Nuclear Counterparts Research Articles

The mRNA-capping enzyme localizes to stress granules in the cytoplasm and maintains cap homeostasis of target mRNAs.

The model of RNA stability has undergone a transformative shift with the revelation of a cytoplasmic capping activity that means a subset of transcripts are recapped autonomously of their nuclear counterparts. The present study demonstrates nucleo-cytoplasmic shuttling of the mRNA-capping enzyme (CE, also known as RNA guanylyltransferase and 5'-phosphatase; RNGTT), traditionally acknowledged for its nuclear localization and functions, elucidating its contribution to cytoplasmic capping activities. A unique nuclear export sequence in CE mediates XPO1-dependent nuclear export of CE. Notably, during sodium arsenite-induced oxidative stress, cytoplasmic CE (cCE) congregates within stress granules (SGs). Through an integrated approach involving molecular docking and subsequent co-immunoprecipitation, we identify eIF3b, a constituent of SGs, as an interactive associate of CE, implying that it has a potential role in guiding cCE to SGs. We measured the cap status of specific mRNA transcripts from U2OS cells that were non-stressed, stressed and recovered from stress, which indicated that cCE-target transcripts lost their caps during stress but remarkably regained cap stability during the recovery phase. This comprehensive study thus uncovers a novel facet of cytoplasmic CE, which facilitates cellular recovery from stress by maintaining cap homeostasis of target mRNAs.

Mitochondrial genome diversity across the subphylum Saccharomycotina.

Eukaryotic life depends on the functional elements encoded by both the nuclear genome and organellar genomes, such as those contained within the mitochondria. The content, size, and structure of the mitochondrial genome varies across organisms with potentially large implications for phenotypic variance and resulting evolutionary trajectories. Among yeasts in the subphylum Saccharomycotina, extensive differences have been observed in various species relative to the model yeast Saccharomyces cerevisiae, but mitochondrial genome sampling across many groups has been scarce, even as hundreds of nuclear genomes have become available. By extracting mitochondrial assemblies from existing short-read genome sequence datasets, we have greatly expanded both the number of available genomes and the coverage across sparsely sampled clades. Comparison of 353 yeast mitochondrial genomes revealed that, while size and GC content were fairly consistent across species, those in the genera Metschnikowia and Saccharomyces trended larger, while several species in the order Saccharomycetales, which includes S. cerevisiae, exhibited lower GC content. Extreme examples for both size and GC content were scattered throughout the subphylum. All mitochondrial genomes shared a core set of protein-coding genes for Complexes III, IV, and V, but they varied in the presence or absence of mitochondrially-encoded canonical Complex I genes. We traced the loss of Complex I genes to a major event in the ancestor of the orders Saccharomycetales and Saccharomycodales, but we also observed several independent losses in the orders Phaffomycetales, Pichiales, and Dipodascales. In contrast to prior hypotheses based on smaller-scale datasets, comparison of evolutionary rates in protein-coding genes showed no bias towards elevated rates among aerobically fermenting (Crabtree/Warburg-positive) yeasts. Mitochondrial introns were widely distributed, but they were highly enriched in some groups. The majority of mitochondrial introns were poorly conserved within groups, but several were shared within groups, between groups, and even across taxonomic orders, which is consistent with horizontal gene transfer, likely involving homing endonucleases acting as selfish elements. As the number of available fungal nuclear genomes continues to expand, the methods described here to retrieve mitochondrial genome sequences from these datasets will prove invaluable to ensuring that studies of fungal mitochondrial genomes keep pace with their nuclear counterparts.

