Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2022.09.13.506888

The persistent homology of mitochondrial ATP synthases

Sinha, S. D.·Wideman, J. G.
View original source ↗Export metadata ↓

Abstract

While mitochondrial ATP synthase has been thoroughly studied in animals and fungi, relatively little is known about the structures of protists. Among those that have been studied, protist ATP synthases possess divergent structures distinct from those of yeast or animals. Therefore, we aimed to clarify the subunit composition and evolution of ATP synthase across all major eukaryotic lineages. We used sensitive homology detection methods and molecular modelling tools to demonstrate the persistence of a near-complete ancestral set of 17 subunits in most major eukaryotic taxa even despite major divergence. These data demonstrate that most eukaryotes possess an ancestral-like ATP synthase structure similar to those of animals, fungi, and plants, but a number have diverged drastically (e.g., ciliates, myzozoans, euglenozoans, and likely retarians and heteroloboseans). In addition, we identified the first synapomorphy of the SAR (stramenopile, alveolate, rhizaria) supergroup - a ~1 billion-year-old gene fusion between ATP synthase stator subunits. Our comparative approach highlights the persistence of ancestral subunits even amidst major structural changes. We conclude by urging that more ATP synthase structures (e.g., from jakobids, heteroloboseans, stramenopiles, rhizarians) are needed to provide a complete picture of the evolution of structural diversity of this ancient and essential complex.

Source connections

Explore related subjects

evolutionary biologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Sinha, S. D., Wideman, J. G.. 2022-09-15. The persistent homology of mitochondrial ATP synthases. https://doi.org/10.1101/2022.09.13.506888

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Evolutionary dynamics of RNA viruses during persistent infection in Drosophila melanogaster

Persistent viral infections provide an extended window for viral evolution, yet their intra-host trajectories across the host lifespan remain underexplored. Here, we tracked the longitudinal evolution of three single-stranded RNA (ssRNA) viruses (Drosophila A virus [DAV], Drosophila C virus [DCV], and Nora virus) and one double-stranded RNA (dsRNA) virus (Bloomfield virus) during persistent infection in Drosophila melanogaster. By analyzing viral populations across early, intermediate, and late infection stages, we mapped dynamic shifts in the viral quasispecies and the emergence of adaptive mutations. These data demonstrate that long-term persistence drives viral evolution in a viral species-specific manner. DAV evolution was defined by clonal interference, driven by the continuous turnover of competing haplotypes. Nora virus exhibited prolonged evolutionary stasis punctuated by a late-stage sweep, suggesting adaptation to the senescing host environment. In contrast, standard DCV populations were locked under strong purifying selection, where no adaptive mutations were detected. However, this constraint collapsed in high-titer DCV infections, triggering extensive mutational diversification. Distinct from the ssRNA dynamics, the multi-segmented dsRNA Bloomfield virus maintained higher sequence fidelity and a stable genomic formula. Ultimately, these results demonstrate that viral evolution during persistent infection is governed by the interplay between specific host-pathogen interactions and the physiological decline of the host.

evolutionary biology↗
bioRxiv2026

A new cell type facilitated live-bearing and multiple independent origins of placentation in fish

The origin of new organs has fascinated biologists since Darwin. Yet the molecular and evolutionary steps that give rise to new organs remain difficult to resolve, largely because most organs have ancient origins. The fish family Poeciliidae offers a rare exception. Within poeciliids, placentas have independently evolved at least nine times, including within the last ~10 million years. Here, we study the molecular and cellular drivers of five independent origins of a placenta, using pairs of sister species with and without a placenta. We identified a new maternal cell type that emerged in the common ancestor of poeciliids and likely enabled the family to transition from egg-laying to live-bearing through egg retention. This new cell type originated by partly co-opting the existing gene regulatory network of another ovarian cell type. Subsequently, this same new maternal cell type, together with the embryonic yolk sac, was repeatedly and independently co-opted to form a placenta in all five origins. The evolution of these placentas involved high levels of convergence at the pathway level (e.g., lipid metabolism and vesicle-mediated transport), although these functional changes relied primarily on distinct genes across species. Our analyses show how the evolution and modification of a new cell type enabled the evolution of live birth and placentation, providing the cellular and genetic foundations for the repeated evolution of a new organ.

evolutionary biology↗
bioRxiv2026

The extracellular morphology and behaviour of the last common ancestor of animals and choanoflagellates

Choanoflagellates, the closest known living relatives of animals, provide a powerful comparative system for investigating the evolution of extracellular morphology and cell behaviour on the animal stem lineage. Although all choanoflagellates share a conserved cellular architecture including a flagellum and collar of microvilli, they display a wide diversity of extracellular structures and behaviours throughout the life cycle. Their extracellular features, historically used for species identification, have long been suspected to reflect a mixture of evolutionary inheritance and ecological plasticity. Yet, the majority of choanoflagellate diversity remains undescribed, and the extent to which their extracellular traits map onto their phylogeny has remained unclear, impeding comparative reconstructions of the evolutionary history of extracellular structures with the earliest animals. Here, we integrate super-resolution fluorescence imaging, electron microscopy and transcriptomic analysis to characterize the extracellular structures and behaviours across both currently described lineages of choanoflagellates (Craspedida and Acanthoecida), by studying pairs of closely related species in conjunction with novel isolates representing previously unexplored clades. Our results reveal strong conservation of extracellular morphology between close relatives, whereas deeper evolutionary distances uncover unexpected innovations, such as sheath-like layers, bipartite thecae, crawling stages and atypical inverted division patterns. Furthermore, the inclusion of early-branching taxa sister to the loricates supports the hypothesis that the silicified extracellular lorica is a derived trait rather than an ancestral feature. Together, our findings suggest that the last choanoflagellate common ancestor possessed an organic non-silicified extracellular covering composed of one or more layers and that it was capable of both swimming and crawling behaviours, refining the cellular context from which animals evolved.

evolutionary biology↗