The New Tree of Eukaryotes

Sex Determination: Genetic Dominance in Oomycete Sex

Oomycetes are notorious plant pathogens. It is known that genetically distinct oomycete strains can mate to increase their genetic diversity and virulence. A new paper finally reveals the genomic locus that may govern sexual compatibility in one oomycete species.

Sequential production of gametes during meiosis in trypanosomes

Meiosis is a core feature of eukaryotes that occurs in all major groups, including the early diverging excavates. In this group, meiosis and production of haploid gametes have been described in the pathogenic protist, Trypanosoma brucei, and mating occurs in the salivary glands of the insect vector, the tsetse fly. Here, we searched for intermediate meiotic stages among trypanosomes from tsetse salivary glands. Many different cell types were recovered, including trypanosomes in Meiosis I and gametes. Significantly, we found trypanosomes containing three nuclei with a 1:2:1 ratio of DNA contents. Some of these cells were undergoing cytokinesis, yielding a mononucleate gamete and a binucleate cell with a nuclear DNA content ratio of 1:2. This cell subsequently produced three more gametes in two further rounds of division. Expression of the cell fusion protein HAP2 (GCS1) was not confined to gametes, but also extended to meiotic intermediates. We propose a model whereby the two nuclei resulting from Meiosis I undergo asynchronous Meiosis II divisions with sequential production of haploid gametes.

Shared evolutionary footprints suggest mitochondrial oxidative damage underlies multiple complex I losses in fungi

Oxidative phosphorylation is among the most conserved mitochondrial pathways. However, one of the cornerstones of this pathway, the multi-protein complex NADH : ubiquinone oxidoreductase (complex I) has been lost multiple independent times in diverse eukaryotic lineages. The causes and consequences of these convergent losses remain poorly understood. Here, we used a comparative genomics approach to reconstruct evolutionary paths leading to complex I loss and infer possible evolutionary scenarios. By mining available mitochondrial and nuclear genomes, we identified eight independent events of mitochondrial complex I loss across eukaryotes, of which six occurred in fungal lineages. We focused on three recent loss events that affect closely related fungal species, and inferred genomic changes convergently associated with complex I loss. Based on these results, we predict novel complex I functional partners and relate the loss of complex I with the presence of increased mitochondrial antioxidants, higher fermentative capabilities, duplications of alternative dehydrogenases, loss of alternative oxidases and adaptation to antifungal compounds. To explain these findings, we hypothesize that a combination of previously acquired compensatory mechanisms and exposure to environmental triggers of oxidative stress (such as hypoxia and/or toxic chemicals) induced complex I loss in fungi.

Lipid Droplets in Unicellular Photosynthetic Stramenopiles

The Heterokonta or Stramenopile phylum comprises clades of unicellular photosynthetic species, which are promising for a broad range of biotechnological applications, based on their capacity to capture atmospheric CO₂ via photosynthesis and produce biomolecules of interest. These molecules include triacylglycerol (TAG) loaded inside specific cytosolic bodies, called the lipid droplets (LDs). Understanding TAG production and LD biogenesis and function in photosynthetic stramenopiles is therefore essential, and is mostly based on the study of a few emerging models, such as the pennate diatom Phaeodactylum tricornutum and eustigmatophytes, such as Nannochloropsis and Microchloropsis species. The biogenesis of cytosolic LD usually occurs at the level of the endoplasmic reticulum. However, stramenopile cells contain a complex plastid deriving from a secondary endosymbiosis, limited by four membranes, the outermost one being connected to the endomembrane system. Recent cell imaging and proteomic studies suggest that at least some cytosolic LDs might be associated to the surface of the complex plastid, via still uncharacterized contact sites. The carbon length and number of double bonds of the acyl groups contained in the TAG molecules depend on their origin. De novo synthesis produces long-chain saturated or monounsaturated fatty acids (SFA, MUFA), whereas subsequent maturation processes lead to very long-chain polyunsaturated FA (VLC-PUFA). TAG composition in SFA, MUFA, and VLC-PUFA reflects therefore the metabolic context that gave rise to the formation of the LD, either via an early partitioning of carbon following FA de novo synthesis and/or a recycling of FA from membrane lipids, e.g., plastid galactolipids or endomembrane phosphor- or betaine lipids. In this review, we address the relationship between cytosolic LDs and the complex membrane compartmentalization within stramenopile cells, the metabolic routes leading to TAG accumulation, and the physiological conditions that trigger LD production, in response to various environmental factors.

Animals, protists and bacteria share marine biogeographic patterns

Over millennia, ecological and evolutionary mechanisms have shaped macroecological patterns across the tree of life. Research describing these patterns at both regional and global scales has traditionally focused on the study of metazoan species. Consequently, there is a limited understanding of cross-phylum biogeographic structuring and an escalating need to understand the macroecology of both microscopic and macroscopic organisms. Here we used environmental DNA (eDNA) metabarcoding to explore the biodiversity of marine metazoans, protists and bacteria along an extensive and highly heterogeneous coastline. Our results showed remarkably consistent biogeographic structure across the kingdoms of life despite billions of years of evolution. Analyses investigating the drivers of these patterns for each taxonomic kingdom found that environmental conditions (such as temperature) and, to a lesser extent, anthropogenic stressors (such as fishing pressure and pollution) explained some of the observed variation. Additionally, metazoans displayed biogeographic patterns that suggested regional biotic homogenization. Against the backdrop of global pervasive anthropogenic environmental change, our work highlights the importance of considering multiple domains of life to understand the maintenance and drivers of biodiversity patterns across broad taxonomic, ecological and geographical scales.

The sexual side of parasitic protists

Much of the vast evolutionary landscape occupied by Eukaryotes is dominated by protists. Though parasitism has arisen in many lineages, there are three main groups of parasitic protists of relevance to human and livestock health: the Apicomplexa, including the malaria parasite Plasmodium and coccidian pathogens of livestock such as Eimeria; the excavate flagellates, encompassing a diverse range of protist pathogens including trypanosomes, Leishmania, Giardia and Trichomonas; and the Amoebozoa, including pathogenic amoebae such as Entamoeba. These three groups represent separate, deep branches of the eukaryote tree, underlining their divergent evolutionary histories. Here, I explore what is known about sex in these three main groups of parasitic protists.

Mechanisms of enhancer action: the known and the unknown

Differential gene expression mechanisms ensure cellular differentiation and plasticity to shape ontogenetic and phylogenetic diversity of cell types. A key regulator of differential gene expression programs are the enhancers, the gene-distal cis-regulatory sequences that govern spatiotemporal and quantitative expression dynamics of target genes. Enhancers are widely believed to physically contact the target promoters to effect transcriptional activation. However, our understanding of the full complement of regulatory proteins and the definitive mechanics of enhancer action is incomplete. Here, we review recent findings to present some emerging concepts on enhancer action and also outline a set of outstanding questions.

