Comparative Analysis of Ralstonia solanacearum Methylomes

Erill, Ivan; Puigvert, Marina; Legrand, Ludovic; Guarischi-Sousa, Rodrigo; Vandecasteele, Céline; Setúbal, João Carlos; Genin, Stéphane; Guidot, Alice; Valls, Marc

doi:10.3389/fpls.2017.00504

Cited by 17 publications

(17 citation statements)

References 58 publications

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“…Two of the B. pseudomallei MTases (M.BpsI and M.BpsII) are homologous to the B. cenocepacia MTases BCAL3494 and BCAM0992. In Ralstonia solanacearum , an important plant pathogen that is phylogenetically related to B. cenocepacia , the GTWWAC methylation motif cooccurs with the respective homolog of the BCAM0992 MTase, whereas a BCAL3494 MTase homolog and methylation of CACAG are absent ( 42 ). As in B. cenocepacia , the BCAM0992 homolog in R. solanacearum is an orphan DNA MTase.…”

Section: Discussionmentioning

confidence: 99%

DNA Methylation Epigenetically Regulates Gene Expression in Burkholderia cenocepacia and Controls Biofilm Formation, Cell Aggregation, and Motility

Vandenbussche

Saß

Pinto‐Carbó

et al. 2020

mSphere

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CF patients diagnosed with Burkholderia cenocepacia infections often experience rapid deterioration of lung function, known as cepacia syndrome. B. cenocepacia has a large multireplicon genome, and much remains to be learned about regulation of gene expression in this organism. From studies in other (model) organisms, it is known that epigenetic changes through DNA methylation play an important role in this regulation. The identification of B. cenocepacia genes of which the expression is regulated by DNA methylation and identification of the regulatory systems involved in this methylation are likely to advance the biological understanding of B. cenocepacia cell adaptation via epigenetic regulation. In time, this might lead to novel approaches to tackle B. cenocepacia infections in CF patients.

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Section: Discussionmentioning

confidence: 99%

DNA Methylation Epigenetically Regulates Gene Expression in Burkholderia cenocepacia and Controls Biofilm Formation, Cell Aggregation, and Motility

Vandenbussche

Saß

Pinto‐Carbó

et al. 2020

mSphere

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“…There has been a recent surge in bacterial methylomic data released 32 , 33 , 35 , 37 – 39 , 48 . However, in these studies, SMRT sequencing only allowed the analysis of m6A and m4C modification marks, as the thorough identification of the third known DNA methylation mark (i.e.…”

Section: Discussionmentioning

confidence: 99%

The complete methylome of an entomopathogenic bacterium reveals the existence of loci with unmethylated Adenines

Payelleville

Legrand

Ogier

et al. 2018

Sci Rep

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DNA methylation can serve to control diverse phenomena in eukaryotes and prokaryotes, including gene regulation leading to cell differentiation. In bacteria, DNA methylomes (i.e., methylation state of each base of the whole genome) have been described for several species, but methylome profile variation during the lifecycle has rarely been studied, and only in a few model organisms. Moreover, major phenotypic changes have been reported in several bacterial strains with a deregulated methyltransferase, but the corresponding methylome has rarely been described. Here we report the first methylome description of an entomopathogenic bacterium, Photorhabdus luminescens. Eight motifs displaying a high rate of methylation (>94%) were identified. The methylome was strikingly stable over course of growth, but also in a subpopulation responsible for a critical step in the bacterium’s lifecycle: successful survival and proliferation in insects. The rare unmethylated GATC motifs were preferentially located in putative promoter regions, and most of them were methylated after Dam methyltransferase overexpression, suggesting that DNA methylation is involved in gene regulation. Our findings bring key insight into bacterial methylomes and encourage further research to decipher the role of loci protected from DNA methylation in gene regulation.

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“…In N. gonnorhoeae , three cytosine-related MTases, part of restriction-modification systems, were able to methylate 17–50 % of corresponding 4mC and 5mC motifs, while in R. solanacearum , 32.8 % of the predicted motif G C CGGC was 4mC-methylated [29, 30].…”

Section: Resultsmentioning

confidence: 99%

Detection of cytosine methylation in Burkholderia cenocepacia by single-molecule real-time sequencing and whole-genome bisulfite sequencing

et al. 2021

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Research on prokaryotic epigenetics, the study of heritable changes in gene expression independent of sequence changes, led to the identification of DNA methylation as a versatile regulator of diverse cellular processes. Methylation of adenine bases is often linked to regulation of gene expression in bacteria, but cytosine methylation is also frequently observed. In this study, we present a complete overview of the cytosine methylome in Burkholderia cenocepacia , an opportunistic respiratory pathogen in cystic fibrosis patients. Single-molecule real-time (SMRT) sequencing was used to map all 4mC-modified cytosines, as analysis of the predicted MTases in the B. cenocepacia genome revealed the presence of a 4mC-specific phage MTase, M.BceJII, targeting GGCC sequences. Methylation motif GCGGCCGC was identified, and out of 6850 motifs detected across the genome, 2051 (29.9 %) were methylated at the fifth position. Whole-genome bisulfite sequencing (WGBS) was performed to map 5mC methylation and 1635 5mC-modified cytosines were identified in CpG motifs. A comparison of the genomic positions of the modified bases called by each method revealed no overlap, which confirmed the authenticity of the detected 4mC and 5mC methylation by SMRT sequencing and WGBS, respectively. Large inter-strain variation of the 4mC-methylated cytosines was observed when B. cenocepacia strains J2315 and K56-2 were compared, which suggests that GGCC methylation patterns in B. cenocepacia are strain-specific. It seems likely that 4mC methylation of GGCC is not involved in regulation of gene expression but rather is a remnant of bacteriophage invasion, in which methylation of the phage genome was crucial for protection against restriction-modification systems of B. cenocepacia .

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Comparative Analysis of Ralstonia solanacearum Methylomes

Cited by 17 publications

References 58 publications

DNA Methylation Epigenetically Regulates Gene Expression in Burkholderia cenocepacia and Controls Biofilm Formation, Cell Aggregation, and Motility

DNA Methylation Epigenetically Regulates Gene Expression in Burkholderia cenocepacia and Controls Biofilm Formation, Cell Aggregation, and Motility

The complete methylome of an entomopathogenic bacterium reveals the existence of loci with unmethylated Adenines

Detection of cytosine methylation in Burkholderia cenocepacia by single-molecule real-time sequencing and whole-genome bisulfite sequencing

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