Characterization of a Novel Superoxide Dismutase from a Deep-sea Sea Cucumber (Psychoropotes verruciaudatus).

At present, deep-sea enzymes are a research hotspot. In this study, a novel copper-zinc superoxide dismutase (CuZnSOD) was successfully cloned and characterized from a new species of sea cucumber Psychropotes verruciaudatus (PVCuZnSOD). The relative molecular weight of the PVCuZnSOD monomer is 15 kDa. The optimum temperature of PVCuZnSOD is 20 °C, and it maintains high activity in the range of 0-60 °C. It also has high thermal stability when incubated at 37 °C. PVCuZnSOD has a maximum activity of more than 50% in the pH range of 4-11 and a high activity at pH 11. In addition, PVCuZnSOD has strong tolerance to Ni2+, Mg2+, Ba2+, and Ca2+, and it can withstand chemical reagents, such as Tween20, TritonX-100, ethanol, glycerol, isopropanol, DMSO, urea, and GuHCl. PVCuZnSOD also shows great stability to gastrointestinal fluid compared with bovine SOD. These characteristics show that PVCuZnSOD has great application potential in medicine, food, and other products.

Saponin and Fatty Acid Profiling of the Sea Cucumber Holothuria atra, α-Glucosidase Inhibitory Activity and the Identification of a Novel Triterpene Glycoside.

Saponin-rich sea cucumber extracts have shown antidiabetic effects in a few reports. Although the triterpene glycosides of sea cucumbers are commonly isolated from their Cuvierian tubules, these are absent in Holothuria atra Jaeger. Therefore, this study intended to investigate the saponin profile in the body wall of H. atra, as well as to assess the α-glucosidase inhibitory activity of the H. atra extracts. The chemical profiling of sea cucumber extracts was conducted by UPLC-HRMS analysis. This resulted in the tentative identification of 11 compounds, 7 of which have not been reported in the H. Atra body wall before. Additionally, two triterpene glycosides were purified and their structures were elucidated based on HRMS and NMR data: desholothurin B (1), and a novel epimer, 12-epi-desholothurin B (2). Moreover, the fatty acid profile of the H. atra body wall was investigated by GC-MS. It was found that the Me90 fraction of the H. atra body wall showed the strongest α-glucosidase inhibitory activity (IC50 value 0.158 ± 0.002 mg/mL), thus making it more potent than acarbose (IC50 value 2.340 ± 0.044 mg/mL).

The digestive tract sections of the sea cucumber Isostichopus badionotus reveal differences in composition, diversity, and functionality of the gut microbiota.

For the first time, this study analyses the composition and diversity of the gut microbiota of Isostichopus badionotus in captivity, using high-throughput 16S rRNA sequencing, and predicts the metagenomic functions of the microbiota. The results revealed a different composition of the gut microbiota for the foregut (FG) and midgut (MG) compared to the hindgut (HG), with a predominance of Proteobacteria, followed by Actinobacteria, Bacteroidetes, and Firmicutes. The FG and MG demonstrated a greater bacterial diversity compared to the HG. In addition, a complex network of interactions was observed at the genus level and identified some strains with probiotic and bioremediation potentials, such as Acinetobacter, Ruegeria, Streptococcus, Lactobacillus, Pseudomonas, Enterobacter, Aeromonas, Rhodopseudomonas, Agarivorans, Bacillus, Enterococcus, Micrococcus, Bifidobacterium, and Shewanella. Predicting metabolic pathways revealed that the bacterial composition in each section of the intestine participates in different physiological processes such as metabolism, genetic and environmental information processing, organismal systems, and cellular processes. Understanding and manipulating microbe--host-environment interactions and their associated functional capacity could substantially contribute to achieving more sustainable aquaculture systems for I. badionotus.

Global knowledge on the commercial sea cucumber Holothuria scabra.

Holothuria scabra is one of the most intensively studied holothuroids, or sea cucumbers (Echinodermata: Holothuroidea), having been discussed in the literature since the early 19th century. The species is important for several reasons: (1) it is widely distributed and historically abundant in several shallow soft-bottom habitats throughout the Indo-Pacific, (2) it has a high commercial value on the Asian markets, where it is mainly sold as a dried product (beche-de-mer) and (3) it is the only tropical holothuroid species that can currently be mass-produced in hatcheries. Over 20 years have elapsed since the last comprehensive review on H. scabra published in 2001. Research on H. scabra has continued to accumulate, fuelled by intense commercial exploitation, and further declines in wild stocks over the entire distribution range. This review compiles data from over 950 publications pertaining to the biology, ecology, physiology, biochemical composition, aquaculture, fishery, processing and trade of H. scabra, presenting the most complete synthesis to date, including scientific papers and material published by local institutions and/or in foreign languages. The main goal of this project was to summarize and critically discuss the abundant literature on this species, making it more readily accessible to all stakeholders aiming to conduct fundamental and applied research on H. scabra, or wishing to develop aquaculture, stock enhancement and management programs across its geographic range.

