DNA transfer between two different species mediated by heterologous cell fusion in Clostridium coculture
Date
2024-01-12
Journal Title
Journal ISSN
Volume Title
Publisher
mBio
Abstract
Prokaryotic evolution is driven by random mutations and horizontal gene transfer (HGT). HGT occurs via transformation, transduction, or conjugation. We have previously shown that in syntrophic cocultures of Clostridium acetobutylicum and Clostridium ljungdahlii, heterologous cell fusion leads to a large-scale exchange of proteins and RNA between the two organisms. Here, we present evidence that heterologous cell fusion facilitates the exchange of DNA between the two organisms. Using selective subculturing, we isolated C. acetobutylicum cells which acquired and integrated into their genome portions of plasmid DNA from a plasmid-carrying C. ljungdahlii strain. Limiting-dilution plating and DNA methylation data based on PacBio Single-Molecule Real Time (SMRT) sequencing support the existence of hybrid C. acetobutylicum/C. ljungdahlii cells. These findings expand our understanding of multi-species microbiomes, their survival strategies, and evolution.
IMPORTANCE
Investigations of natural multispecies microbiomes and synthetic microbial cocultures are attracting renewed interest for their potential application in biotechnology, ecology, and medical fields. Previously, we have shown the syntrophic coculture of C. acetobutylicum and C. ljungdahlii undergoes heterologous cell-to-cell fusion, which facilitates the exchange of cytoplasmic protein and RNA between the two organisms. We now show that heterologous cell fusion between the two Clostridium organisms can facilitate the exchange of DNA. By applying selective pressures to this coculture system, we isolated clones of wild-type C. acetobutylicum which acquired the erythromycin resistance (erm) gene from the C. ljungdahlii strain carrying a plasmid with the erm gene. Single-molecule real-time sequencing revealed that the erm gene was integrated into the genome in a mosaic fashion. Our data also support the persistence of hybrid C. acetobutylicum/C. ljungdahlii cells displaying hybrid DNA-methylation patterns.
Description
This article was originally published in mBio. The version of record is available at: https://doi.org/10.1128/mbio.03133-23. Copyright © 2024 Charubin et al. This is an open access article distributed under the terms of the Creative Commons Attribution 4.0 International
license. This research was featured in UDaily on 1/12/2024 at: https://www.udel.edu/udaily/2024/january/terry-papoutsakis-bacterial-evolution-adaptation-genome-biotechnology/
Keywords
Clostridium ljungdahlii, Clostridium acetobutylicum, syntrophy, heterologous cell fusion, DNA exchange, DNA integration, plasmid DNA
Citation
Charubin K, Hill JD, Papoutsakis ET. 2024. DNA transfer between two different species mediated by heterologous cell fusion in Clostridium coculture. mBio 15:e03133-23. https://doi.org/10.1128/mbio.03133-23