TABLE 3.
Reconstructed FAD regulons in gamma- and betaproteobacteriad
| Taxonomic groupa and organism(s) | PsrA/FadR/FadP regulationb | FA degradation gene(s)c | Other coregulated gene(s)c |
|---|---|---|---|
| Gammaproteobacteria | |||
| Enterobacteriales (5 genomes) | R | fadBA, fadH, fadD, fadIJ, fadE, fadL (4) | fabB (4), fabA (3), ybaW (4), iclR (2), aceBA (1) |
| Pasteurellales (7 genomes) | R | fadL | fabA |
| Haemophilus influenzae | R | - | fabA |
| Haemophilus ducreyi | R | fadL | fabA, fabB, fabDG, accA |
| Actinobacillus pleuropneumoniae | R | fadL | fabA, fabB, fabI, accAD |
| Alteromonadales | |||
| Shewanella spp. (13 genomes) | A, R | fadBA, fadH, fadD; [fadIJ], fadE, acdH, etfBA (10); etfD (11); echH; fadL | aceBA, sdh, SO2935 (11), SO0881 (12), SO4716 (11), SO0572, SO0080 (6) |
| Idiomarina loihiensis | A, R | fadBA, fadH, fadIJ, fadE, acdH | SO2935, IL-0656 |
| Colwellia psychrerythraea | A, R | fadBA, fadD, fadIJ, fadE, acdH, etfBA, etfD | SO2935 |
| Pseudoalteromonas haloplanktis | R | fadIJ, fadH | |
| Pseudoalteromonas atlantica | R | fadBA, fadIJ | |
| Saccharophagus degradans | A | fadBA, acdH | |
| Vibrionales | |||
| Vibrio cholerae | A, R | [fadBA], fadH, fadD, fadIJ, fadE1, fadE2 | mdh, plsB |
| Vibrio parahaemolyticus | A, R | fadBA, fadH, fadD, fadIJ, fadE1, fadE2, fadL | mdh, plsB |
| Vibrio vulnificus | A, R | fadBA, fadH, fadD, fadIJ, fadE1, fadE2 | mdh, plsB |
| Photobacterium profundum | A, R | fadBA, fadH, fadD, fadIJ, fadE1, fadE2, fadL1, fadL2 | echH |
| Vibrio fischeri | R | fadBA, fadH, fadE, fadL | plsB |
| Pseudomonadales (5 genomes) | A | fadBA, fadH (2), acdH, etfBA, etfD, scp | rpoS, algQ, PA1831, PP4195 (4) |
| Xanthomonadales (3 genomes) | A | acdAB | fabAB, accBC, aroQ |
| Oceanospirillales | |||
| Hahella chejuensis | A | fadBA, acdH, etfBA, etfD, scp | |
| Chromohalobacter salexigens | A | fadBA, fadH, fadD, fadE, acdH, etfBA, etfD, scp | |
| Alcanivorax borkumensis | A | fadD, acdH, etfBA, etfD | |
| Betaproteobacteria | |||
| Chromobacterium (1 genome) | A | acdAB, fadD, fadE, acdH, etfBA, etfD, fadL | mdh, accBC, fabK, fabF, aroQ |
| Rhodocyclales | |||
| Dechloromonas aromatica | A | fadBA, acdAB, fadD, fadE, acdH, fadL | |
| Azoarcus sp. | A | fadBA, acdAB, fadE, fadL, echH | |
| Burkholderiales | |||
| Bordetella spp. (3 genomes) | A, P | fadBA, acdAB, fadD, fadE, fadL | BP3678 |
| Ralstonia solanacearum | A, P | fadE, fadAB, acdABH, fadD, etfAB, etfD, echIH | acdQP, maoC, bktB, alkK |
| Ralstonia eutropha, R. metallidurans | A, P | fadAB, acdABH, fadD, etfAB, etfD, echIH, acsA | acdQP, maoC, bktB, alkK, fab |
| Burkholderia xenovorans | A, P | fadAB, acdABH, fadD1, etfAB, etfD, echIH, fadA1, fadD2, fadE | acdQP, maoC, fab |
| Burkholderia spp. (4 genomes) | A, P | fadAB, acdABH, fadD1, etfAB, etfD, echIH, fadD2 | acdQP, maoC, fab |
| Methylibium petroleiphilum | P | fadAB, acdABH, etfAB, etfD, echH | |
| Polaromonas sp. | P | fadAB, acdABH, etfAB | |
| Rhodoferax ferrireducens | P | fadAB, acdABH, etfAB, etfD | acdQP |
Numbers of complete genomes with the analyzed regulon(s) are shown in parentheses.
The existence and copy number of candidate regulators of FAD genes, FadR, PsrA, and FadP, are shown by “R,” “A,” and “P,” respectively.
Candidate FadR-regulated genes are underlined. Candidate PsrA-regulated genes are shown in lightface type. Candidate FadP-regulated genes are shown in boldface type. Operon structures of genes are not shown. For candidate regulon members that are not always regulated within a taxonomic group, the number of genomes that have regulated orthologs is given in parentheses. Genes that are regulated by both FadR and PsrA are in square brackets.
Functional roles of genes are listed in Table S8 in the supplemental material. Locus tags are given for groups of orthologous genes that lack a conventional common name. The genome-specific locus tags of candidate regulon members are given in Tables S4 to S6 in the supplemental material.