Vestiges of the Bacterial Signal Recognition Particle-Based Protein Targeting in Mitochondria

The main bacterial pathway for inserting proteins into the plasma membrane relies on the signal recognition particle (SRP), composed of the Ffh protein and an associated RNA component, and the SRP-docking protein FtsY. Eukaryotes use an equivalent system of archaeal origin to deliver proteins into the endoplasmic reticulum, whereas a bacteria-derived SRP and FtsY function in the plastid. Here we report on the presence of homologs of the bacterial Ffh and FtsY proteins in various unrelated plastid-lacking unicellular eukaryotes, namely Heterolobosea, Alveida, Goniomonas, and Hemimastigophora. The monophyly of novel eukaryotic Ffh and FtsY groups, predicted mitochondrial localization experimentally confirmed for Naegleria gruberi, and a strong alphaproteobacterial affinity of the Ffh group, collectively suggest that they constitute parts of an ancestral mitochondrial signal peptide-based protein-targeting system inherited from the last eukaryotic common ancestor, but lost from the majority of extant eukaryotes. The ability of putative signal peptides, predicted in a subset of mitochondrial-encoded N. gruberi proteins, to target a reporter fluorescent protein into the endoplasmic reticulum of Trypanosoma brucei, likely through their interaction with the cytosolic SRP, provided further support for this notion. We also illustrate that known mitochondrial ribosome-interacting proteins implicated in membrane protein targeting in opisthokonts (Mba1, Mdm38, and Mrx15) are broadly conserved in eukaryotes and nonredundant with the mitochondrial SRP system. Finally, we identified a novel mitochondrial protein (MAP67) present in diverse eukaryotes and related to the signal peptide-binding domain of Ffh, which may well be a hitherto unrecognized component of the mitochondrial membrane protein-targeting machinery.

Ca2+-regulated mitochondrial carriers of ATP-Mg2+/Pi: Evolutionary insights in protozoans

In addition to its uptake across the Ca²⁺ uniporter, intracellular calcium signals can stimulate mitochondrial metabolism activating metabolite exchangers of the inner mitochondrial membrane belonging to the mitochondrial carrier family (SLC25). One of these Ca²⁺-regulated mitochondrial carriers (CaMCs) are the reversible ATP-Mg²⁺/Pi transporters, or SCaMCs, required for maintaining optimal adenine nucleotide (AdN) levels in the mitochondrial matrix representing an alternative transporter to the ADP/ATP translocases (AAC). This CaMC has a distinctive Calmodulin-like (CaM-like) domain fused to the carrier domain that makes its transport activity strictly dependent on cytosolic Ca²⁺ signals. Here we investigate about its origin analysing its distribution and features in unicellular eukaryotes. Unexpectedly, we find two types of ATP-Mg²⁺/Pi carriers, the canonical ones and shortened variants lacking the CaM-like domain. Phylogenetic analysis shows that both SCaMC variants have a common origin, unrelated to AACs, suggesting in turn that recurrent losses of the regulatory module have occurred in the different phyla. They are excluding variants that show a more limited distribution and less conservation than AACs. Interestingly, these truncated variants of SCaMC are found almost exclusively in parasitic protists, such as apicomplexans, kinetoplastides or animal-patogenic oomycetes, and in green algae, suggesting that its lost could be related to certain life-styles. In addition, we find an intricate structural diversity in these variants that may be associated with their pathogenicity. The consequences on SCaMC functions of these new SCaMC-b variants are discussed.

Pyrenoids: CO2-fixing phase separated liquid organelles

Pyrenoids are non-membrane bound organelles found in chloroplasts of algae and hornwort plants that can be seen by light-microscopy. Pyrenoids are formed by liquid-liquid phase separation (LLPS) of Rubisco, the primary CO₂ fixing enzyme, with an intrinsically disordered multivalent Rubisco-binding protein. Pyrenoids are the heart of algal and hornwort biophysical CO₂ concentrating mechanisms, which accelerate photosynthesis and mediate about 30% of global carbon fixation. Even though LLPS may underlie the apparent convergent evolution of pyrenoids, our current molecular understanding of pyrenoid formation comes from a single example, the model alga Chlamydomonas reinhardtii. In this review, we summarise current knowledge about pyrenoid assembly, regulation and structural organization in Chlamydomonas and highlight evidence that LLPS is the general principle underlying pyrenoid formation across algal lineages and hornworts. Detailed understanding of the principles behind pyrenoid assembly, regulation and structural organization within diverse lineages will provide a fundamental understanding of this biogeochemically important organelle and help guide ongoing efforts to engineer pyrenoids into crops to increase photosynthetic performance and yields.².

Cytoskeletal diversification across 1 billion years: What red algae can teach us about the cytoskeleton, and vice versa

The cytoskeleton has a central role in eukaryotic biology, enabling cells to organize internally, polarize, and translocate. Studying cytoskeletal machinery across the tree of life can identify common elements, illuminate fundamental mechanisms, and provide insight into processes specific to less-characterized organisms. Red algae represent an ancient lineage that is diverse, ecologically significant, and biomedically relevant. Recent genomic analysis shows that red algae have a surprising paucity of cytoskeletal elements, particularly molecular motors. Here, we review the genomic and cell biological evidence and propose testable models of how red algal cells might perform processes including cell motility, cytokinesis, intracellular transport, and secretion, given their reduced cytoskeletons. In addition to enhancing understanding of red algae and lineages that evolved from red algal endosymbioses (e.g., apicomplexan parasites), these ideas may also provide insight into cytoskeletal processes in animal cells.

Novel metric for hyperbolic phylogenetic tree embeddings

Advances in experimental technologies, such as DNA sequencing, have opened up new avenues for the applications of phylogenetic methods to various fields beyond their traditional application in evolutionary investigations, extending to the fields of development, differentiation, cancer genomics, and immunogenomics. Thus, the importance of phylogenetic methods is increasingly being recognized, and the development of a novel phylogenetic approach can contribute to several areas of research. Recently, the use of hyperbolic geometry has attracted attention in artificial intelligence research. Hyperbolic space can better represent a hierarchical structure compared to Euclidean space, and can therefore be useful for describing and analyzing a phylogenetic tree. In this study, we developed a novel metric that considers the characteristics of a phylogenetic tree for representation in hyperbolic space. We compared the performance of the proposed hyperbolic embeddings, general hyperbolic embeddings, and Euclidean embeddings, and confirmed that our method could be used to more precisely reconstruct evolutionary distance. We also demonstrate that our approach is useful for predicting the nearest-neighbor node in a partial phylogenetic tree with missing nodes. Furthermore, we proposed a novel approach based on our metric to integrate multiple trees for analyzing tree nodes or imputing missing distances. This study highlights the utility of adopting a geometric approach for further advancing the applications of phylogenetic methods.

