Hayakawa, E. | bioRxiv Science

bioRxiv2024

A transphyletic study of metazoan β-catenin protein complexes

{beta}-catenin is essential for various biological processes, such as body axis determination and cell differentiation, during embryonic development in metazoans. {beta}-catenin functions are thought to be exerted through complexes formed with various types of proteins. Although {beta}-catenin complex proteins have been identified in several bilaterians, little is known about the structural and functional properties of {beta}-catenin complexes in early metazoan evolution. In this study, we performed a comparative analysis of {beta}-catenin sequences in nonbilaterian lineages that diverged early in metazoan evolution. We also carried out transphyletic function experiments with {beta}-catenin from nonbilaterian metazoans using developing Xenopus embryos, which included secondary axis induction in embryos and proteomic analysis of {beta}-catenin protein complexes. Comparative functional analysis of nonbilaterian {beta}-catenins demonstrated sequence characteristics important for {beta}-catenin functions, and the deep origin and evolutionary conservation of the cadherin-catenin complex. Proteins co-immunoprecipitated with {beta}-catenin included several proteins conserved among metazoans. These data provide new insights into the conserved repertoire of {beta}-catenin complexes.

evolutionary biology↗

bioRxiv2019

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

Neuropeptides are a class of bioactive peptides and are responsible for various physiological processes including metabolism, development and reproduction. Although accumulated genome and transcriptome data have reported a number of neuropeptide candidates, it still remains difficult to obtain a comprehensive view of neuropeptide repertoires due to their small and variable nature. Neuropeptide prediction tools usually work only for those peptides for which sequentially related homologs have previously been identified. Recent peptidomics technology has enabled systematic structural identification of neuropeptides by using the combination of liquid chromatography and tandem mass spectrometry. However, obtaining reliable identifications of endogenous peptides is still difficult using a conventional tandem mass spectrometry-based peptide identification approach using protein database because a large search space has to be scanned due to the absence of a cleavage enzyme specification. We developed a pipeline consisting of the prediction of in silico cleaved endogenous neuropeptides followed by peptide-spectrum matching enabling highly sensitive and reliable neuropeptide identification. This approach effectively reduces the search space of peptide-spectrum matching, and thus increases search sensitivity. To identify neuropeptides in Nematostella vectensis, a basal eumetazoan having one of the most primitive nervous systems, we scanned the Nematostella protein database for sequences displaying structural hallmarks of metazoan neuropeptides, including C/N-terminal structures and modifications. Peptide-spectrum matching was performed against the in silico cleaved peptides and successfully identified dozens of neuropeptides at high confidence. The identification of Nematostella neuropeptides structurally related the tachykinin, GnRH/AKH, neuromedin-U/pyrokinin peptide families indicate that these peptides already originated in the eumetazoan ancestor of all animal species, most likely concomitantly with the development of a nervous system.

biochemistry↗