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--- bacteria:t3e:xopd [2020/07/01 10:20]
rkoebnik [References]
+++ bacteria:t3e:xopd [2020/07/08 18:27] (current)
rkoebnik [Biological function]
@@ Line 1: / Line 1: @@
 ====== XopD ======
-Author: Monika Kaluzna\\
+Author: [[https://www.researchgate.net/profile/Monika_Kaluzna|Monika Kałużna]]\\
-Internal reviewer: Alice Boulanger\\
+Internal reviewer: [[https://www.researchgate.net/profile/Alice_Castaing|Alice Boulanger]]\\
 Expert reviewer: FIXME
 Class: XopD (Xanthomonas outer protein D)\\
-Family: family C48 (Rawlings //et al//., 2006)\\
+Family: XopD\\
-Prototype: XopD (//Xanthomonas// outer protein D ; //Xanthomonas euvesicatoria// pv. //euvesicatoria// aka //Xanthomonas campestris// pv. //vescicatoria//; strain 85-10)\\
+Prototype: XopD (//Xanthomonas euvesicatoria// pv. //euvesicatoria//, ex //Xanthomonas campestris// pv. //vesicatoria//; strain 85-10)\\
 RefSeq ID: [[https://www.ncbi.nlm.nih.gov/protein/CAJ22068|CAJ22068]] (545 aa); [[https://www.ncbi.nlm.nih.gov/protein/DAA34040|DAA34040]] (760 aa) new annotation\\
-D structure : [[https://www.rcsb.org/structure/5JP3|5JP3]], Crystal structure available in (Chosed //et al//., 2007), [[http://www.rcsb.org/pdb/explore/jmol.do?structureId=2OIV&edMap=PO4|PDB-2OIV]]
+D structure: [[https://www.rcsb.org/structure/2OIV|2OIV]], [[https://www.rcsb.org/structure/2OIX|2OIX]] (Chosed //et al//., 2007); [[https://www.rcsb.org/structure/5JP1|5JP1]], [[https://www.rcsb.org/structure/5JP3|5JP3]] ( Pruneda //et al.//, 2016 )
 ===== Biological function =====
@@ Line 16: / Line 15: @@
 XopD was discovered in a cDNA-AFLP screen and reverse transcription-PCR analyses (Noël //et al//., 2002).
 === (Experimental) evidence for being a T3E ===
-XopD is a desumoylating enzyme with strict specificity for its plant small ubiquitin-like modifier (SUMO) substrates (Chosed //et al//., 2007). C-terminus of XopD (amino acids 322–520) shares primary sequence similarity with the C48 family of cysteine peptidases. In the XopD polypeptide, amino acid positions 309–481 are most homologous to the C-terminal catalytic domain of the Ulp1 ubiquitin-like protease protein family, which is highly conserved (Hotson //et al//., 2003; Li & Hochstrasser, 1999). Unlike yeast Ulp1 which process a variety of SUMO substrates, XopD exhibits rigid SUMO substrate specificity, it will process only certain plant SUMOs, //i.e.// T-SUMO, //At//SUMO-1, and //At//SUMO-2 (Chosed //et al//., 2007). However, another study has shoxn that XopD shows a mixed activity, being a (tomato)-SUMO and Ubiquitin isopeptidase. The capacity to efficiently recognize both substrates suggest a large evolutionary pressure to become a multifunctionnal protease (Pruneda //et al//., 2016).
+XopD is a desumoylating enzyme with strict specificity for its plant small ubiquitin-like modifier (SUMO) substrates (Chosed //et al//., 2007). C-terminus of XopD (amino acids 322–520) shares primary sequence similarity with the C48 family of cysteine peptidases (Rawlings //et al//., 2006). In the XopD polypeptide, amino acid positions 309–481 are most homologous to the C-terminal catalytic domain of the Ulp1 ubiquitin-like protease protein family, which is highly conserved (Li & Hochstrasser, 1999; Hotson //et al//., 2003). Unlike yeast Ulp1 which process a variety of SUMO substrates, XopD exhibits rigid SUMO substrate specificity, it will process only certain plant SUMOs, //i.e.// T-SUMO, //At//SUMO-1, and //At//SUMO-2 (Chosed //et al//., 2007). However, another study has shoxn that XopD shows a mixed activity, being a (tomato)-SUMO and Ubiquitin isopeptidase. The capacity to efficiently recognize both substrates suggest a large evolutionary pressure to become a multifunctionnal protease (Pruneda //et al//., 2016).
