Bacterial phenotypic plasticity often arises as an adaptation to fluctuating environments, enabling the colonization of soil and the infection of plants and mammals. This phenotypic plasticity can be observed as colony morphotype variation (CMV) in the Burkholderia genus. It has been reported that some Burkholderia pseudomallei strains undergo distinct genomic changes and gene expression adaptations during infection. In contrast, Burkholderia cepacia complex species are known to lose their virulence megaplasmids (pc3), generating CMV and impacting virulence factor production.
In this study, we found that six out of eight published Burkholderia ambifaria (Ba) clinical isolate variants with altered phenotypes, indeed, lost their pc3 (e.g., isolate CEP0996). The other two retain an intact megaplasmid (e.g., isolate HSJ1), indicating phase variation as a second CMV mechanism. Thus, we aimed to compare both types of CMV and understand how phase variation is controlled in Ba HSJ1 by using genomic, proteomic and phenomic analyses.
Even though the two representative group models demonstrated significant genomic differences, they showed common traits in virulence factor production regulated by the Cep quorum sensing (QS) system when compared. Although variant strains are not deficient in producing Cep QS signal molecules, we confirmed that the Cep QS system is necessary for phase variant emergence in Ba HSJ1. Given that DNA methylation is a key epigenetic factor in bacterial phase variation and regulates some Burkholderia cenocepacia (Bc) virulence factors, we hypothesized that adenosine DNA methylation could actively influence Ba phase variation. By individually deleting three putative adenosine DNA methyltransferases, we discovered that DNA methyltransferase (DNA MTase) 2 inhibits variant emergence, whereas DNA MTase 1 regulates virulence factor genes.
This study is the first to report that QS and DNA methylation act as antagonistic systems in controlling Ba phase variation, with DNA MTase 2 activating the production of the CEP2 QS signal molecule.