|
|
|
| Cloning and Expression Analysis of Tudor Domain-containing Protein 3 (TDRD3) Gene in Strongylocentrotus intermedius |
| LI Hao-Wen, ZHANG Xi-Ying, WANG Heng*, LI Jia-Lin, LI Xi-Yu, DING Jun, CHANG Ya-Qing |
| Key Laboratory of Seawater Enhancement and Aquaculture in North China, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian 116023, China |
|
|
|
|
Abstract Germline factors not only regulate germ cell development but may also play important roles in somatic cells. The previous study found that the Tudor domain-containing protein 3 (TDRD3) gene, a member of the TDRD family of germline factors, is significantly upregulated in the gonads of Strongylocentrotus intermedius, which is rich in high concentration of polyunsaturated fatty acids. To investigate the roles and regulatory mechanisms of TDRD3 in non-germline cells and embryonic development, S. intermedius was used as the material, bioinformatics and quantitative molecular approaches were applied to identify and characterize the TDRD3 gene, and to analyze its sequence features as well as its expression patterns across different tissues and developmental stages. The results showed that the full-length cDNA of the TDRD3 gene (GenBank No. PP496300.1) was 4 361 bp, containing a 2 814 bp open reading frame that encoded a protein of 937 amino acids. The predicted protein was hydrophilic and unstable, with 1 conserved Tudor domain. Expression analysis demonstrated that TDRD3 was broadly expressed in various adult tissues and throughout embryonic development in S. intermedius, suggesting that it played essential roles across the organism's life cycle. Notably, TDRD3 expression was significantly elevated in the ovary and during embryogenesis, indicating its potential involvement in gonadal growth and development. This study provides a theoretical foundation for elucidating the molecular mechanisms underlying gonadal and embryonic development in S. intermedius, and offers insights that may contribute to the sustainable aquaculture of this species.
|
|
Received: 11 June 2025
|
|
|
|
Corresponding Authors:
* hengwang@dlou.edu.cn
|
|
|
|
[1] 常亚青. 1997. 虾夷马粪海胆筏式人工养殖研究[J]. 大连水产学院学报, (02): 9-16.
(Chang Y Q. 1997. Culture research of yuzawa feces sea urchin in raft farming[J]. Journal of Dalian Ocean University, (02): 9-16.)
[2] 常亚青, 张伟杰, 丁君, 等. 2010. 虾夷马粪海胆不同家系和性别间性腺性状的比较[J]. 水产学报, 34(7): 1080-1088.
(Chang Y Q, Zhang W J, Ding J, et al.2010. Comparison of gonadal traits of different families and sexes of yuzawa feces sea urchin[J]. Journal of Fisheries of China, 34(7): 1080-1088.)
[3] 甘冰. 2021. 人源TDRD蛋白Tudor结构域识别不同甲基化修饰PIWI蛋白的特异性研究[D]. 硕士学位论文, 华中师范大学, 导师: 闵金荣, pp. 20-21.
(Gan B.2021. Specificity of human TDRD protein Tudor domain in recognizing different methylated PIWI proteins[D]. Thesis for M.S., Central China Normal University, Supervisor: Min J R, pp. 20-21)
[4] 刚德报, 王姮, 关文娟, 等. 2022. 中国北方海域四种海胆消化道组织结构[J]. 广东海洋大学学报, 42(2): 38-45.
(Gang D B, Wang H, Guan W J, et al.2022. The structure of the digestive tract tissue of four species of sea urchins in the northern waters of China[J]. Journal of Guangdong Ocean University, 42(2): 38-45.)
[5] 胡泽超, 邹孝翠, 孙健, 等. 2021. 草鱼脂肪组织及脂肪细胞qRT-PCR内参基因的筛选[J]. 水产学报, 45(3): 432-440.
(Hu Z C, Zou X C, Sun J, et al.2021. Screening of reference genes for qRT-PCR in grass carp adipose tissue and adipocytes[J]. Journal of Fisheries of China, 45(3): 432-440.)
[6] 李鹏琛, 刘炳正, 苏唯一, 等. 2022. 基于全长转录组测序挖掘中间球海胆性腺发育相关基因[J]. 基因组学与应用生物学, 41: 2062-2075.
(Li P C, Liu B Z, Su W Y, et al.2022. Mining gonad development-related genes of intermediate sea urchin based on full-length transcriptome sequencing[J]. Genomics and Applied Biology, 41: 2062-2075.)
[7] 李霞. 2021. 水产动物组织学与胚胎学彩色图谱[M]. 中国农业出版社, 北京. pp. 169-179.
(Li X.2021. Color Atlas of Histology and Embryology of Aquatic Animals[M]. China Agriculture Press, Beijing. pp. 169-179.)
[8] 王姮, 刚德报, 魏仁杰, 等. 2023. 无脊椎动物脂肪酸结合蛋白的研究进展[J]. 南方农业学报, 54(10): 3100-3113.
(Wang H, Gang D B, Wei R J, et al.2023. Research progress on fatty acid-binding proteins in invertebrates[J]. Journal of Southern Agriculture, 54(10): 3100-3113.)
[9] 许伟定, 何平, 王丽梅, 等. 2009. 光棘球海胆性腺氨基酸组成的研究[J]. 大连水产学院学报, 24(6): 583-586.
(Xu W D, He P, Wang L M, et al.2009. The amino acid compositions of gonads in sea urchin Strongylocentrotus nudus[J]. Journal of Dalian Ocean University, 24(6): 583-586.)
[10] 张瀚予. 2023. TDRD3 Tudor结构域识别甲基化G3BP1并调控液液相分离的机制研究[D]. 硕士学位论文, 中国科学技术大学, 导师: 阮科, pp. 18-21.
