Ukr.Biochem.J. 2015; Volume 87, Issue 5, Sep-Oct, pp. 24-37


Legume-rhizobium symbiosis proteomics: achievements and perspectives

Iu. Iu. Kondratiuk, P. M. Mamenko, S. Ya. Kots

Institute of Plant Physiology and Genetics, National Academy of Sciences of Ukraine, Kyiv;

The present review contains results of proteo­mic­ researches of legume-rhizobium symbiosis. The technical difficulties associated with the methods of obtaining protein extracts from symbiotic structures and ways of overcoming them were discussed. The changes of protein synthesis under formation and functioning of symbiotic structures were shown.  Special attention has been given to the importance of proteomic studies of plant-microbe structures in the formation of adaptation strategies under adverse environmental conditions. The technical and conceptual perspectives of legume-rhizobium symbiosis proteomics were shown.

Keywords: , , , , , ,


  1. Udvardi M, Poole PS. Transport and metabolism in legume-rhizobia symbioses. Annu Rev Plant Biol. 2013;64:781-805. Review. PubMed, CrossRef
  2. Herridge DF, Peoples MB, Boddey RM. Global inputs of biological nitrogen fixation in agricultural systems. Plant Soil. 2008 Jul;311(1-2):1-18. CrossRef
  3. Graham PH, Vance CP. Nitrogen fixation in perspective: an overview of research and extension needs. Field Crop Res. 2000;65(2-3):93-106. CrossRef
  4. Cooper RL. A delayed flowering barrier to higher soybean yields. Field Crop Res. 2003 Mar;82(1):27-35. CrossRef
  5.  Petrychenko VF, Kots SYa. Symbiotic systems in modern agricultural manufacture. Bulletin NAS Ukraine. 2014;(3):57-66. (in Ukrainian).
  6. Kots SYa, Morgun VV, Tyhonovych IA, Provorov NA,Patyka VF, Petrychenko VF, Melnykova NM, Mamenko PM. Biological nitrogen fixation: legume-rhizobial symbiosis. Kyiv: Logos, 2011;1: 404 p. (in Ukrainian)
  7. Komatsu S, Toorchi M, Yukawa K. Soybean proteomics. Curr Proteomics. 2007;4(3):182-186. CrossRef
  8. van Wijk KJ. Challenges and prospects of plant proteomics. Plant Physiol. 2001 Jul. 126(2):501-508. PubMedPubMedCentralCrossRef
  9. Rose JKC, Bashir S, Giovannoni JJ, Jahn MM, Saravanan RS. Tackling the plant proteome: practical approaches, hurdles and experimental tools. Plant J. 2004 Sep;39(5):715-33. PubMedCrossRef
  10.  Salekden GH, Komatsu S. Crop proteomics: aim at sustainable agriculture of tomorrow. Proteomics. 2007 Aug;7(16):2976-96. PubMedCrossRef
  11. International Rice Genome Sequencing Project. The map-based sequence of the rice genome. Nature. 2005 Aug 11;436(7052):793-800. PubMed
  12.  Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 2000 Dec 14;408(6814):796-815.
  13. Young ND, Cannon SB, Sato S, Kim D, Cook  DR, Town CD, Roe BA, Tabata S. Sequencing the Genespaces of Medicago truncatula and Lotus japonicas. Plant Physiol. 2005 Apr;137(4):1174-1181. PubMedPubMedCentralCrossRef
  14.  Komatsu S, Ahsan N. Soybean proteomics and its application to functional analysis. J Proteomics. 2009 Apr;72(3):325-336. PubMedCrossRef
  15.  Jain SM, Brar DS. Molecular techniques in crop improvement. Netherlands: Springer-Sience+Business Media B.V. 2009.  772 p.
  16. Kots SYa, Morgun VV, Patyka VF, Malichenko SM, Mamenko PM, Kiriziy DA, Mykhalkiv LM, Beregovenko SK, Melnykova NM. Biological nitrogen fixation: legume-rhizobial symbiosis. Kyiv: Logos, 2010;2:523 p. (in Ukrainian)
  17. Rolfe BG, Mathesius U, Djordjevic M, Weinman J, Hocart C, Weiler G, Bauer WD. Proteomic analysis of legume-microbe interactions. Comp Funct Genomics. 2003;4(2):225-228. PubMedPubMedCentralCrossRef
  18. Cho WCS. Proteomics technologies and challenges. Geno Prot Bioinfo. 2007;5(2):77-85. CrossRef
  19.  Mooney BP, Krishnan HB, Thelen JJ. High-throughput peptide mass fingerprinting of soybean seed proteins: automated workflow and utility of UniGene expressed sequence tag databases for protein identification. Phytochemistry. 2004 Jun;65(12):1733-1744. CrossRef
  20. Isaacson T, Damasceno CMB, Saravanan RS, He Y, Catala C, Saladie M, Rose JKC. Sample extraction techniques for enhanced proteomic analysis of plant tissues. Nat Protoc. 2006;1(2):769-774. PubMed, CrossRef
