Cellular and Genomic Properties of Haloferax gibbonsii LR2-5, the Host of Euryarchaeal Virus HFTV1

Tittes, Collin; Schwarzer, Sabine; Pfeiffer, Friedhelm; Dyall‐Smith, Mike; Rodriguez‐Franco, Marta; Oksanen, Hanna M.; Quax, Tessa E. F.

doi:10.3389/fmicb.2021.625599

Cited by 9 publications

(23 citation statements)

References 98 publications

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“…The quantitative plaque assay also allowed for the determination of the viral titer on the Haloferax host, which is an indication of the efficiency of infection. As a summary, we did not find any true virus-host pairs on any of the Haloferax strains, except on strain Haloferax gibbonsii LR2-5, which was isolated a few years ago from Lake Retba in Senegal at the same time as HFTV1 [59,60]. All LR2-5 infecting viruses had either Halorubrum or Haloarcula as their own host and their titers varied between 10 3 and 10 10 PFU/mL on LR2-5 (Table 1).…”

Section: Virusmentioning

confidence: 83%

“…Thus, we explored in more detail the antiviral defense mechanisms of the host and the viral escape mechanisms to determine if any of these factors could explain the differences in the ability to infect LR2-5 between viruses from the same family. LR2-5 does not have a CRISPR-cas system but encodes a predicted type I restriction modification (RM) system [60]. These antiviral mechanisms are based on methylation of host DNA (to protect it) and cleavage of unmethylated DNA (viral DNA).…”

Section: Restriction-modification Systemsmentioning

confidence: 99%

“…Methylated motifs in the genome of LR2-5 were previously predicted [60]. We searched for sequences in viral genomes that might be recognized by the host methyltransferases.…”

Section: Restriction-modification Systemsmentioning

confidence: 99%

“…volcanii, and a defective provirus of Haloferax mediterranei has been identified, both of which are no longer available (M. Dyall-Smith, personal communication) [57,58]. At the moment, Haloferax tailed virus 1 (HFTV1) is only one virus isolated from a Haloferax host, and it was recently isolated together with its host Haloferax gibbonsii LR2-5 from the hypersaline Lake Retba in Senegal [59,60].…”

Section: Introductionmentioning

confidence: 99%

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The Viral Susceptibility of the Haloferax Species

Sourrouille

Schwarzer

Lequime

et al. 2022

Viruses

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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.

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Section: Virusmentioning

confidence: 83%

Section: Restriction-modification Systemsmentioning

confidence: 99%

“…Methylated motifs in the genome of LR2-5 were previously predicted [60]. We searched for sequences in viral genomes that might be recognized by the host methyltransferases.…”

Section: Restriction-modification Systemsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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The Viral Susceptibility of the Haloferax Species

Sourrouille

Schwarzer

Lequime

et al. 2022

Viruses

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“…The Hfx. volcanii genome annotation is continuously scrutinized, especially when a closely related genome is annotated [ 70 ].…”

Section: Methodsmentioning

confidence: 99%

Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea

Pfeiffer

Dyall‐Smith

2021

Genes

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Background: Annotation ambiguities and annotation errors are a general challenge in genomics. While a reliable protein function assignment can be obtained by experimental characterization, this is expensive and time-consuming, and the number of such Gold Standard Proteins (GSP) with experimental support remains very low compared to proteins annotated by sequence homology, usually through automated pipelines. Even a GSP may give a misleading assignment when used as a reference: the homolog may be close enough to support isofunctionality, but the substrate of the GSP is absent from the species being annotated. In such cases, the enzymes cannot be isofunctional. Here, we examined a variety of such issues in halophilic archaea (class Halobacteria), with a strong focus on the model haloarchaeon Haloferax volcanii. Results: Annotated proteins of Hfx. volcanii were identified for which public databases tend to assign a function that is probably incorrect. In some cases, an alternative, probably correct, function can be predicted or inferred from the available evidence, but this has not been adopted by public databases because experimental validation is lacking. In other cases, a probably invalid specific function is predicted by homology, and while there is evidence that this assigned function is unlikely, the true function remains elusive. We listed 50 of those cases, each with detailed background information, so that a conclusion about the most likely biological function can be drawn. For reasons of brevity and comprehension, only the key aspects are listed in the main text, with detailed information being provided in a corresponding section of the Supplementary Materials. Conclusions: Compiling, describing and summarizing these open annotation issues and functional predictions will benefit the scientific community in the general effort to improve the evaluation of protein function assignments and more thoroughly detail them. By highlighting the gaps and likely annotation errors currently in the databases, we hope this study will provide a framework for experimentalists to systematically confirm (or disprove) our function predictions or to uncover yet more unexpected functions.

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Methods to Analyze Motility in Eury- and Crenarchaea

Patro

Wolferen

et al. 2022

Archaea

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Cellular and Genomic Properties of Haloferax gibbonsii LR2-5, the Host of Euryarchaeal Virus HFTV1

Cited by 9 publications

References 98 publications

The Viral Susceptibility of the Haloferax Species

The Viral Susceptibility of the Haloferax Species

Open Issues for Protein Function Assignment in Haloferax volcanii and Other Halophilic Archaea

Methods to Analyze Motility in Eury- and Crenarchaea

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