Phage biology articles within Nature Communications

In this work, the authors report a system for production of short versions of a filamentous phage enables the structure to be determined by cryo-electron microscopy. Structure combined with mutagenesis allows the identification of phage domains that are important in bacterial attack and for release of new viral progeny.

Phage-plasmids are bacterial extrachromosomal elements that act both as plasmids and as viruses. Here, Shan et al. show that segregational drift and loss-of-function mutations play key roles in the infection dynamics of a cosmopolitan phage-plasmid, allowing it to create continuous productive infections in marine bacteria.

Bacteriophage therapy is evolving as a promising approach to tackling bacterial infection, even in the case of emerging antibiotic resistance. In this work, authors present the topical application of numerous Cutibacterium acnes phage in an in vivo mouse model of acne vulgaris.

To protect from host attack, numerous jumbo bacteriophages establish a micron-scale, protein-based structure to enclose their replicating DNA. Using cryoEM, the authors show that the 2D crystal enclosing this so-called phage nucleus is an assembly of tetramers linked by flexible loops and tails.

Bacteria are equipped with diverse immune strategies to fight bacteriophage infections, including restriction nucleases, abortive infection and CRISPR-Cas systems. Here, Arias et al. use mathematical models of immune responses in individual bacterial cells to highlight the importance of the timing and coordination of different antiviral systems, and present hypotheses that may inspire future research.

Numerous viruses use a portal system for dsDNA entry and exit from their capsid. Here the authors report the atomic structure of phage SPP1 portal DNA gatekeeper and its mechanism of assembly. They also identify evolution breakpoints between different tailed bacteriophages morphotypes and herpesviruses.

The jumbo contractile bacteriophage, Kp24, has been isolated from clinical strains of Klebsiella pneumonia. Here, the authors present structural and functional insight into the capsid, tail and tail fibres and how this impacts infectivity.

Previous bioinformatic analyses have indicated that bacteriophages can use genetic codes different from those of their host bacteria. Here, Peters et al. use metaproteomics to provide experimental evidence of reassignment of stop codon TAG to glutamine in phages found in the human gut microbiome.

E. coli phage SU10 has a short non-contractile tail. Here, the authors show that after cell binding, nozzle proteins and tail fibers of SU10 change conformation to form a nozzle that enables the delivery of the phage DNA into the bacterial cytoplasm.

The arbitrium system is a peptide-based communication system to coordinate the lysis-lysogenic cycle of phages infecting bacteria. Here Gallego del Sol et al. provide the crystal structure of Aim-receptor of Katmira phage infecting B. subtilis in apo, peptide-bound and DNA-bound form.

Here, the authors characterize gut viromes in a cohort of individuals with metabolic syndrome, which they find associated with a highly widespread family of gut bacteriophages they name Candidatus Heliusviridae.

Phages can use ACR proteins that inhibit the adaptive immunity activities of bacterial CRISPR-Cas systems. Here, Philippe et al. show that these systems can block ACR-containing phages by targeting the acr gene, and this can select for phage mutants carrying a deletion within acr that does not block DNA cleavage (interference) but prevents the addition of new immunity (spacer acquisition).

Phages use anti-CRISPR proteins (Acrs) to counteract the bacterial CRISPR-Cas systems. Here, the authors characterize AcrIF24, which functions as an Aca (Acr-associated) to repress and regulate its own transcription, dimerizes the Csy complex, blocks the hybridization of target DNA, and tethers non-sequence-specific DNA to the Csy complex.

Here, Johansen et al. develop an approach, Phages from Metagenomics Binning (PHAMB), that allows the binning of thousands of viral genomes directly from bulk metagenomics data, while simultaneously enabling clustering of viral genomes into accurate taxonomic viral populations, unveiling viral-microbial host interactions in the gut.

In viruses, multi-subunit ring-ATPases are involved in genome packaging. Here, using single-molecule techniques, the authors determine that the active bacteriophage T4 DNA packaging motor is a pentamer and show that the motor can tolerate inactive subunits, suggesting that strict coordination between the subunits is not crucial.

An outcome of phage infection, lateral transduction, has been shown to mobilize chromosomal genes between bacterial cells at rates that exceed those of mobile genetic elements such as plasmids. Does this mean that the bacterial chromosome should be considered a mobile genetic element?

New virions of Ff bacteriophages are extruded from the host cell via the channel built from phage protein pIV, homologous to bacterial secretins. Here, the authors report the structure of this channel from the f1 filamentous bacteriophage and propose its use as an adjuvant to increase the uptake and efficacy of antibiotics.

Here, the authors report a large-scale comparative analysis of <30,000 Diversity-Generating Retroelements (DGRs) across ~9000 metagenomes (representing diverse taxa and biomes), to identify patterns in terms of prevalence and activity. Combined with examination of longitudinal data on <100 metagenomes part of time series, they demonstrate that DGRs are broadly and consistently active, implying an important role in microbiota ecology and evolution.

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.

Virus speciation cannot be fully explained by the evolution of different host specificities. Here, Chaikeeratisak et al. identify ways viruses can remain genetically isolated despite co-infecting the same cell, providing insight into how new virus species evolve.

Bacteriophages and their hosts are involved in a constant evolutionary arms race that should lead to divergence between phage genes over time. Here, the authors recruit metagenomic reads to virus reference genomes and genome fragments in samples from cryoconite holes and show that phages with near-identical core genomes maintain diversity by possession of numerous flexible gene modules, where homologous genes present in the pan-genome interchange to create new phage variants.

