| Aspect | Finding | Evidence / method | Source (date, URL/DOI) | Citation |
|---|---|---|---|---|
| Gene/protein identity | In *Pseudomonas putida* KT2440, **cbrB = PP_4696**, the response regulator of the **CbrA/CbrB** two-component system; it is functionally described as a **σ54-dependent response regulator** controlling nutritional adaptation and carbon/catabolite regulation. This supports identification of Q88DX2 with **cbrB/PP_4696**, not the separate alginate regulator **AlgB** locus found elsewhere in *P. putida*. | Gene deletion/complementation, pathway analysis, review synthesis; PP_4696 explicitly named cbrB in KT2440. | Wirtz et al., 2020-03, https://doi.org/10.1038/s41598-020-62337-9; Thompson et al., 2020-10-15, https://doi.org/10.1128/AEM.01665-20; Reva et al., 2006-06, https://doi.org/10.1128/JB.00101-06 | (pqac-00000004, pqac-00000009, pqac-00000007) |
| Ambiguity check: cbrB vs AlgB | Available KT2440 literature consistently uses **cbrB (PP_4696)** for the CbrAB response regulator, whereas **AlgB** appears as a different alginate-associated regulator in other loci/contexts. Thus, cbrB and AlgB should be treated as **distinct annotations unless sequence-level database reconciliation is shown**. | Cross-comparison of KT2440 locus-specific papers and alginate-related annotations. | Wirtz et al., 2020-03, https://doi.org/10.1038/s41598-020-62337-9; Reva et al., 2006-06, https://doi.org/10.1128/JB.00101-06; Gülez et al., 2012-02, https://doi.org/10.1128/AEM.06150-11 | (pqac-00000004, pqac-00000007) |
| Domain architecture | Q88DX2 is annotated with a **receiver (CheY-like / response-regulator receiver)** domain plus a **central AAA+ / P-loop NTPase ATPase** region and **σ54 enhancer-binding transcriptional activator** features, matching an **NtrC-family bacterial enhancer-binding protein**. | Domain assignment from UniProt/interpro-style annotation integrated with literature describing CbrB as σ54-dependent transcriptional activator. | Moreno & Rojo, 2024-01, https://doi.org/10.1111/1751-7915.14407; Monteagudo-Cascales et al., 2019-06, https://doi.org/10.1038/s41598-019-45554-9 | (pqac-00000010, pqac-00000003) |
| Cellular localization / molecular role | CbrB acts in the **cytoplasm** as the **DNA-binding transcriptional response regulator** activated by phosphorylation from the inner-membrane sensor kinase **CbrA**. | Two-component signaling model; biochemical phosphotransfer from CbrA to CbrB; transcriptional activation of target promoters. | Wirtz et al., 2020-03, https://doi.org/10.1038/s41598-020-62337-9; Moreno & Rojo, 2024-01, https://doi.org/10.1111/1751-7915.14407 | (pqac-00000002, pqac-00000010) |
| Core pathway | **CbrA/CbrB → activation of crcZ and crcY → sequestration/antagonism of Crc with Hfq → relief of carbon catabolite repression (CCR)** on many catabolic genes. | Reporter assays, mutant phenotypes, review of promoter logic and RNA-mediated antagonism. | Moreno & Rojo, 2024-01, https://doi.org/10.1111/1751-7915.14407; Monteagudo-Cascales et al., 2019-06, https://doi.org/10.1038/s41598-019-45554-9; Wirtz et al., 2020-03, https://doi.org/10.1038/s41598-020-62337-9 | (pqac-00000010, pqac-00000001, pqac-00000002) |
| Promoter logic / σ54 dependence | **PcrcZ** is a **strong σ54-dependent promoter** activated by CbrB; a weaker **PcbrB** promoter provides basal cbrB/crcZ transcription. CbrB also regulates other **σN-dependent metabolic genes**. | Promoter analyses and transcriptional model summarized from genetic studies and review. | Moreno & Rojo, 2024-01, https://doi.org/10.1111/1751-7915.14407; Monteagudo-Cascales et al., 2019-06, https://doi.org/10.1038/s41598-019-45554-9 | (pqac-00000010, pqac-00000001) |
