The functional and structural characterization of Xanthomonas campestris pv. campestris core effector XopP revealed a new kinase activity.
Exo70B1
exocyst complex
novel kinase function
pathogen XopP effector
plant defense
protein structure prediction
Journal
The Plant journal : for cell and molecular biology
ISSN: 1365-313X
Titre abrégé: Plant J
Pays: England
ID NLM: 9207397
Informations de publication
Date de publication:
10 2023
10 2023
Historique:
revised:
15
06
2023
received:
16
11
2022
accepted:
20
06
2023
medline:
26
9
2023
pubmed:
22
6
2023
entrez:
22
6
2023
Statut:
ppublish
Résumé
Exo70B1 is a protein subunit of the exocyst complex with a crucial role in a variety of cell mechanisms, including immune responses against pathogens. The calcium-dependent kinase 5 (CPK5) of Arabidopsis thaliana (hereafter Arabidopsis), phosphorylates AtExo70B1 upon functional disruption. We previously reported that, the Xanthomonas campestris pv. campestris effector XopP compromises AtExo70B1, while bypassing the host's hypersensitive response, in a way that is still unclear. Herein we designed an experimental approach, which includes biophysical, biochemical, and molecular assays and is based on structural and functional predictions, utilizing AplhaFold and DALI online servers, respectively, in order to characterize the in vivo XccXopP function. The interaction between AtExo70B1 and XccXopP was found very stable in high temperatures, while AtExo70B1 appeared to be phosphorylated at XccXopP-expressing transgenic Arabidopsis. XccXopP revealed similarities with known mammalian kinases and phosphorylated AtExo70B1 at Ser107, Ser111, Ser248, Thr309, and Thr364. Moreover, XccXopP protected AtExo70B1 from AtCPK5 phosphorylation. Together these findings show that XccXopP is an effector, which not only functions as a novel serine/threonine kinase upon its host target AtExo70B1 but also protects the latter from the innate AtCPK5 phosphorylation, in order to bypass the host's immune responses. Data are available via ProteomeXchange with the identifier PXD041405.
Substances chimiques
Arabidopsis Proteins
0
Bacterial Proteins
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
100-111Informations de copyright
© 2023 Society for Experimental Biology and John Wiley & Sons Ltd.
Références
Ahmed, S.M., Nishida-Fukuda, H., Li, Y., McDonald, W.H., Gradinaru, C.C. & Macara, I.G. (2018) Exocyst dynamics during vesicle tethering and fusion. Nature Communications, 9(1), 5140. Available from: https://doi.org/10.1038/s41467-018-07467-5
Baxevanis, A.D. (2000) The molecular biology database collection: an online compilation of relevant database resources. Nucleic Acids Research, 28(1), 1-7.
Bogdanove, A.J., Koebnik, R., Lu, H., Furutani, A., Angiuoli, S.V., Patil, P.B. et al. (2011) Two new complete genome sequences offer insight into host and tissue specificity of plant pathogenic Xanthomonas spp. Journal of Bacteriology, 193(19), 5450-5464. Available from: https://doi.org/10.1128/JB.05262-11
Brabham, H.J., Hernández-Pinzón, I., Holden, S., Lorang, J. & Moscou, M.J. (2018) An ancient integration in a plant NLR is maintained as a trans-species polymorphism. bioRxiv. Available from: https://doi.org/10.1101/239541
Brillada, C., Teh, O.-K., Ditengou, F.A., Lee, C.-W., Klecker, T., Saeed, B. et al. (2020) Exocyst subunit Exo70B2 is linked to immune signaling and autophagy. The Plant Cell, 33(2), 404-419. Available from: https://doi.org/10.1093/plcell/koaa022
Bryksin, A.V. & Matsumura, I. (2010) Overlap extension PCR cloning: a simple and reliable way to create recombinant plasmids. BioTechniques, 48(6), 463-465. Available from: https://doi.org/10.2144/000113418
Büttner, D. & Bonas, U. (2003) Common infection strategies of plant and animal pathogenic bacteria. Current Opinion in Plant Biology, 6(4), 312-319. Available from: https://doi.org/10.1016/S1369-5266(03)00064-5
Büttner, D. & He, S.Y. (2009) Type III protein secretion in plant pathogenic bacteria. Plant Physiology, 150(4), 1656-1664. Available from: https://doi.org/10.1104/pp.109.139089
Daskalov, A., Habenstein, B., Martinez, D., Debets, A.J., Sabaté, R., Loquet, A. et al. (2015) Signal transduction by a fungal NOD-like receptor based on propagation of a prion amyloid fold. PLoS Biology, 13(2), e1002059. Available from: https://doi.org/10.1371/journal.pbio.1002059
Deutsch, E.W., Bandeira, N., Perez-Riverol, Y., Sharma, V., Carver, J.J., Mendoza, L. et al. (2023) The ProteomeXchange consortium at 10 years: 2023 update. Nucleic Acids Research, 51, 1539-1548.