Flagellotropic phages spin down flagella to reach the bacterial surface and must withstand remarkable drag forces. Here authors show how two nested sets of chainmail stabilise the viral head and a beta-hairpin regulates the formation of the robust yet pliable tail, characteristic of siphoviruses.

Gene transfer agents (GTAs) are phage-like particles that mediate lateral gene exchange. Here, the authors provide the structure of the GTA of Rhodobacter capsulatus (RcGTA), which resembles a tailed phage, and describe the conformational changes required for DNA ejection.

In icosahedral viruses, a symmetry-mismatched portal vertex is assembled by inserting a 12-fold-symmetric portal complex into a 5-fold-symmetric capsid environment. Here, the authors report a near-atomic-resolution in situ cryo-electron microscopy structure of this symmetrically mismatched viral vertex from bacteriophage T4.

The impact of bacteriophages in the human gut microbiome remains poorly understood. Here, the authors characterize coliphages isolated from a large cohort of 1-year-old infants and show that temperate coliphages dominate, while virulent ones have greater infectivity and broader host range.

Bacteria use CRISPR-Cas systems to protect themselves against viral infections. Here, Watson et al. show that a type I CRISPR-Cas system can induce abortive viral infection, where infected cells do not survive but viral propagation is decreased, thus protecting the bacterial population.

Bacterial pathogens often carry multiple phage-derived elements within their genome. Here, the authors show that two phage elements are co-regulated in Listeria monocytogenes, the first one controlling the induction of the second one, which in turn regulates virulence of their bacterial host.

Prophages are viral genomes integrated within bacterial genomes. Here, Rezaei Javan et al. identify nearly 800 prophages and satellite prophages in > 1300 Streptococcus genomes, and show that a satellite prophage is associated with virulence in a mouse model of pneumococcal infection.

Staphylococcus aureus pathogenicity islands (SaPIs) encode the master repressor Stl and after bacteriophage infection Stl interacts with specific phage proteins leading to a derepression of SaPIs. Here the authors provide structural insights into this family of repressors by determining the crystal structures of SaPIbov1 Stl alone and in complex with two structurally unrelated phage dUTPases.

Single-stranded RNA bacteriophages use a single maturation protein (Mat) to attach to a retractile pilus of the bacterial host. Here, the authors report the structures of the MS2 phage bound to the host receptor F-pili and define the orientations of Mat relative to the cell and emanating F-pili, providing new insights into the F-like type IV secretion systems.

Gene transfer agents (GTAs) are ‘domesticated’ bacteriophages that can transfer any genes between bacteria. Here, Paul Fogg identifies a protein that directly regulates transcription of GTA genes and whose expression is in turn controlled by a global cell-cycle regulator and a quorum-sensing regulator.

Smacoviruses are found in the intestinal tract of humans and animals but their precise host remains elusive. Here, the authors identify smacovirus-matching CRISPR spacer sequences in the faecal archaeon Candidatus Methanomassiliicoccus intestinalis, implicating Archaea as a potential host.

Some phages carry genes coding for anti-CRISPR (Acr) proteins that interfere with the activity of bacterial CRISPR-Cas systems. Here, Hynes et al. characterize a new Acr family from streptococcal phages and investigate its potential in genome-editing applications.

Mobile genetic elements called PLEs protect Vibrio cholerae from infection with phage ICP1 by unclear mechanisms. Here, McKitterick and Seed show that a PLE-encoded large serine recombinase exploits an ICP1 protein as a recombination directionality factor to excise this PLE in response to phage infection.

You et al. show that SrpA, a small protein widely conserved among bacteria, controls core cellular processes in response to phage infection and environmental signals in Pseudomonas aeruginosa, including cell motility, chemotaxis, biofilm formation, and virulence.

Host cell recognition is mediated by the phage tail tip proteins, which then triggers viral genome delivery via the phage tail. Here, the authors combine crystallography and cryoEM to structurally characterise the bacteriophage T5 tail tube structure before and after interaction with its host receptor.

Eukaryotic organisms are continuously exposed to bacteriophages, but these are not thought to enter non-phagocytic cells. Here, Lehti et al. show that a bacteriophage can bind to a specific receptor on the surface of human neuroblastoma cells in vitro, and be internalized via the endolysosomal route.

Virophages are recently-identified small viruses that infect larger viruses, yet their diversity and ecological roles are poorly understood. Here, Roux and colleagues present time series metagenomics data revealing new virophage genera and their putative ecological interactions in two freshwater lakes.

Tailed bacteriophages assemble empty precursor capsids known as procapsids that are subsequently filled with viral DNA by a genome-packaging motor. Here the authors present a structure-based analysis that suggests the signal for termination of genome packaging is achieved through a DNA-dependent symmetrization of portal protein.

MS2 is a single-stranded RNA bacteriophage that infects its host via adsorption to bacterial pili. Here the authors visualize the MS2 virion with asymmetric cryo-EM reconstruction, revealing that the genome of MS2 adopts a specific structure of asymmetrically distributed stem-loops connected to the capsid.

The bacterial ‘adaptive’ immune system known as CRISPR-Cas destroys foreign DNA molecules, such as viral genomes, to which the cells have previously been exposed. Here, Hynes et al.show that this gain of immunity is favoured by exposure to defective viruses, a result reminiscent of vaccination.