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Mills J, Gebhard LJ, Schubotz F, Shevchenko A, Speth DR, Liao Y, Duggin IG, Marchfelder A, Erdmann S. Extracellular vesicle formation in Euryarchaeota is driven by a small GTPase. Proc Natl Acad Sci U S A 2024; 121:e2311321121. [PMID: 38408251 DOI: 10.1073/pnas.2311321121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 01/14/2024] [Indexed: 02/28/2024] Open
Abstract
Since their discovery, extracellular vesicles (EVs) have changed our view on how organisms interact with their extracellular world. EVs are able to traffic a diverse array of molecules across different species and even domains, facilitating numerous functions. In this study, we investigate EV production in Euryarchaeota, using the model organism Haloferax volcanii. We uncover that EVs enclose RNA, with specific transcripts preferentially enriched, including those with regulatory potential, and conclude that EVs can act as an RNA communication system between haloarchaea. We demonstrate the key role of an EV-associated small GTPase for EV formation in H. volcanii that is also present across other diverse evolutionary branches of Archaea. We propose the name, ArvA, for the identified family of archaeal vesiculating GTPases. Additionally, we show that two genes in the same operon with arvA (arvB and arvC) are also involved in EV formation. Both, arvB and arvC, are closely associated with arvA in the majority of other archaea encoding ArvA. Our work demonstrates that small GTPases involved in membrane deformation and vesiculation, ubiquitous in Eukaryotes, are also present in Archaea and are widely distributed across diverse archaeal phyla.
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Affiliation(s)
- Joshua Mills
- Archaeal Virology, Max Planck Institute for Marine Microbiology, Bremen 28359, Germany
| | - L Johanna Gebhard
- Archaeal Virology, Max Planck Institute for Marine Microbiology, Bremen 28359, Germany
| | - Florence Schubotz
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen 28359, Germany
| | - Anna Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden 01307, Germany
| | - Daan R Speth
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Bremen 28359, Germany
| | - Yan Liao
- The Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Iain G Duggin
- The Australian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, NSW 2007, Australia
| | | | - Susanne Erdmann
- Archaeal Virology, Max Planck Institute for Marine Microbiology, Bremen 28359, Germany
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2
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Isolation of a virus causing a chronic infection in the archaeal model organism Haloferax volcanii reveals antiviral activities of a provirus. Proc Natl Acad Sci U S A 2022; 119:e2205037119. [PMID: 35994644 PMCID: PMC9436352 DOI: 10.1073/pnas.2205037119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Viruses are important ecological, biogeochemical, and evolutionary drivers in every environment. Upon infection, they often cause the lysis of the host cell. However, some viruses exhibit alternative life cycles, such as chronic infections without cell lysis. The nature and the impact of chronic infections in prokaryotic host organisms remains largely unknown. Here, we characterize a novel haloarchaeal virus, Haloferax volcanii pleomorphic virus 1 (HFPV-1), which is currently the only virus infecting the model haloarchaeon Haloferax volcanii DS2, and demonstrate that HFPV-1 and H. volcanii are a great model system to study virus-host interactions in archaea. HFPV-1 is a pleomorphic virus that causes a chronic infection with continuous release of virus particles, but host and virus coexist without cell lysis or the appearance of resistant cells. Despite an only minor impact of the infection on host growth, we uncovered an extensive remodeling of the transcriptional program of the host (up to 1,049 differentially expressed genes). These changes are highlighted by a down-regulation of two endogenous provirus regions in the host genome, and we show that HFPV-1 infection is strongly influenced by a cross-talk between HFPV-1 and one of the proviruses mediated by a superinfection-like exclusion mechanism. Furthermore, HFPV-1 has a surprisingly wide host range among haloarchaea, and purified virus DNA can cause an infection after transformation into the host, making HFPV-1 a candidate for being developed into a genetic tool for a range of so far inaccessible haloarchaea.
