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PubMed2026

Infection cycles of viruses of the phylum Nucleocytoviricota.

The phylum Nucleocytoviricota, formerly known as nucleocytoplasmic large DNA viruses (NCLDVs), comprises evolutionarily related viruses with remarkably diverse genome sizes, coding capacities and virion morphologies. These viruses infect hosts across the eukaryotic tree of life, from protists to humans, and are believed to have emerged during the early stages of eukaryotic evolution. How the basic aspects of virus-host interaction have evolved in different lineages and whether they share a conserved infection cycle remain unclear. In this Review, we synthesize the information on the infection cycles of model representatives from the major orders within the phylum, revealing both shared traits and lineage-specific innovations. We compare the information available for the extensively studied poxviruses, asfiviruses, iridoviruses and chloroviruses with insights from the rapidly expanding literature on the mimiviruses, pandoraviruses, marseilleviruses and pithoviruses. We provide an overview of the molecular details underlying the key stages of Nucleocytoviricota infection cycles: entry via membrane fusion, formation of viral factories organized via phase separation, genome replication, virion morphogenesis through a crescent intermediate, and egress. We highlight outstanding questions in the field, unify concepts across traditionally separated research areas, and provide a conceptual framework to guide future cell biology studies on large double-stranded DNA viruses.

DNA Viruses↗

PubMed2025

Inactivation of β-1,3-glucan synthase-like 5 confers broad-spectrum resistance to Plasmodiophora brassicae pathotypes in cruciferous plants.

Clubroot disease, caused by the obligate intracellular rhizarian protist Plasmodiophora brassicae, is devastating to cruciferous crops worldwide. Widespread field P. brassicae pathotypes frequently overcome the pathotype-specific resistance of modern varieties, posing a challenge for durable control of this disease. Here a genome-wide association study of 3 years of data comprising field clubroot phenotyping of 244 genome-resequenced Brassica napus accessions identified a strong association of β-1,3-glucan synthase-like 5 (GSL5) with clubroot susceptibility. GSL5 was evolutionarily conserved, and inactivation of GSL5 by genome editing in Arabidopsis, B. napus, Brassica rapa and Brassica oleracea conferred broad-spectrum, high-level resistance to P. brassicae pathotypes without yield penalties in B. napus. GSL5 inactivation derepressed the jasmonic acid-mediated immunity during P. brassicae secondary infection, and this immune repression was possibly reinforced through stabilization of GSL5 by a P. brassicae effector, facilitating clubroot susceptibility. Our study provides durable resistance resources for cruciferous clubroot disease control and insights into plant resistance against intracellular eukaryotic phytopathogens.

Disease Resistance↗

PubMed2026

A compendium of horizontal gene transfers in Metazoa.

With more eukaryotic genomes available for study researchers have been able to identify a growing number of horizontal gene transfer (HGT) candidates. We compiled 9,495 protein coding genes that were identified as horizontally transferred to metazoan hosts in the published literature. This dataset contains gene transfers from bacteria, fungi, archaea and protists to metazoans. We assigned a confidence score to each gene based on the methods used in the scientific paper reporting HGT. All the coding sequences and protein sequences for the HGT genes are stored in a fig share repository. This dataset can be used to identify trends in genome and protein evolution and provide a foundation for creating a centralized HGT database for eukaryotes.

Gene Transfer, Horizontal↗

PubMed1979

Unity and diversity in biochemistry.

A consideration of A Biochemical Phylogeny of the Protists, by M.A. Ragan and D.J. Chapman (Academic Press, 1978) and Biochemical Adaptation to Environmental Change, ed. by R.M.S. Smellie and J.F. Pennock (the Biochemical Society, 1976), within some thoughts on biochemical evolution.

Animals↗

PubMed2026

CoMR: an integrative scoring pipeline for comprehensive mitochondrial proteome reconstruction across eukaryotes.