  21.  Thiellement H. Plant proteomics: Methods and protocols. Humana Press, 2007. 416 p.
  22. Espagne C, Martinez A, Valot B, Meinnel T, Giglione C. Alternative and effective proteomic analysis in Arabidopsis. Proteomics. 2007 Sep;7(20):3788-3799. PubMedCrossRef
  23.  Granier F. Extraction of plant proteins for two-dimensional electrophoresis. Electrophoresis. 1988 Nov;9(11):712-8. PubMed, CrossRef
  24. Mesquita RO, Soares EA, Barros EG, Loureiro ME. Method optimization for proteomic analysis of soybean leaf: improvements in identification of new and low-abundance proteins. Genet Mol Biol. 2012 Jun;35(1 (suppl)):353-61.  PubMed, PubMedCentral, CrossRef
  25. Herman EM, Helm RM, Jung R, Kinney AJ. Genetic modification removes an immunodominant allergen from soybean. Plant Physiol. 2003 May;132(1):36-43. PubMed, PubMedCentral, CrossRef
  26. Toorchi M., Nouri M.Z., Tsumura M., Komatsu S. Acoustic technology for high-performance disruption and extraction of plant proteins. Proteome Res. 2008 Jul;7(7):3035-41. PubMed, CrossRef
  27. Natarajan S., Xu C., Bae H., Caperna T.J., Garrett W.M. Characterization of storage proteins in wild (Glycine soja) and cultivated (Glycine max) soybean seeds using proteomic analysis. J Agric Food Chem. 2006 Apr 19;54(8):3114-20. PubMed, CrossRef
  28. Zhen Y, Qi JL, Wang SS, Su J, Xu HG, Zhang MS. Comparative proteome analysis of differentially expressed proteins induced by Al toxicity in soybean. Physiol Plant. 2007 Dec;131(4):542-54. PubMed, CrossRef
  29. Sobhanian H, Razavizadeh R, Nanjo Y, Ehsanpour  AA, Jazii FR, Motamed  N, Komatsu S. Proteome analysis of soybean leaves, hypocotyls and roots under salt stress. Proteome Sci. 2010 Mar 29;8:19.  PubMedCrossRef
  30. Sarma AD, Oehrle NW, Emerch DW. Plant protein isolation and stabilization for enhanced resolution of two-dimensional polyacrylamide gel electrophoresis. Anal Biochem. 2008 Aug 15;379(2):192-5. PubMed, CrossRef
  31. Mamenko PM, Kots SYa, Drozdenko GM, Zhemojda AV. The protein content of soybean nodules, inoculated by strains and Tn5-mutants of Bradyrhizobium japonicum with different efficiency. Physiol Biochem Cultivated Plants. 2008;40(6):525-531. (in Ukrainian).
