More than just a metabolic regulator - elucidation and validation of new targets of PdhR in Escherichia coli

Abstract

BackgroundThe pyruvate dehydrogenase regulator protein (PdhR) of Escherichia coli acts as a transcriptional regulator in a pyruvate dependent manner to control central metabolic fluxes. However, the complete PdhR regulon has not yet been uncovered. To achieve an extended understanding of its gene regulatory network, we combined large-scale network inference and experimental verification of results obtained by a systems biology approach.Results22 new genes contained in two operons controlled by PdhR (previously only 20 regulatory targets in eight operons were known) were identified by analysing a large-scale dataset of E. coli from the Many Microbes Microarray Database and novel expression data from a pdhR knockout strain, as well as a PdhR overproducing strain. We identified a regulation of the glycolate utilization operon glcDEFGBA using chromatin immunoprecipitation and gel shift assays. We show that this regulation could be part of a cross-induction between genes necessary for acetate and pyruvate utilisation controlled through PdhR. Moreover, a link of PdhR regulation to the replication machinery of the cell via control of the transcription of the dcw-cluster was verified in experiments. This augments our knowledge of the functions of the PdhR-regulon and demonstrates its central importance for further cellular processes in E. coli.ConclusionsWe extended the PdhR regulon by 22 new genes contained in two operons and validated the regulation of the glcDEFGBA operon for glycolate utilisation and the dcw-cluster for cell division proteins experimentally. Our results provide, for the first time, a plausible regulatory link between the nutritional status of the cell and cell replication mediated by PdhR.

PdhR, the pyruvate dehydrogenase repressor, does not regulate lipoic acid synthesis

“…Our data demonstrate that the conclusion of Kaleta and coworkers [24, 21] that PdhR regulates lipA expression is incorrect.…”

The functional landscape bound to the transcription factors of Escherichia coli K-12

“…Finally, PdhR, "Pyruvate Dehydrogenase complex Regulator," regulates around 40 genes involved in the pyruvate dehydrogenase complex. This protein has been proposed as a master regulator for the formation of the PDH complex and the respiratory electron transport system (Gohler et al, 2011;Ogasawara et al, 2007a). Therefore, in this cluster well-defined global regulators and some TFs that could also be considered as master regulators were included, indeed these global TFs are regulating around 60% of the total genes described in the known regulatory network in this bacterium.…”

Shigella reroutes host cell central metabolism to obtain high-flux nutrient supply for vigorous intracellular growth

“…coli (26). We deleted multiple tentative candidates [yhjE (27); actP, a homolog of mctC (28); ycaM and ybaT, putative transporter genes up-regulated in E. coli on pyruvate-containing media (29)], but the resulting combination mutant was still able to grow rapidly on pyruvate in vitro, showing the presence of other yet unidentified pyruvate import mechanisms.…”