Table 1.
Putative diguanylate cyclases investigated in this study
| Locus tag | Name or homologuea | DGC motifb | PDE motif | Other domain(s)c | Biofilm phenotyped | Mutatione |
|---|---|---|---|---|---|---|
| Pfl01_0050 | GGEEF | No change | Insertion | |||
| Pfl01_0190 | GGEEF | PAS 3 | No change | Insertion | ||
| Pfl01_0192 | GGDEF | EAL | TM, PAS | Increased | Insertion | |
| Pfl01_0623 | GcbA | GGDEF | REC | Decreased | Deletion, Tn | |
| Pfl01_0692 | AwsR/YfiN (19, 21) | GGDEF | TM, HAMP | No change | Insertion | |
| Pfl01_1058 | WspR (12, 20) | GGEEF | REC | Decreased | Insertion | |
| Pfl01_1252 | SwsR (21) | GGDEF | EAL | TM, MHYT | No change | Insertion |
| Pfl01_1323 | GGDEF | PAS 3, GAF | No change | Insertion | ||
| Pfl01_1336 | GGEEF | TM | No change | Insertion | ||
| Pfl01_1789 | GcbB | GGEEF | TM, CHASE, PAS | Decreased | Deletion | |
| Pfl01_1887 | GGDEF | EAL | PAS, PAS 3, PAS 4 | Increased | Insertion | |
| Pfl01_2049 | Similar to AdrA (16) | GGDEF | MASE2, TM | No change | Insertion | |
| Pfl01_2170 | GGDEF | 7 TM | No change | Insertion | ||
| Pfl01_2176 | GGDEF | GAF | No change | Insertion | ||
| Pfl01_2297 | GGEEF | TM, CACHE_1 | No change | Insertion | ||
| Pfl01_2525 | Similar to MucR (11) | GGDEF | EAL | TM, MHYT | No change | Insertion |
| Pfl01_2709 | GGDEF | EAL | TM, CHASE4, PAS | Increased | Insertion | |
| Pfl01_3508 | GGDEF | TM, PAS 3 | No change | Insertion | ||
| Pfl01_3550 | GGDEF | TM, HAMP | No change | Insertion | ||
| Pfl01_3800 | GGDEF | TM | No change | Insertion | ||
| Pfl01_4084 | GGEEF | No change | Deletion | |||
| Pfl01_4086 | RbdA (1) | GGDEF | EIL | TM, PAS | Increased | Insertion |
| Pfl01_4307 | GGDEF | MASE2, TM | No change | Insertion | ||
| Pfl01_4451 | Similar to SadC (22) | GGDEF | 7 TM | No change | Insertion | |
| Pfl01_4551 | GGDEF | aaq | PAS, PAC, REC | No change | Insertion | |
| Pfl01_4666 | GcbC | GGEEF | TM, CACHE_1 | Decreased | Deletion | |
| Pfl01_4876 | MwsR/MorA (4, 21) | GGDEF | EAL | TM, PAS | Increased | Insertion |
| Pfl01_5150 | GGDEF | EAL | SBP bac3, TM, PAS | No change | Insertion | |
| Pfl01_5168 | GGEEF | 7 TM | No change | Insertion | ||
| Pfl01_5255 | GGDEF | EAL | REC, PAS | No change | Insertion |
Names for DGCs characterized in this study, or homologues (≥65% amino acid identity) that have been characterized in other organisms, are given with references indicated. “Similar to” indicates <65% amino acid identity but similar domain structures.
Amino acid sequences at the signature GGDEF and EAL motifs are given. Lowercase letters indicate degenerate sequence, and boldface letters indicate phenotypic evidence suggesting the domain is enzymatically active in P. fluorescens Pf0-1.
Other predicted domains are indicated using Pfam symbols (http://pfam.sanger.ac.uk/).
Biofilm phenotypes are given relative to that of WT P. fluorescens Pf0-1 in K10T-1 medium.
The type of mutant(s) tested for each locus is given: Tn, Tn5 insertion; insertion, single-crossover insertion of pKO3; deletion, unmarked deletion of the entire gene.