Du, Y., Mpina, M.H., Birch, P.R., Bouwmeester, K. & Govers, F. (2015) Phytophthora infestans RXLR effector AVR1 interacts with exocyst component Sec5 to manipulate plant immunity. Plant Physiology, 169, 01169.1990. Available from: https://doi.org/10.1104/pp.15.01169
Gu, Y. & Innes, R.W. (2012) The KEEP ON GOING protein of Arabidopsis regulates intracellular protein trafficking and is degraded during fungal infection. The Plant Cell, 24(11), 4717-4730. Available from: https://doi.org/10.1105/tpc.112.105254
Holm, L. (2020) Using Dali for protein structure comparison. Methods in Molecular Biology, 2112, 29-42. Available from: https://doi.org/10.1007/978-1-0716-0270-6_3
Holtzer, M.E. & Holtzer, A. (1992) Alpha-helix to random coil transitions: determination of peptide concentration from the CD at the isodichroic point. Biopolymers, 32(12), 1675-1677. Available from: https://doi.org/10.1002/bip.360321209
Hong, D., Jeon, B.W., Kim, S.Y., Hwang, J.U. & Lee, Y. (2016) The ROP-RIC 7 pathway negatively regulates light-induced stomatal opening by inhibiting exocyst subunit Exo70B1 in Arabidopsis. New Phytologist, 209(2), 624-635. Available from: https://doi.org/10.1111/nph.13625
Ishikawa, K., Yamaguchi, K., Sakamoto, K., Yoshimura, S., Inoue, K., Tsuge, S. et al. (2014) Bacterial effector modulation of host E3 ligase activity suppresses PAMP-triggered immunity in rice. Nature Communications, 5(1), 5430. Available from: https://doi.org/10.1038/ncomms6430
Jones, J.D.G. & Dangl, J.L. (2006) The plant immune system. Nature, 444, 323-329.
Kotsaridis, K., Tsakiri, D. & Sarris, P.F. (2022) Understanding enemy's weapons to an effective prevention: common virulence effects across microbial phytopathogens kingdoms. Critical Reviews in Microbiology, 1-15. Available from: https://doi.org/10.1080/1040841X.2022.2083939
Kulich, I., Pečenková, T., Sekereš, J., Smetana, O., Fendrych, M., Foissner, I. et al. (2013) Arabidopsis exocyst subcomplex containing subunit EXO70B1 is involved in autophagy-related transport to the vacuole. Traffic, 14(11), 1155-1165. Available from: https://doi.org/10.1111/tra.12101
LeBlanc, M.-A., Fink, M.R., Perkins, T.T. & Sousa, M.C. (2021) Type III secretion system effector proteins are mechanically labile. Proceedings of the National Academy of Sciences of the United States of America, 118(12), e2019566118. Available from: https://doi.org/10.1073/pnas.2019566118
Lee, B., Park, Y.J., Park, D.S., Kang, H.W., Kim, J.G., Song, E.S. et al. (2005) The genome sequence of Xanthomonas oryzae pathovar oryzae KACC10331, the bacterial blight pathogen of rice. Nucleic Acids Research, 33(2), 577-586. Available from: https://doi.org/10.1093/nar/gki206
Liu, N., Hake, K., Wang, W., Zhao, T., Romeis, T. & Tang, D. (2017) Calcium-dependent protein kinase5 associates with the truncated NLR protein TIR-NBS2 to contribute to exo70B1-mediated immunity. Plant Cell, 29(4), 746-759. Available from: https://doi.org/10.1105/tpc.16.00822
Mak, H. & Thurston, T.L.M. (2021) Interesting biochemistries in the structure and function of bacterial effectors. Frontiers in Cellular and Infection Microbiology, 11, 608860. Available from: https://doi.org/10.3389/fcimb.2021.608860
