Recommended regulons for experimental verification
The regulons presented in the RegPrecise database were tentatively reconstructed
by using the computational genomic approach and comparisons between closely related
genomes. The reconstructed regulatory network needs to be integrated with functionally
related networks and keynote regulatory interactions representing novel regulons need
to be experimentally validated. Here we list the most important from our point of view
regulons for experimental validation.
Transcription factor LiuR controls pathways of degradation of branch-chain amino acids
(Leu, Ile, Val) in Proteobacteria. LiuR is a novel regulator from the MerR family and has
no orthologs in E. coli. The LiuR regulon and its DNA-binding motif were first discovered
by application of the comparative genomic approach in the Shewanella lineage. For instance,
the LiuR regulator in Shewanella oneidensis MR-1 (encoded by the SO1898 gene) has 9 targets
sites that presumably control expression of 29 genes organized in 9 operons. These genes encode
enzymes from the Leu-Ile-Val degradation pathways (see operons picture below and LiuR regulog in
Shewanella), and also enzymes from other amino acid metabolic pathways (thrABC, gltBD) and TCA
cycle (aceBA). The predicted effectors for LiuR are intermediates of the Leu-Ile-Val degradation
pathways, in particular isovalerate-CoA, isobutyryl-CoA, and 2-methybutanoyl-CoA.
[Kazakov et al., 2008]
Transcription factor PsrA controls the fatty acid degradation pathway in Proteobacteria.
PsrA is a novel regulator from the TetR family and no orthologs in E. coli. The PsrA regulon
and its DNA-binding motif were discovered by application of the comparative genomic approach to
the fatty acid degradation genes in the Shewanella lineage. For instance, the PsrA regulator in
Shewanella oneidensis MR-1 (encoded by the SO2493 gene) has 15 targets sites that presumably control
expression of 25 genes organized in 16 operons. These genes encode enzymes from the fatty acid degradation
pathway (see PsrA regulog in Shewanella), and also enzymes from the TCA cycle (aceBA, sdhCAB, gltA).
The predicted effector for PsrA are fatty acids.
[Kazakov et al., 2008]
Transcription factor HexR controls the central carbohydrate metabolism in Shewanella. HexR is a novel
regulator from the RpiR family; its ortholog in E. coli is a local uncharacterized regulator that presumably
controls only one target operon. The HexR regulon and its DNA-binding motif were discovered by application of
the comparative genomic approach to the central carbohydrate metabolism in the Shewanella lineage. For instance,
the HexR regulator in Shewanella oneidensis MR-1 (encoded by the SO2490 gene) has 14 targets sites that presumably
control expression of 27 genes organized in 14 operons. These genes encode enzymes from the glycolysis, the
pentose-phosphate and Entner-Doudoroff pathways, deoxynucleoside utilization, and glycine cleavage system
(see HexR regulog in Shewanella). The predicted effector for HexR is glucose-6-phosphate.
