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--- bacteria:t3e:xopad [2020/05/28 13:18] – lnoel
+++ bacteria:t3e:xopad [2025/07/24 23:15] (current) – jfpothier
@@ Line 1: / Line 1: @@
-====== XopAD ======
+====== The Type III Effector XopAD from //Xanthomonas// ======
-Author: David Studholme\\
+Author: [[https://www.researchgate.net/profile/David_Studholme|David J. Studholme]]\\
-Internal reviewer: Laurent Noël\\
+Internal reviewer: [[https://www.researchgate.net/profile/Laurent_Noel|Laurent D. Noël]]\\
-Expert reviewer: FIXME
 Class: XopAD\\
 Family: XopAD\\
-Prototype: XopAD (//Xanthomonas euvesicatoria// pv. //euvesicatoria// aka //Xanthomonas campestris// pv. //vescicatoria//; strain 85-10)\\
+Prototypes: XAC4213 (//Xanthomonas citri// pv. //citri//; strain 306), XOO4145 (//Xanthomonas oryzae// pv. //oryzae//; strain T7174)\\
-RefSeq ID: not found in RefSeq. GenBank accession: [[https://www.ncbi.nlm.nih.gov/protein/CAJ26046.1|CAJ26046.1]] (614 aa)\\
+GenBank ID (XAC4213): [[https://www.ncbi.nlm.nih.gov/protein/AAM39048.1|AAM39048.1]] (2883 aa)\\
+GenBank ID (XOO4145): [[https://www.ncbi.nlm.nih.gov/protein/BAE70900.1|BAE70900.1]] (2927 aa)\\
+RefSeq ID: [[https://www.ncbi.nlm.nih.gov/protein/WP_011409710.1|WP_011409710.1]] (2927 aa)\\
 D structure: Unknown
@@ Line 15: / Line 16: @@
 === How discovered? ===
-XopAD was discovered using a machine-learning approach (Teper //et al//., 2016).
+XopAD was first described as a homologue of a type 3 effector from //Ralstonia solanacearum// ([[https://www.ncbi.nlm.nih.gov/protein/BAH47290.1|BAH47290.1]]) (White //et al.//, 2009) and later re-discovered using a machine-learning approach (Teper //et al.//, 2016).
 === (Experimental) evidence for being a T3E ===
 XopAD fused to the AvrBs2 reporter domain, was shown to translocate into plant cells in an //hrpF//-dependent manner.
 === Regulation ===
-Not known. No PIP box was found in the promoter region of //xopAD// in //X. euvesicatoria// strain 85-10 (Teper //et al//., 2016).
+No PIP box was found in the promoter region of //xopAD// in //X. euvesicatoria// pv. //euvesicatoria// strain 85-10 (Teper //et al.//, 2016).
+qRT-PCR revealed that transcript levels of 15 out of 18 tested non-TAL effector genes (as well as the regulatory genes //hrpG// and //hrpX//), including //xopAD//, were significantly reduced in the //Xanthomonas oryzae// pv. //oryzae// Δ//xrvC// mutant compared with those in the wild-type strain PXO99<sup>A</sup> (Liu //et al.//, 2016).
 === Phenotypes ===
-Deletion of //xopAD// does not alter //X. citri// pv. //citri// (//Xci//) pathogenicity (Escalon //et al//., 2013).
+Deletion of //xopAD// does not alter //X. citri// pv. //citri// pathogenicity (Escalon //et al.//, 2013).
 === Localization ===
@@ Line 31: / Line 38: @@
 === Enzymatic function ===
-Not known. However, the 614 amino acid protein consists of multiple [[https://www.ebi.ac.uk/interpro/beta/entry/InterPro/IPR011989/|armadillo repeats]] of semi-conserved 42 amino acids. The C-terminal domain, which is absent in //Xcv// 85-10 XopAD but present in the ~2880 amino acid homologues (see below), encodes a putative RelA-like nucleotidyltransferase domain (Teper //et al//., 2016).
+Not known. However, the 614 amino acid protein consists of multiple [[https://www.ebi.ac.uk/interpro/beta/entry/InterPro/IPR011989/|armadillo repeats]] of semi-conserved 42 amino acids. The C-terminal domain, which is absent in //Xcv// 85-10 XopAD but present in the ~2880 amino acid homologues (see below), encodes a putative RelA-like nucleotidyltransferase domain (Teper //et al.//, 2016).
