Biology subjects

Stairs, C. W.

Publications and source records attributed to Stairs, C. W..

9 recordsLinked to original sources

bioRxiv2026

Proteomics reveals conserved features of histone biology in dinoflagellates

Current knowledge of DNA packaging in eukaryotic nuclei largely centers on its basic unit, the nucleosome. Multiple lineages have, however, diverged from this paradigm, most notably dinoflagellates. Among other molecular oddities, these enigmatic protists have enormous genomes, permanently condensed chromosomes and a foreign gene encoding Dinoflagellate Viral Nucleoprotein (DVNP), which is used for packing DNA. Some dinoflagellates also have Histone-like Proteins (HLPs) acquired from bacteria via lateral gene transfer. Dinoflagellates were long thought to lack histones entirely, but canonical histone genes have been identified by transcriptomics. Here, we performed proteomics on purified nuclei and confirmed the presence of all four core histone classes, along with variants, and DVNP in the dinoflagellates Oxyrrhis marina and Amphidinium carterae and HLPs in A. carterae. We also identified putative histone post-translational modifications found in canonical eukaryotes. Comparative genomics of dinoflagellates revealed histone-handling and modification machinery alongside an apparent reduction in, or diversification of, machinery responsible for replication-dependent nucleosome deposition (CAF-1), consistent with a predominantly transcription-associated role for nucleosomes. Furthermore, proteomics revealed modifications of DVNP and HLP, raising the possibility of machinery co-opting. These observations support a new model of a dinoflagellate chromatin that includes the localization of canonical nucleosomes to insulated chromatin territories (INTs).

evolutionary biology↗

bioRxiv2026

A hydrogen-producing mitochondrion in an anaerobic eukaryotrophic rhizarian

Diverse eukaryotes thrive under low oxygen conditions, in part through highly modified mitochondrion-related organelles (MROs) that use alternate metabolic pathways to support ATP production and cofactor recycling. Anaerobic lifestyles have evolved repeatedly across the eukaryotic tree of life, each providing an independent opportunity to understand how eukaryotes adapt to life in low oxygen conditions. Here, we use single-cell transcriptomics to reconstruct the MRO metabolism of PCE SSF, a benthic eukaryotrophic flagellate and the first cultivated representative of Novel Clade 12 (NC12; Rhizaria), an independently anaerobic rhizarian lineage. PCE SSF possesses an anaerobic hydrogen-producing mitochondrion capable of hydrogenosome-type substrate-level phosphorylation. It also retains a nearly complete but likely branched tricarboxylic acid pathway that lacks citrate synthase and malate dehydrogenase. The function of citrate synthase may instead be fulfilled by the typically cytosolic ATP citrate lyase, previously reported in this context only in the anaerobic cercozoan, Brevimastigomonas motovehiculus. Unlike B. motovehiculus, however, PCE SSF retains only Complex II and the NuoE/NuoF subunits of the electron transport chain and lacks a mitochondrial genome. Together, these features indicate an atypical and reduced mitochondrial metabolism, highlighting the diversity of evolutionary solutions to anaerobic energy metabolism in eukaryotes.

genomics↗

bioRxiv2026

Lateral gene transfer introduced the microbial anaerobiosis-related gene rquA into early animals

Lateral gene transfer (LGT) enables rapid metabolic innovation in microbes, but its evolutionary importance in animals remains debated. Among metabolic traits with major ecological consequences, adaptations to low-oxygen conditions often involve modifications of mitochondrial electron transport and the quinones that mediate electron flow. Rhodoquinone-based anaerobic metabolism occurs in several eukaryotic lineages, yet the evolutionary routes by which animals acquired this capability are poorly understood. Here we show that freshwater sponges possess a rhodoquinone biosynthesis gene, rquA, previously restricted to microbial lineages, which was acquired by lateral gene transfer and functionally integrated into sponge metabolism. Heterologous expression of rquA from the model freshwater sponge Ephydatia muelleri enables rhodoquinone production in yeast, consistent with functional conservation. In E. muelleri, the rquA gene is upregulated under hypoxia and rhodoquinone is detectable across all lifestages, however, it is most abundant in early development in the pluiripotent gemmules. Using comparative genomics, we find that the presence of rquA in freshwater sponges correlates with loss of key genes of the ubiquinone biosynthesis pathway, suggesting these animals cannot synthesize ubiquinone de novo and we show that E. muelleri can convert exogenous ubiquinone to rhodoquinone. Rhodoquinone levels were significantly higher in rquA-encoding freshwater sponges compared to marine sponges that were sampled from natural environments. This study reveals that an early animal lineage acquired a microbial metabolism-related gene via lateral gene transfer during or before the transition to freshwater environments, enabling rhodoquinone utilization and potentially enhancing tolerance to oxygen fluctuations. Thereby, demonstrating how LGT shapes energy metabolism even in multicellular organisms.

