In contrast to many human organs, only the human liver can self-regenerate, to some degree. Some marine echinoderms are convenient objects for studying the processes of regenerations of organs and tissues. For example, sea cucumbers Eupentacta fraudatrix can completely restore within several weeks, the internal organs and the whole body after their division into two or three parts. Therefore, these cucumbers are a very convenient model for studying the general mechanisms of regeneration. However, there is no literature data yet on which biomolecules of these cucumbers can stimulate the regeneration of organs and the whole-body processes. Studying the mechanisms of restoration is very important for modern biology and medicine, since it can help researchers to understand which proteins, enzymes, hormones, or possible complexes can play an essential role in regeneration. This work is the first to analyze the possible content of very stable protein complexes in sea cucumbers Eupentacta fraudatrix. It has been shown that their organisms contain a very stable multiprotein complex of about 2000 kDa. This complex contains 15 proteins with molecular masses (MMs) >10 kDa and 21 small proteins and peptides with MMs 2.0–8.6 kDa. It is effectively destroyed only in the presence of 3.0 M MgCl₂ and, to a lesser extent, 3.0 M NaCl, while the best dissociation occurs in the presence of 8.0 M urea + 0.1 M EDTA. Our data indicate that forming a very stable proteins complex occurs due to the combination of bridges formed by metal ions, electrostatic contacts, and hydrogen bonds.

Only some human organs, including the liver, are capable of very weak self-regeneration. Some marine echinoderms are very useful for studying the self-regeneration processes of organs and tissues. For example, sea cucumbers Eupentacta fraudatrix (holothurians) demonstrate complete restoration of all organs and the body within several weeks after their division into two parts. Therefore, these cucumbers are a prospective model for studying the general mechanisms of self-regeneration. However, there is no data available yet concerning biomolecules of holothurians, which can stimulate the processes of organ and whole-body regeneration. Investigation of these restoration mechanisms is very important for modern medicine and biology because it can help to understand which hormones, nucleic acids, proteins, enzymes, or complexes play an essential role in self-regeneration. It is possible that stable, polyfunctional, high-molecular-weight protein complexes play an essential role in these processes. It has recently been shown that sea cucumbers Eupentacta fraudatrix contain a very stable multiprotein complex of about 2000 kDa. The first analysis of possible enzymatic activities of a stable protein complex was carried out in this work, revealing that the complex possesses several protease and DNase activities. The complex metalloprotease is activated by several metal ions (Zn²⁺ > Mn²⁺ > Mg²⁺). The relative contribution of metalloproteases (~63.4%), serine-like protease (~30.5%), and thiol protease (~6.1%) to the total protease activity of the complex was estimated. Metal-independent proteases of the complex hydrolyze proteins at trypsin-specific sites (after Lys and Arg). The complex contains both metal-dependent and metal-independent DNases. Mg²⁺, Mn²⁺, and Co²⁺ ions were found to strongly increase the DNase activity of the complex.

It was recently shown that IgGs from sera of multiple sclerosis (MS) patients are active in the hydrolysis of DNA and myelin basic protein (MBP). We first analyzed the relative concentration of antibodies against five histones (H1, H2a, H2b, H3, and H4) in the cerebrospinal fluid (CSF) and serum of patients with MS. The relative concentrations of blood and CSF IgGs against histones and their activity in the hydrolysis of five histones varied greatly from patient to patient. However, all 28 IgG preparations were hydrolyzed from one to five histones. Relative activities and correlation coefficients among the activities of IgGs from serum and CSF in the hydrolysis of five histones (H1, H2a, H2b, H3, and H4), DNA, and MBP were calculated. It was shown that auto-IgGs from CSF and sera of MS patients are extremely heterogeneous in their affinity to histones, MBP, and DNA. The heterogeneity of IgG-abzymes hydrolyzing DNA, MBP, and histones from CSF and sera was also demonstrated using their isoelectrofocusing. The isofocusing profiles DNase, MBP-, and histone-hydrolyzing activities of IgGs may be very different for various individuals, but the total IgG subfractions with all their activities are distributed from pH 3 to 10.

