1887

Abstract

strains have been used as plant-growth-promoting rhizobacteria (PGPR) of cereal crops, but their adaptation to the root remains poorly understood. Here, we used a global approach based on differential fluorescence induction (DFI) promoter trapping to identify genes of the wheat isolate Sp245 that are induced in the presence of spring wheat seed extracts. Fluorescence-based flow cytometry sorting of Sp245 cells was validated using P, P and P promoters and . A random promoter library was constructed by cloning 1–3 kb Sp245 fragments upstream of a promoterless version of in the promoter-trap plasmid pOT1e (genome coverage estimated at threefold). Exposure to spring wheat seed extracts obtained using a methanol solution led to the detection of 300 induced DFI clones, and upregulation by seed extracts was confirmed for 46 clones. Sequencing of 21 clones enabled identification of seven promoter regions. Five of them displayed upregulation once inoculated onto spring wheat seedlings. Their downstream sequence was similar to (i) a predicted transcriptional regulator, (ii) a serine/threonine protein kinase, (iii) two conserved hypothetical proteins, or (iv) the copper-containing dissimilatory nitrite reductase NirK. Two of them were also upregulated when inoculated on winter wheat and pea but not on maize, whereas the three others (including P) were upregulated on the three hosts. The amounts of nitrate and/or nitrite present in spring wheat seed extracts were sufficient for P upregulation. Overall, DFI promoter trapping was useful to reveal genes involved in the interaction with the plant.

Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.2007/009381-0
2007-10-01
2019-11-22
Loading full text...

Full text loading...

/deliver/fulltext/micro/153/10/3608.html?itemId=/content/journal/micro/10.1099/mic.0.2007/009381-0&mimeType=html&fmt=ahah

