====== The Type III Effector XopD from //Xanthomonas// ======

Author: [[https://www.researchgate.net/profile/Monika_Kaluzna|Monika Kałużna]]\\
Internal reviewer: [[https://www.researchgate.net/profile/Alice_Castaing|Alice Boulanger]]\\
Expert reviewer: **WANTED!**

Class: XopD (Xanthomonas outer protein D)\\
Family: XopD\\
Prototype: XCV0437 (//Xanthomonas euvesicatoria// pv. //euvesicatoria//, ex //Xanthomonas campestris// pv. //vesicatoria//; strain 85-10)\\
GenBank ID: [[https://www.ncbi.nlm.nih.gov/protein/CAJ22068.1|CAJ22068.1]] (545 aa; original but wrong structural annotation)\\
GenBank ID: [[https://www.ncbi.nlm.nih.gov/protein/DAA34040.1|DAA34040.1]] (760 aa; new structural annotation)\\
RefSeq ID: [[https://www.ncbi.nlm.nih.gov/protein/WP_228949438.1|WP_228949438.1]] (760 aa; new structural annotation)\\
3D 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 =====

=== How discovered? ===

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 (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 (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 (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 ===

XopD is a unique virulence factor that promotes tolerance to //Xcv// 85-10 in infected host leaves and affects bacteria miltiplication (Kim //et al//., 2008). It was found that delays the onset leaf chlorosis and necrosis, two phenotypes associated with pathogen-triggered immunity (PTI) activation (Kim //et al//., 2008). Delaying in tissue damages and lower chlorophyll loss corelate with reduced host defense transcription and reduced salicylic acid (SA) levels-plant defense hormone that limits the spread of pathogens in infected host plant. Moreover, expression of XopD //in planta// is sufficient to repress not only SA- but also jasmonic acid–induced gene transcription (Hotson //et al//., 2003; Kim //et al//., 2008; Kim //et al//., 2011). It was also shown that XopD highly induces the tomato transcription factor, bHLH132 (Kim //et al//., 2019). This induction is dependant of XopD SUMO protease activity. This sutdy has shown that is involved in both plant development and plant defense regulation and that silencing bHLH132 mRNA expression results in stuned tomato with enhanced susceptibility to //Xcv// infection.

For instance, XcvΔ//xopD// mutants grow poorly in infected tomato leaves because defenses dependent from SA were not stifled (Kim //et al//., 2008). It is also known that XopD<sub>Xcv85-10</sub> directly interacts with tomato ethylene responsive transcription factor SlERF4. XopD desumoylates SlERF4 and suppress its activity in ethylene production, which is required for anti-Xcv ethylene stimulated immunity and symptom development (Kim //et al//., 2013). XopD<sub>XccB100</sub> from the// Xanthomonas campestris// pv. //campestris// (//Xcc//) strain B100 specifically interacts with MYB30 to suppress its activity in activating plant defense responses required for anti-//Xcc// immunity (Canonne //et al//., 2011).

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).
=== 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).
=== Enzymatic function ===

Peptidase, isopeptidase or desumoylating enzyme (Hotson// et al//., 2003).
=== Interaction partners ===

Unknown.

===== Conservation =====

=== In xanthomonads ===

Yes (e.g. //Xanthomonas campestris// pv. //vesicatoria//, //X. campestris// pv. //campestris// (Kim //et al//., 2011).
=== In other plant pathogens/symbionts ===

Yes (//Acidovorax// and //Pseudomonas// spp., //e.g.//, //A. avenae// subsp. //citrulli//, //A. avenae// subsp. //avenae//, //P. savastanoi// pv. //savastanoi//, //P. syringae// pv. //eriobotryae//, //P. syringae// pv. //myricae//, //P. savastanoi// pv. //savastanoi//, //P. syringae// pv. //dendropanacis// (Kim //et al//., 2011).
===== References =====

Canonne J, Marino D, Jauneau A, Pouzet C, Brière C, Roby D, Rivas S (2011). The //Xanthomonas// type III effector XopD targets the //Arabidopsis// transcription factor MYB30 to suppress plant defense. Plant Cell 23: 3498-3511. DOI: [[https://doi.org/10.1105/tpc.111.088815|10.1105/tpc.111.088815]]. **Retraction in: Plant Cell (2018) 30: 253.** DOI: [[https://doi.org/10.1105/tpc.17.00567|10.1105/tpc.17.00567]]

