Biology subjects

Ruperti, F.

Publications and source records attributed to Ruperti, F..

6 recordsLinked to original sources

bioRxiv2026

From promiscuity to specialization: The origin of cholinergic and monoaminergic signaling is pre-bilaterian

The emergence of chemical neurotransmission was key to the evolution of nervous systems, yet when the different transmitter systems arose remains unclear. Biogenic amines (here, acetylcholine and the monoamines) have been reported in non-bilaterian animals and even outside Metazoa, but their physiological role has only recently begun to be resolved, and phylogenetic surveys of the bilaterian machinery have restricted dedicated monoaminergic signaling to Bilateria. Combining targeted metabolomics, molecular phylogenies, structural modeling and binding-affinity prediction, single-cell expression analysis and immunochemistry, we show that cholinergic and monoaminergic signaling predate Bilateria. We detect acetylcholine, dopamine, histamine, adrenaline, tyramine, 2-phenylethylamine and tryptamine in a sponge and two cnidarians, and identify broad-specificity enzymes and transporters able to produce and load them. These genes are co-expressed in both neuronal and non-neuronal cell types, indicating that amine signaling was never confined to the nervous system. Two Hydra vulgaris muscarinic receptor orthologs retain a fully conserved orthosteric site and are predicted to bind acetylcholine as strongly as their bilaterian counterparts, and muscle-type nicotinic receptor subunits are co-expressed with Rapsyn-related genes in cnidarian muscle cells, placing cholinergic neuromuscular signaling in the cnidarian-bilaterian ancestor. Specialization came later in Bilateria, where gene duplications produced substrate-specific enzymes (ChAT, TH, TPH), dedicated vesicular transporters (VAChT, VMAT) and ligand-selective receptors. Biogenic amine signaling is thus not a bilaterian innovation but an ancient mode of cellular communication that evolved from generalist to specialist machinery.

evolutionary biology↗

bioRxiv2026

A mobile optical coherence microscope for studying aquatic organisms in- and outside the laboratory

High-resolution, three-dimensional imaging of live organisms has largely depended on laboratory-bound microscopes, limiting quantitative analysis of morphology and dynamics to species that survive transport and thrive under lab-controlled conditions. Here we present a mobile optical coherence microscopy (OCM) platform that overcomes this constraint, delivering [~]2.5 {micro}m axial resolution, label-free, volumetric imaging of live aquatic organisms in both laboratory and remote field environments. We demonstrate the platform across a broad range of aquatic organisms from the lab and field, spanning multiple phyla - including cnidarians, poriferans, annelids, arthropods and echinoderms - resolving internal anatomy, tissue boundaries and organismal morphology at micrometer scale without fixation, fluorescent labeling, or specialized sample preparation. High-speed acquisition, with up to 250 kHz A-line rate and 7.7 Hz volume rate, further enabled morphodynamic imaging of live biological processes, including cellular aggregate motility, embryonic cell division, and organ-level peristaltic dynamics in intact, living animals. To demonstrate field deployability, the platform was operated during the EMBL TREC pan-European expedition, enabling on-site, label-free imaging of marine organisms and plankton immediately upon collection. By decoupling high-resolution volumetric imaging from fixed laboratory settings, mobile OCM opens a path toward field-ready quantitative morphological and dynamic phenotyping of aquatic life.

bioengineering↗

bioRxiv2026

Interallelic cis-regulatory dominance promotes robustness and evolutionary innovation

Dominance is a central principle of genetics, yet the mechanistic basis and the evolutionary consequences of dominance arising from cis-regulatory variation remain poorly understood. We examined the evolutionary trajectories of a pleiotropic developmental enhancer in Drosophila. A genotype-phenotype map between D. melanogaster and D. simulans enhancer sequences reveals extensive epistasis, and many homozygous evolutionary paths reduce transcriptional output. In heterozygotes, however, regulatory dominance masks variants that reduce gene expression, potentially relaxing evolutionary constraints. Using allele-specific reporters and imaging, we show that this dominance arises from interallelic interactions (also known as transvection) reinforced by transcriptional hubs. Importantly, this enhancer dominance is cell-type specific, raising the possibility that it conceals deleterious effects in essential tissues while revealing novel, ectopic activity in others. Interallelic regulatory hubs may therefore expand the range of mutational paths available to diploid genomes while preserving essential transcriptional output.

evolutionary biology↗

bioRxiv2024

Proteomic analysis of the Aggregation Factor from the sponge Clathria (Microciona) prolifera suggests an ancient protein domain toolkit for allorecognition in animals

