1887

Microbiology

Volume 150, Issue 3

Characterization of a new internal promoter (P) for hydrogenase accessory genes Free

Abstract

Synthesis of the [NiFe] hydrogenase requires the participation of 16 accessory genes () besides the genes encoding the structural proteins (). Transcription of is controlled by a −24/−12-type promoter (P), located upstream of and regulated by NifA. In this work, a second −24/−12-type promoter (P), located upstream of the gene and transcribing genes in pea ( L.) bacteroids, has been identified in the gene cluster. Promoter P was also active in free-living cells, as evidenced by genetic complementation of hydrogenase mutants. Both NifA and NtrC activated P expression in the heterologous host . Also, P activity was highly stimulated by NifA in . This NifA activation of P expression only required the -binding site, and it was independent of any -acting element upstream of the box, which suggests a direct interaction of free NifA with the RNA polymerase holoenzyme. P-dependent expression in pea nodules started in interzone II/III, spanned through nitrogen-fixing zone III, and was coincident with the NifA-dependent expression pattern. However, P was dispensable for transcription and hydrogenase activity in pea bacteroids due to transcription initiated at P. This fact and the lack of an activator recruitment system suggest that P plays a secondary role in symbiotic expression.

  • Received:
  • Accepted:
  • Revised:
  • Published Online:
Keyword(s): IHF, integration host factor and UAS, upstream activating sequence
© SGM
Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.26623-0
2004-03-01
2019-11-12
Loading full text...

Full text loading...

/deliver/fulltext/micro/150/3/mic1500665.html?itemId=/content/journal/micro/10.1099/mic.0.26623-0&mimeType=html&fmt=ahah

