DNA Methylation by Restriction Modification Systems Affects the Global Transcriptome Profile in Borrelia burgdorferi.

Single Molecule Real Time (SMRT) sequencing was utilized to map the genome-wide DNA methylation pattern, and to identify consensus modified motifs in B. burgdorferi as well as isogenic methyltransferase mutants. Four conserved m6A modification motifs were identified, and were fully attributable to the presence of specific methyltransferases. Next, RNA-seq was compared between strains to determine the effects of altering global DNA methylation patterns on gene expression. Whole-genome transcriptome changes were observed in conjunction with the loss of methyltransferase enzymes, indicating that DNA methylation by restriction modification systems has effects on gene expression in B. burgdorferi. In vitro log-phase cultures of wild-type Borrelia burgdorferi isolate B31 (A3) and mutant strains lacking methyltransferases bbe02 (A3-NP1) or bbeo2 and bbq67 (5A18-NP1) were grown intriplicate. Genomic DNA was isolated and pooled for each strain for methylome analysis using PacBio SMRT sequencing. Transcriptomes were generated for each replicate by deep sequencing using Illumina miseq. Note: one replicate of A3-NP1 was discarded for transcriptome analysis.