dataesr/scientific-paragraphs-categorization huggingface dataset:
Discovery of novel starfish representatives of bilaterian neuropeptide and peptide hormone families 3. 3. 1. Precursor of a vasopressin/oxytocin-type neuropeptide (asterotocin) A VP/OT-type neuropeptide precursor in A. rubens was identified as a 147-residue protein comprising a predicted 23-residue N-terminal signal peptide, a VP/OT-type neuropeptide sequence (CLVQDCPEGG) followed by a dibasic cleavage site and a neurophysin domain (figure  9a ; GenBank: KT601711). This structure of the precursor conforms to the evolutionarily conserved organization of VP/OT-type neuropeptide precursors throughout the Bilateria  [5, 133]. Mature VP/OT-type neuropeptides are typically C-terminally amidated and have a disulfide bridge between two highly conserved cysteine residues, which are crucial for biological activity  [134] [135] [136].
Precursor of NGFFYamide, a neuropeptide-S/NG peptide/ crustacean cardioactive peptide-type neuropeptide Discovery of the A. rubens NGFFYamide precursor was reported recently  [156]  and was accomplished by analysis of the same neural transcriptome dataset analysed here; therefore, it is included here for sake of completeness. The NGFFYamide precursor is a 239-residue protein comprising a predicted 23-residue N-terminal signal peptide, two copies of the sequence NGFFYG bounded by dibasic cleavage sites and a C-terminal neurophysin domain containing 14 cysteine residues (figure  9b ; GenBank: KC977457), which is a conserved feature of neurophysins. Post-translational conversion of the C-terminal glycine residue of the NGFFYG peptide to an amide group has been confirmed by mass spectrometry  [156].
Precursor of gonadotropin-releasing hormone-type peptide 1 (ArGnRH1P) A GnRH-type neuropeptide precursor in A. rubens (ArGnRH1P) was identified as a 121-residue protein comprising a predicted 27-residue N-terminal signal peptide rsob. royalsocietypublishing. org Open Biol. 6: 150224 and a GnRH-type peptide sequence (QIHYKNPGWGPG) followed by a dibasic cleavage site (figure  9c ; GenBank: KT601712). The presence of an N-terminal glutamine residue and a C-terminal glycine residue are indicative of posttranslational modifications giving rise to an N-terminal pyroglutamate residue and a C-terminal amide group in the putative mature peptide ( pQIHYKNPGWGPG-NH 2 ; ArGnRH1), which would be consistent with GnRHtype neuropeptides that have been identified in other species  [161]. GnRH-type peptides have a widespread phylogenetic distribution indicative of an evolutionary origin dating back to the common ancestor of bilaterians  [5, 6].
Precursor of gonadotropin-releasing hormone-type peptide 2 (ArGnRH2P) A second GnRH-type neuropeptide precursor in A. rubens (ArGnRHP2) was identified as a 99-residue protein comprising a predicted 23-residue N-terminal signal peptide and a putative GnRH-type peptide sequence (HNTFTMGGQN RWKAGG) followed by a dibasic cleavage site (figure  9d ; GenBank: KT601713). The presence of a C-terminal glycine residue is indicative of a post-translational modification that gives rise to a C-terminal amide group on the mature peptide (HNTFTMGGQNRWKAG-NH 2 ). However, the absence of an N-terminal pyroglutamate residue is atypical for GnRH-type neuropeptides  [161]. ArGnRHP2 was identified on account of its sequence similarity with Spnp12, a putative neuropeptide precursor previously identified in the sea urchin S.
Precursor of thyrotropin-releasing hormone (TRH)-type peptides (ArTRHP) A TRH-type neuropeptide precursor in A. rubens (ArTRHP) was identified as a 225-residue protein comprising a predicted 23-residue N-terminal signal peptide and 12 putative TRHtype peptides bounded by dibasic cleavage sites (figure  9e ; GenBank: KT601714). These include a single copy of the peptide sequence QYPGGAPIGLDG and 11 copies of the peptide sequence QWYTG. The presence of an N-terminal glutamine residue and a C-terminal glycine residue in these peptide sequences are indicative of potential post-translational modification to an N-terminal pyroglutamate and a C-terminal amide group in the mature peptides, which would be consistent with the structure of TRH in mammals ( pQHP-NH 2 ). Hence the predicted structure of the multi-copy TRH-type peptide in A.