3C 120 Disk/Corona vs. Jet Variability in X-rays

The 3C120 (Mrk 1506, UGC 03087, Mrk 9014) is a type 1 Seyfert (Sy1)/broad-line radio galaxy (BLRG) with intriguing variable jet activity featuring “dip” and “outburst” phases. Significant X-ray observational datasets have been collected for 3C120 by INTEGRAL, XMM-Newton, SWIFT, Suzaku, and other X-ray observational facilities. The overall X-ray spectrum of 3C 120 is too soft for typical radio-loud AGN, likely due to both variable spectral shape and jet contamination. Separating the “jet base” and nuclear (disc/corona) counterparts in the X-ray spectrum of 3C 120 can provide us with the possibility to investigate its variability in a more detailed way. Our objectives are to estimate separately the time variations of the accretion disc/corona and SSC/IC jet emission counterparts in the 3C 120 X-ray spectra and to analyze the physical state of the nucleus during different phases. Here, we attempt to use the connections between the synchrotron radio- and X-ray SSC/IC jet spectra and their photon indices and the dependence between the nuclear continuum and Fe-K iron luminescent line emission near 6.4 keV to separate the nuclear and jet base contributions to the total X-ray continuum. Using the X-ray observational dataset of 3C 120, we obtained separated fluxes that were interpreted as originating from the nucleus (disc/corona) and non-thermal SSC/IC jet base contributions. After this component separation, we identified the accretion disc/corona and jet states during different phases and compared them with the “jet/disk cycle” (Lohfink) and “magnetic plasmoid reconnection” (Shukla/Manheim) models.

Comparative analyses of three complete Primula mitogenomes with insights into mitogenome size variation in Ericales

BackgroundAlthough knowledge of the sizes, contents, and forms of plant mitochondrial genomes (mitogenomes) is increasing, little is known about the mechanisms underlying their structural diversity. Evolutionary information on the mitogenomes of Primula, an important ornamental taxon, is more limited than the information on their nuclear and plastid counterparts, which has hindered the comprehensive understanding of Primula mitogenomic diversity and evolution. The present study reported and compared three Primula mitogenomes and discussed the size expansion of mitogenomes in Ericales.ResultsMitogenome master circles were sequenced and successfully assembled for three Primula taxa and were compared with publicly available Ericales mitogenomes. The three mitogenomes contained similar gene contents and varied primarily in their structures. The Primula mitogenomes possessed relatively high nucleotide diversity among all examined plant lineages. In addition, high nucleotide diversity was found among Primula species between the Mediterranean and Himalaya-Hengduan Mountains. Most predicted RNA editing sites appeared in the second amino acid codon, increasing the hydrophobic character of the protein. An early stop in atp6 caused by RNA editing was conserved across all examined Ericales species. The interfamilial relationships within Ericales and interspecific relationships within Primula could be well resolved based on mitochondrial data. Transfer of the two longest mitochondrial plastid sequences (MTPTs) occurred before the divergence of Primula and its close relatives, and multiple independent transfers could also occur in a single MTPT sequence. Foreign sequence [MTPTs and mitochondrial nuclear DNA sequences (NUMTs)] uptake and repeats were to some extent associated with changes in Ericales mitogenome size, although none of these relationships were significant overall.ConclusionsThe present study revealed relatively conserved gene contents, gene clusters, RNA editing, and MTPTs but considerable structural variation in Primula mitogenomes. Relatively high nucleotide diversity was found in the Primula mitogenomes. In addition, mitogenomic genes, collinear gene clusters, and locally collinear blocks (LCBs) all showed phylogenetic signals. The evolutionary history of MTPTs in Primula was complicated, even in a single MTPT sequence. Various reasons for the size variation observed in Ericales mitogenomes were found.

Evolution and codon usage bias of mitochondrial and nuclear genomes in Aspergillus section Flavi.

