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19 pages, 2611 KiB

Open AccessArticle

Influence of N-Glycosylation on Virus–Host Interactions in Halorubrum lacusprofundi

by L. Johanna Gebhard, Zlata Vershinin, Tomás Alarcón-Schumacher, Jerry Eichler and Susanne Erdmann

Viruses 2023, 15(7), 1469; https://0-doi-org.brum.beds.ac.uk/10.3390/v15071469 - 28 Jun 2023

Cited by 2 | Viewed by 1334

N-glycosylation is a post-translational modification of proteins that occurs across all three domains of life. In Archaea, N-glycosylation is crucial for cell stability and motility, but importantly also has significant implications for virus–host interactions. While some archaeal viruses present glycosylated proteins or interact [...] Read more.

N-glycosylation is a post-translational modification of proteins that occurs across all three domains of life. In Archaea, N-glycosylation is crucial for cell stability and motility, but importantly also has significant implications for virus–host interactions. While some archaeal viruses present glycosylated proteins or interact with glycosylated host proteins, the direct influence of N-glycosylation on archaeal virus–host interactions remains to be elucidated. In this study, we generated an N-glycosylation-deficient mutant of Halorubrum lacusprofundi, a halophilic archaeon commonly used to study cold adaptation, and examined the impact of compromised N-glycosylation on the infection dynamics of two very diverse viruses. While compromised N-glycosylation had no influence on the life cycle of the head-tailed virus HRTV-DL1, we observed a significant effect on membrane-containing virus HFPV-1. Both intracellular genome numbers and extracellular virus particle numbers of HFPV-1 were increased in the mutant strain, which we attribute to instability of the surface-layer which builds the protein envelope of the cell. When testing the impact of compromised N-glycosylation on the life cycle of plasmid vesicles, specialized membrane vesicles that transfer a plasmid between host cells, we determined that plasmid vesicle stability is strongly dependent on the host glycosylation machinery. Our study thus provides important insight into the role of N-glycosylation in virus–host interactions in Archaea, while pointing to how this influence strongly differs amongst various viruses and virus-like elements. Full article

(This article belongs to the Special Issue Archaeal Virology)

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16 pages, 2159 KiB

Open AccessArticle

Virus-Host Dynamics in Archaeal Groundwater Biofilms and the Associated Bacterial Community Composition

by Victoria Turzynski, Lea Griesdorn, Cristina Moraru, André R. Soares, Sophie A. Simon, Tom L. Stach, Janina Rahlff, Sarah P. Esser and Alexander J. Probst

Viruses 2023, 15(4), 910; https://0-doi-org.brum.beds.ac.uk/10.3390/v15040910 - 31 Mar 2023

Cited by 1 | Viewed by 1628

Abstract

Spatial and temporal distribution of lytic viruses in deep groundwater remains unexplored so far. Here, we tackle this gap of knowledge by studying viral infections of Altivir_1_MSI in biofilms dominated by the uncultivated host Candidatus Altiarchaeum hamiconexum sampled from deep anoxic groundwater over [...] Read more.

Spatial and temporal distribution of lytic viruses in deep groundwater remains unexplored so far. Here, we tackle this gap of knowledge by studying viral infections of Altivir_1_MSI in biofilms dominated by the uncultivated host Candidatus Altiarchaeum hamiconexum sampled from deep anoxic groundwater over a period of four years. Using virus-targeted direct-geneFISH (virusFISH) whose detection efficiency for individual viral particles was 15%, we show a significant and steady increase of virus infections from 2019 to 2022. Based on fluorescence micrographs of individual biofilm flocks, we determined different stages of viral infections in biofilms for single sampling events, demonstrating the progression of infection of biofilms in deep groundwater. Biofilms associated with many host cells undergoing lysis showed a substantial accumulation of filamentous microbes around infected cells probably feeding off host cell debris. Using 16S rRNA gene sequencing across ten individual biofilm flocks from one sampling event, we determined that the associated bacterial community remains relatively constant and was dominated by sulfate-reducing members affiliated with Desulfobacterota. Given the stability of the virus-host interaction in these deep groundwater samples, we postulate that the uncultivated virus-host system described herein represents a suitable model system for studying deep biosphere virus-host interactions in future research endeavors. Full article

