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Molecular Diagnosis and Diversity for Regulated Xanthomonas
Bacterial virulence factors
This DokuWiki is based upon work from COST Action CA16107 EuroXanth, supported by COST (European Cooperation in Science and Technology)
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Link to the original Xanthomonas //Resource @ xanthomonas.org
Multi-FASTA-formatted list of type III effectors from Xanthomonas
List of type III effectors in Xanthomonas (for download from NCBI)
Pseudomonas–Plant Interaction website (Lindeberg et al., 2005)
RalstoT3Edb (Peeters et al., 2013; Sabbagh et al., 2019)
Review papers on type III effectors
| Class | Family | Synonyms | Related proteins | RefSeq ID (GenBank ID) | Function / Features |
|---|---|---|---|---|---|
| AvrBs1 | AvrBs1 | AvrA | WP_011037255.1 | ||
| AvrBs2 | AvrBs2 | WP_039418336.1 | Glycerophosphodiester phosphodiesterase domain | ||
| AvrBs3 | AvrBs3 | PthA, PthB, PthN, PthXo, AvrXa7, AvrXa27, TALE | RipTAL | WP_011052943.1 | TAL effector repeat; Transcription activator in eukaryotic host cell; Nuclear localization |
| XopB | XopB | HopD1 (HopPtoD1, AvrPphD1), RipD | WP_039417318.1 | ||
| XopC | XopC1 | RipC2 | WP_011347616.1 | Phosphoribosyltransferase domain; Haloacid dehalogenase-like hydrolase | |
| XopC | XopC2 | RipC1 | WP_041183113.1 | ||
| XopD | XopD | WP_228949438.1 | C48-family SUMO cysteine protease (Ulp1 protease family); EAR motif; DNA binding; Nuclear localization | ||
| XopE | XopE1 | AvrXacE1 | HopX (AvrPphE), RipE1 | WP_011345998.1 | Putative transglutaminase |
| XopE | XopE2 | AvrXacE3, AvrXccE1 | HopX (AvrPphE), RipE1 | WP_011347479.1 | Putative transglutaminase |
| XopE | XopE3 | AvrXacE2 | HopX (AvrPphE), RipE1 | WP_011052114.1 | Putative transglutaminase |
| XopE | XopE4 | RipE1 | WP_244170787.1 | Putative transglutaminase | |
| XopE | XopE5 | HopX (AvrPphE), RipE1 | WP_260607984.1 | Putative transglutaminase | |
| XopF | XopF1 | Hpa4 | WP_011346095.1 | ||
| XopF | XopF2 | WP_011348008.1 | |||
| XopF | XopF3 | WP_039005675.1 | |||
| XopG | XopG1 | HopH (HopPtoH), RipAX2 | WP_011346758.1 | Peptidase_M91 superfamily; HEXXH motif, typical of zinc metallopeptidases | |
| XopG | XopG2 | HopH (HopPtoH), RipAX2 | WP_011038360.1 | Peptidase_M91 superfamily; HEXXH motif, typical of zinc metallopeptidases | |
| XopG | XopG3 | HopH (HopPtoH), RipAX1 | WP_084217840.1 | Peptidase_M91 superfamily; HEXXH motif, typical of zinc metallopeptidases | |
| XopH | XopH1 | AvrBs1.1, AvrBs7 | HopAO1 (HopPtoD2), RipBL | WP_011345706.1 | Protein tyrosine phosphatase-like phytase; Tyrosine-specific protein phosphatase |
| XopH | XopH2 | HopAO1 (HopPtoD2), RipBL | WP_010377341.1 | Protein tyrosine phosphatase-like phytase; Tyrosine-specific protein phosphatase | |
| XopI | XopI1 | WP_011346406.1 | F-box domain | ||
| XopI | XopI2 | WP_010367684.1 | F-box domain | ||
| XopJ | XopJ1 | HopZ1, RipP1 | WP_011347382.1 | Ser/Thr acetyltransferase | |
| XopJ | XopJ2 | AvrBsT | HopZ1, RipP1 | WP_074052319.1 | Ser/Thr acetyltransferase |
| XopJ | XopJ3 | AvrRxv | HopZ1, RipP1 | WP_011346137.1 | Ser/Thr acetyltransferase |
| XopJ | XopJ4 | AvrXv4 | HopZ1, RipP1 (formerly PopP1) | WP_008572727.1 | Ser/Thr acetyltransferase |
