Nitrogen Control in Corynebacterium glutamicum: Proteins, Mechanisms, Signals

  • Burkovski, Burkovski (Lehrstuhl fur Mikrobiologie, Friedrich-Alexander-Universital Erlangen-Nurnberg) ;
  • Andreas, Andreas (Lehrstuhl fur Mikrobiologie, Friedrich-Alexander-Universital Erlangen-Nurnberg)
  • Published : 2007.02.28

Abstract

In order to utilize different nitrogen sources and to survive in a situation of nitrogen limitation, microorganisms have developed sophisticated mechanisms to adapt their metabolism to a changing nitrogen supply. In this communication, the recent knowledge of nitrogen regulation in the amino acid producer Corynebacterium glutamicum is summarized. The core adaptations of C. glutamicum to nitrogen limitation on the level of transcription are controlled by the global regulator AmtR. Further components of the signal pathway are GlnK, a $P_{II}-type$ signal transduction protein, and GlnD. Mechanisms involved in nitrogen control in C. glutamicum regulating gene expression and protein activity are repression of transcription, protein-complex formation, protein modification by adenylylation, change of intracellular localization, and proteolysis.

Keywords

References

  1. Arcondeguy, T., R. Jack, and M. Merrick. 2001. PII signal transduction proteins, pivotal players in microbial nitrogen control. Microbiol. Mol. Biol. Rev. 65: 80-105 https://doi.org/10.1128/MMBR.65.1.80-105.2001
  2. Beckers, G., L. Nolden, and A. Burkovski. 2001. Glutamate synthase of Corynebacterium glutamicum is not essential for glutamate synthesis and is regulated by the nitrogen status. Microbiology 147: 2961-2970 https://doi.org/10.1099/00221287-147-11-2961
  3. Beckers, G., A. K. Bendt, R. Kramer, and A. Burkovski. 2004. Molecular identification of the urea uptake system and transcriptional analysis of urea transporter- and ureaseencoding genes in Corynebacterium glutamicum. J. Bacteriol. 186: 7645-7652 https://doi.org/10.1128/JB.186.22.7645-7652.2004
  4. Beckers, G., J. Strosser, U. Hildebrandt, J. Kalinowski, M. Farwick, R. Kramer, and A. Burkovski. 2005. Regulation of AmtR-controlled gene expression in Corynebacterium glutamicum: Mechanism and characterization of the AmtR regulon. Mol. Microbiol. 58: 580-595 https://doi.org/10.1111/j.1365-2958.2005.04855.x
  5. Bendt, A. K., G. Beckers, M. Silberbach, A. Wittmann, and A. Burkovski. 2004. Utilization of creatinine as an alternative nitrogen source in Corynebacterium glutamicum. Arch. Microbiol. 181: 443-450 https://doi.org/10.1007/s00203-004-0679-z
  6. Blauwkamp, T. A. and A. J. Ninfa. 2003. Antagonism of PII signalling by the AmtB protein of Escherichia coli. Mol. Microbiol. 48: 1017-1028
  7. Bormann, E. R., B. J. Eikmanns, and H. Sahm. 1992. Molecular analysis of the Corynebacterium glutamicum gdh gene encoding glutamate dehydrogenase. Mol. Microbiol. 6: 317-326 https://doi.org/10.1111/j.1365-2958.1992.tb01474.x
  8. Bott, M. and L. Eggeling (eds.) Handbook of Corynebacterium glutamicum. CRC Press LLC, Boca Raton, FL
  9. Brune, I., K. Brinkrolf, J. Kalinowski, A. Puhler, and A. Tauch. 2005. The individual and common repertoire of DNA-binding transcriptional regulators of Corynebacterium glutamicum, Corynebacterium efficiens, Corynebacterium diphtheriae and Corynebacterium jeikeium deduced from the complete genome sequences. BMC Genomics 6: 86
