Two small RNAs, CrcY and CrcZ, act in concert to sequester the Crc global regulator in Pseudomonas putida, modulating catabolite repression

Abstract

SummaryThe Crc protein is a translational repressor that recognizes a specific target at some mRNAs, controlling catabolite repression and co-ordinating carbon metabolism in pseudomonads. In Pseudomonas aeruginosa, the levels of free Crc protein are controlled by CrcZ, a sRNA that sequesters Crc, acting as an antagonist. We show that, in Pseudomonas putida, the levels of free Crc are controlled by CrcZ and by a novel 368 nt sRNA named CrcY. CrcZ and CrcY, which contain six potential targets for Crc, were able to bind Crc specifically in vitro. The levels of CrcZ and CrcY were low under conditions generating a strong catabolite repression, and increased strongly when catabolite repression was absent. Deletion of either crcZ or crcY had no effect on catabolite repression, but the simultaneous absence of both sRNAs led to constitutive catabolite repression that compromised growth on some carbon sources. Overproduction of CrcZ or CrcY significantly reduced repression. We propose that CrcZ and CrcY act in concert, sequestering and modulating the levels of free Crc according to metabolic conditions. The CbrA/CbrB two-component system activated crcZ transcription, but had little effect on crcY. CrcY was detected in P. putida, Pseudomonas fluorescens and Pseudomonas syringae, but not in P. aeruginosa.

Hierarchical management of carbon sources is regulated similarly by the CbrA/B systems in Pseudomonas aeruginosa and Pseudomonas putida

“…succinate or glucose (Hester et al, 2000a;Moreno et al, 2012;Sonnleitner et al, 2009). Therefore, to investigate any possible difference between the signals regulating the CbrA/B/CrcZ(Y) systems of P. aeruginosa and P. putida, we monitored crcZ expression in a P. putida KT2442 WT strain growing in rich LB medium and in minimal media amended with various carbon sources as done above for P. aeruginosa PAO1 (Figs 1b, S1b and S2b).…”

“…In the literature, succinate has been used as a carbon source to observe CCR in P. aeruginosa and as the non-CCR condition in P. putida (Moreno et al, 2012;Sonnleitner et al, 2009). In this study, we used the same growth conditions for the two strains for the first time, in order to be able to compare them.…”

Pleiotropic Role of the RNA Chaperone Protein Hfq in the Human Pathogen Clostridium difficile

“…Interestingly, in E. coli, an Hfqdependent sRNA, SgrS, is involved in glucose uptake regulation in response to phosphosugar stress by targeting the ptsG mRNA degradation (84). More generally, sRNA-based regulation has been linked to catabolite repression control in several bacteria (85)(86)(87)(88)(89). We may thus hypothesize that Hfq-dependent control of sugar uptake in C. difficile is also mediated by still uncharacterized sRNAs.…”

CrcZ and CrcX regulate carbon source utilization inPseudomonas syringaepathovartomatostrain DC3000

“…CrcZ levels also vary according to the carbon source being used and are low in succinate medium (a preferred carbon source for P. aeruginosa), at an intermediate level in glucose medium and at a high level in mannitol medium (a non-preferred carbon source and a growth condition that does not generate catabolite repression). 5 P. putida contains crcZ and an additional ncRNA, crcY, 6 homologous to psr3 in DC3000. The crcZ and crcY ncRNAs were found to function similarly and modulate levels of RpoN in P. syringae DC3000, but expression was not completely eliminated.…”