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--- bacteria:t3e:xopj8 [2025/07/24 12:20] – [The Type III Effector XopJ8 from //Xanthomonas//] rkoebnik
+++ bacteria:t3e:xopj8 [2025/07/24 23:30] (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: XopJ8\\
-Prototype: E4A48_06420 (//Xanthomonas// //cerealis// pv. //cerealis//, strain 01)\\
+Prototype: FZ025_RS03100 (//Xanthomonas// //hyacinthi//, strain CFBP 1156)\\
-GenBank ID: [[https://www.ncbi.nlm.nih.gov/protein/QDI05802.1|QDI05802.1]] (493 aa)\\
+GenBank ID: [[https://www.ncbi.nlm.nih.gov/protein/QGY75705.1|QGY75705.1]] (362 aa)\\
-RefSeq ID: [[https://www.ncbi.nlm.nih.gov/protein/WP_280117184.1|WP_280117184.1]] (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.\\
+RefSeq ID: [[https://www.ncbi.nlm.nih.gov/protein/WP_104559054.1|WP_104559054.1]] (362 aa).\\
 D structure: Unknown
@@ Line 15: / Line 15: @@
 === How discovered? ===
-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). Additional evidence came from the presence of a conserved palmitoylation signal, which was 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.
+XopJ8 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 at the N terminus (Nimchuk //et al.//, 2000; Thieme //et al.//, 2007). The protein was also predicted as a type III effector by [[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 prototype gene in //X. hyacinthi// strain CFBP 1156 is flanked by two IS//3//-family insertion sequences.
 === (Experimental) evidence for being a T3E ===
-XopJ7 was shown to have a functional type III secretion signal using a reporter fusion with AvrBs1 (Zhao //et al.//, 2013).
+XopJ8 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 //xopJ7// 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 //xopJ8// 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 ===
-The presence of a conserved palmitoylation signal at the N terminus suggests that the protein is localized to the plasma membrane in the plant host cell (Thieme //et al.//, 2007).
+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 41: / Line 45: @@
 === In xanthomonads ===
-Yes (//e.g.//, //X. euvesicatoria//, //X. campestris//, //X. hortorum//).
+Yes (//e.g.//, //X. citri//, frameshifted versions of the gene exist in //X. graminis// pv. //graminis//).
 === In other plant pathogens/symbionts ===
-Yes (e.g., //Acidovorax/////Paracidovorax// ssp., //Burkholderia/////Paraburkholderia// ssp; remote homologs in //Ralstonia// ssp.].
+Yes (e.g., //Pseudomonas syringae//, //Ralstonia// ssp.].
 ===== References =====
 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]]
+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.
 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]]
+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 41: btaf272. DOI: [[https://doi.org/10.1093/bioinformatics/btaf272|10.1093/bioinformatics/btaf272]]
 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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