References

  1. Alexandre, G., Greer, S. E. & Zhulin, I. B. ( 2000; ). Energy taxis is the dominant behavior in Azospirillum brasilense. J Bacteriol 182, 6042–6048.[CrossRef]
    [Google Scholar]
  2. Allaway, D., Schofield, N. A., Leonard, M. E., Gilardoni, L., Finan, T. M. & Poole, P. S. ( 2001; ). Use of differential fluorescence induction and optical trapping to isolate environmentally induced genes. Environ Microbiol 3, 397–406.[CrossRef]
    [Google Scholar]
  3. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. ( 1997; ). Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res 25, 3389–3402.[CrossRef]
    [Google Scholar]
  4. Baek, S.-H. & Shapleigh, J. P. ( 2005; ). Expression of nitrite and nitric oxide reductases in free-living and plant-associated Agrobacterium tumefaciens C58 cells. Appl Environ Microbiol 71, 4427–4436.[CrossRef]
    [Google Scholar]
  5. Baldani, V. L. D., Baldani, J. I. & Döbereiner, J. ( 1983; ). Effects of Azospirillum inoculation on root infection and nitrogen incorporation in wheat. Can J Microbiol 29, 924–929.[CrossRef]
    [Google Scholar]
  6. Bashan, Y., Holguin, G. & de-Bashan, L. E. ( 2004; ). Azospirillum–plant relationships: physiological, molecular, agricultural, and environmental advances (1997–2003). Can J Microbiol 50, 521–577.[CrossRef]
    [Google Scholar]
  7. Bendtsen, J., Nielsen, H., von Heijne, G. & Brunak, S. ( 2004; ). Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 340, 783–795.[CrossRef]
    [Google Scholar]
  8. Bhagwat, A. A. & Keister, D. L. ( 1992; ). Identification and cloning of Bradyrhizobium japonicum genes expressed strain selectively in soil and rhizosphere. Appl Environ Microbiol 58, 1490–1495.
    [Google Scholar]
  9. Binnerup, S. J. & Sørensen, J. ( 1992; ). Nitrate and nitrite microgradients in barley rhizosphere as detected by a highly sensitive denitrification bioassay. Appl Environ Microbiol 58, 2375–2380.
    [Google Scholar]
  10. Blaha, D., Prigent-Combaret, C., Mirza, M. S. & Moënne-Loccoz, Y. ( 2006; ). Phylogeny of the 1-aminocyclopropane-1-carboxylic acid deaminase-encoding gene acdS in phytobeneficial and pathogenic Proteobacteria and relation with strain biogeography. FEMS Microbiol Ecol 56, 455–470.[CrossRef]
    [Google Scholar]
  11. Bloemberg, G. V., Wijfjes, A. H., Lamers, G. E., Stuurman, N. & Lugtenberg, B. J. ( 2000; ). Simultaneous imaging of Pseudomonas fluorescens WCS365 populations expressing three different autofluorescent proteins in the rhizosphere: new perspectives for studying microbial communities. Mol Plant Microbe Interact 13, 1170–1176.[CrossRef]
    [Google Scholar]
  12. Camilli, A. & Mekalanos, J. J. ( 1995; ). Use of recombinase gene fusions to identify Vibrio cholerae genes induced during infection. Mol Microbiol 18, 671–683.[CrossRef]
    [Google Scholar]
  13. Chilton, M.-D., Currier, T. C., Farrand, S. K., Bendich, A. J., Gordon, M. P. & Nester, E. W. ( 1974; ). Agrobacterium tumefaciens DNA and PS8 bacteriophage DNA not detected in crown gall tumors. Proc Natl Acad Sci U S A 71, 3672–3676.[CrossRef]
    [Google Scholar]
  14. Clarke, L. & Carbon, J. ( 1976; ). A colony bank containing synthetic ColEl hybrid plasmids representative of the entire E. coli genome. Cell 9, 91–99.[CrossRef]
    [Google Scholar]
  15. Cormack, B. P., Valdivia, R. H. & Falkow, S. ( 1996; ). FACS-optimized mutants of the green fluorescent protein (GFP). Gene 173, 33–38.[CrossRef]
    [Google Scholar]
  16. Creus, C. M., Graziano, M., Casanovas, E. M., Pereyra, M. A., Simontacchi, M., Puntarulo, S., Barassi, C. A. & Lamattina, L. ( 2005; ). Nitric oxide is involved in the Azospirillum brasilense-induced lateral root formation in tomato. Planta 221, 297–303.[CrossRef]
    [Google Scholar]
  17. Daugherty, P. S., Iverson, B. L. & Georgiou, G. ( 2000; ). Flow cytometric screening of cell-based libraries. J Immunol Methods 243, 211–227.[CrossRef]
    [Google Scholar]
  18. de Lorenzo, V. & Timmis, K. N. ( 1994; ). Analysis and construction of stable phenotypes in gram-negative bacteria with Tn5- and Tn10-derived minitransposons. Methods Enzymol 235, 386–405.
    [Google Scholar]
  19. de Zamaroczy, M., Delorme, F. & Elmerich, C. ( 1989; ). Regulation of transcription and promoter mapping of the structural genes for nitrogenase (nifHDK) of Azospirillum brasilense Sp7. Mol Gen Genet 220, 88–94.[CrossRef]
