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The MAMP Peptide Patterns of Bacterial Flagellins and Their Interaction with Plant Receptors: Bioinformatic and Coevolutionary Aspects
- Authors: Shchyogolev S.Y.1, Burygin G.L.1, Krasova Y.V.1, Matora L.Y.1
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Affiliations:
- Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences
- Issue: Vol 93, No 2 (2024)
- Pages: 179-188
- Section: SHORT COMMUNICATIONS
- URL: https://journal-vniispk.ru/0026-3656/article/view/262517
- DOI: https://doi.org/10.31857/S0026365624020155
- ID: 262517
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Abstract
Conservative motifs (peptide patterns) determining the elicitor properties of plant-pathogenic bacteria were revealed in amino acid sequences of the flagellins of phytopathogenic, associated, and root nodule microflora. In plant growth-promoting rhizobacteria (PGPR), analogs of one (flg22) out of two (flg22 and flgII-28) specific peptides, characterizing pathogens were revealed. Instead of glycine G18, characteristic of an elicitor, tyrosine Y18 was identified in flg22 analogs of most PGPR, which prevents actuation of the phytoimmunity mechanism against PGPR. Molecular docking with the AlphaFold software complex demonstrated reliability of the interaction between the plant receptor FLS2 and the canonical peptide flg22 and its analogs from a plant pathogen and an Azospirillum. However, in the case of the FLS3 plant receptor only its interactions with the canonical peptide flgII-28 and its analog from the plant pathogen were reliable.
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About the authors
S. Yu. Shchyogolev
Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences
Author for correspondence.
Email: shegolev_s@ibppm.ru
Russian Federation, Saratov, 410049
G. L. Burygin
Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences
Email: shegolev_s@ibppm.ru
Russian Federation, Saratov, 410049
Yu. V. Krasova
Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences
Email: shegolev_s@ibppm.ru
Russian Federation, Saratov, 410049
L. Yu. Matora
Institute of Biochemistry and Physiology of Plants and Microorganisms, Saratov Scientific Centre of the Russian Academy of Sciences
Email: shegolev_s@ibppm.ru
Russian Federation, Saratov, 410049
References
- Проворов Н.А., Тихонович И.А., Воробъев Н.И. Симбиоз и симбиогенез. СПб.: Информ-Навигатор, 2018. 464 с.
- Щеголев С.Ю., Тихонов К.С., Андрейченко Д.К. Об опыте инсталляции и использования программного комплекса AlphaFold2 и его оптимизированных версий для определения 3D-структур белков и белковых комплексов // Методы компьютерной диагностики в биологии и медицине — 2022: Сборник статей Всероссийской школы-семинара / Ред. Ан.В. Скрипаль. Саратов: Изд-во “Саратовский источник”, 2022. С. 100‒106.
- Bryant P., Pozzati G., Elofsson A. Improved prediction of protein-protein interactions using AlphaFold2 // Nat. Commun. 2022. V. 13. Art. 1265. P. 1‒11.
- Cai R., Lewis J., Yan S., Liu H., Clarke C.R., Campanile F., Almeida N.F., Studholme D.J., Lindeberg M., Schneider D., Zaccardelli M., Setubal J.C., Morales-Lizcano N.P., Bernal A., Coaker G., Baker C., Bender C.L., Leman S., Vinatzer B.A. The plant pathogen Pseudomonas syringae pv. tomato is genetically monomorphic and under strong selection to evade tomato immunity // PLoS Pathog. 2011. V. 7. Art. e1002130. P. 1‒15.
- Felix G., Duran J.D., Volko S., Boller T. Plants have a sensitive perception system for the most conserved domain of bacterial flagellin // Plant J. 1999. V. 18. P. 265‒276.
- Fliegmann J., Felix G. Immunity: flagellin seen from all sides // Nature Plants. 2016. V. 2. Art. 16136. P. 1‒2.
- Garcia A.V., Charriera A., Schikorab A., Bigearda J., Pateyronc S., de Tauzia-Moreaua M.-L., Evrarda A., Mithöferd A., Martin-Magniettea M. L., Virlogeux-Payantg I., Hirta H. Salmonella enterica flagellin is recognized via FLS2 and activates PAMP-triggered immunity in Arabidopsis thaliana // Mol. Plant. 2014. V. 7. P. 657‒674.
- Gómez-Gómez L., Boller T. FLS2: a LRR receptor-like kinase involved in recognition of the flagellin elicitor in Arabidopsis // Mol. Cell. 2000. V. 5. P. 1‒20.
- Hind S.R., Strickler S.R., Boyle P.C., Dunham D.M., Bao Z., O’Doherty I.M., Baccile J.A., Hoki J.S., Viox E.G., Clarke C.R., Vinatzer B.A., Schroeder F.C., Martin G.B. Tomato receptor FLAGELLIN-SENSING 3 binds flgII-28 and activates the plant immune system // Nature Plants. 2016. V. 2. Art. 16128. P. 1‒8.
