Repertoire, unified nomenclature and evolution of the Type III effector gene set in the Ralstonia solanacearum species complex

Peeters, Nemo; Carrère, Sébastien; Anisimova, Maria; Plener, Laure; Cazalé, Anne-Claire; Genin, Stephane

doi:10.1186/1471-2164-14-859

Table 1 List of the T3E genes currently identified in the R. solanacearum species complex and proposal for a unified nomenclature

From: Repertoire, unified nomenclature and evolution of the Type III effector gene set in the Ralstonia solanacearum species complex

Proposed T3E family name	Representative gene member	Former/other name	Hop/Xop homolo-gues	Functional domain/motif or Function	Evidence for T3SS-dependent secretion or translocation
RipA1	RSc2139	AWR1			RipA1 [23]
RipA2	RSp0099	RipA, Rip29, Hpx31, AWR2			RipA [5], Rip29 [6]
RipA3	RSp0846	Rip44, Hpx32, AWR3			Rip44 [6]
RipA4	RSp0847	Rip45, Hpx4, AWR4			Rip45 [6]
RipA5	RSp1024	Rip56, Hpx10, AWR5			Rip56 [6]
RipB	Rsc0245	RipB, Rip2, Hpx11	HopQ/XopQ	Nucleoside N-ribohydrolase	RipB [5], Rip2 [6]
RipC1	RSp1239	Rip62	XopC		Rip62 [6]
RipC2	CFBP2957 RCFBP_mp20032		XopC
RipD	RSp0304	Rip34, Hpx25, Brg8	HopD/XopB		Rip34 [6]
RipE1	RSc3369	Rip26, Brg9	HopX/XopE		Rip26 [6]
RipE2	CFBP2957 RCFBP_mp10565		HopX/XopE
RipF1	RSp1555	PopF1, PopF2, Rip70		T3SS translocator	RipF1 [6], PopF1 [35]
RipF2	CFBP2957 RCFBP_mp30453			T3SS translocator
RipG1	RSp0914	Gala1, Rip53		F-box Leucine-Rich Repeats	Rip53 [6]
RipG2	RSp0672	Gala2, Rip37, Hpx20		F-box LRR protein	Rip37 [6]
RipG3	RSp0023	Gala3, Rip28		F-box LRR protein	Rip28 [6]
RipG4	RSc1800	Gala4, Rip17, Hpx15		F-box LRR protein	Rip17 [6]
RipG5	RSc1801	Gala5, Rip18, Hpx16		F-box LRR protein	Rip18 [6]
RipG6	RSc1356	RipG, Gala6, Rip13, Hpx13		F-box LRR protein	RipG [5], Rip13 [6]
RipG7	RSc1357	Gala7, Rip14, Hpx14		F-box LRR protein	Gala7 [16], Rip14 [6]
RipG8	CMR15 CMR15v4_10224	Gala8
RipH1	RSc1386	HLK1, Rip15, Brg19	XopP		Rip15 [6]
RipH2	RSp0215	HLK2, Rip32	XopP		Rip32 [6]
RipH3	RSp0160	HLK3, Rip30, Brg18	XopP		Rip30 [6]
RipH4	Psi07 RPSI07_mp0161	HLK4	XopP
RipI	RSc0041	Rip1			Rip1 [6]
RipJ	RSc2132	Rip22	HopZ/XopJ	Putative acetyltransferase	Rip22 [6]
RipK	CFBP2957 RCFBP_mp10024			YopJ acetyltransferase domain
RipL	RSp0193	Rip31, Brg22		Pentatricopeptide Repeats	Rip31 [6]
RipM	RSc1475	Rip16, Brg42			Rip16 [6]
RipN	RSp1130	Rip58, Hpx26, Brg44		Nudix hydrolase domain	Rip58 [6]
RipO1	RSp0323	Rip35, Brg12	HopG		Rip35 [6]
RipO2	R. syzygii RALSY_mp30159		HopG
RipP1	RSc0826	PopP1, Rip7	HopZ/XopJ	Putative acetyltransferase	Rip7 [6], PopP1 [36]
RipP2	RSc0868	PopP2, Rip8	HopZ/XopJ	Acetyltransferase	PopP2 [5], Rip8 [6]
RipP3	UW163 [GenBank accession : CAF32358.1]	PopP3	HopZ/XopJ	Putative acetyltransferase
RipQ	RSp1277	Rip63, Hpx23	HopAA		Rip63 [6]
RipR	RSp1281	Rip64, Hpx24, Brg15, PopS	HopR		Rip64 [6]
RipS1	RSc3401	SKWP1, Rip27, Hpx37	XopAD	Heat/Armadillo repeat domain	Rip27 [6]
RipS2	RSp1374	SKWP2, Rip65, Hpx36		Heat/Armadillo repeat domain	Rip65 [6]
RipS3	RSp0930	SKWP3, Rip54		Heat/Armadillo repeat domain	Rip54 [6]
RipS4	RSc1839	SKWP4, Rip20, Hpx30		Heat/Armadillo repeat domain	Rip20 [6]
