Evolution recovers the fitness of Acinetobacter baylyi strains with large deletions through mutations in deletion-specific targets and global post-transcriptional regulators

• DOI: 10.1371/journal.pgen.1011306
• Publication Date: 2024-09-16T17:57:57Z
• Authors: Isaac Gifford; Gabriel A. Suárez; Jeffrey E. Barrick
• Keywords: Bacterial genome size

Organelles and endosymbionts have naturally evolved dramatically reduced genome sizes compared to their free-living ancestors. Synthetic biologists purposefully engineered streamlined microbial genomes create more efficient cellular chassis define the minimal components of life. During natural or streamlining, deletion many non-essential genes in combination often reduces bacterial fitness for idiosyncratic unknown reasons. We investigated how what extent laboratory evolution could overcome these defects six variants transposon-free Acinetobacter baylyi strain ADP1-ISx that each had a different 22- 42-kilobase region two strains with larger deletions 70 293 kilobases. replicate populations ~300 generations chemically defined medium complex sequenced endpoint clonal isolates. Fitness increased all cases were examined except ancestors failed improve one environments. Mutations affecting nine protein-coding small RNAs significantly associated environments certain The global post-transcriptional regulators rnd (ribonuclease D), csrA (RNA-binding carbon storage regulator), hfq protein chaperone) frequently mutated across strains, though incidence effects mutations on gene function varied ancestral environment. this regulatory network likely compensate an earlier transposon ancestor restored function. More generally, our results demonstrate lost during streamlining can usually be regained rapidly through recovery tends occur deletion-specific compensation adjustments.