An excavate root for the eukaryote tree of life

Hypothesis that ancestral eukaryotes sexually proliferated without kinetochores or mitosis

Eukaryotes possess two different mechanisms to transmit genetic material - mitosis and meiosis. Because mitosis is universal in all present-day eukaryotes, it has been widely assumed, despite the absence of definitive evidence, that meiosis evolved from mitosis during eukaryogenesis. In both processes, chromosome movement depends on interactions between spindle microtubules and a macromolecular protein complex called the kinetochore that assembles onto centromere DNA. Spindle microtubules consist of α- and β-tubulin subunits, which are conserved in all studied eukaryotes. Similarly, canonical kinetochore components are found in almost all eukaryotes. However, an evolutionarily divergent group of organisms called kinetoplastids has a unique set of kinetochore proteins. It remains unclear why and when different types of kinetochores evolved. In this Hypothesis article, I propose that the last eukaryotic common ancestor (LECA) did not have a kinetochore and that these two kinetochore systems evolved independently - one in the ancestor of kinetoplastids and another in the ancestor of all other eukaryotes. Based on the notion that archaea and the LECA possessed cell fusion and genetic exchange machineries, I further propose that key aspects of meiosis evolved prior to mitosis, challenging the dogma that meiosis evolved from mitosis.

Renal Intercalated Cells: Alien Cells Inside Us?

Mammalian renal intercalated cells are known for their role in acid secretion and maintaining acid-base balance. Herein, we discuss the theoretical reasons behind their development based on published data, focusing on the unique characteristics of renal intercalated cell biology that distinguish them from other mammalian cell types, while simultaneously attempting to explain the persistence of cells similar to intercalated cells throughout evolution. In addition, we traced these characteristics phylogenetically back to the simplest organisms. Intercalated cells have several functions and attributes. First, they contribute to kidney defense mechanisms in response to both infectious and non-infectious kidney damage. Second, intercalated cells are energized by V-ATPases in a manner similar to that of protozoa. Third, they possess T-antigens, which are commonly found in embryonic and cancer cells and which confer invasive abilities to these cells. Fourth, their plasticity enables the regeneration of other epithelial cells. These observations indicate that the origins of renal intercalated cells may be traceable back to amoeboid cells that originated from an evolutionary lineage including protists, or even to the last eukaryote common ancestor. The theoretical framework presented herein supports two predictions: first, that sponge amoebocytes possess membrane V-ATPase and are sensitive to bafilomycin, but not to ouabain; and second, that sponge amoebocytes-along with cells from diploblasts (such as Xenacoelomorpha), cnidarians, worms, fish and mollusk ionocytes, and the entire cell lineage containing V-ATPase, carbonic anhydrase, and anion exchangers (HCO3-/Cl-)-have innate immunity, cellular dedifferentiation, and regeneration capabilities.

Chimeric origins and dynamic evolution of central carbon metabolism in eukaryotes

The origin of eukaryotes was a key event in the history of life. Current leading hypotheses propose that a symbiosis between an asgardarchaeal host cell and an alphaproteobacterial endosymbiont represented a crucial step in eukaryotic origin and that metabolic cross-feeding between the partners provided the basis for their subsequent evolutionary integration. A major unanswered question is whether the metabolism of modern eukaryotes bears any vestige of this ancestral syntrophy. Here we systematically analyse the evolutionary origins of the eukaryotic gene repertoires mediating central carbon metabolism. Our phylogenetic and sequence analyses reveal that this gene repertoire is chimeric, with ancestral contributions from Asgardarchaeota and Alphaproteobacteria operating predominantly in glycolysis and the tricarboxylic acid cycle, respectively. Our analyses also reveal the extent to which this ancestral metabolic interplay has been remodelled via gene loss, transfer and subcellular retargeting in the >2 billion years since the origin of eukaryotic cells, and we identify genetic contributions from other prokaryotic sources in addition to the asgardarchaeal host and alphaproteobacterial endosymbiont. Our work demonstrates that, in contrast to previous assumptions, modern eukaryotic metabolism preserves information about the nature of the original asgardarchaeal-alphaproteobacterial interactions and supports syntrophy scenarios for the origin of the eukaryotic cell.

