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--- bacteria:t3e:xopj7 [2025/07/24 09:50] – [The Type III Effector XopBH from //Xanthomonas//] rkoebnik
+++ bacteria:t3e:xopj7 [2025/07/24 23:28] (current) – jfpothier
@@ Line 2: / Line 2: @@
 Author: Anna Passelergue\\
-Internal reviewer: [[https://www.researchgate.net/profile/Ralf_Koebnik|Ralf Koebnik]]
+Internal reviewer: [[https://www.researchgate.net/profile/Ralf_Koebnik|Ralf Koebnik]]\\
 Class: XopJ\\
 Family: XopJ7\\
-Prototype: XTG_RS02340 (//Xanthomonas euroxanthea//, strain CPBF 424) Attention: The prototype sequence is too long because codons 18 to 39 overlap with the plant-inducible promoter (see below; Koebnik //et al.//, 2006).\\
+Prototype: E4A48_06420 (//Xanthomonas// //cerealis// pv. //cerealis//, strain 01)\\
-GenBank ID: [[https://www.ncbi.nlm.nih.gov/protein/CAE1133144.1|CAJ22212.1]] (286 aa)\\
+GenBank ID: [[https://www.ncbi.nlm.nih.gov/protein/QDI05802.1|QDI05802.1]] (493 aa)\\
-RefSeq ID: [[https://www.ncbi.nlm.nih.gov/protein/WP_212580660.1|WP_039417318.1]] (216 aa)\\
+RefSeq ID: [[https://www.ncbi.nlm.nih.gov/protein/WP_185910725.1|WP_185910725.1]] (389 aa). Attention: The RefSeq sequence is too short because 104 codons encoding the N-terminal region, including the type III secretion signal, are missing.\\
 D structure: Unknown
@@ Line 15: / Line 15: @@
 === How discovered? ===
-XopBH was discovered by a [[https://effectidor.tau.ac.il|Effectidor II]], a pan-genomic AI-based algorithm for the prediction of type III secretion system effectors (Wagner //et al.//, 2025). The //xopBH// gene of strain CPBF 424 is located near the T3SS gene cluster, next to [[:bacteria:t3e:xopz|xopZ]] and [[:bacteria:t3e:xopf|xopF]], which are all encoded between //hrpE// and //hrpF// (Huguet & Bonas, 1997; Weber //et al.//, 2005).
+XopJ7 was discovered as an ORF that is encoded downstream of a PIP box and a properly spaced ‐10 promoter motif (TTCGB‐N<sub>15</sub> ‐TTCGB‐N<sub>30–32</sub> ‐YANNNT) (Passelergue, 2025). Additional evidence came from the presence of conserved myristoylation and palmitoylation signals (Nimchuk //et al.//, 2000; Thieme //et al.//, 2007), which were in frame with the ORF. Based on this observation, the translation initiation codon is likely 104 codons upstream of the annotated codon for the locus E4A48_RS06415.
 === (Experimental) evidence for being a T3E ===
-XopBH was shown to have a functional type III secretion signal using a reporter fusion with AvrBs1 (Zhao //et al.//, 2013).
+XopJ7 was shown to have a functional type III secretion signal using a reporter fusion with AvrBs1 (Zhao //et al.//, 2013).
 === Regulation ===
-The presence of a PIP box and a properly spaced ‐10 promoter motif (TTCGB‐N<sub>15</sub> ‐TTCGB‐N<sub>30–32</sub> ‐YANNNT) suggests that the //xopBH// gene is under control of HrpG and HrpX (Wengelnik & Bonas, 1996; Wengelnik //et al.//, 1996; Koebnik //et al.//, 2006).
+The presence of a PIP box and a properly spaced ‐10 promoter motif (TTCGB‐N<sub>15</sub> ‐TTCGB‐N<sub>30–32</sub> ‐YANNNT) suggests that the //xopJ7// gene is under control of HrpG and HrpX (Wengelnik & Bonas, 1996; Wengelnik //et al.//, 1996; Koebnik //et al.//, 2006).
