Literature summary for 3.1.4.52 extracted from

He, Y.W.; Boon, C.; Zhou, L.; Zhang, L.H.
Co-regulation of Xanthomonas campestris virulence by quorum sensing and a novel two-component regulatory system RavS/RavR (2009), Mol. Microbiol., 71, 1464-1476.

Cloned(Commentary)

Cloned (Comment)	Organism
DNA fragments encoding GGDEF (1-172 aa) and GGDEF-EAL domain (10-426 aa) amplified separately and fused to the GST coding region in pGEX-6p-1, transformation of Escherichia coli BL21. Deletion of Xcc1959 in Xcc strain XC1 or 8004 had no significant effect on virulence factor production in vitro	Xanthomonas campestris pv. campestris
mutated DAA domain cloned in expression vector pLAFR3 (lac promoter) for complementation analysis in a Xanthomonas campestris XC1 mutant lacking ravR. Deletion of ravR results in decreased virulence factor production. RavS and RavR constitute a two-component regulatory system (ravS gene deleted inframe in Xanthomonas campestris strains XC1 and 8004): no effect on bacterial growth in YEB and LB medium, similar phenotype changes compared to Xanthomonas campestris XC1 mutant lacking ravR. RavR is a c-di-GMP phosphodiesterase: fusionated domains GGDEF and EAL (cloned separately into the expression vector pLAFR3 for in trans expression in the mutant deltaravR). RavS/RavR 2-component system regulates diverse functions in Xanthomonas campestris XC1	Xanthomonas campestris pv. campestris

Cloned (Comment)

Organism

DNA fragments encoding GGDEF (1-172 aa) and GGDEF-EAL domain (10-426 aa) amplified separately and fused to the GST coding region in pGEX-6p-1, transformation of Escherichia coli BL21. Deletion of Xcc1959 in Xcc strain XC1 or 8004 had no significant effect on virulence factor production in vitro

Xanthomonas campestris pv. campestris

mutated DAA domain cloned in expression vector pLAFR3 (lac promoter) for complementation analysis in a Xanthomonas campestris XC1 mutant lacking ravR. Deletion of ravR results in decreased virulence factor production. RavS and RavR constitute a two-component regulatory system (ravS gene deleted inframe in Xanthomonas campestris strains XC1 and 8004): no effect on bacterial growth in YEB and LB medium, similar phenotype changes compared to Xanthomonas campestris XC1 mutant lacking ravR. RavR is a c-di-GMP phosphodiesterase: fusionated domains GGDEF and EAL (cloned separately into the expression vector pLAFR3 for in trans expression in the mutant deltaravR). RavS/RavR 2-component system regulates diverse functions in Xanthomonas campestris XC1

Xanthomonas campestris pv. campestris

Protein Variants

Protein Variants	Comment	Organism
DAA	EAL domain of ravR mutated (DAA): key residues E and L are substituted by D and A	Xanthomonas campestris pv. campestris

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
c-di-GMP + H2O	Xanthomonas campestris pv. campestris	-	?	-	?
c-di-GMP + H2O	Xanthomonas campestris pv. campestris XC1	-	?	-	?

Organism

Organism	UniProt	Comment	Textmining
Xanthomonas campestris pv. campestris	-	strain ATCC33913	-
Xanthomonas campestris pv. campestris	Q8P947	-	-
Xanthomonas campestris pv. campestris	Q8P9A5	-	-
Xanthomonas campestris pv. campestris ATCC 33913	-	strain ATCC33913	-
Xanthomonas campestris pv. campestris X1	Q8P9A5	-	-
Xanthomonas campestris pv. campestris XC1	Q8P947	-	-

Purification (Commentary)

Purification (Comment)	Organism
GGDEF domain and GGDEF-EAL fusion domains: GST-affinity chromatography	Xanthomonas campestris pv. campestris

Specific Activity [micromol/min/mg]

Specific Activity Minimum [µmol/min/mg]	Specific Activity Maximum [µmol/min/mg]	Comment	Organism
additional information	-	Xanthomonas campestris XC1 wild-type activity 100%, Xanthomonas campestris XC1 mutant lacking ravR 62%, Xanthomonas campestris XC1 mutant lacking ravR transformed with GGDEFEAL fusion domain almost 100%, Xanthomonas campestris XC1 mutant lacking ravR transformed with GGDEF domain 62%, Xanthomonas campestris XC1 mutant lacking ravR transformed with EAL domain almost 100%, Xanthomonas campestris XC1 mutant lacking ravR transformed with mutated EAL domain (DAA): 62%	Xanthomonas campestris pv. campestris

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
c-di-GMP + H2O	-	Xanthomonas campestris pv. campestris	?	-	?
c-di-GMP + H2O	-	Xanthomonas campestris pv. campestris XC1	?	-	?

Subunits

Subunits	Comment	Organism
?	Xcc1959 encodes a GGDEF and EAL fusion domain protein with two PAS domains	Xanthomonas campestris pv. campestris

Synonyms

Synonyms	Comment	Organism
PdeA	containing HD-GYP or EAL domains (associated with c-di-GMP degradation), RavR (Xcc1958, originally named RdeA) encodes a response regulator with an GGDEFEAL fusion domain, RavS (regulation of adaptation and virulence, sensor) encoded by Xcc1960. ravS and ravR belong to the same operon in strain XC1	Xanthomonas campestris pv. campestris
PdeA	containing HD-GYP or EAL domains (associated with cyclic di-3',5'-guanylate degradation), RavR (Xcc1958, originally named PdeA) encodes a response regulator with an GGDEF-EAL fusion domain, RavS (regulation of adaptation and virulence, sensor) encoded by Xcc1960, in the genome of Xanthomonas campestris pv. campestris strain ATCC33913	Xanthomonas campestris pv. campestris
Putative uncharacterized protein	-	Xanthomonas campestris pv. campestris
RavR	-	Xanthomonas campestris pv. campestris