  10. Burkovski, A. 2003. Ammonium assimilation and nitrogen control in Corynebacterium glutamicum and its relatives: An example for new regulatory mechanisms in actinomycetes. FEMS Microbiol. Rev. 27: 617-628 https://doi.org/10.1016/S0168-6445(03)00067-6
  11. Burkovski, A. 2003. I do it my way: Regulation of ammonium uptake and ammonium assimilation in Corynebacterium glutamicum. Arch. Microbiol. 179: 83-88 https://doi.org/10.1007/s00203-002-0505-4
  12. Burkovski, A. 2005. Nitrogen metabolism and its regulation, pp. 333-349. In Bott, M. and L. Eggeling (eds.), Handbook of Corynebacterium glutamicum. CRC Press LLC, Boca Raton, FL
  13. Cerdeno-Tarraga, A. M., A. Efstratiou, L. G. Dover, M. T. G. Holden, M. Pallen, S. D. Bentley, G. S. Besra, C. Churcher, K. D. James, A. De Zoysa, T. Chillingworth, A. Cronin, L. Dowd, T. Feltwell, N. Hamlin, S. Holroyd, K. Jagels, S. Moule, M. A. Quail, E. Rabbinowitch, K. M. Rutherford, N. R. Thomson, L. Unwin, S. Whitehead, B. G. Barrell, and J. Parkhill. 2003. The complete genome sequence and analysis of Corynebacterium diphtheriae NCTC13129. Nucleic Acids Res. 31: 6516-6523
  14. Coutts, G., G. Thomas, D. Blakey, and M. Merrick. 2002 Membrane sequestration of the signal transduction protein GlnK by the ammonium transporter AmtB. EMBO J. 21: 536-545 https://doi.org/10.1093/emboj/21.4.536
  15. Dandekar, T., B. Snel, M. Huynen, and P. Bork. 1998. Conservation of gene order: A fingerprint of proteins that physically interact. Trends Biochem. Sci. 23: 324-328 https://doi.org/10.1016/S0968-0004(98)01274-2
  16. Detsch, C. and J. Stülke. 2003. Ammonium utilization in Bacillus subtilis: Transport and regulatory functions of NrgA and NrgB. Microbiology 149: 3289-3297 https://doi.org/10.1099/mic.0.26512-0
  17. Fisher, S. H. 1999. Regulation of nitrogen metabolism in Bacillus subtilis: Vive la difference! Mol. Microbiol. 32: 223-232
  18. Fisher, S. H. and M. Débarbouille. 2002. Nitrogen source utilization and its regulation, pp. 181-191. In Sonenshein, A. C., J. A. Hoch, and R. Losick (eds.), Bacillus subtilis and its Closest Relatives: From Genes to Cells. ASM, Washington DC
  19. Fudou, R., Y. Jojima, A. Seto, K. Yamada, E. Rimura, T. Nakamatsu, A. Hirashi, and S. Yamanaka. 2002. Corynebacterium efficiens sp. Nov., a glutamic-acidproducing species from soil and plant material. Int. J. Syst. Evol. Microbiol. 52: 1127-1131
  20. He, L., E. Soupene, and S. Kustu. 1997. NtrC is required for control of Klebsiella pneumoniae NifL activity. J. Bacteriol. 179: 7446-7455 https://doi.org/10.1128/jb.179.23.7446-7455.1997
  21. Hermann, T. 2003. Industrial production of amino acids by coryneform bacteria. J. Biotechnol. 104: 155-172 https://doi.org/10.1016/S0168-1656(03)00149-4
  22. Hesketh, A., D. Fink, B. Gust, H.-U. Rexer, B. Scheel, K. Chater, W. Wohlleben, and A. Engels. 2002. The GlnD and GlnK homologues of Streptomyces coelicolor A3(2) are functionally dissimilar to their nitrogen regulatory system counterparts from enteric bacteria. Mol. Microbiol. 46: 319- 330 https://doi.org/10.1046/j.1365-2958.2002.03149.x
  23. Hu, P., T. Leighton, G. Ishkhanova, and S. Kustu. 1999. Sensing of nitrogen limitation by Bacillus subtilis: Comparison to enteric bacteria. J. Bacteriol. 181: 5042-5050
