Advertisement

Synthetic Plasmids to Challenge Symbiotic Nitrogen Fixation Between Rhizobia and Legumes

  • Jovelyn Unay
  • Xavier PerretEmail author
Chapter
Part of the Rhizosphere Biology book series (RHBIO)

Abstract

Growth of most angiosperms, including cereal crops, is constrained by a limited accessibility of nitrogen in soils. Until now, agriculture relied extensively upon chemical fertilizers to compensate for NPK deficiencies in fields, often at considerable ecological costs. Making better use of plant-bacteria associations could lower the environmental impact of agriculture while retaining good yields. For example, soil bacteria known as rhizobia reduce enough atmospheric nitrogen (N2) to secure growth and seed production of legumes. The positive impact on soil fertility of growing legumes in fields and pastures has been known for centuries. Yet, molecular mechanisms governing rhizobia-legume symbioses were only extensively deciphered recently. Conversion of N2 into ammonia by rhizobia nitrogenase occurs almost exclusively inside plant cells of specialized root (or more rarely stem) organs called nodules. Thus, rhizobia established on root surfaces must infect plant tissues and gain access to the cytoplasm of nodule cells before becoming proficient symbionts. Concomitantly, host plants must also prevent systemic infections by non-symbiotic bacteria while securing the development of the nodule organs. Bacterial infection and nodule development are coordinated by molecular signals exchanged by legumes and rhizobia. Amongst these signals, plant-made flavonoids and rhizobial nodulation (Nod) factors are instrumental in securing harmonious symbiosis. As many symbiotic signals and cognate receptors/sensors have been identified in recent years, genetic engineering offers new opportunities to study but also to harness the benefits of legume-rhizobia symbioses. Here, we review the major molecular mechanisms involved in the development of proficient nodules and describe a framework for assembling a subset of symbiotic loci into small synthetic plasmids capable of converting soil bacteria into beneficial plant symbionts. As proof of concept, the nodulation phenotype conferred by the synthetic plasmid pMSym2 is detailed.

Notes

Acknowledgements

We would like to thank Natalia Giot for her help in many aspects of this work. Financial support for this project was provided by the University of Geneva and the Swiss National Science Foundation (grants no. 31003A-146,548 and 31003A-173,191).