Mitochondrial proteome reconstruction from eukaryotic sequence data typically relies on prediction of mitochondrial targeting signals (MTSs). However, MTS predictors are primarily trained on model organisms and may perform poorly in phylogenetically divergent lineages or in organisms with atypical or reduced targeting sequences. Accurate reconstruction therefore requires integration of complementary sources of evidence beyond targeting prediction alone. We developed Comprehensive Mitochondrial Reconstructor (CoMR), an integrative workflow that combines targeting prediction, curated homology searches, large-scale similarity searches, and automated phylogenetic analysis within a unified scoring framework. Benchmarking on the model yeast Saccharomyces cerevisiae yielded strong discriminatory performance [receiver operating characteristic (ROC)-area under the curve (AUC) = 0.92], exceeding standalone prediction with TargetP2, a predictor of N-terminal targeting peptides (ROC-AUC = 0.72). In the divergent anaerobic protist Paratrimastix pyriformis, CoMR maintained robust performance (ROC-AUC = 0.86) validated with an experimental proteome despite extreme class imbalance, achieving a precision-recall AUC of 0.183 (~78-fold enrichment over random expectation and ~10-fold improvement over TargetP2). Ablation analyses demonstrate that predictive performance is robust to individual evidence-layer removal, while overlap analyses showed that homology-based searches recovered candidates missed by targeting predictors, particularly in P. pyriformis. Overall, CoMR improves mitochondrial proteome reconstruction over targeting prediction alone and provides a reproducible workflow for predicting mitochondrial and mitochondrion-related organelle protein repertoires across eukaryotes to aid investigations of organelle evolution and proteome reduction.

Proteome↗

PubMed1977

Physarum polycephalum malate dehydrogenase: inhibitor analyses of the mitochondrial and supernatant isozymes.

The effects of naturally occurring metabolites were tested on the malate dehydrogenase (L-malate: NAD+oxidoreductase, EC 1.1.1.37) isozymes from the eucaryotic protist Physarum polycephalum. Several of the Krebs cycle intermediates were inhibitors for each isozyme indicating that a similar catalytic process was involved for both forms. The metabolites ATP, ADP, and AMP were inhibitors competitive with NAD for the mitochondrial isozyme but not the supernatant form. Several other nucleoside phosphates had no effects. Tests of protein sulfhydryl, arginine- and tyrosine-modifying reagents revealed a similar functional sensitivity by both isozymes to these reagents. Those results are compared with data on isozymes from more complex tissue with comments on the physiological significance of those combined data.

Carboxylic Acids↗

PubMed2026

Long-read transcriptomics corrects Trichomonas vaginalis intron annotations and refines transcript-end features.

BACKGROUND: Trichomonas vaginalis causes the most prevalent non-viral sexually transmitted infection worldwide. Despite its large genome (181.5 Mb; 36,310 predicted protein-coding genes in NYU_TvagG3_2), intron annotations remain limited and inconsistently validated. A recent short-read RNA-seq study reported 63 putative active introns, but short reads can misassign splice boundaries and cannot resolve complete transcript structures. METHODS: We integrated Oxford Nanopore direct RNA sequencing (DRS), ONT cDNA long-read sequencing, and Illumina RNA-seq to refine intron annotations, transcript-end features, and UTR boundaries in T. vaginalis. Candidate introns were validated by targeted PCR and Sanger sequencing, and representative splicing events were further assessed using public SRA datasets. RESULTS: Starting from 31 historically annotated introns, motif-guided long-read screening and orthogonal validation identified 17 additional validated introns, increasing the curated set to 48 confirmed introns. Among these 17 events, three were previously unrecognized in the current NYU_TvagG3_2 reference annotation. We also corrected five reported loci, including two false-positive introns, two splice-coordinate misannotations, and one gene-sequence error. DRS further supported transcript termination site mapping, UAAA polyadenylation-signal profiling relative to poly(A) addition sites, and single-molecule poly(A)-tail estimation. StringTie mixed-mode assemblies provided updated UTR boundaries for intron-bearing transcripts and transcripts without curated introns. CONCLUSIONS: This study provides a rigorously validated, long-read-refined resource of intron annotations, UTR boundaries, and UAAA-guided transcript-end features for T. vaginalis, together with a reproducible workflow for non-model protists. These refinements improve the current reference annotation and support future studies of functional genomics, parasite biology, pathogenesis, and diagnostic development.

Trichomonas vaginalis↗

PubMed1979

The ultrastructure of mitosis in Plasmodiophora brassicae (Plasmodiophorales).