Analysis of Complete Mitochondrial Genome of Bohadschia argus (Jaeger, 1833) (Aspidochirotida, Holothuriidae).

Bohadschia argu is a kind of sea cucumber with high economic value; it is the only undisputed species in the genus Bohadschia. In this study, the complete mitochondrial genome (mitogenome) of B. argus was acquired through high-throughput sequencing. The mitochondrial genome of B. argus was 15,656 bp in total length and contained a putative control region (CR) and 37 typical genes of animal mitochondrial genomes, including 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rrnS and rrnL) and 22 transfer RNA genes (tRNA). The sizes of the PCGs ranged from 168 bp to 1833 bp, and all PCGs except nad6 were encoded on the heavy chain (H). Both rrnS and rrnL were also encoded on the H chain. Twenty-two tRNA genes had positive AT skew and GC skew. All tRNAs had a typical cloverleaf secondary structure except for trnI, in which an arm of dihydrouridine was missing. B. argus shared the same gene arrangement order (the echinoderm ground pattern) as other species in Aspidochirotida. Phylogenetic analysis clearly revealed that B. argus belongs as a member of the Holothuriidae, and it is closely related to members of Actinopyga and Holothuria.

Molecular mechanisms mediating stiffening in the mechanically adaptable connective tissues of sea cucumbers.

Mutable collagenous tissues (MCTs) from echinoderms (e.g., sea stars, sea urchins) possess the remarkable ability to change their mechanical properties rapidly and reversibly thanks to the release of effector molecules regulating the number of cross-links between collagen fibrils. Among these effector molecules, tensilin has been identified as a stiffening factor in sea cucumber MCTs. Since its discovery and description twenty years ago, tensilin orthologs have been identified in a few sea cucumber species but no novel information about its molecular mode of action has been reported. In this study, using a combination of in silico analyses, we identified the tensilin present in the dermis of Holothuria forskali, Hf-(D)Tensilin. Anti-peptide antibodies showed that this protein is localised in the secretory granules of type 2 juxtaligamental-like cells, a MCT specific cell type. We then used the bacterium E. coli to produce recombinantly Hf-(D)Tensilin and confirmed its stiffening effect on pieces of the dermis and its aggregation effect on collagen fibrils extracted from the sea cucumber dermis. To investigate how tensilin can cross-bridge collagen fibrils, truncated recombinant tensilins were also produced and used in combination with various compounds. Results suggest that two types of interactions contribute to the aggregation effect of tensilin on the fibrils: (1) the N-terminal NTR TIMP like domain of the protein interacts strongly with sulfated GAGs attached to the surface of the collagen fibrils, and (2) the C-terminal part of the protein is involved in its dimerisation/oligomerisation through ionic but possibly also cation-π and hydrophobic interactions.

The Concentration of ProAKAP4 and Other Indicators of Cryopotential of Spermatozoa Cryopreserved in Extender with Holothuroidea Extract Addition.

The aim of this study was to determine the concentration of proAKAP4 and other indicators of cryopotential of spermatozoa cryopreserved in extender with Holothuroidea extract addition. Nine Holstein Friesian bulls, 3.5 years old, of known health status, were used for the study. The animals were kept and fed equally. Semen was collected once a week using an artificial vagina. The commercially available Holothuroidea extract was used as a supplement to the commercial extender (0, 2, 4 and 6 µL/mL) before the freezing/thawing process. The viability, motility, motion parameters, and acrosome integrity of the sperm were analyzed with (test) or without (control) extract samples. Furthermore, the concentration of the proAKAP4 biomarker in frozen sperm was assessed. It was shown that the addition of 4 and 6 µL of the extract may have a positive effect on the quality parameters of the sperm after thawing. The results indicate that extender supplementation with the above extract modulates (increases) the concentration of proAKAP4 in sperm at all tested levels. Additionally, this indicator has become helpful in identifying sperm of poor biological quality. Moreover, it has been proven that the proAKAP4 biomarker can be successfully used to evaluate the effectiveness of the use of various extenders for semen cryopreservation.

