| Topic | Key findings | Evidence type | Quantitative/statistical data (if any) | Organism/strain | Citation |
|---|---|---|---|---|---|
| Identity | PP_4099 in *Pseudomonas putida* KT2440 is the response regulator GacA, described as the cognate partner of GacS and as the Pseudomonad counterpart of the BarA/UvrY system in *E. coli*; this matches UniProt Q88FJ6 (uvrY/gacA). (pqac-00000002, pqac-00000003) | Genome annotation; comparative functional genomics | RB-TnSeq meta-analysis showed strong gacS/gacA phenocopy in *P. putida* (r² = 0.997). (pqac-00000015) | *P. putida* KT2440 | *Transcriptional Regulatory Systems in Pseudomonas* (2025) https://doi.org/10.3390/ijms26104677; *High Throughput Fitness Profiling Reveals Loss Of GacS-GacA Regulation Improves Indigoidine Production In Pseudomonas putida* (2021) https://doi.org/10.1101/2021.02.02.429437 |
| Domains | GacA-family proteins are described as having an N-terminal receiver (REC) domain with a conserved phospho-accepting Asp and a C-terminal helix-turn-helix DNA-binding domain; this is consistent with the UniProt/InterPro assignment for Q88FJ6. (pqac-00000007, pqac-00000029) | Domain/structure-function analysis; TCS review | Conserved phospho-accepting residue reported as Asp-54 in GacA-family regulator. (pqac-00000007) | Pseudomonads (applied by homology to KT2440 GacA) | *Regulatory Mechanisms Underlying Biological Control Activity of Pseudomonas chlororaphis PA23* (2012) DOI not available in gathered evidence |
| Activation mechanism | GacS autophosphorylates in response to unknown signals and transfers phosphate to GacA; phosphorylated GacA is proposed to act as a transcription factor, likely via dimerization, to activate downstream sRNA genes. (pqac-00000000, pqac-00000017, pqac-00000029, pqac-00000030) | Genetic/regulatory model; promoter analysis | GacS phosphorelay residues reported in one pseudomonad model: His-294, Asp-717, His-863 → GacA Asp-54. (pqac-00000007) | *P. putida* KT2440 and related *Pseudomonas* spp. | *Self-Regulation and Interplay of Rsm Family Proteins Modulate the Lifestyle of Pseudomonas putida* (2016) https://doi.org/10.1128/AEM.01724-16; *GacA-Controlled Activation of Promoters for Small RNA Genes in Pseudomonas fluorescens* (2010) https://doi.org/10.1128/AEM.02014-09 |
| Direct regulatory output | Activated GacA primarily induces transcription of small RNAs in the Gac-Rsm pathway rather than controlling a large direct protein-coding regulon; in Pseudomonads these sRNAs are RsmX/RsmY/RsmZ. (pqac-00000000, pqac-00000031, pqac-00000033, pqac-00000034) | Genetic/regulatory cascade analysis | No KT2440-specific fold change available in gathered evidence. | *P. putida* KT2440 and related *Pseudomonas* spp. | *Self-Regulation and Interplay of Rsm Family Proteins Modulate the Lifestyle of Pseudomonas putida* (2016) https://doi.org/10.1128/AEM.01724-16 |
| sRNA promoter control | GacA-dependent rsmY/rsmZ promoters contain a conserved palindromic upstream activating sequence (UAS); the UAS is necessary but not sufficient, and auxiliary factors such as PsrA and IHF contribute to activation. (pqac-00000008, pqac-00000010, pqac-00000030) | Promoter dissection; in vitro DNA-binding/regulatory analysis | UAS length ~18 bp; consensus reported as TGTAAGNNATNNCTTACA; example rsmZ UAS sequence TGTAAGCAAAGGCTTACT. (pqac-00000010) | *P. fluorescens* CHA0; *P. chlororaphis* PA23 | *GacA-Controlled Activation of Promoters for Small RNA Genes in Pseudomonas fluorescens* (2010) https://doi.org/10.1128/AEM.02014-09 |
| Downstream post-transcriptional mechanism | RsmX/Y/Z sRNAs contain repeated unpaired GGA motifs and sequester RsmA/E-family RNA-binding proteins, relieving translational repression of target mRNAs; Rsm proteins act near ribosome-binding sites. (pqac-00000000, pqac-00000009, pqac-00000030, pqac-00000032, pqac-00000034) | RNA-protein regulatory mechanism; genetic analysis | RsmA/CsrA optimal dual-site spacing on RNA reported around ~18 nt in one structural model. (pqac-00000032) | *P. putida* KT2440 and related *Pseudomonas* spp. | *Self-Regulation and Interplay of Rsm Family Proteins Modulate the Lifestyle of Pseudomonas putida* (2016) https://doi.org/10.1128/AEM.01724-16; *GacA-Controlled Activation of Promoters for Small RNA Genes in Pseudomonas fluorescens* (2010) https://doi.org/10.1128/AEM.02014-09 |