(This article belongs to the Special Issue Archaeal Virology)

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22 pages, 2339 KiB

Open AccessArticle

Diversity of SIRV-like Viruses from a North American Population

by Joseph R. Fackler, Michael Dworjan, Khaled S. Gazi and Dennis W. Grogan

Viruses 2022, 14(7), 1439; https://0-doi-org.brum.beds.ac.uk/10.3390/v14071439 - 30 Jun 2022

Cited by 1 | Viewed by 1331

Abstract

A small subset of acidic hot springs sampled in Yellowstone National Park yielded rod-shaped viruses which lysed liquid host cultures and formed clear plaques on lawns of host cells. Three isolates chosen for detailed analysis were found to be genetically related to previously [...] Read more.

A small subset of acidic hot springs sampled in Yellowstone National Park yielded rod-shaped viruses which lysed liquid host cultures and formed clear plaques on lawns of host cells. Three isolates chosen for detailed analysis were found to be genetically related to previously described isolates of the Sulfolobus islandicus rod-shaped virus (SIRV), but distinct from them and from each other. Functional stability of the new isolates was assessed in a series of inactivation experiments. UV-C radiation inactivated one of the isolates somewhat faster than bacteriophage λ, suggesting that encapsidation in the SIRV-like virion did not confer unusual protection of the DNA from UV damage. With respect to high temperature, the new isolates were extremely, but not equally, stable. Several chemical treatments were found to inactivate the virions and, in some cases, to reveal apparent differences in virion stability among the isolates. Screening a larger set of isolates identified greater variation of these stability properties but found few correlations among the resulting profiles. The majority of host cells infected by the new isolates were killed, but survivors exhibited heritable resistance, which could not be attributed to CRISPR spacer acquisition or the loss of the pilus-related genes identified by earlier studies. Virus-resistant host variants arose at high frequency and most were resistant to multiple viral strains; conversely, resistant host clones generated virus-sensitive variants, also at high frequency. Virus-resistant cells lacked the ability of virus-sensitive cells to bind virions in liquid suspensions. Rapid interconversion of sensitive and resistant forms of a host strain suggests the operation of a yet-unidentified mechanism that acts to allow both the lytic virus and its host to propagate in highly localized natural populations, whereas variation of virion-stability phenotypes among the new viral isolates suggests that multiple molecular features contribute to the biological durability of these viruses. Full article

(This article belongs to the Special Issue Archaeal Virology)

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15 pages, 2496 KiB

Open AccessArticle

The Viral Susceptibility of the Haloferax Species

by Zaloa Aguirre Sourrouille, Sabine Schwarzer, Sebastian Lequime, Hanna M. Oksanen and Tessa E. F. Quax

Viruses 2022, 14(6), 1344; https://0-doi-org.brum.beds.ac.uk/10.3390/v14061344 - 20 Jun 2022

Cited by 5 | Viewed by 2663

Abstract

Viruses can infect members of all three domains of life. However, little is known about viruses infecting archaea and the mechanisms that determine their host interactions are poorly understood. Investigations of molecular mechanisms of viral infection rely on genetically accessible virus–host model systems. [...] Read more.