evolutionary biology↗

bioRxiv2026

Semi-permeable capsules enable parallel cultivation and live microscopic observations of microbial eukaryotes

Semi-permeable capsules (SPCs) create enclosed porous microenvironments, diffusible to only small proteins and macromolecules. This presents a powerful tool for single cell observation, isolation, and sequencing. However, their range of use for sustaining viable microbial eukaryotes is largely unexplored. Single-cell eukaryotes are often understudied, with a wealth of unknown lifecycles, culturing methods and inter-microbial interactions, which are difficult to visualize. Here, we show that eukaryotes from eight different supergroups can be captured and propagated in SPCs. Encapsulation allowed observations of cell stages, motility and growth in a traceable and parallelized manner.

microbiology↗

bioRxiv2026

CoMR: an integrative scoring pipeline for Comprehensive Mitochondrial proteome Reconstruction across eukaryotes

Mitochondrial proteome reconstruction from eukaryotic sequence data typically relies on prediction of mitochondrial targeting signals (MTSs). However, MTS predictors are primarily trained on model organisms and may perform poorly in phylogenetically divergent lineages or in organisms with atypical or reduced targeting sequences. Accurate reconstruction therefore requires integration of complementary sources of evidence beyond targeting prediction alone. We developed CoMR (Comprehensive Mitochondrial Reconstructor), an integrative workflow that combines targeting prediction, curated homology searches, large-scale similarity searches, and automated phylogenetic analysis within a unified scoring framework. Benchmarking on the model yeast Saccharomyces cerevisiae yielded strong discriminatory performance (ROC-AUC = 0.92), exceeding standalone TargetP2 prediction (ROC-AUC = 0.72). In the divergent anaerobic protist Paratrimastix pyriformis, CoMR maintained robust performance (ROC-AUC = 0.86) validated with an experimental proteome despite extreme class imbalance, achieving a precision-recall AUC of 0.183 ([~]78-fold enrichment over random expectation and [~]10-fold improvement over TargetP2). Ablation analyses demonstrate that predictive performance is robust to individual evidence-layer removal and that the relative contribution of homology sources depends on phylogenetic context. Together, these results show that integrative evidence scoring improves mitochondrial proteome reconstruction across both model and non-model eukaryotes.

bioinformatics↗

bioRxiv2023

Extreme mitochondrial reduction in a novel group of free-living metamonads.

Metamonads are a diverse group of heterotrophic microbial eukaryotes adapted to living in hypoxic environments. All metamonads but one harbour metabolically altered mitochondrion-related organelles (MROs) with reduced functions relative to aerobic mitochondria, however the degree of reduction varies markedly over the metamonad tree. To further investigate metamonad MRO diversity, we generated high quality draft genomes, transcriptomes, and predicted proteomes for five recently discovered free-living metamonads. Phylogenomic analyses placed these organisms in a group we informally named the BaSk (Barthelonids+Skoliomonads) clade, which emerges as a deeply branching sister group to the Fornicata, a metamonad phylum that includes parasitic and free-living flagellates. Extensive bioinformatic analyses of the manually curated gene models showed that these organisms are predicted to have extremely reduced MRO proteomes in comparison to other free-living metamonads. Loss of the mitochondrial iron-sulfur cluster (ISC) assembly system in some organisms in this group appears to be linked to the acquisition in their common ancestral lineage of a SUF-like minimal system (SMS) Fe/S cluster pathway through lateral gene transfer (LGT). One of the isolates, Skoliomonas litria, appears to have undergone further mitochondrial reduction having lost all other known MRO pathways. No proteins were confidently assigned to the predicted MRO proteome of this organism suggesting that the organelle has been lost. The extreme mitochondrial reduction observed within this free-living anaerobic protistan clade is unprecedented and demonstrates that mitochondrial functions, under some conditions, may be completely lost even in free-living organisms.

