Nucleotide triphosphate (NTP)-dependent molecular switches regulate essential cellular processes by cycling between active and inactive states thro...

Nucleocytoplasmic large DNA viruses (NCLDVs) encode multi-subunit RNA polymerases (msRNAPs) that challenge conventional views of viral evolution. Phylogenetic and structural studies reveal that NCLDV RNAP catalytic cores share deep evolutionary roots with eukaryotic counterparts, implicating ancient gene transfers that shaped the last eukaryotic common ancestor (LECA), underscoring NCLDVs’ pivotal role in eukaryotic origins. NCLDV RNAP retains the fundamental architecture of cellular RNAPs while evolving and adapting for viral gene regulation. This review summarizes structural and functional divergences between viral and cellular RNAPs, synthesizes evidence for virus-driven RNAP evolution, and evaluates emerging hypotheses of viral eukaryogenesis. Viewing viruses as evolutionary collaborators offers new insights into RNAP adaptability and bridges virology, evolutionary biology, and synthetic biology across diverse biological contexts.

Evading infection in Cellulophaga baltica comes with cellular changes that alter carbon cycling, metabolite secretion and sedimentation rates.

RFdiffusion2, an extension of the RFdiffusion framework, builds de novo enzyme active sites using atom-level functional group constraints.

Analysis of eukaryotic gene sequences using a relaxed molecular clock methodology indicate that eukaryotes emerged 3.0–2.25 billion years ago as a result of mitochondrial endosymbiosis with complex archaea that already possessed an elaborated cytoskeleton, membrane trafficking, endomembrane, phagocytotic machinery and a nucleus.

AbstractMotivation. Biomolecular condensates have been implicated in key cellular processes such as gene regulation, stress response, and signaling, and dy

The constant arms race of bacteriophages and their bacterial hosts has inspired major breakthroughs in biotechnology and shaped phages as fierce predators with great clinical potential to fight multidrug-resistant bacterial pathogens. However, the vast amount of genomic “dark matter” composed of genes of unknown function in phage genomes remains a major obstacle for the molecular understanding of phage-host interactions. Here we present HIDEN-SEQ, a transposon-insertion sequencing method for phages that systematically links viral genes to selectable phenotypes. Using model phage T4, we show that HIDEN-SEQ readily reproduces the gene essentiality map established over decades of research. Subsequently, we show that our method is easily portable to different phages far beyond classical laboratory models. Across a panel of bacterial hosts and growth conditions, HIDEN-SEQ reveals many conditionally essential phage genes, including previously unknown viral anti-defense factors that we could match to specific antiviral defenses of the respective hosts. Compared to analogous techniques, HIDEN-SEQ provides unprecedented depth and near base-pair resolution as well as great ease of use and portability. We therefore anticipate that HIDEN-SEQ will accelerate discoveries in phage biology by uncovering functions of viral dark matter with direct relevance for microbial ecology, biotechnology, and improvements of phage therapy. ### Competing Interest Statement J.W.V. is a scientific advisory board member at i-Seq Biotechnology. The remaining authors declare no competing interests. Swiss National Science Foundation, https://ror.org/00yjd3n13, PZ00P3_180085, TMSGI3_211369, grant number 180541

Picocyanobacteria from the genera Prochlorococcus and Synechococcus thrive across the globe in aqueous environments, have relatively small genomes, and have growth dynamics regulated by both viral interactions and abiotic conditions, making them excellent model organisms for exploring host-pathogen coevolution. The Salish Sea, located in the Western coastal waters bordering the USA and Canada, is at the current northern boundary (defined by Prochlorococcus versus Synechococcus prevalence ratios) of the range of Prochlorococcus. Predictions suggest that this boundary will shift as warmer waters move northward, providing an excellent system to study host-pathogen dynamics and coevolution in a changing environmental context. In preparation for such studies, we developed and refined methods to sample and sequence cyanobacteria, cyanophages, and their abiotic environment. In addition to basic methodological questions focused on the physical sampling, filtering, viral precipitation, DNA extraction, and technical replicability, we explored how well our filtering and extraction protocols enrich for our main target, picocyanobacteria. The protocol described herein can successfully discriminate large-cell eukaryotic organisms, but size fractionation of picocyanobacteria appears to be affected by the presence of free DNA, multicellular structures, and abundant tycheposons. Our preferred final protocol at the conclusion of these experiments based on yield and processing time is presented. We recovered substantial Prochlorococcus, Synechococcus and amoeba-like sequences in most samples, and preliminary exploration of relative taxon sequence read recoveries across locations, over time, and tidal conditions are also discussed. Approaches described here may be useful to other efforts such as harmful algal bloom monitoring, species isolation and enrichment, water quality assessments, anti-viral discovery, and understanding picocyanobacterial population changes over space and time. ### Competing Interest Statement The authors have declared no competing interest. Office of Biological and Environmental Research, 81832 Office of Science, DE-AC05-76RL01830 Department of Energy, DE-AC05-76RL01830