RipS5	RSp0296	SKWP5, Rip33, Hpx34		Heat/Armadillo repeat domain	Rip33 [6]
RipS6	RSc2130	SKWP6		Heat/Armadillo repeat domain
RipS7	Molk2 RSMK02658	SKWP7		Heat/Armadillo repeat domain
RipS8	Psi07 RSPsi07_1850	SKWP8		Heat/Armadillo repeat domain
RipT	RSc3212	RipT, Rip25	HopC	Putative cysteine protease	RipT [5], Rip25 [6]
RipU	RSp1212	Rip59			Rip59 [6]
RipV1	RSc1349	Rip12, Hpx29, Brg17		Ubiquitin ligase domain	Rip12 [6]
RipV2	Psi07 RSPsi07_1895			Ubiquitin ligase domain
RipW	RSc2775	PopW, Rip24		Harpin, Pectate lyase	Rip24 [6], PopW [34]
RipX	RSp0877	PopA, Rip49		Harpin	Rip49 [6], PopA [74]
RipY	RSc0257	Rip3, Brg23		Ankyrin Repeats	Rip3 [6]
RipZ	RSp1031	Rip57, Brg38			Rip57 [6]
RipAA	RSc0608	AvrA, Rip5, Brg46			AvrA [31], Rip5 [6]
RipAB	RSp0876	PopB, Rip48			Rip48 [6], PopB [33]
RipAC	RSp0875	PopC, Rip47	XopAE	Leucine-Rich Repeats	Rip47 [6], PopC [33]
RipAD	RSp1601	Rip72			Rip72 [6]
RipAE	RSc0321	Rip4	HopZ/XopJ	Putative acetyltransferase	Rip4 [6]
RipAF1	RSp0822	Rip40	HopF	PutativeADP-ribosyltransferase	Rip40 [6]
RipAF2	R. syzygii RALSY_20037		HopF	PutativeADP-ribosyltransferase
RipAG	RSc0824	Rip6			Rip6 [6]
RipAH	RSc0895	Rip11			Rip11 [6]
RipAI	RSp0838	Rip41			Rip41 [6]
RipAJ	RSc2101	Rip21, Hpx18			Rip21 [6]
RipAK	RSc2359	Rip23, Hpx28, Brg36			Rip23 [6]
RipAL	UW551 RRSL_02221	Rip38		Lipase domain	Rip38 [6]
RipAM	RSc3272	Brg40			This work Additional file 3
RipAN	RSp0845	Rip43, Hpx33, Brg33			Rip43 [6]
RipAO	RSp0879	Rip50, Hpx2, Brg34			Rip50 [6]
RipAP	UW551 RRSL_04655	Rip60		Ankyrin Repeats	Rip60 [6]
RipAQ	RSp0885	Rip51, Brg35			Rip51 [6]
RipAR	RSp1236	Rip61		Ubiquitin ligase domain	Rip61 [6]
RipAS	RSp1384	Rip66, Hpx9, Brg43			Rip66 [6]
RipAT	RSp1388	Rip67, Brg48			Rip67 [6]
RipAU	RSp1460	Rip68, Hpx8, Brg45			Rip68 [6]
RipAV	RSp0732	Rip39, Hpx27, Brg39	HopAV		Rip39 [6]
RipAW	RSp1475	Rip69		Ubiquitin ligase domain	Rip69 [6]
RipAX1	RSc3290	Brg13	HopH/XopG
RipAX2	RSp0572	Rip36, Brg14	HopH/XopG		Rip36 [6]
RipAY	RSp1022	Rip55, Hpx21, Brg37			Rip55 [6]
RipAZ1	RSp1582	Rip71			Rip71 [6]
RipAZ2	R. syzygii RALSY_20407
RipBA	RSc0227, RSp0228 [pseudogene]		AvrRpm1
RipBB	Psi07 RPSI07_mp0573			Ankyrin repeats
RipBC	CFBP2957 RCFBP_mp30170			YopJ acetyltransferase domain & Ankyrin Repeats
RipBD	R. syzygii RALSY_20184		HopAF
RipBE	RS1000 Rip10	Rip10	XopAR		Rip10 [6]
RipBF	Psi07 RPSI07_2863		HopV
RipBG	Molk2 RSMK00763		HopAB	Ubiquitin ligase domain
RipBH	Psi07 RPSI07_mp1715			Shigella flexneri OspD family
RipBI	CFBP2957 RCFBP_mp30113		XopX
RipTAL1	RSc1815	Rip19, Hpx17, Brg11	TAL	Putative transcription factor	Rip19 [6]
RipTPS	RSp0731			Trehalose-phosphate synthase	Manuscript in preparation

A representative gene member for each family is provided (gene nomenclature from strain GMI1000 unless otherwise stated) with other names published in the literature. Homologues T3E from Pseudomonas syringae sp. (Hop) or Xanthomonas sp. (Xop) are indicated. The last column lists T3E for which Type 3 secretion system-dependent secretion or translocation was experimentally demonstrated.

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ISSN: 1471-2164

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