A robustly rooted tree of eukaryotes reveals their excavate ancestry

The eukaryote Tree of Life (eToL) depicts the relationships among all eukaryotic organisms; its root represents the Last Eukaryotic Common Ancestor (LECA) from which all extant complex lifeforms are descended1. Locating this root is crucial for reconstructing the features of LECA, both as the endpoint of eukaryogenesis and the start point for the evolution of the myriad complex traits underpinning the diversification of living eukaryotes. However, the position of the root remains contentious due to pervasive phylogenetic artefacts stemming from inadequate evolutionary models, poor taxon sampling and limited phylogenetic signal1. Here we estimate the root of the eToL with unprecedented resolution on the basis of a new, much larger, dataset of mitochondrial proteins that includes all known eukaryotic supergroups. Our analyses of a 100 taxon × 93 protein dataset with state-of-the-art phylogenetic models and an extensive evaluation of alternative hypotheses show that the eukaryotic root lies between two multi-supergroup assemblages: 'Opimoda+' and 'Diphoda+'. This position is consistently supported across different models and robustness analyses. Notably, groups containing 'typical excavates' are placed on both sides of the root, suggesting the complex features of the 'excavate' cell architecture trace back to LECA. This study sheds light on the ancestral cells from which extant eukaryotes arose and provides a crucial framework for investigating the origin and evolution of canonical eukaryotic features.

A hypothesis for nucleosome evolution based on mutational analysis

Nucleosomes are complexes of DNA and histone proteins that form the basis of eukaryotic chromatin. Eukaryotic histones are descended from archaeal homologs; however, how this occurred remains unclear. Our previous genetic analysis of the budding yeast nucleosome identified 26 histone residues conserved between Saccharomyces cerevisiae and Trypanosoma brucei: 15 that are lethal when mutated and 11 that are synthetically lethal with deletion of the FEN1 nuclease. These residues are partially conserved in nucleosomes of a variety of giant viruses, allowing us to follow the route by which they were established in the LECA (last eukaryotic common ancestor). We analyzed yeast nucleosome genetic data to generate a model for the emergence of the eukaryotic nucleosome. In our model, histone H2B-H2A and H4-H3 doublets found in giant virus nucleosomes facilitated the formation of the acidic patch surface and nucleosome entry sites of the eukaryotic nucleosome, respectively. Splitting of the H2B-H2A doublet resulted in the H2A variant H2A.Z, and subsequent splitting of the H4-H3 doublet led to a eukaryote-specific domain required for chromatin binding of H2A.Z. We propose that the LECA emerged when the newly split H3 N-terminus horizontally acquired a common N-tail found in extinct pre-LECA lineages and some extant giant viruses. This hypothesis predicts that the emergence of the H3 variant CENP-A and the establishment of CENP-A-dependent chromosome segregation occurred after the emergence of the LECA, implying that the root of all eukaryotes is assigned within Euglenida.

Trypanosome doublet microtubule structures reveal flagellum assembly and motility mechanisms

The flagellum of Trypanosoma brucei drives the parasite's characteristic screw-like motion and is essential for its replication, transmission, and pathogenesis. However, the molecular details of this process remain unclear. Here, we present high-resolution (up to 2.8 angstrom) cryo-electron microscopy structures of T. brucei flagellar doublet microtubules (DMTs). Integrated modeling identified 154 different axonemal proteins inside and outside the DMT and, together with genetic and proteomic interrogation, revealed conserved and trypanosome-specific foundations of flagellum assembly and motility. We captured axonemal dynein motors in their pre-power stroke state. Comparing atomic models between pre- and post-power strokes defined how dynein structural changes drive sliding of adjacent DMTs during flagellar beating. This study illuminates structural dynamics underlying flagellar motility and identifies pathogen-specific proteins to consider for therapeutic interventions targeting neglected diseases.