-Besides C-terminal SUMO protease domain (Chosed //et al//., 2007; Hotson //et al//., 2003), XopD has a unique N-terminal region with a host range determining non-specific DNA-binding domain (DBD) (Kim //et al//., 2011) and a central domain with two internal ERF-associated amphiphilic repression (EAR) motifs (L/FDLNL/FXP)(Ohta //et al//., 2001), which were found in plant repressors that regulate stress induced transcription. XopD might repress host transcription during //Xcv// infection (Ohta //et al//., 2001; Kim //et al//., 2011).
+Besides C-terminal SUMO protease domain (Hotson //et al//., 2003; Chosed //et al//., 2007), XopD has a unique N-terminal region with a host range determining non-specific DNA-binding domain (DBD) (Kim //et al//., 2011) and a central domain with two internal ERF-associated amphiphilic repression (EAR) motifs (L/FDLNL/FXP) (Ohta //et al//., 2001), which were found in plant repressors that regulate stress induced transcription. XopD might repress host transcription during //Xcv// infection (Ohta //et al//., 2001; Kim //et al//., 2011).
 === Regulation ===
-The //xopD// gene expression is induced in a //hrpG//- and //hrpX//-dependent manner (Noel //et al//., 2002). It was described that, XopD promoter does not contain a PIP box, but a //hrp// box, which is found in all //hrpL//-dependent promoters in //P.syringae// and //Erwinia// spp. (GGAACTNA-N13-CGACNNA; consensus: GGAACcNa-N13/14-cCACNNA) (Noel //et al//., 2002; Innes //et al//., 1993). However, after carefully inspected the intergenic region of the //Xanthomonas euvesicatoria// pv. //euvesicatoria// 85-10 genome (Xcv 85-10) between the //XCV0436// locus and the //xopD// locus for an alternative promoter and start site (Kim //et al//., 2011), identified a putative PIP box and ATG just downstream of the //XCV0436// locus. Using ATG as the putative start codon, the respective //xopD// ORF predicts a protein with 760 aa with a longer N-terminal domain (Kim //et al//., 2011).
+The //xopD// gene expression is induced in a //hrpG//- and //hrpX//-dependent manner (Noël //et al//., 2002). It was described that, XopD promoter does not contain a PIP box, but a //hrp// box, which is found in all //hrpL//-dependent promoters in //P.syringae// and //Erwinia// spp. (GGAACTNA-N13-CGACNNA; consensus: GGAACcNa-N13/14-cCACNNA) (Noël //et al//., 2002; Innes //et al//., 1993). However, after carefully inspected the intergenic region of the //Xanthomonas euvesicatoria// pv. //euvesicatoria// 85-10 genome (Xcv 85-10) between the //XCV0436// locus and the //xopD// locus for an alternative promoter and start site (Kim //et al//., 2011), identified a putative PIP box and ATG just downstream of the //XCV0436// locus. Using ATG as the putative start codon, the respective //xopD// ORF predicts a protein with 760 aa with a longer N-terminal domain (Kim //et al//., 2011).
 === Phenotypes ===
@@ Line 35: / Line 31: @@
 Comparative analysis of the XopD effector family in other phytopathogenic bacteria revealed that so called XopD-like proteins presents differences in sequence and length of their N-terminal domains. This suggests that the N-terminal domain of XopD and XopD-like effectors might impart substrate and/or host specificity.
-Transgenic expression of XopD<sub>Xcc8004</sub> in //Arabidopsis// has shown an accumulation of host defense response in a SA-dependent way (Tan //et al.//, 2015). Another study showed that //psvA//<sub>Xcc8004</sub> and //psvA//<sub>XccATCC33913</sub> (Castaneda //et al//., 2005) are not required for //Xcc// virulence in their host plants. Moreover, XopD<sub>XccB100</sub>, although having high sequence similarity with XopD<sub>Xcv85–10</sub> except for the KAE-rich domain localized in N-terminal region (Canonne //et al//., 2012), was not required for //Xcc// B100 virulence in //Arabidopsis//, //N. benthamiana//, and radish. These findings suggest that XopD-like effectors are not important for //Xcc//-plant interactions (Kim //et al//., 2011).
