Table 1.
Restriction-Modifications systems (RMS) and target motifs in N. gonorrhoeae.
| RMS type | RMS | Subtype (REBASE) | Motif | Methylation type | Detected? | PacBio/ REBASE | Methylated fraction F: % 5′-3′ R: % 3′-5′ | Number of strains |
|---|---|---|---|---|---|---|---|---|
| I | NgoAV | Gamma |
5′-GACN{6}TGC-3′ 3′-CTGN{6}ACG-5′ |
6mA | Yes | PacBio |
F: 95.0-100 R: 91.3-99.6 |
2/25 |
|
5′-GACN{7}TGC-3′ 3′-CTGN{7}ACG-5′ |
6mA | Yes | PacBio |
F: 100 R: 100 |
4/25 | |||
|
5′-GCAN{8}TGC-3′ 3′-CGTN{8}ACG-5′ |
6mA | Yes | PacBio |
F: 99.8-99.9 R: 99.8-99.9 |
2/25 | |||
| NgoAXVII | Gamma |
5′-GAGN{5}TAC-3′ 3′-CTCN{5}ATG-5′ |
6mA | Yes | PacBio |
F: 100 R: 100 |
22/25 | |
| 5′-BGAGN{4}GTTAC-3′ | 6mA | Yes | PacBio | F: 87.5 | 1/25 | |||
| II | NgoAI | P |
5′-RGCGCY-3′ 3′-YCGCGR-5′ |
5mC | Yes | REBASE | — | 25/25 |
| NgoAII | P |
5′-GGCC-3′ 3′-CCGG-5′ |
5mC | Yes | REBASE | — | 25/25 | |
| NgoAIII | P |
5′-CCGCGG-3′ 3′-GGCGCC-5′ |
4mC | Yes | PacBio | 50.4 | 21/25 | |
| NgoAIV | P |
5′-GCCGGC-3′ 3′-CGGCCG-5′ |
5mC | Yes | REBASE | — | 25/25 | |
| NgoAVII | S |
5′-GCGGC-3' 3′-CGCCG-5′ |
5mC | Yes | PacBio | 36.3–39.7 | 25/25 | |
| NgoAVIII | G,S |
5′-GACN{5}TGA-3′ 3′-CTGN{5}ACT-5′ |
6mA | No | REBASE (base undetermined) | — | — | |
| NgoAXI (Dam) | Beta |
5′-GATC-3′ 3′-CTAG-5′ |
6mA | Yes | PacBio |
F: 98.6–99.0 R: 98.6–99.0 |
2/25 | |
| NgoAXIII | — | Unknown | Unknown | No | REBASE | — | — | |
| NgoAXIV | P |
5′-CCGG-3′ 3'-GGCC-5′ |
5mC | Yes | REBASE | — | 25/25 | |
| NgoAXV | P |
5′-GGNNCC-3′ 3'-CCNNGG-5′ |
5mC | Yes | REBASE | — | 25/25 | |
| NgoAXVI | S |
5′-GGTGA-3′ 3′-CCACT-5′ |
Forward 6mA Reverse 5mC |
Yes | PacBio | F: 93.1–99.9 | 25/25 | |
| Unknown | Unknown |
5′-AAANCGGTTNNC-3′ 3′-TTTNGCCAANNG-5′ |
m4C | Yes | PacBio | F: 17.5–20.6 | >14/25 | |
| III | NgoAX | — | 5′-CCACC-3′ | 6mA | Yes | PacBio | F: 97.3–100 | 6/25 |
| NgoAXII | — | 5′-GCAGA-3′ | 6mA | Yes | PacBio | F: 95.4–98.2 | 3/25 |
Those detected as methylated by the PacBio SMRT pipeline are marked as such and the fraction of modified motifs in the genomes indicated as a range (F: forward, R: reverse). For those not directly detected by the pipeline, the associated motifs in REBASE are shown and marked as detected if a significant difference in IPD ratios is found between the target base and the unmethylated equivalent by a Mann-Whitney test.