  32. Toldra F, Nollet LML. Proteomics in foods. Principles and applications. Germany: Springer, 2013. 589 pp.   CrossRef
  33. Chen S, Harmon AC. Advances in plant proteomics. Proteomics. 2005;6(20:5504-16. CrossRef
  34. Kawaguchi M, Minamisawa K. Plant-microbe communications for symbiosis. Plant Cell Physiol. 2010 Sep;51(9):1377-80. PubMedCrossRef
  35. Ferguson BJ, Indrasumunar A, Hayashi S, Lin MH, Lin YH, Reid DE, Gresshoff PM. Molecular analysis of legume nodule development and autoregulation. J Integr Plant Biol. 2010 Jan;52(1):61-76. PubMed, CrossRef
  36. Reid D.E., Hayashi S., Lorenc M., Stiller J., Edwards D., Gresshoff P.M., Ferguson B.J. Identification of systemic responses in soybean nodulation by xylem sap feeding and complete transcriptome sequencing reveal a novel component of the autoregulation pathway. Plant Biotechnol J. 2012 Aug;10(6):680-9. PubMed, CrossRef
  37. Deakin WJ, Broughton WJ. Symbiotic use of pathogenic strategies: rhizobial protein secretion systems. Nat Rev Microbiol. 2009 Apr;7(4):312-20. PubMed, CrossRef
  38. Oldroyd G.E., Downie J.A. Coordinating nodule morphogenesis with rhizobial infection in legumes. Annu Rev Plant Biol. 2008;59(1):519-46. PubMed, CrossRef
  39. Spaink HP. Root nodulation and infection factors produced by rhizobial bacteria. Annu Rev Microbiol. 2000 Oct;54(1):257-88. PubMed, CrossRef
  40. Libault M, Farmer A, Brechenmacher L, Drnevich J, Langley RJ, Bilgin DD, Radwan O, Neece DJ, Clough SJ, May GD, Stacey G. Complete transcriptome of the soybean root hair cell, a single-cell model, and its alteration in response to Bradyrhizobium japonicum infection.  Plant Physiol. 2010 Feb;152(2):541-52. PubMed, PubMedCentralCrossRef
  41. Wan J, Torres M, Ganapathy A, Thelen J, DaGue BB, Mooney B, Xu D, Stacey G. Proteomic analysis of soybean root hairs after infection by Bradyrhizobium japonicum. Plant Microbe Interact. 2005 May;18(5):458-67. PubMed, CrossRef
  42. Nguyen THN, Brechenmacher L, Aldrich JT, Clauss TR, Gritsenko MA, Hixson KK, Libault M, Tanaka K, Yang F, Yao Q, Pasa-Tolic L, Xu D, Nguyen HT, Stacey G. Quantitative Phosphoproteomic Analysis of Soybean Root Hairs Inoculated with Bradyrhizobium japonicum. Mol Cell Proteomics. 2012 Nov;11(11):1140-55. PubMed, PubMedCentral, CrossRef
  43. Clarke VC, Loughlin PC, Gavrin A, Chen C, Brear EM, Day DA, Smith PMC. Proteomic analysis of the soybean symbiosome identifies new symbiotic proteins. Mol Cell Proteomics. 2015 May;14(5):1301-22. PubMed, PubMedCentralCrossRef
  44. Oehrle NW, Sarma AD, Waters JK, Emerich DW. Proteomic analysis of soybean nodule cytosol. Phytochemistry. 2008 Oct;69(13):2426-38. PubMed, CrossRef
  45. Dam S, Dyrlund TF, Ussatjuk A, Jochimsen B, Nielsen K, Goffard N, Ventosa M, Lorentzen A, Gupta V, Andersen SU, Enghild JJ, Ronson CW, Roepstorff P, Stougaard J. Proteome reference maps of the Lotus japonicus nodule and root. Proteomics. 2014 Feb;14(2-3):230-40. PubMedCrossRef
  46. Natera SHA, Guerreiro N, Djordjevic NA.  Proteome analysis  of  differentially  displayed  proteins  as  a  tool  for the  investigation  of  symbiosis. Mol Plant Microbe Interact. 2000 Sep;13(9):995-1009. PubMedCrossRef
  47. Han S-K, Wagner D. Role of chromatin in water stress responses in plants. J Exp Bot. 2014 Jun;65(10):2785-99. PubMedPubMedCentral, CrossRef
  48. Muneer S, Ahmad J, Bashir H, Qureshi MI. Proteomics of nitrogen fixing nodules under various environmental stresses. Plant Omics J. 2012;5(2):167-176.