References

  1. Beringer, J. E. ( 1974; ). R factor transfer in Rhizobium leguminosarum. J Gen Microbiol 84, 188–198.[CrossRef]
    [Google Scholar]
  2. Bernhard, M., Schwartz, E., Rietdorf, J. & Friedrich, B. ( 1996; ). The Alcaligenes eutrophus membrane-bound hydrogenase gene locus encodes functions involved in maturation and electron transport coupling. J Bacteriol 178, 4522–4529.
     [Google Scholar]
  3. Bernhard, M., Buhrke, T., Bleijlevens, B., De Lacey, A. L., Fernández, V. M., Albracht, S. P. & Friedrich, B. ( 2001; ). The H2 sensor of Ralstonia eutropha. Biochemical characteristics, spectroscopic properties, and its interaction with a histidine protein kinase. J Biol Chem 276, 15592–15597.[CrossRef]
    [Google Scholar]
  4. Better, M., Ditta, G. & Helinski, D. ( 1985; ). Deletion analysis of Rhizobium meliloti symbiotic promoters. EMBO J 4, 2419–2424.
     [Google Scholar]
  5. Black, L. K., Fu, C. & Maier, J. R. ( 1994; ). Sequence and characterization of hupU and hupV genes of Bradyrhizobium japonicum encoding a possible nickel-sensing complex involved in hydrogenase expression. J Bacteriol 176, 7102–7106.
     [Google Scholar]
  6. Brito, B., Palacios, J. M., Hidalgo, E., Imperial, J. & Ruiz-Argüeso, T. ( 1994; ). Nickel availability to pea (Pisum sativum L.) plants limits hydrogenase activity of Rhizobium leguminosarum bv. viciae bacteroids by affecting the processing of the hydrogenase structural subunits. J Bacteriol 176, 5297–5303.
     [Google Scholar]
  7. Brito, B., Palacios, J. M., Imperial, J. & 8 other authors ( 1995; ). Temporal and spatial co-expression of hydrogenase and nitrogenase genes from Rhizobium leguminosarum bv. viciae in pea (Pisum sativum L.) root nodules. Mol Plant–Microbe Interact 8, 235–240.[CrossRef]
    [Google Scholar]
  8. Brito, B., Martínez, M., Fernández, D., Rey, L., Cabrera, E., Palacios, J. M., Imperial, J. & Ruiz-Argüeso, T. ( 1997; ). Hydrogenase genes from Rhizobium leguminosarum bv. viciae are controlled by the nitrogen fixation regulatory protein NifA. Proc Natl Acad Sci U S A 94, 6019–6024.[CrossRef]
    [Google Scholar]
  9. Brito, B., Palacios, J. M., Imperial, J. & Ruiz-Argüeso, T. ( 2002; ). Engineering the Rhizobium leguminosarum bv. viciae hydrogenase system for expression in free-living microaerobic cells and increased symbiotic hydrogenase activity. Appl Environ Microbiol 68, 2461–2467.[CrossRef]
    [Google Scholar]
  10. Casalot, L. & Rousset, M. ( 2001; ). Maturation of the [NiFe] hydrogenases. Trends Microbiol 9, 228–237.[CrossRef]
    [Google Scholar]
  11. Chiurazzi, M. & Iaccarino, M. ( 1990; ). Transcriptional analysis of the glnB-glnA region of Rhizobium leguminosarum biovar viciae. Mol Microbiol 4, 1727–1735.[CrossRef]
    [Google Scholar]
  12. Colombo, M. V., Gutiérrez, D., Palacios, J. M., Imperial, J. & Ruiz-Argüeso, T. ( 2000; ). A novel autoregulation mechanism of fnrN expression in Rhizobium leguminosarum bv. viciae. Mol Microbiol 36, 477–486.[CrossRef]
    [Google Scholar]
  13. Drummond, M., Clements, J., Merrick, M. & Dixon, R. ( 1983; ). Positive control and autogenous regulation of the nifLA promoter in Klebsiella pneumoniae. Nature 301, 302–307.[CrossRef]
    [Google Scholar]
  14. Durmowicz, M. C. & Maier, R. J. ( 1998; ). The FixK2 protein is involved in regulation of symbiotic hydrogenase expression in Bradyrhizobium japonicum. J Bacteriol 180, 3253–3256.
     [Google Scholar]
  15. Elsen, S., Colbeau, A., Chabert, J. & Vignais, P. M. ( 1996; ). The hupTUV operon is involved in negative control of hydrogenase synthesis in Rhodobacter capsulatus. J Bacteriol 178, 5174–5181.
     [Google Scholar]
  16. Friedrich, B. & Schwartz, E. ( 1993; ). Molecular biology of hydrogen utilization in aerobic chemolithotrophs. Annu Rev Microbiol 47, 351–383.[CrossRef]
    [Google Scholar]
  17. Fu, C. & Maier, R. J. ( 1994; ). Organization of the hydrogenase gene cluster from Bradyrhizobium japonicum: sequences and analysis of five more hydrogenase-related genes. Gene 145, 91–96.[CrossRef]
    [Google Scholar]
  18. Gutiérrez, D., Hernando, Y., Palacios, J. M., Imperial, J. & Ruiz-Argüeso, T. ( 1997; ). FnrN controls symbiotic nitrogen fixation and hydrogenase activities in Rhizobium leguminosarum bv. viciae UPM791. J Bacteriol 179, 5264–5270.
