{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T17:06:14Z","timestamp":1790701574741,"version":"4.1.0"},"reference-count":34,"publisher":"IMR Press","issue":"3","license":[{"start":{"date-parts":[[2026,7,15]],"date-time":"2026-07-15T00:00:00Z","timestamp":1784073600000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Russian State-funded budget project of ICBFM SB RAS","award":["125012300658-9"],"award-info":[{"award-number":["125012300658-9"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Front. Biosci. (Schol Ed)"],"abstract":"<jats:p>Background: The sea cucumber Eupentacta fraudatrix is a highly interesting model organism for research due to the remarkable ability of the organism to regenerate lost organs following evisceration. In animals after evisceration, increased expression levels of genes such as Sox (SRY-related HMG-box, transcription factors), MMP (matrix metalloproteinases), TIMP (tissue inhibitors of metalloproteinases), and PIWI (ribonuclease-active proteins) have been observed. Since ribonucleases release nucleotides for the synthesis of new molecules and regulate cellular processes by acting on various RNA species, these enzymes are hypothesized to play a significant role in regeneration. Methods: Holothurian homogenate was fractionated chromatographically into several protein fractions. Ribonuclease activity was analyzed using a specific microRNA (miRNA) as a substrate, as well as by an in-gel activity assay. Results: This study examined the ribonuclease activity of E. fraudatrix proteins precipitated with ammonium sulfate from whole-organism homogenates, focusing on pH dependence and substrate specificity. The optimal pH for hydrolyzing a specific miRNA related to the sea cucumber Apostichopus japonicus and a non-specific homo-oligonucleotide, (pA)23, was 5.0 and 6.0, respectively. Inhibition of ribonuclease activity in the presence of EDTA (ethylenediaminetetraacetic acid), Mg2+, and Ca2+ indicates dependence on metal ions. Hydrolysis of the specific substrate was about 25% higher than that of the non-specific substrate and produced five cleavage sites. Using in-gel activity analysis, five protein bands with ribonuclease activity were detected in E. fraudatrix homogenate, with apparent molecular masses ranging from 15 to 77 kDa. Conclusions: This work represents the first report describing the biochemical properties of a ribonuclease from this holothurian species. Five protein forms with ribonuclease activity, differing in electrophoretic mobility, were identified. The biochemical characteristics of these enzymes resemble those of ribonucleases from other echinoderms. Ribonucleases from echinoderms are promising tools for molecular biology applications, including DNA purification, RNA analysis and mapping, as well as for biomedicine, particularly in the development of antiviral agents.<\/jats:p>","DOI":"10.31083\/fbs48977","type":"journal-article","created":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T16:26:53Z","timestamp":1790699213000},"source":"Crossref","is-referenced-by-count":0,"title":["Biochemical Characterization of Ribonuclease Activities From the Sea Cucumber Eupentacta fraudatrix"],"prefix":"10.31083","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7430-3683","authenticated-orcid":true,"given":"Svetlana E.","family":"Soboleva","sequence":"first","affiliation":[{"name":"Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, 630090 Novosibirsk, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-0951-156X","authenticated-orcid":true,"given":"Valeria