Precursor of two cholecystokinin-type peptides (ArCCKP) A cholecystokinin (CCK)-type neuropeptide precursor in A. rubens (ArCCKP) was identified as a 163-residue protein comprising a predicted 22-residue N-terminal signal peptide and two putative CCK-type neuropeptides bounded by dibasic cleavage sites: RQSKVDDYGHGLFWG (ArCCK1) and GGDDQYGFGLFFG (ArCCK2) (figure  9g ; GenBank: KT601716). The presence of C-terminal glycine residues in both of these sequences is indicative of post-translational modifications giving rise to a C-terminal amide group on the mature peptides. Furthermore, an additional potential post-translational modification for these peptides is sulfation of the tyrosine residues (underlined above), as this is a common characteristic of CCK-type neuropeptides in other species  [189].
Precursors of orexin-type peptides (ArOXP1 and ArOXP2) An orexin (OX)-type neuropeptide precursor in A. rubens (ArOXP1) was identified as a 112-residue protein comprising a predicted 24-residue N-terminal signal peptide and an OXtype peptide sequence followed by a dibasic cleavage site (figure  9h ; GenBank: KT601717). The presence of a C-terminal glycine residue is indicative of a post-translational modification that gives rise to a C-terminal amide group on the mature peptide. It is noteworthy that the putative OX-type peptide contains six cysteine residues, which may form up to three disulfide bridges. This contrasts with OXtype peptides in vertebrates that have two intra-chain disulfide bridges formed by four cysteine residues  [210]. A second OX-type neuropeptide precursor in A. rubens (ArOXP2) was identified as a 161-residue protein comprising a predicted 26-residue N-terminal signal peptide and an OXtype peptide sequence, followed by a dibasic cleavage site (figure  9i ; GenBank: KT601718).
Precursor of a luqin-type neuropeptide (ArLQP) A luqin (LQ)-type neuropeptide precursor in A. rubens (ArLQP) was identified as a 106-residue protein comprising a predicted 44-residue N-terminal signal peptide and a putative LQ-type peptide sequence (EEKTRFPKFMRWG) followed by a dibasic cleavage site (figure  9j ; GenBank: KT601719). The presence of a C-terminal glycine residue is indicative of a post-translational modification giving rise to a C-terminal amide group on the putative mature peptide (EEKTRFPKFMRW-NH 2 ). Comparison of the LQ-type neuropeptide precursor in A. rubens with LQ-type precursor proteins that have been identified in other species reveals similarities (figure  16 ). Thus, in A. rubens, the precursor comprises a single putative neuropeptide (EEKTRFPKFMRW-NH 2 ), which is also a feature of LQ-type precursors in other echinoderms (e.
Precursor of pedal peptide-type neuropeptides (ArPPLNP) A partial 325-residue sequence of a pedal peptide (PP)-type precursor (ArPPLNP) was identified in A. rubens, comprising a 31-residue N-terminal signal peptide and seven putative neuropeptides bounded by dibasic cleavage sites (figure  9k ; GenBank: KT601720). The putative peptides derived from ArPPLNP share sequence similarity with peptides derived from two PP-type precursors that were recently identified in the sea urchin S. purpuratus (SpPPLNP1 and SpPPLNP2)  [9]. Furthermore, as illustrated in figure  17 , representative neuropeptides derived from ArPPLNP, SpPPLNP1 and SpPPLNP2 share sequence similarity with PP-type peptides in lophotrochozoans (e. g. Capitella, Lottia) and orcokinintype peptides in arthropods (e. g. Drosophila). Indeed, it was the discovery of SpPPLNP1 and SpPPLNP2 in S.