The discovery that sponges (Porifera) can fully regenerate from aggregates of dissociated cells launched them as one of the earliest experimental models for cell adhesion and allorecognition studies in animals. This process depends on an extracellular glycoprotein complex called the Aggregation Factor (AF). However, our understanding of how animal adhesion and allorecognition mechanisms first evolved is complicated by the fact that the known components of the AF are thought to be unique to sponges. We used label-free quantitative proteomics to identify additional AF components and interacting proteins in the classical model Clathria prolifera and compare them to proteins involved in cell interactions in Bilateria. Our results confirm MAFp3/p4 as the primary components of the AF, but implicate related proteins with calx-beta and wreath domains as additional components. Using AlphaFold, we unveiled close structural similarities of AF components to distant homologs in other animals, previously masked by the stark decay of sequence similarity. The wreath domain, believed to be unique to the AF, was predicted to contain a central beta-sandwich of the same organization as the vWFD domain in extracellular, gel-forming gly-coproteins in other animals. Additionally, we co-purified candidate AF-interacting proteins that share a conserved C-terminus, containing divergent Ig-like and Fn3 domains, a combination also known from IgCAMs. One of these, MAFAP1, may function to link the AF to the surface of cells. Our results highlight the existence of an ancient toolkit of conserved protein domains regulating cell-cell and cell-ECM interactions in all animals, and likely reflect a common origin of cell-adhesion and allorecognition.

biochemistry↗

bioRxiv2023

Molecular profiling of sponge deflation reveals an ancient relaxant-inflammatory response

A hallmark of animals is the coordination of whole-body movement. Neurons and muscles are central to this, yet coordinated movements also exist in sponges that lack these cell types. Sponges are sessile animals with a complex canal system for filter-feeding. They undergo whole-body movements resembling "contractions" that lead to canal closure and water expulsion. Here, we combine 3D optical coherence microscopy, pharmacology, and functional proteomics to elucidate anatomy, molecular physiology, and control of these movements. We find them driven by the relaxation of actomyosin stress fibers in epithelial canal cells, which leads to whole-body deflation via collapse of the incurrent and expansion of the excurrent system, controlled by an Akt/NO/PKG/A pathway. A concomitant increase in reactive oxygen species and secretion of proteinases and cytokines indicate an inflammation-like state reminiscent of vascular endothelial cells experiencing oscillatory shear stress. This suggests an ancient relaxant-inflammatory response of perturbed fluid-carrying systems in animals. HighlightsO_LISponge deflation is driven by tension release in actomyosin stress fibers of epithelial pinacocytes C_LIO_LIAkt kinase/Nitric oxide/Protein kinase G/A regulate actomyosin relaxation C_LIO_LIAgitation-induced deflation coincides with an inflammatory state C_LIO_LIThe sponge relaxant-inflammatory response is evolutionary related to similar responses in the vertebrate vascular system C_LI

molecular biology↗

bioRxiv2022

Cross-phyla protein annotation beyond sequence similarity through structural prediction and alignment

BackgroundAnnotating protein function is a major goal in molecular biology, yet experimentally determined knowledge is often limited to a few model organisms. In non-model species, the sequence-based prediction of gene orthology can be used to infer function, however this approach loses predictive power with longer evolutionary distances. Here we propose a pipeline for the functional annotation of proteins using structural similarity, exploiting the fact that protein structures are directly linked to function and can be more conserved than protein sequences. ResultsWe propose a pipeline of openly available tools for the functional annotation of proteins via structural similarity (MorF: MorphologFinder) and use it to annotate the complete proteome of a sponge. Sponges are highly relevant for inferring the early history of animals, yet their proteomes remain sparsely annotated. MorF accurately predicts the functions of proteins with known homology in >90% cases, and annotates an additional 50% of the proteome beyond standard sequence-based methods. Using this, we uncover new functions for sponge cell types, including extensive FGF, TGF and Ephrin signalling in sponge epithelia, and redox metabolism and control in myopeptidocytes. Notably, we also annotate genes specific to the enigmatic sponge mesocytes, proposing they function to digest cell walls. ConclusionsOur work demonstrates that structural similarity is a powerful approach that complements and extends sequence similarity searches to identify homologous proteins over long evolutionary distances. We anticipate this to be a powerful approach that boosts discovery in numerous -omics datasets, especially for non-model organisms.

evolutionary biology↗