Mitosis was examined in plasmodia of Plasmodiophora brassicae within artifically inoculated cabbage roots, using light- and electron microscopy. Mitotic nuclear divisions are characterized by a persistent nucleolus, bipolar centrioles paired end-to-end, densely staining chromatin, and a complex array of membranes that surround and ramify through the spindle. Chromatin begins to condense in prophase, and is aligned at metaphase in a reticulate plate on the nuclear equator. The chromatin is not resolvable into distinct chromosomes at metaphase, and a chromosome count is not possible. Large amounts of membrane cisternae within the spindle are most clearly visible at metaphase, and apparently represent the remains of the nuclear envelope. The nuclear envelope is disrupted during prometaphase and may become entangled in the spindle when centriolar microtubules enter the nucleus. Several concentric sheets of perinuclear endoplasmic reticulum surround the spindle and give the mitotic nucleus the superficial appearance of having an intact nuclear envelope. This interpretation of the identity of nucleus-associated membranes differs from those previously reported for other protists, including members of the Plasmodiophorales.

Actinomycetales↗

PubMed2022

CMTr mediated 2'-O-ribose methylation status of cap-adjacent nucleotides across animals.

Cap methyltransferases (CMTrs) O methylate the 2' position of the ribose (cOMe) of cap-adjacent nucleotides of animal, protist, and viral mRNAs. Animals generally have two CMTrs, whereas trypanosomes have three, and many viruses encode one in their genome. In the splice leader of mRNAs in trypanosomes, the first four nucleotides contain cOMe, but little is known about the status of cOMe in animals. Here, we show that cOMe is prominently present on the first two cap-adjacent nucleotides with species- and tissue-specific variations in Caenorhabditis elegans, honeybees, zebrafish, mouse, and human cell lines. In contrast, Drosophila contains cOMe primarily on the first cap-adjacent nucleotide. De novo RoseTTA modeling of CMTrs reveals close similarities of the overall structure and near identity for the catalytic tetrad, and for cap and cofactor binding for human, Drosophila and C. elegans CMTrs. Although viral CMTrs maintain the overall structure and catalytic tetrad, they have diverged in cap and cofactor binding. Consistent with the structural similarity, both CMTrs from Drosophila and humans methylate the first cap-adjacent nucleotide of an AGU consensus start. Because the second nucleotide is also methylated upon heat stress in Drosophila, these findings argue for regulated cOMe important for gene expression regulation.

Animals↗

PubMed1976

Do evolutionary changes in cytochrome c structure reflect functional adaptations?

Following the demonstration that the rate of evolutionary change in the amino acid sequences of cytochromes c of eukaryotic species was not constant either for a single line of phylogenetic descent during different evolutionary intervals or for separate lines of descent, the concept that neutral mutations account for the vast majority of the evolutionary variations could no longer be accepted. Previous studies had shown that all eukaryotic cytochromes c tested appeared to be functionally indistinguishable in their reaction with mitochondrial respiratory chain components. However, an examination of the kinetics at low ionic strength led to the discovery of a high affinity reaction of cytochrome c with cytochrome c oxidase that revealed large differences in activity between the cytochromes of the horse, baker's yeast and the protist Euglena. Observed Km values for this reaction of 10(-7) to 10(-8) M appear to represent actual dissociation constants, as demonstrated by direct binding studies of cytochrome c with purified cytochrome c oxidase. The high affinity reaction is sensitive to ionic strength and inhibited by ADP and ATP in the range of physiological concentrations, ATP being three times as effective as ADP. The possibility is discussed that this effect of ATP on cytochrome c binding to its oxidase could provide the basis of a mechanism for mitochondrial respiratory control. The demonstration of differences between cytochrome c of various species in this kinetic system opens the way to a systematic study of the possible evolutionary adaptations of cytochromes c to their oxidases.

Amino Acid Sequence↗

PubMedDate not supplied

[Preliminary results on a microsporidosis of Atherina boyeri Risso, 1810, from the Languedoc lagoons (author's transl)].