     [Google Scholar]
  19. Hernando, Y., Palacios, J. M., Imperial, J. & Ruiz-Argüeso, T. ( 1995; ). The hypBFCDE operon from Rhizobium leguminosarum biovar viciae is expressed from an Fnr-type promoter that escapes mutagenesis of the fnrN gene. J Bacteriol 177, 5661–5669.
     [Google Scholar]
  20. Hidalgo, E., Palacios, J. M., Murillo, J. & Ruiz-Argüeso, T. ( 1992; ). Nucleotide sequence and characterization of four additional genes of the hydrogenase structural operon from Rhizobium leguminosarum bv. viciae. J Bacteriol 174, 4130–4139.
     [Google Scholar]
  21. Imperial, J., Ugalde, R. A., Shah, V. K. & Brill, W. J. ( 1984; ). Role of the nifQ gene product in the incorporation of molybdenum into nitrogenase in Klebsiella pneumoniae. J Bacteriol 158, 187–194.
     [Google Scholar]
  22. Kennedy, C. ( 1977; ). Linkage map of the nitrogen fixation (nif) genes in Klebsiella pneumoniae. Mol Gen Genet 157, 199–204.[CrossRef]
    [Google Scholar]
  23. Leyva, A., Palacios, J. M., Mozo, T. & Ruiz-Argüeso, T. ( 1987; ). Cloning and characterization of hydrogen uptake genes from Rhizobium leguminosarum. J Bacteriol 169, 4929–4934.
     [Google Scholar]
  24. Leyva, A., Palacios, J. M., Murillo, J. & Ruiz-Argüeso, T. ( 1990; ). Genetic organization of the hydrogen uptake (hup) cluster from Rhizobium leguminosarum. J Bacteriol 172, 1647–1655.
     [Google Scholar]
  25. MacNeil, T., Roberts, G. P., MacNeil, D. & Tyler, B. ( 1982; ). The products of glnL and glnG are bifunctional regulatory proteins. Mol Gen Genet 188, 325–333.[CrossRef]
    [Google Scholar]
  26. Menon, N. K., Robbins, J., Wendt, J. C., Shanmugam, K. T. & Przybyla, A. E. ( 1991; ). Mutational analysis and characterization of the Escherichia coli hya operon, which encodes [NiFe] hydrogenase 1. J Bacteriol 173, 4851–4861.
     [Google Scholar]
  27. Miller, J. H. ( 1972; ). Experiments in Molecular Genetics. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
  28. Molina-López, J. A., Govantes, F. & Santero, E. ( 1994; ). Geometry of the process of activation at the σ 54-dependent nifH promoter of Klebsiella pneumoniae. J Biol Chem 269, 25419–25425.
     [Google Scholar]
  29. Morett, E. & Buck, M. ( 1988; ). NifA-dependent in vivo protection demonstrates that the upstream activator sequence of nif promoters is a protein binding site. Proc Natl Acad Sci U S A 85, 9401–9405.[CrossRef]
    [Google Scholar]
  30. Morett, E. & Segovia, L. ( 1993; ). The σ 54 bacterial enhancer-binding protein family: mechanism of activation and phylogenetic relationship of their functional domains. J Bacteriol 175, 6067–6074.
     [Google Scholar]
  31. O'Gara, F. & Shanmugam, K. T. ( 1976; ). Regulation of nitrogen fixation by rhizobia: export of fixed N2 as . Biochem Biophys Acta 437, 313–321.[CrossRef]
    [Google Scholar]
  32. Parry, S. K., Sharma, S. B. & Terzaghi, E. A. ( 1994; ). Construction of a bidirectional promoter probe vector and its use in analysing nod gene expression in Rhizobium loti. Gene 150, 105–109.[CrossRef]
    [Google Scholar]
  33. Pérez-Martín, J. & de Lorenzo, V. ( 1995; ). Integration host factor suppresses promiscuous activation of the σ 54-dependent promoter Pu of Pseudomonas putida. Proc Natl Acad Sci U S A 92, 7277–7281.[CrossRef]
    [Google Scholar]
  34. Rey, L., Hidalgo, E., Palacios, J. & Ruiz-Argüeso, T. ( 1992; ). Nucleotide sequence and organization of an H2-uptake gene cluster from Rhizobium leguminosarum bv. viciae containing a rubredoxin-like gene and four additional open reading frames. J Mol Biol 228, 998–1002.[CrossRef]
    [Google Scholar]
  35. Ruiz-Argüeso, T., Hanus, F. J. & Evans, H. J. ( 1978; ). Hydrogen production and uptake by pea nodules as affected by strains of Rhizobium leguminosarum. Arch Microbiol 116, 113–118.[CrossRef]
    [Google Scholar]
  36. Ruiz-Argüeso, T., Palacios, J. M. & Imperial, J. ( 2001; ). Regulation of the hydrogenase system in Rhizobium leguminosarum. Plant Soil 230, 49–57.[CrossRef]
    [Google Scholar]
  37. Sambrook, J., Fritsch, E. F. & Maniatis, T. ( 1989; ). Molecular Cloning: a Laboratory Manual. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
