1887

Microbiology Society logo

Volume 150, Issue 6

Characterization of genes responsive to nutrient limitation Free

Abstract

The low bioavailability of nutrients and oxygen in the soil environment has hampered successful expression of biodegradation and biocontrol genes that are driven by promoters highly active during routine laboratory conditions of high availability of nutrients and oxygen. Hence, in the present study, expression of the -tagged genes in 12 Tn mutants of the soil microbe PNL-MK25 were examined under various conditions chosen to mimic the soil environment: low carbon, phosphate, nitrate or oxygen, and in the rhizosphere. Based on their expression profiles, three nutrient-responsive mutant (NRM) strains, NRM5, NRM7 and NRM17, were selected for identification of the tagged genes. In strain NRM5, expression of the glutamate dehydrogenase () gene was increased 4·9–26·4-fold under various low-nutrient conditions. In NRM7, expression of the novel NADPH : quinone oxidoreductase-like () gene was consistently amongst the highest and was synergistically upregulated by low-nutrient and anoxic conditions. The gene in NRM17, which encodes the fourth subunit of the cytochrome ubiquinol oxidase complex, had decreased expression in low-nutrient conditions but its absolute expression level was still amongst the highest. Additionally, it was independent of oxygen availability, in contrast to that in .

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): ADH, alcohol dehydrogenase , CCR, carbon catabolite repression , GUS, β-glucuronidase , NRM, nutrient-responsive mutant , QOR, quinone oxidoreductase and RE, root exudate
SGM
Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.26657-0
2004-06-01
2024-04-20
Loading full text...

Full text loading...

/deliver/fulltext/micro/150/6/mic1501661.html?itemId=/content/journal/micro/10.1099/mic.0.26657-0&mimeType=html&fmt=ahah

