One ligand, two regulators and three binding sites: How KDPG controls primary carbon metabolism in Pseudomonas.

Richard H. Little,Rowena K. Y. Fung,Simona Pepe,Jacob G. Malone,Josep Casadesús,Rosaria Campilongo,Eleftheria Trampari,Lucia Grenga,Davide Roncarati,Clare E. M. Stevenson,Govind Chandra

doi:10.1371/journal.pgen.1006839

Abstract

Effective regulation of primary carbon metabolism is critically important for bacteria to successfully adapt to different environments. We have identified an uncharacterised transcriptional regulator; RccR, that controls this process in response to carbon source availability. Disruption of rccR in the plant-associated microbe Pseudomonas fluorescens inhibits growth in defined media, and compromises its ability to colonise the wheat rhizosphere. Structurally, RccR is almost identical to the Entner-Doudoroff (ED) pathway regulator HexR, and both proteins are controlled by the same ED-intermediate; 2-keto-3-deoxy-6-phosphogluconate (KDPG). Despite these similarities, HexR and RccR control entirely different aspects of primary metabolism, with RccR regulating pyruvate metabolism (aceEF), the glyoxylate shunt (aceA, glcB, pntAA) and gluconeogenesis (pckA, gap). RccR displays complex and unusual regulatory behaviour; switching repression between the pyruvate metabolism and glyoxylate shunt/gluconeogenesis loci depending on the available carbon source. This regulatory complexity is enabled by two distinct pseudo-palindromic binding sites, differing only in the length of their linker regions, with KDPG binding increasing affinity for the 28 bp aceA binding site but decreasing affinity for the 15 bp aceE site. Thus, RccR is able to simultaneously suppress and activate gene expression in response to carbon source availability. Together, the RccR and HexR regulators enable the rapid coordination of multiple aspects of primary carbon metabolism, in response to levels of a single key intermediate.

Highlights

Soil-dwelling Pseudomonas spp. are exposed to a complex and dynamic physical and chemical environment, and must constantly adapt their cell physiology by changing the expression patterns of membrane proteins, secreted small molecules, and enzymes [1]
We propose that the coordinated activity of HexR and RccR tightly controls the remodelling of central metabolism in response to intracellular KDPG levels, maximizing bacterial proliferation and fitness, and optimising enzyme synthesis to most effectively respond to nutrient availability in the environment
Following the observation that rccR seems to play a Transcriptional control of Pseudomonas metabolism role in the plant environment [30] we decided to examine the locus in more detail

Summary

Introduction

Soil-dwelling Pseudomonas spp. are exposed to a complex and dynamic physical and chemical environment, and must constantly adapt their cell physiology by changing the expression patterns of membrane proteins, secreted small molecules, and enzymes [1]. This ability to gauge the surroundings and modulate gene expression is crucial for effective environmental adaptation [2]. Transcription factors belonging to the RpiR family control the expression of enzymes involved in carbon metabolism [9] Members of this family are characterized by a helix-turn-helix DNA-binding domain at the N-terminus and a sugar isomerase domain (SIS) at the C-terminus [10, 11]. HexR binds KDPG via its SIS domain, signalling glucose availability and causing HexR to dissociate from DNA, inducing expression of its gene targets and stimulating glucose uptake and metabolism [14]

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Results

Discussion

Conclusion