A.","family":"Ivaschenko","sequence":"additional","affiliation":[{"name":"Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, 630090 Novosibirsk, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0987-7066","authenticated-orcid":true,"given":"Irina A.","family":"Kostrikina","sequence":"additional","affiliation":[{"name":"Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, 630090 Novosibirsk, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4988-8923","authenticated-orcid":true,"given":"Georgy A.","family":"Nevinsky","sequence":"additional","affiliation":[{"name":"Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, 630090 Novosibirsk, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"16242","published-online":{"date-parts":[[2026,7,15]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","unstructured":"Garc\u00eda-Arrar\u00e1s JE, L\u00e1zaro-Pe\u00f1a MI, D\u00edaz-Balzac CA. Holothurians as a Model System to Study Regeneration. Results and Problems in Cell Differentiation. 2018; 65: 255\u2013283.","DOI":"10.1007\/978-3-319-92486-1_13"},{"key":"ref2","doi-asserted-by":"publisher","unstructured":"Dolmatov IY, Kalacheva NV, Tkacheva ES, Shulga AP, Zavalnaya EG, Shamshurina EV, et al. Expression of Piwi, MMP, TIMP, and Sox during Gut Regeneration in Holothurian Eupentacta fraudatrix (Holothuroidea, Dendrochirotida). Genes. 2021; 12: 1292.","DOI":"10.3390\/genes12081292"},{"key":"ref3","doi-asserted-by":"publisher","unstructured":"Girich AS, Isaeva MP, Dolmatov IY. Wnt and frizzled expression during regeneration of internal organs in the holothurian Eupentacta fraudatrix. Wound Repair and Regeneration. 2017; 25: 828\u2013835.","DOI":"10.1111\/wrr.12591"},{"key":"ref4","doi-asserted-by":"publisher","unstructured":"Su F, Dolmatov IY, Wang T, Yang H, Ding K, Zhang L, et al. LncRNA-miRNA interplay regulate intestinal regeneration in the sea cucumber Apostichopus japonicus. Computational and Structural Biotechnology Journal. 2025; 27: 1383\u20131393.","DOI":"10.1016\/j.csbj.2025.03.047"},{"key":"ref5","doi-asserted-by":"publisher","unstructured":"Su F, Huo D, Yang H, Sun L. CircRNA8388 functions as the sponge for miR-2392 during intestinal regeneration in sea cucumber Apostichopus japonicus. International Journal of Biological Macromolecules. 2024; 274: 133302.","DOI":"10.1016\/j.ijbiomac.2024.133302"},{"key":"ref6","doi-asserted-by":"publisher","unstructured":"Bernstein E, Caudy AA, Hammond SM, Hannon GJ. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature. 2001; 409: 363\u2013366.","DOI":"10.1038\/35053110"},{"key":"ref7","doi-asserted-by":"publisher","unstructured":"Hoffend NC, Magner WJ, Tomasi TB. The modulation of Dicer regulates tumor immunogenicity in melanoma. Oncotarget. 2016; 7: 47663\u201347673.","DOI":"10.18632\/oncotarget.10273"},{"key":"ref8","doi-asserted-by":"publisher","unstructured":"Braun T, Klepzig H, Herling M. AGO2 in T-prolymphocytic leukemia: its canonical and non-canonical deregulation and function. Oncotarget. 2023; 14: 395\u2013397.","DOI":"10.18632\/oncotarget.28378"},{"key":"ref9","doi-asserted-by":"publisher","unstructured":"Motoyoshi N, Kobayashi H, Itagaki T, Inokuchi N. Amino acid sequence analysis and characterization of a ribonuclease from starfish Asterias amurensis. Journal of Biochemistry. 2016; 160: 131\u2013139.","DOI":"10.1093\/jb\/mvw017"},{"key":"ref10","doi-asserted-by":"publisher","unstructured":"Sanda A, Kiyomoto M, Iwama M, Ohgi K, Irie M. Marked changes in the ribonuclease activity of mature and immature gonads of sea urchins Hemicentrotus pulcherrimus and Anthocidaris crassispina. Biological & Pharmaceutical Bulletin. 