Precursors of GPA2-type and GPB5-type glycoprotein hormones A glycoprotein hormone a-2 (GPA2)-type precursor in A. rubens (ArGPAP2-1) was identified as a 135-residue protein comprising a predicted 24-residue N-terminal signal peptide followed by a 111-residue polypeptide that shares sequence similarity with GPA2-type subunits (figure  18a ; GenBank: KT601721). A second GPA2-type precursor (ArGPAP2-2) was identified as a 130-residue protein comprising a predicted 28-residue N-terminal signal peptide followed by a 102-residue polypeptide that shares sequence similarity with GPA2-type subunits (figure  18b ; GenBank: KT601722). It is noteworthy that both ArGPA2-1 and ArGPA2-2 contain 10 cysteine residues (figure  18a, b ), which, in accordance with glycoprotein hormone subunits in other phyla, are likely to form five disulfide bridges  [125].
A glycoprotein hormone b-5 (GPB5)-type precursor in A. rubens (ArGPBP5-1) was identified as a 136-residue protein comprising a predicted 24-residue N-terminal signal peptide followed by a 112-residue polypeptide that shares sequence similarity with GPB5-type subunits (figure  18c ; GenBank: KT601723). A second GPB5-type precursor (ArGPBP5-2) was identified as a 141-residue protein comprising a predicted 31-residue N-terminal signal peptide followed by a 110-residue polypeptide that shares sequence similarity with GPB5-type subunits (figure  18d ; GenBank: KT601724). A third GPB5-type precursor (ArGPBP5-3) was identified as a 130-residue protein comprising a predicted 30-residue N-terminal signal peptide followed by a 100-residue polypeptide sequence sharing sequence similarity with GPB5-type subunits (figure  18e ; GenBank: KT601725).
Precursors of bursicon-type hormones (ArBAP and ArBBP) A bursicon-a-type precursor in A. rubens (ArBAP) was identified as a 139-residue protein comprising a predicted 35-residue N-terminal signal peptide followed by a 104-residue polypeptide sequence sharing sequence similarity with bursicon-a-type subunits (figure  18f ; GenBank: KT601726). A bursicon-b-type precursor in A. rubens (ArBBP) was identified as a 142-residue protein comprising a predicted 30-residue N-terminal signal peptide followed by a 112-residue polypeptide sequence sharing sequence similarity with bursicon-b-type subunits (figure  18g ; Gen-Bank: KT601727). Both ArBAP and ArBBP contain 11 cysteine residues, in common with the prototypical bursicon-type subunits in insects (figure  19 ). Bursicon was originally discovered in insects on account of its effect in causing cuticular tanning  [246].
Precursor of relaxin-like gonad-stimulating peptide (ArRGPP) A relaxin-like gonad-stimulating peptide precursor in A. rubens (ArRGPP) was identified as a 109-residue protein comprising sequentially (i) a predicted 26-residue N-terminal signal peptide, (ii) a 20-residue polypeptide comprising two cysteine residues (B-chain), (iii) a dibasic cleavage site, (iv) a connecting peptide (C-peptide) domain (residues rsob. royalsocietypublishing. org Open Biol. 6: 150224 49-82), (v) a dibasic cleavage site and (vi) a 25-residue polypeptide comprising four cysteine residues (A-chain) (figure  18h ; GenBank: KT601728). The A-chain has the cysteine motif CCxxx CxxxxxxxxC, which is characteristic of the insulin/insulin-like growth factor (IGF)/relaxin superfamily (figure  20 ). More specifically, the final residue of the A-chain is a cysteine, which is characteristic of the relaxin/ insulin-like (INSL) sub-class as opposed to the insulin/ IGF sub-class  [252].
Precursor of relaxin-like peptide 2 (ArRLPP2) A second relaxin-like peptide precursor in A. rubens (ArRLPP2) was identified as a 119-residue protein comprising sequentially (i) a predicted 30-residue N-terminal signal peptide, (ii) a 26-residue polypeptide comprising two cysteine residues (B chain), (iii) a dibasic cleavage site, (iv) a C-peptide domain (residues 59-91), (v) a dibasic cleavage site and (vi) a 26-residue polypeptide comprising four cysteine residues (A-chain) (figure  18i ; GenBank: KT601729). It is noteworthy that the N-terminal glutamine residue in the B-chain could be subject to post-translational conversion to a pyroglutamate. Similarly to ArRGPP (or 'ArRLPP1'), the A-chain has the cysteine motif CCxxxCxxxxxxxxC, while the B-chain has the cysteine motif CxxxxxxxxxxxC characteristic of the insulin/IGF/relaxin superfamily (figure  20 ).
