TABLE 1.
Novel designations for GGDEF/EAL domain-encoding genes of E. coli
| Gene name | b no. | UniProt entry | New gene name | Other gene named | Domain architecturea | Comment and/or reference(s)e |
|---|---|---|---|---|---|---|
| Genes encoding diguanylate cyclases (intact GGDEF domains) | ||||||
| yaiC | b0385 | P0AAP1 | dgcC | adrA* | MASE2b-GGDEF | 12, 15–17 |
| ycdT | b1025 | P75908 | dgcT | MASE4b-GGDEF | (18) | |
| ydaM | b1341 | P77302 | dgcM | PAS-PAS-GGDEF | 19–21 | |
| yddV | b1490 | P0AA89 | dgcO | dosC | Globin sensor GGDEF | 22 |
| ydeH | b1535 | P31129 | dgcZ | CZB-GGDEF | 23 | |
| yeaJ | b1786 | P76237 | dgcJ | GAPES1c-GGDEF | 21 | |
| yeaP | b1794 | P76245 | dgcP | GAF-GGDEF | ||
| yedQ | b1956 | P76330 | dgcQ | CHASE7c-xCache-GGDEF | 21, 24, 25 | |
| yegE | b2067 | P38097 | dgcE | MASE1b-PAS-PAS-PAS-GGDEF-xEAL | 12, 21, 26 | |
| yfiN | b2604 | P46139 | dgcN | tpbB* | CHASE8c-HAMP-GGDEF | 26–28 |
| yliF | b0834 | P75801 | dgcI | GAPES2c-GGDEF | ||
| yneF | b1522 | P76147 | dgcF | xMASE1-GGDEF | Promoter and first 4 TM segments deleted in E. coli K-12 (18) | |
| EC55989_0813 | B7LBD9 | dgcX | MASE4b-GGDEF | Extra DGC in EAEC (18) | ||
| EcSMS35_1716 | B1LFF9 | dgcY | MASE5b-GGDEF | Extra DGC in E. coli SMS35 and NMEC 07:K1 strain CE10 (29) | ||
| Genes encoding c-di-GMP phosphodiesterases (intact EAL domains) | ||||||
| rtn | b2176 | P76446 | pdeN | CSSc-EAL | ||
| yahA | b0315 | P21514 | pdeL | LuxR-EAL | 30, 31 | |
| ycgG | b1168 | P75995 | pdeG | CSSc-EAL | ||
| yciR | b1285 | P77334 | pdeR | gmr | PAS-GGDEF-EAL | 19, 20 |
| yddU | b1489 | P76129 | pdeO | dosP | PAS-PAS-xGAF-xGGDEF-EAL | 22, 30, 32, 33 |
| yfeA | b2395 | P23842 | pdeA | MASE1b-xGGDEF-EAL | ||
| yfgF | b2503 | P77172 | pdeF | MASE1b-xGGDEF-EAL | 34, 35 | |
| yhjH | b3525 | P37646 | pdeH | EAL | 21, 26, 36 | |
| yhjK | b3529 | P37649 | pdeK | hmsP* | GAPES3c-HAMP-xGGDEF-EAL | |
| yjcC | b4061 | P32701 | pdeC | CSSc-EAL | ||
| ylaB | b0457 | P77473 | pdeB | CSSc-EAL | ||
| yliE | b0833 | P75800 | pdeI | CHASE9c-xCache-HAMP-xGGDEF-EAL | ||
| yoaD | b1815 | P76261 | pdeD | adrB | CSSc-EAL | 37 |
| Z1528 | Q8XAQ9 | pdeT | vmpA | CSSc-EAL | Extra PDE in EHEC O157:H7 (18, 38) | |
| EcE24377A_E0053 | A7ZH68 | pdeW | EAL | Extra PDE in ETEC E24377A (29) | ||
| ECP_2965 | Q707K1 | pdeX | EAL | Extra PDE in UPEC 536 (29) | ||
| UTI89_C1116 | Q1RDG4 | pdeY | sfaY | EAL | Extra PDE in several ExPEC strains (29, 39) | |
| Genes encoding proteins with degenerate GGDEF and EAL domains | ||||||
| ycgF | b1163 | P75990 | bluF | BLUF-xEAL | 9, 40 | |
| yeaI | b1785 | P76236 | cdgI | MASE4b-xGGDEF | ||
| ydiV | b1707 | P76204 | rflP | xEAL | Regulator of FlhDC proteolysis (10, 11) | |
| yhdA | b3252 | P13518 | csrD | GAPES4c-xGGDEF-xEAL | 8, 41 |
The domain names indicate the following Pfam entries: BLUF, PF04940; Cache, PF02743; CHASE7, PF17151; CHASE8, PF17152; CHASE9, PF17153; CSS, PF12792; CZB, PF13682; EAL, PF00563; GAF, PF01590 or PF13492; GAPES1, PF17155; GAPES2, PF17156; GAPES3, PF17154; GAPES4, PF17157; GGDEF, PF00990; globin sensor, PF11563; HAMP, PF00672; LuxR, PF00196; MASE1, PF05231; MASE2, PF05230; MASE4, PF17158; MASE5, PF17178; PAS, PF08448 or PF13426. An “x” in front of a domain name indicates an enzymatically inactive or highly divergent domain. The Pfam entries for new sensor domains are to appear in the 29th release of the Pfam database (48).
An integral membrane domain.
Predicted periplasmic domain.
Asterisks indicate designations used for homologous genes in other genera or species as follows: adrA, Salmonella (occasionally, adrA has also been used for E. coli); tpbB, Pseudomonas aeruginosa; hmsP, Yersinia.
ETEC, enterotoxigenic E. coli; ExPEC, extraintestinal pathogenic E. coli; NMEC, neonatal meningitis E. coli; EAEC, enteraggregative E. coli; TM, transmembrane.