rocR (PA3947, Q9HX69) review notes

Summary of the literature

RocR is a 392-aa response regulator with an N-terminal receiver (REC) domain
(phosphorylatable Asp56) and a C-terminal EAL domain. It is part of the
RocS1-RocR-RocA1 (SadARS) system.

Purified RocR hydrolyses c-di-GMP by a Mg2+-assisted general-base mechanism
PMID:18344366. UniProt records Km 3.2 uM and kcat 0.67/s, and
no activity on cAMP or cGMP.
Loop 6 of the EAL domain and the D56 phosphorylation site modulate activity
PMID:19376848.
The crystal structure (R286W mutant) is an unusual tetramer, and RocR is
tetrameric in solution PMID:22753070. RocR has no predicted transmembrane
segment in UniProt; it is a soluble cytoplasmic response regulator.
Genetics: RocR antagonises RocA1, the DNA-binding activator of cupB/cupC
PMID:15659157. The SadARS system is needed
for late biofilm maturation and type III secretion gene expression
PMID:15687209.
Kulesekara et al. 2006 (PMID:16477007). I read the full text on the PMC web page
(PMC1413825); the cached copy is abstract-only. The PDE assay was a lysate assay:
"The ability of the PDE-containing proteins to hydrolyze c-di-GMP was tested by
adding synthetic c-di-GMP to lysates of strains overexpressing these proteins and
measuring the disappearance of the dinucleotide from the reaction mixture". In
Table 1 PDE activity is "measured as percent of the added synthetic c-diGMP
degraded". The rows for genes in this batch and its neighbours read: "PA2133 ETL
— +(71) PA2200 EAL +(61)", "PA3311 AGDEF EAL — —", "PA2818 EAL —", "PA3825 EVL
+(27) PA3947 EVL +(100)", and "PA4367 GGDQF EAL — —". A rocR insertion abolished
TTSS cytotoxicity and virulence in mice.

PseudoCAP IBA-seed assessment

PTN node	node term	n_seeds	leaf IBAs	seed annotation (term, evidence, PMID)	verdict	rationale	other seeds	IBD stands without this seed?
PTN002105365	GO:0071111 cyclic-guanylate-specific phosphodiesterase activity	18	162 (24 taxa)	GO:0071111, IDA, PMID:16477007 (PseudoCAP); also EXP PMID:18344366, PMID:19376848 (UniProt)	SOUND	Lysate of a RocR-overexpressing strain degraded 100% of added c-di-GMP (full text read). Purified-enzyme kinetics (UniProt EXP rows) confirm the activity directly.	E. coli PdeA, PdeB, PdeC, PdeF, PdeH, PdeI, PdeK, PdeL, PdeN, DosP; M. tuberculosis P9WM13; P. aeruginosa bifA, PA2133, PA2200, nbdA, PA2567, PA3825	Yes. Many seeds have purified-enzyme evidence (e.g. PdeH, PdeL, PdeF, RocR's own EXP rows).

Node-level GO_CENTRAL defects for PTN002105365 (recorded here, once)

RocR has the most direct biochemical evidence among the P. aeruginosa seeds, so the
node-level defects for the shared node PTN002105365 are recorded in this review and
cross-referenced from bifA, PA2133, PA2200 and nbdA.

GO:0071111 reaches degenerate EAL proteins. The leaf GAF
(.cache/paint/leaf.gaf.gz, queried 2026-11-05) shows IBA GO:0071111 from this
node on E. coli CsrD (P13518), YdiV (P76204), Salmonella YdiV (Q8ZPS6) and BluF
(P75990), with no NOT annotation. CsrD is experimentally not a c-di-GMP PDE
PMID:16980588. UniProt describes YdiV as an anti-FlhD4C2 factor and
BluF as a blue-light BluR antirepressor. The node term is right for the clade as a
whole, and the IBD does not depend on any one P. aeruginosa seed; what is missing
is NOT/loss annotations on the degenerate branches. Confidence PROBABLE.
GO:0005886 plasma membrane (is_active_in) on the same node. The PM IBD is
seeded by membrane-anchored E. coli proteins, but the clade includes soluble EAL
proteins: RocR (REC-EAL, tetramer in solution, no TM) and PA2133 (285 aa, a lone
EAL domain, no TM). The PM term does not suit the whole clade. Confidence
PROBABLE.

Annotation decisions

GO:0071111 rows (IBA, IEA, EXP x2, IDA): ACCEPT; core function.
GO:0005886 IBA: MARK_AS_OVER_ANNOTATED; RocR is soluble.
GO:0000160 phosphorelay signal transduction system (IEA, REC domain): ACCEPT; RocR
is the receiver of the RocS1 phosphorelay.
GO:0045892 negative regulation of DNA-templated transcription (IMP,
PMID:15659157): KEEP_AS_NON_CORE. RocR is not a DNA-binding protein; it acts by
antagonising RocA1, the transcription factor. The full text was not read.