    [Google Scholar]
  20. Delledonne, M. ( 2005; ). NO news is good news for plants. Curr Opin Plant Biol 8, 390–396.[CrossRef]
    [Google Scholar]
  21. Dobbelaere, S., Croonenborghs, A., Thys, A., Vande Broek, A. & Vanderleyden, J. ( 1999; ). Phytostimulatory effect of Azospirillum brasilense wild type and mutant strains altered in IAA production on wheat. Plant Soil 212, 153–162.[CrossRef]
    [Google Scholar]
  22. Dobbelaere, S., Croonenborghs, A., Amber, T., Ptacek, D., Vanderleyden, J., Dutto, P., Labandera-Conzalez, C., Caballero-Mellado, J., Aguirre, J. F. & other authors ( 2001; ). Responses of agronomically important crops to inoculation with Azospirillum. Aust J Plant Physiol 28, 871–879.
    [Google Scholar]
  23. Dobbelaere, S., Croonenborghs, A., Thys, A., Ptacek, D., Okon, Y. & Vanderleyden, J. ( 2002; ). Effect of inoculation with wild type Azospirillum brasilense and A. irakense strains on development and nitrogen uptake of spring wheat and grain maize. Biol Fertil Soils 36, 284–297.[CrossRef]
    [Google Scholar]
  24. Dozois, C. M., Daigle, F. & Curtiss, R., III ( 2003; ). Identification of pathogen-specific and conserved genes expressed in vivo by an avian pathogenic Escherichia coli strain. Proc Natl Acad Sci U S A 100, 247–252.[CrossRef]
    [Google Scholar]
  25. El Zemrany, H., Cortet, J., Lutz, P. M., Chabert, A., Baudoin, E., Haurat, J., Maughan, N., Félix, D., Défago, G. & other authors ( 2006; ). Field survival of the phytostimulator Azospirillum lipoferum CRT1 and functional impact on maize crop, biodegradation of crop residues, and soil faunal indicators in a context of decreasing nitrogen fertilisation. Soil Biol Biochem 38, 1712–1726.[CrossRef]
    [Google Scholar]
  26. Fan, T. W., Lane, A. N., Shenker, M., Bartley, J. P., Crowley, D. & Higashi, R. M. ( 2001; ). Comprehensive chemical profiling of gramineous plant root exudates using high-resolution NMR and MS. Phytochemistry 57, 209–221.[CrossRef]
    [Google Scholar]
  27. Fedi, S., Montaini, P. & Favilli, F. ( 1992; ). Chemotactic response of Azospirillum toward root exudates of C3 and C4 plants. Symbiosis 13, 101–105.
    [Google Scholar]
  28. Ferrari, B. C., Oregaard, G. & Sørensen, S. J. ( 2004; ). Recovery of GFP-labeled bacteria for culturing and molecular analysis after cell sorting using a benchtop flow cytometer. Microb Ecol 48, 239–245.
    [Google Scholar]
  29. Figurski, D. H. & Helinski, D. R. ( 1979; ). Replication of an origin-containing derivative of plasmid RK2 dependent on a plasmid function provided in trans. Proc Natl Acad Sci U S A 76, 1648–1652.[CrossRef]
    [Google Scholar]
  30. Ghiglione, J.-F., Richaume, A., Philippot, L. & Lensi, R. ( 2002; ). Relative involvement of nitrate and nitrite reduction in the competitiveness of Pseudomonas fluorescens in the rhizosphere of maize under non-limiting nitrate conditions. FEMS Microbiol Ecol 39, 121–127.[CrossRef]
    [Google Scholar]
  31. Glick, B. R., Penrose, D. M. & Li, J. ( 1998; ). A model for the lowering of plant ethylene concentrations by plant growth-promoting bacteria. J Theor Biol 190, 63–68.[CrossRef]
    [Google Scholar]
  32. Guerreiro, N., Redmond, J. W., Rolfe, B. G. & Djordjevic, M. A. ( 1997; ). New Rhizobium leguminosarum flavonoid-induced proteins revealed by proteome analysis of differentially displayed proteins. Mol Plant Microbe Interact 10, 506–516.[CrossRef]
    [Google Scholar]
  33. Højberg, O., Schnider, U., Winteler, H. V., Sørensen, J. & Haas, D. ( 1999; ). Oxygen-sensing reporter strain of Pseudomonas fluorescens for monitoring the distribution of low-oxygen habitats in soil. Appl Environ Microbiol 65, 4085–4093.
    [Google Scholar]
  34. Ishikawa, J. & Hotta, K. ( 1999; ). FramePlot: a new implementation of the frame analysis for predicting protein-coding regions in bacterial DNA with a high G+C content. FEMS Microbiol Lett 174, 251–253.[CrossRef]
    [Google Scholar]
  35. Jacoud, C., Faure, D., Wadoux, P. & Bally, R. ( 1998; ). Development of a strain-specific probe to follow inoculated Azospirillum lipoferum CRT1 under field conditions and enhancement of maize root development by inoculation. FEMS Microbiol Ecol 27, 43–51.[CrossRef]
