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. 2013;9(1):e1003191.
doi: 10.1371/journal.pgen.1003191. Epub 2013 Jan 3.

Comprehensive Methylome Characterization of Mycoplasma Genitalium and Mycoplasma Pneumoniae at Single-Base Resolution

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Free PMC article

Comprehensive Methylome Characterization of Mycoplasma Genitalium and Mycoplasma Pneumoniae at Single-Base Resolution

Maria Lluch-Senar et al. PLoS Genet. .
Free PMC article

Abstract

In the bacterial world, methylation is most commonly associated with restriction-modification systems that provide a defense mechanism against invading foreign genomes. In addition, it is known that methylation plays functionally important roles, including timing of DNA replication, chromosome partitioning, DNA repair, and regulation of gene expression. However, full DNA methylome analyses are scarce due to a lack of a simple methodology for rapid and sensitive detection of common epigenetic marks (ie N(6)-methyladenine (6 mA) and N(4)-methylcytosine (4 mC)), in these organisms. Here, we use Single-Molecule Real-Time (SMRT) sequencing to determine the methylomes of two related human pathogen species, Mycoplasma genitalium G-37 and Mycoplasma pneumoniae M129, with single-base resolution. Our analysis identified two new methylation motifs not previously described in bacteria: a widespread 6 mA methylation motif common to both bacteria (5'-CTAT-3'), as well as a more complex Type I m6A sequence motif in M. pneumoniae (5'-GAN(7)TAY-3'/3'-CTN(7)ATR-5'). We identify the methyltransferase responsible for the common motif and suggest the one involved in M. pneumoniae only. 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. To our knowledge, this is one of the first direct methylome profiling studies with single-base resolution from a bacterial organism.

Conflict of interest statement

KL, TAC, KS, SWT, and JK are full-time employees at PacificBiosciences, a company commercializing single-molecule, real-time nucleic acid sequencing technologies.

Figures

Figure 1
Figure 1. Methylome determination of M. pneumoniae by SMRT sequencing.
(A) Circos plot of kinetic variation across the genome. Red tracks represent the Qmod (−10log(Pvalue) from t-test) values of the forward (outer track) and reverse (inner track) strands. Blue and green tracks represent the location of the 5′-CTAT-3′ and Type I motifs discovered by filtering on Qmod values as shown in (C). (B) Example of IPD ratio plots of the two discovered motifs for a section of the genome. The top plot shows 3 instances of 5′-CTAT-3′, two of them are asymmetrically methylated. The bottom plot shows 2 Type I examples, where each one is fully methylated; that is each Type I recognition site is methylated on both strands. (C) Qmod distribution showing the filtering threshold of 100 used (black dash line) for determining modified positions.
Figure 2
Figure 2. Genome-wide distribution of 5′-CT
A T-3′ motif. (A) Hot spots of methylation for the 5′-CTAT-3′ motif. The graph represents the number of motifs per 1 kb window. The red line indicates the threshold (5). Regions with more than five 5′-CTAT-3′ motifs are considered “hot spots of methylation”. Red arrows indicate the most enriched regions. (B) Circular representation of the M. pneumoniae genome. Red marks indicate genome locations of the three main enriched regions of methylation. (C) Methylation in the putative origin of replication of M. pneumoniae. Blue boxes indicate putative DnaA boxes. Red arrows and lines indicate methylation sites. Black arrows indicated a common distance (24 bp) from methylation sites to the TSSs of the three MPNs. (D) Motif sequences of two putative cell division “check points” (L, left and R, right). Noteworthy only in L motif contains the recognition motif 5′-CTAT-3′ (showed in red letters) on the complementary strand. In contrast, the R motif contains 5′-TTAT-3′ (showed in blue letters) on the complementary strand instead. The three large grey arrows are the three non-coding RNAs (MPNs200, MPNs201 and MPNs381).
Figure 3
Figure 3. Genome-wide distribution of 5′-GAN7TAY-3′/3′-CTN7 ATR-5′ motif.
(A) Map of the genome of M. pneumoniae representing the enriched regions for the 5′-GAN7TAY-3′/3′-CTN7 ATR-5′ motif. (B) Schematic representation of the cytadherence operon. The red square indicates the main “hot spot” of methylation for the Type I motif. (C) Upstream sequence of MPNs383. Red stars indicate the methylation by M.MpnI and blue stars indicate methylation by M.MpnII. The black arrow shows the transcriptional start site (TSS) of the MPNs383 and the red box the promoter sequence of this antisense RNA.
Figure 4
Figure 4. Unmethylated sites.
A) IPD ratio plot of a 5′-CTAT-3′ site not detected as methylated (shadowed in yellow). B) IPD ratio plot of an unmethylated 5′-GAN7TAY-3′/3′-CTN7 ATR-5′ motif (shadowed in yellow). For comparison of signal intensity, a methylated 5′-CTAT-3′ is also shown in the bottom plot (shadowed in red).
Figure 5
Figure 5. Histogram of distances of methylation motifs to TSS in the promoter regions.
(A) Distances for the 5′-CTAT-3′ motif to TSS. (B) Distances for the 5′-GAN7TAY-3′/3′-CTN7 ATR-5′ motif to TSS.
Figure 6
Figure 6. Qmod distributions.
Qmod distributions of 5′-CTAT-3′ (A) and 5′-GAN7TAY-3′/3′-CTN7 ATR-5′ motifs (B) for M. pneumoniae genome at exponential (6 h, red line) and stationary (96 h, blue line) phases of growth.

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