The fungal genus Aspergillus contains a diversity of species divided into taxonomic sections of closely related species. Section Flavi contains 33 species, many of industrial, agricultural, or medical relevance. Here, we analyze the mitochondrial genomes (mitogenomes) of 20 Flavi species-including 18 newly assembled mitogenomes-and compare their evolutionary history and codon usage bias patterns to their nuclear counterparts. Codon usage bias refers to variable frequencies of synonymous codons in coding DNA and is shaped by a balance of neutral processes and natural selection. All mitogenomes were circular DNA molecules with highly conserved gene content and order. As expected, genomic content, including GC content, and genome size differed greatly between mitochondrial and nuclear genomes. Phylogenetic analysis based on 14 concatenated mitochondrial genes predicted evolutionary relationships largely consistent with those predicted by a phylogeny constructed from 2,422 nuclear genes. Comparing similarities in interspecies patterns of codon usage bias between mitochondrial and nuclear genomes showed that species grouped differently by patterns of codon usage bias depending on whether analyses were performed using mitochondrial or nuclear relative synonymous usage values. We found that patterns of codon usage bias at gene level are more similar between mitogenomes of different species than the mitogenome and nuclear genome of the same species. Finally, we inferred that, although most genes-both nuclear and mitochondrial-deviated from the neutral expectation for codon usage, mitogenomes were not under translational selection while nuclear genomes were under moderate translational selection. These results contribute to the study of mitochondrial genome evolution in filamentous fungi.

Purification of Mitochondrial Ribosomal Complexes from Trypanosoma cruzi and Leishmania tarentolae for Cryo-EM Analysis.

Kinetoplastids are unicellular eukaryotic parasites responsible for human pathologies such as Chagas disease, sleeping sickness or Leishmaniasis, caused by Trypanosoma cruzi, Trypanosoma brucei, and various Leishmania spp., respectively. They harbor a single large mitochondrion that is essential for the survival of the parasite. Interestingly, most of the mitochondrial gene expression machineries and processes present significant differences from their nuclear and cytosolic counterparts. A striking example concerns their mitochondrial ribosomes, in charge of translating the few essential mRNAs encoded by mitochondrial genomes. Here, we present a detailed protocol including the specific procedures to isolate mitochondria from two species of kinetoplastids, T. cruzi and L. tarentolae, by differential centrifugations. Then, we detail the protocol to purify mitochondrial ribosomal complexes from these two species of parasites (including ribosomal maturating complexes) by a sucrose gradient approach. Finally, we describe how to prepare cryo-electron microscopy (cryo-EM) grids from these two sorts of samples. This protocol will be useful for further studies aiming at analyzing mitochondrial translation regulation.

Membrane-Initiated Estrogen, Androgen, and Progesterone Receptor Signaling in Health and Disease.

Rapid effects of steroid hormones were discovered in the early 1950s, but the subject was dominated in the 1970s by discoveries of estradiol and progesterone stimulating protein synthesis. This led to the paradigm that steroid hormones regulate growth, differentiation, and metabolism via binding a receptor in the nucleus. It took 30 years to appreciate not only that some cellular functions arise solely from membrane-localized steroid receptor (SR) actions, but that rapid sex steroid signaling from membrane-localized SRs is a prerequisite for the phosphorylation, nuclear import, and potentiation of the transcriptional activity of nuclear SR counterparts. Here, we provide a review and update on the current state of knowledge of membrane-initiated estrogen (ER), androgen (AR) and progesterone (PR) receptor signaling, the mechanisms of membrane-associated SR potentiation of their nuclear SR homologues, and the importance of this membrane-nuclear SR collaboration in physiology and disease. We also highlight potential clinical implications of pathway-selective modulation of membrane-associated SR.

Mitochondrial protein import as a quality control sensor.

