Linked symbiotic populations: analysis of polymorphism in nfr5 receptor gene by using molecular doking

Open Access Open Access
Restricted Access Access granted
Restricted Access Subscription or Fee Access

Abstract


In the present work a molecular genetic analysis of the receptor part of the nfr5 gene in 15 plants of the conjugate collection (the plant component Melilotus albus, the bacterial component Sinorhizobium meliloti) has been done. Was studied the LysM domains structure and found a high level of the nucleotide polymorphism in LysM domains of this gene. A clear relationship of nucleotide and amino acid polymorphism in the receptor region of the nfr5 gene with the genetic diversity of the rhizobial component (bacterial symbiotic locus nodD) was observed. Based on these data, the computer modeling of binding of the bacterial Nod-factor with two different variants of the plant receptor was performed.

Keywords

About the authors

Yuri B Porozov

ITMO University, Saint-Petersburg, RF

Email: porozov@ifc.cnr.it

Aleksey N Muntyan

All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, RF

Email: genet@yandex.ru

Elena P Chizhevskaya

All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, RF

Email: chizhevskaya@yandex.ru, Podbelskiy chausse, 3, Saint-Petersburg, Pushkin, 196608

Boris V Simarov

All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, RF

Email: genet@yandex.ru

Evgeniy E Andronov

All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, RF

Email: eeandr@gmail.com

References

  1. Андронов Е. Е., Румянцева М. Л., Сагуленко В. В., Симаров Б. В., 1999. Влияние растения-хозяина на генетическое разнообразие природной популяции Sinorhizobium meliloti//Генетика. №10, С. 1169-1177.
  2. Мунтян А. Н., и др. 2012. Сопраженные симбиотические популяции. Часть I: анализ генетического разнообразия ризобального компонента.//Экологическая генетика. Т. 1, N1, С. 3-11
  3. Albrecht C., Geurts R., Bisseling T., 1999. Legume nodulation and mycorrhizae formation; two extremes in host specificity meet//The EMBO journal. Vol. 18. № 2. P. 281-288.
  4. Arnold K., Kiefer F., Kopp J. et al., 2009. The Protein Model Portal//Journal of structural and functional genomics. Vol. 10. № 1. P. 1-8.
  5. Arrighi J. F., Barre A., Ben Amor B. et al., 2006. The Medicago truncatula lysin [corrected] motifreceptor-like kinase gene family includes NFP and new nodule-expressed genes//Plant physiology. Vol. 142. № 1. P. 265-279.
  6. Banks J. L., Beard H. S., Cao Y. et al., 2005. Integrated Modeling Program, Applied Chemical Theory (IMPA CT)//Journal of Computational Chemistry. Vol. 26. № 16. P. 1752-1780.
  7. Bellows M. L., Floudas C. A., 2010. 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//Current drug targets. Vol. 11. № 3. P. 264-278.
  8. Boutard N., Jamieson A. G., Ong H. et al., 2010. Structure-activity analysis of the growth hormone secretagogue GHRP-6 by alpha-and beta-amino gamma-lactam positional scanning//Chem Biol Drug Des. Vol. 75. № 1. P. 40-50.
  9. Byington C. L., Dunbrack R. L., Jr., Cohen F. E. et al., 1997. Molecular modeling of phosphofructokinase from Entamoeba histolytica for the prediction of new antiparasitic agents//Archives of medical research. Vol. 28. Spec №. P. 86-88.
  10. Denarie J., F. Debelle. 1996. Rhizobium lipo-chitooligos accharide nodulation factors: signaling molecules mediating recognition and morphogenesis//Annu Rev. Biochem. Vol. 65. P. 503-535.
  11. Diévart A, Clark S E., 2003. Using mutant alleles to determine the structure and function of leucinerich repeat receptor-like kinases//Curr Opin Plant Biol. Vol. 6. № 5. P. 507-516.
  12. Eswar N., Webb B., Marti-Renom M. A. et al., 2006. Comparative protein structure modeling using Modeller//Current protocols in bioinformatics/editoral board, Andreas D. Baxevanis et al., Chapter 5.P. Unit 5 6.
  13. Feng Z., Chen L., Maddula H. et al., 2004. Ligand Depot: a data warehouse for ligands bound to macromolecules//Bioinformatics. Vol. 20. № 13. P. 2153-2155.