Beyond Static Tethering at Membrane Contact Sites: Structural Dynamics and Functional Implications of VAP Proteins

The membranes surrounding the eukaryotic cell and its organelles are continuously invaginating, budding, and undergoing membrane fusion-fission events, which enable them to perform functions not found in prokaryotic cells. In addition, organelles come into close contact with each other at membrane contact sites (MCSs), which involve many types of proteins, and which regulate the signaling and transport of various molecules. Vesicle-associated membrane protein (VAMP)-associated protein (VAP) is an important factor involved in the tethering and contact of various organelles at MCSs in almost all eukaryotes and has attracted attention for its association with various diseases, mainly neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS). However, the detailed mechanism of its functional expression remains unclear. In this review, we quantitatively discuss the structural dynamics of the entire molecule, including intrinsically disordered regions and intramolecular and intermolecular interactions, focusing on the vertebrate VAP paralogs VAPA and VAPB. Molecular phylogenetic and biophysical considerations are the basis of the work.

Evolution of Transcription Factor-containing Superfamilies in Eukaryotes

Regulation of gene expression helps determine various phenotypes in most cellular life forms. It is orchestrated at different levels and at the point of transcription initiation by transcription factors (TFs). TFs bind to DNA through domains that are evolutionarily related, by shared membership of the same superfamilies (TF-SFs), to those found in other nucleic acid binding and protein-binding functions (nTFs for non-TFs). Here we ask how TF DNA binding sequence families in eukaryotes have evolved in relation to their nTF relatives. TF numbers scale by power law with the total number of protein-coding genes differently in different clades, with fungi usually showing sub-linear powers whereas chordates show super-linear scaling. The LECA probably encoded a complex regulatory machinery with both TFs and nTFs, but with an excess of nTFs when compared to the relative distribution of TFs and nTFs in extant organisms. Losses drive the evolution of TFs and nTFs, with the possible exception of TFs in animals for some tree topologies. TFs are highly dynamic in evolution, showing higher gain and loss rates than nTFs in some TF-SFs though both are conserved to similar extents. Gains of TFs and nTFs are driven by the appearance of a large number of new sequence clusters in a small number of nodes, which determine the presence of as many as a third of extant TFs and nTFs as well as the relative presence of TFs and nTFs. Whereas nodes showing explosion of TF numbers belong to multicellular clades, those for nTFs lie among the fungi and the protists.

The Acrasis kona genome and developmental transcriptomes reveal deep origins of eukaryotic multicellular pathways

Acrasids are amoebae with the capacity to form multicellular fruiting bodies in a process known as aggregative multicellularity (AGM). This makes acrasids the only known example of multicellularity among the earliest branches of eukaryotes (the former Excavata). Here, we report the Acrasis kona genome sequence plus transcriptomes from pre-, mid- and post-developmental stages. The genome is rich in novelty and genes with strong signatures of horizontal transfer, and multigene families encode nearly half of the amoeba's predicted proteome. Development in A. kona appears molecularly simple relative to the AGM model, Dictyostelium discoideum. However, the acrasid also differs from the dictyostelid in that it does not appear to be starving during development. Instead, developing A. kona appears to be very metabolically active, does not induce autophagy and does not up-regulate its proteasomal genes. Together, these observations strongly suggest that starvation is not essential for AGM development. Nonetheless, development in the two amoebae appears to employ remarkably similar pathways for signaling, motility and, potentially, construction of an extracellular matrix surrounding the developing cell mass. Much of this similarity is also shared with animal development, suggesting that much of the basic tool kit for multicellular development arose early in eukaryote evolution.