(Zhang H Y.2023. Mechanism of TDRD3 tudor domain recognizing methylated G3BP1 and regulating liquid-liquid phase separation[D]. Thesis for M. S., University of Science and Technology of China, Supervisor: Ruan K, pp. 18-21.)
[11] 张杨. 2020. 海胆性腺营养成分及加工方法的研究进展[J]. 现代食品, 2020(23): 44-45.
(Zhang Y.2020. Research progress on nutritional and processing methods of sea urchin gonad[J]. Journal of Modern Food, 2020(23): 44-45.)
[12] 朱万龙, 王政昆, 张浩. 2019. 动物能量代谢的研究简述[M]. Scientific Research Publishing, Inc., USA. pp. 61-73.
(Zhu W L, Wang Z K, Zhang H.2019. A Brief Review of Animal Energy Metabolism[M]. Scientific Research Publishing, Inc. USA. pp. 61-73.)
[13] Brown M S, Evans B S, Afonso L O B.2022. Characterization of gonadal development and gene expression during sex differentiation in Atlantic salmon (Salmo salar) from 0 to 79 days post-hatching[J]. Gene, 822: 146393.
[14] Chen C, Nott T, Jin J, et al.2011. Deciphering arginine methylation: Tudor tells the tale[J]. Nature Reviews Molecular Cell Biology, 12(10): 629-642.
[15] Gan B, Chen S, Liu H, et al.2019. Structure and function of eTudor domain containing TDRD proteins[J]. Critical Reviews in Biochemistry and Molecular Biology, 54: 119-132.
[16] Han Y L, Sun Z H, Chang S, et al.2021. Application of SNP in genetic sex identification and effect of estradiol on sex-related gene expression in Strongylocentrotus intermedius[J]. Frontiers in Endocrinology, 12: 756530.
[17] Johnston I A, Bolla S L, Bizuayehu T T, et al.2010. Maternal gene expression in Atlantic halibut (Hippoglossus hippoglossus L.) and its relation to egg quality[J]. BMC Research Notes, 3: 1-11.
[18] Kojima K, Kuramochi-Miyagawa S, Chuma S, et al.2009. Associations between PIWI proteins and TDRD1/MTR-1 are critical for integrated subcellular localization in murine male germ cells[J]. Genes to Cells, 14: 1155-1165.
[19] Li L, Lu X, Dean J.2013. The maternal to zygotic transition in mammals[J]. Molecular Aspects of Medicine, 34(5): 919-938.
[20] Liu K, Guo Y H, Liu H P, et al.2012. Crystal structure of TDRD3 and methyl-arginine binding characterization of TDRD3, SMN and SPF30[J]. PLOS One, 7: e30375.
[21] Liu X L, Chang Y Q, Xiang J H, et al.2003. Estimates of genetic parameters for growth traits of the sea urchin, Strongylocentrotus intermedius[J]. Aquaculture, 243(2005): 27-32.
[22] Liu Z Y, Liu S S, Guo S Y, et al.2022. Evolutionary dynamics and conserved function of the Tudor-domain-containing (TDRD) proteins in teleost fish[J]. Marine Life Science & Technology, 4: 18-30.
[23] Marchler B A, Lu S, Anderson J B, et al.2010. CDD: A conserved domain database for the functional annotation of proteins[J]. Nucleic Acids Research, 39: 225-229.
[24] Ozata D M, Gainetdinov I, Zoch A, et al.2018. PIWI-interacting RNAs: Small RNAs with big functions[J]. Nature Reviews Genetics, 20: 89-108.
[25] Strasser M J, Mackenzie N C, Dumstrei K, et al.2008. Control over the morphology and segregation of zebrafish germ cell granules during embryonic development[J]. BMC Developmental Biology, 8: 58.
[26] Wang B, Wang H Z, Song H F, et al.2019. Evolutionary significance and regulated expression of TDRD family genes in gynogenetic Japanese flounder (Paralichthys olivaceus)[J]. Marine Genomics, 31: 100593.
[27] Wang H, Ding J, Ding S Y, et al.2019. Transcriptome analysis to characterize the genes related to gonad growth and fatty acid metabolism in the sea urchin Strongylocentrotus intermedius[J]. Genes & Genomics, 41(12): 1397-1415.
[28] Wang H, Ding J, Ding S Y, et al.2020. Integrated metabolomic and transcriptomic analyses identify critical genes in eicosapentaenoic acid biosynthesis and metabolism in the sea urchin Strongylocentrotus intermedius[J]. Scientific Reports, 10(1): 1697.
[29] Wang H, Zhao W F, Liu X Y, et al.2022. Comparative lipidome and transcriptome provide novel insight into polyunsaturated fatty acids metabolism of the sea urchin[J]. Frontiers in Marine Science, 9: 777341.
[30] Yang Y, McBride K M, Hensley S, et al.2014. Arginine methylation facilitates the recruitment of TOP3B to chromatin to prevent R-loop accumulation[J]. Molecular Cell, 53(3): 484-497.
[31] Zhang H, Liu K, Izumi N, et al.2021. Tudor-SN-Tdrd3 complex facilitates piRNA amplification in Drosophila ovaries[J]. Proceedings of the National Academy of Sciences of the USA, 118(11): e2016593118.
[32] Zhang K, Sun M, Li M, et al.2022. Tdrd3 acts as a key regulator in zebrafish female germline stem cell maintenance and differentiation[J]. Zebrafish, 19(2): 104-116.
[33] Zhao J, Wang B, Yu H, et al.2018. Tdrd1 is a germline-specific and sexually dimorphically expressed gene in Paralichthys olivaceus[J]. Gene, 673: 61-69. |
|
|
|