Mitochondria are organelles involved in various functions related to cellular metabolism and homoeostasis. Though mitochondria contain own genome, their nuclear counterparts encode most of the different mitochondrial proteins. These are synthesised as precursors in the cytosol and have to be delivered into the mitochondria. These organelles hence have elaborate machineries for the import of precursor proteins from cytosol. The protein import machineries present in both mitochondrial membrane and aqueous compartments show great variability in pre-protein recognition, translocation and sorting across or into it. Mitochondrial protein import machineries also interact transiently with other protein complexes of the respiratory chain or those involved in the maintenance of membrane architecture. Hence mitochondrial protein translocation is an indispensable part of the regulatory network that maintains protein biogenesis, bioenergetics, membrane dynamics and quality control of the organelle. Various stress conditions and diseases that are associated with mitochondrial import defects lead to changes in cellular transcriptomic and proteomic profiles. Dysfunction in mitochondrial protein import also causes over-accumulation of precursor proteins and their aggregation in the cytosol. Multiple pathways may be activated for buffering these harmful consequences. Here, we present a comprehensive picture of import machinery and its role in cellular quality control in response to defective mitochondrial import. We also discuss the pathological consequences of dysfunctional mitochondrial protein import in neurodegeneration and cancer.

Plastid genomes and phylogenomics of liverworts (Marchantiophyta): Conserved genome structure but highest relative plastid substitution rate in land plants

With some 7300 species of small nonvascular spore-producing plants, liverworts represent one of the major lineages of land plants. Although multi-locus molecular phylogenetic studies have elucidated relationships of liverworts at different taxonomic categories, the backbone phylogeny of liverworts is still to be fully resolved, especially for the placement of Ptilidiales and the relationships within Jungermanniales and Marchantiales. Here, we provided phylogenomic inferences of liverworts based on 42 newly sequenced and 24 published liverwort plastid genomes representing all but two orders of liverworts, and characterized the evolution of the plastome in liverworts. The structure of the plastid genome is overall conserved across the phylogeny of liverworts, with only two structural variants detected from simple thalloids, besides 18 out of 43 liverwort genera showing intron variations in their plastomes. Complex thalloid liverworts maintain the most plastid genes, and seem to undergo fewer gene deletions and pseudogenization events than other liverworts. Plastid phylogenetic inferences yielded mostly robustly supported relationships, and consistently resolved Ptilidiales as the sister to Porellales. The relative ratio of silent substitutions across the three genetic compartments (i.e., 1:15:10, for mitochondrial:plastid:nuclear) suggests that liverwort plastid genes have the potential to evolve faster than their nuclear counterparts, unlike in any other major land plant lineages where the mutation rate of nuclear genes overwhelm those of their plastid and mitochondrial counterparts.

Struggle for survival: new insights into NELF condensation for adaptive transcriptional reprogramming

In this issue of Molecular Cell, Rawat etal. (2021) characterize novel stress-induced condensates of the negative elongation factor (NELF) as the nuclear counterparts of cytosolic stress granules. This provides a new perspective on transcription repression orchestrated by phase separation.

Stress-induced nuclear condensation of NELF drives transcriptional downregulation

SummaryIn response to stress, human cells coordinately downregulate transcription and translation of housekeeping genes. To downregulate transcription, the negative elongation factor (NELF) is recruited to gene promoters impairing RNA polymerase II elongation. Here we report that NELF rapidly forms nuclear condensates upon stress in human cells. Condensate formation requires NELF dephosphorylation and SUMOylation induced by stress. The intrinsically disordered region (IDR) in NELFA is necessary for nuclear NELF condensation and can be functionally replaced by the IDR of FUS or EWSR1 protein. We find that biomolecular condensation facilitates enhanced recruitment of NELF to promoters upon stress to drive transcriptional downregulation. Importantly, NELF condensation is required for cellular viability under stressful conditions. We propose that stress-induced NELF condensates reported here are nuclear counterparts of cytosolic stress granules. These two stress-inducible condensates may drive the coordinated downregulation of transcription and translation, likely forming a critical node of the stress survival strategy.