  38. Schäfer, A., Tauch, A., Jäger, W., Kalinowski, J., Thierbach, G. & Pühler, A. ( 1994; ). Small mobilizable multi-purpose cloning vectors derived from the Escherichia coli plasmids pK18 and pK19: selection of defined deletions in the chromosome of Corynebacterium glutamicum. Gene 145, 69–73.[CrossRef]
    [Google Scholar]
  39. Schwartz, E., Buhrke, T., Gerischer, U. & Friedrich, B. ( 1999; ). Positive transcriptional feedback controls hydrogenase expression in Alcaligenes eutrophus H16. J Bacteriol 181, 5684–5692.
     [Google Scholar]
  40. Simon, R., Priefer, U. & Pühler, A. ( 1983; ). A broad host range mobilization system for in vivo genetic engineering: transposon mutagenesis in Gram-negative bacteria. Bio/Technology 1, 784–791.[CrossRef]
    [Google Scholar]
  41. Smith, P. K., Krohn, R. I., Hermanson, G. T. & 7 other authors ( 1985; ). Measurement of protein using bicinchoninic acid. Anal Biochem 150, 76–85.[CrossRef]
    [Google Scholar]
  42. Soupène, E., Foussard, M., Boistard, P., Truchet, G. & Batut, J. ( 1995; ). Oxygen as a key developmental regulator of Rhizobium meliloti N2-fixation gene expression within the alfalfa root nodule. Proc Natl Acad Sci U S A 92, 3759–3763.[CrossRef]
    [Google Scholar]
  43. Spaink, H. P., Okker, R. J. H., Wijffelman, C. A., Peers, E. & Lugtenberg, B. J. J. ( 1987; ). Promoters in the nodulation region of Rhizobium leguminosarum Sym plasmid pRL1JI. Plant Mol Biol 9, 27–39.[CrossRef]
    [Google Scholar]
  44. Summers, W. C. ( 1970; ). A simple method for extraction of RNA from E. coli utilizing diethyl pyrocarbonate. Anal Biochem 33, 459–463.
     [Google Scholar]
  45. Szeto, W. W., Nixon, B. T., Ronson, C. W. & Ausubel, F. M. ( 1987; ). Identification and characterization of the Rhizobium meliloti ntrC gene: R. meliloti has separate regulatory pathways for activation of nitrogen fixation genes in free-living and symbiotic cells. J Bacteriol 169, 1423–1432.
     [Google Scholar]
  46. Van de Wiel, C., Scheres, B., Frassen, H., van Lierop, M. J., van Lammeren, A., van Kammen, A. & Bisseling, T. ( 1990; ). The early nodulin transcript ENOD2 is located in the nodule parenchyma (inner cortex) of pea and soybean root nodules. EMBO J 9, 1–7.
     [Google Scholar]
  47. Van Soom, C., Browaeys, J., Verreth, C. & Vanderleyden, J. ( 1993a; ). Nucleotide sequence analysis of four genes, hupC, hupD, hupF and hupG, downstream of the hydrogenase structural genes in Bradyrhizobium japonicum. J Mol Biol 234, 508–512.[CrossRef]
    [Google Scholar]
  48. Van Soom, C., Verreth, C., Sampaio, M. J. & Vanderleyden, J. ( 1993b; ). Identification of a potential transcriptional regulator of hydrogenase activity in free-living Bradyrhizobium japonicum strains. Mol Gen Genet 239, 235–240.[CrossRef]
    [Google Scholar]
  49. Van Soom, C., Lerouge, I., Vanderleyden, J., Ruiz-Argüeso, T. & Palacios, J. M. ( 1999; ). Identification and characterization of hupT, a gene involved in negative regulation of hydrogen oxidation in Bradyrhizobium japonicum. J Bacteriol 181, 5085–5089.
     [Google Scholar]
  50. Vasse, J., de Billy, F., Camut, S. & Truchet, G. ( 1990; ). Correlation between ultrastructural differentiation of bacteroids and nitrogen fixation in alfalfa nodules. J Bacteriol 172, 4295–4306.
     [Google Scholar]
  51. Vignais, P. M., Billoud, B. & Meyer, J. ( 2001; ). Classification and phylogeny of hydrogenases. FEMS Microbiol Rev 25, 455–501.[CrossRef]
    [Google Scholar]
  52. Vincent, J. M. ( 1970; ). A Manual for the Practical Study of the Root-nodule Bacteria. Oxford: Blackwell Scientific Publications.
  53. Yang, W. C., Horvath, B., Hontelez, J., van Kammen, A. & Bisseling, T. ( 1991; ). In situ localization of Rhizobium mRNAs in pea nodules: nifA and nifH localization. Mol Plant–Microbe Interact 4, 464–468.[CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.26623-0
Loading
Characterization of a new internal promoter (P3) for Rhizobium leguminosarum hydrogenase accessory genes hupGHIJ
Microbiology 150, 665 (2004); https://doi.org/10.1099/mic.0.26623-0
/content/journal/micro/10.1099/mic.0.26623-0
/content/journal/micro/10.1099/mic.0.26623-0
Loading

Data & Media loading...

Most Cited This Month

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