  14. Gilson M. K., Zhou H. X., 2007. Calculation of protein-ligand binding affinities//Annual Review of Biophysics and Biomolecular Structure. Vol. 36. P. 21-42.
  15. Johnson, K. L., Ingram G. C., 2005. Sending the right signals: Regulating receptor kinase activity//Curr. Opin. Plant Biol. Vol. 8. P. 648-656.
  16. Kelley L. A., Sternberg M. J., 2009. Protein structure prediction on the Web: a case study using the Phyre server//Nature protocols. Vol. 4. № 3. P. 363-71.
  17. Kim D. E., Chivian D., Baker D., 2004. Protein structure prediction and analysis using the Robetta server//Nucleic acids research. Vol. 32 (Web Server issue). P. 526-531.
  18. Laskowski R. A., MacArthur M. W., Moss D. S. et al., 1993. PROCHECK: a program to check the stereochemical quality of protein structures//Journal of Applied Crystallography. Vol. 26. № 2. P. 283-291.
  19. Lerouge P., Roche P., Faucher C. et al., 1990. Symbiotic host-specificity of Rhizobium meliloti is determined by a sulphated and acylated glucosamine oligosaccharide signal//Nature. Vol. 344. P. 781-784.
  20. Limpens E., Franken C., Smit P. et al., 2003. LysM domain receptor kinases regulating rhizobial Nod factor-induced infection//Science. Vol. 302. № 5645. P. 630-633.
  21. Madsen E. B., Madsen L. H., Radotoiu S. et al., 2003. A receptor kinase gene of the LysM type is involved in legume perception of rhizobial signals//Nature. Vol. 425. P. 637-640.
  22. Markmann K., Giczey, G., Parniske M., 2008. Functional adaptation of a plant receptor-kinase paved the way for the evolution of intracellular root symbioses with bacteria//PLoS Biol. Vol. 6. P. 496-506.
  23. Morris G. M., Huey R., Lindstrom W. et al., 2009. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility//Journal of Computational Chemistry. Vol. 30. № 16. P. 2785-2791.
  24. Mulder L., Lefebvre B., Cullimore J. et al., 2006. LysM domains of Medicago truncatula NFP protein involved in Nod factor perception. Glycosylation state, molecular modeling and docking of chitooligosaccharides and Nod factors//Glycobiology. Vol. 16. № 9. P. 801-809.
  25. Navarro-Gochicoa M. T., Camut S., Timmers A. C., et al., 2003. 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 physiology. Vol. 133. № 4. P. 1893-910.
  26. Radutoiu S.,Madsen L. H., Madsen E. B. et al., 2003. Plant recognition of symbiotic bacteria requires two LysM receptor-like kinases//Nature. Vol. 425. P. 585-592.
  27. Rockey W. M., Laederach A., Reilly P. J., 2000. Automated docking of alpha-(1-> 4)-and alpha-(1-> 6)-linked glucosyl trisaccharides and maltopentaose into the soybean beta-amylase active site//Proteins. Vol. 40. № 2. P. 299-309.
  28. Rogers S. O., Bendich A. J., 1985. Extraction of DNA from milligram amounts of fresh, herbarium and mummified plant tissues//Plant Mol. Biol. Vol. 5. P. 69-76.
  29. Roy A., Kucukural A., Zhang Y., 2010. I-TASSER: a unified platform for automated protein structure and function prediction//Nature protocols. Vol. 5. № 4. P. 725-738.
  30. Sambrook J., Fritsch E. F., Maniatis T. 1989. Molecular Cloning: A Laboratory Manual//Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.
  31. Torii K. U., 2004. Leucine-rich repeat receptor kinases in plants: Structure, function, and signal transduction pathways//Int. Rev. Cytol. Vol. 234. P. 1-46.
  32. Vriend G., 1990. WHAT IF: a molecular modeling and drug design program//Journal of Molecular Graphics. Vol. 8. № 1. P. 52-56, 29.
  33. Walker J. C., 1994. Structure and function of the receptor-like protein kinases of higher plants//Plant Mol. Biol. Vol. 26. P. 1599-1609.
  34. www.invitrogen.com
  35. www.megasoftware.net.
  36. www.ub.es/dnasp
  37. Zhang Y., 2008. I-TASSER server for protein 3D structure prediction//BMC Bioinformatics. Vol. 9. P. 40.

Statistics

Views

Abstract - 430

PDF (Russian) - 293

Cited-By


Article Metrics

Metrics Loading ...

PlumX

Dimensions


Copyright (c) 2012 Porozov Y.B., Muntyan A.N., Chizhevskaya E.P., Simarov B.V., Andronov E.E.

Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.

This website uses cookies

You consent to our cookies if you continue to use our website.

About Cookies