Assess of contamination of the snow cover for detecting the zones of inhalation chemical risk

Introduction. On the territory with a resistant snow cover, atmospheric pollution accumulates over several months; solid precipitation in the form of snow is an indicator object for assessing the state of the urban environment. Materials and methods. The sampling of snow was carried out on trial plots close to the monitoring points of atmospheric air and reflecting the influence of various stationary and mobile sources of pollution. The methods of gas chromatography-mass spectrometry and the atomic absorption spectrometry were used. Results. The results were obtained on the content of polycyclic aromatic hydrocarbons (PAHs) and heavy metals in snow cover to identify risk zones in the city of Ulan-Ude of the Republic of Buryatiya. The widest range of metals is recorded at points located near a major traffic interchange and in a residential area near the low-rise buildings of the private sector. The determined PAHs in large quantities were established to be contained in the solid sediment of snow samples. Discussion. Snow cover is a depositing and transit component of the environment. Its study gives important information about the chemical state of industrial ecosystems. About 30 thousand tons of chemical impurities enter the air basin of Ulan-Ude from stationary sources per year. Emissions of the total amount of hydrocarbons averaged of 1,741.96 tons over the study period, soot - 822.41 tons, which is by tens and hundreds times higher than that of other toxic substances, therefore, the PAH content in snow samples is higher than that of heavy metals. Conclusion. The accumulation of chemicals of 13 priority PAHs, of which 60-80% of the total amount falls on 3-,4- nuclear counterparts (phenanthrene, anthracene, fluoranthene, pyrene, benzo(a)anthracene, chrysene) occurs in accumulating media. PAHs are associated with water-insoluble (solid phase) PAHs, which indicates to the unity of the main source of pollution (vehicle exhaust gases).

Assess of contamination of the snow cover for detecting the zones of inhalation chemical risk

Introduction. On the territory with a resistant snow cover, atmospheric pollution accumulates over several months; solid precipitation in the form of snow is an indicator object for assessing the state of the urban environment. Materials and methods. The sampling of snow was carried out on trial plots close to the monitoring points of atmospheric air and reflecting the influence of various stationary and mobile sources of pollution. The methods of gas chromatography-mass spectrometry and the atomic absorption spectrometry were used. Results. The results were obtained on the content of polycyclic aromatic hydrocarbons (PAHs) and heavy metals in snow cover to identify risk zones in the city of Ulan-Ude of the Republic of Buryatiya. The widest range of metals is recorded at points located near a major traffic interchange and in a residential area near the low-rise buildings of the private sector. The determined PAHs in large quantities were established to be contained in the solid sediment of snow samples. Discussion. Snow cover is a depositing and transit component of the environment. Its study gives important information about the chemical state of industrial ecosystems. About 30 thousand tons of chemical impurities enter the air basin of Ulan-Ude from stationary sources per year. Emissions of the total amount of hydrocarbons averaged of 1,741.96 tons over the study period, soot - 822.41 tons, which is by tens and hundreds times higher than that of other toxic substances, therefore, the PAH content in snow samples is higher than that of heavy metals. Conclusion. The accumulation of chemicals of 13 priority PAHs, of which 60-80% of the total amount falls on 3-,4- nuclear counterparts (phenanthrene, anthracene, fluoranthene, pyrene, benzo(a)anthracene, chrysene) occurs in accumulating media. PAHs are associated with water-insoluble (solid phase) PAHs, which indicates to the unity of the main source of pollution (vehicle exhaust gases).

The Mitogenome of Norway Spruce and a Reappraisal of Mitochondrial Recombination in Plants.