| XopJ | XopJ5 | AvrXccB | HopZ1, RipK, RipP1 | WP_228442257.1 | Ser/Thr acetyltransferase |
| XopJ | XopJ6 | RipP2 (formerly PopP2) | WP_196765268.1 | Ser/Thr acetyltransferase | |
| XopK | XopK | WP_027703763.1 | |||
| XopL | XopL | RipAC (formerly PopC) | WP_218498620.1 | LRR motif; LRR domain | |
| XopM | XopM | WP_011346113.1 | |||
| XopN | XopN | HopAU1 | WP_011348010.1 | ARM/HEAT repeat | |
| XopO | XopO | HopK1 (HopPtoK, HolPtoAB) N-terminal domain, AvrRps4 | WP_011346566.1 | AvrRps4 C-terminal region | |
| XopP | XopP | RipH3 (formerly Hlk) | WP_104613784.1 | ||
| XopQ | XopQ | HopQ1 (HolPtoQ), RipB | WP_011349176.1 | Inosine/uridine-preferring nucleoside hydrolase | |
| XopR | XopR | WP_011260681.1 | |||
| XopS | XopS | WP_039418869.1 | |||
| XopT | XopT | WP_199285673.1 | Plectin-repeat | ||
| XopU | XopU | WP_011408937.1 | |||
| XopV | XopV | RipAD | WP_011409498.1 | ||
| XopW | XopW | WP_228329674.1 | |||
| XopX | XopX | HopAE1 (HolPsyAE), RipBI | WP_011346212.1 | ||
| XopY | XopY | WP_011408080.1 | |||
| XopZ | XopZ1 | HopAS1 | WP_011259177.1 | ||
| XopZ | XopZ2 | HopAS1 | WP_039421390.1 | ||
| XopAA | XopAA | Ecf | HopAE1 (HolPsyAE), weakly related to RipBI | WP_041855088.1 | Early chlorosis factor; Proteasome/cyclosome repeat |
| XopAB | XopAB | weakly related to XopN | WP_011409110.1 | ||
| XopAC | XopAC | AvrAC | RipAC (formerly PopC) | WP_011269629.1 | LRR motif; LRR domain; Fido domain; Vascular hypersensitivity in Arabidopsis landrace Col-0 |
| XopAD | XopAD | RipS3 | WP_011409710.1 | SKWP repeat protein; Armadillo-like helical repeat; Armadillo-type fold; RelA/SpoT superfamily | |
| XopAE | XopAE | HpaF/HpaG | RipAC (formerly PopC) | WP_011050288.1 | LRR motif; LRR domain |
| XopAF | XopAF1 | AvrXv3 | HopAF1 (HopPtoJ), RipBD | WP_008577605.1 | |
| XopAF | XopAF2 | HopAF1 (HopPtoJ), RipBD | WP_227479740.1 | ||
| XopAG | XopAG1 | AvrGf1 | HopG1 (HopPtoG), HolPtoW, RipO1 | WP_272820829.1 | |
| XopAG | XopAG2 | AvrGf2 | HopG1 (HopPtoG), HolPtoW, RipO1 | WP_007970248.1 | |
| XopAH | XopAH | AvrXccC | AvrB/AvrC (AvrPphC) | WP_011037263.1 | AvrB/AvrC-family avirulence protein |
| XopAI | XopAI | HopO1 (HopPtoO, HopPtoS), HopAI1 (HolPtoAI) | WP_011052119.1 | NAD:arginine ADP-ribosyltransferase | |
| XopAJ | XopAJ | AvrRxo1 | WP_014504815.1 | P-loop containing nucleoside triphosphate hydrolase | |
| XopAK | XopAK | HopK1 (HopPtoK, HolPtoAB) C-terminal domain, RipBQ | WP_269466020.1 | ||
| XopAL | XopAL1 | Eop3, weakly similar to HopX, RipE2 | WP_274360846.1 | ||
| XopAL | XopAL2 | Eop3, RS_T3E_Hyp14 | WP_012437264.1 | ||
| XopAM | XopAM | HopR1, RipR | WP_012438997.1 | AvrE-family effector | |
| XopAN | XopAN | Replaced by XopAV | |||
| XopAO | XopAO | AvrRpm1, RipBA | WP_162267513.1 | ||
| XopAP | XopAP | RipAL | WP_236504155.1 | α/β hydrolase fold; Class-3 lipase | |
| XopAQ | XopAQ | RipAH/RipAG | WP_233366621.1 | ||
| XopAR | XopAR | RipBE | (APO95022.1) | ||
| XopAS | XopAS | HopAS1 | WP_229015407.1 | ||
| XopAT | XopAT | (AEL06363.1) | |||
| XopAU | XopAU | WP_041855031.1 | Serine/threonine kinase; Protein kinase domain; ATP-binding site | ||
| XopAV | XopAV1 | WP_065628638.1 | |||
| XopAV | XopAV2 | WP_011269951.1 | |||
| XopAW | XopAW | WP_011348129.1 | Calcium-binding protein; EF-hand domain; Calcium-binding site | ||