Precursors of insulin-like growth factors (ArIGFP1 and ArIGFP2) ArIGFP1 is a 355-residue precursor protein comprising a predicted 27-residue N-terminal signal peptide and A-E domains that are characteristic of IGF-type precursors (figure  18j ; GenBank: KT601730). The B-domain contains two cysteine residues (residues 32 and 44) and the A-domain contains four cysteine residues (residues 91, 92, 96 and 105), which are likely to form disulfide bridges and a peptide heterodimer between both chains based on the presence of this feature in the insulin/IGF/relaxin superfamily. ArIGFP1 has dibasic cleavage sites at the C-terminal and N-terminal of the B-domain (residues 28 -55) and A-domain  rsob. royalsocietypublishing. org Open Biol. 6: 150224 (residues 83 -106), respectively, which would allow for the removal of the intervening C-peptide (residues 58 -80) as in vertebrate insulin and relaxin.
However, the ArIGFP1 Adomain also extends to a D-domain (residues 107 -133) and E-domain (residues 134 -355), a feature found in IGF-type precursors  [266]. ArIGFP2 is a 343-residue precursor protein comprising a predicted 22-residue N-terminal signal peptide and characteristic IGF-type A-, B-, C-and E-domains (figure  18k ; GenBank: KT601731). The B-domain contains two cysteine residues (residues 28 and 40) and the A-domain contains four cysteine residues (residues 66, 67, 71 and 80), which are likely to form disulfide bridges, and a peptide heterodimer between both chains based on the presence of this feature in the insulin/IGF/relaxin superfamily. However, unlike vertebrate insulin and relaxin, ArIGFP2 does not have dibasic cleavage sites at the C-terminal and Nterminal of the B-domain (residues 23 -46) and A-domain rsob.
Precursors of SALMFamide neuropeptides The SALMFamide neuropeptides S1 (GFNSALMF-NH 2 ) and S2 (SGPYSFNSGLTF-NH 2 ) were originally isolated from extracts of nerves dissected from A. rubens and the closely related starfish species A. forbesi; they were the first neuropeptides to be identified in an echinoderm species  [21, 22]. Here, we have identified transcripts that encode the S1 and S2 precursor proteins. The S1 precursor is a 210-residue protein comprising a predicted 23-residue N-terminal signal peptide and, bounded by dibasic cleavage sites, seven putative neuropeptide sequences that have a C-terminal glycine residue, which is a potential substrate for C-terminal amidation (figure  21a ; GenBank: KT601732). The predicted neuropeptide products rsob. royalsocietypublishing. org Open Biol.
6: 150224 of the S1 precursor are S1 and six other putative L-type SAL-MFamides, which like S1 have the C-terminal motif S/ TxLxF/Y-NH 2 (where x is variable). Four of the novel SAL-MFamides are octapeptides, like S1, but one peptide is one residue shorter than S1 (LHSALPF-NH 2 ) and another is longer than S1 (PAGASAFHSALSY-NH 2 ). The S2 precursor is a 233-residue protein comprising a predicted 23-residue N-terminal signal peptide and, bounded by dibasic cleavage sites, eight putative neuropeptide sequences that have a C-terminal glycine residue, which is a potential substrate for C-terminal amidation (figure  21b ; GenBank: KP330476). The predicted neuropeptide products of the S2 precursor are S2, which like S1 is an L-type SALMFamide, and seven putative F-type SALMFamides, which have the C-terminal motif F/YxF/Y-NH 2 (where x is variable).
