The Birth of a Symbiont: Epigenome Analysis Reveals Shifting Methylation Profile

A recent publication from scientists at the University of Florida and the University of Missouri used SMRT Sequencing to analyze epigenomic changes that occur when free-living bacteria associate with a host and become symbiotic instead.
Published in the Frontiers in Microbiology journal, “Integrating DNA Methylation and Gene Expression Data in the Development of the Soybean-Bradyrhizobium N₂-Fixing Symbiosis” comes from a team of collaborators including lead author Austin Davis-Richardson and senior author Eric Triplett. The scientists aimed to assess the role of epigenetics in bacterial evolution from free-living to symbiont and chose SMRT Sequencing because it generates base-specific modification information as it sequences DNA.
In its symbiotic state, the nitrogen-fixing Bradyrhizobium diazoefficiens colonizes the roots of soybean plants. Previous studies had reported significant differences in gene expression as the bacterium underwent the transition from free-living to symbiont, leading this team to investigate how much of that could be explained by changes in methylation. They sequenced a free-living bacterium and an endosymbiont, generating a single finished 9 Mb contig representing the genome of the free-living organism. This was used as a reference genome for assembly of the symbiotic strain and made it possible for scientists to identify the 681 kb symbiosis island, which contains genes known to be involved in the infection process.
The methylation analysis found 3,276 changes in five DNA motifs between the strains; 768 of them were associated with differentiation from free-living to symbiotic state, representing more than 9% of all genes and more than 35% of genes with differential expression between the strains. Of the altered genes, 80 were located in the symbiosis island but currently have no known function in the differentiation process. Of the five DNA motifs found, four had increased methylation in the free-living bacterium, and intriguingly, the fifth — the 5’-CCTTG^m6AG-3’ motif — was only seen in the symbiont.
“These associations between methylation and expression changes in many B. diazoefficiens genes suggest an important role of the epigenome in bacterial differentiation to the symbiotic state,” the scientists report, noting that follow-up studies with more replicates will be needed to fully test the hypothesis.