1. Low base‐substitution mutation rate and predominance of insertion‐deletion events in the acidophilic bacteriumAcidobacterium capsulatum
- Author
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Sibel Kucukyildirim, Samuel F. Miller, and Michael Lynch
- Subjects
mutation rate ,Ecology ,acidophile ,mutation spectrum ,QH540-549.5 ,Ecology, Evolution, Behavior and Systematics ,Nature Notes ,Nature and Landscape Conservation - Abstract
Analyses of spontaneous mutation have shown that total genome‐wide mutation rates are quantitatively similar for most prokaryotic organisms. However, this view is mainly based on organisms that grow best around neutral pH values (6.0–8.0). In particular, the whole‐genome mutation rate has not been determined for an acidophilic organism. Here, we have determined the genome‐wide rate of spontaneous mutation in the acidophilic Acidobacterium capsulatum using a direct and unbiased method: a mutation‐accumulation experiment followed by whole‐genome sequencing. Evaluation of 69 mutation accumulation lines of A. capsulatum after an average of ~2900 cell divisions yielded a base‐substitution mutation rate of 1.22 × 10−10 per site per generation or 4 × 10−4 per genome per generation, which is significantly lower than the consensus value (2.5−4.6 × 10−3) of mesothermophilic (~15–40°C) and neutrophilic (pH 6–8) prokaryotic organisms. However, the insertion‐deletion rate (0.43 × 10−10 per site per generation) is high relative to the base‐substitution mutation rate. Organisms with a similar effective population size and a similar expected effect of genetic drift should have similar mutation rates. Because selection operates on the total mutation rate, it is suggested that the relatively high insertion‐deletion rate may be balanced by a low base‐substitution rate in A. capsulatum, with selection operating on the total mutation rate., Investigating organisms adapted to life in extreme habitats may further our understanding of the mechanisms of genome stability. Our methods precisely measure the genome‐wide rate, molecular spectrum, and spatial distribution of spontaneous mutations. To our knowledge, this report is the first experimental result of a genome‐wide mutation profile in an acidophilic prokaryote.
- Published
- 2021