The Crc/CrcZ‐CrcY global regulatory system helps the integration of gluconeogenic and glycolytic metabolism in Pseudomonas putida

Abstract

In metabolically versatile bacteria, carbon catabolite repression (CCR) facilitates the preferential assimilation of the most efficient carbon sources, improving growth rates and fitness. In Pseudomonas putida, the Crc and Hfq proteins and the CrcZ and CrcY small RNAs, which are believed to antagonize Crc/Hfq, are key players in CCR. Unlike that seen in other bacterial species, succinate and glucose elicit weak CCR in this bacterium. In the present work, metabolic, transcriptomic and constraint-based metabolic flux analyses were combined to clarify whether P. putida prefers succinate or glucose, and to identify the role of the Crc protein in the metabolism of these compounds. When provided simultaneously, succinate was consumed faster than glucose, although both compounds were metabolized. CrcZ and CrcY levels were lower when both substrates were present than when only one was provided, suggesting a role for Crc in coordinating metabolism of these compounds. Flux distribution analysis suggested that, when both substrates are present, Crc works to organize a metabolism in which carbon compounds flow in opposite directions: from glucose to pyruvate, and from succinate to pyruvate. Thus, our results support that Crc not only favours the assimilation of preferred compounds, but balances carbon fluxes, optimizing metabolism and growth.

Glucose uptake in Azotobacter vinelandii occurs through a GluP transporter that is under the control of the CbrA/CbrB and Hfq-Crc systems

“…However, we found that gluP expression is under the control of the CbrA/CbrB and Crc/Hfq systems, as it occurs with the gtsABC genes in Pseudomonas spp. 21, 35, 36 . In fact, we showed that during diazotrophic growth the A .…”

Influence of the Hfq and Crc global regulators on the control of iron homeostasis in Pseudomonas putida

“…Both the transcriptomic and proteomic assays indicated that, in the minimal medium with succinate used to culture the cells, the absence of Crc had a significantly smaller influence than that observed in earlier reports in which cells had been cultured in LB complete medium (Moreno et al ., ). This is consistent with the observation that the amount of CrcZ + CrcY present in cells growing exponentially in M9 medium with succinate is more than seven‐fold that seen in cells cultured in LB medium (La Rosa et al ., ). This suggests that when cells grow in M9 succinate medium there is less Crc and/or Hfq available to control gene expression than in LB medium.…”

“…Among the genes for which RNA levels increased in the absence of Crc were those for the high affinity transport system for succinate and fumarate, dctPQM . The expression of these genes is known to be repressed post‐transcriptionally by Crc in both P. putida (La Rosa et al ., ) and P. aeruginosa (Valentini and Lapouge, ). In fact, both P. putida dctP and dctM contain Hfq/Crc binding sites at their translation initiation regions.…”

Unravelling the complexity and redundancy of carbon catabolic repression in Pseudomonas fluorescens SBW25

“…Glycerol does not produce any detectable CCR effects on xut genes expression; thus, it makes sense that addition of glycerol did not restore the fitness cost of CCR for xylose utilization. Interestingly, CCR was advantageous in the complete medium of LB, which had been used as the assay condition for CCR in P. putida strains (La Rosa et al ., ).…”

“…). Influences of CCR on carbon fluxes have been evidenced by metabolomics studies in P. putida and P. aeruginosa (La Rosa et al ., ; La Rosa et al ., ). For example, inactivation of crc causes excretion of acetate and pyruvate when bacteria were grown exponentially in complete LB medium, and these valuable metabolites are later consumed when bacterial growth is slowed down in stationary phase, demonstrating an important role of Crc in balanced bacterial growth (La Rosa et al ., ).…”