Sabine Schwarzer

Archaea can be infected by morphologically diverse viruses, and the study of these viruses is important for understanding viral evolution in general. Archaeal tailed viruses make up the largest group of isolated archaeal viruses and the major class of isolated viruses infecting haloarchaea. Yet, little is known about the infection strategies of these viruses. In this study, we focus on archaeal myoviruses and investigate their infection cycles. HRTV-7 and HRTV-10 are both capable of infecting multiple Halorubrum strains, including Halorubrum salinarum B2-2, which is well suited for light microscopy. Virus lifecycle experiments combined with plaque assays and time-lapse microscopy showed that both viruses have a predominantly lytic life cycle, with complete lysis occurring between 9 and 12 h post-infection. Cells swell considerably just prior to lysis, indicating that the cell envelope becomes compromised. Whole-genome sequencing of virus-insensitive strains suggests that HRTV-10 likely uses the S-layer, the main cell envelope component of these archaea, as a receptor. Interestingly, we observed full-length integration of HRTV-7 in virus-resistant cells, as well as parts of the viral genome within the host genome, suggesting viral resistance based on superinfection exclusion. Together, these findings contribute to our understanding of archaeal virus-host interactions and provide insight into their infection strategies. IMPORTANCE: Viruses of archaea are important to understand the diversity and evolution of all viruses. However, they are little studied. Archaea are ubiquitous microorganisms, of which some thrive at extreme conditions, such as high salt concentrations. Salt-loving haloarchaea are excellent models to study archaeal virus-host interactions due to the high availability of viral isolates and suitability for microscopy. Bacteria and archaea are both infected by tailed viruses; however, in archaea, their infection mechanisms are largely unknown. We used two tailed archaeal viruses infecting the same host to compare their infection strategies. Both viruses induce cell lysis of the host, which is preceded by cell bloating. Interestingly, one of the viruses can integrate into the genome of the host, which renders the strain resistant, suggesting a mechanism of superinfection exclusion. This work provides insight into archaeal virus-host interactions, thereby contributing to the exploration of the unusual archaeal virosphere.

The crystalline surface layer (S-layer) of prokaryotes constitutes a critical macromolecular interface governing virus–host interactions. In this review, we synthesize recent findings regarding the role of S-layer glycoproteins as viral receptors, examine the structural and functional diversity of these systems across prokaryotic lineages, and analyze the molecular strategies that determine virus–host specificity. By integrating perspectives from structural biology, microbiology, and evolutionary studies, we seek to elucidate the fundamental principles and emerging themes that characterize virus–host interactions at the cell surface mediated by the S-layer.

Archaeal symbioses remain among the least understood cellular interactions. Ultra-small Nanobdellati (initially called DPANN) archaea rely on larger hosts for survival, yet their effects on host eco-physiology and their interactions with infecting viruses have not yet been examined experimentally. Here, we established the first stable tripartite co-culture comprising a Nanobdellales symbiont (YN4), its archaeal host (YN4HA), and a virus (MTIV4). We analyzed this system using physiological, genomic, transcriptomic, glycoproteomic, and cryo-electron tomography (cryoET) approaches. CryoET analysis revealed that the Nanobdellales archaeon formed cone-like structures to contact the host, as has been observed in other Nanobdellati-host systems. In this system, the host is infected by the virus. The Nanobdellales archaeon mitigated virus-induced growth inhibition of the host without any detectable fitness cost, indicating a defensive mutualism rather than a strictly parasitic relationship. This protective effect may involve Nanobdellati-driven remodeling of host cell surface glycans, suggesting a previously unrecognized glycan-mediated defense strategy. Overall, our tripartite system provides new insight into complex archaeal interactions in extreme environments that cannot be captured through conventional binary co-culture systems.

Although viruses have been shown to infect all domains of life, our understanding of the genetic program behind the exploitation of host resources to produce progeny virions is thus far limited to several bacterial viruses. Therefore, to elucidate the transcriptome of euryarchaeal viruses and their hosts, we employed RNAseq analysis of samples taken at different time points from Haloferax gibbonsii LR2-5 cultures infected with the lytic model virus Haloferax tailed virus 1 (HFTV1). While following the transcription of viral genes throughout the infective life cycle, we observed a tight temporal regulation of viral transcripts and differential expression from within viral gene clusters. Furthermore, antisense RNAs (asRNAs) appear to play an important role in support of the timing of late-expressed viral genes. Therefore, with many differentially expressed transcripts, including intragenic transcripts and asRNAs, the regulatory machinery employed by HFTV1 contrasts with that of viral model systems (based on phages), in which antitermination and/or alternative polymerases (seemingly lacking in HFTV1) are more widespread. When examining differentially expressed host genes, we observed a strong downregulation of genes involved in motility, such as those encoding the archaellum and chemotaxis machinery, which was confirmed by swimming assays of HFTV1 infected cells. This might be a strategy of the virus to redirect energy flowing into movement toward the production of virions. In conclusion, this work provides a stepping stone for further exploration of the intriguing strategies of viral transcriptional regulation throughout their infection cycle across the domains of life. IMPORTANCE: Viruses infect members of all three domains of life, including Archaea. Euryarchaea are widespread microorganisms found in various environments, such as the human gut and solar salterns. Due to the exceptional availability of cell biology and genetic tools for some salt-loving archaea, they serve as a model system from which insights can be extrapolated. Insights into the regulation of viral infections are of particular importance, especially since HFTV1 has been adopted as a model virus by the archaeal viral community. We found that, while harboring parallels with bacterial viruses, such as tight temporal regulation, HFTV1 harbors an impressive number of differentially expressed transcriptional units. Furthermore, antisense RNAs and intragenic regulatory elements seem to play a much more prominent role in HFTV1 gene expression. Thus, this work challenges current models and provides valuable new insights into the gene regulation of viral infection of archaea, which mark similarities and differences with viruses from other domains of life.

