Bacterial adaptation by a transposition burst of an invading IS element

Abstract

The general importance of transposable elements (TEs) for adaptive evolution remains unclear. This in part reflects a poor understanding of the role of TEs for adaptation in non-model systems. Here, we investigated whether insertion sequence (IS) elements are a major source of beneficial mutations during 400 generations of laboratory evolution of the cyanobacterium Acaryochloris marina strain CCMEE 5410, which has experienced a recent or on-going IS element expansion and has among the highest transposase gene contents for a bacterial genome. Most mutations detected in the eight independent experimental populations were IS transposition events. Surprisingly, however, the majority of these involved the copy-and-paste activity of only a single copy of an unclassified element (ISAm1) that has recently invaded the strain CCMEE 5410 genome. ISAm1 transposition was largely responsible for the highly repeatable evolutionary dynamics observed among populations. Notably, this included mutations in multiple targets involved in the acquisition of inorganic carbon for photosynthesis that were exclusively due to ISAm1 activity. These mutations were associated with an increase in linear growth rate under conditions of reduced carbon availability but did not appear to impact fitness when carbon was readily available. Our study reveals that the activity of a single transposase can fuel adaptation for at least several hundred generations but may also potentially limit the rate of adaptation through clonal interference.

Emergence of novel non-aggregative variants under negative frequency-dependent selection in Klebsiella variicola

“…For long, transposition of IS was associated to fitness loss due to gene inactivation or expression changes. Here, we provide more evidence that IS can increase fitness and play an important role in adaptation, as was already shown across different species ranging from Enterobacteria (Consuegra et al 2021 , Frazão et al 2022 ) to Cyanobacteria (Miller et al 2021 ). A recent study in Bacillus subtilis and Bacillus thuringensis revived end-point populations from four different evolution experiments and showed that, independently of growth in either biotic or abiotic conditions, insertion sequences are critical in adaptation (Hu et al 2023 ).…”

Discovery of Chlorophyll d: Isolation and Characterization of a Far-Red Cyanobacterium from the Original Site of Manning and Strain (1943) at Moss Beach, California

“…strain Awaji, discovered by Murakami, et al [15] in Japan, for which there is no full genome sequence. However, it is closest in full genome comparison to strain S15 from the California coast [65], both epiphytes of red algae in the Pacific. Like strain S15, the Moss Beach strain also lacks complex phycobilisomes, as compared to type strain MBIC11017, perhaps indicating an adaptation to their similar red (or brown for strain Moss Beach) algal epiphyte spectral environment.…”

Diurnal transcriptional variation is reduced in a nitrogen-fixing diatom endosymbiont

“…Paired end short-read sequencing was performed with MiSeq500 v2 (Illumina). For R. gibba , high molecular weight DNA was also extracted using the protocol described elsewhere [ 23 ], prepped using a MinION Ligation Sequencing Kit, and sequenced using a FLO-MIN106 flow cell (Oxford Nanopore). All library preparations and sequencing were performed at the University of Montana Genomics Core.…”