Fatty Acids of Echinoderms: Diversity, Current Applications and Future Opportunities.

The phylum Echinodermata comprising the classes Asteroidea, Ophiuroidea, Echinoidea, Holothuroidea, and Crinodeia, is one of the important invertebrate groups. Members of this phylum live exclusively in marine habitats and are distributed in almost all depths and latitudes. Some of them, such as sea urchins and sea cucumbers, are commercially valuable and constitute a major fishery resource. Echinoderms are increasingly recognized as a unique source of various metabolites with a wide range of biological activities. The importance of dietary polyunsaturated fatty acids, such as eicosapentaenoic acid, in human health has drawn attention to echinoderms as a promising source of essential fatty acids (FAs). Extensive information on the FAs of the phylum has been accumulated to date. The biosynthetic capabilities and feeding habits of echinoderms explain the findings of the unusual FAs in them. Certain common and unusual FAs may serve as chemotaxonomic markers of the classes. The main goal of the review was to gather the relevant information on the distribution of FAs among the echinoderm classes, describe the structures, distribution, biosynthetic pathways, and bioactivity, with an emphasis on the FAs specific for echinoderms. A large part of the review is devoted to the FAs derived from echinoderms that exhibit various biological activities promising for potential therapeutic applications.

Characterization of the complete mitochondrial genome of Thyonella gemmata (Echinodermata: Cucumariidae).

Thyonella gemmata , also known as the Green sea cucumber, is a biomedically and ecologically important species. In this study, the complete mitogenome of T. gemmata (Echinodermata: Holothuroidea) collected from the Florida Panhandle, USA is reported. The mitochondrial genome of T. gemmata consisted of 15,696 base pairs, and was composed of 36.10% A, 28.27% T, 23.18% C, and 12.45% G. There were 13 protein coding genes, 22 tRNA genes, and 2 rRNA genes within the mitogenome of T. gemmata. Mapping out the complete mitochondrial genome of T. gemmata, will help aid in future evolutionary studies and can be applied to future phylogenetic research of holothurians and related species.

Sphingolipids of Asteroidea and Holothuroidea: Structures and Biological Activities.

Sphingolipids are complex lipids widespread in nature as structural components of biomembranes. Commonly, the sphingolipids of marine organisms differ from those of terrestrial animals and plants. The gangliosides are the most complex sphingolipids characteristic of vertebrates that have been found in only the Echinodermata (echinoderms) phylum of invertebrates. Sphingolipids of the representatives of the Asteroidea and Holothuroidea classes are the most studied among all echinoderms. In this review, we have summarized the data on sphingolipids of these two classes of marine invertebrates over the past two decades. Recently established structures, properties, and peculiarities of biogenesis of ceramides, cerebrosides, and gangliosides from starfishes and holothurians are discussed. The purpose of this review is to provide the most complete information on the chemical structures, structural features, and biological activities of sphingolipids of the Asteroidea and Holothuroidea classes.

The complete mitochondrial genome of the chocolate chip sea cucumber Isostichopus badionotus (Echinodermata: Holothuroidea).

The chocolate chip sea cucumber, Isostichopus badionotus (Selenka 1867), is an ecologically and biomedically important species. In this study, we report the complete mitogenome sequence of the sea cucumber, I. badionotus (Echinodermata: Holothuroidea). The mitochondrial genome consisted of 16,319 bp, with 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes. The total nucleotide composition consisted of 31.61% A, 29.20% T, 23.48% C, 15.71% G, with a high A + T content of 60.81%. Phylogenetic analysis using the complete mitochondrial genome of I. badionotus is helpful in studying the evolution of beneficial adaptations to aid in bioremediation and biomedical research and development.

The first two complete mitogenomes of the order Apodida from deep-sea chemoautotrophic environments: New insights into the gene rearrangement, origin and evolution of the deep-sea sea cucumbers.

