First survey and functional annotation of prohormone and convertase genes in the pig

Abstract

BackgroundThe pig is a biomedical model to study human and livestock traits. Many of these traits are controlled by neuropeptides that result from the cleavage of prohormones by prohormone convertases. Only 45 prohormones have been confirmed in the pig. Sequence homology can be ineffective to annotate prohormone genes in sequenced species like the pig due to the multifactorial nature of the prohormone processing. The goal of this study is to undertake the first complete survey of prohormone and prohormone convertases genes in the pig genome. These genes were functionally annotated based on 35 gene expression microarray experiments. The cleavage sites of prohormone sequences into potentially active neuropeptides were predicted.ResultsWe identified 95 unique prohormone genes, 2 alternative calcitonin-related sequences, 8 prohormone convertases and 1 cleavage facilitator in the pig genome 10.2 assembly and trace archives. Of these, 11 pig prohormone genes have not been reported in the UniProt, UniGene or Gene databases. These genes are intermedin, cortistatin, insulin-like 5, orexigenic neuropeptide QRFP, prokineticin 2, prolactin-releasing peptide, parathyroid hormone 2, urocortin, urocortin 2, urocortin 3, and urotensin 2-related peptide. In addition, a novel neuropeptide S was identified in the pig genome correcting the previously reported pig sequence that is identical to the rabbit sequence. Most differentially expressed prohormone genes were under-expressed in pigs experiencing immune challenge relative to the un-challenged controls, in non-pregnant relative to pregnant sows, in old relative to young embryos, and in non-neural relative to neural tissues. The cleavage prediction based on human sequences had the best performance with a correct classification rate of cleaved and non-cleaved sites of 92% suggesting that the processing of prohormones in pigs is similar to humans. The cleavage prediction models did not find conclusive evidence supporting the production of the bioactive neuropeptides urocortin 2, urocortin 3, torsin family 2 member A, tachykinin 4, islet amyloid polypeptide, and calcitonin receptor-stimulating peptide 2 in the pig.ConclusionsThe present genomic and functional characterization supports the use of the pig as an effective animal model to gain a deeper understanding of prohormones, prohormone convertases and neuropeptides in biomedical and agricultural research.

Transcriptomic analysis of Rongchang pig brains and livers

“…Our data showed the detection of most neuropeptide gene transcripts based on the reported information of approximately 100 genes identified in humans, rats, mice, pigs, cows and rhesus monkeys (Porter et al, 2012;Tegge et al, 2008). These derived expression profiles may guide future physiological studies focused on signal transduction and functions of these molecules in these two important tissues.…”

“…Bioinformatic analysis (Porter et al, 2012) indicated a lack of a complete pig genome sequence for UCN1, UCN2 and UCN3 and was not supported by transcript evidence from UniGene, Gene, and UniProt. In our study, the expression of UCN1 and UCN2 was not observed, but UCN3 was expressed in Rongchang pig liver samples (Fig.…”

“…In addition, based on bioinformatic analysis (Porter et al, 2012), neuropeptide genes not expressed in brain or liver samples were identified to include: atrial natriuretic factor (ANF), neuropeptide S (NPS), endothelin 2 (EDN2), gastric inhibitory polypeptide (GIP), gastrin-releasing peptide (GRP), insulin-like 5 (INSL5), neuropeptide B (NPB), neuropeptide FF (NPFF), neuropeptide S (NPS), neuropeptide W (NPW), prokineticin2 (PROK2), prothyroliberin (TRH), urocortin 1 (UCN1), urocortin 2 (UCN2), and neurosecretory protein VGF (VGF) genes.…”

Effects of maternal immune activation in porcine transcript isoforms of neuropeptide and receptor genes

“…Our systematic study of over 200 transcript isoforms produced by genes in the neuropeptide system enabled us to expose various MIA effects within gene and across brain regions that are subsequently exemplified. Transcript isoforms were identified in the hippocampus and hypothalamus for most neuropeptide and receptor genes known in mammals [16,17,38,39]. Transcript isoforms from neuropeptide Y receptor Y6 (NPY6R), insulin (INS) and urocortin 2 (UCN2) were identified in fewer than 5% of the pigs in both regions.…”

Characterization of the prohormone complement in Amphiprion and related fish species integrating genome and transcriptome assemblies

“…Neuropeptides are formed by enzymatic cleavage and chemical post-translational modifications of larger, inactive precursor proteins referred to as prohormones. In order to characterize these neuropeptides, the prohormone complement first needs to be revealed using sequence information and a list of known prohormones [28][29][30][31][32][33][34]. Ideally, the sequence information is obtained from the genome sequencing project of the species of interest but next-generation sequencing of the transcriptome can also be used for identification [35].…”