Cytochromes P450 evolution in the plant terrestrialization context

Plants started to colonize land around 500 million years ago. It meant dealing with new challenges like absence of buoyancy, water and nutrients shortage, increased light radiation, reproduction on land, and interaction with new microorganisms. This obviously required the acquisition of novel functions and metabolic capacities. Cytochrome P450 (CYP) monooxygenases form the largest superfamily of enzymes and are present to catalyse critical and rate-limiting steps in most plant-specific pathways. The different families of CYP enzymes are typically associated with specific functions. CYP family emergence and evolution in the green lineage thus offer the opportunity to obtain a glimpse into the timing of the evolution of the critical functions that were required (or became dispensable) for the plant transition to land. Based on the analysis of currently available genomic data, this review provides an evolutionary history of plant CYPs in the context of plant terrestrialization and describes the associated functions in the different lineages. Without surprise it highlights the relevance of the biosynthesis of antioxidants and UV screens, biopolymers, and critical signalling pathways. It also points to important unsolved questions that would deserve to be answered to improve our understanding of plant adaptation to challenging environments and the management of agricultural traits. This article is part of the theme issue 'The evolution of plant metabolism'.

The secretory pathway in Tetrahymena is organized for efficient constitutive secretion at ciliary pockets

In ciliates, membrane cisternae called alveoli interpose between the plasma membrane and the cytoplasm, posing a barrier to endocytic and exocytic membrane trafficking. One exception to this barrier is plasma membrane invaginations called parasomal sacs, which are adjacent to ciliary basal bodies. By following a fluorescent secretory marker called ESCargo, we imaged secretory compartments and secretion in these cells. A cortical endoplasmic reticulum is organized along cytoskeletal ridges and cradles a cohort of mitochondria. One cohort of Golgi are highly mobile in a subcortical layer, while the remainder appear stably positioned at periodic sites close to basal bodies, except near the cell tip where, interestingly, Golgi are more closely spaced. Strikingly, ESCargo secretion was readily visible at positions aligned with basal bodies and parasomal sacs. Thus peri-ciliary zones in ciliates are organized, like ciliary pockets in the highly unrelated trypanosomids, as unique hubs of exo-endocytic trafficking.

Diverse Genome Structures among Eukaryotes May Have Arisen in Response to Genetic Conflict

In contrast to the typified view of genome cycling only between haploidy and diploidy, there is evidence from across the tree of life of genome dynamics that alter both copy number (i.e. ploidy) and chromosome complements. Here, we highlight examples of such processes, including endoreplication, aneuploidy, inheritance of extrachromosomal DNA, and chromatin extrusion. Synthesizing data on eukaryotic genome dynamics in diverse extant lineages suggests the possibility that such processes were present before the last eukaryotic common ancestor. While present in some prokaryotes, these features appear exaggerated in eukaryotes where they are regulated by eukaryote-specific innovations including the nucleus, complex cytoskeleton, and synaptonemal complex. Based on these observations, we propose a model by which genome conflict drove the transformation of genomes during eukaryogenesis: from the origin of eukaryotes (i.e. first eukaryotic common ancestor) through the evolution of last eukaryotic common ancestor.

Reconstructing the last common ancestor of all eukaryotes

Understanding the origin of eukaryotic cells is one of the most difficult problems in all of biology. A key challenge relevant to the question of eukaryogenesis is reconstructing the gene repertoire of the last eukaryotic common ancestor (LECA). As data sets grow, sketching an accurate genomics-informed picture of early eukaryotic cellular complexity requires provision of analytical resources and a commitment to data sharing. Here, we summarise progress towards understanding the biology of LECA and outline a community approach to inferring its wider gene repertoire. Once assembled, a robust LECA gene set will be a useful tool for evaluating alternative hypotheses about the origin of eukaryotes and understanding the evolution of traits in all descendant lineages, with relevance in diverse fields such as cell biology, microbial ecology, biotechnology, agriculture, and medicine. In this Consensus View, we put forth the status quo and an agreed path forward to reconstruct LECA's gene content.