Viruses can infect members of all three domains of life. However, little is known about viruses infecting archaea and the mechanisms that determine their host interactions are poorly understood. Investigations of molecular mechanisms of viral infection rely on genetically accessible virus–host model systems. Euryarchaea belonging to the genus Haloferax are interesting models, as a reliable genetic system and versatile microscopy methods are available. However, only one virus infecting the Haloferax species is currently available. In this study, we tested ~100 haloarchaeal virus isolates for their infectivity on 14 Haloferax strains. From this, we identified 10 virus isolates in total capable of infecting Haloferax strains, which represented myovirus or siphovirus morphotypes. Surprisingly, the only susceptible strain of all 14 tested was Haloferax gibbonsii LR2-5, which serves as an auspicious host for all of these 10 viruses. By applying comparative genomics, we shed light on factors determining the host range of haloarchaeal viruses on Haloferax. We anticipate our study to be a starting point in the study of haloarchaeal virus–host interactions. Full article

(This article belongs to the Special Issue Archaeal Virology)

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16 pages, 5872 KiB

Open AccessArticle

Halorubrum pleomorphic virus-6 Membrane Fusion Is Triggered by an S-Layer Component of Its Haloarchaeal Host

by Eduardo A. Bignon, Kevin R. Chou, Elina Roine and Nicole D. Tischler

Viruses 2022, 14(2), 254; https://0-doi-org.brum.beds.ac.uk/10.3390/v14020254 - 27 Jan 2022

Cited by 5 | Viewed by 2759

Abstract

(1) Background: Haloarchaea comprise extremely halophilic organisms of the Archaea domain. They are single-cell organisms with distinctive membrane lipids and a protein-based cell wall or surface layer (S-layer) formed by a glycoprotein array. Pleolipoviruses, which infect haloarchaeal cells, have an envelope analogous to [...] Read more.

(1) Background: Haloarchaea comprise extremely halophilic organisms of the Archaea domain. They are single-cell organisms with distinctive membrane lipids and a protein-based cell wall or surface layer (S-layer) formed by a glycoprotein array. Pleolipoviruses, which infect haloarchaeal cells, have an envelope analogous to eukaryotic enveloped viruses. One such member, Halorubrum pleomorphic virus 6 (HRPV-6), has been shown to enter host cells through virus-cell membrane fusion. The HRPV-6 fusion activity was attributed to its VP4-like spike protein, but the physiological trigger required to induce membrane fusion remains yet unknown. (2) Methods: We used SDS-PAGE mass spectroscopy to characterize the S-layer extract, established a proteoliposome system, and used R18-fluorescence dequenching to measure membrane fusion. (3) Results: We show that the S-layer extraction by Mg²⁺ chelating from the HRPV-6 host, Halorubrum sp. SS7-4, abrogates HRPV-6 membrane fusion. When we in turn reconstituted the S-layer extract from Hrr. sp. SS7-4 onto liposomes in the presence of Mg²⁺, HRPV-6 membrane fusion with the proteoliposomes could be readily observed. This was not the case with liposomes alone or with proteoliposomes carrying the S-layer extract from other haloarchaea, such as Haloferax volcanii. (4) Conclusions: The S-layer extract from the host, Hrr. sp. SS7-4, corresponds to the physiological fusion trigger of HRPV-6. Full article

(This article belongs to the Special Issue Archaeal Virology)

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14 pages, 2091 KiB

Open AccessArticle

Halovirus HF2 Intergenic Repeat Sequences Carry Promoters

by Brendan Russ, Friedhelm Pfeiffer and Mike Dyall-Smith

Viruses 2021, 13(12), 2388; https://0-doi-org.brum.beds.ac.uk/10.3390/v13122388 - 29 Nov 2021

Viewed by 1840

Abstract

Halovirus HF2 was the first member of the Haloferacalesvirus genus to have its genome fully sequenced, which revealed two classes of intergenic repeat (IR) sequences: class I repeats of 58 bp in length, and class II repeats of 29 bp in length. Both [...] Read more.

