Phase-variable type I restriction-modification systems: A new characterization methodology for high throughput sequencing data
Creators: name: Mendes, Catarina I.
name: Machado, Miguel P.
name: Melo-Cristino, José
name: Ramirez, Mário
name: Carriço, João A.
Publisher: name: F1000 Research Limited
Year: 2019

description: Background: Restriction-modification systems have long been considered a defense mechanism against foreign DNA. However, recent studies have uncovered a much wider variety of functions, from operon switching to hyper-variable shufflons. Type I systems are the most complex ones,consisting of three polypeptides: R (restriction, encoded by <i>hsdR</i>), M (modification, encoded by <i>hsdM</i>), and S (specificity, encoded by <i>hsdS</i>). A distinct group of type I systems, through phase variation, root epigenetic effects upon gene expression and phenotype.The S subunit contains two variable regions encoding the target recognition domains (TRD),and is usually accompanied by inverted silent <i>hsdS</i> units that, through recombination, allow for phase variation switching events. These phase-variable type I systems have been reported across several families, including Bacillale, Lactobacilliales, Mycoplasma and Bacteriodetes.<br><br>Method: We’ve developed a methodology for the analysis of phase-variable type I restriction-modification system based on mapping approach of short read paired-end high throughput sequencing data. <br>The general conformation of the full locus is evaluated. The presence of all gene units of the locus is assessed via gene coverage by mapping the raw data to each unit using ReMatCh. The proportion of the overall length of target region that was determined to be present and the sequence identity of those positions are considered when assessing the locus as present.<br>As previously demonstrated, the <i>hsdS</i> allele being transcribed cannot be reliably determined using assembly and/or standard mapping approaches due to the structural rearrangement mediating the phase variation. Instead, the conserved <i>hsdS</i> region, flanked by the <i>hsdM </i>gene,is used as target, retrieving the read mates of the sequences that align to this region. By mapping these mates to the optional TRD, the first variable region can be determined, and is then used as the new target sequencing. Retrieving the mates of the sequences that align to this region and mapping them to the second optional TRD allows the determination of the other variable <i>hsdS</i> region. However, it is possible that different alleles are expressed in the same bacterial population, requiring steps of validation to assess the reliability of the results.<br><br>Results &amp; Conclusions: <i>Streptococcus pneumoniae</i> contains two type I restriction-modification systems in its core genome, although only one, the <i>ivr</i> locus, with a six-phase variation, has been associated with epigenetic events that lead to different opacity phenotypes. We’ve developed ivrTyper, a tool for the automated detection of the likely expressed<i> hsdS</i> allele in <i>S. pneumoniae </i>directly from paired-end raw data.<br><br>References &amp; Acknowledgments: The ivrTyper and ReMatCh are available in GitHub at https://github.com/cimendes/ivrTyper and https://github.com/B-UMMI/ReMatCh/.