The Prokaryotic Roots of Eukaryotic Immune Systems

Over the past two decades, studies have revealed profound evolutionary connections between prokaryotic and eukaryotic immune systems, challenging the notion of their unrelatedness. Immune systems across the tree of life share an operational framework, shaping their biochemical logic and evolutionary trajectories. The diversification of immune genes in the prokaryotic superkingdoms, followed by lateral transfer to eukaryotes, was central to the emergence of innate immunity in the latter. These include protein domains related to nucleotide second messenger-dependent systems, NAD+/nucleotide degradation, and P-loop NTPase domains of the STAND and GTPase clades playing pivotal roles in eukaryotic immunity and inflammation. Moreover, several domains orchestrating programmed cell death, ultimately of prokaryotic provenance, suggest an intimate link between immunity and the emergence of multicellularity in eukaryotes such as animals. While eukaryotes directly adopted some proteins from bacterial immune systems, they repurposed others for new immune functions from bacterial interorganismal conflict systems. These emerging immune components hold substantial biotechnological potential.

Foraging mechanisms in excavate flagellates shed light on the functional ecology of early eukaryotes

The phagotrophic flagellates described as "typical excavates" have been hypothesized to be morphologically similar to the Last Eukaryotic Common Ancestor and understanding the functional ecology of excavates may therefore help shed light on the ecology of these early eukaryotes. Typical excavates are characterized by a posterior flagellum equipped with a vane that beats in a ventral groove. Here, we combined flow visualization and observations of prey capture in representatives of the three clades of excavates with computational fluid dynamic modeling, to understand the functional significance of this cell architecture. We record substantial differences amongst species in the orientation of the vane and the beat plane of the posterior flagellum. Clearance rate magnitudes estimated from flow visualization and modeling are both like that of other similarly sized flagellates. The interaction between a vaned flagellum beating in a confinement is modeled to produce a very efficient feeding current at low energy costs, irrespective of the beat plane and vane orientation and of all other morphological variations. Given this predicted uniformity of function, we suggest that the foraging systems of typical excavates studied here may be good proxies to understand those potentially used by our distant ancestors more than 1 billion years ago.

How mitochondrial cristae illuminate the important role of oxygen during eukaryogenesis

Inner membranes of mitochondria are extensively folded, forming cristae. The observed overall correlation between efficient eukaryotic ATP generation and the area of internal mitochondrial inner membranes both in unicellular organisms and metazoan tissues seems to explain why they evolved. However, the crucial use of molecular oxygen (O2) as final acceptor of the electron transport chain is still not sufficiently appreciated. O2 was an essential prerequisite for cristae development during early eukaryogenesis and could be the factor allowing cristae retention upon loss of mitochondrial ATP generation. Here I analyze illuminating bacterial and unicellular eukaryotic examples. I also discuss formative influences of intracellular O2 consumption on the evolution of the last eukaryotic common ancestor (LECA). These considerations bring about an explanation for the many genes coming from other organisms than the archaeon and bacterium merging at the start of eukaryogenesis.

The contours of evolution: In defence of Darwin's tree of life paradigm

Both the concept of a Darwinian tree of life (TOL) and the possibility of its accurate reconstruction have been much criticized. Criticisms mostly revolve around the extensive occurrence of lateral gene transfer (LGT), instances of uptake of complete organisms to become organelles (with the associated subsequent gene transfer to the nucleus), as well as the implications of more subtle aspects of the biological species concept. Here we argue that none of these criticisms are sufficient to abandon the valuable TOL concept and the biological realities it captures. Especially important is the need to conceptually distinguish between organismal trees and gene trees, which necessitates incorporating insights of widely occurring LGT into modern evolutionary theory. We demonstrate that all criticisms, while based on important new findings, do not invalidate the TOL. After considering the implications of these new insights, we find that the contours of evolution are best represented by a TOL.

Microbial Diversity and Open Questions about the Deep Tree of Life

In this perspective, we explore the transformative impact and inherent limitations of metagenomics and single-cell genomics on our understanding of microbial diversity and their integration into the Tree of Life. We delve into the key challenges associated with incorporating new microbial lineages into the Tree of Life through advanced phylogenomic approaches. Additionally, we shed light on enduring debates surrounding various aspects of the microbial Tree of Life, focusing on recent advances in some of its deepest nodes, such as the roots of bacteria, archaea, and eukaryotes. We also bring forth current limitations in genome recovery and phylogenomic methodology, as well as new avenues of research to uncover additional key microbial lineages and resolve the shape of the Tree of Life.

