song, Manzong2,3; Zhi, Ying3; Cai, Yuefeng2,3; Zhang, Haibin1; Shen, Xin2,3
刊名BMC GENOMICS
出版日期2024-10-28
卷号25期号:1页码:20
关键词Vesicomyidae clam Lysine acetylation Cold seep zone Comparative proteomics Post-translational modification Adaptation mechanism
ISSN号1471-2164
DOI10.1186/s12864-024-10916-9
英文摘要Background The deep-sea cold seep zone is characterized by high pressure, low temperature, darkness, and oligotrophy. Vesicomyidae clams are the dominant species within this environment, often forming symbiotic relationships with chemosynthetic microbes. Understanding the mechanisms by which Vesicomyidae clams adapt to the cold seep environment is significant. Acetylation modification of lysine is known to play a crucial role in various metabolic processes. Consequently, investigating the role of lysine acetylation in the adaptation of Vesicomyidae clams to deep-sea environments is worthwhile. So, a comparative study of lysine acetylation in cold seep clam Archivesica marissinica and shallow water shellfish Ruditapes philippinarum was conducted. Results A total of 539 acetylated proteins were identified with 1634 acetylation sites. Conservative motif enrichment analysis revealed that the motifs -KacR-, -KacT-, and -KacF- were the most conserved. Subsequent gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analyses were conducted on significantly differentially expressed acetylated proteins. The GO enrichment analysis indicated that acetylated proteins are crucial in various biological processes, including cellular response to stimulation, and other cellular processes ( p < 0.05 and false discovery rate (FDR) < 0.25). The results of KEGG enrichment analysis indicated that acetylated proteins are involved in various cellular processes, including tight junction, motor proteins, gap junction, phagosome, cGMP-PKG signaling pathways, endocytosis, glycolysis/gluconeogenesis, among others (p < 0.05 and FDR < 0.25). Notably, a high abundance of lysine acetylation was observed in the glycolysis/glycogenesis pathways, and the acetylation of glyceraldehyde 3-phosphate dehydrogenase might facilitate ATP production. Subsequent investigation into acetylation modifications associated with deep-sea adaptation revealed the specific identification of key acetylated proteins. Among these, the adaptation of cold seep clam hemoglobin and heat shock protein to high hydrostatic pressure and low temperature might involve an increase in acetylation levels. Acetylation of arginine kinase might be related to ATP production and interaction with symbiotic bacteria. Myosin heavy chain (Ama01085) has the most acetylation sites and might improve the actomyosin system stability through acetylation. Further validation is required for the acetylation modification from Vesicomyidae clams. Conclusion A novel comparative analysis was undertaken to investigate the acetylation of lysine in Vesicomyidae clams, yielding novel insights into the regulatory role of lysine acetylation in deep-sea organisms. The findings present many potential proteins for further exploration of acetylation functions in cold seep clams and other deep-sea mollusks.
WOS关键词CARBONIC-ANHYDRASE ; HEMOGLOBIN ; SUCCINYLATION ; DIVERSITY ; PROTEINS ; DIOXIDE ; ASPIRIN ; TARGETS ; SURFACE
资助项目Natural Science Foundation of Jiangsu Province ; Explorer 1 scientific research ship of Institute of Deep-sea Science and Engineering (Chinese Academy of Sciences)
WOS研究方向Biotechnology & Applied Microbiology ; Genetics & Heredity
语种英语
WOS记录号WOS:001343697800001
出版者BMC
资助机构Natural Science Foundation of Jiangsu Province ; Explorer 1 scientific research ship of Institute of Deep-sea Science and Engineering (Chinese Academy of Sciences)
源URL[http://ir.idsse.ac.cn/handle/183446/11801]  
专题深海科学研究部_深海生物学研究室_海洋生物生态与进化研究组
通讯作者Shen, Xin
作者单位1.Chinese Acad Sci, Inst Deep Sea Sci & Engn, Sanya 572000, Peoples R China
2.Jiangsu Ocean Univ, Coinnovat Ctr Jiangsu Marine Bioind Technol, Lianyungang 222000, Peoples R China
3.Jiangsu Ocean Univ, Sch Marine Sci & Fisheries, Lianyungang 222000, Peoples R China
推荐引用方式
GB/T 7714		 Kong, Xue,Wang, Wei,Chen, Sunan,et al. Comparative study of lysine acetylation in Vesicomyidae clam Archivesica marissinica and the manila clam Ruditapes philippinarum: adaptation mechanisms in cold seep environments[J]. BMC GENOMICS,2024,25(1):20.
APA Kong, Xue.,Wang, Wei.,Chen, Sunan.,Song, Manzong.,Zhi, Ying.,...&Shen, Xin.(2024).Comparative study of lysine acetylation in Vesicomyidae clam Archivesica marissinica and the manila clam Ruditapes philippinarum: adaptation mechanisms in cold seep environments.BMC GENOMICS,25(1),20.
MLA Kong, Xue,et al."Comparative study of lysine acetylation in Vesicomyidae clam Archivesica marissinica and the manila clam Ruditapes philippinarum: adaptation mechanisms in cold seep environments".BMC GENOMICS 25.1(2024):20.

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来源：深海科学与工程研究所

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