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Papathanasiou P, Erdmann S, Leon-Sobrino C, Sharma K, Urlaub H, Garrett RA, Peng X. 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. RNA Biol 2018; 16:557-565. [PMID: 30146914 DOI: 10.1080/15476286.2018.1511674] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Carrier state viral infection constitutes an equilibrium state in which a limited fraction of a cellular population is infected while the remaining cells are transiently resistant to infection. This type of infection has been characterized for several bacteriophages but not, to date, for archaeal viruses. Here we demonstrate that the rudivirus SIRV3 can produce a host-dependent carrier state infection in the model crenarchaeon Sulfolobus. SIRV3 only infected a fraction of a Sulfolobus islandicus REY15A culture over several days during which host growth was unimpaired and no chromosomal DNA degradation was observed. CRISPR spacer acquisition from SIRV3 DNA was induced by coinfecting with the monocaudavirus SMV1 and it was coincident with increased transcript levels from subtype I-A adaptation and interference cas genes. However, this response did not significantly affect the carrier state infection of SIRV3 and both viruses were maintained in the culture over 12 days during which SIRV3 anti-CRISPR genes were shown to be expressed. Transcriptome and proteome analyses demonstrated that most SIRV3 genes were expressed at varying levels over time whereas SMV1 gene expression was generally low. The study yields insights into the basis for the stable infection of SIRV3 and the resistance to the different host CRISPR-Cas interference mechanisms. It also provides a rationale for the commonly observed coinfection of archaeal cells by different viruses in natural environments.
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Affiliation(s)
- Pavlos Papathanasiou
- a Danish Archaea Centre, Department of Biology , University of Copenhagen , Copenhagen N , Denmark
| | - Susanne Erdmann
- a Danish Archaea Centre, Department of Biology , University of Copenhagen , Copenhagen N , Denmark.,b ithree Institute, University of Technology Sydney , Sydney , Australia
| | - Carlos Leon-Sobrino
- a Danish Archaea Centre, Department of Biology , University of Copenhagen , Copenhagen N , Denmark.,c Centre for Microbial Ecology and Genomics, Department of Genetics , University of Pretoria , Hatfield , South Africa
| | - Kundan Sharma
- d Max Planck Institute of Biophysical Chemistry , Am Faßberg 11, D37077 Göttingen , Germany.,e Ludwig Institute for Cancer Research, University of Oxford , Oxford , UK
| | - Henning Urlaub
- d Max Planck Institute of Biophysical Chemistry , Am Faßberg 11, D37077 Göttingen , Germany.,f Bioanalytics Research Group, Institute of Clinical Chemistry, University Medical Center Göttingen , Göttingen , Germany
| | - Roger A Garrett
- a Danish Archaea Centre, Department of Biology , University of Copenhagen , Copenhagen N , Denmark
| | - Xu Peng
- a Danish Archaea Centre, Department of Biology , University of Copenhagen , Copenhagen N , Denmark
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Efficient CRISPR-Mediated Post-Transcriptional Gene Silencing in a Hyperthermophilic Archaeon Using Multiplexed crRNA Expression. G3-GENES GENOMES GENETICS 2016; 6:3161-3168. [PMID: 27507792 PMCID: PMC5068938 DOI: 10.1534/g3.116.032482] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-mediated RNA degradation is catalyzed by a type III system in the hyperthermophilic archaeon Sulfolobus solfataricus. Earlier work demonstrated that the system can be engineered to target specifically mRNA of an endogenous host reporter gene, namely the β-galactosidase in S. solfataricus. Here, we investigated the effect of single and multiple spacers targeting the mRNA of a second reporter gene, α-amylase, at the same, and at different, locations respectively, using a minimal CRISPR (miniCR) locus supplied on a viral shuttle vector. The use of increasing numbers of spacers reduced mRNA levels at progressively higher levels, with three crRNAs (CRISPR RNAs) leading to ∼ 70–80% reduction, and five spacers resulting in an α-amylase gene knockdown of > 90% measured on both mRNA and protein activity levels. Our results indicate that this technology can be used to increase or modulate gene knockdown for efficient post-transcriptional gene silencing in hyperthermophilic archaea, and potentially also in other organisms.
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