Canonne J, Pichereaux C, Mario D, Roby D, Rossignol M, Rivas S (2012). Identification of the protein sequence of the type III effector XopD from the B100 strain of //Xanthomonas campestris// pv. //campestris//. Plant Signal Behav. 7: 184-187. DOI: [[https://www.tandfonline.com/doi/full/10.4161/psb.18828|10.4161/psb.18828.]]

Castaneda A, Reddy JD, El-Yacoubi B, Gabriel DW (2005). Mutagenesis of all eight //avr// genes in //Xanthomonas campestris// pv. //campestris// had no detected effect on pathogenicity, but one //avr// gene affected race specificity. Mol. Plant Microbe Interact. 18: 1306-1317. DOI: [[https://doi.org/10.1094/MPMI-18-1306|10.1094/MPMI-18-1306]]

Chosed R, Tomchick DR, Brautigam CA, Mukherjee S, Negi VS, Machius M, Orth K (2007). Structural analysis of //Xanthomonas// XopD provides insights into substrate specificity of ubiquitin-like protein proteases. J. Biol. Chem. 282: 6773-6782. DOI: [[https://doi.org/10.1074/jbc.M608730200|10.1074/jbc.M608730200]]

Hotson A, Chosed R, Shu H, Orth K, Mudgett MB (2003). //Xanthomonas// type III effector XopD targets SUMO-conjugated proteins //in planta//. Mol. Microbiol. 50: 377-389. DOI: [[https://doi.org/10.1046/j.1365-2958.2003.03730.x|10.1046/j.1365-2958.2003.03730.x]]

Innes RW, Bent AF, Kunkel BN, Bisgrove SR, Staskawicz BJ (1993). Molecular analysis of avirulence gene //avrRpt2// and identification of a putative regulatory sequence common to all known //Pseudomonas syringae// avirulence genes. J. Bacteriol. 175: 4859-4869. DOI: [[https://doi.org/10.1128/jb.175.15.4859-4869.1993|10.1128/jb.175.15.4859-4869.1993]]

Kim JG, Taylor KW, Hotson A, Keegan M, Schmelz EA, Mudgett MB (2008). XopD SUMO protease affects host transcription, promotes pathogen growth, and delays symptom development in //Xanthomonas//-infected tomato leaves. Plant Cell 20: 1915-1929. DOI: [[https://doi.org/10.1105/tpc.108.058529|10.1105/tpc.108.058529]]

Kim JG, Stork W, Mudgett MB (2013). //Xanthomonas// type III effector XopD desumoylates tomato transcriptionfactor SlERF4 to suppress ethylene responses and promote pathogen. Cell Host Microbe 13: 143-154. DOI: [[https://doi.org/10.1016/j.chom.2013.01.006|10.1016/j.chom.2013.01.006]]

Kim JG, Taylor KW, Mudgett MB (2011). Comparative analysis of the XopD type III secretion (T3S) effector family in plant pathogenic bacteria. Mol. Plant Pathol. 12: 715-730. DOI: [[https://doi.org/10.1111/j.1364-3703.2011.00706.x|10.1111/j.1364-3703.2011.00706.x]]

Li SJ, Hochstrasser M (1999). A new protease required for cell-cycle progression in yeast. Nature 398: 246-251. DOI: [[https://doi.org/10.1038/18457|10.1038/18457]]

Noël L, Thieme F, Nennstiel D, Bonas U (2002). Two novel type III-secreted proteins of //Xanthomonas campestris// pv. //vesicatoria// are encoded within the hrp pathogenicity island. J. Bacteriol. 184: 1340-1348. DOI: [[https://doi.org/10.1128/jb.184.5.1340-1348.2002|10.1128/jb.184.5.1340-1348.2002]]

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]]

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]]

===== Acknowledgements =====

This fact sheet is based upon work from COST Action CA16107 EuroXanth, supported by COST (European Cooperation in Science and Technology).