Precursor of AN peptides (ArANPP) ArANPP is a 274-residue precursor protein comprising a predicted 24-residue N-terminal signal peptide and six putative neuropeptides with an N-terminal alanine (A)/asparagine (N) (AN) motif, which are bounded by putative dibasic cleavage sites (figure  21c ; GenBank: KT601733). Three of the predicted neuropeptides have a C-terminal glycine residue, which may be a substrate for post-translational conversion to an amide group. ArANPP was identified on account of its sequence similarity with the sea urchin AN peptide precursor SpANPP  [9]. The AN peptides are a family of peptides that have to date only been identified in the echinoderms  [9, 10] , and a relationship with neuropeptides identified in other phyla has yet to be determined. Some similarities with TK-type peptides have been noted  [10] , but with the discovery of other TK-type peptides in A.
Arnp11 Arnp11 was identified and named on account of its similarity with Spnp11, a putative neuropeptide precursor in the sea urchin S. purpuratus  [9]. It is a 103-residue precursor protein comprising a 21-residue N-terminal signal peptide followed by an 82-residue polypeptide sequence (residues 22 -103) that contains a putative dibasic cleavage site at residues 45/ 46 (figure  21d ; GenBank: KT601734). The N-terminal region of the protein (residues 22 -44) contains six acidic residues (D or E), which indicates that this part of the protein may be an acidic spacer peptide. We propose that it is the 57-residue polypeptide formed by residues 47 -103 that may be a secreted bioactive neuropeptide. It is noteworthy that the 57-residue polypeptide includes six cysteine residues, which may form up to three intramolecular disulfide bridges.
Arnp15a and Arnp15b Arnp15a and Arnp15b were identified and named on account of their similarity to Spnp15, a putative neuropeptide precursor in the sea urchin S. purpuratus  [9]. Arnp15a is a 111-residue protein comprising a predicted 19-residue N-terminal signal peptide followed by a 92-residue polypeptide sequence (residues 20-111) that contains a dibasic cleavage site at residues 54/55 (figure  21e ; GenBank: KT601735). The N-terminal region of the protein (residues 20-53) contains eight acidic residues (D or E), indicating that this part of the protein is an acidic spacer peptide. We propose that it is the 53-residue polypeptide formed by residues 56-108 that may be a secreted bioactive neuropeptide. The presence of six cysteine residues in the 53-residue polypeptide suggests that there may be up to three intramolecular disulfide bridges.
Alternatively, a homodimeric protein could be formed by up to six intermolecular disulfide bridges. Arnp15b is a 111-residue protein comprising a predicted 25-residue N-terminal signal peptide followed by an 86-residue polypeptide sequence (residues 26 -111) that contains a dibasic cleavage site at residues 63/64 (figure  21f ; GenBank: KT601736). The N-terminal region of the protein (residues 26-62) contains six acidic residues (D or E), indicating that this part of the protein may be an acidic spacer peptide. We propose that it is the 47-residue polypeptide formed by residues 65-111 that may be a secreted bioactive neuropeptide. The presence of six cysteine residues in the 47-residue polypeptide suggests that there may be up to three intramolecular disulfide bridges. Alternatively, a homodimeric protein could be formed by up to six intermolecular disulfide bridges.
Arnp18 Arnp18 was identified and named on account of its similarity to Spnp18, a putative neuropeptide precursor in the sea urchin S. purpuratus  [9]. Arnp18 is a 113-residue protein comprising a predicted 27-residue N-terminal signal peptide followed by an 86-residue polypeptide sequence (residues 28-113) that contains a putative dibasic cleavage site at residues 36/37 (figure  21g ; GenBank: KT601737). We propose that it is the 76-residue polypeptide formed by residues 38 -113 that may be a secreted bioactive neuropeptide (Arn18). It is noteworthy that Arn18 contains nine cysteine residues, which may form up to four intramolecular disulfide bridges. Alternatively, a homodimeric protein could be formed by up to nine intermolecular disulfide bridges. Arn18 and Spn18 do not share any apparent sequence similarity with rsob.