A most likely new microsporidia parasites Atherina boyeri Risso, 1810 and is found from the lagoons south of Montpellier to the Berre lagoon. This Protist establishes itself in the wall of the digestive tract, it forms numerous cysts, as well as in the general cavity of the fish were it evolves into voluminous xenoma (sometimes reatching centimeter in diameter) which present particular histological characteristics. This preliminary report extends from September 1976 to March 1977. The histological, epidemiological and statistical aspects are discussed. Experimental, biochemical and ultrastructural studies are under way.

Animals↗

PubMed2025

Analysis of Leishbuviridae from Trypanosomatids.

Over the last decade, considerable progress has been made in unraveling RNA virus diversity. This has contributed to our understanding of the evolution of these viruses, which include emerging zoonotic human pathogens. Current success has been greatly facilitated by the development of next-generation sequencing platforms instrumental for meta-transcriptomic studies. However, due to the rapid evolution of RNA viruses, there are numerous "blind spots" waiting to be explored; one of those is the RNA virome of unicellular eukaryotes. Here, we present the pipeline, which has been successfully used to characterize various types of RNA viruses, including Leishbuviridae (Bunyaviricetes, Hareavirales) in the parasitic flagellates of the family Trypanosomatidae. The pipeline relies on axenic in vitro cell culture and double-stranded RNA enrichment, followed by direct RNA-sequencing. A detailed procedure description starting from the initial total RNA preparation to the final assembly of the viral segments is provided.

High-Throughput Nucleotide Sequencing↗

PubMed2026

A novel jakobid genus from the soil of an indoor plant.

Jakobids are a group of free-living heterotrophic flagellates that hold a key phylogenetic position for understanding early eukaryote evolution and are particularly notable for their gene-rich, bacteria-like mitochondrial genomes. Although the number of formally described species is small, jakobids are frequently detected in anoxic marine habitats. However, their edaphic diversity remains unexplored, with the few documented isolations from soil over the past two decades, each yielding a new genus. Here, we describe a novel jakobid, Celatomonas quasimodo gen. et sp. nov., isolated from commercial potting soil used for cultivating indoor plants. The organism was characterised by light and scanning electron microscopy, and its phylogenetic position was inferred using 18S rRNA gene phylogenetic analysis. While exhibiting typical jakobid features, the cells adopt a highly unusual curved-triangular morphology during division, which has not been reported for any other jakobid. Phylogenetic analysis placed C. quasimodo as the firmly supported sister lineage of Moramonas marocensis within the family Moramonadidae (suborder Histionina). Despite this close affinity, the two taxa present a level of 18S rRNA gene divergence comparable to that between already recognised genera of Moramonadidae. Together, these data support the recognition of Celatomonas quasimodo as a new genus and species within Moramonadidae. Furthermore, screening of soil environmental DNA datasets revealed the presence of multiple novel jakobid lineages, alongside a novel jakobid clade (JENV-1) of uncertain phylogenetic position from equatorial environments. This newly described jakobid genus provides a valuable model for future comparative studies of cellular ultrastructure and the evolution of jakobid mitochondrial genomes. Combined with the environmental DNA screening results, our findings underscore the importance of soil habitats as reservoirs of unexplored eukaryotic diversity and provide new insights into jakobid systematics.

Phylogeny↗

PubMed2026

An updated checklist of testate amoebae in China.

We present an updated checklist of testate amoebae (TA) in China covering TA records in the literature of the past ∼100 years. In total 363 TA species/subspecies in 53 genera have been included in the current Chinese checklist. The updated Chinese checklist includes five recently discovered TA species (Netzelia mulanensis, Pentagonia zhangduensis, Pontigulasia pentangulostoma, Cornutheca jiuhuensis, and Planhoogenraadia wuchanica) and 24 TA species/subspecies that have been added as new records for China. TA taxonomy and classification in the updated Chinese checklist are based on current knowledge derived from morphological, physiological, and molecular (ribosomal and mitochondrial DNA sequence data, genomics) studies. Corresponding changes in the updated Chinese checklist are outlined and the taxonomy and diversity of (Chinese) TA as well as their biogeography, ecology, and conservation are discussed. As all kinds of TA studies are eventually based on a reliable taxonomy and nomenclature, we are confident that our updated Chinese checklist will be of great value for TA researchers not only in China, but also worldwide.

China↗