References

  1. Andrews M, Andrews ME (2017) Specificity in legume-rhizobia symbioses. Int J Mol Sci 18:705Google Scholar
  2. Brewin NJ (2010) Root nodules (legume-Rhizobium symbiosis). In: Encyclopedia of life sciences (ELS). Wiley, ChichesterGoogle Scholar
  3. Broughton WJ, Heycke N, Meyer ZAH, Pankhurst CE (1984) Plasmid linked nif and nod genes in fast-growing rhizobia that nodulate Glycine max, Psophocarpus tetragonolobus, and Vigna unguiculata. Proc Natl Acad Sci U S A 81:3093–3097CrossRefGoogle Scholar
  4. Broughton WJ, Wong C-H, Lewin A, Samrey U, Myint H, Meyer z AH, Dowling DN, Simon R (1986) Identification of Rhizobium plasmid sequences involved in recognition of Psophocarpus, Vigna, and other legumes. J Cell Biol 102:1173–1182Google Scholar
  5. Broughton WJ, Jabbouri S, Perret X (2000) Keys to symbiotic harmony. J Bacteriol 182:5641–5652CrossRefGoogle Scholar
  6. Broughton WJ, Hanin M, Relić B, Kopciñska J, Golinowski W, Simsek S, Ojanen-Reuhs T, Reuhs B, Marie C, Kobayashi H, Bordogna B, Le Quéré A, Jabbouri S, Fellay R, Perret X, Deakin WJ (2006) Flavonoid-inducible modifications to rhamnan O antigens are necessary for Rhizobium sp. strain NGR234-legume symbioses. J Bacteriol 188:3654–3663CrossRefGoogle Scholar
  7. Buren S, Young EM, Sweeny EA, Lopez-Torrejon G, Veldhuizen M, Voigt CA, Rubio LM (2017) Formation of nitrogenase NifDK tetramers in the mitochondria of Saccharomyces cerevisiae. ACS Synth Biol 6:1043–1055CrossRefGoogle Scholar
  8. D’Antuono AL, Ott T, Krusell L, Voroshilova V, Ugalde RA, Udvardi M, Lepek VC (2008) Defects in rhizobial cyclic glucan and lipopolysaccharide synthesis alter legume gene expression during nodule development. Mol Plant-Microbe Interact 21:50–60CrossRefGoogle Scholar
  9. de Kok S, Stanton LH, Slaby T, Durot M, Holmes VF, Patel KG, Platt D, Shapland EB, Serber Z, Dean J, Newman JD, Chandran SS (2014) Rapid and reliable DNA assembly via ligase cycling reaction. ACS Synth Biol 3:97–106CrossRefGoogle Scholar
  10. Deakin WJ, Broughton WJ (2009) Symbiotic use of pathogenic strategies: rhizobial protein secretion systems. Nat Rev Microbiol 7:312–320CrossRefGoogle Scholar
  11. Demont-Caulet N, Maillet F, Tailler D, Jacquinet JC, Promé JC, Nicolaou KC, Truchet G, Beau JM, Dénarié J (1999) Nodule-inducing activity of synthetic Sinorhizobium meliloti nodulation factors and related lipo-chitooligosaccharides on alfalfa. Importance of the acyl chain structure. Plant Physiol 120:83–92CrossRefGoogle Scholar
  12. Dénarié J, Debellé F, Promé J-C (1996) Rhizobium lipo-chitooligosaccharaide nodulation factors: signaling molecules mediating recognition and morphogenesis. Annu Rev Biochem 65:503–535CrossRefGoogle Scholar
  13. diCenzo GC, Zamani M, Milunovic B, Finan TM (2016) Genomic resources for identification of the minimal N2-fixing symbiotic genome. Environ Microbiol 18:2534–2547CrossRefGoogle Scholar
  14. Dohlemann J, Wagner M, Happel C, Carrillo M, Sobetzko P, Erb TJ, Thanbichler M, Becker A (2017) A family of single copy repABC-type shuttle vectors stably maintained in the alpha-proteobacterium Sinorhizobium meliloti. ACS Synth Biol 6:968–984CrossRefGoogle Scholar
  15. Downie JA (2005) Legume haemoglobins: symbiotic nitrogen fixation needs bloody nodules. Curr Biol 15:R196–R198CrossRefGoogle Scholar
  16. Dreyfus BL, Dommergues YR (1981) Nitrogen fixing nodules induced by Rhizobium on the stem of the tropical legume Sesbania rostrata. FEMS Microbiol Lett 10:313CrossRefGoogle Scholar
