TABLE 1.

Reconstructed ILV degradation regulons in proteobacteriad

Taxonomic groupa and organismLiuR/LiuQ regulationbILV degradation gene(s)cOther coregulated gene(s)c
Gammaproteobacteria
    Alteromonadales
        Shewanella spp. (13 genomes)RliuABCDEFG, ivdABCDEFG, bkd, ldh, etfBAaceBA, gltBA, thrABC, tyrR (8)
        Idiomarina loihiensisRliuABCDE, ivdA, bkd, aacS
        Colwellia psychrerythraeaRliuABCDEFG, ivdAEG, bkd, etfBA, etfD
        Pseudoalteromonas haloplanktisRliuABCDEFG, ivdABCDEFG, bkd, ldh, etfBA, etfDacdH
        Pseudoalteromonas atlanticaRliuABCDEFG, ivdABCDEFG, etfBA, etfD
    Vibrionales (3 genomes)R, RliuABCDE, ivdABCDEFG, etfBA, etfDlivGHMKF (1)
    Pseudomonadales (5 genomes)RliuABCDE, aacS (4), etfBA, etfD (1)
    Oceanospirillales
        Hahella chejuensisRliuABCDE, bkd, aacS
        Alcanivorax borkumensisRliuABCD, aacS
Betaproteobacteria
    Chromobacterium (1 genome)R, RliuABCDE, ivdABCDEFG, aacS
    Rhodocyclales
        Dechloromonas aromaticaRliuABCDE, ivdACcah, paaI, gloB
        Azoarcus sp.RliuAC, ivdAcah, paaH, gloB
    Burkholderiales
        Bordetella spp. (3 genomes)RliuABD, ivdACDFpaaI, aceK (2), sdh/glt, mdh
        Ralstonia solanacearumRliuABCDE, ivdACcah, paaH, aceK, mcm, gloB
        Ralstonia eutrophaR, QliuABDE-1, ivdAC, liuABCDE-2; aacSpaaI, cah, paaH, aceK, bio, gloB
        Ralstonia metalliduransR, QliuAC, ivdAC, liuBDE; aacScah, paaH, aceK, mcm
        Burkholderia xenovoransR, QliuABCD, ivdAC, aacScah, aceK
        Burkholderia spp. (4 genomes)QliuABCD
        Methylibium petroleiphilumQliuABCD
        Polaromonas sp.RliuA, ivdAC, etfBApaaI, cah, paaH, aceK, mcm, acdH
        Rhodoferax ferrireducensR, RliuA, ivdAC, etfBAcah, paaH, aceK, mcm, acdH
Alphaproteobacteria
    Rhodospirillales (1 genome)RliuRABCDE, ivdACEFlivGHMKF
  • a The number of complete genomes with the analyzed regulon(s) is shown in parentheses.

  • b The existence and copy number of candidate regulators of ILV degradation genes, LiuR and/or LiuQ, are shown by “R” and/or “Q,” respectively.

  • c 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.

  • d 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.