Cellular and genomic properties of<i>Haloferax gibbonsii</i>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:10.1101/2020.10.26.354720

Cited by 3 publications

(5 citation statements)

References 99 publications

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“…volcanii [ 15 , 16 , 19 ] and Hfx. gibbonsii [ 42 ], during growth in liquid medium. The exact ODs at which the transition from rod-shaped to plate-shaped cells occurs is species-dependent and different for all strains.…”

Section: Resultsmentioning

confidence: 99%

“…volcanii and Hfx. gibbonsii LR2-5 are linked with motility [ 19 , 42 ], we studied if similar correlation can be found for Haloarcula species. Cells were grown in CA medium and observed at similar ODs as for cell-shape analysis with time lapse microscopy at 42 °C.…”

Section: Resultsmentioning

confidence: 99%

“…volcanii and Hfx. gibbonsii LR2-5 [ 15 , 16 , 19 , 42 ] as also a transition from rod- to plate-shaped cells was observed, although the transition took place later during growth for Har. hispanica compared to Hfx.…”

Section: Discussionmentioning

confidence: 99%

“…(iii) And finally, the Haloarcula strains generally contained a mixture of plate and triangular shaped cells in stationary phase, whereas Haloferax cells are mainly reported plate shaped in this phase, although triangular cells were also reported for Hfx. volcanii [ 11 , 19 , 42 ].…”

Section: Discussionmentioning

confidence: 99%

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Growth Phase Dependent Cell Shape of Haloarcula

et al. 2021

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Several haloarchaea are reported to be pleomorphic, while others exhibit remarkable shapes, such as squares. Recently, Haloferax volcanii was found to alter its morphology during growth. Cells are motile rods in early exponential phase, and immotile plates in stationary phase. It is unknown if this growth phase dependent cell shape alteration is a specific feature of Hfx. volcanii, or conserved amongst haloarchaea. Here, we studied the cell shape and motility of two haloarchaea species Haloarcula hispanica and Haloarcula californiae. With a combination of light and electron microscopy, we observed that both strains undergo a growth phase dependent morphological development, albeit in a slightly different fashion as Hfx. volcanii. For both Haloarcula strains, the cell size is changing throughout growth. Cell shape seems to be related with motility, as highly motile cells on semi-solid agar plates are predominantly rod-shaped. We conclude that the growth phase dependent cell morphology alteration might be a common feature amongst haloarchaea, and that cell shape is generally linked with a motile life style. The conservation of this phenomenon underscores the importance of studies of the molecular mechanisms regulating cell shape in archaea.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Growth Phase Dependent Cell Shape of Haloarcula

et al. 2021

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“…The Hfx. volcanii genome annotation is continuously scrutinized, especially when a closely related genome is annotated (Tittes et al, 2021). The 16 haloarchaeal genomes which are currently under survey are listed in Suppl.…”

Section: Curation Of Genome Annotation and Gold Standard Protein Identificationmentioning

confidence: 99%

Open issues for protein function assignment inHaloferax volcaniiand other halophilic archaea

Pfeiffer

Dyall‐Smith

2021

Preprint

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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 examine 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 list 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 key aspects are listed in the main text, with detailed information being provided in a corresponding section of the Supplementary Material. 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 sytematically confirm (or disprove) our function predictions or to uncover yet 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 ofHaloferax gibbonsiiLR2-5, the host of euryarchaeal virus HFTV1

Cited by 3 publications

References 99 publications

Growth Phase Dependent Cell Shape of Haloarcula

Growth Phase Dependent Cell Shape of Haloarcula

Open issues for protein function assignment inHaloferax volcaniiand other halophilic archaea

Methods to Analyze Motility in Eury- and Crenarchaea

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