Antinuclear antibodies, especially anti-DNA antibodies, are known to be a hallmark of systemic lupus erythematosus (SLE) and represent a diverse pool of autoantibodies with different origins, antigenic properties, and physicochemical features. Antibodies with catalytic properties have been found among the antibody repertoire in SLE, but the specific features and clinical associations of such antibodies have not been sufficiently studied. This study showed that chromatographically purified IgG from the serum of SLE patients effectively hydrolyzed DNA and DNA-associated proteins such as histones and high-mobility group box 1 (HMGB1) compared to healthy individuals. Remarkably, the level of hydrolysis of DNA and DNA-associated proteins was closely correlated. At the same time, these antibodies did not hydrolyze the control protein, tumor necrosis factor-α (TNFα), which does not possess DNA-binding properties. IgG DNase activity levels varied significantly, so patients were divided into high- and low-activity subgroups using the DBSCAN algorithm, with the difference between median values being greater than 49 times. The subgroup with high IgG DNase activity was characterized by an increase in anti-DNA antibodies (p < 0.04) than the subgroup with low activity, which had a shorter duration of the disease (p = 0.03) and was more often characterized by a subacute rather than a non-chronic course of the disease (p = 0.048). High catalase-like activity of IgG was also detected in SLE. Thus, the antibody pool in SLE contains not only high-affinity antinuclear autoantibodies but also catalytic antibodies capable of hydrolyzing DNA and DNA-associated proteins. These findings expand our understanding of the heterogeneity of the repertoire of catalytic autoantibodies among SLE patients.

Sea cucumbers exhibit rapid recovery of all organs and the body following various injuries, making them highly promising models for investigating the mechanisms of self-regeneration. This study provides the first comprehensive comparative analysis of DNase activities in both homogenates and highly stable multiprotein complexes isolated from five distinct organs—gut, respiratory trees, body wall, gonads, and coelomic fluid—of the sea cucumber Paracaudina chilensis. Using in situ zymography following SDS-PAGE with copolymerized polymeric DNA, we systematically profiled the molecular weights, optimal pH values, and metal ion dependencies of DNases across these tissues and their corresponding stable complexes (1.2–1.8 MDa). Our results reveal that each organ possesses a unique DNase repertoire, with at least 25 distinct enzymatic species identified on the basis of molecular masses (~19, 23, 30, 35, 50, 100, 130, and 150 kDa) and pH optima ranging from 4.5 to 9.5. Notably, the gut homogenate contained the greatest diversity of DNases, whereas the respiratory tree and coelomic fluid complexes harbored highly active enzymes that were undetectable in the corresponding homogenates, indicating selective enrichment during complex assembly. Most DNases were Mg²⁺-dependent, with optimal MgCl₂ concentrations between 5 and 10 mM; however, two metal-independent DNases (~50 and ~100 kDa) were identified exclusively in respiratory tree complexes, and their activity was strongly enhanced by EDTA, suggesting suppression by endogenous metal ions. Additionally, Ca²⁺-activated DNases (~19 and ~23 kDa) were found in complexes from body wall, gonads, and coelomic fluid. Several DNases with high relative activity in the complexes were not reliably detected in the corresponding tissue homogenates, whereas some abundant homogenate enzymes were absent from the complexes. This implies that the formation of these supramolecular assemblies is not random but rather involves the specific recruitment of low-abundance enzymes, potentially concentrating them to achieve high local activity for organ-specific functions. The gut, which undergoes complete regeneration after evisceration, contained the most varied set of DNases, hinting at a possible role in DNA metabolism during tissue renewal. Thus, we have shown for the first time that the multiprotein complexes from different organs of the sea cucumber differ not only in molecular weight and protein/peptide composition but also in the number and types of DNases they contain. We propose that in each organ of the sea cucumber, a specific multiprotein complex is formed, which may be necessary to perform additional extended functions of this complex beyond those of canonical individual proteins, peptides, and enzymes.

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.