References

  1. 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]
  2. Atlas R. M. 1991; Bioremediation of fossil fuel contaminated soils. In In Situ Bioreclamation: Applications and Investigations for Hydrocarbon and Contaminated Site Remediation pp. 14–32 Edited by Hinchee R. E., Olfenbuttel E. F. Boston, MA: Butterworth-Heinemann;
     [Google Scholar]
  3. Brenchley J. E., Baker C. A., Patil L. G. 1975; Regulation of the ammonia assimilatory enzymes in Salmonella typhimurium. J Bacteriol 124:182–189
     [Google Scholar]
  4. Cases I., de Lorenzo V. 1998; Expression systems and physiological control of promoter activity in bacteria. Curr Opin Microbiol 1:303–310 [CrossRef]
     [Google Scholar]
  5. Chepuri V., Gennis R. B. 1990; The use of gene fusions to determine the topology of all of the subunits of the cytochrome o terminal oxidase complex of Escherichia coli. J Biol Chem 265:12978–12986
     [Google Scholar]
  6. Chepuri V., Lemieux L., Au D. C. T., Gennis R. B. 1990; The sequence of the cyo operon indicates substantial structural similarities between the cytochrome o ubiquinol oxidase of Escherichia coli and the aa3-type family of cytochrome c oxidases. J Biol Chem 265:11185–11192
     [Google Scholar]
  7. Dashman T., Stotzky G. 1986; Microbial utilization of amino acids and a peptide bound on homoionic montmorillonite and kaolinite. Soil Biol Biochem 18:5–14 [CrossRef]
     [Google Scholar]
  8. Diaz E., Prieto M. A. 2000; Bacterial promoters triggering biodegradation of aromatic pollutants. Curr Opin Biotechnol 11:467–475 [CrossRef]
     [Google Scholar]
  9. Dowling D. N., O'Gara F. 1994; Metabolites of Pseudomonas involved in the biocontrol of plant disease. Trends Biotechnol 12:133–140 [CrossRef]
     [Google Scholar]
  10. Duetz W. A., Wind B., Kamp M., van Andel J. G. 1997; Effect of growth rate, nutrient limitation and succinate on expression of TOL pathway enzymes in response to m-xylene in chemostat cultures of Pseudomonas putida (pWWO). Microbiology 143:2331–2338 [CrossRef]
     [Google Scholar]
  11. Edwards K. J., Barton J. D., Rossjohn J., Thorn J. M., Taylor G. L., Ollis D. L. 1996; Structural and sequence comparisons of quinone oxidoreductase, zeta-crystallin, and glucose and alcohol dehydrogenases. Arch Biochem Biophys 328:173–183 [CrossRef]
     [Google Scholar]
  12. Ertan H. 1992; The effect of various culture conditions on the levels of ammonia assimilatory enzymes of Corynebacterium callunae. Arch Microbiol 158:42–47 [CrossRef]
     [Google Scholar]
  13. Ferenci T. 1999; Regulation by nutrient limitation. Curr Opin Microbiol 2:208–213 [CrossRef]
     [Google Scholar]
  14. Gallagher S. R. 1992 GUS Protocols: Using the gus Gene as a Reporter of Gene Expression San Diego, CA: Academic Press;
  15. Gonzalez P., Rao P. V., Zigler Jr J. S. 1993; Molecular cloning and sequencing of zeta-crystallin/quinone reductase cDNA from human liver. Biochem Biophys Res Commun 191:902–907 [CrossRef]
     [Google Scholar]
  16. Greenland D. J. 1971; Interactions between humic and fulvic acids and clays. Soil Science 111:34–41 [CrossRef]
     [Google Scholar]
  17. Hartline R. A., Gunsalus I. C. 1971; Induction specificity and catabolite repression of the early enzymes in camphor degradation by Pseudomonas putida. J Bacteriol 106:468–478
     [Google Scholar]
  18. Helling R. B. 1994; Why does Escherichia coli have two primary pathways for synthesis of glutamate?. Microbiology 176:4664–4668
     [Google Scholar]
  19. Hirayama H., Takami H., Inoue A., Horikoshi K. 1998; Isolation and characterization of toluene-sensitive mutants from Pseudomonas putida IH-2000. FEMS Microbiol Lett 169:219–225 [CrossRef]
     [Google Scholar]
  20. Hojberg O., Schnider U., Winteler H. V., Sorensen 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]
  21. Jensen L. E., Nybroe O. 1999; Nitrogen availability to Pseudomonas fluorescens DF57 is limited during decomposition of barley straw in bulk soil and in the barley rhizosphere. Appl Environ Microbiol 65:4320–4328
     [Google Scholar]
  22. Jornvall H., Persson B., Jeffrey J. 1987; Characteristics of alcohol/polyol dehydrogenases. The zinc-containing long-chain alcohol dehydrogenases. Eur J Biochem 167:195–201 [CrossRef]
     [Google Scholar]
  23. Kohler T., Epp S. F., Curty L. K., Pechere J. C. 1999; Characterization of MexT, the regulator of the MexE-MexF-OprN multidrug efflux system of Pseudomonas aeruginosa. J Bacteriol 181:6300–6305
     [Google Scholar]
  24. Kozlowski T. T., Kramer P. J., Pallardy S. G. 1991 The Physiological Ecology of Woody Plants San Diego: Academic Press;
  25. Kragelund L., Hosbond C., Nybroe O. 1997; Distribution of metabolic activity and phosphate starvation response of lux-tagged Pseudomonas fluorescens reporter bacteria in the barley rhizosphere. Appl Environ Microbiol 63:4920–4928
     [Google Scholar]
  26. Kranz R. G., Gennis R. B. 1983; Immunological characterization of the cytochrome o terminal oxidase from Escherichia coli. J Biol Chem 258:10614–10621
     [Google Scholar]
  27. Kyte J., Doolittle R. F. 1982; A simple method for displaying the hydropathic character of a protein. J Mol Biol 157:105–132 [CrossRef]
     [Google Scholar]
  28. Leahy J. G., Colwell R. R. 1990; Microbial degradation of hydrocarbons in the environment. Microbiol Rev 54:305–315
     [Google Scholar]
  29. Lin E. C. C., Iuchi S. 1991; Regulation of gene expression in fermentative and respiratory systems in Escherichia coli and related bacteria. Annu Rev Genet 25:361–387 [CrossRef]