Inferring the deep past from molecular data

There is an expectation that analyses of molecular sequences might be able to distinguish between alternative hypotheses for ancient relationships, but the phylogenetic methods used and types of data analyzed are of critical importance in any attempt to recover historical signal. Here, we discuss some common issues that can influence the topology of trees obtained when using overly simple models to analyze molecular data that often display complicated patterns of sequence heterogeneity. To illustrate our discussion, we have used three examples of inferred relationships which have changed radically as models and methods of analysis have improved. In two of these examples, the sister-group relationship between thermophilic Thermus and mesophilic Deinococcus, and the position of long-branch Microsporidia among eukaryotes, we show that recovering what is now generally considered to be the correct tree is critically dependent on the fit between model and data. In the third example, the position of eukaryotes in the tree of life, the hypothesis that is currently supported by the best available methods is fundamentally different from the classical view of relationships between major cellular domains. Since heterogeneity appears to be pervasive and varied among all molecular sequence data, and even the best available models can still struggle to deal with some problems, the issues we discuss are generally relevant to phylogenetic analyses. It remains essential to maintain a critical attitude to all trees as hypotheses of relationship that may change with more data and better methods.

A molecular timescale for eukaryote evolution with implications for the origin of red algal-derived plastids

In modern oceans, eukaryotic phytoplankton is dominated by lineages with red algal-derived plastids such as diatoms, dinoflagellates, and coccolithophores. Despite the ecological importance of these groups and many others representing a huge diversity of forms and lifestyles, we still lack a comprehensive understanding of their evolution and how they obtained their plastids. New hypotheses have emerged to explain the acquisition of red algal-derived plastids by serial endosymbiosis, but the chronology of these putative independent plastid acquisitions remains untested. Here, we establish a timeframe for the origin of red algal-derived plastids under scenarios of serial endosymbiosis, using Bayesian molecular clock analyses applied on a phylogenomic dataset with broad sampling of eukaryote diversity. We find that the hypotheses of serial endosymbiosis are chronologically possible, as the stem lineages of all red plastid-containing groups overlap in time. This period in the Meso- and Neoproterozoic Eras set the stage for the later expansion to dominance of red algal-derived primary production in the contemporary oceans, which profoundly altered the global geochemical and ecological conditions of the Earth.

The actomyosin interface contains an evolutionary conserved core and an ancillary interface involved in specificity

Plasmodium falciparum, the causative agent of malaria, moves by an atypical process called gliding motility. Actomyosin interactions are central to gliding motility. However, the details of these interactions remained elusive until now. Here, we report an atomic structure of the divergent Plasmodium falciparum actomyosin system determined by electron cryomicroscopy at the end of the powerstroke (Rigor state). The structure provides insights into the detailed interactions that are required for the parasite to produce the force and motion required for infectivity. Remarkably, the footprint of the myosin motor on filamentous actin is conserved with respect to higher eukaryotes, despite important variability in the Plasmodium falciparum myosin and actin elements that make up the interface. Comparison with other actomyosin complexes reveals a conserved core interface common to all actomyosin complexes, with an ancillary interface involved in defining the spatial positioning of the motor on actin filaments.

Plasmodium falciparum moves by an atypical process called gliding motility which comprises of atypical myosin A (PfMyoA) and filaments of the dynamic and divergent PfActin-1 (PfAct1). Here authors present the cryo-EM structure of PfMyoA bound to filamentous PfAct1 stabilized with jasplakinolide and provide insights into the interactions that are required for the parasite to produce the force and motion required for infectivity.

The iron-sulfur scaffold protein HCF101 unveils the complexity of organellar evolution in SAR, Haptista and Cryptista

Background

Nbp35-like proteins (Nbp35, Cfd1, HCF101, Ind1, and AbpC) are P-loop NTPases that serve as components of iron-sulfur cluster (FeS) assembly machineries. In eukaryotes, Ind1 is present in mitochondria, and its function is associated with the assembly of FeS clusters in subunits of respiratory Complex I, Nbp35 and Cfd1 are the components of the cytosolic FeS assembly (CIA) pathway, and HCF101 is involved in FeS assembly of photosystem I in plastids of plants (chHCF101). The AbpC protein operates in Bacteria and Archaea. To date, the cellular distribution of these proteins is considered to be highly conserved with only a few exceptions.

Results

We searched for the genes of all members of the Nbp35-like protein family and analyzed their targeting sequences. Nbp35 and Cfd1 were predicted to reside in the cytoplasm with some exceptions of Nbp35 localization to the mitochondria; Ind1was found in the mitochondria, and HCF101 was predicted to reside in plastids (chHCF101) of all photosynthetically active eukaryotes. Surprisingly, we found a second HCF101 paralog in all members of Cryptista, Haptista, and SAR that was predicted to predominantly target mitochondria (mHCF101), whereas Ind1 appeared to be absent in these organisms. We also identified a few exceptions, as apicomplexans possess mHCF101 predicted to localize in the cytosol and Nbp35 in the mitochondria. Our predictions were experimentally confirmed in selected representatives of Apicomplexa (Toxoplasma gondii), Stramenopila (Phaeodactylum tricornutum, Thalassiosira pseudonana), and Ciliophora (Tetrahymena thermophila) by tagging proteins with a transgenic reporter. Phylogenetic analysis suggested that chHCF101 and mHCF101 evolved from a common ancestral HCF101 independently of the Nbp35/Cfd1 and Ind1 proteins. Interestingly, phylogenetic analysis supports rather a lateral gene transfer of ancestral HCF101 from bacteria than its acquisition being associated with either α-proteobacterial or cyanobacterial endosymbionts.

Conclusion

Our searches for Nbp35-like proteins across eukaryotic lineages revealed that SAR, Haptista, and Cryptista possess mitochondrial HCF101. Because plastid localization of HCF101 was only known thus far, the discovery of its mitochondrial paralog explains confusion regarding the presence of HCF101 in organisms that possibly lost secondary plastids (e.g., ciliates, Cryptosporidium) or possess reduced nonphotosynthetic plastids (apicomplexans).

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-021-01777-x.

Ancestral sequence reconstruction - An underused approach to understand the evolution of gene function in plants?

Whilst substantial research effort has been placed on understanding the interactions of plant proteins with their molecular partners, relatively few studies in plants - by contrast to work in other organisms - address how these interactions evolve. It is thought that ancestral proteins were more promiscuous than modern proteins and that specificity often evolved following gene duplication and subsequent functional refining. However, ancestral protein resurrection studies have found that some modern proteins have evolved de novo from ancestors lacking those functions. Intriguingly, the new interactions evolved as a consequence of just a few mutations and, as such, acquisition of new functions appears to be neither difficult nor rare, however, only a few of them are incorporated into biological processes before they are lost to subsequent mutations. Here, we detail the approach of ancestral sequence reconstruction (ASR), providing a primer to reconstruct the sequence of an ancestral gene. We will present case studies from a range of different eukaryotes before discussing the few instances where ancestral reconstructions have been used in plants. As ASR is used to dig into the remote evolutionary past, we will also present some alternative genetic approaches to investigate molecular evolution on shorter timescales. We argue that the study of plant secondary metabolism is particularly well suited for ancestral reconstruction studies. Indeed, its ancient evolutionary roots and highly diverse landscape provide an ideal context in which to address the focal issue around the emergence of evolutionary novelties and how this affects the chemical diversification of plant metabolism.