2008; 31: 1659\u20131662.","DOI":"10.1248\/bpb.31.1659"},{"key":"ref11","doi-asserted-by":"publisher","unstructured":"Boyko AV, Girich AS, Tkacheva ES, Dolmatov IY. The Eupentacta fraudatrix transcriptome provides insights into regulation of cell transdifferentiation. Scientific Reports. 2020; 10: 1522.","DOI":"10.1038\/s41598-020-58470-0"},{"key":"ref12","doi-asserted-by":"publisher","unstructured":"Zavalnaya EG, Shamshurina EV, Eliseikina MG. The Immunocytochemical Identification of PIWI-Positive Cells during the Recovery of a Coelomocyte Population after Evisceration in the Holothurian Eupentacta fraudatrix (Djakonov et Baranova, 1958) (Holothuroidea: Dendrochirota). Russian Journal of Marine Biology. 2020; 46: 97\u2013104.","DOI":"10.1134\/S106307402002011X"},{"key":"ref13","doi-asserted-by":"publisher","unstructured":"Lu TX, Rothenberg ME. MicroRNA. The Journal of Allergy and Clinical Immunology. 2018; 141: 1202\u20131207.","DOI":"10.1016\/j.jaci.2017.08.034"},{"key":"ref14","doi-asserted-by":"publisher","unstructured":"Huo D, Sun L, Li X, Ru X, Liu S, Zhang L, et al. Differential Expression of miRNAs in the Respiratory Tree of the Sea Cucumber Apostichopus japonicus Under Hypoxia Stress. G3 (Bethesda, Md.). 2017; 7: 3681\u20133692.","DOI":"10.1534\/g3.117.1129"},{"key":"ref15","doi-asserted-by":"publisher","unstructured":"Yang Z, Wu J. MicroRNAs and regenerative medicine. DNA and Cell Biology. 2007; 26: 257\u2013264.","DOI":"10.1089\/dna.2006.0548"},{"key":"ref16","doi-asserted-by":"publisher","unstructured":"Ambros V. MicroRNA-mediated gene regulation and the resilience of multicellular animals. Postepy Biochemii. 2024; 70: 62\u201370.","DOI":"10.18388\/pb.2021_515"},{"key":"ref17","doi-asserted-by":"publisher","unstructured":"Ho PTB, Clark IM, Le LTT. MicroRNA-Based Diagnosis and Therapy. International Journal of Molecular Sciences. 2022; 23: 7167.","DOI":"10.3390\/ijms23137167"},{"key":"ref18","doi-asserted-by":"publisher","unstructured":"Sun H, Zhou Z, Dong Y, Yang A, Jiang J, Chen Z, et al. Expression analysis of microRNAs related to the skin ulceration syndrome of sea cucumber Apostichopus japonicus. Fish & Shellfish Immunology. 2016; 49: 205\u2013212.","DOI":"10.1016\/j.fsi.2015.12.036"},{"key":"ref19","doi-asserted-by":"publisher","unstructured":"Sun H, Zhou Z, Dong Y, Yang A, Pan Y, Jiang J, et al. In-depth profiling of miRNA regulation in the body wall of sea cucumber Apostichopus japonicus during skin ulceration syndrome progression. Fish & Shellfish Immunology. 2018; 79: 202\u2013208.","DOI":"10.1016\/j.fsi.2018.05.020"},{"key":"ref20","doi-asserted-by":"publisher","unstructured":"Sun L, Sun J, Li X, Zhang L, Yang H, Wang Q. Understanding regulation of microRNAs on intestine regeneration in the sea cucumber Apostichopus japonicus using high-throughput sequencing. Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics. 2017; 22: 1\u20139.","DOI":"10.1016\/j.cbd.2017.01.001"},{"key":"ref21","doi-asserted-by":"publisher","unstructured":"Jiao R, Wu B, Han S, Cui D, Sun J, Zhao T, et al. miRn-3 inhibits cutaneous wound healing by targeting gelsolin in the sea cucumber Apostichopus japonicus. International Journal of Biological Macromolecules. 2024; 254: 127801.","DOI":"10.1016\/j.ijbiomac.2023.127801"},{"key":"ref22","doi-asserted-by":"publisher","unstructured":"Zhang Y, Shao Y, Lv Z, Li C. MiR-210 regulates coelomocyte proliferation through targeting E2F3 in Apostichopus japonicus. Fish & Shellfish Immunology. 