 === Interaction partners ===
@@ Line 40: / Line 48: @@
 === In xanthomonads ===
-Yes. XopAD has homologues encoded in the genomes of most  //Xanthomonas// species (Teper //et al//., 2016), including //X. axonopodis// (Harrison & Studholme, 2014), //X. vasicola// (Studholme //et al//., 2010; Wasukira //et al//., 2012), //X. nasturtii// (Vicente //et al//., 2010), //X. citri// (Escalon //et al//., 2013). In this respect, //Xanthomonas campestris// appear to be an exception. Escalon and colleagues state “// The analysis of// xopAD //and// xopAG //suggested horizontal transfer between// X. citri //pv.// bilvae//, another citrus pathogen, and some// Xci //strains//” (Escalon //et al//., 2013). The prototype sequence from //X. euvesicatoria// strain 85-10 (Teper //et al//., 2016) is 614 amino acids in length and marked in GenBank as a fragment. Homologues in other genomes of this species range from 2840 (RefSeq: [[https://www.ncbi.nlm.nih.gov/protein/WP_046939801.1|WP_046939801.1]]) to 2885 (RefSeq: [[https://www.ncbi.nlm.nih.gov/protein/WP_033837371.1|WP_033837371.1]]) amino acids in length and the authors of the prototype study state: “//we hypothesize that the ORFs annotated as XCV1197 (XopAV) and XCV1198, and XCV4315 (XopAD), XCV4314 and XCV4313, were originally two complete ORFs that were later truncated by the introduction of early stop codons//” (Teper //et al//., 2016). Therefore, the full-length homologues found in other genomes might not be functionally equivalent to the prototype XopAD. The introduction of early stop codons is explained by presence of an ISXac5-related insertion sequence (Escalon //et al//., 2013).
+Yes. XopAD has homologues encoded in the genomes of most //Xanthomonas// species (Teper //et al.//, 2016), including //X. axonopodis// (Harrison & Studholme, 2014), //X. vasicola// (Studholme //et al//., 2010; Wasukira //et al.//, 2012), //X. nasturtii// (Vicente //et al.//, 2010), //X. citri// (Escalon //et al.//, 2013). In this respect, //Xanthomonas campestris// appears to be an exception. Escalon and colleagues state: “The analysis of //xopAD// //and// //xopAG// suggested horizontal transfer between //X. citri// pv. //bilvae//, another citrus pathogen, and some //X. citri// pv. //citri// strains” (Escalon //et al//., 2013). The prototype sequence from //X. euvesicatoria// pv. //euvesictoria// strain 85-10 (Teper //et al.//, 2016) is 614 amino acids in length and marked in GenBank as a fragment. Homologues in other genomes of this species range from 2840 aa (RefSeq: [[https://www.ncbi.nlm.nih.gov/protein/WP_046939801.1|WP_046939801.1]]) to 2885 aa (RefSeq: [[https://www.ncbi.nlm.nih.gov/protein/WP_033837371.1|WP_033837371.1]]) in length and the authors of the prototype study state: "We hypothesize that the ORFs annotated as XCV1197 (XopAV) and XCV1198, and XCV4315 (XopAD), XCV4314 and XCV4313, were originally two complete ORFs that were later truncated by the introduction of early stop codons" (Teper //et al//., 2016). Therefore, the full-length homologues found in other genomes might not be functionally equivalent to the prototype XopAD. The introduction of early stop codons is explained by presence of an IS//Xac5//-related insertion sequence (Escalon //et al.//, 2013).
 === In other plant pathogens/symbionts ===
-Yes. XopAD is homologous to members of the RipS1 family of effectors in //Ralstonia solanacearum// (Peeters //et al//., 2013).
+Yes. XopAD is homologous to members of the RipS1 family of effectors in //Ralstonia solanacearum// (Peeters //et al.//, 2013).
 ===== References =====
-Escalon A //et al.// (2013). Variations in type III effector repertoires, pathological phenotypes and host range of //Xanthomonas citri// pv. //citri// pathotypes. Mol. Plant Pathol. 14, 483–496. DOI: [[https://doi.org/10.1111/mpp.12019|10.1111/mpp.12019]].
