Analysis of the effect of conserved regions on bacterial plasmid host range

Abstract

Background: Genetic information is shared between different bacteria through mobile genetic elements, among which plasmids. Some plasmids are able to transfer and spread genetic information between different species. Understanding which genes allow plasmids to replicate in different species is useful in containing the antibiotic resistance epidemic, as well as aid in the creation of vectors in the field of genetic engineering. Which characteristics determine plasmid host range is not fully known. Current approaches either use nucleotide composition or a combination of the genes, also called a genetic backbone, comprising replication and conjugation machinery to predict plasmid host range, but these methods are not perfect in their predictions. As research has shown that plasmids have a certain genetic backbone, we test the hypothesis that conserved regions around replication, conjugation genes and post-segregational killing systems affect host range.

We found that the genes in our conserved regions were almost exclusively encountered in that specific order. When studying the functional annotations of genes in a conserved region, they seem to be functionally related and serve a more grand biological function. Although the replication and conjugation machinery, which are often used as predictors for host range, were found to be associated with plasmid host range, the conserved regions were generally similarly or more specific than the combination of these predictors, which suggests that some conserved regions affect plasmid host range. Several genes related to evading bacterial immune systems and partitioning systems were found to be less conserved, with more divergence in their sequence, for which we hypothesize that these genes usually mutate to ameliorate the cost of plasmid carriage.