Evolutionary Sequence Modeling for Discovery of Peptide Hormones

Abstract

There are currently a large number of “orphan” G-protein-coupled receptors (GPCRs) whose endogenous ligands (peptide hormones) are unknown. Identification of these peptide hormones is a difficult and important problem. We describe a computational framework that models spatial structure along the genomic sequence simultaneously with the temporal evolutionary path structure across species and show how such models can be used to discover new functional molecules, in particular peptide hormones, via cross-genomic sequence comparisons. The computational framework incorporates a priori high-level knowledge of structural and evolutionary constraints into a hierarchical grammar of evolutionary probabilistic models. This computational method was used for identifying novel prohormones and the processed peptide sites by producing sequence alignments across many species at the functional-element level. Experimental results with an initial implementation of the algorithm were used to identify potential prohormones by comparing the human and non-human proteins in the Swiss-Prot database of known annotated proteins. In this proof of concept, we identified 45 out of 54 prohormones with only 44 false positives. The comparison of known and hypothetical human and mouse proteins resulted in the identification of a novel putative prohormone with at least four potential neuropeptides. Finally, in order to validate the computational methodology, we present the basic molecular biological characterization of the novel putative peptide hormone, including its identification and regional localization in the brain. This species comparison, HMM-based computational approach succeeded in identifying a previously undiscovered neuropeptide from whole genome protein sequences. This novel putative peptide hormone is found in discreet brain regions as well as other organs. The success of this approach will have a great impact on our understanding of GPCRs and associated pathways and help to identify new targets for drug development.

Decreased Spexin Levels in Patients with Type 1 and Type 2 Diabetes

“…The administration of ACTH was reported to decrease adrenal levels of spexin mRNA in vivo, while the administration of dexamethasone increased the levels of spexin mRNA [11]. Spexin was found to have a direct involvement in the regulation of adrenocortical cell proliferation.…”

Goldfish spexin: solution structure and novel function as a satiety factor in feeding control

“…In humans, SPX appears to be widely expressed, as its sequence was identified in expressed sequence tag databases for cancer cells from a wide range of tissues. By Northern blot and RT-PCR, SPX gene expression was confirmed in human and mouse, especially in the kidney, pancreas, brain, and placenta (19,34). The most extensive study on tissue expression profiling of SPX has been published recently in the rat using immunohistochemical staining (25).…”

“…The gene encoding SPX was independently reported by another group using a different approach by evolutionary probabilistic models based on the genome data reported for different vertebrates (35). The discovery of SPX is a recent example of obtaining the protein structure of novel peptides using bioinformatics prior to its purification/showing of its biological actions.…”

“…The discovery of SPX is a recent example of obtaining the protein structure of novel peptides using bioinformatics prior to its purification/showing of its biological actions. In human, SPX is encoded by the C12orf39 gene in chromosome 12 (48), and its prepropeptide is composed of a hydrophobic signal peptide, followed by the 14-amino acid (AA) SPX mature peptide flanked by two dibasic protein cleavage sites (RR and GRR) (34). Since GRR is the target site for protein processing by peptidylglycine ␣-amidating monooxygenase and the motif is highly conserved in SPX sequences found in different species, the mature peptide of SPX is believed to have ␣-amidation at its COOH terminus.…”

“…The modification would probably enhance the peptide stability and/or increase its binding affinity for its cognate receptor (17). Among the representative species used in the initial studies, SPX mature peptide was found be identical in mammals and birds (19,34). In general, the 14-AA peptide NMTPQAMLYLKGAQ is commonly accepted to be the SPX mature peptide in tetrapods.…”