Conjugate symbiotic populations part II: Analysis of nfr5 receptor gene polymorphisms using molecular docking

  • Yu. B. Porozov
  • A. N. Muntyan
  • E. P. Chizhevskaya
  • B. V. Simarov
  • E. E. Andronov


In this study, an analysis of nucleotide and amino-acid polymorphisms in the receptor part of the nfr5 gene was conducted in 15 plants of the conjugate collection (Melilotus albus was the plant component; Sinorhizobium meliloti was the bacterial component). The domain structure of the studied region was determined and it was demonstrated that the maxima of the nucleotide polymorphisms fall on the LysM domains of this gene. A clear association between nucleotide and amino-acid polymorphisms of the plant receptor region of the nfr5 gene and the genetic diversity of the rhizobial component of the conjugate system (symbiotic nodD locus) was detected. Based on the data that were obtained, computer modeling of bacterial Nod factor binding with two variants of the plant receptor was conducted.


conjugate collection nfr5 Nod factor Melilotus albus molecular modeling docking 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Albrecht, C., Geurts, R., and Bisseling, T., Legume Nodulation and Mycorrhizae Formation; Two Extremes in Host Specificity Meet, EMBO J., 1999, vol. 18, no. 2, pp. 281–288.PubMedCrossRefGoogle Scholar
  2. Andronov, E.E., Rumyantseva, M.L., Sagulenko, V.V., and Simarov, B.V., Effect of the Host Plant on the Genetic Diversity of a Natural Population of Sinorhizobium meliloti, Russ. J. Genet., 1999, vol. 35, no. 10, pp. 1169–1176.Google Scholar
  3. Arnold, K., Kiefer, F., Kopp, J., et al., The Protein Model Portal, J. Struct. Funct. Genomics, vol. 10, no. 1, pp. 1–8.Google Scholar
  4. Arrighi, J.F., Barre, A., Ben Amor, B., et al., The Medicago truncatula Lysine [Corrected] Motif Receptor-Like Kinase Gene Family Includes NFP and New Nodule-Expressed Genes, Plant Physiol., 2006, vol. 142, no. 1, pp. 265–279.PubMedCrossRefGoogle Scholar
  5. Banks, J.L., Beard, H.S., Cao, Y., et al., Integrated Modeling Program, Applied Chemical Theory (IMPA CT), J. Comput. Chem., 2005, vol. 26, no. 16, pp. 1752–1780.PubMedCrossRefGoogle Scholar
  6. Bellows, M.L. and Floudas, C.A., Computational Methods for de novo Protein Design and Its Applications to the Human Immunodeficiency Virus 1, Purine Nucleoside Phosphorylase, Ubiquitin Specific Protease 7, and Histone Demethylases, Curr. Drug Targets, 2010, vol. 11, no. 3, pp. 264–278.PubMedCrossRefGoogle Scholar
  7. Boutard, N., Jamieson, A.G., Ong, H., et al., Structure-Activity Analysis of the Growth Hormone Secretagogue GHRP-6 by Alpha- and Beta-Amino Gamma-Lactam Positional Scanning, Chem. Biol. Drug Des., 2010, vol. 75, no. 1, pp. 40–50.PubMedCrossRefGoogle Scholar
  8. Byington, C.L., Dunbrack, R.L.,Jr., Cohen, F.E., et al., Molecular Modeling of Phosphofructokinase from Entamoeba histolytica for the Prediction of New Antiparasitic Agents, Arch. Med. Res.,, 1997, vol. 28, spec. no., pp. 86–88.PubMedGoogle Scholar
  9. Denarie, J. and Debelle, F., Rhizobium Lipo-Chitooligosaccharide Nodulation Factors: Signaling Molecules Mediating Recognition and Morphogenesis, Ann. Rev. Biochem., 1996, vol. 65, pp. 503–535.PubMedCrossRefGoogle Scholar
  10. Diévart, A. and Clark, S.E., Using Mutant Alleles to Determine the Structure and Function of Leucine-Rich Repeat Receptor-Like Kinases, Curr. Opin. Plant Biol., 2003, vol. 6, no. 5, pp. 507–516.PubMedCrossRefGoogle Scholar
  11. Eswar, N., Webb, B., Marti-Renom, M.A., et al., Comparative Protein Structure Modeling Using Modeller, Current Protocols in Bioinformatics, Editorial Board, A.D. Baxevanis et al., 2006, Chapter 5, Units 5–6.Google Scholar
  12. Feng, Z., Chen, L., Maddula, H., et al., Ligand Depot: A Data Warehouse for Ligands Bound to Macromolecules, Bioinformatics, 2004, vol. 20, no. 13, pp. 2153–2155.PubMedCrossRefGoogle Scholar
  13. Gilson, M.K. and Zhou, H.X., Calculation of Protein-Ligand Binding Affinities, Ann. Rev. Biophys. Biomol. Struct., 2007, vol. 36, pp. 21–42.CrossRefGoogle Scholar
  14. Johnson, K.L. and Ingram, G.C., Sending the Right Signals: Regulating Receptor Kinase Activity, Curr. Opin. Plant Biol., 2005, vol. 8, pp. 648–656.PubMedCrossRefGoogle Scholar
  15. Kelley, L.A. and Sternberg, M.J., Protein Structure Prediction on the Web: A Case Study Using the Phyre Server, Nature Protocols, 2009, vol. 4, no. 3, pp. 363–371.PubMedCrossRefGoogle Scholar
