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Published on: February 23, 2014
Precision Methylome and In Vivo Methylation Kinetics Characterization of Klebsiella pneumoniae
1CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; Department of Oncology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, People's Hospital of Henan University, Zhengzhou 450001, China; University of Chinese Academy of Sciences, Beijing 100049, China.
Abstract:
Klebsiella pneumoniae (K. pneumoniae) is an important pathogen that can cause severe hospital- and community-acquired infections. To systematically investigate its methylation features, we determined the whole-genome sequences of 14 K. pneumoniae strains covering varying serotypes, multilocus sequence types, clonal groups, viscosity/virulence, and drug resistance. Their methylomes were further characterized using Pacific Biosciences single-molecule real-time and bisulfite technologies. We identified 15 methylation motifs [13 N6-methyladenine (6mA) and two 5-methylcytosine (5mC) motifs], among which eight were novel. Their corresponding DNA methyltransferases were also validated. Additionally, we analyzed the genomic distribution of GATC and CCWGG methylation motifs shared by all strains, and identified differential distribution patterns of some hemi-/un-methylated GATC motifs, which tend to be located within intergenic regions (IGRs). Specifically, we characterized the in vivo methylation kinetics at single-base resolution on a genome-wide scale by simulating the dynamic processes of replication-mediated passive demethylation and MTase-catalyzed re-methylation. The slow methylation of the GATC motifs in the replication origin (oriC) regions and IGRs implicates the epigenetic regulation of replication initiation and transcription. Our findings illustrate the first comprehensive dynamic methylome map of K. pneumoniae at single-base resolution, and provide a useful reference to better understand epigenetic regulation in this and other bacterial species.
Insights
This study maps the dynamic methylome of Klebsiella pneumoniae, revealing novel methylation patterns and their role in regulating essential bacterial processes like replication and transcription.
Area of Science:
- Bacteriology and Epigenetics
- Genomics and Molecular Biology
Background:
- Klebsiella pneumoniae is a significant pathogen causing severe infections.
- Understanding its epigenetic mechanisms, particularly DNA methylation, is crucial for combating infections.
Purpose of the Study:
- To comprehensively map the methylome of K. pneumoniae strains.
- To identify novel methylation motifs and their associated enzymes.
- To investigate the dynamic methylation kinetics and its regulatory role.
Main Methods:
- Whole-genome sequencing of 14 K. pneumoniae strains.
- Methylome characterization using single-molecule real-time and bisulfite sequencing.
- Analysis of methylation motif distribution and in vivo methylation kinetics.
Main Results:
- Identified 15 methylation motifs (13 N6-methyladenine and 2 5-methylcytosine), including 8 novel motifs.
- Found differential distribution of GATC motifs in intergenic regions.
- Characterized genome-wide methylation kinetics, showing slow methylation in oriC and IGRs.
Conclusions:
- Provides the first comprehensive dynamic methylome map of K. pneumoniae at single-base resolution.
- Highlights the epigenetic regulation of replication initiation and transcription by DNA methylation.
- Offers a valuable reference for studying bacterial epigenetics.