Encyclopedia of Family A DNA Polymerases Localized in Organelles: Evolutionary Contribution of Bacteria Including the Proto-Mitochondrion

DNA polymerases synthesize DNA from deoxyribonucleotides in a semiconservative manner and serve as the core of DNA replication and repair machinery. In eukaryotic cells, there are 2 genome-containing organelles, mitochondria, and plastids, which were derived from an alphaproteobacterium and a cyanobacterium, respectively. Except for rare cases of genome-lacking mitochondria and plastids, both organelles must be served by nucleus-encoded DNA polymerases that localize and work in them to maintain their genomes. The evolution of organellar DNA polymerases has yet to be fully understood because of 2 unsettled issues. First, the diversity of organellar DNA polymerases has not been elucidated in the full spectrum of eukaryotes. Second, it is unclear when the DNA polymerases that were used originally in the endosymbiotic bacteria giving rise to mitochondria and plastids were discarded, as the organellar DNA polymerases known to date show no phylogenetic affinity to those of the extant alphaproteobacteria or cyanobacteria. In this study, we identified from diverse eukaryotes 134 family A DNA polymerase sequences, which were classified into 10 novel types, and explored their evolutionary origins. The subcellular localizations of selected DNA polymerases were further examined experimentally. The results presented here suggest that the diversity of organellar DNA polymerases has been shaped by multiple transfers of the PolI gene from phylogenetically broad bacteria, and their occurrence in eukaryotes was additionally impacted by secondary plastid endosymbioses. Finally, we propose that the last eukaryotic common ancestor may have possessed 2 mitochondrial DNA polymerases, POP, and a candidate of the direct descendant of the proto-mitochondrial DNA polymerase I, rdxPolA, identified in this study.

Linear motifs regulating protein secretion, sorting and autophagy in Leishmania parasites are diverged with respect to their host equivalents

The pathogenic, tropical Leishmania flagellates belong to an early-branching eukaryotic lineage (Kinetoplastida) with several unique features. Unfortunately, they are poorly understood from a molecular biology perspective, making development of mechanistically novel and selective drugs difficult. Here, we explore three functionally critical targeting short linear motif systems as well as their receptors in depth, using a combination of structural modeling, evolutionary sequence divergence and deep learning. Secretory signal peptides, endoplasmic reticulum (ER) retention motifs (KDEL motifs), and autophagy signals (motifs interacting with ATG8 family members) are ancient and essential components of cellular life. Although expected to be conserved amongst the kinetoplastids, we observe that all three systems show a varying degree of divergence from their better studied equivalents in animals, plants, or fungi. We not only describe their behaviour, but also build models that allow the prediction of localization and potential functions for several uncharacterized Leishmania proteins. The unusually Ala/Val-rich secretory signal peptides, endoplasmic reticulum resident proteins ending in Asp-Leu-COOH and atypical ATG8-like proteins are all unique molecular features of kinetoplastid parasites. Several of their critical protein-protein interactions could serve as targets of selective antimicrobial agents against Leishmaniasis due to their systematic divergence from the host.

Mitochondrial genomes revisited: why do different lineages retain different genes?

The mitochondria contain their own genome derived from an alphaproteobacterial endosymbiont. From thousands of protein-coding genes originally encoded by their ancestor, only between 1 and about 70 are encoded on extant mitochondrial genomes (mitogenomes). Thanks to a dramatically increasing number of sequenced and annotated mitogenomes a coherent picture of why some genes were lost, or relocated to the nucleus, is emerging. In this review, we describe the characteristics of mitochondria-to-nucleus gene transfer and the resulting varied content of mitogenomes across eukaryotes. We introduce a 'burst-upon-drift' model to best explain nuclear-mitochondrial population genetics with flares of transfer due to genetic drift.