genomics↗

bioRxiv2023

A unique symbiosome in an anaerobic single-celled eukaryote

Symbiotic relationships drive evolutionary change and are important sources of novelty. Here we demonstrate a highly structured syntrophic symbiosis between species of the anaerobic protist Anaeramoeba (Anaeramoebae, Metamonada) and bacterial ectosymbionts. We dissected this symbiosis with long-read metagenomics, transcriptomics of host and symbiont cells coupled with fluorescent in situ hybridization (FISH), and microscopy. Genome sequencing, phylogenomic analyses and FISH show that the symbionts belong to the Desulfobacteraceae and were acquired independently in two different Anaeramoeba species. We show that ectosymbionts likely reside deep within cell surface invaginations in a symbiosomal membrane network that is tightly associated with cytoplasmic hydrogenosomes. Metabolic reconstructions based on the genomes and transcriptomes of the symbionts suggest a highly evolved syntrophic interaction. Host hydrogenosomes likely produce hydrogen, acetate, and propionate that are consumed by the symbionts dissimilatory sulfate reduction, Wood-Ljungdahl and methylmalonyl pathways, respectively. Because the host genome sequences encode several vitamin B12-dependent enzymes but appear to lack the ability to biosynthesize this vitamin, we hypothesize that the symbionts supply their hosts with B12. We detected numerous lateral gene transfers from diverse bacteria to Anaeramoeba, including genes involved in oxygen defense and anaerobic metabolism. Gene families encoding membrane-trafficking components that regulate the phagosomal maturation machinery are notably expanded in Anaeramoeba spp. and may be involved in organizing and/or stabilizing the symbiosomal membrane system. Overall, the Anaeramoebae have evolved a dynamic symbiosome comprised of a vacuolar system that facilitates positioning and maintenance of sulfate-reducing bacterial ectosymbionts.

evolutionary biology↗

bioRxiv2020

The integrin-mediated adhesome complex, essential to multicellularity, is present in the most recent common ancestor of animals, fungi, and amoebae

Integrins are transmembrane receptor proteins that activate signal transduction pathways upon extracellular matrix binding. The Integrin Mediated Adhesion Complex (IMAC), mediates various cell physiological process. The IMAC was thought to be an animal specific machinery until over the last decade these complexes were discovered in Obazoa, the group containing animals, fungi, and several microbial eukaryote lineages. Amoebozoa is the eukaryotic supergroup sister to Obazoa. Even though Amoebozoa represents the closest outgroup to Obazoa, little genomic-level data and attention to gene inventories has been given to the supergroup. To examine the evolutionary history of the IMAC, we examine gene inventories of deeply sampled set of 100+ Amoebozoa taxa, including new data from several taxa. From these robust data sampled from the entire breadth of known amoebozoan clades, we show the presence of an ancestral complex of integrin adhesion proteins that predate the evolution of the Amoebozoa. Our results highlight that many of these proteins appear to have evolved earlier in eukaryote evolution than previously thought. Co-option of an ancient protein complex was key to the emergence of animal type multicellularity. The role of the IMAC in a unicellular context is unknown but must also play a critical role for at least some unicellular organisms.

evolutionary biology↗

bioRxiv2018

Complex evolutionary history of translation Elongation Factor 2 and diphthamide biosynthesis in Archaea and parabasalids

Diphthamide is a modified histidine residue which is uniquely present in archaeal and eukaryotic elongation factor 2 (EF-2), an essential GTPase responsible for catalyzing the coordinated translocation of tRNA and mRNA through the ribosome. In part due to the role of diphthamide in maintaining translational fidelity, it was previously assumed that diphthamide biosynthesis genes (dph) are conserved across all eukaryotes and archaea. Here, comparative analysis of new and existing genomes reveals that some archaea (i.e., members of the Asgard superphylum, Geoarchaea, and Korarchaeota) and eukaryotes (i.e., parabasalids) lack dph. In addition, while EF-2 was thought to exist as a single copy in archaea, many of these dph-lacking archaeal genomes encode a second EF-2 paralog missing key-residues required for diphthamide modification and for normal translocase function, perhaps suggesting functional divergence linked to loss of diphthamide biosynthesis. Interestingly, some Heimdallarchaeota previously suggested to be most closely related to the eukaryotic ancestor maintain dph genes and a single gene encoding canonical EF-2. Our findings reveal that the ability to produce diphthamide, once thought to be a universal feature in archaea and eukaryotes, has been lost multiple times during evolution, and suggest that anticipated compensatory mechanisms evolved independently.

microbiology↗