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3
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Chen S, Tu D, Hong T, Luo Y, Shen L, Ren P, Lu P, Chen X. Genomic features of a new head-tail halovirus VOLN27B infecting a Halorubrum strain. Gene 2022; 841:146766. [PMID: 35908623 DOI: 10.1016/j.gene.2022.146766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 06/26/2022] [Accepted: 07/24/2022] [Indexed: 11/04/2022]
Abstract
Relatively few viruses infecting haloarchaea (haloviruses) have been reported. In this study, the genome sequence of VOLN27B, a recently described archaeal tailed virus (arTV) with a myovirus morphotype was described, along with the sequence of its host, Halorubrum spp. LN27. Halovirus VOLN27B contains a linear, dsDNA genome of 76,891 bp which is predicted to encode 109 proteins and four tRNAs (tRNAThr, tRNAArg, tRNAGly and tRNAAsn). The DNA G+C content of VOLN27B genome is 56.1 mol%, nearly 10% lower than that of its host strain. A 315 bp LTR (long terminal repeat) was detected in the genome. The genome of its host strain LN27 was 3,301,211 bp (chromosome and 1 plasmid) with a DNA G+C content of 68.3 mol% and 3,142 annotated protein coding genes. At least two hypothetical proviruses were detected in the genome. It lacked a CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) locus. Sequence similarity and phylogenetic tree reconstructions placed it within the genus Halorubrum as a potential new species. VOLN27B exhibits a distinct difference in the frequency of codon usage against its host strain Halorubrum sp. LN27. The organization of VOLN27B genome shows remarkable synteny and amino acid sequence similarity to the genomes and predicted proteins of HF1-like haloviruses (genus Haloferacalesvirus) and a provirus in the genome of Halorubrum depositum Y78. VOLN27B and its host Halorubrum sp. LN27 comprise a new virus-host system from a hypersaline ecosystem and can be used to further understand the novel biology at extreme salt concentration.
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Affiliation(s)
- Shaoxing Chen
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China.
| | - Demei Tu
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Tao Hong
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Yuqing Luo
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Liang Shen
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Ping Ren
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Peng Lu
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Xiangdong Chen
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan 430072, China.
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4
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VOLN27B: A New Head-Tailed Halovirus Isolated from an Underground Salt Crystal and Infecting Halorubrum. ARCHAEA (VANCOUVER, B.C.) 2022; 2021:8271899. [PMID: 34992502 PMCID: PMC8727067 DOI: 10.1155/2021/8271899] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 09/06/2021] [Accepted: 11/08/2021] [Indexed: 01/04/2023]
Abstract
A novel halovirus, VOLN27B, was isolated from a drill core sample taken at a depth of approximately 430 m, from a layer formed during the Cretaceous period (Anhui, China). VOLN27B infects the halophilic archaeon Halorubrum sp. LN27 and has a head-tailed morphotype with a contractile tail, typical of myoviruses. The average head diameter is 64 ± 2.0 nm, and uncontracted tails are 15 ± 1.0 × 65 ± 2.0 nm. The latent period is about 10 h. The maturing time of VOLN27B in cells of Halorubrum sp. LN27 was nearly 8 h. The adsorption time of VOLN27B on cells of Halorubrum sp. LN27 was less than 1 min. Virus particles are unstable at pH values less than 5 or when the NaCl concentration is below 12% (w/v). VOLN27B and Halorubrum sp. LN27 were recovered from the same hypersaline environment and provide a new virus-host system in haloarchaea.