Marchal, C., Michalopoulou, V.A., Zou, Z., Cevik, V. & Sarris, P.F. (2022) Show me your ID: NLR immune receptors with integrated domains in plants. Essays in Biochemistry, 66(5), 527-539. Available from: https://doi.org/10.1042/EBC20210084
Mei, K. & Guo, W. (2018) The exocyst complex. Current Biology, 28(17), R922-R925. Available from: https://doi.org/10.1016/J.CUB.2018.06.042
Mei, K. & Guo, W. (2019) Exocytosis: a new exocyst movie. Current Biology, 29(1), R30-R32. Available from: https://doi.org/10.1016/j.cub.2018.11.022
Mei, K., Li, Y., Wang, S., Shao, G., Wang, J., Ding, Y. et al. (2018) Cryo-EM structure of the exocyst complex. Nature Structural and Molecular Biology, 25(2), 139-146. Available from: https://doi.org/10.1038/s41594-017-0016-2
Mermigka, G. & Sarris, P.F. (2019) The rise of plant resistosomes. Trends in Immunology, 40(8), 670-673. Available from: https://doi.org/10.1016/j.it.2019.05.008
Michalopoulou, V.A., Mermigka, G., Kotsaridis, K., Mentzelopoulou, A., Celie, P.H.N., Moschou, P.N. et al. (2022) The host exocyst complex is targeted by a conserved bacterial type-III effector that promotes virulence. The Plant Cell, 2, 1-25.
Nishimura, M.T., Anderson, R.G., Cherkis, K.A., Law, T.F., Liu, Q.L., Machius, M. et al. (2017) TIR-only protein RBA1 recognizes a pathogen effector to regulate cell death in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America, 114(10), E2053-E2062. Available from: https://doi.org/10.1073/pnas.1620973114
Perez-Riverol, Y., Bai, J., Bandla, C., García-Seisdedos, D., Hewapathirana, S., Kamatchinathan, S. et al. (2022) The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences. Nucleic Acids Research, 50, 543-552.
Perez-Riverol, Y., Xu, Q.W., Wang, R., Uszkoreit, J., Griss, J., Sanchez, A. et al. (2016) PRIDE inspector Toolsuite: moving toward a universal visualization tool for proteomics data standard formats and quality assessment of ProteomeXchange datasets. Molecular & Cellular Proteomics, 8, 305-317. Available from: https://doi.org/10.1074/mcp.O115.050229
Redditt, T.J., Chung, E.H., Zand Karimi, H., Rodibaugh, N., Zhang, Y., Trinidad, J.C. et al. (2019) AvrRpm1 functions as an ADP-ribosyl transferase to modify NOI-domain containing proteins, including Arabidopsis and soybean RPM1-interacting protein 4. The Plant Cell, 31, 2664-2681. Available from: https://doi.org/10.1105/tpc.19.00020
Roux, B., Bolot, S., Guy, E., Denancé, N., Lautier, M., Jardinaud, M.F. et al. (2015) Genomics and transcriptomics of Xanthomonas campestris species challenge the concept of core type III effectome. BMC Genomics, 16(1), 975. Available from: https://doi.org/10.1186/s12864-015-2190-0
Sabol, P., Kulich, I. & Žárský, V. (2017) RIN4 recruits the exocyst subunit EXO70B1 to the plasma membrane. Journal of Experimental Botany, 68(12), 3253-3265. Available from: https://doi.org/10.1093/jxb/erx007
Salanoubat, M., Genin, S., Artiguenave, F., Gouzy, J., Mangenot, S., Arlat, M. et al. (2002) Genome sequence of the plant pathogen Ralstonia solanacearum. Nature, 415, 497-502.