    [Google Scholar]
  36. Jacoud, C., Job, D., Wadoux, P. & Bally, R. ( 1999; ). Initiation of root growth stimulation by Azospirillum lipoferum CRT1 during maize seed germination. Can J Microbiol 45, 339–342.[CrossRef]
    [Google Scholar]
  37. Jofré, E., Rivalora, V., Balegno, H. & Mori, G. ( 1998; ). Differential gene expression in Azospirillum brasilense Cd under saline stress. Can J Microbiol 44, 929–936.[CrossRef]
    [Google Scholar]
  38. Kiliç, A. O., Herzberg, M. C., Meyer, M. W., Zhao, X. & Tao, L. ( 1999; ). Streptococcal reporter gene-fusion vector for identification of in vivo expressed genes. Plasmid 42, 67–72.[CrossRef]
    [Google Scholar]
  39. Lambrecht, M., Okon, Y., Vande Broek, A. & Vanderleyden, J. ( 2000; ). Indole-3-acetic acid: a reciprocal signalling molecule in bacteria-plant interactions. Trends Microbiol 8, 298–300.[CrossRef]
    [Google Scholar]
  40. Landa, B. B., Mavrodi, O. V., Raaijmakers, J. M., McSpadden Gardener, B. B., Thomashow, L. S. & Weller, D. M. ( 2002; ). Differential ability of genotypes of 2,4-diacetylphloroglucinol-producing Pseudomonas fluorescens strains to colonize the roots of pea plants. Appl Environ Microbiol 68, 3226–3237.[CrossRef]
    [Google Scholar]
  41. Mark, G. L., Dow, J. M., Kiely, P. D., Higgins, H., Haynes, J., Baysse, C., Abbas, A., Foley, T., Franks, A. & other authors ( 2005; ). Transcriptome profiling of bacterial responses to root exudates identifies genes involved in microbe-plant interactions. Proc Natl Acad Sci U S A 102, 17454–17459.[CrossRef]
    [Google Scholar]
  42. Martin-Didonet, C. C., Chubatsu, L. S., Souza, E. M., Kleina, M., Rego, F. G., Rigo, L. U., Yates, M. G. & Pedrosa, F. O. ( 2000; ). Genome structure of the genus Azospirillum. J Bacteriol 182, 4113–4116.[CrossRef]
    [Google Scholar]
  43. McClelland, M., Mathieu-Daude, F. & Welsh, J. ( 1995; ). RNA fingerprinting and differential display using arbitrarily primed PCR. Trends Genet 11, 242–246.[CrossRef]
    [Google Scholar]
  44. Miché, L. & Balandreau, J. ( 2001; ). Effects of rice seed surface sterilization with hypochlorite on inoculated Burkholderia vietnamiensis. Appl Environ Microbiol 67, 3046–3052.[CrossRef]
    [Google Scholar]
  45. Mirza, M. S., Mehnaz, S., Normand, P., Prigent-Combaret, C., Moënne-Loccoz, Y., Bally, R. & Kauser, A. M. ( 2006; ). Molecular characterization and PCR detection of a nitrogen-fixing Pseudomonas strain promoting rice growth. Biol Fertil Soils 43, 163–170.[CrossRef]
    [Google Scholar]
  46. Neuer, G., Kronenberg, A. & Bothe, H. ( 1985; ). Denitrification and nitrogen fixation by Azospirillum. III. Properties of a wheat–Azospirillum association. Arch Microbiol 141, 364–370.[CrossRef]
    [Google Scholar]
  47. Okon, Y. & Kapulnik, Y. ( 1986; ). Development and function of Azospirillum-inoculated roots. Plant Soil 90, 3–16.[CrossRef]
    [Google Scholar]
  48. Okon, Y. & Labandera-Gonzalez, C. A. ( 1994; ). Agronomic applications of Azospirillum: an evaluation of 20 years worldwide field inoculation. Soil Biol Biochem 26, 1591–1601.[CrossRef]
    [Google Scholar]
  49. Rainey, P. B. ( 1999; ). Adaptation of Pseudomonas fluorescens to the plant rhizosphere. Environ Microbiol 1, 243–257.[CrossRef]
    [Google Scholar]
  50. Ramos, H. J., Roncato-Maccari, L. D., Souza, E. M., Soares-Ramos, J. R., Hungria, M. & Pedrosa, F. O. ( 2002; ). Monitoring Azospirillum–wheat interactions using the gfp and gusA genes constitutively expressed from a new broad-host range vector. J Biotechnol 97, 243–252.[CrossRef]
    [Google Scholar]
  51. Rediers, H., Rainey, P. B., Vanderleyden, J. & De Mot, R. ( 2005; ). Unraveling the secret lives of bacteria: use of in vivo expression technology and differential fluorescence induction promoter traps as tools for exploring niche-specific gene expression. Microbiol Mol Biol Rev 69, 217–261.[CrossRef]
    [Google Scholar]
  52. Reinhold, B., Hurek, T. & Fendrik, I. ( 1985; ). Strain-specific chemotaxis of Azospirillum spp. J Bacteriol 162, 190–195.
    [Google Scholar]
  53. Rezzonico, F., Zala, M., Keel, C., Duffy, B., Moënne-Loccoz, Y. & Défago, G. ( 2007; ). Is the ability of biocontrol fluorescent pseudomonads to produce the antifungal metabolite 2,4-diacetylphloroglucinol really synonymous with higher plant protection? New Phytol 173, 861–872.[CrossRef]
