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Estimation of the Genome-Wide Mutation Rate and Spectrum in the Archaeal Species Haloferax volcanii.

ABSTRACT: Organisms adapted to life in extreme habitats (extremophiles) can further our understanding of the mechanisms of genetic stability, particularly replication and repair. Despite the harsh environmental conditions they endure, these extremophiles represent a great deal of the Earth's biodiversity. Here, for the first time in a member of the archaeal domain, we report a genome-wide assay of spontaneous mutations in the halophilic species Haloferax volcanii using a direct and unbiased method: mutation accumulation experiments combined with deep whole-genome sequencing. H. volcanii is a key model organism not only for the study of halophilicity, but also for archaeal biology in general. Our methods measure the genome-wide rate, spectrum, and spatial distribution of spontaneous mutations. The estimated base substitution rate of 3.15 × 10^-10 per site per generation, or 0.0012 per genome per generation, is similar to the value found in mesophilic prokaryotes (optimal growth at ∼20-45°). This study contributes to a comprehensive phylogenetic view of how evolutionary forces and molecular mechanisms shape the rate and molecular spectrum of mutations across the tree of life.

SUBMITTER: Kucukyildirim S

PROVIDER: S-EPMC7404244 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Ubiquitin-like small archaeal modifier proteins (SAMPs) in Haloferax volcanii.

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Specificity of archaeal caspase activity in the extreme halophile Haloferax volcanii.

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Archaeal membrane-associated proteases: insights on Haloferax volcanii and other haloarchaea.

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The archaeal protein SepF is essential for cell division in Haloferax volcanii.

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Assigning a function to a conserved archaeal metallo-β-lactamase from Haloferax volcanii.

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| S-EPMC3296008 | biostudies-literature

The repeatability of genome-wide mutation rate and spectrum estimates.

Project description:Over the last decade, mutation studies have grown in popularity due to the affordability and accessibility of whole genome sequencing. As the number of species in which spontaneous mutation has been directly estimated approaches 20 across two domains of life, questions arise over the repeatability of results in such experiments. Five species were identified in which duplicate mutation studies have been performed. Across these studies the difference in estimated spontaneous mutation rate is at most, weakly significant (p < 0.01). However, a highly significant (p < 10(-5)), threefold difference in the rate of insertions/deletions (indels) exists between two recent studies in Schizosaccharomyces pombe. Upon investigation of the ancestral genome sequence for both studies, a possible anti-mutator allele was identified. The observed variation in indel rate may imply that the use of indel markers, such as microsatellites, for the investigation of genetic diversity within and among populations may be inappropriate because of the assumption of uniform mutation rate within a species.

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Crystal structure of the ubiquitin-like small archaeal modifier protein 2 from Haloferax volcanii.

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Genome-wide gene expression Haloferax volcanii under oxidative stress

Project description:The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) of H. volcanii upon treatment of NaOCl.

2022-05-25 | GSE204840 | GEO

Ionic strength-dependent conformations of a ubiquitin-like small archaeal modifier protein (SAMP1) from Haloferax volcanii.

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