| XopAX | XopAX | WP_041854960.1 | |||
| XopAY | XopAY | Replaced by XopAV | |||
| XopAZ | XopAZ | WP_104549896.1 | SlpA superfamily; FKBP-type peptidyl-prolyl cis-trans isomerase | ||
| XopBA | XopBA | HopW1, RipBP | WP_227478587.1 | ||
| XopBB | XopBB | HopF2 (AvrPphF) | WP_251761698.1 | ||
| XopBC | = XopAV class | ||||
| XopBD | = XopAT class | ||||
| XopBE | = XopC class | ||||
| XopBF | = XopAV class | ||||
| XopBG | XopBG | WP_145953988.1 |
| Name | Synonyms | Related proteins | RefSeq ID (GenBank ID) | Function / Features | Reference |
|---|---|---|---|---|---|
| AvrXccA1 | AvrXca | WP_011039290.1 | Avirulence protein, perhaps not a T3E | Parker et al., 1993 | |
| AvrXccA2 | WP_274318562.1 | Avirulence protein, perhaps not a T3E | |||
| HpaA | WP_011346100.1 | Type III secretion control protein, perhaps not a T3E | Lorenz et al., 2008 | ||
| HpaT | WP_058196718.1 | Putative translocon protein, not a T3E | Pesce et al., 2017 | ||
| HrpB2 | WP_008575450.1 | Putative inner rod protein, not a T3E | Rossier et al., 2000; Scheibner et al., 2016 | ||
| HrpE | HrpE1 | WP_011346098.1 | Major subunit of the Hrp pilus | Weber et al., 2005; Weber & Koebnik, 2005; Weber & Koebnik, 2006; Gottig et al., 2018 | |
| HrpF | RipF (formerly PopF) | WP_011346092.1 | Putative translocon protein, not a T3E | Huguet & Bonas, 1997; Meyer et al., 2006 | |
| HrpW | RipW (formerly PopW) | WP_005926112.1 | Pectate lyase, perhaps not a T3E | Charkowski et al., 1998; Li et al., 2010 | |
| XopA | Hpa1/HpaG | WP_011346111.1 | Harpin, perhaps not a T3E | Zhu et al., 2000; Kim et al., 2004; Sgro et al., 2012; Wang et al., 2018 |
Charkowski AO, Alfano JR, Preston G, Yuan J, He SY, Collmer A (1998). The Pseudomonas syringae pv. tomato HrpW protein has domains similar to harpins and pectate lyases and can elicit the plant hypersensitive response and bind to pectate. J. Bacteriol. 180: 5211-5217. DOI: 10.1128/JB.180.19.5211-5217.1998
Gottig N, Vranych CV, Sgro GG, Piazza A, Ottado J (2018). HrpE, the major component of the Xanthomonas type three protein secretion pilus, elicits plant immunity responses. Sci. Rep. 8: 9842. DOI: 10.1038/s41598-018-27869-1
Huguet E, Bonas U (1997). HrpF of Xanthomonas campestris pv. vesicatoria encodes an 87-kDa protein with homology to NoIX of Rhizobium fredii. Mol. Plant Microbe Interact. 10: 488-498. DOI: 10.1094/MPMI.1997.10.4.488
Kim JG, Jeon E, Oh J, Moon JS, Hwang I (2004). Mutational analysis of Xanthomonas harpin HpaG identifies a key functional region that elicits the hypersensitive response in nonhost plants. J. Bacteriol. 186: 6239-6247. DOI: 10.1128/JB.186.18.6239-6247.2004
Li JG, Liu HX, Cao J, Chen LF, Gu C, Allen C, Guo JH (2010). PopW of Ralstonia solanacearum, a new two-domain harpin targeting the plant cell wall. Mol. Plant Pathol. 11: 371-381. DOI: 10.1111/j.1364-3703.2010.00610.x
Lindeberg M, Stavrinides J, Chang JH, Alfano JR, Collmer A, Dangl JL, Greenberg JT, Mansfield JW, Guttman DS (2005). Proposed guidelines for a unified nomenclature and phylogenetic analysis of type III Hop effector proteins in the plant pathogen Pseudomonas syringae. Mol. Plant Microbe Interact. 18: 275-282. DOI: 10.1094/MPMI-18-0275
Lorenz C, Kirchner O, Egler M, Stuttmann J, Bonas U, Büttner D (2008). HpaA from Xanthomonas is a regulator of type III secretion. Mol. Microbiol. 69: 344-360. DOI: 10.1111/j.1365-2958.2008.06280.x
