Neuropeptide precursors and neuropeptides in the sea cucumber Apostichopus japonicus: a genomic, transcriptomic and proteomic analysis

Abstract

The sea cucumber Apostichopus japonicus is a foodstuff with very high economic value in China, Japan and other countries in south-east Asia. It is at the heart of a multibillion-dollar industry and to meet demand for this product, aquaculture methods and facilities have been established. However, there are challenges associated with optimization of reproduction, feeding and growth in non-natural environments. Therefore, we need to learn more about the biology of A . japonicus , including processes such as aestivation, evisceration, regeneration and albinism. One of the major classes of molecules that regulate physiology and behaviour in animals are neuropeptides, and a few bioactive peptides have already been identified in A . japonicus . To facilitate more comprehensive investigations of neuropeptide function in A . japonicus , here we have analysed genomic and transcriptomic sequence data and proteomic data to identify neuropeptide precursors and neuropeptides in this species. We identified 44 transcripts encoding neuropeptide precursors or putative neuropeptide precursors, and in some instances neuropeptides derived from these precursors were confirmed by mass spectrometry. Furthermore, analysis of genomic sequence data enabled identification of the location of neuropeptide precursor genes on genomic scaffolds and linkage groups (chromosomes) and determination of gene structure. Many of the precursors identified contain homologs of neuropeptides that have been identified in other bilaterian animals. Precursors of neuropeptides that have thus far only been identified in echinoderms were identified, including L- and F-type SALMFamides, AN peptides and others. Precursors of several peptides that act as modulators of neuromuscular activity in A . japonicus were also identified. The discovery of a large repertoire of neuropeptide precursors and neuropeptides provides a basis for experimental studies that investigate the physiological roles of neuropeptide signaling systems in A . japonicus . Looking ahead, some of these neuropeptides may have effects that could be harnessed to enable improvements in the aquaculture of this economically important species.

Evolution and Comparative Physiology of Luqin-Type Neuropeptide Signaling

“…Through analysis of transcriptome/genome sequence data, luqin-type neuropeptide precursors have subsequently been identified in other echinoderm classes, including Holothuroidea (sea cucumbers), Asteroidea (starfish or sea stars), and Ophiuroidea (brittle stars). In the sea cucumbers Apostichopus japonicus, Holothuria glaberrima, Holothuria scabra, and Holothuria leucospilota, the precursor comprises a single neuropeptide with the same predicted structure in all four species-KPYKFMRW-NH 2 (Rowe et al, 2014;Suwansa-Ard et al, 2018;Chen et al, 2019;Chieu et al, 2019). Luqin-type precursors identified in the starfish species A. rubens and Acanthaster planci comprise a single putative neuropeptide with the amino acid sequence EKGRFPKFMRW-NH 2 and EEKTRFPKFMRW-NH 2 , respectively Smith et al, 2017).…”

Comparative and Evolutionary Physiology of Vasopressin/ Oxytocin-Type Neuropeptide Signaling in Invertebrates

“…The other classes of echinoderms that we have yet to consider are the Holothuroidea (sea cucumbers), which are a sister class to the Echinoidea (sea urchins) in the Echinozoan clade of extant echinoderms, and the Crinoidea (e.g., featherstars) that occupy a basal position with respect to the other extant echinoderm classes (135). VP/OT-type precursor transcript sequences have been identified in several sea cucumber species, including Apostichopus japonicus, Holothuria glaberrima, and Holothuria scabra (136,137). The neuropeptides derived from these precursors (e.g., CFITNCPLG-NH 2 in A. japonicus; "holotocin") share more sequence similarity with the sea urchin peptide echinotocin (CFISNCPKG-NH 2 ) than with asterozoan VP/OTtype neuropeptides (e.g., asterotocin) ( Table 1), consistent with the sister group status of sea cucumbers (Holothuroidea) and sea urchins (Echinoidea) in the echinozoan clade of the phylum Echinodermata.…”

“…The neuropeptides derived from these precursors (e.g., CFITNCPLG-NH 2 in A. japonicus; "holotocin") share more sequence similarity with the sea urchin peptide echinotocin (CFISNCPKG-NH 2 ) than with asterozoan VP/OTtype neuropeptides (e.g., asterotocin) ( Table 1), consistent with the sister group status of sea cucumbers (Holothuroidea) and sea urchins (Echinoidea) in the echinozoan clade of the phylum Echinodermata. Currently, nothing is known about the physiological roles of VP/OT-type neuropeptides in sea cucumbers and so this is an important objective for future studies, particularly in the context of potential applications in aquaculture of economically valuable edible species such as A. stichopus and H. scabra (136,137).…”

The Effect of Pedal Peptide-Type Neuropeptide on Locomotor Behavior and Muscle Physiology in the Sea Cucumber Apostichopus japonicus

“…Although the locomotor behavior of A. japonicus was studied thoroughly before (Pan et al, 2015), the mechanisms underlying locomotor behavior in this echinoderm species are still unclear. With the decoding of whole-genome and the application of transcriptomics and proteomics in A. japonicus, the neuropeptides in A. japonicus were recently identified (Chen et al, 2019), which provide the foundation to study the functions of neuropeptides in locomotor behavior in this species.…”

“…A pedal peptidetype neuropeptide (C-terminal serine is amidated, as determined from mass spec data.) from the Ajnp7 precursor protein (Rowe and Elphick, 2012;Chen et al, 2019) was synthesized artificially by biological techniques. The EthoVision XT software was used to analysis the changes of locomotor behavior in A. japonicus after PDP administration.…”