| Lifestyle regulon in KT2440 | In KT2440, GacS/GacA positively regulates both major adhesin genes, *lapA* and *lapF*; *lapA* shows an early transient promoter peak plus a stationary-phase rise, whereas *lapF* is induced late and depends on RpoS. (pqac-00000004, pqac-00000021, pqac-00000022) | Reporter fusions; transcriptional time-course; genetics | In a gacS mutant, *rpoS* expression was abolished; biofilm defect was statistically significant at all measured time points except 24 h. (pqac-00000022, pqac-00000043) | *P. putida* KT2440 | *Roles of Cyclic Di-GMP and the Gac System in Transcriptional Control of the Genes Coding for the Pseudomonas putida Adhesins LapA and LapF* (2014) https://doi.org/10.1128/JB.01287-13 |
| Biofilm and motility phenotypes | GacS/GacA-Rsm signaling is a key determinant of the planktonic-to-sessile transition, affecting motility, biofilm formation/dispersal, adhesin expression, exopolysaccharides, and c-di-GMP-linked lifestyle outputs. (pqac-00000000, pqac-00000034, pqac-00000043) | Mutant phenotyping; lifestyle regulation analysis | In one related pseudomonad example, gac mutants showed ~150% increased swimming motility; KT2440 gacS mutants were impaired in biofilm formation. (pqac-00000005, pqac-00000043) | *P. putida* KT2440 and related *Pseudomonas* spp. | *Self-Regulation and Interplay of Rsm Family Proteins Modulate the Lifestyle of Pseudomonas putida* (2016) https://doi.org/10.1128/AEM.01724-16; *Roles of Cyclic Di-GMP and the Gac System... LapA and LapF* (2014) https://doi.org/10.1128/JB.01287-13 |
| Interaction with c-di-GMP network | High intracellular c-di-GMP stimulates *lapA* transcription but represses *lapF*; FleQ is required for c-di-GMP-dependent activation of *lapA* and has only minor effects on *lapF*, placing GacA within a broader lifestyle network. (pqac-00000004, pqac-00000021, pqac-00000022) | Reporter analysis; regulatory genetics | Qualitative opposite effects on *lapA* vs *lapF*; no fold changes provided in gathered evidence. | *P. putida* KT2440 | *Roles of Cyclic Di-GMP and the Gac System in Transcriptional Control of the Genes Coding for the Pseudomonas putida Adhesins LapA and LapF* (2014) https://doi.org/10.1128/JB.01287-13 |
| Biotechnology application | Deleting *gacA* in KT2440 improved bioreactor fitness and strongly increased heterologous indigoidine production from p-coumarate, suggesting GacA diverts carbon to secondary metabolism/biofilm/iron-sequestration functions under these conditions. (pqac-00000003, pqac-00000012, pqac-00000015, pqac-00000037) | RB-TnSeq fitness profiling; strain reconstruction; fed-batch bioprocess | Yield improved from 0.034 to 0.29 g indigoidine/g pCA (8.5-fold); 29% MTY in fed-batch. (pqac-00000015, pqac-00000037) | *P. putida* KT2440 | *High Throughput Fitness Profiling Reveals Loss Of GacS-GacA Regulation Improves Indigoidine Production In Pseudomonas putida* (2021) https://doi.org/10.1101/2021.02.02.429437 |
| Biocontrol/specialized metabolites | In a recent 2023 study, GacA positively regulated pseudoiodinine biosynthesis in *P. mosselii*; the full *psdABCDEFG* operon was sufficient for heterologous production in *P. putida* KT2440, illustrating a real implementation of a GacA-linked metabolite pathway in KT2440. (pqac-00000011, pqac-00000014, pqac-00000041) | Transcriptomics; gene deletion/complementation; heterologous expression; field/greenhouse assays | Engineered strain achieved 22.4-fold higher pseudoiodinine production, 42.5 mg/L average yield; field biocontrol efficiency >50% at >5 μM. (pqac-00000011, pqac-00000014, pqac-00000041) | *P. mosselii* 923; heterologous production in *P. putida* KT2440 | *The natural pyrazolotriazine pseudoiodinine from Pseudomonas mosselii 923 inhibits plant bacterial and fungal pathogens* (2023) https://doi.org/10.1038/s41467-023-36433-z |
| 2023 network insight | Plasmid-encoded RsmQ can bind host RsmY/RsmZ ncRNAs and heterodimerize with host Rsm proteins, showing that the Gac-Rsm output layer is vulnerable to horizontal regulatory crosstalk; this is relevant to engineered plasmid-bearing Pseudomonads. (pqac-00000013, pqac-00000036) | Structural modeling; SPR; BACTH interaction assays | ~50% of RsmQ-regulated proteins had upstream AnGGA motifs and ~25% had GGA motifs; five tested oligos showed >50% Rmax binding. (pqac-00000013) | *Pseudomonas fluorescens* SBW25/plasmid context | *Plasmids manipulate bacterial behaviour through translational regulatory crosstalk* (2023) https://doi.org/10.1371/journal.pbio.3001988 |


*Table: This table summarizes verified identity, mechanism, phenotype, and application evidence for GacA/UvrY (PP_4099; UniProt Q88FJ6) in *Pseudomonas putida* KT2440 and closely related pseudomonads. It highlights where evidence is KT2440-specific versus inferred from conserved Gac-Rsm biology.*