A novel predicted ADP-ribosyltransferase-like family conserved in eukaryotic evolution

The presence of many completely uncharacterized proteins, even in well-studied organisms such as humans, seriously hampers full understanding of the functioning of the living cells. ADP-ribosylation is a common post-translational modification of proteins; also nucleic acids and small molecules can be modified by the covalent attachment of ADP-ribose. This modification, important in cellular signalling and infection processes, is usually executed by enzymes from the large superfamily of ADP-ribosyltransferases (ARTs). Here, using bioinformatics approaches, we identify a novel putative ADP-ribosyltransferase family, conserved in eukaryotic evolution, with a divergent active site. The hallmark of these proteins is the ART domain nestled between flanking leucine-rich repeat (LRR) domains. LRRs are typically involved in innate immune surveillance. The novel family appears as putative novel ADP-ribosylation-related actors, most likely pseudoenzymes. Sequence divergence and lack of clearly detectable “classical” ART active site suggests the novel domains are pseudoARTs, yet atypical ART activity, or alternative enzymatic activity cannot be excluded. We propose that this family, including its human member LRRC9, may be involved in an ancient defense mechanism, with analogies to the innate immune system, and coupling pathogen detection to ADP-ribosyltransfer or other signalling mechanisms.

A single-cell genomics pipeline for environmental microbial eukaryotes

Single-cell sequencing of environmental microorganisms is an essential component of the microbial ecology toolkit. However, large-scale targeted single-cell sequencing for the whole-genome recovery of uncultivated eukaryotes is lagging. The key challenges are low abundance in environmental communities, large complex genomes, and cell walls that are difficult to break. We describe a pipeline composed of state-of-the art single-cell genomics tools and protocols optimized for poorly studied and uncultivated eukaryotic microorganisms that are found at low abundance. This pipeline consists of seven distinct steps, beginning with sample collection and ending with genome annotation, each equipped with quality review steps to ensure high genome quality at low cost. We tested and evaluated each step on environmental samples and cultures of early-diverging lineages of fungi and Chromista/SAR. We show that genomes produced using this pipeline are almost as good as complete reference genomes for functional and comparative genomics for environmental microbial eukaryotes.

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We optimized single-cell methodology using a broad sample range, for EME

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We combined bioinformatic and bench protocols into a concise workflow

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We benchmarked the pipeline and used it on environmental samples

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We selected a set of QC criteria for best genome quality prediction

Novel Endosymbionts in Rhizarian Amoebae Imply Universal Infection of Unrelated Free-Living Amoebae by Legionellales

Legionellales-infected water is a frequent cause of local outbreaks of Legionnaires’ disease and Pontiac fever. Decontaminations are difficult because Legionellales reproduce in eukaryotic microorganisms (protists). Most often, Legionellales have been isolated from amoebae; however, the culture-based sampling methods are taxonomically biased. Sequencing studies show that amoebae in the cercozoan class Thecofilosea are dominant in soils and wastewater treatment plants, prompting us to screen their capability to serve as potential hosts of endosymbiotic bacteria. Environmental isolates of Thecofilosea contained a surprising richness of endosymbiotic Legionellales, including Legionella. Considering the widespread dispersal of Legionellales in apparently unrelated amoeboid protist taxa, it appears that the morphotype and not the evolutionary origin of amoebae determines their suitability as hosts for Legionellales. We further provide a protocol for gnotobiotic cultivation of Legionellales and their respective hosts, facilitating future genomic and transcriptomic research of host–symbiont relationships.

CARD-FISH in the Sequencing Era: Opening a New Universe of Protistan Ecology

Phagotrophic protists are key players in aquatic food webs. Although sequencing-based studies have revealed their enormous diversity, ecological information on in situ abundance, feeding modes, grazing preferences, and growth rates of specific lineages can be reliably obtained only using microscopy-based molecular methods, such as Catalyzed Reporter Deposition-Fluorescence in situ Hybridization (CARD-FISH). CARD-FISH is commonly applied to study prokaryotes, but less so to microbial eukaryotes. Application of this technique revealed that Paraphysomonas or Spumella-like chrysophytes, considered to be among the most prominent members of protistan communities in pelagic environments, are omnipresent but actually less abundant than expected, in contrast to little known groups such as heterotrophic cryptophyte lineages (e.g., CRY1), cercozoans, katablepharids, or the MAST lineages. Combination of CARD-FISH with tracer techniques and application of double CARD-FISH allow visualization of food vacuole contents of specific flagellate groups, thus considerably challenging our current, simplistic view that they are predominantly bacterivores. Experimental manipulations with natural communities revealed that larger flagellates are actually omnivores ingesting both prokaryotes and other protists. These new findings justify our proposition of an updated model of microbial food webs in pelagic environments, reflecting more authentically the complex trophic interactions and specific roles of flagellated protists, with inclusion of at least two additional trophic levels in the nanoplankton size fraction. Moreover, we provide a detailed CARD-FISH protocol for protists, exemplified on mixo- and heterotrophic nanoplanktonic flagellates, together with tips on probe design, a troubleshooting guide addressing most frequent obstacles, and an exhaustive list of published probes targeting protists.

Utilization of cobalamin is ubiquitous in early-branching fungal phyla

Cobalamin is a cofactor present in essential metabolic pathways in animals and one of the water-soluble vitamins. It is a complex compound synthesized solely by prokaryotes. Cobalamin dependence is scattered across the tree of life. In particular, fungi and plants were deemed devoid of cobalamin. We demonstrate that cobalamin is utilized by all non-Dikarya fungi lineages. This observation is supported by the genomic presence of both B12-dependent enzymes and cobalamin modifying enzymes. Fungal cobalamin-dependent enzymes are highly similar to their animal homologs. Phylogenetic analyses support a scenario of vertical inheritance of the cobalamin usage with several losses. Cobalamin usage was probably lost in Mucorinae and at the base of Dikarya which groups most of the model organisms and which hindered B12-dependent metabolism discovery in fungi. Our results indicate that cobalamin dependence was a widely distributed trait at least in Opisthokonta, across diverse microbial eukaryotes and was likely present in the LECA.

Development of an absolute quantification method for ribosomal RNA gene copy numbers per eukaryotic single cell by digital PCR

Recent increase of Harmful Algal Blooms (HAB) causes world-wide ecological, economical, and health issues, and more attention is paid to frequent coastal monitoring for the early detection of HAB species to prevent or reduce such impacts. Use of molecular tools in addition to traditional microscopy-based observation has become one of the promising methodologies for coastal monitoring. However, as ribosomal RNA (rRNA) genes are commonly targeted in molecular studies, variability in the rRNA gene copy number within and between species must be considered to provide quantitative information in quantitative PCR (qPCR), digital PCR (dPCR), and metabarcoding analyses. Currently, this information is only available for a limited number of species. The present study utilized a dPCR technology to quantify copy numbers of rRNA genes per single cell in 16 phytoplankton species, the majority of which are toxin-producers, using a newly developed universal primer set accompanied by a labeled probe with a fluorophore and a double-quencher. In silico PCR using the newly developed primers allowed the detection of taxa from 8 supergroups, demonstrating universality and broad coverage of the primer set. Chelex buffer was found to be suitable for DNA extraction to obtain DNA fragments with suitable size to avoid underestimation of the copy numbers. The study successfully demonstrated the first comparison of absolute quantification of 18S rRNA copy numbers per cell from 16 phytoplankton species by the dPCR technology.