Meyer D, Cunnac S, Guéneron M, Declercq C, Van Gijsegem F, Lauber E, Boucher C, Arlat M (2006). PopF1 and PopF2, two proteins secreted by the type III protein secretion system of Ralstonia solanacearum, are translocators belonging to the HrpF/NopX family. J. Bacteriol. 188: 4903-4917. DOI: 10.1128/JB.00180-06
Parker JE, Barber CE, Fan MJ, Daniels MJ (1993). Interaction of Xanthomonas campestris with Arabidopsis thaliana: characterization of a gene from X. c. pv. raphani that confers avirulence to most A. thaliana accessions. Mol. Plant Microbe Interact. 6: 216-224. DOI: 10.1094/mpmi-6-216
Peeters N, Carrère S, Anisimova M, Plener L, Cazalé AC, Genin S (2013). Repertoire, unified nomenclature and evolution of the Type III effector gene set in the Ralstonia solanacearum species complex. BMC Genomics 14: 859. DOI: 10.1186/1471-2164-14-859
Pesce C, Jacobs JM, Berthelot E, Perret M, Vancheva T, Bragard C, Koebnik R (2017). Comparative genomics identifies a novel conserved protein, HpaT, in proteobacterial type III secretion systems that do not possess the putative translocon protein HrpF. Front. Microbiol. 8: 1177. DOI: 10.3389/fmicb.2017.01177
Rossier O, Van den Ackerveken G, Bonas U (2000). HrpB2 and HrpF from Xanthomonas are type III-secreted proteins and essential for pathogenicity and recognition by the host plant. Mol. Microbiol. 38: 828-838. DOI: 10.1046/j.1365-2958.2000.02173.x
Sabbagh CRR, Carrere S, Lonjon F, Vailleau F, Macho AP, Genin S, Peeters N (2019). Pangenomic type III effector database of the plant pathogenic Ralstonia spp. PeerJ 7: e7346. DOI: 10.7717/peerj.7346
Scheibner F, Schulz S, Hausner J, Marillonnet S, Büttner D (2016). Type III-dependent translocation of HrpB2 by a nonpathogenic hpaABC mutant of the plant-pathogenic bacterium Xanthomonas campestris pv. vesicatoria. Appl. Environ. Microbiol. 82: 3331-3347. DOI: 10.1128/AEM.00537-16
Sgro GG, Ficarra FA, Dunger G, Scarpeci TE, Valle EM, Cortadi A, Orellano EG, Gottig N, Ottado J (2012). Contribution of a harpin protein from Xanthomonas axonopodis pv. citri to pathogen virulence. Mol. Plant Pathol. 13: 1047-1059. DOI: 10.1111/j.1364-3703.2012.00814.x
Wang X, Zhang L, Ji H, Mo X, Li P, Wang J, Dong H (2018). Hpa1 is a type III translocator in Xanthomonas oryzae pv. oryzae. BMC Microbiol. 18: 105. DOI: 10.1186/s12866-018-1251-3
Weber E, Koebnik R (2005). Domain structure of HrpE, the Hrp pilus subunit of Xanthomonas campestris pv. vesicatoria. J. Bacteriol. 187: 6175-6186. DOI: 10.1128/JB.187.17.6175-6186.2005
Weber E, Koebnik R (2006). Positive selection of the Hrp pilin HrpE of the plant pathogen Xanthomonas. J. Bacteriol. 188: 1405-1410. DOI: 10.1128/JB.188.4.1405-1410.2006
Weber E, Ojanen-Reuhs T, Huguet E, Hause G, Romantschuk M, Korhonen TK, Bonas U, Koebnik R (2005). The type III-dependent Hrp pilus is required for productive interaction of Xanthomonas campestris pv. vesicatoria with pepper host plants. J. Bacteriol. 187: 2458-2468. DOI: 10.1128/JB.187.7.2458-2468.2005
Zhu W, MaGbanua MM, White FF (2000). Identification of two novel hrp-associated genes in the hrp gene cluster of Xanthomonas oryzae pv. oryzae. J. Bacteriol. 182: 1844-1853. DOI: 10.1128/JB.182.7.1844-1853.2000
