Programmed Heterogeneity: Epigenetic Mechanisms in Bacteria

Casadesús, Josep; Low, David A.

doi:10.1074/jbc.r113.472274

Cited by 214 publications

(199 citation statements)

References 101 publications

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“…In contrast, Lobner-Olesen et al (55) and RobbinsMenke et al (56) found that the regulatory regions of differentially expressed genes were not enriched with GATC for both Dam Ϫ and Dam-overproducing mutants. While there are clear cases where methylation directly regulates gene expression in E. coli (57), the last two studies suggest that most differential gene expression in Dam mutants results from indirect effects of variable Dam concentrations on cell physiology, not from direct regulation of expression via methylation. Similarly, Ͼ30% of genes in E. coli C227-11 were differentially expressed after deleting the RM.EcoGIII methyltransferase, yet there were no clear connections to RM.EcoGIII methylation sites for most of these genes (22).…”

Section: Dynamics Of Dna Methylation and Gene Expressionmentioning

confidence: 99%

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

et al. 2013

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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 determined via SMRT sequencing of gene knockout mutants. In addition, we found that S. oneidensis MR-1 cultures grown under various culture conditions displayed different DNA methylation patterns. However, the small number of differentially methylated sites could not be directly linked to the much larger number of differentially expressed genes under these conditions, suggesting that DNA methylation is not a major regulator of gene expression in S. oneidensis MR-1. The enrichment of methylated GATC motifs in the origin of replication indicates that DNA methylation may regulate genome replication in a manner similar to that seen in Escherichia coli. Furthermore, comparative analyses suggest that many Gammaproteobacteria, including all members of the Shewanellaceae family, may also utilize DNA methylation to regulate genome replication.

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Section: Dynamics Of Dna Methylation and Gene Expressionmentioning

confidence: 99%

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

et al. 2013

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“…DNA MTases are ubiquitous enzymes in the prokaryotic world, where they play important roles in several cellular processes, such as host protection and epigenetic regulation (56)(57)(58). The genomes of various lytic and lysogenic phages have been shown to encode multi-and monospecific orphan MTases, which are not associated with any restriction enzymes.…”

Section: Fig 4 Comparison Of Restriction Patterns Of Dammentioning

confidence: 99%

Molecular Characterization of a Novel Temperate Sinorhizobium Bacteriophage, ФLM21, Encoding DNA Methyltransferase with CcrM-Like Specificity

Dziewit

Oscik

Bartosik

et al. 2014

J Virol

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ABSTRACT⌽LM21 is a temperate phage isolated from Sinorhizobium sp. strain LM21 (Alphaproteobacteria). Genomic analysis and electron microscopy suggested that ⌽LM21 is a member of the family Siphoviridae. The phage has an isometric head and a long noncontractile tail. The genome of ⌽LM21 has 50,827 bp of linear double-stranded DNA encoding 72 putative proteins, including proteins responsible for the assembly of the phage particles, DNA packaging, transcription, replication, and lysis. Virion proteins were characterized using mass spectrometry, leading to the identification of the major capsid and tail components, tape measure, and a putative portal protein. We have confirmed the activity of two gene products, a lytic enzyme (a putative chitinase) and a DNA methyltransferase, sharing sequence specificity with the cell cycle-regulating methyltransferase (CcrM) of the bacterial host. Interestingly, the genome of Sinorhizobium phage ⌽LM21 shows very limited similarity to other known phage genome sequences and is thus considered unique. IMPORTANCEProphages are known to play an important role in the genomic diversification of bacteria via horizontal gene transfer. The influence of prophages on pathogenic bacteria is very well documented. However, our knowledge of the overall impact of prophages on the survival of their lysogenic, nonpathogenic bacterial hosts is still limited. In particular, information on prophages of the agronomically important Sinorhizobium species is scarce. In this study, we describe the isolation and molecular characterization of a novel temperate bacteriophage, ⌽LM21, of Sinorhizobium sp. LM21. Since we have not found any similar sequences, we propose that this bacteriophage is a novel species. We conducted a functional analysis of selected proteins. We have demonstrated that the phage DNA methyltransferase has the same sequence specificity as the cell cycle-regulating methyltransferase CcrM of its host. We point out that this phenomenon of mimicking the host regulatory mechanisms by viruses is quite common in bacteriophages.

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“…Additionally, higher bacterial diversity in deep compared to shallow water corals 88,89 suggests that some deep habitat-specific microbes may be involved in nutrient cycling specific to the low-irradiance environments. Both genetic and epigenetic processes contribute to high phenotypic plasticity and rapid evolution in bacteria 90 . In addition, bacterial pathogens and mutualists are known to induce alterations in host epigenomes, leading to potentially long-lasting imprinting effects that provide a form of plasticity to their hosts 91 .…”

Section: Potential Involvement Of Microbes In Coral Acclimatizationmentioning

confidence: 99%

Rapid adaptive responses to climate change in corals

et al. 2017

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Programmed Heterogeneity: Epigenetic Mechanisms in Bacteria

Cited by 214 publications

References 101 publications

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

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

Molecular Characterization of a Novel Temperate Sinorhizobium Bacteriophage, ФLM21, Encoding DNA Methyltransferase with CcrM-Like Specificity

Rapid adaptive responses to climate change in corals

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