Plant mitogenomes can be difficult to assemble because they are structurally dynamic and prone to intergenomic DNA transfers, leading to the unusual situation where an organelle genome is far outnumbered by its nuclear counterparts. As a result, comparative mitogenome studies are in their infancy and some key aspects of genome evolution are still known mainly from pregenomic, qualitative methods. To help address these limitations, we combined machine learning and in silico enrichment of mitochondrial-like long reads to assemble the bacterial-sized mitogenome of Norway spruce (Pinaceae: Picea abies). We conducted comparative analyses of repeat abundance, intergenomic transfers, substitution and rearrangement rates, and estimated repeat-by-repeat homologous recombination rates. Prompted by our discovery of highly recombinogenic small repeats in P. abies, we assessed the genomic support for the prevailing hypothesis that intramolecular recombination is predominantly driven by repeat length, with larger repeats facilitating DNA exchange more readily. Overall, we found mixed support for this view: Recombination dynamics were heterogeneous across vascular plants and highly active small repeats (ca. 200 bp) were present in about one-third of studied mitogenomes. As in previous studies, we did not observe any robust relationships among commonly studied genome attributes, but we identify variation in recombination rates as a underinvestigated source of plant mitogenome diversity.

Role of Mitochondrial DNA Damage in ROS-Mediated Pathogenesis of Age-Related Macular Degeneration (AMD).

Age-related macular degeneration (AMD) is a complex eye disease that affects millions of people worldwide and is the main reason for legal blindness and vision loss in the elderly in developed countries. Although the cause of AMD pathogenesis is not known, oxidative stress-related damage to retinal pigment epithelium (RPE) is considered an early event in AMD induction. However, the precise cause of such damage and of the induction of oxidative stress, including related oxidative effects occurring in RPE and the onset and progression of AMD, are not well understood. Many results point to mitochondria as a source of elevated levels of reactive oxygen species (ROS) in AMD. This ROS increase can be associated with aging and effects induced by other AMD risk factors and is correlated with damage to mitochondrial DNA. Therefore, mitochondrial DNA (mtDNA) damage can be an essential element of AMD pathogenesis. This is supported by many studies that show a greater susceptibility of mtDNA than nuclear DNA to DNA-damaging agents in AMD. Therefore, the mitochondrial DNA damage reaction (mtDDR) is important in AMD prevention and in slowing down its progression as is ROS-targeting AMD therapy. However, we know far less about mtDNA than its nuclear counterparts. Further research should measure DNA damage in order to compare it in mitochondria and the nucleus, as current methods have serious disadvantages.

Biochemical Studies Provide Insights into the Necessity for Multiple Arabidopsis thaliana Protein-Only RNase P Isoenzymes

RNase P catalyzes removal of the 5′ leader from precursor tRNAs (pre-tRNAs) in all three domains of life. Some eukaryotic cells contain multiple forms of the protein-only RNase P (PRORP) variant, prompting efforts to unravel this seeming redundancy. Previous studies concluded that there were only modest differences in the processing of typical pre-tRNAs by the three isoforms in Arabidopsis thaliana [AtPRORP1 (organellar), AtPRORP2 and AtPRORP3 (nuclear)]. Here, we investigated if different physical attributes of the three isoforms might engender payoffs under specific conditions. Our temperature–activity profiling studies revealed that AtPRORPs display substrate-identity dependent behavior at elevated temperatures (37–45 °C), with the organellar variant outperforming the nuclear counterparts. Echoing these findings, molecular dynamics simulations revealed that AtPRORP2 relative to AtPRORP1 samples a wider conformational ensemble that deviates from the crystal structure. Results from our biochemical studies and molecular dynamics simulations support the idea that AtPRORPs have overlapping but not necessarily redundant attributes and inspire new perspectives on the suitability of each variant to perform its function(s) in a specific cellular locale.

The Multiple Levels of Mitonuclear Coregulation.

Together, the nuclear and mitochondrial genomes encode the oxidative phosphorylation (OXPHOS) complexes that reside in the mitochondrial inner membrane and enable aerobic life. Mitochondria maintain their own genome that is expressed and regulated by factors distinct from their nuclear counterparts. For optimal function, the cell must ensure proper stoichiometric production of OXPHOS subunits by coordinating two physically separated and evolutionarily distinct gene expression systems. Here, we review our current understanding of mitonuclear coregulation primarily at the levels of transcription and translation. Additionally, we discuss other levels of coregulation that may exist but remain largely unexplored, including mRNA modification and stability and posttranslational protein degradation.

