CODON USAGE ADAPTATION LEADS TO HIGHER LIKELIHOOD FOR MAINTENANCE OF GENES HORIZONTALLY ACQUIRED BY BACTERIA FROM PHAGES

Horizontal gene transfer (HGT) accounts for much of the interspecies genetic diversity in bacteria. By introducing entire genes into the organism`s genome in a single event, HGT allows for acquisition of traits de novo. It may occur through one of the following: (i) conjugation, transfer of a plasmid by direct contact; (ii) transformation, uptake of genetic material from the environment; or (iii) transduction, transfer of genetic material via a bacteriophage.

Using pangenomes to analyze the genetic composition of bacteria, we divided the protein-coding genes of Escherichia coli into groups according to their relative abundance in species` genomes. Additionally, we classified each gene as either viral, i.e. belonging to a putative viral insert, or non-viral. This allowed us to observe that genes classified as viral tend to be better at remaining in the bacterial genome compared to genes acquired from other sources. This phenomenon can be viewed through the pangenome in two ways: (i) the percentage of viral genes is higher among pangenes considered as “rare” (genes that have orthologs in more than one genome and up to 25% of total genomes) than it is among pangenes considered as “unique” (genes that have orthologs in one genome); (ii) the percent of viral genes among pangenes considered as “core” (genes that have orthologs in all genomes) is higher than expected.

To try and explain this, we looked at the pangenes` codon usage patterns and ascertained that viral genes tend to be more biased than non-viral genes upon acquisition. This makes them more adapted to the host genome compared to other horizontally transferred genes and thereby increases their likelihood of remaining in the host genome.