RNA Viruses in Aquatic Unicellular Eukaryotes

Increasing sequence information indicates that RNA viruses constitute a major fraction of marine virus assemblages. However, only 12 RNA virus species have been described, infecting known host species of marine single-celled eukaryotes. Eight of these use diatoms as hosts, while four are resident in dinoflagellate, raphidophyte, thraustochytrid, or prasinophyte species. Most of these belong to the order Picornavirales, while two are divergent and fall into the families Alvernaviridae and Reoviridae. However, a very recent study has suggested that there is extraordinary diversity in aquatic RNA viromes, describing thousands of viruses, many of which likely use protist hosts. Thus, RNA viruses are expected to play a major ecological role for marine unicellular eukaryotic hosts. In this review, we describe in detail what has to date been discovered concerning viruses with RNA genomes that infect aquatic unicellular eukaryotes.

Quantifying the taxonomic bias in enzymology

The ongoing biotechnological revolution is rooted in our knowledge of enzymes. However, metagenomics is showing how little we know about Earth's enzyme repertoire. Deep sequencing has revolutionized our view of the tree of life. The genomes of newly‐discovered organisms are replete with novel sequences, emphasizing the trove of enzyme structures and functions waiting to be explored by biochemists. Here, we sought to draw attention to the vastness of the “enzymatic dark matter” within the tree of life by placing enzymological knowledge in the context of phylogeny. We used kinetic parameters from the BRaunschweig ENzyme DAtabase (BRENDA) as our proxy for enzymological knowledge. Mapping 12,677 BRENDA entries onto the phylogenetic tree revealed that 55% of these data were from eukaryotes, even though they are the least diverse part of the tree. At the next taxonomic level, only four of 18 archaeal phyla and 24 of 111 bacterial phyla are represented in the BRENDA dataset. One phylum, the Proteobacteria, accounts for over half of all bacterial entries. Similarly, the supergroup Amorphea, which includes animals and fungi, contains over half the data on eukaryotes. Many major taxonomic groups are notable for their complete absence from BRENDA, including the ultra‐diverse bacterial Candidate Phyla Radiation. At the species level, five mammals (including human) contribute 15% of BRENDA entries. The taxonomic bias in enzymology is strong, but in the era of gene synthesis we now have the tools to address it. Doing so promises to enrich our biochemical understanding of life and uncover powerful new biocatalysts.

HERMES: An improved method to test mitochondrial genome molecular synapomorphies among clades

Mitochondrial chromosomes have diversified among eukaryotes and many different architectures and features are now acknowledged for this genome. Here we present the improved HERMES index, which can measure and quantify the amount of molecular change experienced by mitochondrial genomes. We test the improved approach with ten molecular phylogenetic studies based on complete mitochondrial genomes, representing six bilaterian Phyla. In most cases, HERMES analysis spotted out clades or single species with peculiar molecular synapomorphies, allowing to identify phylogenetic and ecological patterns. The software presented herein handles linear, circular, and multi-chromosome genomes, thus widening the HERMES scope to the complete eukaryotic domain.

Multiple Origins of Extracellular DNA Traps

Extracellular DNA traps (ETs) are evolutionarily conserved antimicrobial mechanisms present in protozoa, plants, and animals. In this review, we compare their similarities in species of different taxa, and put forward the hypothesis that ETs have multiple origins. Our results are consistent with a process of evolutionary convergence in multicellular organisms through the application of a congruency test. Furthermore, we discuss why multicellularity is related to the presence of a mechanism initiating the formation of ETs.

Molecular Pathotyping of Plasmodiophora brassicae-Genomes, Marker Genes, and Obstacles

Here we review the usefulness of the currently available genomic information for the molecular identification of pathotypes. We focused on effector candidates and genes implied to be pathotype specific and tried to connect reported marker genes to Plasmodiophora brassicae genome information. The potentials for practical applications, current obstacles and future perspectives are discussed.

Determinants of genome-wide distribution and evolution of uORFs in eukaryotes

Upstream open reading frames (uORFs) play widespread regulatory functions in modulating mRNA translation in eukaryotes, but the principles underlying the genomic distribution and evolution of uORFs remain poorly understood. Here, we analyze ~17 million putative canonical uORFs in 478 eukaryotic species that span most of the extant taxa of eukaryotes. We demonstrate how positive and purifying selection, coupled with differences in effective population size (Ne), has shaped the contents of uORFs in eukaryotes. Besides, gene expression level is important in influencing uORF occurrences across genes in a species. Our analyses suggest that most uORFs might play regulatory roles rather than encode functional peptides. We also show that the Kozak sequence context of uORFs has evolved across eukaryotic clades, and that noncanonical uORFs tend to have weaker suppressive effects than canonical uORFs in translation regulation. This study provides insights into the driving forces underlying uORF evolution in eukaryotes.

Mitochondrial copper and phosphate transporter specificity was defined early in the evolution of eukaryotes

The mitochondrial carrier family protein SLC25A3 transports both copper and phosphate in mammals, yet in Saccharomyces cerevisiae the transport of these substrates is partitioned across two paralogs: PIC2 and MIR1. To understand the ancestral state of copper and phosphate transport in mitochondria, we explored the evolutionary relationships of PIC2 and MIR1 orthologs across the eukaryotic tree of life. Phylogenetic analyses revealed that PIC2-like and MIR1-like orthologs are present in all major eukaryotic supergroups, indicating an ancient gene duplication created these paralogs. To link this phylogenetic signal to protein function, we used structural modeling and site-directed mutagenesis to identify residues involved in copper and phosphate transport. Based on these analyses, we generated an L175A variant of mouse SLC25A3 that retains the ability to transport copper but not phosphate. This work highlights the utility of using an evolutionary framework to uncover amino acids involved in substrate recognition by mitochondrial carrier family proteins.

Silicon Cycling in Soils Revisited

Silicon (Si) speciation and availability in soils is highly important for ecosystem functioning, because Si is a beneficial element for plant growth. Si chemistry is highly complex compared to other elements in soils, because Si reaction rates are relatively slow and dependent on Si species. Consequently, we review the occurrence of different Si species in soil solution and their changes by polymerization, depolymerization, and condensation in relation to important soil processes. We show that an argumentation based on thermodynamic endmembers of Si dependent processes, as currently done, is often difficult, because some reactions such as mineral crystallization require months to years (sometimes even centuries or millennia). Furthermore, we give an overview of Si reactions in soil solution and the predominance of certain solid compounds, which is a neglected but important parameter controlling the availability, reactivity, and function of Si in soils. We further discuss the drivers of soil Si cycling and how humans interfere with these processes. The soil Si cycle is of major importance for ecosystem functioning; therefore, a deeper understanding of drivers of Si cycling (e.g., predominant speciation), human disturbances and the implication for important soil properties (water storage, nutrient availability, and micro aggregate stability) is of fundamental relevance.

