TABLE 1.
Reconstructed ILV degradation regulons in proteobacteriad
| Taxonomic groupa and organism | LiuR/LiuQ regulationb | ILV degradation gene(s)c | Other coregulated gene(s)c |
|---|---|---|---|
| Gammaproteobacteria | |||
| Alteromonadales | |||
| Shewanella spp. (13 genomes) | R | liuABCDEFG, ivdABCDEFG, bkd, ldh, etfBA | aceBA, gltBA, thrABC, tyrR (8) |
| Idiomarina loihiensis | R | liuABCDE, ivdA, bkd, aacS | |
| Colwellia psychrerythraea | R | liuABCDEFG, ivdAEG, bkd, etfBA, etfD | |
| Pseudoalteromonas haloplanktis | R | liuABCDEFG, ivdABCDEFG, bkd, ldh, etfBA, etfD | acdH |
| Pseudoalteromonas atlantica | R | liuABCDEFG, ivdABCDEFG, etfBA, etfD | |
| Vibrionales (3 genomes) | R, R | liuABCDE, ivdABCDEFG, etfBA, etfD | livGHMKF (1) |
| Pseudomonadales (5 genomes) | R | liuABCDE, aacS (4), etfBA, etfD (1) | |
| Oceanospirillales | |||
| Hahella chejuensis | R | liuABCDE, bkd, aacS | |
| Alcanivorax borkumensis | R | liuABCD, aacS | |
| Betaproteobacteria | |||
| Chromobacterium (1 genome) | R, R | liuABCDE, ivdABCDEFG, aacS | |
| Rhodocyclales | |||
| Dechloromonas aromatica | R | liuABCDE, ivdAC | cah, paaI, gloB |
| Azoarcus sp. | R | liuAC, ivdA | cah, paaH, gloB |
| Burkholderiales | |||
| Bordetella spp. (3 genomes) | R | liuABD, ivdACDF | paaI, aceK (2), sdh/glt, mdh |
| Ralstonia solanacearum | R | liuABCDE, ivdAC | cah, paaH, aceK, mcm, gloB |
| Ralstonia eutropha | R, Q | liuABDE-1, ivdAC, liuABCDE-2; aacS | paaI, cah, paaH, aceK, bio, gloB |
| Ralstonia metallidurans | R, Q | liuAC, ivdAC, liuBDE; aacS | cah, paaH, aceK, mcm |
| Burkholderia xenovorans | R, Q | liuABCD, ivdAC, aacS | cah, aceK |
| Burkholderia spp. (4 genomes) | Q | liuABCD | |
| Methylibium petroleiphilum | Q | liuABCD | |
| Polaromonas sp. | R | liuA, ivdAC, etfBA | paaI, cah, paaH, aceK, mcm, acdH |
| Rhodoferax ferrireducens | R, R | liuA, ivdAC, etfBA | cah, paaH, aceK, mcm, acdH |
| Alphaproteobacteria | |||
| Rhodospirillales (1 genome) | R | liuRABCDE, ivdACEF | livGHMKF |
The number of complete genomes with the analyzed regulon(s) is shown in parentheses.
The existence and copy number of candidate regulators of ILV degradation genes, LiuR and/or LiuQ, are shown by “R” and/or “Q,” respectively.
Candidate LiuR-regulated genes are shown in lightface type. Candidate LiuQ-regulated genes are underlined and in boldface. Genes are grouped (form stretches) only when they have the same first three letters in their names. The operon structure of genes is 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.
Functional roles of genes are listed in Table S7 in the supplemental material. The genome-specific locus tags of candidate regulon members are given in Tables S1 and S2 in the supplemental material.