The deep-sea ecosystem is considered as the largest and most remote biome of the world. It is meaningful and important to elucidate the life origins by exploring the origin and adaptive genetic mechanisms of the large deep-sea organisms. Sea cucumbers (Holothuroidea) are abundant and economically important group of echinoderms, living from the shallow-waters to deep-sea. In this study, we present the mitochondrial genomes of the sea cucumber Chiridota heheva and Chiridota sp. collected from the deep-sea cold seep and hydrothermal vent, respectively. This is the first reported mitochondrial genomes from the order Apodida. The mitochondrial genomes of C. heheva (17,200 bp) and Chiridota sp. (17,199 bp) display novel gene arrangements with the first protein-coding gene rearrangements in the class Holothuroidea. Bases composition analysis showed that the A + T content of deep-sea holothurians were significantly higher than that of the shallow-water groups. We compared the arrangement of genes from the 24 available holothurian mitogenomes and found that the transposition, reverse transposition and tandem-duplication-random-losses (TDRL) may be involved in the evolution of mitochondrial gene arrangements in Holothuroidea. Phylogenetic analysis revealed that the Apodida clustered with Elasipodida, forming two basal deep-sea holothurian clades. The divergence between the deep-sea and shallow-water holothurians was located at 386.93 Mya, during the Late Devonian. Mitochondrial protein-coding genes of deep-sea holothurians underwent relaxed purifying selection. There are 57 positive selected amino acids sites for some mitochondrial genes of the three deep-sea clades, implying they may involve in the adaption of deep-sea sea cucumbers.

The complete mitochondrial genome of Pink warty sea cucumber (Cercodemas anceps Selenka, 1867).

In this study, we sequenced the circular mitochondrial genome (mitogenome) of Cercodemas anceps. This genome was determined to measure 16,539 bp in length and contain 13 protein-coding genes (PCGs), 22 tRNA genes, and 2 rRNA genes. The longest gene was observed to be nad5, which measures 1,641 bp in length and is located at position 6,540 ∼ 8,180 of the C. anceps mitogenome. One PCG, nad6, and five tRNA genes (tRNASer(UCN) , tRNAGln , tRNAAla , tRNAVal, and tRNAAsp ) were located on the light chain, and the other genes were located on the heavy chain. A phylogenetic tree was constructed with the mitogenome sequences of 26 types of echinoderm species, and the results show that C. anceps is most closely related to C. quadrangularis.

Primer registro del género Leptopentacta (Cucumariidae: Colochirinae) en el Caribe nicaragüense / First record of the genus Leptopentacta (Cucumariidae: Colochirinae) for the Nicaraguan Caribbean

Introducción: El género Leptopentacta solo ha sido reportado previamente en Florida, Cuba, Colombia, Costa Rica y Surinam. Objetivo: Presentar el primer registro del género para Nicaragua. Métodos: Los caracteres morfológicos del material nicaragüense del Smithsonian Institution (USNM 1014529), fueron corroborados con la descripción original. Resultados: Los cinco especímenes recolectados en el Caribe nicaragüense coinciden con el género. Conclusiones: Leptopentacta se reporta por primera vez en el Mar Caribe de Nicaragua. Esto aumenta el número de equinodermos nicaragüenses a 194 especies.

Introduction: The genus Leptopentacta has only been previously reported from Florida, Cuba, Colombia, Costa Rica, and Suriname. Objective: To present the first record of the genus for Nicaragua. Methods: The morphological characters of Nicaraguan material at the Smithsonian Institution (USNM 1014529), were corroborated with the original description. Results: The five specimens collected in the Nicaraguan Caribbean match the genus. Conclusions: Leptopentacta is reported for the first time from the Nicaraguan Caribbean Sea. This increases the number of Nicaraguan echinoderms to 194 species.

Exploring the macrostructural anatomy of dendrochirotid sea cucumber's (Echinodermata) calcareous rings under micro-computed tomography and its bearing on phylogeny.

Despite descending from heavily calcified ancestors, the holothuroid skeleton is fully internal and composed of microscopic ossicles and a ring of plates bound by connective tissue, the calcareous ring. The calcareous ring exhibits a complex and poorly understood morphology; as a result, establishing unambiguous homology statements about its macrostructure has been challenging and phylogenetic studies have had to simplify this important structure. Here, we provide the first broad comparative study of Dendrochirotida calcareous rings using micro-computed tomography (µCT). A detailed description of the three-dimensional macrostructure of the calcareous ring of 10 sea cucumber species, including rare and type specimens, is presented. The structures observed were highly variable at the subfamily level, especially at the point of tissue attachment. The relationship between the calcareous ring and its associated organs, and their functional morphology are discussed. To aid future phylogenetic studies, we listed 22 characters and performed a preliminary cladistic analysis. The topology obtained supports the idea that the simple, cucumariid ring is ancestral to the mosaic-like phyllophorid ring; however, it did not support the monophyly of the cucumariids. It also did not support the family Sclerodactylidae, which was described based on the ring morphology. Differently from the dermal ossicles, which are highly homoplastic, the general homoplasy index of the calcareous ring characters was relatively low. This result highlights the importance of this structure for phylogenetic inference. Unfortunately, time since collection, rough collection methods and fixation can damage the skeleton, and the calcareous ring is often overlooked in taxonomic descriptions. The data presented here will improve our understanding of holothuroid relationships and facilitate studies on holothuroid functional morphology and biomechanics.