    [Google Scholar]
  54. Sambrook, J., Fritsch, E. F. & Maniatis, T. ( 1989; ). Molecular Cloning: a Laboratory Manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
  55. Silby, M. W. & Levy, S. B. ( 2004; ). Use of in vivo expression technology to identify genes important in growth and survival of Pseudomonas fluorescens Pf0-1 in soil: discovery of expressed sequences with novel genetic organization. J Bacteriol 186, 7411–7419.[CrossRef]
    [Google Scholar]
  56. Silby, M. W., Rainey, P. B. & Levy, S. B. ( 2004; ). IVET experiments in Pseudomonas fluorescens reveal cryptic promoters at loci associated with recognizable overlapping genes. Microbiology 150, 518–520.[CrossRef]
    [Google Scholar]
  57. Steenhoudt, O. & Vanderleyden, J. ( 2000; ). Azospirillum, a free-living nitrogen-fixing bacterium closely associated with grasses: genetic, biochemical and ecological aspects. FEMS Microbiol Rev 24, 487–506.[CrossRef]
    [Google Scholar]
  58. Tang, X., Lu, B. F. & Pan, S. Q. ( 1999; ). A bifunctional transposon mini-Tn5gfp-km which can be used to select for promoter fusions and report gene expression levels in Agrobacterium tumefaciens. FEMS Microbiol Lett 179, 37–42.[CrossRef]
    [Google Scholar]
  59. Valverde, A., Okon, Y. & Burdman, S. ( 2006; ). cDNA-AFLP reveals differentially expressed genes related to cell aggregation of Azospirillum brasilense. FEMS Microbiol Lett 265, 186–194.[CrossRef]
    [Google Scholar]
  60. Van Bastelaere, E., De Mot, R., Michiels, K. & Vanderleyden, J. ( 1993; ). Differential gene expression in Azospirillum spp. by plant root exudates: analysis of protein profiles by two-dimensional polyacrylamide gel electrophoresis. FEMS Microbiol Lett 112, 335–342.[CrossRef]
    [Google Scholar]
  61. Vancura, V. & Hanzlikova, A. ( 1972; ). Root exudates of plants. IV. Differences in chemical composition of seed and seedlings exudates. Plant Soil 36, 271–282.[CrossRef]
    [Google Scholar]
  62. Vande Broek, A., Lambrecht, M. & Vanderleyden, J. ( 1998; ). Bacterial chemotactic motility is important for the initiation of wheat root colonization by Azospirillum brasilense. Microbiology 144, 2599–2606.[CrossRef]
    [Google Scholar]
  63. Velasco, L., Mesa, S., Delgado, M. J. & Bedmar, E. J. ( 2001; ). Characterization of the nirK gene encoding the respiratory, Cu-containing nitrite reductase of Bradyrhizobium japonicum. Biochim Biophys Acta 1521, 130–134.[CrossRef]
    [Google Scholar]
  64. Vial, L., Pothier, J. F., Normand, P., Moënne-Loccoz, Y., Bally, R. & Wisniewski-Dyé, F. ( 2004; ). Construction of a recA mutant of Azospirillum lipoferum and involvement of recA in phase variation. FEMS Microbiol Lett 236, 291–299.
    [Google Scholar]
  65. Wang, J., Li, C., Yang, H., Mushegian, A. & Jin, S. ( 1998; ). A novel serine/threonine protein kinase homologue of Pseudomonas aeruginosa is specifically inducible within the host infection site and is required for full virulence in neutropenic mice. J Bacteriol 180, 6764–6768.
    [Google Scholar]
  66. Zhang, X. X., George, A., Bailey, M. J. & Rainey, P. B. ( 2006; ). The histidine utilization (hut) genes of Pseudomonas fluorescens SBW25 are active on plant surfaces, but are not required for competitive colonization of sugar beet seedlings. Microbiology 152, 1867–1875.[CrossRef]
    [Google Scholar]
  67. Zhu, G.-Y., Dobbelaere, S. & Vanderleyden, J. ( 2002; ). Use of green fluorescent protein to visualize rice root colonization by Azospirillum irakense and A. brasilense. Funct Plant Biol 29, 1279–1285.[CrossRef]
    [Google Scholar]
  68. Zumft, W. G. ( 2002; ). Nitric oxide signaling and NO dependent transcriptional control in bacterial denitrification by members of the FNR-CRP regulator family. J Mol Microbiol Biotechnol 4, 277–286.
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.2007/009381-0
Loading
/content/journal/micro/10.1099/mic.0.2007/009381-0
Loading

Data & Media loading...

Supplements

vol. , part 10, pp. 3608 - 3622

Spring wheat seed extract-inducible cryptic fusions identified by DFI in A. brasilense Sp245 [ PDF] (19 kb)



PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error