Biological implications of SNPs in signal peptide domains of human proteins

Abstract

Proteins destined for secretion or membrane compartments possess signal peptides for insertion into the membrane. The signal peptide is therefore critical for localization and function of cell surface receptors and ligands that mediate cell-cell communication. About 4% of all human proteins listed in UniProt database have signal peptide domains in their N terminals. A comprehensive literature survey was performed to retrieve functional and disease associated genetic variants in the signal peptide domains of human proteins. In 21 human proteins we have identified 26 disease associated mutations within their signal peptide domains, 14 mutations of which have been experimentally shown to impair the signal peptide function and thus influence protein transportation. We took advantage of SignalP 3.0 predictions to characterize the signal peptide prediction score differences between the mutant and the wild-type alleles of each mutation, as well as 189 previously uncharacterized single nucleotide polymorphisms (SNPs) found to be located in the signal peptide domains of 165 human proteins. Comparisons of signal peptide prediction outcomes of mutations and SNPs, have implicated SNPs potentially impacting the signal peptide function, and thus the cellular localization of the human proteins. The majority of the top candidate proteins represented membrane and secreted proteins that are associated with molecular transport, cell signaling and cell to cell interaction processes of the cell. This is the first study that systematically characterizes genetic variation occurring in the signal peptides of all human proteins. This study represents a useful strategy for prioritization of SNPs occurring within the signal peptide domains of human proteins. Functional evaluation of candidates identified herein may reveal effects on major cellular processes including immune cell function, cell recognition and adhesion, and signal transduction.

Creation of Apolipoprotein C-II (ApoC-II) Mutant Mice and Correction of Their Hypertriglyceridemia with an ApoC-II Mimetic Peptide

“…1). Mutations leading to the retention of signal peptides often interfere with protein secretion, because the hydrophobic signal peptide binds to lipids in endoplasmic reticulum membranes (Jarjanazi et al, 2008). In the case of ApoC-II, perhaps because it associates with lipoproteins, the retained signal peptide could instead bind to lipids on the lipoprotein particle and thereby be secreted normally.…”

Tissue expression and predicted protein structures of the bovine ANGPTL3 and association of novel SNPs with growth and meat quality traits

“…Signal peptide is critical for localization and function of cell surface receptors and ligands that mediate cell-cell communication (Jarjanazi et al, 2008).…”

Significant association between SCGB1D4 gene polymorphisms and susceptibility to adenoid hypertrophy in a pediatric population*

“…org/uniprot/Q6XE38#section_seq). The minor allele of this synonymous SNP (sSNP), which does not change the amino acid sequence, might lead to the vitiated signal activity of the protein through influencing gene expression biology and posttranscriptional regulation mechanisms involving conformation and stability of pre-mRNA, translation initiation, and stability and folding of protein (30,31). Therefore, the gene may be a modifying factor for AH.…”