  24. Ikeda, M. and S. Nakagawa. 2003. The Corynebacterium glutamicum genome: Features and impacts on biotechnological processes. Appl. Microbiol. Biotechnol. 62: 99-109 https://doi.org/10.1007/s00253-003-1328-1
  25. Ikeda, T. P., A. E. Shauger, and S. Kustu. 1996. Salmonella typhimurium apparently perceives external nitrogen limitation as internal glutamine limitation. J. Mol. Biol. 259: 589- 607 https://doi.org/10.1006/jmbi.1996.0342
  26. Jakoby, M., M. Tesch, H. Sahm, R. Krämer, and A. Burkovski. 1997. Isolation of the Corynebacterium glutamicum glnA gene encoding glutamine synthetase I. FEMS Microbiol. Lett. 154: 81-88 https://doi.org/10.1111/j.1574-6968.1997.tb12627.x
  27. Jakoby, M., R. Kramer, and A. Burkovski. 1999. Nitrogen regulation in Corynebacterium glutamicum: Isolation of genes involved and biochemical characterization of corresponding proteins. FEMS Microbiol. Lett. 173: 303-310 https://doi.org/10.1111/j.1574-6968.1999.tb13518.x
  28. Jakoby, M., L. Nolden, J. Meier-Wagner, R. Kramer, and A. Burkovski. 2000. AmtR, a global repressor in the nitrogen regulation system of Corynebacterium glutamicum. Mol. Microbiol. 37: 964-977 https://doi.org/10.1046/j.1365-2958.2000.02073.x
  29. Javelle, A., E. Severi, J. Thornton, and M. Merrick. 2004. Ammonium sensing in Escherichia coli. Role of the ammonium transporter AmtB and AmtB-GlnK complex formation. J. Biol. Chem. 279: 8530-8538 https://doi.org/10.1074/jbc.M312399200
  30. Javelle, A. and M. Merrick. 2005. Complex formation between AmtB and GlnK: An ancestral role in prokaryotic nitrogen control. Biochem. Soc. Trans. 33: 170-172 https://doi.org/10.1042/BST0330170
  31. Kalinowski, J. 2005. The genomes of amino acid-producing corynebacteria, pp. 37-56. In Bott, M. and L. Eggeling (eds.), Handbook of Corynebacterium glutamicum. CRC Press LLC, Boca Raton, FL
  32. Kalinowski, J., B. Bathe, N. Bischoff, M. Bott, A. Burkovski, N. Dusch, L. Eggeling, B. J. Eikmanns, L. Gaigalat, A. Goesmann, M. Hartmann, K. Huthmacher, R. Kramer, B. Linke, A. C. McHardy, F. Meyer, B. Mockel, W. Pfefferle, A. Puhler, D. Rey, C. Rückert, H. Sahm, V. F. Wendisch, I. Wiegräbe, and A. Tauch. 2003. The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins. J. Biotechnol. 104: 5-25 https://doi.org/10.1016/S0168-1656(03)00154-8
  33. Kimura, K. 1962. The significance of glutamic dehydrogenase in glutamic acid fermentation. J. Gen. Appl. Microbiol. 8: 253-260 https://doi.org/10.2323/jgam.8.253
  34. Kinoshita, S., S. Udaka, and M. Shimono. 1957. Amino acid fermentation. I. Production of L-glutamic acid by various microorganisms. J. Gen. Appl. Microbiol. 3: 193-205 https://doi.org/10.2323/jgam.3.193
  35. Kronemeyer, W., N. Peekhaus, R. Kramer, L. Eggeling, and H. Sahm. 1995. Structure of the gluABCD cluster encoding the glutamate uptake system of Corynebacterium glutamicum. J. Bacteriol. 177: 1152-1158 https://doi.org/10.1128/jb.177.5.1152-1158.1995
  36. Leuchtenberger, W. 1996. Amino acids - technical production and use, pp. 465-502. In Rehm, H. and G. Reed (eds.), Products of Primary Metabolism. Biotechnology, Volume 6. VCH Verlagsgesellschaft GmbH, Weinheim, Germany
  37. Leuchtenberger, W., K. Huthmacher, and K. Drauz. 2005. Biotechnological production of amino acids and derivatives: Current status and prospects. Appl. Microbiol. Biotechnol. 69: 1-8 https://doi.org/10.1007/s00253-005-0155-y