Determinants, and implications, of the shape and size of thylakoids and cristae

Thylakoids are flattened sacs isolated from other membranes; cristae are attached to the rest of the inner mitochondrial membrane by the crista junction, but the crista lumen is separated from the intermembrane space. The shape of thylakoids and cristae involves membranes with small (5-30 nm) radii of curvature. While the mechanism of curvature is not entirely clear, it seems to be largely a function of Curt proteins in thylakoids and Mitochondrial Organising Site and Crista Organising Centre proteins and oligomeric F_OF₁ ATP synthase in cristae. A subordinate, or minimal, role is attributable to lipids with areas of their head group area greater (convex leaflet) or smaller (concave leaflet) than the area of the lipid tail; examples of the latter group are monogalactosyldiglyceride in thylakoids and cardiolipin in cristae. The volume per unit area on the lumen side of the membrane is less than that of the chloroplast stroma or cyanobacterial cytosol for thylakoids, and mitochondrial matrix for cristae. A low volume per unit area of thylakoids and cristae means a small lumen width that is the average of wider spaces between lipid parts of the membranes and the narrower gaps dominated by extra-membrane components of transmembrane proteins. These structural constraints have important implications for the movement of the electron carriers plastocyanin and cytochrome c₆ (thylakoids) and cytochrome c (cristae) and hence the separation of the membrane-associated electron donors to, and electron acceptors from, these water-soluble electron carriers. The donor/acceptor pairs, are the cytochrome fb₆Fe_nh complex and P₇₀₀⁺ in thylakoids, and Complex III and Complex IV of cristae. The other energy flux parallel to the membranes is that of the proton motive force generated by redox-powered H⁺ pumps into the lumen to the proton motive force use in ATP synthesis by H⁺ flux from the lumen through the ATP synthase. For both the electron transport and proton motive force movement, concentration differences of reduced and oxidised electron carriers and protonated and deprotonated pH buffers are involved. The need for diffusion along a congested route of these energy transfer agents may limit the separation of sources and sinks parallel to the membranes of thylakoids and cristae.

Convergence of sphingolipid desaturation across over 500 million years of plant evolution

For plants, acclimation to low temperatures is fundamental to survival. This process involves the modification of lipids to maintain membrane fluidity. We previously identified a new cold-induced putative desaturase in Physcomitrium (Physcomitrella) patens. Lipid profiles of null mutants of this gene lack sphingolipids containing monounsaturated C24 fatty acids, classifying the new protein as sphingolipid fatty acid denaturase (PpSFD). PpSFD mutants showed a cold-sensitive phenotype as well as higher susceptibility to the oomycete Pythium, assigning functions in stress tolerance for PpSFD. Ectopic expression of PpSFD in the Atads2.1 (acyl coenzyme A desaturase-like 2) Arabidopsis thaliana mutant functionally complemented its cold-sensitive phenotype. While these two enzymes catalyse a similar reaction, their evolutionary origin is clearly different since AtADS2 is a methyl-end desaturase whereas PpSFD is a cytochrome b₅ fusion desaturase. Altogether, we suggest that adjustment of membrane fluidity evolved independently in mosses and seed plants, which diverged more than 500 million years ago.

Abundantly expressed class of noncoding RNAs conserved through the multicellular evolution of dictyostelid social amoebas

Aggregative multicellularity has evolved multiple times in diverse groups of eukaryotes, exemplified by the well-studied development of dictyostelid social amoebas, for example, Dictyostelium discoideum However, it is still poorly understood why multicellularity emerged in these amoebas while the majority of other members of Amoebozoa are unicellular. Previously, a novel type of noncoding RNA, Class I RNAs, was identified in D. discoideum and shown to be important for normal multicellular development. Here, we investigated Class I RNA evolution and its connection to multicellular development. We identified a large number of new Class I RNA genes by constructing a covariance model combined with a scoring system based on conserved upstream sequences. Multiple genes were predicted in representatives of each major group of Dictyostelia and expression analysis confirmed that our search approach identifies expressed Class I RNA genes with high accuracy and sensitivity and that the RNAs are developmentally regulated. Further studies showed that Class I RNAs are ubiquitous in Dictyostelia and share highly conserved structure and sequence motifs. In addition, Class I RNA genes appear to be unique to dictyostelid social amoebas because they could not be identified in outgroup genomes, including their closest known relatives. Our results show that Class I RNA is an ancient class of ncRNAs, likely to have been present in the last common ancestor of Dictyostelia dating back at least 600 million years. Based on previous functional analyses and the presented evolutionary investigation, we hypothesize that Class I RNAs were involved in evolution of multicellularity in Dictyostelia.

Evolution of ribosomal protein network architectures

To perform an accurate protein synthesis, ribosomes accomplish complex tasks involving the long-range communication between its functional centres such as the peptidyl transfer centre, the tRNA bindings sites and the peptide exit tunnel. How information is transmitted between these sites remains one of the major challenges in current ribosome research. Many experimental studies have revealed that some r-proteins play essential roles in remote communication and the possible involvement of r-protein networks in these processes have been recently proposed. Our phylogenetic, structural and mathematical study reveals that of the three kingdom's r-protein networks converged towards non-random graphs where r-proteins collectively coevolved to optimize interconnection between functional centres. The massive acquisition of conserved aromatic residues at the interfaces and along the extensions of the newly connected eukaryotic r-proteins also highlights that a strong selective pressure acts on their sequences probably for the formation of new allosteric pathways in the network.

Glycomics, Glycoproteomics, and Glycogenomics: An Inter-Taxa Evolutionary Perspective

Glycosylation is a highly diverse set of co- and posttranslational modifications of proteins. For mammalian glycoproteins, glycosylation is often site-, tissue-, and species-specific and diversified by microheterogeneity. Multitudinous biochemical, cellular, physiological, and organismic effects of their glycans have been revealed, either intrinsic to the carrier proteins or mediated by endogenous reader proteins with carbohydrate recognition domains. Furthermore, glycans frequently form the first line of access by or defense from foreign invaders, and new roles for nucleocytoplasmic glycosylation are blossoming. We now know enough to conclude that the same general principles apply in invertebrate animals and unicellular eukaryotes-different branches of which spawned the plants or fungi and animals. The two major driving forces for exploring the glycomes of invertebrates and protists are (i) to understand the biochemical basis of glycan-driven biology in these organisms, especially of pathogens, and (ii) to uncover the evolutionary relationships between glycans, their biosynthetic enzyme genes, and biological functions for new glycobiological insights. With an emphasis on emerging areas of protist glycobiology, here we offer an overview of glycan diversity and evolution, to promote future access to this treasure trove of glycobiological processes.

