Intragenic DNA inversions expand bacterial coding capacity

Rachael B. Chanin, Patrick T. West, Jakob Wirbel, Matthew O. Gill, Gabriella Z. M. Green, Ryan M. Park, Nora Enright, Arjun M. Miklos, Angela S. Hickey, Erin F. Brooks, Krystal K. Lum, Ileana M. Cristea and Ami S. Bhatt ()
Additional contact information
Rachael B. Chanin: Stanford University
Patrick T. West: Stanford University
Jakob Wirbel: Stanford University
Matthew O. Gill: Stanford University
Gabriella Z. M. Green: Stanford University
Ryan M. Park: Stanford University
Nora Enright: Stanford University
Arjun M. Miklos: Stanford University
Angela S. Hickey: Stanford University
Erin F. Brooks: Stanford University
Krystal K. Lum: Princeton University
Ileana M. Cristea: Princeton University
Ami S. Bhatt: Stanford University

Nature, 2024, vol. 634, issue 8032, 234-242

Abstract: Abstract Bacterial populations that originate from a single bacterium are not strictly clonal and often contain subgroups with distinct phenotypes1. Bacteria can generate heterogeneity through phase variation—a preprogrammed, reversible mechanism that alters gene expression levels across a population1. One well-studied type of phase variation involves enzyme-mediated inversion of specific regions of genomic DNA2. Frequently, these DNA inversions flip the orientation of promoters, turning transcription of adjacent coding regions on or off2. Through this mechanism, inversion can affect fitness, survival or group dynamics3,4. Here, we describe the development of PhaVa, a computational tool that identifies DNA inversions using long-read datasets. We also identify 372 ‘intragenic invertons’, a novel class of DNA inversions found entirely within genes, in genomes of bacterial and archaeal isolates. Intragenic invertons allow a gene to encode two or more versions of a protein by flipping a DNA sequence within the coding region, thereby increasing coding capacity without increasing genome size. We validate ten intragenic invertons in the gut commensal Bacteroides thetaiotaomicron, and experimentally characterize an intragenic inverton in the thiamine biosynthesis gene thiC.

Date: 2024
References: Add references at CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/s41586-024-07970-4 Abstract (text/html)
Access to the full text of the articles in this series is restricted.

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:nature:v:634:y:2024:i:8032:d:10.1038_s41586-024-07970-4

Ordering information: This journal article can be ordered from
https://www.nature.com/

DOI: 10.1038/s41586-024-07970-4

Access Statistics for this article

Nature is currently edited by Magdalena Skipper

More articles in Nature from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().