The dynamic subcellular localisation of Rad1 is cell cycle dependent in Leishmania major

The subcellular localisation of Rad1, a subunit of the Leishmania major 9-1-1 complex, remains unexplored. Herein, we reveal that Rad1 localises predominantly to the nucleus. Upon hydroxyurea treatment, the diffuse nuclear localisation of Rad1 becomes more punctate, suggesting that Rad1 is responsive to replication stress. Moreover, Rad1 localisation correlates with cell cycle progression. In the majority of G1 to early S-phase cells, Rad1 localises predominantly to the nucleus. As cells progress from late-S phase to mitosis, Rad1 relocalizes to both the nucleus and the cytoplasm in ∼90 % of cells. This pattern of distribution is different from Rad9 and Hus1, which remain nuclear throughout the cell cycle, suggesting Leishmania Rad1 may regulate 9-1-1 activities and/or perform relevant functions outside the 9-1-1 complex.

Insights into the conservation and diversification of the molecular functions of YTHDF proteins

YT521-B homology (YTH) domain proteins act as readers of N6-methyladenosine (m6A) in mRNA. Members of the YTHDF clade determine properties of m6A-containing mRNAs in the cytoplasm. Vertebrates encode three YTHDF proteins whose possible functional specialization is debated. In land plants, the YTHDF clade has expanded from one member in basal lineages to eleven so-called EVOLUTIONARILY CONSERVED C-TERMINAL REGION1-11 (ECT1-11) proteins in Arabidopsis thaliana, named after the conserved YTH domain placed behind a long N-terminal intrinsically disordered region (IDR). ECT2, ECT3 and ECT4 show genetic redundancy in stimulation of primed stem cell division, but the origin and implications of YTHDF expansion in higher plants are unknown, as it is unclear whether it involves acquisition of fundamentally different molecular properties, in particular of their divergent IDRs. Here, we use functional complementation of ect2/ect3/ect4 mutants to test whether different YTHDF proteins can perform the same function when similarly expressed in leaf primordia. We show that stimulation of primordial cell division relies on an ancestral molecular function of the m6A-YTHDF axis in land plants that is present in bryophytes and is conserved over YTHDF diversification, as it appears in all major clades of YTHDF proteins in flowering plants. Importantly, although our results indicate that the YTH domains of all arabidopsis ECT proteins have m6A-binding capacity, lineage-specific neo-functionalization of ECT1, ECT9 and ECT11 happened after late duplication events, and involves altered properties of both the YTH domains, and, especially, of the IDRs. We also identify two biophysical properties recurrent in IDRs of YTHDF proteins able to complement ect2 ect3 ect4 mutants, a clear phase separation propensity and a charge distribution that creates electric dipoles. Human and fly YTHDFs do not have IDRs with this combination of properties and cannot replace ECT2/3/4 function in arabidopsis, perhaps suggesting different molecular activities of YTHDF proteins between major taxa.

Defining eukaryotes to dissect eukaryogenesis

The origin of eukaryotes is among the most contentious debates in evolutionary biology, attracting multiple seemingly incompatible theories seeking to explain the sequence in which eukaryotic characteristics were acquired. Much of the controversy arises from differing views on the defining characteristics of eukaryotes. We argue that eukaryotes should be defined phylogenetically, and that doing so clarifies where competing hypotheses of eukaryogenesis agree and how we may test among aspects of disagreement. Some hypotheses make predictions about the phylogenetic origins of eukaryotic genes and are distinguishable on that basis. However, other hypotheses differ only in the order of key evolutionary steps, like mitochondrial endosymbiosis and nuclear assembly, which cannot currently be distinguished phylogenetically. Stages within eukaryogenesis may be made identifiable through the absolute dating of gene duplicates that map to eukaryotic traits, such as in genes of host or mitochondrial origin that duplicated and diverged functionally prior to emergence of the last eukaryotic common ancestor. In this way, it may finally be possible to distinguish heat from light in the debate over eukaryogenesis.