| Phosphorylation and signal transduction | CbrA **autophosphorylates** and **transfers phosphate to CbrB**; in vitro, **CbrA-dependent dephosphorylation of CbrB~P was not detected**. Less-favorable carbon sources are associated with increased signaling output to CbrB targets. | Biochemical phosphotransfer assays plus PcrcZ::lux reporter experiments. | Wirtz et al., 2020-03, https://doi.org/10.1038/s41598-020-62337-9 | (pqac-00000002, pqac-00000005) |
| Reporter evidence for crcZ activation | In **ΔcbrA** and **ΔcbrB** mutants carrying **PcrcZ::luxCDABE**, crcZ expression was lost and restored only by complementation with the cognate gene, demonstrating that **CbrB is required for crcZ transcriptional activation** in KT2440. | Luciferase reporter in wild type, deletion mutants, and complemented strains. | Wirtz et al., 2020-03, https://doi.org/10.1038/s41598-020-62337-9 | (pqac-00000005, pqac-00000011) |
| Carbon-source responsiveness | **crcZ** expression is low on preferred carbon sources such as **succinate/LB** and maximal on less favorable sources such as **L-histidine, L-arginine, oxaloacetate**, consistent with CbrB-mediated relief of CCR when preferred substrates are absent. | Carbon-source-dependent PcrcZ::lux assays and review of CCR physiology. | Wirtz et al., 2020-03, https://doi.org/10.1038/s41598-020-62337-9; Moreno & Rojo, 2024-01, https://doi.org/10.1111/1751-7915.14407 | (pqac-00000005, pqac-00000010) |
| Additional validated targets / regulon | CbrB activity in KT2440 was monitored through transcription of **crcZ, crcY, and PP2810**, with maximal induction under non-preferred carbon sources; CbrB is also described as directly regulating σ54-dependent catabolic pathways such as the **hut** system. | Target-gene assays and prior pathway characterization. | Monteagudo-Cascales et al., 2019-06, https://doi.org/10.1038/s41598-019-45554-9; Wirtz et al., 2020-03, https://doi.org/10.1038/s41598-020-62337-9 | (pqac-00000001, pqac-00000004) |
| Growth and motility phenotypes | A **ΔcbrB-like phenotype** includes inability or severe defect in use of **citrate** and **histidine**, a **longer lag on succinate**, and **reduced swimming motility**; these phenotypes were mirrored by CbrA signaling mutants and rescued by complementation. | Mutant phenotype analysis in defined media and motility assays. | Monteagudo-Cascales et al., 2019-06, https://doi.org/10.1038/s41598-019-45554-9 | (pqac-00000001, pqac-00000003) |
| Stress-related phenotype | A transposon screen found the **CbrAB sensor kinase system** essential for coping with **cold stress** in KT2440, indicating CbrB-linked nutritional/stress adaptation extends beyond single catabolic operons. | Genome-wide mutant screening and transcriptomics under abiotic stress. | Reva et al., 2006-06, https://doi.org/10.1128/JB.00101-06 | (pqac-00000007) |
| Genome-scale fitness signal | In RB-TnSeq, **cbrB (PP_4696)** showed **pentanol-specific fitness defects**, supporting a role for CbrB in broader central carbon metabolism and assimilation of nonpreferred substrates relevant to biotechnology. | Random barcode transposon sequencing across alcohol/fatty-acid conditions. | Thompson et al., 2020-10-15, https://doi.org/10.1128/AEM.01665-20 | (pqac-00000009) |
| Current mechanistic uncertainty | Recent review consensus is that CbrB is central to CCR control, but the **signal sensed upstream of CbrA/CbrB remains unresolved**; evidence points to an **intracellular metabolite or metabolic ratio**, and unphosphorylated CbrB may retain partial activity in vitro. | Expert review synthesizing primary studies. | Moreno & Rojo, 2024-01, https://doi.org/10.1111/1751-7915.14407 | (pqac-00000010) |


*Table: This table summarizes locus-specific evidence supporting the identity and function of Pseudomonas putida KT2440 cbrB (PP_4696; UniProt Q88DX2). It highlights domain-based functional inference, the CbrA/CbrB–crcZ/crcY–Crc/Hfq pathway, and key experiments establishing its role in carbon catabolite regulation and adaptive metabolism.*