Stable maintenance of the rudivirus SIRV3 in a carrier state in <i>Sulfolobus islandicus</i> despite activation of the CRISPR-Cas immune response by a second virus SMV1

Papathanasiou, Pavlos; Erdmann, Susanne; León‐Sobrino, Carlos; Sharma, K. C.; Urlaub, Henning; Garrett, Roger A.; Peng, Xu

doi:10.1080/15476286.2018.1511674

Cited by 12 publications

(8 citation statements)

References 43 publications

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“…The SIFV infection cycle starts with rapid virion adsorption to the host cell surface. The high rate of adsorption, similar to that documented for other hyperthermophilic archaeal viruses (8,9,12,46), is likely to be important for limiting the exposure of the viral particles to extreme environmental conditions. Notably, however, unlike many other hyperthermophilic archaeal viruses which recognize their hosts through pili (12,(47)(48)(49), SIFV has been suggested to bind the receptor located directly within the cellular membrane (26).…”

Section: Discussionmentioning

confidence: 54%

A filamentous archaeal virus is enveloped inside the cell and released through pyramidal portals

Baquero

Gazi

Sachse

et al. 2021

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

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The majority of viruses infecting hyperthermophilic archaea display unique virion architectures and are evolutionarily unrelated to viruses of bacteria and eukaryotes. The lack of relationships to other known viruses suggests that the mechanisms of virus–host interaction in Archaea are also likely to be distinct. To gain insights into archaeal virus–host interactions, we studied the life cycle of the enveloped, ∼2-μm-long Sulfolobus islandicus filamentous virus (SIFV), a member of the family Lipothrixviridae infecting a hyperthermophilic and acidophilic archaeon Saccharolobus islandicus LAL14/1. Using dual-axis electron tomography and convolutional neural network analysis, we characterize the life cycle of SIFV and show that the virions, which are nearly two times longer than the host cell diameter, are assembled in the cell cytoplasm, forming twisted virion bundles organized on a nonperfect hexagonal lattice. Remarkably, our results indicate that envelopment of the helical nucleocapsids takes place inside the cell rather than by budding as in the case of most other known enveloped viruses. The mature virions are released from the cell through large (up to 220 nm in diameter), six-sided pyramidal portals, which are built from multiple copies of a single 89-amino-acid-long viral protein gp43. The overexpression of this protein in Escherichia coli leads to pyramid formation in the bacterial membrane. Collectively, our results provide insights into the assembly and release of enveloped filamentous viruses and illuminate the evolution of virus–host interactions in Archaea.

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Section: Discussionmentioning

confidence: 54%

A filamentous archaeal virus is enveloped inside the cell and released through pyramidal portals

Baquero

Gazi

Sachse

et al. 2021

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

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“…Having investigated population-level CRISPR-Cas immunity to the non-lytic SSVs, we next compared these results with a lytic family of viruses. The SIRVs have large linear genomes that can use a lytic replication cycle or establish a carrier (non-integrated) infection state that does not include integration into the host genome [72,73]. For this study, we used five previously reported SIRVs identified from the same Nymph Lake hot springs as our Yellowstone S. islandicus strains, but from 2 years earlier (table 1) [43].…”

Section: (C) Crispr Immunity Differs With Geographical Location and Timementioning

confidence: 99%

Diversified local CRISPR-Cas immunity to viruses ofSulfolobus islandicus

Pauly

Bautista

Black

et al. 2019

Phil. Trans. R. Soc. B

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The population diversity and structure of CRISPR-Cas immunity provides key insights into virus–host interactions. Here, we examined two geographically and genetically distinct natural populations of the thermophilic crenarchaeon Sulfolobus islandicus and their interactions with Sulfolobus spindle-shaped viruses (SSVs) and S. islandicus rod-shaped viruses (SIRVs). We found that both virus families can be targeted with high population distributed immunity, whereby most immune strains target a virus using unique unshared CRISPR spacers. In Kamchatka, Russia, we observed high immunity to chronic SSVs that increases over time. In this context, we found that some SSVs had shortened genomes lacking genes that are highly targeted by the S. islandicus population, indicating a potential mechanism of immune evasion. By contrast, in Yellowstone National Park, we found high inter- and intra-strain immune diversity targeting lytic SIRVs and low immunity to chronic SSVs. In this population, we observed evidence of SIRVs evolving immunity through mutations concentrated in the first five bases of protospacers. These results indicate that diversity and structure of antiviral CRISPR-Cas immunity for a single microbial species can differ by both the population and virus type, and suggest that different virus families use different mechanisms to evade CRISPR-Cas immunity. This article is part of a discussion meeting issue ‘The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems’.

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“…The crenarchaeon Sulfolobus islandicus LAL14/1 carries one subtype I-D CRISPR–Cas locus containing spacers matching the genome of the lytic rod-shaped virus, Sulfolobus islandicus rod-shaped virus 2 (SIRV2), for which it is a laboratory host 21 . To counter the CRISPR–Cas immunity, SIRV2 on its part expresses a 12.2 kDa anti-CRISPR (Acr) protein, AcrID1, which is conserved in many archaeal viruses including Sulfolobus islandicus rod-shaped virus 3 (SIRV3) 22 . SIRV3 AcrID1 was shown to inhibit type I-D immunity in S. islandicus through direct binding to the large subunit of the effector complex, Cas10d 23 .…”

Section: Resultsmentioning

confidence: 99%

Structural basis for inhibition of an archaeal CRISPR–Cas type I-D large subunit by an anti-CRISPR protein

et al. 2020

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A hallmark of type I CRISPR–Cas systems is the presence of Cas3, which contains both the nuclease and helicase activities required for DNA cleavage during interference. In subtype I-D systems, however, the histidine-aspartate (HD) nuclease domain is encoded as part of a Cas10-like large effector complex subunit and the helicase activity in a separate Cas3’ subunit, but the functional and mechanistic consequences of this organisation are not currently understood. Here we show that the Sulfolobus islandicus type I-D Cas10d large subunit exhibits an unusual domain architecture consisting of a Cas3-like HD nuclease domain fused to a degenerate polymerase fold and a C-terminal domain structurally similar to Cas11. Crystal structures of Cas10d both in isolation and bound to S. islandicus rod-shaped virus 3 AcrID1 reveal that the anti-CRISPR protein sequesters the large subunit in a non-functional state unable to form a cleavage-competent effector complex. The architecture of Cas10d suggests that the type I-D effector complex is similar to those found in type III CRISPR–Cas systems and that this feature is specifically exploited by phages for anti-CRISPR defence.

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Stable maintenance of the rudivirus SIRV3 in a carrier state in Sulfolobus islandicus despite activation of the CRISPR-Cas immune response by a second virus SMV1

Cited by 12 publications

References 43 publications

A filamentous archaeal virus is enveloped inside the cell and released through pyramidal portals

A filamentous archaeal virus is enveloped inside the cell and released through pyramidal portals

Diversified local CRISPR-Cas immunity to viruses ofSulfolobus islandicus

Structural basis for inhibition of an archaeal CRISPR–Cas type I-D large subunit by an anti-CRISPR protein

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