2020; 106: 583\u2013590.","DOI":"10.1016\/j.fsi.2020.08.036"},{"key":"ref23","doi-asserted-by":"publisher","unstructured":"Chen M, Zhang X, Liu J, Storey KB. High-throughput sequencing reveals differential expression of miRNAs in intestine from sea cucumber during aestivation. PloS One. 2013; 8: e76120.","DOI":"10.1371\/journal.pone.0076120"},{"key":"ref24","doi-asserted-by":"publisher","unstructured":"Huo D, Su F, Yang H, Sun L. Exosomal microRNAs regulate the heat stress response in sea cucumber Apostichopus japonicus. Ecotoxicology and Environmental Safety. 2023; 249: 114419.","DOI":"10.1016\/j.ecoenv.2022.114419"},{"key":"ref25","doi-asserted-by":"publisher","unstructured":"Tian Y, Shang Y, Guo R, Chang Y, Jiang Y. Salinity stress-induced differentially expressed miRNAs and target genes in sea cucumbers Apostichopus japonicus. Cell Stress & Chaperones. 2019; 24: 719\u2013733.","DOI":"10.1007\/s12192-019-00996-y"},{"key":"ref26","doi-asserted-by":"publisher","unstructured":"Huo D, Sun L, Sun J, Zhang L, Liu S, Su F, et al. Sea cucumbers in a high temperature and low dissolved oxygen world: Roles of miRNAs in the regulation of environmental stresses. Environmental Pollution (Barking, Essex: 1987). 2021; 268: 115509.","DOI":"10.1016\/j.envpol.2020.115509"},{"key":"ref27","doi-asserted-by":"publisher","unstructured":"Timofeeva AM, Kostrikina IA, Dmitrenok PS, Soboleva SE, Nevinsky GA. Very Stable Two Mega Dalton High-Molecular-Mass Multiprotein Complex from Sea Cucumber Eupentacta fraudatrix. Molecules (Basel, Switzerland). 2021; 26: 5703.","DOI":"10.3390\/molecules26185703"},{"key":"ref28","doi-asserted-by":"publisher","unstructured":"Timofeeva AM, Kostrikina IA, Dmitrenok PS, Soboleva SE, Nevinsky GA. Protease and DNase Activities of a Very Stable High-Molecular-Mass Multiprotein Complex from Sea Cucumber Eupentacta fraudatrix. International Journal of Molecular Sciences. 2022; 23: 6677.","DOI":"10.3390\/ijms23126677"},{"key":"ref29","doi-asserted-by":"publisher","unstructured":"Martinez E. Multi-protein complexes in eukaryotic gene transcription. Plant Molecular Biology. 2002; 50: 925\u2013947.","DOI":"10.1023\/a:1021258713850"},{"key":"ref30","doi-asserted-by":"publisher","unstructured":"Zhang L, Song X, Hamel JF, Mercier A. Aquaculture, stock enhancement, and restocking. Developments in Aquaculture and Fisheries Science. In Hamel JF and Mercier A. The sea cucumber Apostichopus japonicus: History, biology and aquaculture, 289\u2013322. Academic Press (Elsevier): London. 2015.","DOI":"10.1016\/B978-0-12-799953-1.00016-7"},{"key":"ref31","doi-asserted-by":"publisher","unstructured":"Warner JF, Lyons DC, McClay DR. Left-right asymmetry in the sea urchin embryo: BMP and the asymmetrical origins of the adult. PLoS Biology. 2012; 10: e1001404.","DOI":"10.1371\/journal.pbio.1001404"},{"key":"ref32","doi-asserted-by":"publisher","unstructured":"Liu C, Yuan J, Zhang X, Jin S, Li F, Xiang J. Clustering genomic organization of sea cucumber miRNAs impacts their evolution and expression. Genomics. 2021; 113: 3544\u20133555.","DOI":"10.1016\/j.ygeno.2021.08.003"},{"key":"ref33","doi-asserted-by":"publisher","unstructured":"Pang J, Guo Q, Lu Z. The catalytic mechanism, metal dependence, substrate specificity, and biodiversity of ribonuclease H. Frontiers in Microbiology. 2022; 13: 1034811.","DOI":"10.3389\/fmicb.2022.1034811"},{"key":"ref34","doi-asserted-by":"publisher","unstructured":"Rosta E, Yang W, Hummer G. Calcium inhibition of ribonuclease H1 two-metal ion catalysis. 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