The Roles of Mutation, Selection, and Expression in Determining Relative Rates of Evolution in Mitochondrial versus Nuclear Genomes.

Eukaryotes rely on proteins encoded by the nuclear and mitochondrial (mt) genomes, which interact within multisubunit complexes such as oxidative-phosphorylation enzymes. Although selection is thought to be less efficient on the asexual mt genome, in bilaterian animals the ratio of nonsynonymous to synonymous substitutions (ω) is lower in mt- compared with nuclear-encoded OXPHOS subunits, suggesting stronger effects of purifying selection in the mt genome. Because high levels of gene expression constrain protein sequence evolution, one proposed resolution to this paradox is that mt genes are expressed more highly than nuclear genes. To test this hypothesis, we investigated expression and sequence evolution of mt and nuclear genes from 84 diverse eukaryotes that vary in mt gene content and mutation rate. We found that the relationship between mt and nuclear ω values varied dramatically across eukaryotes. In contrast, transcript abundance is consistently higher for mt genes than nuclear genes, regardless of which genes happen to be in the mt genome. Consequently, expression levels cannot be responsible for the differences in ω Rather, 84% of the variance in the ratio of ω values between mt and nuclear genes could be explained by differences in mutation rate between the two genomes. We relate these findings to the hypothesis that high rates of mt mutation select for compensatory changes in the nuclear genome. We also propose an explanation for why mt transcripts consistently outnumber their nuclear counterparts, with implications for mitonuclear protein imbalance and aging.

Blurring the line between nuclear and nonnuclear weapons: Increasing the risk of accidental nuclear war?

ABSTRACTIn the past few months, there have been a number of provocative events between Russia and the West: Russian jets buzz US warships in the Black Sea. Turkey, a NATO member, shoots down a Russian warplane involved in the Syria conflict. Russian government media talk publicly about turning the United States to ashes. NATO and Russia both reposition military assets and conduct exercises reminiscent of the darkest days of the Cold War. All this raises fear that misplaced bravado and brinksmanship could lead to the use of nuclear weapons. But there is a subtler, easily overlooked trend as well, which could make the situation even worse: a gradual blurring of the line – particularly in Russia – that separates conventional weapons and their delivery systems from their nuclear counterparts. Uncertainty about the actual capability of a weapon system can be a significant factor in managing a conflict, whether political or military. This is probably the calculation behind a number of Russian programs that are particularly vague about their nuclear dimension.

TopIb, a phylogenetic hallmark gene of Thaumarchaeota encodes a functional eukaryote-like topoisomerase IB.

Type IB DNA topoisomerases can eliminate torsional stresses produced during replication and transcription. These enzymes are found in all eukaryotes and a short version is present in some bacteria and viruses. Among prokaryotes, the long eukaryotic version is only observed in archaea of the phylum Thaumarchaeota. However, the activities and the roles of these topoisomerases have remained an open question. Here, we demonstrate that all available thaumarchaeal genomes contain a topoisomerase IB gene that defines a monophyletic group closely related to the eukaryotic enzymes. We show that the topIB gene is expressed in the model thaumarchaeon Nitrososphaera viennensis and we purified the recombinant enzyme from the uncultivated thaumarchaeon Candidatus Caldiarchaeum subterraneum. This enzyme is active in vitro at high temperature, making it the first thermophilic topoisomerase IB characterized so far. We have compared this archaeal type IB enzyme to its human mitochondrial and nuclear counterparts. The archaeal enzyme relaxes both negatively and positively supercoiled DNA like the eukaryotic enzymes. However, its pattern of DNA cleavage specificity is different and it is resistant to camptothecins (CPTs) and non-CPT Top1 inhibitors, LMP744 and lamellarin D. This newly described thermostable topoisomerases IB should be a promising new model for evolutionary, mechanistic and structural studies.