Pseudomonadaceae CbrA/CbrB carbon catabolite control via Crc/Hfq

The CbrA/CbrB two-component system of the Pseudomonadaceae and the post-transcriptional machinery it controls, which together set carbon catabolite repression and balance carbon against nitrogen utilization. The membrane sensor histidine kinase CbrA phosphorylates the conserved receiver aspartate of CbrB, and CbrB acts as a sigma-54-dependent enhancer-binding activator of the genes for the CrcZ-family small RNAs (CrcZ, and CrcY or CrcX in some species). Those small RNAs act as decoys for the Hfq/Crc translational repressor: Hfq binds A-rich catabolite-activity motifs near the ribosome-binding sites of catabolic mRNAs through its distal face, and the catalytically inactive co-repressor Crc stabilises the repressive Hfq/RNA assemblies. When favoured carbon sources are scarce, CrcZ-family RNA levels rise, Hfq/Crc is sequestered, and translational repression of catabolic mRNAs is relieved. The module spans sensing, phosphotransfer, sigma-54-dependent small-RNA induction, and the translational repression step that the small RNAs antagonise.

Scope. The CbrA/CbrB-CrcZ-Crc/Hfq arrangement is characterised in Pseudomonas putida, P. aeruginosa, P. fluorescens and P. syringae, and in Azotobacter vinelandii, where both systems are functionally conserved; it is absent from Enterobacteria, which use cAMP-CRP and PTS-based catabolite control instead. The module is therefore a concrete Pseudomonadaceae realisation rather than a pan-bacterial motif, with P. putida KT2440 proteins as exemplars (all five have complete gene reviews). Grounding. CbrA, both CbrB roles, the Hfq/Crc translational repressor step and Crc are grounded as concrete KT2440 gene products: the PANTHER families that classify them are much broader than the role (CbrA sits in a generic sensor-histidine-kinase family; CbrB's subfamily PTHR32071:SF117 also holds receiver-less NifA and XylR, so phosphorelay response-regulator activity and control of the CrcZ-family promoters are not subfamily properties, and P. putida XylR is a Pseudomonadaceae SF117 member that does not drive them; the Hfq translation repressor role depends on the Crc partnership, which is restricted to the Pseudomonadaceae, so it is not asserted for the pan-bacterial Hfq family; Crc sits in the catalytic exonuclease III family whose nuclease activity it has lost). Sigma-54 and the Hfq sRNA-stabilisation role are grounded to their PANTHER families, whose reviewed family-wide activities match the annotons. Bulk family groundings proposed elsewhere that add A. vinelandii NifA (P09570) to an SF117-grounded CbrB activator role and Desulfovibrio RpoN (Q72BK7) to the sigma-54 role were not adopted as module exemplars, because neither organism's protein acts in this catabolite-control circuit; both are recorded as representatives in the PTHR32071 and PTHR32248 family reviews instead. Phosphorelay motif. The CbrA -> CbrB step is a simple two-component system that conforms to MODULE:two_component_relay WITH_DEVIATIONS: the histidine-phosphotransfer (Hpt) tier is absent, so the validator's tier-count, tier-function and topology advisories for this node are the expected output of that declared deviation. Small RNAs. The CrcZ-family decoy RNAs are non-coding and appear as the described input to the repression step rather than as protein participants. Naming. UniProt entry Q88DX2 carries the name AlgB by homology while the KT2440 literature studies this locus as CbrB, and Q88C91 (Crc) is named exodeoxyribonuclease III by family rule; the gene reviews record both. The wider CbrB regulon and the downstream catabolic pathways whose mRNAs are repressed are separate modules.