DNA methylome regulates virulence and metabolism in Pseudomonas syringae
- Department of Biomedical Sciences, City University of Hong Kong, China
- Shenzhen Research Institute, City University of Hong Kong, Shenzhen, China
- Chengdu Research Institute, City University of Hong Kong, China
- Institute of Digital Medicine, City University of Hong Kong, China
- Tung Research Centre, City University of Hong Kong, China
Figures
Figure 1 with 1 supplement
Genome-wide identification of P. syringae DNA methylation.
(A) The circle map displays the distribution of 6mA, 5mC, and 4mC in Psph WT. (B) The Venn plot reveals overlapped genes within three types of DNA methylation of Psph WT. (C) The circle map displays …
Figure 1—figure supplement 1
Distribution patterns of methylation sites in three model strains.
(A) Bar plot shows the distribution of modified sites located in different regions of coding sequence (CDS), intergenic region, and non-coding RNA. (B) GC contents distribution of 6mA between three P…
Figure 2 with 1 supplement
Functional enrichment analysis of methylation sites in three P. syringae strains.
(A) Repartition of the total pool of modified genes among strains. (B) Proportion of methylated genes detected in one, two, or three genomes for all P. syringae strains and conserved DNA methylation …
Figure 2—figure supplement 1
Cluster of Orthologous Group (COG) analysis of methylation sites in P. syringae.
(A) COG classification of three DNA methylations in Psph. (B) COG classification of three DNA methylations in Pst. (C) COG classification of three DNA methylations in Pss.
Figure 3 with 3 supplements
DNA methylation motifs in P. syringae.
(A) 6mA methylation motifs found in Psph using SMRT-seq. The black arrows indicate the site of adenine methylation. (B) Bar plot shows the abundance of methylated numbers throughout all motif sites …
Figure 3—figure supplement 1
Comparative genomic analysis of Type I RM system among bacterial genus.
Different species are highlighted in different colors. The color key indicates the %identity compared to the MTases in Psph.
Figure 3—figure supplement 2
Identification of Type I DNA methyltransferase in Psph.
(A) Growth curve of Psph WT, ΔhsdMSR, and complemented strains at 28°C in KB medium. (B) HsdMSR can catalyze 6mA formation in Psph. (C) The circle map displays the distribution of 6mA, 5mC, and 4mC …
Figure 3—figure supplement 3
Effects of growth phases on methylation in P. syringae.
(A) Dot blot results of three P. syringae strains in logarithmic and stationary phases. (B) Overexpression of HsdM showed a higher 6mA modification level than that in wild-type (WT). (C) …
Figure 4
Transcriptional changes profiling of hsdMSR mutant in Psph.
(A) The volcano plot reveals differentially expressed genes (DEGs) between Psph WT and ΔhsdMSR. The DEGs were (|log2FC| > 1 and adjusted p-value <0.05) in blue (ribosomal protein), pink (alginate …
Figure 5 with 1 supplement
Influence of HsdMSR on virulence and metabolism in Psph.
(A) HsdMSR negatively regulated T3SS-related genes. Data are shown as means ± SD (n = 3). Statistical significance was determined using two-tailed Student's t-test (*p < 0.05). (B) Disease symptoms …
Figure 5—figure supplement 1
Number of genes with significant translational efficiency (TE) changes.
(A) The gene ontology (GO) terms for the genes in which TE changed more than 1-FC. (B) The GO terms for the genes in which TE changed less than 1-FC.
Figure 6
6mA methylation regulates gene transcription based on fully methylated.
(A) Upstream region sequence of hrpF carrying the HsdMSR motif. Adenine methylation is highlighted in red. (B) Constantly lux activity detection of the hrpF between Psph WT and ΔhsdMSR. Data are …
Additional files
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Supplementary file 1
Restriction–modification systems predicted in P. syringae.
- https://cdn.elifesciences.org/articles/96290/elife-96290-supp1-v1.docx
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Supplementary file 2
Modified genes conserved in three P. syringae strains.
- https://cdn.elifesciences.org/articles/96290/elife-96290-supp2-v1.csv
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Supplementary file 3
Differentially expressed genes (DEGs) between Psph WT and ΔhsdMSR.
- https://cdn.elifesciences.org/articles/96290/elife-96290-supp3-v1.csv
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Supplementary file 4
Differentially expressed genes (DEGs) carrying HsdMSR motif in their putative promoter regions.
- https://cdn.elifesciences.org/articles/96290/elife-96290-supp4-v1.csv
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Supplementary file 5
Genes with changed translational efficiency (TE) between Psph WT and ΔhsdMSR.
- https://cdn.elifesciences.org/articles/96290/elife-96290-supp5-v1.csv
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Supplementary file 6
Strains, plasmids, and primers.
- https://cdn.elifesciences.org/articles/96290/elife-96290-supp6-v1.xlsx
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MDAR checklist
- https://cdn.elifesciences.org/articles/96290/elife-96290-mdarchecklist1-v1.docx
