Analysis of mouse brain peptides using mass spectrometry-based peptidomics: implications for novel functions ranging from non-classical neuropeptides to microproteins

Abstract

Peptides are known to play many important physiological roles in signaling. A large number of peptides have been detected in mouse brain extracts using mass spectrometry-based peptidomics studies, and 850 peptides have been identified. Half of these peptides are derived from secretory pathway proteins and many are known bioactive neuropeptides which activate G protein-coupled receptors; these are termed "classical neuropeptides." In addition, 427 peptides were identified that are derived from non-secretory pathway proteins; the majority are cystosolic, and the remainder are mitochondrial, nuclear, lysosomal, or membrane proteins. Many of these peptides represent the Nor C-terminus of the protein, rather than internal fragments, raising the possibility that they are formed by selective processing rather than protein degradation. In addition to consideration of the cleavage site required to generate the intracellular peptides, their potential functions are discussed. Several of the cytosolic peptides were previously found to interact with receptors and/or otherwise influence cellular activity; examples include hemophins, hemopressins, diazepam binding inhibitor, and hippocampal cholinergic neurostimulating peptide. The possibility that these peptides are secreted from cells and function in cell-cell signaling is discussed. If these intracellular peptides can be shown to be secreted in levels sufficient to produce a biological effect, they would appropriately be called "non-classical neuropeptides" by analogy with non-classical neurotransmitters such as nitric oxide and anandamide. It is also possible that intracellular peptides function as "microproteins" and modulate protein-protein interactions; evidence for this function is discussed, along with future directions that are needed to establish this and other possible functions for peptides.

High Identification Rates of Endogenous Neuropeptides from Mouse Brain

“…2,9,38−40 The formation of peptide fragments may come from in vivo peptide/protein processing, which are performed by intracellular proteolysis or by extracellular peptide decay after their release from neurons. 41 These processes are not fully understood yet. However, a line of evidence showed that many peptide fragments have distinct physiological functions, for example, activating particular receptors or inhibiting enzymes.…”

“…However, a line of evidence showed that many peptide fragments have distinct physiological functions, for example, activating particular receptors or inhibiting enzymes. 41,42 The identification of novel peptides therefore provided possible candidates for bioactive neuropeptides.…”

Neuropeptide alterations in the tree shrew hypothalamus during volatile anesthesia

“…1A), based on the list of reported neuropeptides, precursors and additional candidate [17,18] (see Supplementary Table 1). Current studies showed that neuropeptides are produced from their precursors by different neuropeptide-processing enzymes in different pathways.…”

“…The database was constructed by first downloading a list of 2405 protein precursors [17,18] from the Uniprot database (http:// www.uniprot.org/, 7 July 2010) restricted to Euarchontoglires species. All these sequences were then submitted to an in silico peptide cleavage using custom made software written in Perl, according to the following template:…”

O-Glycosylation of a Secretory Granule Membrane Enzyme Is Essential for Its Endocytic Trafficking

“…Although N-glycosylation occurs at predictable sites (-Asn-Xaa-Ser/Thr-, where Xaa is not Pro) and must be initiated in the endoplasmic reticulum, O-glycosylation sites cannot be predicted based on primary sequence (14,15). Based on earlier studies using [ 3 H]galactose, [ 35 SO 4 2Ϫ Met], and [ 35 S]Met, sulfated galactose-containing O-linked sugars are found on at least two Ser/Thr residues in the exon 16 region of PAM-1 (3,15). A prohormone convertase 1-mediated cleavage at the Lys-Lys site in exon 16 separates soluble PHM from membrane PAL, and at least one O-glycosylation site is found in each product.…”