A viral reckoning: viruses emerge as essential manipulators of global ecosystems

Roux, Simon; Brum, Jennifer R.

doi:10.1111/1758-2229.12700

Cited by 5 publications

(4 citation statements)

References 59 publications

(65 reference statements)

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“…Viruses are the master manipulators of their hosts at both cellular and population levels (50). Studies on virus-host interactions have greatly contributed to uncovering many fundamental aspects of cell biology, especially in eukaryotes, including mechanisms of membrane fusion, membrane scission by the ESCRT machinery, apoptosis, cytoskeleton remodeling, functioning of plasmodesmata in plants, and many more (51)(52)(53)(54).…”

Section: Discussionmentioning

confidence: 99%

Virus-induced cell gigantism and asymmetric cell division in archaea

Liu

Cvirkaitė-Krupovič

Baquero

et al. 2021

Proc. Natl. Acad. Sci. U.S.A.

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Archaeal viruses represent one of the most mysterious parts of the global virosphere, with many virus groups sharing no evolutionary relationship to viruses of bacteria or eukaryotes. How these viruses interact with their hosts remains largely unexplored. Here we show that nonlytic lemon-shaped virus STSV2 interferes with the cell cycle control of its host, hyperthermophilic and acidophilic archaeon Sulfolobus islandicus, arresting the cell cycle in the S phase. STSV2 infection leads to transcriptional repression of the cell division machinery, which is homologous to the eukaryotic endosomal sorting complexes required for transport (ESCRT) system. The infected cells grow up to 20-fold larger in size, have 8,000-fold larger volume compared to noninfected cells, and accumulate massive amounts of viral and cellular DNA. Whereas noninfected Sulfolobus cells divide symmetrically by binary fission, the STSV2-infected cells undergo asymmetric division, whereby giant cells release normal-sized cells by budding, resembling the division of budding yeast. Reinfection of the normal-sized cells produces a new generation of giant cells. If the CRISPR-Cas system is present, the giant cells acquire virus-derived spacers and terminate the virus spread, whereas in its absence, the cycle continues, suggesting that CRISPR-Cas is the primary defense system in Sulfolobus against STSV2. Collectively, our results show how an archaeal virus manipulates the cell cycle, transforming the cell into a giant virion-producing factory.

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Section: Discussionmentioning

confidence: 99%

Virus-induced cell gigantism and asymmetric cell division in archaea

Liu

Cvirkaitė-Krupovič

Baquero

et al. 2021

Proc. Natl. Acad. Sci. U.S.A.

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“…In the networks, 14 viral elements were predicted to infect multiple hosts that are from different phyla (8) or domains (6) (Supplemental Table S1). Following curation based on length of CRISPR-array containing scaffolds, quality of MAGs, and taxonomic consistency between MAGs and CRISPR-array encoding scaffolds, we predict that four cross-phylum viral infections are legitimate, one of which was identified in two networks.…”

Section: Cross-phylum/cross-domain Infectionmentioning

confidence: 99%

“…Metagenomics-based methods have identified a multitude of new viruses from a variety of environments 1-6 , but there is a recognized need for better representation from soil, plant-associated, and engineered environments 5 . Through their host interactions, prokaryotic viruses can disrupt microbial ecosystem services by reducing or eliminating the hosts responsible 4,5,7,8 , augment host metabolism with Auxiliary Metabolic Genes (AMGs) [9][10][11][12][13] , stimulate gene flow within microbial populations through horizontal gene transfer [14][15][16] , or alter host immunity through virallyencoded CRISPR arrays 17,18 that can also drive interviral conflicts 18,19 . While prokaryotic viruses are expected to be host-specific, recent research has provided evidence for non-specific prokaryotic viral infection across taxonomic orders 20 and even across phyla 5,21,22 .Current computational methods for matching microbial viruses to their putative hosts vary in accuracy and sensitivity 23 .…”

mentioning

confidence: 99%

CRISPR-resolved virus-host interactions in a municipal landfill include non-specific viruses, hyper-targeted viral populations, and interviral conflicts

George

Hug

2023

Sci Rep

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Viruses are the most abundant microbial guild on the planet, impacting microbial community structure and ecosystem services. Viruses are specifically understudied in engineered environments, including examinations of their host interactions. We examined host-virus interactions via host CRISPR spacer to viral protospacer mapping in a municipal landfill across two years. Viruses comprised ~ 4% of both the unassembled reads and assembled basepairs. A total of 458 unique virus-host connections captured hyper-targeted viral populations and host CRISPR array adaptation over time. Four viruses were predicted to infect across multiple phyla, suggesting that some viruses are far less host-specific than is currently understood. We detected 161 viral elements that encode CRISPR arrays, including one with 187 spacers, the longest virally-encoded CRISPR array described to date. Virally-encoded CRISPR arrays targeted other viral elements in interviral conflicts. CRISPR-encoding proviruses integrated into host chromosomes were latent examples of CRISPR-immunity-based superinfection exclusion. The bulk of the observed virus-host interactions fit the one-virus-one-host paradigm, but with limited geographic specificity. Our networks highlight rare and previously undescribed complex interactions influencing the ecology of this dynamic engineered system. Our observations indicate landfills, as heterogeneous contaminated sites with unique selective pressures, are key locations for atypical virus-host dynamics.

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“…Finally, we are currently exploring the use of targeted metagenomics and time-series analysis to understand the eco-evolutionary drivers and constraints on virus-host dynamics in nature. Eventually, we envision that a full viral ecogenomics toolkit will soon empower researchers to scrutinize viral communities and virus-host interactions with an unprecedented level of detail and resolution, enabling us to revisit long-standing biological questions and possibly inspiring new technologies for microbiome manipulation [45][46][47][48].…”

Section: Viral Ecogenomics: Exploring Viral Diversity and Virus-host Interactions From Metagenomes-by Simon Rouxmentioning

confidence: 99%

The International Virus Bioinformatics Meeting 2020

Hufsky

Beerenwinkel

Meyer

et al. 2020

Viruses

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The International Virus Bioinformatics Meeting 2020 was originally planned to take place in Bern, Switzerland, in March 2020. However, the COVID-19 pandemic put a spoke in the wheel of almost all conferences to be held in 2020. After moving the conference to 8–9 October 2020, we got hit by the second wave and finally decided at short notice to go fully online. On the other hand, the pandemic has made us even more aware of the importance of accelerating research in viral bioinformatics. Advances in bioinformatics have led to improved approaches to investigate viral infections and outbreaks. The International Virus Bioinformatics Meeting 2020 has attracted approximately 120 experts in virology and bioinformatics from all over the world to join the two-day virtual meeting. Despite concerns being raised that virtual meetings lack possibilities for face-to-face discussion, the participants from this small community created a highly interactive scientific environment, engaging in lively and inspiring discussions and suggesting new research directions and questions. The meeting featured five invited and twelve contributed talks, on the four main topics: (1) proteome and RNAome of RNA viruses, (2) viral metagenomics and ecology, (3) virus evolution and classification and (4) viral infections and immunology. Further, the meeting featured 20 oral poster presentations, all of which focused on specific areas of virus bioinformatics. This report summarizes the main research findings and highlights presented at the meeting.

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A viral reckoning: viruses emerge as essential manipulators of global ecosystems

Cited by 5 publications

References 59 publications

Virus-induced cell gigantism and asymmetric cell division in archaea

Virus-induced cell gigantism and asymmetric cell division in archaea

CRISPR-resolved virus-host interactions in a municipal landfill include non-specific viruses, hyper-targeted viral populations, and interviral conflicts

The International Virus Bioinformatics Meeting 2020

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