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--- bacteria:t3e:xopad [2020/07/02 16:04]
rkoebnik [Biological function]
+++ bacteria:t3e:xopad [2020/08/11 11:07] (current)
rkoebnik [Conservation]
@@ Line 1: / Line 1: @@
 ====== XopAD ======
-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)\\
+Prototype: XopAD (//Xanthomonas euvesicatoria// pv. //euvesicatoria//, ex //Xanthomonas campestris// pv. //vescicatoria//; strain 85-10)\\
 RefSeq ID: not found in RefSeq. GenBank accession: [[https://www.ncbi.nlm.nih.gov/protein/CAJ26046.1|CAJ26046.1]] (614 aa)\\
 D structure: Unknown
@@ Line 23: / Line 23: @@
 No PIP box was found in the promoter region of //xopAD// in //X. 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 ===
@@ Line 42: / Line 42: @@
 === 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 //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).
 === In other plant pathogens/symbionts ===
 Yes. XopAD is homologous to members of the RipS1 family of effectors in //Ralstonia solanacearum// (Peeters //et al//., 2013).
 ===== References =====
@@ Line 52: / Line 52: @@
 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]]

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