Sandstrom, A., Mitchell, P.S., Goers, L., Mu, E.W., Lesser, C.F. & Vance, R.E. (2019) Functional degradation: a mechanism of NLRP1 inflammasome activation by diverse pathogen enzymes. Science, 364(6435), 1330. Available from: https://doi.org/10.1126/science.aau1330
Sarris, P.F., Cevik, V., Dagdas, G., Jones, J.D.G. & Krasileva, K.V. (2016) Comparative analysis of plant immune receptor architectures uncovers host proteins likely targeted by pathogens. BMC Biology, 14(1), 8. Available from: https://doi.org/10.1186/s12915-016-0228-7
Sertedakis, M., Kotsaridis, K., Tsakiri, D., Mermigka, G., Dominguez-Ferreras, A., Ntoukakis, V. et al. (2022) Expression of putative effectors of different Xylella fastidiosa strains triggers cell death-like responses in various nicotiana model plants. Molecular Plant Pathology, 23(1), 148-156. Available from: https://doi.org/10.1111/mpp.13147
Stegmann, M., Anderson, R.G., Ichimura, K., Pecenkova, T., Reuter, P., Žárský, V. et al. (2012) The ubiquitin ligase PUB22 targets a subunit of the exocyst complex required for PAMP-triggered responses in Arabidopsis. The Plant Cell, 24(11), 4703-4716. Available from: https://doi.org/10.1105/tpc.112.104463
Stegmann, M., Anderson, R.G., Westphal, L., Rosahl, S., McDowell, J. & Trujillo, M. (2014) The exocyst subunit Exo70B1 is involved in the immune response of Arabidopsis thaliana to different pathogens and cell death. Plant Signaling and Behavior, 8(12), 1-5. Available from: https://doi.org/10.4161/psb.27421
Synek, L., Pleskot, R., Sekereš, J., Serrano, N., Vukašinović, N., Ortmannová, J. et al. (2021) Plasma membrane phospholipid signature recruits the plant exocyst complex via the EXO70A1 subunit. Proceedings of the National Academy of Sciences of the United States of America, 118(36), e2105287118. Available from: https://doi.org/10.1073/pnas.2105287118
Tang, J.L., Tang, D.J., Dubrow, Z.E., Bogdanove, A. & An, S.Q. (2021) Xanthomonas campestris pathovars. Trends in Microbiology, 29(2), 182-183. Available from: https://doi.org/10.1016/j.tim.2020.06.003
Taus, T., Köcher, T., Pichler, P., Paschke, C., Schmidt, A., Henrich, C. et al. (2011) Universal and confident phosphorylation site localization using phosphoRS. Journal of Proteome Research, 10, 5354-5362.
The PyMOL Molecular Graphics System. (n.d.) Version 2.0. Schrödinger, LLC.
