Table 1.

Cyclic di-GMP receptors and corresponding non-binding homologues

Cyclic di-GMP receptors or corresponding non-binding homologues	Representatives	Organism	Function	Cyclic di-GMP binding site	Reference
PilZ domain proteins
xPilZ-PilZ	YcgR	E. coli	protein-protein interaction	RXXXR (D/N)xSxxG	[173]
xPilZ-PilZ	PlzA	Borellia burgdorferi	DNA/RNA binding of PilZ domain not binding cyclic di-GMP	RXXXR (D/N)xSxxG	[174]
effector-PilZ	BcsA	E. coli	cellulose synthase activity	RXXXR (D/N)xSxxG	[173]
xPilZ	PilZ	Xanthomonas spp.	interacts with cyclic di-GMP receptor FimX	no binding	[108]
PilZ	MapZ	P. aeruginosa	adaptor in chemosensory pathway	RXXXR (D/N)xSxxG	[175]
Transcription factors
Clp/Crp transcriptional regulator	Clp (Xac0483, BCAM1349)	Xanthomonas spp., Burkholderia , Stenotrophomonas maltophilia , Lysobacter enzymogenes	regulator of biofilm formation and virulence	E RS/T TS/T/N, glutamate E99 required for cyclic di-GMP binding	[113–117, 119, 176]
	CRP	E. coli , Pseudomonas putida , P. aeruginosa , V. cholerae	catabolite repression ( E. coli )	cAMP binding
	CRP	Mycobacterium tuberculosis		cAMP binding
	CRP	Rhodospirillum centenum	encystment	cGMP binding	[177]
CsgD subgroup LuxR type transcriptional regulator	VpsT	V. cholerae	biofilm activator	W[F/L/M][T/S]R	[111]
	CsgD	S. typhimurium , E. coli	biofilm activator	no binding	[112]
YajQ family	XC_3703/Smlt4090/PA4395/CdgL	Xanthomonas campestris pv campestris, S. maltophilia , P. aeruginosa , L. enzymogenes	interacts with LysR family transcription factor	n.d.*	[90]
	YajQ	E. coli , Clostridium sp., Bacillus cereus	interacts with transcription factor	ATP/GTP binding	[90]
P-loop NTPase lineage
AAA +ATPase domain proteins
NtrC type	FleQ/FlrA	P. aeruginosa , V. cholerae	sigma54 enhancer-binding transcription factor	LFRS RN ExxxR	[127, 178]
	FlrA	V. cholerae	sigma54 enhancer-binding transcription factor		[128]
	VpsR	V. cholerae	sigma54 enhancer-binding transcription factor, sigma70 associated	E R YxxxxxxRExxxQxxxxR	[129]
	Lon	P. aeruginosa ; V. cholerae	proteolysis	n.d.*	[130]
PilB/GspE type	MshE (PilB, VC0405)	V. cholerae	polymerizing type IV pili ATPase	RLGxx(L/V/I) (L/V/I)xxG(L/V/I)(L/V/I)xxxxLxx xLxxQ	[15]
	MshE (GspE, PA14_29490)	P. aeruginosa	type II secretion system ATPase	RLGxx(L/V/I) (L/V/I)xxG(L/V/I)(L/V/I)xxxxLxx xLxxQ	[133]
	PilB	Xanthomonas spp., P. aeruginosa	polymerizing type IV pili ATPase	no binding
PilT/VirD4 ATPases	PilT	V. cholerae	depolymerizing type IV pili ATPase	no binding
RecA ATPases	RecA	M. tuberculosis , Mycobacterium smegmatis	recombinase	c-di-GMP and c-di-AMP binding; C-terminus	[135]
	RecA	E. coli	recombinase	c-di-GMP binding; C-terminus	[135]
Hybrid Hsp100 ATPases	ClpB2 (ClpV1)	V. cholerae	type VI secretion	c-di-GMP binding; n.d.	[134]
FliI/HrcN type ATPases	FliI/HrcN	P. fluorescens , S. typhimurium , Sinorhizobium meliloti / Pseudomonas syringae	flagella/type three secretion system	R E R on different subunits	[134]
Degenerated cyclic di-GMP turnover proteins
Degenerated EAL domains	FimX	Xanthomonas, P. aeruginosa	type IV pili biosynthesis, type III secretion system expression	EXLXR	[94]
	LapD/BpfD	P. fluorescens, Bordetella bronchiseptica, Legionella pneumophila, Shewanella putrefaciens	regulation of periplasmic LapG protease activity	EXLXR	[10, 120]
CsrD paralogues	CsrD	Erwinia amylovora	binding of CsrB/CsrC small RNAs for RNaseE degradation	EXLXR	[106]
	CsrD/MshH	E. coli, S. typhimurium/V. cholerae	binding of CsrB/CsrC small RNAs for RNaseE degradation	EXMXR, no binding	[107]
	PigX	Serratia sp.	CsrD homologue, apparent in vivo phosphodiesterase activity	catalytic activity	[105]
Degenerated GGDEF domain (examples)	PelD	P. aeruginosa	Pel polysaccharide biosynthesis	RxxD	[104]
	PopA	C. vibrioides	degradation of replication initiation inhibitor CtrA	RxxD	[179]
Receiver domain
Pseudo-REC	ShkA	C. vibrioides	stimulation of phosphotransfer from histidine kinase to bEBP TacA	Y338	[136]
Pseudo-REC	Cle	C. vibrioides	interact with FliM upon cyclic di-GMP binding	[Y/F]XGPX[R/K]R	[137]
Conventional REC	PleD	C. vibrioides	phosphorylation of conserved aspartate 59 stimulates activity of output domain	no binding	[180]
Ribosomal components
Elongation factor P	EF-P	A. baumanii; Acinetobacter albensis	facilitates relieve of stalling of proline-rich regions	K47, E69	[138, 139]
	EF-P	E. coli, P. aeruginosa, and Burkholderia cenocepacia	relieve of stalling of proline-rich regions	no binding	[138, 139]
Glycosyltransferase type 2
	PgaC/PgaD complex	E. coli	PNAG (PGA/Ica) biosynthesis	R222A of PgaC	[140]
	PgaC/PgaD complex	S. aureus , S. epidermidis	PNAG biosynthesis	stimulation of PNAG synthesis does not require cyclic di-GMP	[56]

*n.d.=binding site not identified.