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Prichard A, Pogliano J. The intricate organizational strategy of nucleus-forming phages. Curr Opin Microbiol 2024; 79:102457. [PMID: 38581914 DOI: 10.1016/j.mib.2024.102457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/01/2024] [Accepted: 03/08/2024] [Indexed: 04/08/2024]
Abstract
Nucleus-forming phages (chimalliviruses) encode numerous genes responsible for creating intricate structures for viral replication. Research on this newly appreciated family of phages has begun to reveal the mechanisms underlying the subcellular organization of the nucleus-based phage replication cycle. These discoveries include the structure of the phage nuclear shell, the identification of a membrane-bound early phage infection intermediate, the dynamic localization of phage RNA polymerases, the phylogeny and core genome of chimalliviruses, and the variation in replication mechanisms across diverse nucleus-forming phages. This research is being propelled forward through the application of fluorescence microscopy and cryo-electron microscopy and the innovative use of new tools such as proximity labeling and RNA-targeting Clustered Regularly Interspaced Short Palindromic Repeats-Cas systems.
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Affiliation(s)
- Amy Prichard
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Joe Pogliano
- School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA.
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2
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Ding S, Hamm JN, Bale NJ, Sinninghe Damsté JS, Spang A. Selective lipid recruitment by an archaeal DPANN symbiont from its host. Nat Commun 2024; 15:3405. [PMID: 38649682 PMCID: PMC11035636 DOI: 10.1038/s41467-024-47750-2] [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: 12/06/2023] [Accepted: 04/11/2024] [Indexed: 04/25/2024] Open
Abstract
The symbiont Ca. Nanohaloarchaeum antarcticus is obligately dependent on its host Halorubrum lacusprofundi for lipids and other metabolites due to its lack of certain biosynthetic genes. However, it remains unclear which specific lipids or metabolites are acquired from its host, and how the host responds to infection. Here, we explored the lipidome dynamics of the Ca. Nha. antarcticus - Hrr. lacusprofundi symbiotic relationship during co-cultivation. By using a comprehensive untargeted lipidomic methodology, our study reveals that Ca. Nha. antarcticus selectively recruits 110 lipid species from its host, i.e., nearly two-thirds of the total number of host lipids. Lipid profiles of co-cultures displayed shifts in abundances of bacterioruberins and menaquinones and changes in degree of bilayer-forming glycerolipid unsaturation. This likely results in increased membrane fluidity and improved resistance to membrane disruptions, consistent with compensation for higher metabolic load and mechanical stress on host membranes when in contact with Ca. Nha. antarcticus cells. Notably, our findings differ from previous observations of other DPANN symbiont-host systems, where no differences in lipidome composition were reported. Altogether, our work emphasizes the strength of employing untargeted lipidomics approaches to provide details into the dynamics underlying a DPANN symbiont-host system.
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Affiliation(s)
- Su Ding
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, Texel, The Netherlands.
| | - Joshua N Hamm
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, Texel, The Netherlands.
| | - Nicole J Bale
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, Texel, The Netherlands
| | - Jaap S Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, Texel, The Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, The Netherlands
| | - Anja Spang
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, Texel, The Netherlands
- Department of Evolutionary & Population Biology, Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
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Kuiper BP, Schöntag AMC, Oksanen HM, Daum B, Quax TEF. Archaeal virus entry and egress. MICROLIFE 2024; 5:uqad048. [PMID: 38234448 PMCID: PMC10791045 DOI: 10.1093/femsml/uqad048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 11/08/2023] [Accepted: 01/02/2024] [Indexed: 01/19/2024]
Abstract
Archaeal viruses display a high degree of structural and genomic diversity. Few details are known about the mechanisms by which these viruses enter and exit their host cells. Research on archaeal viruses has lately made significant progress due to advances in genetic tools and imaging techniques, such as cryo-electron tomography (cryo-ET). In recent years, a steady output of newly identified archaeal viral receptors and egress mechanisms has offered the first insight into how archaeal viruses interact with the archaeal cell envelope. As more details about archaeal viral entry and egress are unravelled, patterns are starting to emerge. This helps to better understand the interactions between viruses and the archaeal cell envelope and how these compare to infection strategies of viruses in other domains of life. Here, we provide an overview of recent developments in the field of archaeal viral entry and egress, shedding light onto the most elusive part of the virosphere.
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Affiliation(s)
- Bastiaan P Kuiper
- Biology of Archaea and Viruses, Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, Faculty for Science and Engineering, University of Groningen, 7th floor, Nijenborgh 7, 9747 AG Groningen, the Netherlands
| | - Anna M C Schöntag
- Biology of Archaea and Viruses, Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, Faculty for Science and Engineering, University of Groningen, 7th floor, Nijenborgh 7, 9747 AG Groningen, the Netherlands
| | - Hanna M Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland
| | - Bertram Daum
- Living Systems Institute, Faculty of Health and Life Sciences, University of Exeter, Exeter EX4 4QD, United Kingdom
| | - Tessa E F Quax
- Biology of Archaea and Viruses, Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, Faculty for Science and Engineering, University of Groningen, 7th floor, Nijenborgh 7, 9747 AG Groningen, the Netherlands
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Overton MS, Manuel RD, Lawrence CM, Snyder JC. Viruses of the Turriviridae: an emerging model system for studying archaeal virus-host interactions. Front Microbiol 2023; 14:1258997. [PMID: 37808280 PMCID: PMC10551542 DOI: 10.3389/fmicb.2023.1258997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 09/04/2023] [Indexed: 10/10/2023] Open
Abstract
Viruses have played a central role in the evolution and ecology of cellular life since it first arose. Investigations into viral molecular biology and ecological dynamics have propelled abundant progress in our understanding of living systems, including genetic inheritance, cellular signaling and trafficking, and organismal development. As well, the discovery of viral lineages that infect members of all three domains suggest that these lineages originated at the earliest stages of biological evolution. Research into these viruses is helping to elucidate the conditions under which life arose, and the dynamics that directed its early development. Archaeal viruses have only recently become a subject of intense study, but investigations have already produced intriguing and exciting results. STIV was originally discovered in Yellowstone National Park and has been the focus of concentrated research. Through this research, a viral genetic system was created, a novel lysis mechanism was discovered, and the interaction of the virus with cellular ESCRT machinery was revealed. This review will summarize the discoveries within this group of viruses and will also discuss future work.
