Exploring the Roles of DNA Methylation in the Metal-Reducing Bacterium Shewanella oneidensis MR-1

@article{Bendall2013ExploringTR,
  title={Exploring the Roles of DNA Methylation in the Metal-Reducing Bacterium Shewanella oneidensis MR-1},
  author={Matthew L. Bendall and Khai Luong and Kelly M. Wetmore and Matthew J. Blow and Jonas Korlach and Adam M. Deutschbauer and Rex R. Malmstrom},
  journal={Journal of Bacteriology},
  year={2013},
  volume={195},
  pages={4966 - 4974}
}
ABSTRACT We performed whole-genome analyses of DNA methylation in Shewanella oneidensis MR-1 to examine its possible role in regulating gene expression and other cellular processes. Single-molecule real-time (SMRT) sequencing revealed extensive methylation of adenine (N6mA) throughout the genome. These methylated bases were located in five sequence motifs, including three novel targets for type I restriction/modification enzymes. The sequence motifs targeted by putative methyltranferases were… 
The Epigenomic Landscape of Prokaryotes
TLDR
The results reveal the pervasive presence ofDNA methylation throughout the prokaryotic kingdoms, as well as the diversity of sequence specificities and potential functions of DNA methylation systems.
A novel DNA methylation motif identified in Bacillus pumilus BA06 and possible roles in the regulation of gene expression
TLDR
Single-molecule real-time sequencing can be used to identify a wide variety of chemical modifications of the genome, such as methylation, and it was found that deletion of the R-M system Bpu6ORFCP induced transcriptional changes in many genes and led to increased gene expression in pathways related to ABC transporters, sulfur metabolism, ribosomes, cysteine and methionine metabolism and starch and sucrose metabolism.
Genome-Wide Methylation Patterns in Salmonella enterica Subsp. enterica Serovars
TLDR
Using single molecule real-time (SMRT) DNA-sequencing, the complete genomes of eleven Salmonella enterica isolates from nine different serovars were sequenced and the whole-genome methylation patterns of each genome were analysed.
Deciphering bacterial epigenomes using modern sequencing technologies
TLDR
Advances in DNA sequencing technology have provided new opportunities for systematic detection of all three forms of methylated DNA at a genome-wide scale and offer unprecedented opportunities for achieving a more complete understanding of bacterial epigenomes.
DNA Methylation Assessed by SMRT Sequencing Is Linked to Mutations in Neisseria meningitidis Isolates
TLDR
A more diverse role of DNA methylation and Restriction-Modification systems in the evolution of prokaryotic genomes is suggested, including in isolates from asymptomatic carriers.
Pan-genome analyses of 24 Shewanella strains re-emphasize the diversification of their functions yet evolutionary dynamics of metal-reducing pathway
TLDR
The diversity of genes present in the accessory and specific genomes of Shewanella strains indicates that each strain uses different strategies to adapt to diverse environments.
Methyltransferases acquired by lactococcal 936-type phage provide protection against restriction endonuclease activity
TLDR
SMRT sequencing technology enabled the identification of the target motifs of MTases encoded by the genomes of three lytic 936-type phages and these MTases represent the first functional MTases identified in this species of phage.
Application of DNA adductomics to soil bacterium Sphingobium sp. strain KK22
TLDR
This work demonstrated the first application of DNA adductomics to examine DNA damage in a bacterium and sets a foundation for future work.
A new recombineering system for precise genome-editing in Shewanella oneidensis strain MR-1 using single-stranded oligonucleotides
TLDR
Development of a robust and simple electroporation method in S. oneidensis that allows an efficiency of ~4.0 x 106 transformants/µg DNA and a new prophage-mediated genome engineering (recombineering) system using a λ Red Beta homolog from Shewanella sp.
...
...

References

SHOWING 1-10 OF 99 REFERENCES
Comprehensive Methylome Characterization of Mycoplasma genitalium and Mycoplasma pneumoniae at Single-Base Resolution
TLDR
Analysis of the distribution of methylation sites across the genome of M. pneumoniae suggests a potential role for methylation in regulating the cell cycle, as well as in regulation of gene expression, in one of the first direct methylome profiling studies with single-base resolution from a bacterial organism.
Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing
TLDR
It is found that deletion of a phage-encoded methyltransferase-endonuclease (restriction-modification; RM) system induced global transcriptional changes and led to gene amplification, suggesting that the role of RM systems extends beyond protecting host genomes from foreign DNA.
Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing
TLDR
SMRT sequencing confirms the identity and position of the methylated base in cases where the MTase specificity was previously established by other methods and finds evidence of unanticipated MTase promiscuity with some enzymes apparently also modifying sequences that are related, but not identical to the cognate site.
An Epigenetic Switch Involving Overlapping Fur and DNA Methylation Optimizes Expression of a Type VI Secretion Gene Cluster
TLDR
It is shown that the sci1 gene cluster expression is under the control of an epigenetic switch depending on methylation: fur binding prevents methylation of a GATC motif, whereas methylation at this specific site decreases the affinity of Fur for its binding box.
Epigenetic Gene Regulation in the Bacterial World
TLDR
DNA adenine methylation plays roles in the virulence of diverse pathogens of humans and livestock animals, including pathogenic Escherichia coli, Salmonella, Vibrio, Yersinia, Haemophilus, and Brucella.
Whole Methylome Analysis by Ultra-Deep Sequencing Using Two-Base Encoding
TLDR
A whole methylome sequencing study that compares two different bisulfite conversion methods (in solution versus in gel), utilizing the high throughput of the SOLiD™ System is presented.
A whole genome approach to in vivo DNA-protein interactions in E. coli
TLDR
The in vivo protection at the Dam site upstream of the car operon was correlated with a downregulation of car expression, as expected of a feedback represser-binding model.
Quantitative whole-genome analysis of DNA-protein interactions by in vivo methylase protection in E. coli
TLDR
A global methylation-based technique was used to identify, display, and quantitate the in vivo occupancy of numerous protein-binding sites within the Escherichia coli genome, providing insights into their function based on a common pattern of transcriptional regulation.
Evidence-Based Annotation of Gene Function in Shewanella oneidensis MR-1 Using Genome-Wide Fitness Profiling across 121 Conditions
TLDR
Pools of tagged transposon mutants in the metal-reducing bacterium Shewanella oneidensis MR-1 are used to probe the mutant fitness of 3,355 genes in 121 diverse conditions including different growth substrates, alternative electron acceptors, stresses, and motility and it is found that genes in all functional categories have phenotypes, and that potentially redundant genes are likely to have distinct phenotypes.
Genome sequence of the dissimilatory metal ion–reducing bacterium Shewanella oneidensis
TLDR
This genome sequence represents a critical step in the elucidation of the pathways for reduction (and bioremediation) of pollutants such as uranium (U) and chromium (Cr), and offers a starting point for defining this organism's complex electron transport systems and metal ion–reducing capabilities.
...
...