Halovirus HF2 was the first member of the Haloferacalesvirus genus to have its genome fully sequenced, which revealed two classes of intergenic repeat (IR) sequences: class I repeats of 58 bp in length, and class II repeats of 29 bp in length. Both classes of repeat contain AT-rich motifs that were conjectured to represent promoters. In the present study, nine IRs were cloned upstream of the bgaH reporter gene, and all displayed promoter activity, providing experimental evidence for the previous conjecture. Comparative genomics showed that IR sequences and their relative genomic positions were strongly conserved among other members of the same virus genus. The transcription of HF2 was also examined by the reverse-transcriptase-PCR (RT-PCR) method, which demonstrated very long transcripts were produced that together covered most of the genome, and from both strands. The presence of long counter transcripts suggests a regulatory role or possibly unrecognized coding potential. Full article

(This article belongs to the Special Issue Archaeal Virology)

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13 pages, 1836 KiB

Open AccessArticle

Characterization of Blf4, an Archaeal Lytic Virus Targeting a Member of the Methanomicrobiales

by Katrin Weidenbach, Sandro Wolf, Anne Kupczok, Tobias Kern, Martin A. Fischer, Jochen Reetz, Natalia Urbańska, Sven Künzel, Ruth A. Schmitz and Michael Rother

Viruses 2021, 13(10), 1934; https://0-doi-org.brum.beds.ac.uk/10.3390/v13101934 - 26 Sep 2021

Cited by 8 | Viewed by 2599

Abstract

Today, the number of known viruses infecting methanogenic archaea is limited. Here, we report on a novel lytic virus, designated Blf4, and its host strain Methanoculleus bourgensis E02.3, a methanogenic archaeon belonging to the Methanomicrobiales, both isolated from a commercial biogas plant in [...] Read more.

Today, the number of known viruses infecting methanogenic archaea is limited. Here, we report on a novel lytic virus, designated Blf4, and its host strain Methanoculleus bourgensis E02.3, a methanogenic archaeon belonging to the Methanomicrobiales, both isolated from a commercial biogas plant in Germany. The virus consists of an icosahedral head 60 nm in diameter and a long non-contractile tail of 125 nm in length, which is consistent with the new isolate belonging to the Siphoviridae family. Electron microscopy revealed that Blf4 attaches to the vegetative cells of M. bourgensis E02.3 as well as to cellular appendages. Apart from M. bourgensis E02.3, none of the tested Methanoculleus strains were lysed by Blf4, indicating a narrow host range. The complete 37 kb dsDNA genome of Blf4 contains 63 open reading frames (ORFs), all organized in the same transcriptional direction. For most of the ORFs, potential functions were predicted. In addition, the genome of the host M. bourgensis E02.3 was sequenced and assembled, resulting in a 2.6 Mbp draft genome consisting of nine contigs. All genes required for a hydrogenotrophic lifestyle were predicted. A CRISPR/Cas system (type I-U) was identified with six spacers directed against Blf4, indicating that this defense system might not be very efficient in fending off invading Blf4 virus. Full article

(This article belongs to the Special Issue Archaeal Virology)

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Review

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18 pages, 3151 KiB

Open AccessReview

Genomics, Transcriptomics, and Proteomics of SSV1 and Related Fusellovirus: A Minireview

by Martina Aulitto, Laura Martinez-Alvarez, Salvatore Fusco, Qunxin She, Simonetta Bartolucci, Xu Peng and Patrizia Contursi

Viruses 2022, 14(10), 2082; https://0-doi-org.brum.beds.ac.uk/10.3390/v14102082 - 20 Sep 2022

Cited by 3 | Viewed by 1948

Abstract

Saccharolobus spindle-shaped virus 1 (SSV1) was one of the first viruses identified in the archaeal kingdom. Originally isolated from a Japanese species of Saccharolobus back in 1984, it has been extensively used as a model system for genomic, transcriptomic, and proteomic studies, as [...] Read more.

Saccharolobus spindle-shaped virus 1 (SSV1) was one of the first viruses identified in the archaeal kingdom. Originally isolated from a Japanese species of Saccharolobus back in 1984, it has been extensively used as a model system for genomic, transcriptomic, and proteomic studies, as well as to unveil the molecular mechanisms governing the host–virus interaction. The purpose of this mini review is to supply a compendium of four decades of research on the SSV1 virus. Full article

(This article belongs to the Special Issue Archaeal Virology)

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