+Transgenic expression of XopD<sub>Xcc8004</sub> in //Arabidopsis// has shown an accumulation of host defense response in a SA-dependent way (Tan //et al.//, 2015). Another study showed that //psvA// <sub>Xcc8004</sub> and //psvA// <sub>XccATCC33913</sub> (Castaneda //et al//., 2005) are not required for //Xcc// virulence in their host plants. Moreover, XopD<sub>XccB100</sub>, although having high sequence similarity with XopD<sub>Xcv85–10</sub> except for the KAE-rich domain localized in N-terminal region (Canonne //et al//., 2012), was not required for //Xcc// B100 virulence in //Arabidopsis//, //N. benthamiana//, and radish. These findings suggest that XopD-like effectors are not important for //Xcc//-plant interactions (Kim //et al//., 2011).
 === Localization ===
-XopD localizes to subnuclear foci. The N terminus of XopD is required for targeting the effector to the plant nucleus; C-terminal domain encodes a Cys protease that cleaves SUMO-conjugated proteins (Hotson //et al//., 2003; Kim //et al//., 2008)).
+XopD localizes to subnuclear foci. The N terminus of XopD is required for targeting the effector to the plant nucleus; C-terminal domain encodes a Cys protease that cleaves SUMO-conjugated proteins (Hotson //et al//., 2003; Kim //et al//., 2008).
 === Enzymatic function ===
-Peptidase, isopeptidase or desumoylating enzyme (Hotson//et al//., 2003).
+Peptidase, isopeptidase or desumoylating enzyme (Hotson// et al//., 2003).
 === Interaction partners ===
@@ Line 54: / Line 47: @@
 Yes (e.g. //Xanthomonas campestris// pv. //vesicatoria//, //X. campestris// pv. //campestris// (Kim //et al//., 2011).
 === In other plant pathogens/symbionts ===
@@ Line 84: / Line 76: @@
 Ohta M, Matsui K, Hiratsu K, Shinshi H, Ohme-Takagi M (2001). Repression domains of class II ERF transcriptional repressors share an essential motif for active repression. Plant Cell 13: 1959-1968. DOI: [[https://doi.org/10.1105/tpc.010127|10.1105/tpc.010127]]
-Pruneda JN, Durkin CH, Geurink PP, Ovaa H, Santhanam B, Holden DW, Komander D. (2016). The molecular basis for ubiquitin and ubiquitin-like specificities in bacterial effector proteases. Mol. Cell 63: 261-276. DOI: [[https://doi.org/10.1016/j.molcel.2016.06.015|10.1016/j.molcel.2016.06.015]]
+Pruneda JN, Durkin CH, Geurink PP, Ovaa H, Santhanam B, Holden DW, Komander D (2016). The molecular basis for ubiquitin and ubiquitin-like specificities in bacterial effector proteases. Mol. Cell 63: 261-276. DOI: [[https://doi.org/10.1016/j.molcel.2016.06.015|10.1016/j.molcel.2016.06.015]]
 Rawlings ND, Morton FR, Barrett AJ (2006). MEROPS: the peptidase database. Nucl. Acids Res. 34: D270-D272. DOI: [[https://doi.org/10.1093/nar/gkj089|10.1093/nar/gkj089]]
 Tan CM, Li MY, Yang PY, Chang SH, Ho YP, Lin H, Deng WL, Yang JY (2015). //Arabidopsis// HFR1 is a potential nuclear substrate regulated by the //Xanthomonas// type III effector XopD<sub>//Xcc//8004</sub>. PLoS One 10: e0117067. DOI: [[http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0117067|10.1371/journal.pone.0117067]]
+===== Further reading =====
+Canonne J, Marino D, Noël LD, Arechaga I, Pichereaux C, Rossignol M, Roby D, Rivas S (2010). Detection and functional characterization of a 215 amino acid N-terminal extension in the //Xanthomonas// type III effector XopD. PLoS One 5: e15773. DOI: [[https://doi.org/10.1371/journal.pone.0015773|10.1371/journal.pone.0015773]]. **Retraction in: PLoS One (2018) 13: e0190773.** DOI: [[https://doi.org/10.1371/journal.pone.0190773|10.1371/journal.pone.0190773 ]]
+Raffaele S, Rivas S (2013). Regulate and be regulated: integration of defense and other signals by the AtMYB30 transcription factor. Front. Plant Sci. 4: 98. DOI: [[https://doi.org/10.3389/fpls.2013.00098|10.3389/fpls.2013.00098]]
+Tan L, Rong W, Luo H, Chen Y, He C (2014). The //Xanthomonas campestris// effector protein XopD<sub>Xcc8004</sub> triggers plant disease tolerance by targeting DELLA proteins. New Phytol. 204: 595-608. DOI: [[https://doi.org/10.1111/nph.12918|10.1111/nph.12918]]

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