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.

Figure 1

A. japonicus neuropeptide precursor proteins that are precursors of neuropeptides belonging to known bilaterian neuropeptide families. Predicted signal peptides are shown in blue, putative neuropeptides are shown in red [with cysteine (C) residues highlighted in grey], C-terminal glycine (G) residues that are putative substrates for amidation are shown in orange and putative monobasic/dibasic cleavage sites are shown in green. Peptides confirmed by mass spectrometry are shown with light yellow highlighting. For peptides with a C-terminal glycine residue (orange) highlighted in yellow, mass spectrometric analysis confirmed that the C-terminal glycine residue is converted to an amide group. The positions of introns in the open reading frame of the gene encoding each neuropeptide precursor are indicated by underlining the amino acid residue(s) whose codon(s) are interrupted by introns.

Figure 2

A. japonicus neuropeptide precursor proteins that are precursors of neuropeptides belonging to known bilaterian neuropeptide families. Predicted signal peptides are shown in blue, putative neuropeptides are shown in red [with cysteine (C) residues highlighted in grey], C-terminal glycine (G) residues that are putative substrates for amidation are shown in orange and putative monobasic/dibasic cleavage sites are shown in green. Peptides confirmed by mass spectrometry are shown with light yellow highlighting. For peptides with a C-terminal glycine residue (orange) highlighted in yellow, mass spectrometric analysis confirmed that the C-terminal glycine residue is converted to an amide group. The positions of introns in the open reading frame of the gene encoding each neuropeptide precursor are indicated by underlining the amino acid residue(s) whose codon(s) are interrupted by introns.

Figure 3

A. japonicus neuropeptide precursor proteins that are precursors of neuropeptides belonging to known bilaterian neuropeptide families. Predicted signal peptides are shown in blue, putative neuropeptides are shown in red [with cysteine (C) residues highlighted in grey] and putative monobasic/dibasic cleavage sites are shown in green. The positions of introns in the open reading frame of the gene encoding each neuropeptide precursor are indicated by underlining the amino acid residue(s) whose codon(s) are interrupted by introns.

Figure 4

A. japonicus proteins that are precursors of neuropeptides (SALMFamides and AN peptides) and putative neuropeptides (Ajn8, 9 and 11) that have thus far been found only in echinoderms. Predicted signal peptides are shown in blue, putative neuropeptides are shown in red [with cysteine (C) residues highlighted in grey], C-terminal glycine (G) residues that are putative substrates for amidation are shown in orange and putative monobasic/dibasic cleavage sites are shown in green. Peptides confirmed by mass spectrometry are shown with light yellow highlighting. For peptides with a C-terminal glycine residue (orange) highlighted in yellow, mass spectrometric analysis confirmed that the C-terminal glycine residue is converted to an amide group. The positions of introns in the open reading frame of the gene encoding each neuropeptide precursor are indicated by underlining the amino acid residue(s) whose codon(s) are interrupted by introns.

Figure 5

A. japonicus proteins that are precursors of putative neuropeptides that have thus far been found only in echinoderms. Predicted signal peptides are shown in blue, putative neuropeptides are shown in red [with cysteine (C) residues highlighted in grey], C-terminal glycine (G) residues that are putative substrates for amidation are shown in orange and putative dibasic cleavage sites are shown in green. Peptides confirmed by mass spectrometry are shown with light yellow highlighting. The positions of introns in the open reading frame of the gene encoding each neuropeptide precursor are indicated by underlining the amino acid residue(s) whose codon(s) are interrupted by introns.

Figure 6

Neuropeptide precursors that are precursors of bioactive peptides have been discovered previously in A. japonicus. Predicted signal peptides are shown in blue, putative neuropeptides are shown in red [with cysteine (C) residues highlighted in grey], C-terminal glycine (G) residues that are putative substrates for amidation are shown in orange and putative monobasic/dibasic cleavage sites are shown in green. Peptides confirmed by mass spectrometry are shown with light yellow highlighting. For peptides with a C-terminal glycine residue (orange) highlighted in yellow, mass spectrometric analysis confirmed that the C-terminal glycine residue is converted to an amide group. The positions of introns in the open reading frame of the gene encoding each neuropeptide precursor are indicated by underlining the amino acid residue(s) whose codon(s) are interrupted by introns.

Figure 7

Novel putative neuropeptide precursors in A. japonicus based on NP search analysis or BLAST analysis using known A. japonicus neuropeptide precursors as queries. Predicted signal peptides are shown in blue, putative neuropeptides are shown in red [with cysteine (C) residues highlighted in grey], C-terminal glycine (G) residues that are putative substrates for amidation are shown in orange and putative monobasic/dibasic cleavage sites are shown in green. The positions of introns in the open reading frame of the gene encoding each neuropeptide precursor are indicated by underlining the amino acid residue(s) whose codon(s) are interrupted by introns.