The Ecology and Evolution of Amoeba-Bacterium Interactions

Amoebae are protists that have complicated relationships with bacteria, covering the whole spectrum of symbiosis. Amoeba-bacterium interactions contribute to the study of predation, symbiosis, pathogenesis, and human health. Given the complexity of their relationships, it is necessary to understand the ecology and evolution of their interactions. In this paper, we provide an updated review of the current understanding of amoeba-bacterium interactions. We start by discussing the diversity of amoebae and their bacterial partners. We also define three types of ecological interactions between amoebae and bacteria and discuss their different outcomes. Finally, we focus on the implications of amoeba-bacterium interactions on human health, horizontal gene transfer, drinking water safety, and the evolution of symbiosis. In conclusion, amoeba-bacterium interactions are excellent model systems to investigate a wide range of scientific questions. Future studies should utilize advanced techniques to address research gaps, such as detecting hidden diversity, lack of amoeba genomes, and the impacts of amoeba predation on the microbiome.

αα-Hub domains and intrinsically disordered proteins: A decisive combo

Hub proteins are central nodes in protein-protein interaction networks with critical importance to all living organisms. Recently, a new group of folded hub domains, the αα-hubs, was defined based on a shared αα-hairpin supersecondary structural foundation. The members PAH, RST, TAFH, NCBD, and HHD are found in large proteins such as Sin3, RCD1, TAF4, CBP, and harmonin, which organize disordered transcriptional regulators and membrane scaffolds in interactomes of importance to human diseases and plant quality. In this review, studies of structures, functions, and complexes across the αα-hubs are described and compared to provide a unified description of the group. This analysis expands the associated molecular concepts of "one domain-one binding site", motif-based ligand binding, and coupled folding and binding of intrinsically disordered ligands to additional concepts of importance to signal fidelity. These include context, motif reversibility, multivalency, complex heterogeneity, synergistic αα-hub:ligand folding, accessory binding sites, and supramodules. We propose that these multifaceted protein-protein interaction properties are made possible by the characteristics of the αα-hub fold, including supersite properties, dynamics, variable topologies, accessory helices, and malleability and abetted by adaptability of the disordered ligands. Critically, these features provide additional filters for specificity. With the presentations of new concepts, this review opens for new research questions addressing properties across the group, which are driven from concepts discovered in studies of the individual members. Combined, the members of the αα-hubs are ideal models for deconvoluting signal fidelity maintained by folded hubs and their interactions with intrinsically disordered ligands.

Step-by-Step Evolution of Telomeres: Lessons from Yeasts

In virtually every eukaryotic species, the ends of nuclear chromosomes are protected by telomeres, nucleoprotein structures counteracting the end-replication problem and suppressing recombination and undue DNA repair. Although in most cases, the primary structure of telomeric DNA is conserved, there are several exceptions to this rule. One is represented by the telomeric repeats of ascomycetous yeasts, which encompass a great variety of sequences, whose evolutionary origin has been puzzling for several decades. At present, the key questions concerning the driving force behind their rapid evolution and the means of co-evolution of telomeric repeats and telomere-binding proteins remain largely unanswered. Previously published studies addressed mostly the general concepts of the evolutionary origin of telomeres, key properties of telomeric proteins as well as the molecular mechanisms of telomere maintenance; however, the evolutionary process itself has not been analyzed thoroughly. Here, we aimed to inspect the evolution of telomeres in ascomycetous yeasts from the subphyla Saccharomycotina and Taphrinomycotina, with special focus on the evolutionary origin of species-specific telomeric repeats. We analyzed the sequences of telomeric repeats from 204 yeast species classified into 20 families and as a result, we propose a step-by-step model, which integrates the diversity of telomeric repeats, telomerase RNAs, telomere-binding protein complexes and explains a propensity of certain species to generate the repeat heterogeneity within a single telomeric array.

High Sequence Divergence but Limited Architectural Rearrangements in Organelle Genomes of Cyanophora (Glaucophyta) Species

Cyanophora is the glaucophyte model taxon. Following the sequencing of the nuclear genome of C. paradoxa, studies based on single organelle and nuclear molecular markers revealed previously unrecognized species diversity within this glaucophyte genus. Here, we present the complete plastid (ptDNA) and mitochondrial (mtDNA) genomes of C. kugrensii, C. sudae, and C. biloba. The respective sizes and coding capacities of both ptDNAs and mtDNAs are conserved among Cyanophora species with only minor differences due to specific gene duplications. Organelle phylogenomic analyses consistently recover the species C. kugrensii and C. paradoxa as a clade and C. sudae and C. biloba as a separate group. The phylogenetic affiliations of the four Cyanophora species are consistent with architectural similarities shared at the organelle genomic level. Genetic distance estimations from both organelle sequences are also consistent with phylogenetic and architecture evidence. Comparative analyses confirm that the Cyanophora mitochondrial genes accumulate substitutions at 3-fold higher rates than plastid counterparts, suggesting that mtDNA markers are more appropriate to investigate glaucophyte diversity and evolutionary events that occur at a population level. The study of complete organelle genomes is becoming the standard for species delimitation and is particularly relevant to study cryptic diversity in microbial groups.

Environmental drivers of plankton protist communities along latitudinal and vertical gradients in the oldest and deepest freshwater lake

Identifying which abiotic and biotic factors determine microbial community assembly is crucial to understand ecological processes and predict how communities will respond to environmental change. While global surveys aim at addressing this question in the world's oceans, equivalent studies in large freshwater systems are virtually lacking. Being the oldest, deepest and most voluminous freshwater lake on Earth, Lake Baikal offers a unique opportunity to test the effect of horizontal versus vertical gradients in community structure. Here, we characterized the structure of planktonic microbial eukaryotic communities (0.2-30 μm cell size) along a North-South latitudinal gradient (~600 km) from samples collected in coastal and pelagic waters and from surface to the deepest zones (5-1400 m) using an 18S rRNA gene metabarcoding approach. Our results show complex and diverse protist communities dominated by alveolates (ciliates and dinoflagellates), ochrophytes and holomycotan lineages, with cryptophytes, haptophytes, katablepharids and telonemids in moderate abundance and many low-frequency lineages, including several typical marine members, such as diplonemids, syndinians and radiolarians. Depth had a strong significant effect on protist community stratification. By contrast, the effect of the latitudinal gradient was marginal and no significant difference was observed between coastal and surface open water communities. Co-occurrence network analyses showed that epipelagic communities were significantly more interconnected than communities from the dark water column and suggest specific biotic interactions between autotrophic, heterotrophic and parasitic lineages that influence protist community structure. Since climate change is rapidly affecting Siberia and Lake Baikal, our comprehensive protist survey constitutes a useful reference to monitor ongoing community shifts.