 === Phenotypes ===
@@ Line 28: / Line 31: @@
 === Localization ===
-Unknown.
+The presence of conserved myristoylation and palmitoylation signals at the N terminus suggests that the protein is localized to the plasma membrane in the plant host cell (Nimchuk //et al.//, 2000; Thieme //et al.//, 2007).
 === Enzymatic function ===
@@ Line 42: / Line 44: @@
 === In xanthomonads ===
-Yes (//e.g.//, //X. arboricola//, //X. campestris// pv. //papavericola//, //X. hortorum//).
+Yes (//e.g.//, //X. euvesicatoria//, //X. campestris//, //X. hortorum//).
-=== In other plant pathogens/symbionts ===
+=
+== In other plant pathogens/symbionts ===
-No.
+Yes (e.g., //Acidovorax/////Paracidovorax// ssp., //Burkholderia/////Paraburkholderia// ssp; remote homologs in //Ralstonia// ssp.].
 ===== References =====
-Huguet E, Bonas U (1997). //hrpF// of //Xanthomonas campestris// pv. //vesicatoria// encodes an 87-kDa protein with homology to NoIX of //Rhizobium fredii//. Mo.l Plant Microbe Interact. 10: 488-498. DOI: [[https://doi.org/10.1094/MPMI.1997.10.4.488|10.1094/MPMI.1997.10.4.488]]
 Koebnik R, Krüger A, Thieme F, Urban A, Bonas U (2006). Specific binding of the //Xanthomonas campestris// pv. //vesicatoria// AraC-type transcriptional activator HrpX to plant-inducible promoter boxes. J. Bacteriol. 188: 7652-7660. DOI: [[https://doi.org/10.1128/JB.00795-06|10.1128/JB.00795-06]]
-Wagner N, Baumer E, Lyubman I, Shimony Y, Bracha N, Martins L, Potnis N, Chang JH, Teper D, Koebnik R, Pupko T (2025). Effectidor II: A pan-genomic AI-based algorithm for the prediction of type III secretion system effectors. Bioinformatics, in press. DOI: [[https://doi.org/10.1093/bioinformatics/btaf272|10.1093/bioinformatics/btaf272]]
+Nimchuk Z, Marois E, Kjemtrup S, Leister RT, Katagiri F, Dangl JL (2000). Eukaryotic fatty acylation drives plasma membrane targeting and enhances function of several type III effector proteins from //Pseudomonas syringae//. Cell 101: 353-363. DOI: [[https://doi.org/10.1016/s0092-8674(00)80846-6|10.1016/s0092-8674(00)80846-6]]
+Passelergue A (2025). Discovery of eight type III effector genes harboring the PIP box in clade-I xanthomonads. Master's thesis, Université de Montpellier, France.
-Weber E, Ojanen-Reuhs T, Huguet E, Hause G, Romantschuk M, Korhonen TK, Bonas U, Koebnik R (2005). The type III-dependent Hrp pilus is required for productive interaction of //Xanthomonas campestris// pv. //vesicatoria// with pepper host plants. J. Bacteriol. 187: 2458-2468. DOI: [[https://doi.org/10.1128/JB.187.7.2458-2468.2005|10.1128/JB.187.7.2458-2468.2005]]
+Thieme F, Szczesny R, Urban A, Kirchner O, Hause G, Bonas U (2007). New type III effectors from //Xanthomonas campestris// pv. //vesicatoria// trigger plant reactions dependent on a conserved N-myristoylation motif. Mol. Plant Microbe Interact. 20: 1250-1261. DOI: [[https://doi.org/10.1094/MPMI-20-10-1250|10.1094/MPMI-20-10-1250]]
 Wengelnik K, Bonas U (1996). HrpXv, an AraC-type regulator, activates expression of five of the six loci in the hrp cluster of //Xanthomonas campestris// pv. //vesicatoria//. J. Bacteriol. 178: 3462-3469. DOI: [[https://doi.org/10.1128/jb.178.12.3462-3469.1996|10.1128/jb.178.12.3462-3469.1996]]

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