  16. Kim, D.E., Chivian, D., and Baker, D., Protein Structure Prediction and Analysis Using the Robetta Server, Nucleic Acids Res., 2004, vol. 32, Web Server issue, pp. 526–531.CrossRefGoogle Scholar
  17. Laskowski, R.A., MacArthur, M.W., Moss, D.S., et al., PROCHECK: A Program to Check the Stereochemical Quality of Protein Structures, J. Appl. Crystallogr., 1993, vol. 26, no. 2, pp. 283–291.CrossRefGoogle Scholar
  18. Lerouge, P., Roche, P., Faucher, C., et al., Symbiotic Host-Specificity of Rhizobium meliloti Is Determined by a Sulphated and Acylated Glucosamine Oligosaccharide Signal, Nature, 1990, vol. 344, pp. 781–784.PubMedCrossRefGoogle Scholar
  19. Limpens, E., Franken, C., Smit, P., et al., LysM Domain Receptor Kinases Regulating Rhizobial Nod Factor-Induced Infection, Science, 2003, vol. 302, no. 5645, pp. 630–633.PubMedCrossRefGoogle Scholar
  20. Madsen, E.B., Madsen, L.H., Radotoiu, S., et al., A Receptor Kinase Gene of the LysM Type Is Involved in Legume Perception of Rhizobial Signals, Nature, 2003, vol. 425, pp. 637–640.PubMedCrossRefGoogle Scholar
  21. Markmann, K., Giczey, G., and Parniske, M., Functional Adaptation of a Plant Receptor-Kinase Paved the Way for the Evolution of Intracellular Root Symbioses with Bacteria, PLoS Biol, 2008, vol. 6, pp. 496–506.CrossRefGoogle Scholar
  22. Morris, G.M., Huey, R., Lindstrom, W., et al., AutoDock4 and AutoDockTools4: Automated Docking with Selective Receptor Flexibility, J. Comput. Chem., 2009, vol. 30, no. 16, pp. 2785–2791.PubMedCrossRefGoogle Scholar
  23. Mulder, L., Lefebvre, B., Cullimore, J., et al., LysM Domains of Medicago truncatula NFP Protein Involved in Nod Factor Perception. Glycosylation State, Molecular Modeling and Docking of Chitooligosaccharides and Nod Factors, Glycobiology, 2006, vol. 16, no. 9, pp. 801–809.PubMedCrossRefGoogle Scholar
  24. Muntyan, A.N., et al., Coupled Symbiotic Populations. Part I: Analysis of Genetic Diversity of the Rhizobial Component, Ekol. Genet., 2012, vol. 1, no. 1, pp. 1169–1177.Google Scholar
  25. Navarro-Gochicoa, M.T., Camut, S., Timmers, A.C., et al., Characterization of Four Lectin-Like Receptor Kinases Expressed in Roots of Medicago truncatula. Structure, Location, Regulation of Expression, and Potential Role in the Symbiosis with Sinorhizobium meliloti, Plant Physiol., 2003, vol. 133, no. 4, pp. 1893–910.PubMedCrossRefGoogle Scholar
  26. Radutoiu, S., Madsen, L.H., Madsen, E.B., et al., Plant Recognition of Symbiotic Bacteria Requires Two LysM Receptor-Like Kinases, Nature, 2003, vol. 425, pp. 585–592.PubMedCrossRefGoogle Scholar
  27. Rockey, W.M., Laederach, A., and Reilly, P.J., Automated Docking of Alpha-(1 → 4)- and Alpha-(1 → 6)-Linked Glucosyl Trisaccharides and Maltopentaose into the Soybean Beta-Amylase Active Site, Proteins, 2000, vol. 40, no. 2, pp. 299–309.PubMedCrossRefGoogle Scholar
  28. Rogers, S.O. and Bendich, A.J., Extraction of DNA from Milligram Amounts of Fresh, Herbarium and Mummified Plant Tissues, Plant. Mol. Biol., 1985, vol. 5, pp. 69–76.CrossRefGoogle Scholar
  29. Roy, A., Kucukural, A., and Zhang, Y., I-TASSER: a Unified Platform for Automated Protein Structure and Function Prediction, Nature Protocols, 2010, vol. 5, no. 4, pp. 725–738.PubMedCrossRefGoogle Scholar
  30. Sambrook, J., Fritsch, E.F., and Maniatis, T., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor: Cold Spring Harbor Laboratory Press, 1989.Google Scholar
  31. Torii, K.U., Leucine-Rich Repeat Receptor Kinases in Plants: Structure, Function, and Signal Transduction Pathways, Int. Rev. Cytol., 2004, vol. 234, pp. 1–46.PubMedCrossRefGoogle Scholar
  32. Vriend, G., WHAT IF: A Molecular Modeling and Drug Design Program, J. Mol. Graphics, 1990, vol. 8, no. 1, p. 29.CrossRefGoogle Scholar
  33. Walker, J.C., Structure and Function of the Receptor-Like Protein Kinases of Higher Plants, Plant. Mol. Biol., 1994, vol. 26, pp. 1599–1609.PubMedCrossRefGoogle Scholar
  34. Zhang, Y., I-TASSER Server for Protein 3D Structure Prediction, BMC Bioinformatics, 2008, vol. 9, p. 40.PubMedCrossRefGoogle Scholar

Copyright information

© Pleiades Publishing, Ltd. 2013

Authors and Affiliations

  • Yu. B. Porozov
    • 1
  • A. N. Muntyan
    • 2
  • E. P. Chizhevskaya
    • 2
  • B. V. Simarov
    • 2
  • E. E. Andronov
    • 2
  1. 1.St. Petersburg National Research University of Information Technologies, Mechanics, and OpticsSt. PetersburgRussia
  2. 2.All-Russia Research Institute for Agricultural MicrobiologySt. PetersburgRussia

Personalised recommendations