Biology subjects

Pittis, A. A.

Publications and source records attributed to Pittis, A. A..

7 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

Pre-neuronal origins of monoamine and acetylcholine synthesis and transport

Neuronal architecture is highly modular and individual components can be found in non-neuronal cell types or even neuronless animals, suggesting some functions predate neurons. However, the evolutionary origins of neurotransmitter synthesis, transport and synaptic vesicle biogenesis outside animals remain obscure. To our knowledge, no previous work has systematically addressed the function of neuronal protein homologs outside animals. Our phylogenetic analysis indicates that orthologs of synaptic vesicle (SV) neurotransmitter transporters (SLC18) and synthesis enzymes are widespread in fungi, which, together with animals and sister taxa, form the clade Opisthokonta. Comparing them with their synaptic counterparts can shed light on the emergence of key functions at the animal-fungi split. Here, we combine extensive phylogenetic profiling and statistical analysis with the generation of functional data for these protein families in fungi. We show that monoamine synthesis, orthologous to that of neurons, is present in fungi and places its origin in the opisthokont common ancestor. We also annotate the orthologs of SLC18 transporters showing that they retain an exporter profile and reside predominantly in the endolysosomal system. Building on this observation, we couple deep-learning localization predictions and GO enrichment analysis to show that the phylogenetic context of SVs is lysosomal throughout the Opisthokonta tree, with implications for their phylogenetic origin. In addition, we monitor fungal gene expression in the presence of monoamines showing that they modulate secondary metabolism, hinting at their physiological significance in a neuronless clade. We propose that the machinery associated with neurotransmission originated before animals.

evolutionary biology↗

bioRxiv2026

KEDROS: A Comparative Genomics and High-Resolution Phylogenetic Profiling Workspace

Phylogenetic profiling infers gene function from the presence and absence of genes across genomes, but it loses resolution in eukaryotes, where many protein families contain several functionally distinct paralogs. Existing resources address parts of this problem separately: web services build trees for one family at a time, orthology databases provide precomputed orthologous groups for predefined species sets, and tree-profiling tools require users to supply their own trees and groupings. Here, we present KEDROS, a web platform that builds gene trees for any protein family across UniProt reference proteomes, splits each tree into subfamilies at inferred gene duplications, and profiles each subfamily separately. The organisms, the families and the taxonomic depth at which trees are split are all chosen by the user, so the same workflow serves any question that can be posed as a contrast between two sets of organisms: a pathogen and its host, a pest and non-target species, or lineages with and without a trait. KEDROS answers such contrasts at two levels. Across families and subfamilies, it ranks those present in one set and absent from the other, pointing to lineage-specific genes and candidate targets. Within a subfamily shared by both sets, it identifies amino acid positions that differ consistently between them and may underlie functional divergence, and displays them on AlphaFold structures. All analyses run in a web browser, with no installation or programming. Each of these steps exists in some form elsewhere, but to our knowledge no other resource runs them end to end, at the scale of whole proteomes, on organism sets defined by the user. We illustrate KEDROS with two cases. In the trypanothione reductase family of trypanosomatids, it recovers parasite-specific subfamilies and the substrate-binding substitutions that separate the parasite enzyme from human glutathione reductase. In the bacterial phylum Bacillota, it recovers the sporulation machinery from phenotype labels alone across 1,218 proteomes, and ranks an uncharacterized family among the strongest markers of the trait. KEDROS thus offers a general, code-free route from a comparative question to testable hypotheses about genes and residues. KEDROS is freely available at https://kedros.cgenomicslab.org.

bioinformatics↗

bioRxiv2026

Gene duplication shaped the origin and evolution of the vertebrate olfactory combinatorial code

Animals read their chemical environment through olfactory receptors, which form part of the class A GPCRs and are the largest gene family devoted to a single function in animals. Each odorant molecule activates a different combination of receptors, projects distinctly in the brain, and so yields a distinct odour percept. The principles of this coding are well described, and the evolution and regulation of these genes are actively researched. However, how the code was initially assembled and evolved has not been examined. Here we combine phylogenetics, receptor-ligand interactions predicted by paired protein and chemical language models, ancestral sequence reconstruction, and chemical-space analysis. Predicted activation profiles group odorants into six clusters -each enriched for its own set of odour descriptors- so that molecules read by similar receptor combinations tend to smell alike. Reconstructed ancestors place the origin of the code at the first duplication of the family, in the gnathostome ancestor, at the class I/class II split. The first duplicates then diverged asymmetrically into distinct chemical subspaces. One kept a third of the ancestral ligands; the other re-tuned almost completely and took up carboxylic acids -the polar chemistry long associated with class I. Aromatics were retained and enriched on the class II side. Combinatorial coding was not really invented: it arose once, at the first duplication, and was never lost.

evolutionary biology↗

bioRxiv2025

Expansion, functional diversification and gene fusion events in the Ato protein family