  17. Fauvart M, Michiels J (2008) Rhizobial secreted proteins as determinants of host specificity in the rhizobium-legume symbiosis. FEMS Microbiol Lett 285:1–9CrossRefGoogle Scholar
  18. Fellay R, Hanin M, Montorzi G, Frey J, Freiberg C, Golinowski W, Staehelin C, Broughton WJ, Jabbouri S (1998) nodD2 of Rhizobium sp. NGR234 is involved in the repression of the nodABC operon. Mol Microbiol 27:1039–1050CrossRefGoogle Scholar
  19. Ferguson BJ, Indrasumunar A, Hayashi S, Lin MH, Lin YH, Reid DE, Gresshoff PM (2010) Molecular analysis of legume nodule development and autoregulation. J Integr Plant Biol 52:61–76CrossRefGoogle Scholar
  20. Fischer HM (1994) Genetic regulation of nitrogen fixation in rhizobia. Microbiol Rev 58:352–386PubMedPubMedCentralGoogle Scholar
  21. Fisher RF, Long SR (1993) Interactions of NodD at the nod box - NodD binds to 2 distinct sites on the same face of the helix and induces a bend in the DNA. J Mol Biol 233:336–348CrossRefGoogle Scholar
  22. Fliegmann J, Bono JJ (2015) Lipo-chitooligosaccharidic nodulation factors and their perception by plant receptors. Glycoconj J 32:455–464CrossRefGoogle Scholar
  23. Fraysse N, Jabbouri S, Treilhou M, Couderc F, Poinsot V (2002) Symbiotic conditions induce structural modifications of Sinorhizobium sp. NGR234 surface polysaccharides. Glycobiology 12:741–748CrossRefGoogle Scholar
  24. Fred EB, Baldwin IL, McCoy E (1932) Root nodule bacteria and leguminous plants. University of Wisconsin Press, MadisonGoogle Scholar
  25. Freiberg C, Fellay R, Bairoch A, Broughton WJ, Rosenthal A, Perret X (1997) Molecular basis of symbiosis between Rhizobium and legumes. Nature 387:394–401CrossRefGoogle Scholar
  26. Fumeaux C, Bakkou N, Kopćinska J, Golinowski W, Westenberg DJ, Müller P, Perret X (2011) Functional analysis of the nifQdctA1y4vGHIJ operon of Sinorhizobium fredii strain NGR234 using a transposon with a NifA-dependent read-out promoter. Microbiology 157:2745–2758CrossRefGoogle Scholar
  27. Gage DJ (2004) Infection and invasion of roots by symbiotic, nitrogen-fixing rhizobia during nodulation of temperate legumes. Microbiol Mol Biol Rev 68:280–300CrossRefGoogle Scholar
  28. Gibson DG (2012) Gibson Assembly – building a synthetic biology toolset. NEB Expressions, 3–5Google Scholar
  29. Gibson KE, Kobayashi H, Walker GC (2008) Molecular determinants of a symbiotic chronic infection. Annu Rev Genet 42:413–441CrossRefGoogle Scholar
  30. Gourion B, Berrabah F, Ratet P, Stacey G (2015) Rhizobium-legume symbioses: the crucial role of plant immunity. Trends Plant Sci 20:186–194CrossRefGoogle Scholar
  31. Gresshoff PM, Hayashi S, Biswas B, Mirzaei S, Indrasumunar A, Reid D, Samuel S, Tollenaere A, van Hameren B, Hastwell A, Scott P, Ferguson BJ (2015) The value of biodiversity in legume symbiotic nitrogen fixation and nodulation for biofuel and food production. J Plant Physiol 172:128–136CrossRefGoogle Scholar
  32. Hubber A, Vergunst AC, Sullivan JT, Hooykaas PJ, Ronson CW (2004) Symbiotic phenotypes and translocated effector proteins of the Mesorhizobium loti strain R7A VirB/D4 type IV secretion system. Mol Microbiol 54:561–574CrossRefGoogle Scholar
  33. Jabbouri S, Fellay R, Talmont F, Kamalaprija P, Burger U, Relić B, Promé JC, Broughton WJ (1995) Involvement of nodS in N-methylation and nodU in 6-O-carbamoylation of Rhizobium sp. NGR234 nod factors. J Biol Chem 270:22968–22973CrossRefGoogle Scholar
  34. Jackson LE, Burger M, Cavagnaro TR (2008) Roots, nitrogen transformations, and ecosystem services. Annu Rev Plant Biol 59:341–363CrossRefGoogle Scholar