Description of Imasa heleensis, gen. nov., sp. nov. (Imasidae, fam. nov.), a Deep-Branching Marine Malawimonad and Possible Key Taxon in Understanding Early Eukaryotic Evolution

Malawimonadida is a deep-level (arguably "kingdom-scale") lineage of eukaryotes whose phylogenetic affinities are uncertain but of great evolutionary interest, as the group is suspected to branch close to the root of the tree of eukaryotes. Part of the difficulty in placing Malawimonadida phylogenetically is its tiny circumscription: at present, it comprises only two described and one cultured but undescribed species, all of them are freshwater suspension-feeding nanoflagellates. In this study, we cultivated and characterised Imasa heleensis gen. nov., sp. nov. (Imasidae fam. nov.), the first marine malawimonad to be described. Light and electron microscopy observations show that Imasa is largely similar to other malawimonads, but more frequently adheres to the substrate, often by means of a pliable posterior extension. Phylogenetic analyses based on two ribosomal RNA genes and four translated protein-coding genes using three different taxon sets place Imasa as sister to the three freshwater malawimonad strains with strong support. Imasa's mitochondrial genome is circular-mapping and shows a similar gene complement to other known malawimonads. We conclude that Imasa represents an important expansion of the range of taxa available for future evolutionary study.

Inorganic carbon concentrating mechanisms in free-living and symbiotic dinoflagellates and chromerids

Photosynthetic dinoflagellates are ecologically and biogeochemically important in marine and freshwater environments. However, surprisingly little is known of how this group acquires inorganic carbon or how these diverse processes evolved. Consequently, how CO₂ availability ultimately influences the success of dinoflagellates over space and time remains poorly resolved compared to other microalgal groups. Here we review the evidence. Photosynthetic core dinoflagellates have a Form II RuBisCO (replaced by Form IB or Form ID in derived dinoflagellates). The in vitro kinetics of the Form II RuBisCO from dinoflagellates are largely unknown, but dinoflagellates with Form II (and other) RuBisCOs have inorganic carbon concentrating mechanisms (CCMs), as indicated by in vivo internal inorganic C accumulation and affinity for external inorganic C. However, the location of the membrane(s) at which the essential active transport component(s) of the CCM occur(s) is (are) unresolved; isolation and characterization of functionally competent chloroplasts would help in this respect. Endosymbiotic Symbiodiniaceae (in Foraminifera, Acantharia, Radiolaria, Ciliata, Porifera, Acoela, Cnidaria, and Mollusca) obtain inorganic C by transport from seawater through host tissue. In corals this transport apparently provides an inorganic C concentration around the photobiont that obviates the need for photobiont CCM. This is not the case for tridacnid bivalves, medusae, or, possibly, Foraminifera. Overcoming these long-standing knowledge gaps relies on technical advances (e.g., the in vitro kinetics of Form II RuBisCO) that can functionally track the fate of inorganic C forms.

Free-living amoebae and other neglected protistan pathogens: Health emergency signals?

Protistan parasites have an undisputed global health impact. However, outside of a few key exceptions, e.g. the agent of malaria, most of these infectious agents are neglected as important health threats. The Symposium entitled "Free-living amoebae and neglected pathogenic protozoa: health emergency signals?" held at the European Congress of Protistology in Rome, July 2019, brought together researchers addressing scientific and clinical questions about some of these fascinating organisms. Topics presented included the molecular basis of pathogenicity in Acanthamoeba; genomics of Naegleria fowleri; and epidemiology of poorly diagnosed enteric protistan species, including Giardia, Cryptosporidium, Blastocystis, Dientamoeba. The Symposium aim was to excite the audience about the opportunities and challenges of research in these underexplored organisms and to underline the public health implications of currently under-appreciated protistan infections. The major take home message is that any knowledge that we gain about these organisms will allow us to better address them, in terms of monitoring and treatment, as sources of future health emergencies.

A Field Guide to Eukaryotic Transposable Elements

Transposable elements (TEs) are mobile DNA sequences that propagate within genomes. Through diverse invasion strategies, TEs have come to occupy a substantial fraction of nearly all eukaryotic genomes, and they represent a major source of genetic variation and novelty. Here we review the defining features of each major group of eukaryotic TEs and explore their evolutionary origins and relationships. We discuss how the unique biology of different TEs influences their propagation and distribution within and across genomes. Environmental and genetic factors acting at the level of the host species further modulate the activity, diversification, and fate of TEs, producing the dramatic variation in TE content observed across eukaryotes. We argue that cataloging TE diversity and dissecting the idiosyncratic behavior of individual elements are crucial to expanding our comprehension of their impact on the biology of genomes and the evolution of species.

Evolution of the centrosome, from the periphery to the center

Centrosomes are central organelles that organize microtubules (MTs) in animals, fungi and several other eukaryotic lineages. Despite an important diversity of structure, the centrosomes of different lineages share the same functions and part of their molecular components. To uncover how divergent centrosomes are related to each other, we need to trace the evolutionary history of MT organization. Careful assessment of cytoskeletal architecture in extant eukaryotic species can help us infer the ancestral state and identify the subsequent changes that took place during evolution. This led to the finding that the last common ancestor of all eukaryotes was very likely a biflagellate cell with a surprisingly complex cytoskeletal organization. Centrosomes are likely derived from the basal bodies of such flagellate, but when and how many times this happened remains unclear. Here, we discuss different hypotheses for how centrosomes evolved in a eukaryotic lineage called Amorphea, to which animals, fungi and amoebozoans belong.

Host Range and Coding Potential of Eukaryotic Giant Viruses

Giant viruses are a group of eukaryotic double-stranded DNA viruses with large virion and genome size that challenged the traditional view of virus. Newly isolated strains and sequenced genomes in the last two decades have substantially advanced our knowledge of their host diversity, gene functions, and evolutionary history. Giant viruses are now known to infect hosts from all major supergroups in the eukaryotic tree of life, which predominantly comprises microbial organisms. The seven well-recognized viral clades (taxonomic families) have drastically different host range. Mimiviridae and Phycodnaviridae, both with notable intrafamilial genome variation and high abundance in environmental samples, have members that infect the most diverse eukaryotic lineages. Laboratory experiments and comparative genomics have shed light on the unprecedented functional potential of giant viruses, encoding proteins for genetic information flow, energy metabolism, synthesis of biomolecules, membrane transport, and sensing that allow for sophisticated control of intracellular conditions and cell-environment interactions. Evolutionary genomics can illuminate how current and past hosts shape viral gene repertoires, although it becomes more obscure with divergent sequences and deep phylogenies. Continued works to characterize giant viruses from marine and other environments will further contribute to our understanding of their host range, coding potential, and virus-host coevolution.

Unorthodox Mechanisms to Initiate Translation Open Novel Paths for Gene Expression

Translation in eukaryotes is dependent on the activity of translation initiation factor (eIF) 4G family of proteins, a scaffold protein that, during the initiation step, coordinates the activity of other eIFs to recruit the 40S ribosomal subunit to the mRNA. Three decades of research on protein synthesis and its regulation has provided a wealth of evidence supporting the crucial role of cap-dependent translation initiation, which involves eIF4G. However, the recent discovery of a surprising variety of alternative mechanisms to initiate translation in the absence of eIF4G has stirred the orthodox view of how protein synthesis is performed. These mechanisms involve novel interactions among known eIFs, or between known eIFs and other proteins not previously linked to translation. Thus, a new picture is emerging in which the unorthodox translation initiation complexes contribute to the diversity of mechanisms that regulate gene expression in eukaryotes.