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Cryo-electron microscopy structures of three large ornate natural bacterial RNA molecules reveal their quaternary structures and intra- and intermolecular interactions that stabilize them.

A survey of the reconstructed gene set of the last eukaryotic common ancestor shows a consistent link between Asgard archaea and the origin of numerous, functionally diverse eukaryotic genes, demonstrating the dominant Asgard contribution to eukaryogenesis.

Owing to their ability to couple ion movement with ATP hydrolysis or synthesis, F-type and V-type ATPases constitute the cornerstone of cellular bioenergetics and are present in all three domains of life. In this Opinion, Eugene Koonin and colleagues use sequence and structural data to develop an evolutionary scenario for these ubiquitous molecular machines.

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

Nagahata, Kato and Yamada et al. provide cryo-electron microscopy structures of four phylogenetically diverse RNA-guided nucleases—HfmIscB, TbaIscB, YnpsCas9 and NbaCas9—each in complex with its guide RNA and target DNA, providing insights into CRISPR–Cas9 evolution.

Photosynthesis reaction centre barrel proteins are important components of the FtsZ-based cell division apparatus in Haloferax volcanii and other archaea.

The widespread prokaryotic immune systems, in particular restriction–modification, CRISPR–Cas and defensive toxin–antitoxin systems, are absent in eukaryotes, whereas relatively rare ones, such as Argonautes and antiviral STAND NTPases, became central to eukaryotic innate immunity. In this Comment, we hypothesize that the cause of this paradox is the drastic reduction of horizontal gene transfer rate in eukaryotes.

An exploration of previously undescribed variants from the long tail of the CRISPR–Cas distribution.

A cryo-electron microscopy reconstruction of the virus ΦcrAss001 provides insights into the functions of the viral gene products in capsid assembly and infection.

The CRISPR–Cas (clustered regularly interspaced short palindromic repeats–CRISPR-associated proteins) systems are immunity systems that are present in many bacteria and archaea. Here, Koonin and colleagues present a new classification of these systems and introduce a new nomenclature of the genes in the CRISPR–casloci that better reflects the relationships between the proteins.

The natural progression of tumours and their treatment can influence tumour evolution. Here, authors analyse whole-exome sequencing data from various cancer cohorts, finding that treatment-resistant tumors shift toward neutral evolution, which correlates with worse prognosis, and monitoring this shift may guide treatment decisions.

In this Analysis article, Makarova and colleagues provide an overview of the cell division and membrane budding systems of the Archaea. They show that at least four different systems regulate these processes, providing insight into the evolutionary history of archaeal and eukaryotic cells.

Virus-host competition drives evolution of diverse antiviral defences in bacteria and antidefense systems in their viruses (phages). Here, Silas et al. use a functional screen of phage accessory genes to show how bacterial cell-surface sugars can be major determinants of phage host-range, and how some phage proteins injected into bacterial cells inhibit host immunity.

CRISPR–Cas systems provide bacteria and archaea with adaptive immunity to invading foreign DNA. In an Analysis article, Koonin and colleagues update a previous classification of these systems to incorporate the large volume of genomic data generated in recent years.

CRISPR–Cas systems in bacteria and archaea have multifaceted evolutionary relationships with mobile genetic elements (MGEs), including viruses, plasmids and transposons. CRISPR–Cas systems or their components have also been recruited by MGEs on many independent occasions. In this Analysis article, Koonin and colleagues investigate and substantially expand the range of CRISPR–Cas components carried by MGEs.

The vast resource of viral genome sequences has been exploited to carry out a genomic comparison and phylogenetic analysis of the picorna-like superfamily. The authors conclude that the diverse groups of picorna-like viruses probably evolved in a 'Big Bang' that came after the evolution of the main groups of eukaryotes.

A significant proportion of the molecular evolution of bacteria and archaea occurs through gene gain and loss. Here Iranzo et al. develop a mathematical model that explains observed differential patterns of sequence evolution vs. gene content evolution as a consequence of homologous recombination.

Here, the authors analyze 4907 Circular Metagenome Assembled Genomes from human microbiomes and identify and characterize nearly 600 diverse genomes of crAss-like phages, finding two putative families with unusual genomic features, including high density of self-splicing introns and inteins.

Comparative analysis of 162 genomes of Asgard archaea results in six newly proposed phyla, including a deep branch that is provisionally named Wukongarchaeota, and sheds light on the evolutionary history of this clade.

The COVID-19 pandemic highlighted the need to understand the emergence of viral variants, given that these can have implications for vaccination success. A bioinformatics tool offers a way to predict viral evolution.

The interplay between driver mutations and aneuploidy during tumorigenesis is largely unexplored. Here, the authors show two types of associations, leading to different therapeutic vulnerabilities and prognoses.

CRISPR-Cas is a host adaptive immunity system and viruses harbor diverse anti-CRISPR proteins (Acrs). Here, the authors develop a random forest machine-learning approach to predict Acrs, identifying 2500 candidate Acr families, which expand the current repertoire of predicted Acrs by two orders of magnitude.

Polintons are large DNA transposons that are widespread in the genomes of eukaryotes. Here, Krupovic and Koonin propose that Polintons were the first group of eukaryotic double-stranded DNA viruses to evolve from bacteriophages and that they gave rise to most large DNA viruses of eukaryotes and various other selfish elements.

Transposable elements are key drivers of evolutionary innovation across many species. This Opinion article proposes evolutionary scenarios in which transposable elements have acted on innate immunity loci to generate adaptive immune systems and discusses striking parallels between the evolution of different adaptive immune systems: CRISPR–Cas in bacteria and archaea, and V(D)J recombination in vertebrates.

Protein repeats may be considered a paradox, being evolutionarily conserved yet also hotspots of protein evolution associated with innovation. Here, the authors use a novel method to show that new repeats undergo rapid divergence within species, but are then fixed and conserved between species.

Bacteria of the genus Streptomyces have complex life cycles involving cellular differentiation and multicellular structures that have never been observed in archaea. Here, the authors show that several halophilic archaea display a life cycle resembling that of Streptomyces bacteria, undergoing cellular differentiation into mycelia and spores.

The concepts of orthology and paralogy are fundamental to comparative genomics and are also frequently used for the functional annotation of uncharacterized genes. However, assumptions regarding function have recently been challenged, and the implications of assigning genes as orthologues or paralogues are far from straightforward.

Incessant encounters of all cellular life forms with mobile genetic elements (MGEs) have driven the evolution of diverse defence mechanisms, including CRISPR–Cas and restriction–modification systems. In this Perspective, Koonin, Makarova, Wolf and Krupovic describe the surprisingly intricate interplay between MGEs and host defence systems. Not only do defence systems commonly show high horizontal mobility but many molecular components are ‘guns for hire’ that have been co-opted by defence systems from MGEs and vice versa.

The authors describe the structure and function of two evolutionarily diverged RNA polymerases of a thermophilic phage. One of the polymerases is fused to the phage tape measure protein, a virion component dictating the length of the phage tail.

Metagenomic analysis of a single RNA virome from the Yangshan Deep-Water Harbour in China enabled the recovery of more than 4,500 distinct RNA viruses, doubling the known set of RNA viruses to date, and provided insights into their biology.

Methanonatronarchaeia are a distinct class-level lineage of extremely halophilic methanogens, which lack features of classical methanogenesis and have a high intracellular concentration of potassium, suggesting potassium-based osmoprotection.