  35. Kawaharada Y, Kelly S, Nielsen MW, Hjuler CT, Gysel K, Muszynski A, Carlson RW, Thygesen MB, Sandal N, Asmussen MH, Vinther M, Andersen SU, Krusell L, Thirup S, Jensen KJ, Ronson CW, Blaise M, Radutoiu S, Stougaard J (2015) Receptor-mediated exopolysaccharide perception controls bacterial infection. Nature 523:308–312CrossRefGoogle Scholar
  36. Kelly S, Radutoiu S, Stougaard J (2017) Legume LysM receptors mediate symbiotic and pathogenic signalling. Curr Opin Plant Biol 39:152–158CrossRefGoogle Scholar
  37. Kereszt A, Mergaert P, Kondorosi E (2011) Bacteroid development in legume nodules: evolution of mutual benefit or of sacrificial victims? Mol Plant-Microbe Interact 24:1300–1309CrossRefGoogle Scholar
  38. Kobayashi H, Naciri-Graven Y, Broughton WJ, Perret X (2004) Flavonoids induce temporal shifts in gene-expression of nod-box controlled loci in Rhizobium sp. NGR234. Mol Microbiol 51:335–347CrossRefGoogle Scholar
  39. Le Strange KK, Bender GL, Djordjevic MA, Rolfe BG, Redmond JW (1990) The Rhizobium strain NGR234 nodD1 gene product responds to activation by simple phenolic compounds vanillin and isovanillin present in wheat seedling extracts. Mol Plant-Microbe Interact 3:214–220CrossRefGoogle Scholar
  40. Lewin A, Rosenberg C, Meyer ZAH, Wong CH, Nelson L, Manen J-F, Stanley J, Dowling DN, Dénarié J, Broughton WJ (1987) Multiple host-specificity loci of the broad host range Rhizobium sp. NGR234 selected using the widely compatible legume Vigna unguiculata. Plant Mol Biol 8:447–459CrossRefGoogle Scholar
  41. Lewin A, Cervantes E, Wong C-H, Broughton WJ (1990) nodSU, two new nod genes of the broad host range Rhizobium strain NGR234 encode host-specific nodulation of the tropical tree Leucaena leucocephala. Mol Plant-Microbe Interact 3:317–326CrossRefGoogle Scholar
  42. Long SR (2015) Receptive to infection. Nature 523:298–299CrossRefGoogle Scholar
  43. Marchetti M, Catrice O, Batut J, Masson-Boivin C (2011) Cupriavidus taiwanensis bacteroids in Mimosa pudica indeterminate nodules are not terminally differentiated. Appl Environ Microbiol 77:2161–2164CrossRefGoogle Scholar
  44. Marie C, Deakin WJ, Viprey V, Kopciñska J, Golinowski W, Krishnan HB, Perret X, Broughton WJ (2003) Characterisation of Nops, Nodulation outer proteins, secreted via the type III secretion system of NGR234. Mol Plant-Microbe Interact 16:743–751CrossRefGoogle Scholar
  45. Marie C, Deakin WJ, Ojanen-Reuhs T, Diallo E, Reuhs B, Broughton WJ, Perret X (2004) TtsI, a key regulator of Rhizobium species NGR234 is required for type III-dependent protein secretion and synthesis of rhamnose-rich polysaccharides. Mol Plant-Microbe Interact 17:958–966CrossRefGoogle Scholar
  46. Masson-Boivin C, Sachs JL (2017) Symbiotic nitrogen fixation by rhizobia-the roots of a success story. Curr Opin Plant Biol 44:7–15CrossRefGoogle Scholar
  47. Masson-Boivin C, Giraud E, Perret X, Batut J (2009) Establishing nitrogen-fixing symbiosis with legumes: how many rhizobium recipes? Trends Microbiol 17:458–466CrossRefGoogle Scholar
  48. Mergaert P, Uchiumi T, Alunni B, Evanno G, Cheron A, Catrice O, Mausset AE, Barloy-Hubler F, Galibert F, Kondorosi A, Kondorosi E (2006) Eukaryotic control on bacterial cell cycle and differentiation in the Rhizobium-legume symbiosis. Proc Natl Acad Sci U S A 103:5230–5235CrossRefGoogle Scholar
  49. Miwa H, Okazaki S (2017) How effectors promote beneficial interactions. Curr Opin Plant Biol 38:148–154CrossRefGoogle Scholar
  50. Morrison NA, Hau CY, Trinick MJ, Shine J, Rolfe BG (1983) Heat curing of a Sym plasmid in a fast-growing Rhizobium sp. that is able to nodulate legumes and the nonlegume Parasponia sp. J Bacteriol 153:527–531PubMedPubMedCentralGoogle Scholar