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Wörtz J, Smith V, Fallmann J, König S, Thuraisingam T, Walther P, Urlaub H, Stadler PF, Allers T, Hille F, Marchfelder A. Cas1 and Fen1 Display Equivalent Functions During Archaeal DNA Repair. Front Microbiol 2022; 13:822304. [PMID: 35495653 PMCID: PMC9051519 DOI: 10.3389/fmicb.2022.822304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 02/21/2022] [Indexed: 12/12/2022] Open
Abstract
CRISPR-Cas constitutes an adaptive prokaryotic defence system against invasive nucleic acids like viruses and plasmids. Beyond their role in immunity, CRISPR-Cas systems have been shown to closely interact with components of cellular DNA repair pathways, either by regulating their expression or via direct protein-protein contact and enzymatic activity. The integrase Cas1 is usually involved in the adaptation phase of CRISPR-Cas immunity but an additional role in cellular DNA repair pathways has been proposed previously. Here, we analysed the capacity of an archaeal Cas1 from Haloferax volcanii to act upon DNA damage induced by oxidative stress and found that a deletion of the cas1 gene led to reduced survival rates following stress induction. In addition, our results indicate that Cas1 is directly involved in DNA repair as the enzymatically active site of the protein is crucial for growth under oxidative conditions. Based on biochemical assays, we propose a mechanism by which Cas1 plays a similar function to DNA repair protein Fen1 by cleaving branched intermediate structures. The present study broadens our understanding of the functional link between CRISPR-Cas immunity and DNA repair by demonstrating that Cas1 and Fen1 display equivalent roles during archaeal DNA damage repair.
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Affiliation(s)
| | - Victoria Smith
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Jörg Fallmann
- Department of Computer Science, Bioinformatics Group, Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
| | - Sabine König
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Institute of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | | | - Paul Walther
- Central Facility for Electron Microscopy, Ulm University, Ulm, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
- Institute of Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Peter F. Stadler
- Department of Computer Science, Bioinformatics Group, Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Competence Center for Scalable Data Services and Solutions, Leipzig Research Center for Civilization Diseases, University Leipzig, Leipzig, Germany
- Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia
- Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria
- Center for RNA in Technology and Health, University of Copenhagen, Copenhagen, Denmark
- Santa Fe Institute, Santa Fe, NM, United States
- Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany
| | - Thorsten Allers
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | | | - Anita Marchfelder
- Biology II, Ulm University, Ulm, Germany
- *Correspondence: Anita Marchfelder,
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Liu Y, Demina TA, Roux S, Aiewsakun P, Kazlauskas D, Simmonds P, Prangishvili D, Oksanen HM, Krupovic M. Diversity, taxonomy, and evolution of archaeal viruses of the class Caudoviricetes. PLoS Biol 2021; 19:e3001442. [PMID: 34752450 PMCID: PMC8651126 DOI: 10.1371/journal.pbio.3001442] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 12/07/2021] [Accepted: 10/17/2021] [Indexed: 11/19/2022] Open
Abstract
The archaeal tailed viruses (arTV), evolutionarily related to tailed double-stranded DNA (dsDNA) bacteriophages of the class Caudoviricetes, represent the most common isolates infecting halophilic archaea. Only a handful of these viruses have been genomically characterized, limiting our appreciation of their ecological impacts and evolution. Here, we present 37 new genomes of haloarchaeal tailed virus isolates, more than doubling the current number of sequenced arTVs. Analysis of all 63 available complete genomes of arTVs, which we propose to classify into 14 new families and 3 orders, suggests ancient divergence of archaeal and bacterial tailed viruses and points to an extensive sharing of genes involved in DNA metabolism and counterdefense mechanisms, illuminating common strategies of virus-host interactions with tailed bacteriophages. Coupling of the comparative genomics with the host range analysis on a broad panel of haloarchaeal species uncovered 4 distinct groups of viral tail fiber adhesins controlling the host range expansion. The survey of metagenomes using viral hallmark genes suggests that the global architecture of the arTV community is shaped through recurrent transfers between different biomes, including hypersaline, marine, and anoxic environments.
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Affiliation(s)
- Ying Liu
- Institut Pasteur, Université de Paris, Archaeal Virology Unit, Paris, France
| | - Tatiana A. Demina
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Pakorn Aiewsakun
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Darius Kazlauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - David Prangishvili
- Institut Pasteur, Université de Paris, Archaeal Virology Unit, Paris, France
- Ivane Javakhishvili Tbilisi State University, Tbilisi, Georgia
| | - Hanna M. Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Mart Krupovic
- Institut Pasteur, Université de Paris, Archaeal Virology Unit, Paris, France
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