While archaeal viruses show a stunning diversity of morphologies, many bear a notable resemblance to tailed bacterial phages. This raises fundamental questions: Do all tailed viruses share a common origin and do they infect their hosts in similar ways? Answering these questions requires high-resolution structural insights, yet no complete atomic models of archaeal viruses have been available. Here, we present the near-atomic resolution structure of Haloferax tailed virus 1 (HFTV1), an archaeal virus thriving in extreme salinity. Using cryo–electron microscopy, we resolve the architecture and assembly of all structural proteins and capture conformational transitions associated with DNA ejection. Our data reveal genome spooling within the capsid and identify putative receptor-binding and catalytic sites for host recognition and infection. These findings uncover key mechanisms of archaeal virus assembly, principles of virus-host interactions, and evolutionary links connecting archaeal, bacterial, and eukaryotic viruses.

Although viruses have been shown to infect all domains of life, our understanding of the genetic program behind the exploitation of host resources to produce progeny virions is thus far limited to several bacterial viruses. Therefore, to elucidate the transcriptome of euryarchaeal viruses and their hosts, we employed RNAseq analysis of samples taken at different time points from Haloferax gibbonsii LR2-5 cultures infected with the lytic model virus Haloferax Tailed Virus 1 (HFTV1). While following the transcription of viral genes throughout the infective life cycle, we observed a tight temporal regulation of viral transcripts as well as differential expression from within viral gene clusters. Furthermore, anti-sense RNAs (asRNAs) appear to play an important role in support of the timing of late-expressed viral genes. Therefore, with many differentially expressed transcripts, including intragenic transcripts and asRNAs, the regulatory machinery employed by HFTV1 contrasts with viral model systems (based on phages), in which antitermination and/or alternative polymerases (seemingly lacking in HFTV1) are more widespread. When looking into differentially expressed host genes, we observed a strong downregulation of genes involved in motility, such as the archaellum and chemotaxis machinery, which was confirmed with swimming assays of HFTV1 infected cells. This might be a strategy of the virus to redirect energy flowing into movement towards the production of virions. In conclusion, this work thus provides a stepping stone for further exploration of the intriguing strategies of viral transcriptional regulation of their infection cycle across the domains of life.

Outnumbering their hosts by at least a factor of 10, viruses are the most common biological entity on Earth, are major drivers of evolution, and greatly impact on the dynamics of our planet’s ecosystems. While viruses infecting bacteria and eukaryotes have been extensively studied, the viruses roaming the archaeal domain remain largely unexplored. In recent years, a growing number of archaeal viruses have been described, revealing a stunningly diverse range of morphologies that appear unique to archaea. Detailed structural studies are paramount to fully understand how archaeal viruses infect their hosts. However, no complete atomic models of archaeal viruses are available to date. Using electron cryo-microscopy, we investigated the structure of the archaeal virus Haloferax tailed virus 1 (HFTV1), which infects the halophile Haloferax gibbonsii LR2-5 originating from the Senegalese salt lake Retba. Through single particle analysis, we achieved near-atomic resolution for the entire set of HFTV1’s structural proteins, enabling the building of a full atomic model of the virion. Comparing the structures of DNA filled and empty capsids, we visualise structural changes occurring upon DNA ejection. By investigating the double-stranded DNA inside the capsid, we elucidate how the genome is spooled upon loading. Furthermore, our structure reveals putative cell-surface receptor-binding and catalytic roles of capsid turret, baseplate, and tail fibre proteins. Together, our data provide new insights into the mechanisms of HFTV1 assembly and infection, unveiling new perspectives on general rules of host-virus interactions in archaea and their evolutionary links to bacterial and eukaryotic viruses.

Archaeal viruses are the most enigmatic members of the virosphere. These viruses infect ubiquitous archaea and display an unusually high structural and genetic diversity.