Identification and Positive Selection Analysis of Metallothionein fromDeep Sea Clams in Vesicomyidae
KONG Xue1,2,3, CHEN Sunan1, ZHU Xinhui1, WU Ke1, CAI Yuefeng1,2, ZHI Ying1, LI Yanan4, ZHANG Haibin5, SHEN Xin1,2
1. School of Marine Science and Fisheries, Jiangsu Ocean University, Lianyungang 222000, China; 2. Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of MarineBiotechnology, Jiangsu Ocean University, Lianyungang 222000, China; 3. Key Laboratory of MarineBiogenetic Resources, Ministry of Natural Resources, Xiamen 361000, China; 4. College of Animal Science andTehnology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; 5. Institute ofDeep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
Abstract：Deep-sea cold seep and hydrothermal ecosystems are characterized by extreme physical and chemical environments, including high hydrostatic pressure, darkness, high concentrations of heavy metals and nutrient limitation. As the dominant taxa in this habitat, clams in Vesicomyidae provide an ideal model for analyzing the adaptive evolution of deep-sea organisms. In this study, we conducted phylogenetic analysis and positive selection pressure detection of metallothioneins (MTs) in deep/shallow-sea bivalves with the aim of elucidating the molecular basis of their adaptation to the deep-sea environment. Five MTs coding sequences with molecular weight of 6—7 ku and isoelectric point of 7.2—8.5 were identified from the omics data of four species in Vesicomyidae. Multiple sequence comparisons revealed that MT-10 isoforms contained 19 conserved cysteine residues in both deep- and shallow-sea species, forming nine CXC conserved motifs, except for CmagMT-10Ⅱ. The phylogenetic evolutionary tree showed that the species (AmMT-10, ApMT-10, CmagMT-10Ⅰ, PoMT-10) in Vesicomyidae were clustered into a single branch and clustered into a bigger evolutionary branch with shallow-water clams MT-10s. Then, a branch-site model for selection pressure analysis, with the deep-sea clam MT-10 as the foreground branch and the shallow sea shellfish MT-10 as the background branch, showed that ω (non-synonymous substitution rate/synonymous substitution rate) was 30.705 2 (P<0.05). The assay identified two strong selection sites (30E, 46T) with amino acid substitution patterns (30P/S/A → E; 46V/A → T) leading to a shift in charge properties. Protein stability prediction by DUET and DDGun showed that these substitutions resulted in a negative shift in ΔΔG values (maximum -1.1 kcal/mol), suggesting that increased structural flexibility may enhance substrate/ligand binding efficiency.It is hypothesized that under the selective pressure of the deep-sea environment, the clam MT-10s in Vesicomyidae achieves functional adaptive evolution through charge modification at key sites. The finding provides new molecular evidence for understanding of the extreme environmental adaptation of deep-sea organisms.
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2026, Vol. 45 