Timilsina, S., Potnis, N., Newberry, E.A., Liyanapathiranage, P., Iruegas-Bocardo, F., White, F.F. et al. (2020) Xanthomonas diversity, virulence and plant-pathogen interactions. Nature Reviews Microbiology, 18(8), 415-427. Available from: https://doi.org/10.1038/s41579-020-0361-8
Tsakiri, D., Kotsaridis, K., Michalopoulou, V.A., Kokkinidis, M. & Sarris, P.F. (2022) Ralstonia solanacearum core effector RipE1 interacts and cleaves the Arabidopsis exocyst component. bioRxiV. Available from: https://doi.org/10.1101/2022.08.31.506019
Tunyasuvunakool, K. (2022) The prospects and opportunities of protein structure prediction with AI. Nature Reviews Molecular Cell Biology, 23(7), 445-446. Available from: https://doi.org/10.1038/s41580-022-00488-5
van Wijk, K.J., Friso, G., Walther, D. & Schulze, W.X. (2014) Meta-analysis of Arabidopsis thaliana phospho-proteomics data reveals compartmentalization of phosphorylation motifs. The Plant Cell, 26, 2367-2389. Available from: https://doi.org/10.1105/tpc.114.125815
Vicente, J.G. & Holub, E.B. (2013) Xanthomonas campestris pv. campestris (cause of black rot of crucifers) in the genomic era is still a worldwide threat to brassica crops. Molecular Plant Pathology, 14(1), 2-18. Available from: https://doi.org/10.1111/j.1364-3703.2012.00833.x
Wang, W., Liu, N., Gao, C., Cai, H., Romeis, T. & Tang, D. (2020) The Arabidopsis exocyst subunits EXO70B1 and EXO70B2 regulate FLS2 homeostasis at the plasma membrane. The New Phytologist, 227, 529-544. Available from: https://doi.org/10.1111/nph.16515
Wang, W., Liu, N., Gao, C., Rui, L. & Tang, D. (2019) The Pseudomonas syringae effector AvrPtoB associates with and ubiquitinates Arabidopsis exocyst. Frontiers in Plant Science, 10, 1027. Available from: https://doi.org/10.3389/fpls.2019.01027
White, F.F., Potnis, N., Jones, J.B. & Koebnik, R. (2009) The type III effectors of Xanthomonas. Molecular Plant Pathology, 10(6), 749-766. Available from: https://doi.org/10.1111/j.1364-3703.2009.00590.x
Whitmore, L. & Wallace, B.A. (2008) Protein secondary structure analyses from circular dichroism spectroscopy: methods and reference databases. Biopolymers, 89(5), 392-400. Available from: https://doi.org/10.1002/bip.20853
Yang, H., Rudge, D.G., Koos, J.D., Vaidialingam, B., Yang, H.J. & Pavletich, N.P. (2013) mTOR kinase structure, mechanism and regulation. Nature, 497, 217-223. Available from: https://doi.org/10.1038/nature12122
Yuan, M., Ngou, B.P.M., Ding, P. & Xin, X.F. (2021) PTI-ETI crosstalk: an integrative view of plant immunity. Current Opinion in Plant Biology, 62, 102030. Available from: https://doi.org/10.1016/j.pbi.2021.102030
Zaman, A., Wu, X., Lemoff, A., Yadavalli, S., Lee, J., Wang, C. et al. (2021) Exocyst protein subnetworks integrate hippo and mTOR signaling to promote virus detection and cancer ll exocyst protein subnetworks integrate hippo and mTOR signaling to promote virus detection and cancer. Cell Reports, 36(5), 109491. Available from: https://doi.org/10.1016/j.celrep.2021.109491
Žárský, V., Sekereš, J., Kubátová, Z., Pečenková, T. & Cvrčková, F. (2020) Three subfamilies of exocyst EXO70 family subunits in land plants: early divergence and ongoing functional specialization. Journal of Experimental Botany, 71(1), 49-62. Available from: https://doi.org/10.1093/jxb/erz423
Zhao, J., Zhang, X., Wan, W., Zhang, H., Liu, J., Li, M. et al. (2019) Identification and characterization of the EXO70 gene family in polyploid wheat and related species. International Journal of Molecular Sciences, 20(1), 1-22. Available from: https://doi.org/10.3390/ijms20010060
Zhao, T., Rui, L., Li, J., Nishimura, M.T., Vogel, J.P., Liu, N. et al. (2015) A truncated NLR protein, TIR-NBS2, is required for activated defense responses in the exo70B1 mutant. PLoS Genetics, 11(1), 1-28. Available from: https://doi.org/10.1371/journal.pgen.1004945
Zulawski, M., Schulze, G., Braginets, R., Hartmann, S. & Schulze, W.X. (2014) The Arabidopsis kinome: phylogeny and evolutionary insights into functional diversification. BMC Genomics, 15(1), 548. Available from: https://doi.org/10.1186/1471-2164-15-548
Zulawski, M. & Schulze, W.X. (2015) The plant kinome. Methods in Molecular Biology, 1306, 1-23. Available from: https://doi.org/10.1007/978-1-4939-2648-0