The first complete mitochondrial genome of Actinopyga from Actinopyga echinites (Aspidochirotida: Holothuriidae).

The deep-water redfish, Actinopyga echinites, is an ecologically and economically important holothuroid in China due to its valuable nutrition and pharmacological compounds. However, the taxonomy and phylogeny of the Actinopyga have been debated and misidentifications have been reported recently. Moreover, there remain considerable doubts about cryptic species complex within Actinopyga. In this study, we report the first complete mitochondrial genome of Actinopyga from A. echinites. The mitogenome has 15,619 base pairs (62.9% A + T content) and made up of a total of 37 genes (13 protein-coding, 22 transfer RNAs, and 2 ribosomal RNAs), and a putative control region. This study was the first available complete mitogenome of Actinopyga and will provide useful genetic information for future phylogenetic and taxonomic classification of Holothuriidae.

Pentamera fonsecae n. sp. a new species of sea cucumber from the Pacific coast of Costa Rica (Holothuroidea: Dendrochirotida: Thyonidae).

Pentamera fonsecae n. sp. is described from seven specimens as a new species of Thyonidae from the Pacific coast of Costa Rica. It is distinguished from its congeners by having tables with ladder-shaped spires in the body wall, and tube feet with curved support tables of variable height and tables as those found in the body wall slightly smaller than those from the body wall. This species is distributed in Guanacaste, Costa Rica, from 28.5 to 40 m on muddy bottoms.

Two new species of holothurians of the genus Echinopsolus Gutt, 1990(Echinodermata: Dendrochirotida: Cucumariidae) from the North-Western Pacific.

Two new species of the genus Echinopsolus-E. sanamyanorum and E. onekotanensis are described. This genus is new for North-Western Pacific marine fauna. Echinopsolus sanamyanorum was collected in the Avacha Gulf (south-east coast of Kamchatka), E. onekotanensis-near the Onekotan Island (The Kuril Islands).

First records and new information on the associations of echinoderms with other phyla in the rocky reefs of northern Chocó, Colombian Pacific.

Rocky reefs of the northern Colombian Pacific (Chocó) are diverse ecosystems that are poorly studied. Echinoderms are one of the principal groups in these ecosystems with associations to different species, including benthic organisms in which they live and other species that use them as hosts. These relationships include fishes, sponges, seaweeds, cnidarians, polychaetes, bryozoans, crustaceans, mollusks, and other echinoderms. For this area, 22 associations were registered, including commensalism, epibionts and parasitism. This work constitutes the first report for the associations of Eucidaris thouarsii with Suberites aff. ficus, E. thouarsii with Ophiothela mirabilis, and Holothuria (Thymiosicia) impatiens with Encheliophis vermicularis. Associations of Pentaceraster cumingi with Zenopontonia soror, and Ophionereis annulata with Malmgreniella cf. variegata are new records for Colombia. This work also expands the range of hosts previously described for Ophiothela mirabilis and expands the distribution of the association between Diadema mexicanum and Echineulima cf. robusta.

Complete sequence of mitochondrial DNA of a deep-sea holothurian species of the genus Synallactes (Synallactida: Synallactidae).

One complete mitochondrial genome (mitogenome) was determined for a deep-sea holothurian species of the genus Synallactes (Synallactida: Synallactidae). The mitochondrial genome size of the sea cucumber was 15,920 bp. The sequence contains 2 ribosomal RNA genes (12S and 16S), 22 transfer RNA genes, and 13 protein-coding genes, as found in most previously determined holothurian mitogenomes. The A + T content of the complete mitochondrial genome sequence was 64.45%. The base composition showed a tendency of AT. The resulted maximum likelihood (ML) tree of Holothuroidea supported that Synallactes sp. is a species of Synallactida.