Characterization of the prohormone complement in cattle using genomic libraries and cleavage prediction approaches

Southey, Bruce R.; Rodriguez-Zas, Sandra L.; Sweedler, Jonathan V.

doi:10.1186/1471-2164-10-228

Cited by 23 publications

(28 citation statements)

References 45 publications

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“…[19,50]. The initial list of candidate prohormone genes was derived from known mammalian genes supplemented by known or homologous avian genes identified by Delfino et al .…”

Section: Methodsmentioning

confidence: 99%

The zebra finch neuropeptidome: prediction, detection and expression

et al. 2010

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BackgroundAmong songbirds, the zebra finch (Taeniopygia guttata) is an excellent model system for investigating the neural mechanisms underlying complex behaviours such as vocal communication, learning and social interactions. Neuropeptides and peptide hormones are cell-to-cell signalling molecules known to mediate similar behaviours in other animals. However, in the zebra finch, this information is limited. With the newly-released zebra finch genome as a foundation, we combined bioinformatics, mass-spectrometry (MS)-enabled peptidomics and molecular techniques to identify the complete suite of neuropeptide prohormones and final peptide products and their distributions.ResultsComplementary bioinformatic resources were integrated to survey the zebra finch genome, identifying 70 putative prohormones. Ninety peptides derived from 24 predicted prohormones were characterized using several MS platforms; tandem MS confirmed a majority of the sequences. Most of the peptides described here were not known in the zebra finch or other avian species, although homologous prohormones exist in the chicken genome. Among the zebra finch peptides discovered were several unique vasoactive intestinal and adenylate cyclase activating polypeptide 1 peptides created by cleavage at sites previously unreported in mammalian prohormones. MS-based profiling of brain areas required for singing detected 13 peptides within one brain nucleus, HVC; in situ hybridization detected 13 of the 15 prohormone genes examined within at least one major song control nucleus. Expression mapping also identified prohormone messenger RNAs in areas associated with spatial learning and social behaviours. Based on the whole-genome analysis, 40 prohormone probes were found on a commonly used zebra finch brain microarray. Analysis of these newly annotated transcripts revealed that six prohormone probes showed altered expression after birds heard song playbacks in a paradigm of song recognition learning; we partially verify this result experimentally.ConclusionsThe zebra finch peptidome and prohormone complement is now characterized. Based on previous microarray results on zebra finch vocal learning and synaptic plasticity, a number of these prohormones show significant changes during learning. Interestingly, most mammalian prohormones have counterparts in the zebra finch, demonstrating that this songbird uses similar biochemical pathways for neurotransmission and hormonal regulation. These findings enhance investigation into neuropeptide-mediated mechanisms of brain function, learning and behaviour in this model.

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“…[19,50]. The initial list of candidate prohormone genes was derived from known mammalian genes supplemented by known or homologous avian genes identified by Delfino et al .…”

Section: Methodsmentioning

confidence: 99%

The zebra finch neuropeptidome: prediction, detection and expression

et al. 2010

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“…A master list of candidate genes was generated based on known human and chicken prohormone gene sequences available in public databases and a literature review (Amare et al, 2006; Southey et al, 2008; Southey et al, 2009). The human sequences offer a good representation of the mammalian genes (Tegge et al, 2008) and were complemented with already known chicken sequences not detected in mammalian species.…”

Section: Methodsmentioning

confidence: 99%

“…Several models have been proposed to predict the cleavage of prohormone proteins coded by neuropeptide genes (Hummon et al, 2005; Southey et al, 2006b; Tegge et al, 2008; Southey et al 2008; Southey et al 2009). However, no cleavage model has been trained on avian species.…”