  38. Meier-Wagner, J., L. Nolden, M. Jakoby, R. M. Siewe, R. Krämer, and A. Burkovski. 2001. Multiplicity of ammonium uptake systems in Corynebacterium glutamicum: Role of Amt and AmtB. Microbiology 147: 135-143 https://doi.org/10.1099/00221287-147-1-135
  39. Merkens, H., G. Beckers, A. Wirtz, and A. Burkovski. 2005. Vanillate metabolism in Corynebacterium glutamicum. Curr. Microbiol. 51: 59-65 https://doi.org/10.1007/s00284-005-4531-8
  40. Muller, T., J. Strosser, S. Buchinger, L. Nolden, A. Wirtz, R. Kramer, and A. Burkovski. 2006. Mutation-induced metabolite pool alterations in Corynebacterium glutamicum: Towards the identification of nitrogen control signals. J. Biotechnol. (electronic publication ahead of print)
  41. Nolden, L., M. Farwick, R. Kramer, and A. Burkovski. 2001. Glutamine synthetases of Corynebacterium glutamicum: Transcriptional control and regulation of activity. FEMS Microbiol. Lett. 201: 91-98 https://doi.org/10.1111/j.1574-6968.2001.tb10738.x
  42. Nolden, L., C.-E. Ngouoto-Nkili, A. K. Bendt, R. Kramer, and A. Burkovski. 2001. Sensing nitrogen limitation in Corynebacterium glutamicum: The role of glnK and glnD. Mol. Microbiol. 42: 1281-1295 https://doi.org/10.1046/j.1365-2958.2001.02694.x
  43. Nolden, L., G. Beckers, and A. Burkovski. 2002. Nitrogen assimilation in Corynebacterium diphtheriae: Pathways and regulatory cascades. FEMS Microbiol. Lett. 208: 287-293 https://doi.org/10.1111/j.1574-6968.2002.tb11096.x
  44. Oshima, K., K. Tanaka, and S. Kinoshita. 1964. Studies on glutamic acid fermentation. XI. Purification and properties of L-glutamic acid dehydrogenase from Micrococcus glutamicus. Agric. Biol. Chem. 28: 714-722 https://doi.org/10.1271/bbb1961.28.714
  45. Ramos, J. L., M. Martinez-Bueno, A. J. Molina-Henares, W. Teran, K. Watanabe, X. Zhang, M. T. Gallegos, R. Brennan, and R. Tobes. 2005. The TetR family of transcriptional repressors. Microbiol. Mol. Biol. Rev. 69: 326-356 https://doi.org/10.1128/MMBR.69.2.326-356.2005
  46. Reuter, J. and W. Wohlleben. 2006. Nitrogen metabolism in Streptomyces coelicolor: Transcriptional and post-transcriptional regulation. J. Mol. Microbiol. Biotechnol. (In press)
  47. Schmitz, R. A. 2000. Internal glutamine and glutamate pools in Klebsiella pneumoniae grown under different conditions of nitrogen availability. Curr. Microbiol. 41: 357-362 https://doi.org/10.1007/s002840010149
  48. Schulz, A. A., H. J. Collett, and S. J. Reid. 2001. Nitrogen and carbon regulation of glutamine synthetase and glutamate synthase in Corynebacterium glutamicum ATCC 13032. FEMS Microbiol. Lett. 205: 361-367 https://doi.org/10.1111/j.1574-6968.2001.tb10973.x
  49. Shiio, I. and H. Ozaki. 1970. Regulation of nicotinamide adenine dinucleotide phosphate-specific glutamate dehydrogenase from Brevibacterium flavum, a glutamate-producing bacterium. J. Biochem. 68: 633-647 https://doi.org/10.1093/oxfordjournals.jbchem.a129397
  50. Siewe, R. M., B. Weil, A. Burkovski, B. J. Eikmanns, M. Eikmanns, and R. Kramer. 1996. Functional and genetic characterization of the (methyl)ammonium uptake carrier of Corynebacterium glutamicum. J. Biol. Chem. 271: 5398- 5403 https://doi.org/10.1074/jbc.271.10.5398