Candida albicans, a commensal opportunistic pathogen, exhibits remarkable metabolic flexibility and adaptability to environmental changes. In glucose-limited niches, it utilizes alternative carbon sources such as carboxylic acids, which may influence its pathogenicity. In Saccharomyces cerevisiae, the uptake of monocarboxylates occurs through regulated plasma membrane (PM) transport proteins, such as Ato1 (Ady2), which belongs to the Acetate Uptake Transporter (AceTr) family. In C. albicans, these proteins are notably expanded, consisting of ten Ato-like proteins (ATO1-ATO10), whose functions remain unknown. Here, we investigated the role of Ato proteins in carboxylic acid utilization by C. albicans using in-silico and functional analysis. Our data revealed that several C. albicans Atos retain conserved AceTr motifs but possess distinct structural features, including differences in pore radius and binding sites for acetate and lactate. Expression analysis revealed that Ato1, Ato2, Ato3, and Ato6 exhibit distinct cellular localization and expression levels on the plasma membrane, depending on the presence or absence of monocarboxylates. Remarkably, deletion of ATO1 impaired Ato2 and Ato3 expression and caused ER retention of a distinct form of Ato2, suggesting a central regulatory role for Ato1 in the Ato transport system. Finally, we identified a novel Ato-related protein family in vertebrates. This family has three consecutive 6-helix transport domains and a unique C-terminal fusion with Sua5/YciO/YrdC, an enzyme involved in tRNA modification. Overall, our data suggests that the Ato protein family might play a critical role in the utilization of acetic or lactic acids in C. albicans. It also proposes potential functional redundancy among its members, which may contribute to rapid environmental adaptation and pathogenicity.

microbiology↗

bioRxiv2020

Discovery of EMRE in fungi resolves the true evolutionary history of the mitochondrial calciumuniporter

Mitochondrial calcium (mt-Ca2+) uptake is central for the regulation of numerous cellular processes in eukaryotes1. This occurs through a highly selective Ca2+ uniporter located at the inner mitochondrial membrane and driven by the membrane potential2-4. While the physiological role of the uniporter was extensively studied for decades, its genetic identity was only recently determined, with MCU5,6, MICU17 and EMRE8 constituting pore-forming and regulatory subunits. Preliminary evolutionary analyses suggested an ancient eukaryotic origin of mt-Ca2+ uptake, but also pinpointed inconsistent phylogenetic distributions of MCU, MICU1, and EMRE within fungi, where homologs of MCU were present in the absence of the supposedly essential regulators, MICU1 and EMRE9,10. Here, we perform the most comprehensive phylogenomic analysis of the mt-Ca2+ uptake system and trace its evolution across 1,156 fully-sequenced eukaryotes. In contrast to earlier assumptions9-11 we find compelling evidence that previously identified animal and fungal MCUs, the targets of several structural and functional efforts11-16, represent two distinct paralogous subfamilies originating from an ancestral duplication. We further uncover a complete "animal-like" uniporter complex within chytrid fungi, including bona-fide orthologs of MCU, MICU1, and EMRE. This first identification of EMRE outside Holozoa (animals and their unicellular relatives) and its strong coevolution with "animal-like" MICU1 and MCU indicates that these three components formed the core of the ancestral opisthokont uniporter. We confirm this finding experimentally, by showing that chytrid EMRE orthologs in combination with either human or "animal-like" MCUs, but not with "fungal-specific" MCUs, can reconstitute mt-Ca2+ uptake in vivo in the yeast Saccharomyces cerevisiae. Hence, we here solve a purported evolutionary paradox: the presence of MCU homologs in fungal species devoid of other uniporter components and with no detectable mt-Ca2+ uptake. Altogether, our study clarifies the evolution of the mt-Ca2+ uniporter and identifies new important targets for comparative structural and functional studies.

evolutionary biology↗

bioRxiv2018

MICU1 modulates MCU ion selectivity and tolerance to manganese stress

The mitochondrial calcium uniporter is a highly selective ion channel composed of species-and tissue-specific structural and regulatory subunits. However, the contribution of each component to uniporter-mediated activity still remains unclear. Here, we employ an evolutionary and synthetic biology approach to investigate the functional inter-dependence between the pore-forming subunit MCU and the EF-hand protein MICU1. Using phylogenetic profiling and genetic complementation analyses, we show that MCU and MICU1 constitute the minimal eukaryotic unit of the uniporter, pointing towards a strong selective pressure behind their co-occurrence. Heterologous reconstitution of MCU-mediated and MICU1-gated mitochondrial calcium entry in vivo in yeast cells demonstrates that MICU1 per se is essential to protect yeast from MCU-dependent manganese cytotoxicity. Accordingly, MICU1 deletion significantly sensitizes human HEK-293 cells to manganese-induced stress. Our study identifies a critical role of MICU1 in the regulation of MCU ion selectivity, with potential implications for patients with MICU1 deficiency.

cell biology↗