  51. Mulligan JT, Long SR (1985) Induction of Rhizobium meliloti nodC expression by plant exudate requires nodD. Proc Natl Acad Sci U S A 82:6609–6613CrossRefGoogle Scholar
  52. Mus F, Crook MB, Garcia K, Garcia Costas A, Geddes BA, Kouri ED, Paramasivan P, Ryu MH, Oldroyd GED, Poole PS, Udvardi MK, Voigt CA, Ane JM, Peters JW (2016) Symbiotic nitrogen fixation and the challenges to its extension to nonlegumes. Appl Environ Microbiol 82:3698–3710CrossRefGoogle Scholar
  53. Okazaki S, Kaneko T, Sato S, Saeki K (2013) Hijacking of leguminous nodulation signaling by the rhizobial type III secretion system. In: Proc. Natl. Acad. Sci. USA, vol 110, pp 17131–17136Google Scholar
  54. Okazaki S, Tittabutr P, Teulet A, Thouin J, Fardoux J, Chaintreuil C, Gully D, Arrighi JF, Furuta N, Miwa H, Yasuda M, Nouwen N, Teaumroong N, Giraud E (2016) Rhizobium-legume symbiosis in the absence of Nod factors: two possible scenarios with or without the T3SS. ISME J 10:64–74CrossRefGoogle Scholar
  55. Oldroyd GE, Downie JA (2008) Coordinating nodule morphogenesis with rhizobial infection in legumes. Annu Rev Plant Biol 59:519–546CrossRefGoogle Scholar
  56. Oldroyd GE, Murray JD, Poole PS, Downie JA (2011) The rule of engagement in the legume-rhizobial symbiosis. Annu Rev Genet 45:119–144CrossRefGoogle Scholar
  57. Pankhurst CE, Broughton WJ, Bachem C, Kondorosi E, Kondorosi A (1983) Identification of nitrogen fixation and nodulation genes on a large plasmid from a broad host range Rhizobium sp. In: Pühler A (ed) Molecular genetics of the bacteria-plant interaction. Springler, Berlin, pp 169–176CrossRefGoogle Scholar
  58. Perret X, Staehelin C, Broughton WJ (2000) Molecular basis of symbiotic promiscuity. Microbiol Mol Biol Rev 64:180–201CrossRefGoogle Scholar
  59. Perret X, Kobayashi H, Collado-Vides J (2003) Regulation of expression of symbiotic genes in Rhizobium sp. NGR234. Indian J Exp Biol 41:1101–1113PubMedGoogle Scholar
  60. Poole P, Ramachandran V, Terpolilli J (2018) Rhizobia: from saprophytes to endosymbionts. Nat Rev Microbiol 16:291–303CrossRefGoogle Scholar
  61. Price NP, Relić B, Talmont F, Lewin A, Promé D, Pueppke SG, Maillet F, Dénarié J, Promé JC, Broughton WJ (1992) Broad-host-range Rhizobium species strain NGR234 secretes a family of carbamoylated, and fucosylated, nodulation signals that are O-acetylated or sulphated. Mol Microbiol 6:3575–3584CrossRefGoogle Scholar
  62. Price NP, Talmont F, Wieruszeski JM, Promé D, Promé JC (1996) Structural determination of symbiotic nodulation factors from the broad host-range Rhizobium species NGR234. Carbohydr Res 289:115–136CrossRefGoogle Scholar
  63. Pueppke SG, Broughton WJ (1999) Rhizobium sp. strain NGR234 and R. fredii USDA257 share exceptionally broad, nested host ranges. Mol Plant-Microbe Interact 12:293–318CrossRefGoogle Scholar
  64. Raetz CR, Whitfield C (2002) Lipopolysaccharide endotoxins. Annu Rev Biochem 71:635–700CrossRefGoogle Scholar
  65. Relić B, Fellay R, Lewin A, Perret X, Price NPJ, Rochepeau P, Broughton WJ (1993) nod genes and Nod factors of Rhizobium species NGR234. In: Palacios R, Mora J, Newton WE (eds) New horizons in nitrogen fixation. Kluwer Academic Publishers, Dordrecht, pp 183–189CrossRefGoogle Scholar
  66. Relić B, Staehelin C, Fellay R, Jabbouri S, Boller T, Broughton WJ (1994a) Do Nod-factor levels play a role in host-specificity? In: Kiss GB, Endre G (eds) Proceedings of the 1st European nitrogen fixation conference. Officina Press, Szeged, pp 69–75Google Scholar