+Escalon A, Javegny S, Vernière C, Noël LD, Vital K, Poussier S, Hajri A, Boureau T, Pruvost O, Arlat M, Gagnevin L (2013). Variations in type III effector repertoires, pathological phenotypes and host range of //Xanthomonas citri// pv. //citri// pathotypes. Mol. Plant Pathol. 14: 483-496. DOI: [[https://doi.org/10.1111/mpp.12019|10.1111/mpp.12019]]
+Harrison J, Studholme DJ (2014). Draft genome sequence of //Xanthomonas axonopodis// pathovar //vasculorum// NCPPB 900. FEMS Microbiol. Lett. 360: 113-116. DOI: [[https://doi.org/10.1111/1574-6968.12607|10.1111/1574-6968.12607]]
+Liu Y, Long J, Shen D, Song C (2016). //Xanthomonas oryzae// pv. //oryzae// requires H-NS-family protein XrvC to regulate virulence during rice infection. FEMS Microbiol. Lett. 363: fnw067. DOI: [[https://doi.org/10.1093/femsle/fnw067|10.1093/femsle/fnw067]]
+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: [[https://doi.org/10.1186/1471-2164-14-859|10.1186/1471-2164-14-859]]
+Studholme DJ, Kemen E, MacLean D, Schornack S, Aritua V, Thwaites R, Grant M, Smith J, Jones JD (2010). Genome-wide sequencing data reveals virulence factors implicated in banana //Xanthomonas// wilt. FEMS Microbiol. Lett. 310: 182-192. DOI: [[https://doi.org/10.1111/j.1574-6968.2010.02065.x|10.1111/j.1574-6968.2010.02065.x]]
-Harrison J & Studholme DJ (2014). Draft genome sequence of //Xanthomonas axonopodis// pathovar //vasculorum// NCPPB 900. FEMS Microbiol. Lett. 360: 113–116. DOI: [[https://doi.org/10.1111/1574-6968.12607|10.1111/1574-6968.12607]].
+Teper D, Burstein D, Salomon D, Gershovitz M, Pupko T, Sessa G (2016). Identification of novel //Xanthomonas euvesicatoria// type III effector proteins by a machine-learning approach. Mol. Plant Pathol. 17: 398-411. DOI: [[https://doi.org/10.1111/mpp.12288|10.1111/mpp.12288]]
-Peeters N //et al.// (2013). Repertoire, unified nomenclature and evolution of the Type III effector gene set in the //Ralstonia solanacearum// species complex. BMC Genomics 14: 859. DOI: [[https://doi.org/10.1186/1471-2164-14-859|10.1186/1471-2164-14-859]].
+Vicente JG, Rothwell S, Holub EB, Studholme DJ (2017). Pathogenic, phenotypic and molecular characterisation of //Xanthomonas nasturtii// sp. nov. and //Xanthomonas floridensis// sp. nov., new species of //Xanthomonas// associated with watercress production in Florida. Int. J. Syst. Evol. Microbiol. 67: 3645-3654. DOI: [[https://doi.org/10.1099/ijsem.0.002189|10.1099/ijsem.0.002189]]
-Studholme DJ //et al.// (2010). Genome-wide sequencing data reveals virulence factors implicated in banana //Xanthomonas// wilt. FEMS Microbiol. Lett. 310: 182–192. DOI: [[https://doi.org/10.1111/j.1574-6968.2010.02065.x|10.1111/j.1574-6968.2010.02065.x]].
+Wasukira A, Tayebwa J, Thwaites R, Paszkiewicz K, Aritua V, Kubiriba J, Smith J, Grant M, Studholme DJ (2012). Genome-wide sequencing reveals two major sub-lineages in the genetically monomorphic pathogen //Xanthomonas campestris// pathovar //musacearum//. Genes (Basel) 3: 361-377. DOI: [[https://doi.org/10.3390/genes3030361|10.3390/genes3030361]]
-Teper D //et al.// (2016). Identification of novel //Xanthomonas euvesicatoria// type III effector proteins by a machine-learning approach. Mol. Plant Pathol. 17: 398–411. DOI: [[https://doi.org/10.1111/mpp.12288|10.1111/mpp.12288]].
+White FF, Potnis N, Jones JB, Koebnik R (2009). The type III effectors of //Xanthomonas//. Mol. Plant Pathol. 10: 749-66. DOI: [[https://doi.org/10.1111/j.1364-3703.2009.00590.x|10.1111/j.1364-3703.2009.00590.x]]
-Vicente JG, Rothwell S, Holub EB, Studholme DJ (2017). Pathogenic, phenotypic and molecular characterisation of //Xanthomonas nasturtii// sp. nov. and //Xanthomonas floridensis// sp. nov., new species of //Xanthomonas// associated with watercress production in Florida. Int. J. Syst. Evol. Microbiol. 67: 3645–3654. DOI: [[https://doi.org/10.1099/ijsem.0.002189|10.1099/ijsem.0.002189]].
+===== Acknowledgements =====
-Wasukira A //et al.// (2012). Genome-wide sequencing reveals two major sub-lineages in the genetically monomorphic pathogen //Xanthomonas campestris// pathovar //musacearum//. Genes (Basel) 3: 361–377. DOI: [[https://doi.org/10.3390/genes3030361|10.3390/genes3030361]].
+This fact sheet is based upon work from COST Action CA16107 EuroXanth, supported by COST (European Cooperation in Science and Technology).

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