- Hu D., Reevesa P.R. The remarkable dual-level diversity of prokaryotic flagellins // mSystems. 2020. V. 5. Art. e00705-19.
- Sun Y., Li L., Macho A.P., Han Z., Hu Z., Zipfel C., Zhou J.-M., Chai J. Structural basis for flg22-induced activation of the Arabidopsis FLS2-BAK1 immune complex // Science. 2013. V. 342. P. 624‒628.
- Thomson N.M., Rossmann F.M., Ferreira J.L., Matthews-Palmer T.R., Beeby M., Pallen M.J. Bacterial flagellins: does size matter? // Trends Microbiol. 2018. V. 26. P. 575‒581.
Supplementary files
Supplementary Files
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Fig. 1. Fragments of MVP with peptides flg22 (A, C), flgII-28 (B) and FliC274 sequences from representatives of Azospirillaceae (A, B); fragment of MVP with peptide flg22 and FliC sequences from representatives of PGPR (C). A. — Azospirillum, B. — Brucella, S. — Sinorhizobium.
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3.
Fig. 2. Molecular docking of plant receptors FLS2 (Ar. thaliana) (A‒D), FLS3 (S. lycopersicum) (E‒G) with bacterial peptides flg22 (A‒D), flgII-28 (E‒G) and their analogues from phytopathogen and PGPR: P. aeruginosa ATCC700888 (A); Pc. atrosepticum SCRI1043 (B, F); A. baldaniorum Sp245, “long” flagellin (C); A. baldaniorum Sp245, “short” flagellin (D, G); P. syringae pv. tomato T1 (E). Oval in Fig. 2; G, the values of the parameters indicating the ineffectiveness of the interaction for this pair — receptor + peptide are highlighted.
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4.
Fig. S1. Fragments of the logo of the FliC sequence profile from P. aeruginosa ATCC 700888 with 500 homologous sequences demonstrate a very significant difference in the level of conservativeness of the N- and C-terminal sections of proteins from their highly variable intermediate part marked with arrows, in which the logo signal is vanishingly small compared to the rest of the logo.
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5.
Figure S2. A fragment of multiple sequence alignment (MVP) with flg22 for FliC bacteria — pathogenic (A) and PGPR of the Azospirillaceae family (B) — demonstrates the presence of G18 residue in pathogens — key for their elicitory properties — but its replacement with other residues in Azospirillaceae.
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6.
Figure S3. 3D models of AlphaFold-Multimer dimer complexes FliC621(A, C)+FliC274 (B,D) for A. brasilense Sp7 (A, B) and A. baldaniorum Sp245 (C, D). pDpckQ values ≥ 0.23 indicate a sufficiently high quality of modeling and the principal affiliation of the FliC621 dimer+FliC274 belongs to the category of truly interacting proteins (Bryant et al., 2022).
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7.
Figure S4. The fragment of the MVP with flg22 for the flagellin FliC414=Laf1 of the lateral flagellum of representatives of the genus Azospirillum demonstrates the replacement of glycine G18 with tyrosine Y18, which excludes the presence of elicitor properties in Laf1. The lines shown reflect the species diversity of the objects used. MVP with the same set of Laf1 sequences showed the absence of analogues of flgII-28 in them.
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8.
Fig. S5. The fragment of the MVP with flg22 for FliC300 representatives of the Brucellaceae family demonstrates the replacement of glycine G18 with tyrosine Y18, which excludes the presence of elicitor properties in FliC300. The lines shown reflect the species diversity of the objects used. MVP with the same set of FliC300 sequences showed the absence of analogues of flgII-28 in them.
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9.
Figure S6. The fragment of the MVP with flg22 for FliC320 representatives of the Rhizobiaceae family demonstrates the replacement of glycine G18 with tyrosine Y18, which excludes the presence of elicitor properties in FliC320. A similar result was obtained with more numerous sets of homologous rhizobium flagellins FliC320 and FliC395 in the number of several dozen. MVP with the same set of FliC320 sequences showed the absence of analogues of flgII-28 in them.
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10.
Figure S7. Fragments of MVP with flg22 for FlgL representatives of the genus Azospirillum demonstrate the absence of structures homologous to the flg22 peptide in these proteins, since only separate, gap-separated parts of flg2 2 are aligned in the MVP regions outside the highly conserved site corresponding to flg22 in the flagellin of FliC bacteria (see Fig. S1), which is very similar in ٣D structure to FlgL (Hu, Reevesa, 2020).
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11.
S8. Fragments of MVP with flgII-28 for FlgL representatives of the genus Azospirillum demonstrate the absence of structures homologous to the flgII-28 peptide in these proteins, since only separate, gap-separated parts of flgII-28 are aligned in the MVP regions outside the highly conserved site corresponding to flgII-28 in the flagellin of FliC bacteria (see Fig. S1), which is very similar in 3D structure to FlgL (Hu, Reevesa, 2020).
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