Supra-operonic clusters of functionally related genes (SOCs) are a source of horizontal gene co-transfers

TL;DR

This study reveals that supra-operonic clusters (SOCs) are a fundamental unit of horizontal gene transfer in bacteria, extending beyond operons and influencing the size distribution of transferred DNA segments.

Contribution

It identifies and characterizes supra-operonic clusters as a key structural unit in bacterial horizontal gene transfer, expanding understanding beyond operons.

Findings

Most co-gained gene pairs are transferred within 30 kb.

Larger distances often involve phage-related gene transfer.

Distribution of gene transfer sizes aligns with SOCs, not operons.

Abstract

Adaptation of bacteria occurs predominantly via horizontal gene transfer (HGT). While it is widely recognized that horizontal acquisitions frequently encompass multiple genes, it is unclear what the size distribution of successfully transferred DNA segments looks like and what evolutionary forces shape this distribution. Here, we identified 1790 gene family pairs that were consistently co-gained on the same branches across a phylogeny of 53 E. coli strains. We estimated a lower limit of their genomic distances at the time they were transferred to their host genomes; this distribution shows a sharp upper bound at 30 kb. The same gene-pairs can have larger distances (up to 70 kb) in other genomes. These more distant pairs likely represent recent acquisitions via transduction that involve the co-transfer of excised prophage genes, as they are almost always associated with intervening phage-associated genes. The observed distribution of genomic distances of co-transferred genes is much broader than expected from a model based on the co-transfer of genes within operons; instead, this distribution is highly consistent with the size distribution of supra-operonic clusters (SOCs), groups of co-occurring and co-functioning genes that extend beyond operons. Thus, we propose that SOCs form a basic unit of horizontal gene transfer.