  49. Zahran HH. Rhizobium-legume symbiosis and nitrogen fixation under severe conditions and in an arid climate. Microbiol Mol Biol Rev. 1999 Dec;63(4):968-89. PubMedPubMedCentral
  50. Chaves MM, Flexas J, Pinheiro C. Photosynthesis under drought and salt stress: regulation mechanisms from whole plant to cell. Ann Bot. 2009 Feb;103(4):551-60. PubMedPubMedCentralCrossRef
  51. Gil-Quintana E, Larrainzar E, Seminario A, Díaz-Leal JL, Alamillo JM, Pineda M, Arrese-Igor C, Wienkoop S, González EM. Local inhibition of nitrogen fixation and nodule metabolism in drought-stressed soybea. J Exp Bot. 2013 May;64(8):2171-82. PubMed, PubMedCentral, CrossRef
  52. Coleto I, Pineda M,  Rodino AP, De Ron AM, Alamillo JM. Comparison of inhibition of N2 fixation and ureide accumulation under water deficit in four common bean genotypes of contrasting drought tolerance. Ann Bot. 2014 May;113(6):1071-82. PubMed, PubMedCentral, CrossRef
  53. Durand  JL,  Sheehy JE, Minchin FR.  Nitrogenase activity, photosynthesis and nodule water potential in soybean plants experiencing water deprivation. J Exp Bot. 1987;38(2):311-321. CrossRef
  54. Sinclair TR, Serraj R. Legume nitrogen fixation and drought. Nature. 1995 Nov;378(6555):334. CrossRef
  55. Valentine AJ, Benedito VA, Kang Y. Legume nitrogen fixation and soil abiotic stress: from physiology to genomics and beyond. Annu Plant Rev. 2011;42:207-248. CrossRef
  56. Ramos MLG, Gordon AJ, Minchin FR, Sprent JI, Parsons R. Effect of water stress on nodule physiology and biochemistry of a drought tolerant cultivar of common bean (Phaseolus vulgaris L.). Ann Bot. 1999 Jan;83(1):57-63. CrossRef
  57. Guerin V, Trinchant JC, Rigaud J. Nitrogen fixation (C2H2 reduction) by broad bean (Vicia faba L.) nodules and bacteroids under water-restricted conditions. Plant Physiol. 1990 Mar;92(3):595-601. PubMed, CrossRef
  58. Aranjuelo I, Molero G, Erice G, Avice JC, Nogues S. Plant physiology and proteomics reveals the leaf response to drought in alfalfa (Medicago sativa L.). J Exp Bot. 2011 Jan;62(1):111-23. PubMed, PubMedCentral, CrossRef
  59. Bestel-Corre G, Dumas-Gaudot E, Poinsot V, Dieu M, Dierick JF, van TD, Remacle J, Gianinazzi-Pearson V, Gianinazzi S. Proteome analysis and identification of symbiosis-related proteins from Medicago  trancatula by two-dimensional gel electrophoresis and mass spectrometry. Electrophoresis. 2002 Jan;23(1):122-37. PubMed, CrossRef
  60. Chen H, Higgins J, Oresnik IJ, Hynes MF, Natera S, Djordjevic MA, Weinman JJ, Rolfe BG. Proteome analysis demonstrates complex replicon and luteolin interactions in pSyma-cured derivatives ofSinorhizobium meliloti strain 2011.  Electrophoresis. 2000 Nov;21(17):3833-42. PubMed, CrossRef
  61. Fester T, Kiess M, Strack D. A mycorrhiza-responsive protein in wheat roots. Mycorrhiza. 2002 Aug;12(4):219-22. Epub 2002 May 1. PubMed, CrossRef
  62. Larrainzar E, Wienkoop S, Weckwerth W, Ladrera R, Arrese-Igor C, Gonzalez EM. Medicago truncatula root nodule proteome analysis reveals differential plant and bacteroid responses to drought stress. Plant Physiol. 2007 Jul;144(3):1495-507. PubMed, PubMedCentral, CrossRef
  63.  Aghaei K, Komatsu S. Crop and medicinal plants proteomics in response to salt stress.  Fron Plant Sci. 2014;4(8):1-9. PubMed, PubMedCentral, CrossRef
  64. Sobhaniana H., Aghaei K., Komatsu S. Changes in the plant proteome resulting from salt stress: Toward the creation of salt-tolerant crops? J Proteomics. 2011 Aug 12;74(8):1323-37. PubMed, CrossRef
  65. Elsheikh EAE,  Wood  M.  Nodulation  and  N2-fixiation by soybean  inoculated with salt-tolerant rhizobia or salt-sensitive Bradyrhizobium  in  saline  soil. Soil Biol Biochem. 1995 Apr;27(4-5):657-661. CrossRef
  66. Aghaei  K,  Ehsanpour  AA,  Shah  AH,  Komatsu  S.  Proteome  analysis  of  soybean  hypocotyl  and  root  under salt stress.  Amino Acids. 2009 Jan;36(1):91-8. PubMed, CrossRef