     [Google Scholar]
  30. Liu X., Taber H. W. 1998; Catabolite regulation of the Bacillus subtilis ctaBCDEF gene cluster. J Bacteriol 180:6154–6163
     [Google Scholar]
  31. Marschner P., Crowley D. E. 1996a; Physiological activity of a bioluminescent Pseudomonas fluorescens (strain 2-79) in the rhizosphere of mycorrhizal and non-mycorrhizal pepper (Capsicum annuum L. Soil Biol Biochem 28:869–876 [CrossRef]
     [Google Scholar]
  32. Marschner P., Crowley D. E. 1996b; Root colonization of mycorrhizal and non-mycorrhizal pepper (Capsicum annuum) byPseudomonas fluorescens 2-79RL. New Phytol 134:115–122 [CrossRef]
     [Google Scholar]
  33. Meikle A., Amin-Hanjani S., Glover A., Killham K., Prosser J. I. 1995; Matric potential and the survival and activity of a Pseudomonas fluorescens inoculum in soil. Soil Biol Biochem 27:881–892 [CrossRef]
     [Google Scholar]
  34. Minagawa J., Nakamura H., Yamato I., Mogi T., Anraku Y. 1990; Transcriptional regulation of the cytochrome b562-o complex in Escherichia coli: gene expression and molecular characterization of the promoter. J Biol Chem 265:11198–11203
     [Google Scholar]
  35. Normander B., Hendriksen N. B., Nybroe O. 1999; Green fluorescent protein-marked Pseudomonas fluorescens: localization, viability, and activity in the natural barley rhizosphere. Appl Environ Microbiol 65:4646–4651
     [Google Scholar]
  36. O'Connor K., Duetz W., Wind B., Dobson A. D. 1996; The effect of nutrient limitation on styrene metabolism in Pseudomonas putida CA-3. Appl Environ Microbiol 62:3594–3599
     [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. Sawers R. G. 1991; Identification and molecular characterization of a transcriptional regulator from Pseudomonas aeruginosa PAO1 exhibiting structural and functional similarity to the FNR protein of Escherichia coli. Mol Microbiol 5:1469–1481 [CrossRef]
     [Google Scholar]
  39. Schell M. A. 1993; Molecular biology of the LysR family of transcriptional regulators. Annu Rev Microbiol 47:597–626 [CrossRef]
     [Google Scholar]
  40. Sharma S. B., Signer E. R. 1990; Temporal and spatial regulation of the symbiotic genes of Rhizobium meliloti in planta revealed by transposon Tn5-gusA. Genes Dev 4:344–356 [CrossRef]
     [Google Scholar]
  41. Spiro S., Guest J. R. 1991; Adaptive responses to oxygen limitation in Escherichia coli. Trends Biochem Sci 16:310–314 [CrossRef]
     [Google Scholar]
  42. Stanier R. Y., Palleroni N. J., Doudoroff M. 1966; The aerobic pseudomonads: a taxonomic study. J Gen Microbiol 43:159–271 [CrossRef]
     [Google Scholar]
  43. Stretton S., Goodman A. E. 1998; Carbon dioxide as a regulator of gene expression in microorganisms. Antonie van Leeuwenhoek 73:79–85 [CrossRef]
     [Google Scholar]
  44. Syn C. K. C., Swarup S. 2000; A scalable protocol for the isolation of large-sized genomic DNA within an hour from several bacteria. Anal Biochem 278:86–90 [CrossRef]
     [Google Scholar]
  45. Tao H., Bausch C., Richmond C., Blattner F. R., Conway T. 1999; Functional genomics: expression analysis of Escherichia coli growing on minimal and rich media. J Bacteriol 181:6425–6440
     [Google Scholar]
  46. Thompson J. D., Higgins D. G., Gibson T. J. 1994; Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680 [CrossRef]
     [Google Scholar]
  47. Timmis K. N., Pieper D. H. 1999; Bacteria designed for bioremediation. Trends Biotechnol 17:200–204
     [Google Scholar]
  48. Vande Broek A., Michiels J., Vanderleyden J., van Gool A. 1993; Spatial-temporal colonization patterns of Azospirillum brasilense on the wheat root surface and expression of bacterial nifH gene during association. Mol Plant–Microbe Interact 6:592–600 [CrossRef]
     [Google Scholar]
  49. van Overbeek L. S., van Elsas J. D. 1995; Root exudates-induced promoter activity in Pseudomonas fluorescens mutants in the wheat rhizosphere. Appl Environ Microbiol 61:890–898
     [Google Scholar]
  50. van Overbeek L. S., van Elsas J. D. 1997; Adaptation of bacteria to soil conditions: applications of molecular physiology in soil microbiology. In Modern Soil Microbiology pp. 441–477 Edited by Wellington E. M. H., Trevors J. T., van Elsas J. D. New York: Marcel Dekker;
     [Google Scholar]
  51. Williams S. T. 1985; Oligotrophy in soil: fact or fiction?. In Bacteria in the Natural Environment: the Effect of Nutrient Conditions pp. 81–110 Edited by Fletcher M., Floodgate G. London: Academic Press;
     [Google Scholar]
  52. Ye R. W., Haas D., Ka J. O., Krishnapillai V., Zimmerman A., Baird C., Tiedje J. M. 1995; Anaerobic activation of the entire denitrification pathway in Pseudomonas aeruginosa requires Anr, an analog of Fnr. J Bacteriol 177:3606–3609
     [Google Scholar]
  53. Zimmerman A., Reimann C., Galimand M., Haas D. 1991; Anaerobic growth and cyanide synthesis of Pseudomonas aeruginosa depends on anr, a regulatory gene homologous with fnr of Escherichia coli. Mol Microbiol 5:1483–1490 [CrossRef]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.26657-0
Loading
Characterization of Pseudomonas putida genes responsive to nutrient limitation
Microbiology 150, 1661 (2004); https://doi.org/10.1099/mic.0.26657-0
/content/journal/micro/10.1099/mic.0.26657-0
/content/journal/micro/10.1099/mic.0.26657-0
Loading

Data & Media loading...

Most cited Most Cited RSS feed

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