  51. Silberbach, M. and A. Burkovski. 2006. Application of global analysis techniques to Corynebacterium glutamicum: New insights into nitrogen regulation. J. Biotechnol. (electronic publication ahead of print)
  52. Silberbach, M., A. Huser, J. Kalinowski, A. Puhler, B. Walter, R. Kramer, and A. Burkovski. 2005. DNA microarray analysis of the nitrogen starvation response of Corynebacterium glutamicum. J. Biotechnol.119: 357-367 https://doi.org/10.1016/j.jbiotec.2005.04.007
  53. Silberbach, M., M. Schafer, A. Huser, J. Kalinowski, A. Puhler, R. Kramer, and A. Burkovski. 2005. Adaptation of Corynebacterium glutamicum to ammonium-limitation: A global analysis using transcriptome and proteome techniques. Appl. Environ. Microbiol. 71: 2391-2402 https://doi.org/10.1128/AEM.71.5.2391-2402.2005
  54. Strosser, J., A. Ludke, S. Schaffer, R. Kramer, and A. Burkovski. 2004. Regulation of GlnK activity: Modification, membrane sequestration, and proteolysis as regulatory principles in the network of nitrogen control in Corynebacterium glutamicum. Mol. Microbiol. 54: 132-147 https://doi.org/10.1111/j.1365-2958.2004.04247.x
  55. Tauch, A., O. Kaiser, T. Hain, A. Goesmann, B. Weisshaar, A. Albersmeier, T. Bekel, N. Bischoff, I. Brune, T. Chakraborty, J. Kalinowski, F. Meyer, O. Rupp, S. Schneiker, P. Viehoever, and A. Pühler. 2005. Complete genome sequence and analysis of the multiresistant nosocomial pathogen Corynebacterium jeikeium K411, a lipid-requiring bacterium of the human skin flora. J. Bacteriol. 187: 4671-4682 https://doi.org/10.1128/JB.187.13.4671-4682.2005
  56. Tesch, M., B. J. Eikmanns, A. A. de Graaf, and H. Sahm. 1998. Ammonia assimilation in Corynebacterium glutamicum and a glutamate dehydrogenase-deficient mutant. Biotechnol. Lett. 20: 953-957 https://doi.org/10.1023/A:1005442618575
  57. Tesch, M., A. A. de Graaf, and H. Sahm. 1999. In vivo fluxes in the ammonium-assimilatory pathways in Corynebacterium glutamicum studied by $^{15}$N nuclear magnetic resonance. Appl. Environ. Microbiol. 65: 1099-1109
  58. Thomas, G., G. Coutts, and M. Merrick. 2000. The glnKamtB operon. A conserved gene pair in prokaryotes. Trends Genet. 16: 11-14
  59. Tondervik, A., H. R. Torgersen, H. K. Botnmark, and A. R. Strom. 2006. Transposon mutations in the 5' end of glnD, the gene for a nitrogen regulatory sensor, that suppress the osmosensitive phenotype caused by otsBA lesions in Escherichia coli. J. Bacteriol. 188: 4218-4226 https://doi.org/10.1128/JB.00513-05
  60. Trotschel, C., S. Kandirali, P. Diaz-Achirica, A. Meinhardt, S. Morbach, R. Kramer, and A. Burkovski. 2003. GltS, the sodium-coupled L-glutamate uptake system of Corynebacterium glutamicum: Identification of the corresponding gene and impact on L-glutamate production. Appl. Microbiol. Biotechnol. 60: 738-742 https://doi.org/10.1007/s00253-002-1170-x
  61. Udaka, S. 1960. Screening method for microorganisms accumulating metabolites and its use in the isolation of Micrococcus glutamicus. J. Bacteriol. 79: 745-755
  62. Walter, B., E. HanBler, J. Kalinowski, and A. Burkovski. 2006. Nitrogen metabolism and nitrogen control in corynebacteria: Variations of a common theme. J. Mol. Microbiol. Biotechnol. (In press)
  63. Wendisch, V. F., M. Bott, J. Kalinowski, M. Oldiges, and W. Wiechert. 2006. Emerging Corynebacterium glutamicum systems biology. J. Biotechnol. 124: 74-92 https://doi.org/10.1016/j.jbiotec.2005.12.002