Arnp21 Arnp21 is a 102-residue protein comprising a predicted 22-residue N-terminal signal peptide followed by an 80-residue polypeptide sequence (residues 23-102) that contains putative dibasic cleavage sites at residues 45/46 and 67/68 (figure  21h ; GenBank: KT601738). We propose that it is the 22-residue peptide formed by residues 23 -44 (Arn21a) and the 20-residue peptide formed by residues 47-66 (Arn21b) that may be secreted bioactive neuropeptides. The presence of C-terminal glycine residues on both of these peptides is indicative of post-translational modifications giving rise to a C-terminal amide group on the mature peptides.
Arnp22 Arnp22 is a 157-residue protein comprising a predicted 24residue N-terminal signal peptide followed by a 133-residue polypeptide sequence (residues 25 -157) that contains putative dibasic cleavage sites at residues 86/87, 112/113, 126/ 127, 136/137 and 151/152 (figure  21i ; GenBank: KT601739). We propose that it is the 24-residue polypeptide formed by residues 88-111 (Arn22a) and the 23-residue polypeptide formed between residues 128 -150 (Arn22b) that may form secreted bioactive neuropeptides. It is noteworthy that both Arn22a and Arn22b contain two cysteine residues that are separated by four amino acid residues and that may form intramolecular disulfide bridges. Alternatively, heterodimeric polypeptides could be formed by up to two intermolecular disulfide bridges. It is also noteworthy that both Arn22a and Arn22b have the same C-terminal pentapeptide sequence-NQRGW.
Arnp23 Arnp23 is a 118-residue protein comprising a predicted 24-residue N-terminal signal peptide followed by a 94-residue polypeptide sequence (residues 25-118) that contains putative dibasic cleavage sites at residues 51/52, 75/76 and 111/112 (figure  21j ; GenBank: KT601740). We propose that it is the 22-residue polypeptide formed by residues 53-74 (Arn23a) and the 34-residue polypeptide formed by residues 77-110 (Arn23b) that may form secreted bioactive neuropeptides. It is noteworthy that both Arn23a and Arn23b contain two cysteine residues that are separated by four amino acid residues and that may form intramolecular disulfide bridges. Alternatively, a heterodimeric protein could be formed by up to two intermolecular disulfide bridges. Interestingly, both Arn23a and Arn23b have the same C-terminal tripeptide sequence (RGW), which, as highlighted above, is a feature of Arn22a and Arn22b.
Arnp24 Arnp24 is an 83-residue protein comprising a predicted 16-residue N-terminal signal peptide followed by a 67-residue polypeptide sequence (residues 17-83) that contains putative dibasic cleavage sites at residues 60/61 and 76/77 (figure  21k ; GenBank: KT601741). We propose that it is the 14-residue peptide formed by residues 62 -75 that may form a secreted bioactive neuropeptide. The presence of a C-terminal glycine residue on the peptide is indicative of post-translational modification giving rise to a C-terminal amide group on the mature peptide. The putative neuropeptide (Arn24) contains two cysteine residues, which may form an intramolecular disulfide bridge. Alternatively, a homodimeric protein could be formed by up to two intermolecular disulfide bridges. Finally, it is noteworthy that the position of Arn24 in the C-terminal region of the precursor and the presence of two cysteine residues is reminiscent of SS/MCH-type neuropeptides (see above), which may provide clues towards functional characterization of Arn24 as a putative neuropeptide.
Arnp25 Arnp25 is a 97-residue protein comprising a predicted 31residue N-terminal signal peptide followed by a 66-residue polypeptide sequence (residues 32 -97) that contains a putative dibasic cleavage site at residues 46/47 (figure  21l ; GenBank: KT601742). We propose that it is the 14-residue peptide formed by residues 32 -45 that may form a secreted bioactive neuropeptide. The presence of a C-terminal glycine residue on the peptide is indicative of post-translational modification giving rise to a C-terminal amide group on the mature peptide. It is also noteworthy that the putative neuropeptide (Arn25) contains two cysteine residues, which may form an intramolecular disulfide bridge. Alternatively, a homodimeric protein could be formed by up to two intermolecular disulfide bridges. It should also be noted that the two arginine residues preceding the first cysteine residue represent a potential dibasic cleavage site.