  67. Relić B, Perret X, Estrada-Garcia MT, Kopcinska J, Golinowski W, Krishnan HB, Pueppke SG, Broughton WJ (1994b) Nod factors of Rhizobium are a key to the legume door. Mol Microbiol 13:171–178CrossRefGoogle Scholar
  68. Reuhs BL, Relić B, Forsberg LS, Marie C, Ojanen-Reuhs T, Stephens SB, Wong CH, Jabbouri S, Broughton WJ (2005) Structural characterization of a flavonoid-inducible Pseudomonas aeruginosa A-band-like O antigen of Rhizobium sp. strain NGR234, required for the formation of nitrogen-fixing nodules. J Bacteriol 187:6479–6487CrossRefGoogle Scholar
  69. Roth LE, Jeon KW, Stacey G (1988) Homology in endosymbiotic systems: the term ‘symbiosome’. In: Palacios RAVDPS (ed) Molecular genetics of plant-microbe interactions. APS Press, St-Paul, pp 220–225Google Scholar
  70. Saad M, Crèvecoeur M, Masson-Boivin C, Perret X (2012) The T3SS of Cupriavidus taiwanensis strain LMG19424 compromizes symbiosis with Leucaena leucocephala. Appl Environ Microbiol 78:7476–7479CrossRefGoogle Scholar
  71. Schmeisser C, Liesegang H, Krysciak D, Bakkou N, Le Quéré A, Wollherr A, Heinemeyer I, Morgenstern B, Pommerening-Röser A, Flores M, Palacios R, Brenner S, Gottschalk G, Schmitz RA, Broughton WJ, Perret X, Strittmatter AW, Streit WR (2009) Rhizobium sp. NGR234 possesses a remarkable number of secretion systems. Appl Environ Microbiol 75:4035–4045CrossRefGoogle Scholar
  72. Sprent JI, Ardley J, James EK (2017) Biogeography of nodulated legumes and their nitrogen-fixing symbionts. New Phytol 215:40–56CrossRefGoogle Scholar
  73. Staehelin C, Krishnan HB (2015) Nodulation outer proteins: double-edged swords of symbiotic rhizobia. Biochem J 470:263–274CrossRefGoogle Scholar
  74. Streeter JG (1994) Failure of inoculant rhizobia to overcome the dominance of indigenous strains for nodule formation. Can J Microbiol 40:513–522CrossRefGoogle Scholar
  75. Sullivan JT, Trzebiatowski JR, Cruickshank RW, Gouzy J, Brown SD, Elliot RM, Fleetwood DJ, McCallum NG, Rossbach U, Stuart GS, Weaver JE, Webby RJ, De Bruijn FJ, Ronson CW (2002) Comparative sequence analysis of the symbiosis island of Mesorhizobium loti strain R7A. J Bacteriol 184:3086–3095CrossRefGoogle Scholar
  76. Trinick MJ (1980) Relationships amongst the fast-growing rhizobia of Lablab purpureus, Leucaena leucocephala, Mimosa spp., Acacia farnesiana and Sesbania grandiflora and their affinities with other rhizobial groups. J Appl Bacteriol 49:39–53CrossRefGoogle Scholar
  77. Trinick MJ, Galbraith J (1980) The Rhizobium requirements of the non-legume Parasponia andersonii in relationship to the cross-inoculation group concept of legumes. New Phytol 86:17–26CrossRefGoogle Scholar
  78. Viprey V, Del Greco A, Golinowski W, Broughton WJ, Perret X (1998) Symbiotic implications of type III protein secretion machinery in Rhizobium. Mol Microbiol 28:1381–1389CrossRefGoogle Scholar
  79. Vlassak KM, de Wilde P, Snoeck C, Luyten E, van Rhijn P, Vanderleyden J (1998) The Rhizobium sp. BR816 nodD3 gene is regulated by a transcriptional regulator of the AraC/XylS family. Mol Gen Genet 258:558–561CrossRefGoogle Scholar
  80. Waelkens F, Voets T, Vlassak K, Vanderleyden J, van Rhijn P (1995) The nodS gene of Rhizobium tropici strain CIAT899 is necessary for nodulation on Phaseolus vulgaris and on Leucaena leucocephala. Mol Plant-Microbe Interact 8:147–154CrossRefGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2019

Authors and Affiliations

  1. 1.Department of Botany and Plant Biology, Sciences IIIUniversity of GenevaGenevaSwitzerland

Personalised recommendations