Characteristics of the modification motif ANCNNNNCCT.

Mean Score–mean Modification QV of instances of this motif that were detected as modified; Mean IPD Ratio–mean interpulse duration (IPD) ratio of instances of this motif that were detected as modified; Mean Coverage–mean coverage of instances of this motif that were detected as modified.</p

Genome alignment of Mycoplasma gallisepticum strains obtained using the program Mauve.

RM system MgaS6I is marked in orange, variable lipoproteins vlhA clusters in green, the CRISPR system in blue. M. gallisepticum S6 genome is on the top, below the genomes of the other strains. A–whole genome representation, B–fragment of genomes near MgaS6I genomic context. (PDF)</p

Phylogenetic tree of TRDs of specificity subunits of <i>M</i>. <i>gallisepticum</i> S6 and other TRDs with similar specificity.

The names in the leaves represent the TRD names, which consist of the REBASE name of the HsdS and its sequence specificity. The numbers on the nodes are distance measures calculated using BLOSUM62 substitution matrices.</p

The efficiency of <i>camR</i> insertion into wild-type <i>M</i>. <i>gallisepticum</i>, ΔS.MgaS6I strain, and four strains with <i>tetM</i> insertion in various intergenic regions.

CFUs of strains with significant difference, as compared to the CFU of ΔS.MgaS6I strain (Student’s t-test, P<0.05), have been indicated using asterisks.</p

Fig 8 -

A–Difference between the expression levels of paired genes for mutants with EGFP genes under synthetic promoters, with or without methylation sites. For each pair, the difference for EGFP gene in comparison with control genes eno, gadp, tuf, ligA, and gyrB is shown. Genes with significant difference between promoters with or without the methylation site (Student’s t-test, Benjamini–Hochberg correction, PEGFP promoters with or without methylated sites in -10 box, -35 box, between -35 and -10 boxes, and in the TSS. Methylation sites are underlined; methylated adenines in forward and reverse strands are in bold; -10 boxes are in blue and highlighted with blue boxes; -35 boxes are highlighted with green boxes and the sequence with strong consensus to the -35 box is in green; TSSs are in red and marked with red arrows; sequence differences between paired methylated or non-methylated promoters are in pink.</p

Methylated fraction of each methylation site.

A–Number of sites with different fractions of methylation. Colors represent sites located in one of the four parts of the genome: between the origin and midpoint of the chromosome, on the plus or minus strand. The panel on the right schematically shows the methylation sites that were counted in each group. B–Number of sites with different fractions of methylation. In this figure, the location of sites in the genome has not been considered. Colors represent the sites on the ANCNNNNCCT or AGGNNNNGNT strands in the double-stranded methylation motif. The panel on the right schematically shows the methylation sites that were counted in each group.</p

Restriction-modification systems of <i>M</i>. <i>gallisepticum</i> S6.

Arrows represent the ORFs; grey, blue, green, and orange colors indicate genes hsdC (controller protein), hsdM (methyltransferase), hsdS (specificity subunit), and hsdR (restriction subunit), respectively. Ori–origin of replication. Faded colors represent disrupted genes.</p

Differences in expression levels of genes with DNA methylations sites between WT and ΔS.MgaS6I strains.

Groups of control genes eno, gadp, tuf, ligA, gyrB, dnaJ_2, and dnaJ_6; genes with the methylation motif in promoters topA, dnaJ_4, tktA_1, scpA, osmC_2, trxA_1, yebC, and dnaB; genes with different numbers of methylation sites or with hemi-methylation status ligA, gyrB, dnaB, hup_2, ung, uvrB, and groEL; genes of methyltransferases hsdM from MgaS6I and mraW have been presented. Genes with significant difference between strains (Student’s t-test, Benjamini–Hochberg correction, P<0.05) are shown using red boxes and asterisks.</p

Supplementary tables S1-S8.

(XLSX)</p

Distribution of DNA modification sites along the genome of <i>M</i>. <i>gallisepticum</i> S6.

A–Annotated features: RM systems are in orange, vlhA clusters in green, the CRISPR system in grey, the virulence cluster in blue, and mobile elements in black. B and С –Whole-genome representation of the DNA modification motif ANCNNNNCCT for plus and minus strand, respectively. The lines indicate positions of sites, and the colors from red to blue represent percentage of methylation in each site. Percentage of methylation was calculated using the build-in SMRT protocol, as the fraction of reads aligning to the position that has a modified base. D–Density of methylation sites. Maximum density of methylation is highlighted in orange, while minimum is highlighted in green. E–GC content. Maximum GC content is highlighted in red, while minimum is highlighted in blue. F–Hypo-methylated sites are in green, hemi-methylated sites in orange and blue (for plus and minus strands, respectively); proteins with differential abundance (as assessed using 2D-DIGE) between WT and ΔS.MgaS6I strains are in grey.</p