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--- bacteria:t3e:xopad [2020/08/11 10:07] – [Conservation] rkoebnik
+++ bacteria:t3e:xopad [2025/02/13 13:33] (current) – jfpothier
@@ Line 1: / Line 1: @@
-====== XopAD ======
+====== The Type III Effector XopAD from //Xanthomonas// ======
 Author: [[https://www.researchgate.net/profile/David_Studholme|David J. Studholme]]\\
 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//, ex //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 ===
@@ Line 21: / Line 22: @@
 === Regulation ===
-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).
+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 33: / Line 34: @@
 === 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 42: / Line 43: @@
 === 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// 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 //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 IS//Xac5//-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 =====
@@ Line 64: / Line 64: @@
 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]]
+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]]
+===== Acknowledgements =====
+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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