A combined strategy of neuropeptide prediction and tandem mass spectrometry identifies evolutionarily conserved ancient neuropeptides in the sea anemone Nematostella vectensis

Autoři: Eisuke Hayakawa aff001;  Hiroshi Watanabe aff002;  Gerben Menschaert aff004;  Thomas W. Holstein aff003;  Geert Baggerman aff005;  Liliane Schoofs aff001
Působiště autorů: Research Group of Functional Genomics and Proteomics, KU Leuven, Leuven, Belgium aff001;  Evolutionary Neurobiology Unit, Okinawa Institute of Science & Technology, Okinawa, Japan aff002;  Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany aff003;  Faculty of Bioscience Engineering, Laboratory for Bioinformatics and Computational Genomics, Ghent University, Ghent, Belgium aff004;  CFP/Ceproma, University Antwerpen, Antwerpen, Belgium aff005;  VITO, Applied Bio & molecular Systems (ABS), Mol, Belgium aff006
Vyšlo v časopise: PLoS ONE 14(9)
Kategorie: Research Article
doi: 10.1371/journal.pone.0215185


Neuropeptides are a class of bioactive peptides shown to be involved in various physiological processes, including metabolism, development, and reproduction. Although neuropeptide candidates have been predicted from genomic and transcriptomic data, comprehensive characterization of neuropeptide repertoires remains a challenge owing to their small size and variable sequences. De novo prediction of neuropeptides from genome or transcriptome data is difficult and usually only efficient for those peptides that have identified orthologs in other animal species. Recent peptidomics technology has enabled systematic structural identification of neuropeptides by using the combination of liquid chromatography and tandem mass spectrometry. However, reliable identification of naturally occurring peptides using a conventional tandem mass spectrometry approach, scanning spectra against a protein database, remains difficult because a large search space must be scanned due to the absence of a cleavage enzyme specification. We developed a pipeline consisting of in silico prediction of candidate neuropeptides followed by peptide-spectrum matching. This approach enables highly sensitive and reliable neuropeptide identification, as the search space for peptide-spectrum matching is highly reduced. Nematostella vectensis is a basal eumetazoan with one of the most ancient nervous systems. We scanned the Nematostella protein database for sequences displaying structural hallmarks typical of eumetazoan neuropeptide precursors, including amino- and carboxyterminal motifs and associated modifications. Peptide-spectrum matching was performed against a dataset of peptides that are cleaved in silico from these putative peptide precursors. The dozens of newly identified neuropeptides display structural similarities to bilaterian neuropeptides including tachykinin, myoinhibitory peptide, and neuromedin-U/pyrokinin, suggesting these neuropeptides occurred in the eumetazoan ancestor of all animal species.

Klíčová slova:

Database searching – Protein extraction – Sequence databases – Sequence motif analysis – Sequence similarity searching – Signal peptides – Animal evolution – Amidation


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