Archaeal transcription is a hybrid of eukaryotic and prokaryotic features: an RNA polymerase II (RNAPII)-like polymerase transcribes genes organized i…

The growing antimicrobial resistance crisis has sparked renewed interest in using bacteriophage (phage) as a treatment for antibiotic-resistant infections. Phage are viruses that infect and often kill bacteria, and have served as key models for many molecular biology studies. There are many complex phage-bacterial interactions that dictate the success or failure of the phage life cycle, but many of these are not well understood or characterised. These include the specific interactions to recognize a bacterium during the infection process, bacterial phage defence mechanisms and metabolic pathways that are key to phage replication. In this study a novel Escherichia coli phage, Arnold, is characterised and the genome sequence is reported. We then use transposon-directed insertion sequencing (TraDIS) to screen a library of E. coli mutants to identify over 200 genes involved in Arnold phage infection or in phage resistance. Using this approach, we identified both an outer membrane protein (BtuB, vitamin B12 transporter) and an inner membrane protein (SdaC, serine/proton symporter) involved in phage infection. Deletions in these genes were shown to provide immunity to infection by this phage. Understanding the genetic basis of phage infection and phage resistance should allow us to select or design phage to target specific bacterial pathogens in the future.

Crawling motility is a hallmark of eukaryotic cells and requires a dynamic actin cytoskeleton, regulated adhesion, and spatially organized signalling pathways1–3. Asgard archaea (phylum Promethearchaeota) which are considered the closest known prokaryotic relatives of eukaryotes potentially encode these functions within their large set of ‘eukaryotic signature proteins’[4][1]–[9][2]. The few cultivated members show a complex cell morphology, consisting of a central cell body from which several protrusions extend, filled with an actin-based cytoskeleton[10][3],[11][4]. Here, live cell microscopy of two organisms of the Loki- and Hodarchaea lineages[10][3],[12][5] showed that they dynamically and drastically change their cell shape on a minute time scale and grow and retract their extensive protrusions with a speed of 1.5 to 5.3 µm/min, respectively. After adhering to a glass surface, cells employ their protrusions to undergo active crawling motion. In the presence of selected actin inhibitors however, the observed dynamics were arrested, suggesting a central role of actin in these processes. The observed cellular plasticity and motility are unique features among prokaryotes and might have been crucial for the emergence of the first eukaryotic cells that are thought to have formed through the association of a member of the Promethearchaeota and an alphaproteobacterium, the ancestor of mitochondria. ### Competing Interest Statement The authors have declared no competing interest. Deutsche Forschungsgemeinschaft, 5170 Japan Society for the Promotion of Science, 22H0498 Chan Zuckerberg Initiative (United States), https://doi.org/10.37921/120055ratwvi, DAF2020-225401 FWF Austrian Science Fund, W1257, EFP 25 [1]: #ref-4 [2]: #ref-9 [3]: #ref-10 [4]: #ref-11 [5]: #ref-12

The Retron-Eco7 is a genetic element involved in anti-phage defense that encodes two effector proteins (PtuA and PtuB) and cleaves the host tRNA. Here, the authors solved the Retron-Eco7 complex structure using cryo-EM.

Something from nothing: The birth of new phage defense genes

Diel study revealed fine scale coupling between microbial activity and DOM biogeochemistry in the oligotrophic ocean.

Abstract. Viruses are the most abundant biological entities on Earth, yet their global diversity remains largely unexplored. Here, we present VIRE, a compr

While viruses affect the flow of elements and energy at a planet-wide scale through lysis, gene transfer, and metabolic reprogramming, they are yet to be inc...

Abstract. Extracting and directly amplifying DNA from small-volume, low-biomass samples would enable rapid, ultra-high-throughput analyses, facilitating th

Chloroflexus aurantiacus succinate dehydrogenase at apo- and MK-bound forms reveal electron transfer pathways connecting succinate oxidation to menaquinone reduction at a canonical QP site and a newly identified QD site with atypical configuration.

Environmental metagenomic explorations show that Mirusviricota lineages lack essential replication and transcription genes and contain spliceosomal introns, suggesting nuclear reproduction.