  67. Sobhanian H, Razavizade R, Nanjo Y, Ehsanpour AA, Jazii FR, Motamed N, Komatsu S. Proteome analysis of soybean leaves, hypocotyls and roots under salt stress. Proteome Sci. 2010 Mar 29;8:19. PubMed, PubMedCentral, CrossRef
  68. Li DY, Inoue H, Takahashi M, Kojima T, Shiraiwa M, Takahara H. Molecular characterization of a novel salt-inducible gene for an OSBP (oxysterolbinding protein)-homologue from soybean. Gene. 2008 Jan 15;407(1-2):12-20. PubMed, CrossRef
  69. Onishi M., Tachi H., Kojima T., Shiraiwa M., Takahara H. Molecular cloning and characterization of a novel salt-inducible gene encoding an acidic isoform of PR-5 protein in soybean (Glycine max [L.] Merr.). Plant Physiol Biochem. 2006 Oct;44(10):574-80. Epub 2006 Oct 9. PubMed, CrossRef
  70. Liao H, Wong FL, Phang TH, Cheung MY, Li WYF, Shao G, Yan X, Lam HM. GmPAP3, a novel purple acid phosphatase-like gene in soybean induced by NaCl stress but not phosphorus deficiency. Gene. 2003 Oct 30;318:103-11. PubMed, CrossRef
  71. Chen M, Wang QY, Cheng XG, Xu ZS, Li LC, Ye XG, Xia LQ, Ma YZ. GmDREB2, a soybean DRE-binding transcription factor, conferred drought and high-salt tolerance in transgenic plants. Biochem Biophys Res Commun. 2007 Feb 9;353(2):299-305. PubMed, CrossRef
  72. Wahid A, Gelani S, Ashraf M, Foolad MR. Heat tolerance in plants: an overview. Environ Exp Bot. 2007 Dec;61(3):199-223. CrossRef
  73. Hungria M., Kaschuk G. Regulation of N2 fixation and NO3‾/NH4+ assimilation in nodulated and N-fertilized Phaseolus vulgaris L. exposed to high temperature stress.  Environ Exp Bot. 2014; 98:32-39. CrossRef
  74. Miura K, Furumoto T. Cold signaling and cold response in plants. Int J Mol Sci. 2013 Mar 6;14(3):5312-37. PubMed, CrossRef
  75. Aranjuelo I, Arrese-Igor C, Molero G. Nodule performance within a changing environmental context. J Plant Physiol. 2014 Jul 15;171(12):1076-90.PubMed, CrossRef
  76. Rodziewicz P, Swarcewicz B, Chmielewska K, Wojakowska A, Stobiecki M. Influence of abiotic stresses on plant proteome and metabolome changes.  Acta Physiol Plant. 2014;36(1):1-19. CrossRef
  77. Wang W, Vinocur B, Shoseyov O, Altman A. Role of plant heat-shock proteins and molecular chaperones in the abiotic stress response. Trends Plant Sci. 2004 May;9(5):244-52. PubMed, CrossRef
  78. Swigonska S, Weidner S. Proteomic analysis of response to long-term continuous stress in roots of germinating soybean seeds. J Plant Physiol. 2013 Mar 15;170(5):470-9.PubMed, CrossRef
  79. Cvjetko P, Zovko M, Balen B. Proteomics of heavy metal toxicity in plant. Arch Indust Hygiene Toxicol. 2014 Jan;65(1):1-18. PubMed, CrossRef
  80. Sobkowiak R, Deckert J. Proteins induced by cadmium in soybean cells. J Plant Physiol. 2006 Nov;163(11):1203-6. PubMed, CrossRef
  81. Ahsan N, Nakamura T, Komatsu S. Differential responses of microsomal proteins and metabolites in two contrasting cadmium (Cd) accumulating soybean cultivars under Cd stress. Amino Acids. 2012 Jan;42(1):317-27. PubMed, CrossRef
  82. Hossain Z, Hajika M, Komatsu S. Comparative proteome analysis of high and low cadmium accumulating soybeans under cadmium stress. Amino Acids. 2012 Dec;43(6):2393-416. PubMedCrossRef
  83. Barkla BJ,  Vera-Estrella R, Pantoja O. Progress and challenges for abiotic stress proteomics of crop plants. Proteomics. 2013 Jun;13(12-13):1801-15. PubMed, CrossRef
  84. Kosakivska IV, Bluma DA, Ustinova AYu, Demirevska K. Influence of stress temperatures on proteins of Brassica napus var. оleifera varieties.  Physiol Biochem Cultivated Plants. 2011;43(6):492-497. (in Ukrainian).
  85. Kav NNV, Srivastava S, Yajima W, Nidhi S. Application of proteomics to  investigate  рlant-microbe іnteractions. Curr Proteomic. 2007 Apr;4(1):28-43. CrossRef
  86. Christof R, Muralli S. The application of proteomics to plant biology: a review. Can J Bot. 2006 Jun;84(6):883-892. CrossRef

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