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Affiliation(s)
- Michael S. Overton
- Department of Biological Sciences, Cal Poly Pomona, Pomona, CA, United States
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Robert D. Manuel
- Department of Biological Sciences, Cal Poly Pomona, Pomona, CA, United States
| | - C. Martin Lawrence
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
| | - Jamie C. Snyder
- Department of Biological Sciences, Cal Poly Pomona, Pomona, CA, United States
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Feng X, Li Y, Tian C, Yang W, Liu X, Zhang C, Zeng Z. Isolation of archaeal viruses with lipid membrane from Tengchong acidic hot springs. Front Microbiol 2023; 14:1134935. [PMID: 37065132 PMCID: PMC10101205 DOI: 10.3389/fmicb.2023.1134935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 03/14/2023] [Indexed: 03/31/2023] Open
Abstract
Archaeal viruses are one of the most mysterious parts of the virosphere because of their diverse morphologies and unique genome contents. The crenarchaeal viruses are commonly found in high temperature and acidic hot springs, and the number of identified crenarchaeal viruses is being rapidly increased in recent two decades. Over fifty viruses infecting the members of the order Sulfolobales have been identified, most of which are from hot springs distributed in the United States, Russia, Iceland, Japan, and Italy. To further expand the reservoir of viruses infecting strains of Sulfolobaceae, we investigated virus diversity through cultivation-dependent approaches in hot springs in Tengchong, Yunnan, China. Eight different virus-like particles were detected in enrichment cultures, among which five new archaeal viruses were isolated and characterized. We showed that these viruses can infect acidophilic hyperthermophiles belonging to three different genera of the family Sulfolobaceae, namely, Saccharolobus, Sulfolobus, and Metallosphaera. We also compared the lipid compositions of the viral and cellular membranes and found that the lipid composition of some viral envelopes was very different from that of the host membrane. Collectively, our results showed that the Tengchong hot springs harbor highly diverse viruses, providing excellent models for archaeal virus-host studies.
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Affiliation(s)
- Xi Feng
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Yanan Li
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Chang Tian
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Wei Yang
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Xinyu Liu
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Changyi Zhang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- *Correspondence: Zhirui Zeng, ; Changyi Zhang,
| | - Zhirui Zeng
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
- *Correspondence: Zhirui Zeng, ; Changyi Zhang,
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Yu F, Luo W, Xie W, Li Y, Meng S, Kan J, Ye X, Peng T, Wang H, Huang T, Hu Z. Community reassemblies of eukaryotes, prokaryotes, and viruses in the hexabromocyclododecanes-contaminated microcosms. JOURNAL OF HAZARDOUS MATERIALS 2022; 436:129159. [PMID: 35643009 DOI: 10.1016/j.jhazmat.2022.129159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/28/2022] [Accepted: 05/12/2022] [Indexed: 06/15/2023]
Abstract
The microbial community in seriously contaminated environment were not well known. This research investigated the community reassemblies in microcosms made of two distinct mangrove sediments amended with high levels of hexabromocyclododecanes (HBCDs). After eight months of contamination, the transformation of HBCDs yielded various lower brominated products and resulted in acidification (pH ~2). Therefore, the degraders and dehalogenase homologous genes involved in transformation of HBCDs only presented in low abundance to avoid further deterioration of the habitats. Moreover, in these deteriorated habitats, 1344 bacterial, 969 archaeal, 599 eukaryotic (excluded fungi), 187 fungal OTUs, and 10 viral genera, were reduced compared with controls. Specifically, in two groups of microcosms, Zetaproteobacteria, Deinococcus-Thermus, Spirochaetes, Bacteroidetes, Euryarchaeota, and Ascomycota, were positively responding taxa to HBCDs. Caloneis (Bacillariophyta) and Ascomycota turned to the dominant eukaryotic and fungal taxa. Most of predominant taxa were related to the contamination of brominated flame retardants (BFRs). Microbial communities were reassembled in divergent and sediment-dependent manner. The long-term contamination of HBCDs leaded to the change of relations between many taxa, included some of the environmental viruses and their known hosts. This research highlight the importance of monitoring the ecological effects around plants producing or processing halogenated compounds.
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Affiliation(s)
- Fei Yu
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China
| | - Wenqi Luo
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China
| | - Wei Xie
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China
| | - Yuyang Li
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China
| | - Shanshan Meng
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China
| | - Jie Kan
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China
| | - Xueying Ye
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China
| | - Tao Peng
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China
| | - Hui Wang
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China
| | - Tongwang Huang
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China
| | - Zhong Hu
- Department of Biology, College of Science, Shantou University, Guangdong Province, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, Guangdong, PR China.
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