Section: Methodsmentioning

confidence: 99%

Genome-wide census and expression profiling of chicken neuropeptide and prohormone convertase genes

et al. 2010

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Neuropeptides regulate cell-cell signaling and influence many biological processes in vertebrates, including development, growth, and reproduction. The complex processing of neuropeptides from prohormone proteins by prohormone convertases, combined with the evolutionary distance between the chicken and mammalian species that have experienced extensive neuropeptide research, has led to the empirical confirmation of only 18 chicken prohormone proteins. To expand our knowledge of the neuropeptide and prohormone convertase gene complement, we performed an exhaustive survey of the chicken genomic, EST, and proteomic databases using a list of 95 neuropeptide and 7 prohormone convertase genes known in other species. Analysis of the EST resources and 22 microarray studies offered a comprehensive portrait of gene expression across multiple conditions. Five neuropeptide genes (apelin, cocaine-and amphetamine-regulated transcript protein, insulin-like 5, neuropeptide S, and neuropeptide B) previously unknown in chicken were identified and 62 genes were confirmed. Although most neuropeptide gene families known in human are present in chicken, there are several gene not present in the chicken. Conversely, several chicken neuropeptide genes are absent from mammalian species, including C-RF amide, c-type natriuretic peptide 1 precursor, and renal natriuretic peptide. The prohormone convertases, with one exception, were found in the chicken genome. Bioinformatic models used to predict prohormone cleavages confirm that the processing of prohormone proteins into neuropeptides is similar between species. Neuropeptide genes are most frequently expressed in the brain and head, followed by the ovary and small intestine. Microarray analyses revealed that the expression of adrenomedullin, chromogranin-A, augurin, neuromedin-U, platelet-derived growth factor A and D, proenkephalin, relaxin-3, prepronociceptin, and insulin-like growth factor I was most susceptible (P-value < 0.001) to changes in developmental stage, gender, and genetic line among other conditions studied. Our complete survey and characterization facilitates understanding of neuropeptides genes in the chicken, an animal of importance to biomedical and agricultural research.

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“…Unlike prototypic tumor suppressor genes (Lee and Muller, 2010; Rothenberg and Settleman, 2010), however, bioinformatic algorithms predict that Ecrg4 is not an intracellular cytoplasmic protein (Mirabeau et al, 2007; Schuster-Bockler and Bateman, 2007; Southey et al, 2009; Tegge et al, 2008). Instead, Ecrg4 resembles a ligand encoding a neuropeptide-like precursor characteristic of the human secretome (Clark et al, 2003; Hathout, 2007; Mustafa et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

Cell-specific processing and release of the hormone-like precursor and candidate tumor suppressor gene product, Ecrg4

et al. 2012

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The human open reading frame C2orf40 encodes esophageal cancer related gene-4 (Ecrg4), a newly recognized neuropeptide-like precursor protein whose gene expression by cells in vitro, over-expression in mice in vivo and knock-down in zebrafish affects cell proliferation, migration and senescence, progenitor cell survival and differentiation and inflammatory function. Unlike traditionally secreted neuropeptide precursors however, we find that Ecrg4 localizes to the epithelial cell surface and remains tethered after secretion. Here, we used cell surface biotinylation to establish that 14kDa Ecrg4 localizes to the cell surface of prostate (PC3), or kidney (HEK) epithelial cells after transfection. Accordingly, this Ecrg4 is resistant to washing cells with neutral, high salt (2M NaCl), acidic (50 mM glycine, pH 2.8) or basic (100 mM Na2CO3, pH 11) buffers. Mutagenesis of Ecrg4 established that cell tethering was mediated by an NH2-terminus hydrophobic leader sequence that enabled both trafficking to the surface and tethering. Immunoblotting analyses however showed that different cells process Ecrg4 differently. Whereas PC3 cells release cell surface Ecrg4 to generate soluble Ecrg4 peptides of 6 to 14 kDa, HEK cells do neither and the 14kDa precursor resembles a sentinel attached to the cell surface. Because a phorbol ester treatment of PC3 cells stimulated Ecrg4 release from, and processing at, the cell surface, these data are consistent with a multifunctional role for Ecrg4 that is dependent on its cell of origin and the molecular form produced.

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Characterization of the prohormone complement in cattle using genomic libraries and cleavage prediction approaches

Cited by 23 publications

References 45 publications

The zebra finch neuropeptidome: prediction, detection and expression

The zebra finch neuropeptidome: prediction, detection and expression

Genome-wide census and expression profiling of chicken neuropeptide and prohormone convertase genes

Cell-specific processing and release of the hormone-like precursor and candidate tumor suppressor gene product, Ecrg4

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