A genomic view on nitrogen metabolism and nitrogen control in mycobacteria

Journal of Molecular Microbiology and Biotechnology

Volumn 17, Issue 1, 2009, Pages 20-29

  Amon, Johannes ^a   Titgemeyer, Fritz ^a   Burkovski, Andreas ^a  

^a UNIVERSITY OF ERLANGEN NUREMBERG   (Germany)

Author keywords

Ammonium; GlnR; Glutamine synthetase; Mycobacterium; Nitrogen control; Nitrogen regulation

Indexed keywords

AMMONIA; GLUTAMATE DEHYDROGENASE; GLUTAMATE SYNTHASE; HEXOSE 1 PHOSPHATE URIDYLYLTRANSFERASE; NITRATE; NITRATE REDUCTASE; NITRITE REDUCTASE; NITROGEN; NITROGEN REGULATORY PROTEIN; UREA; UREASE;

ARTICLE; BACTERIAL GENE; CONTROLLED STUDY; GENE SEQUENCE; GENETIC SCREENING; GENOME ANALYSIS; GENOMICS; MYCOBACTERIUM; MYCOBACTERIUM AVIUM; MYCOBACTERIUM LEPRAE; MYCOBACTERIUM PARATUBERCULOSIS; MYCOBACTERIUM SMEGMATIS; MYCOBACTERIUM TUBERCULOSIS; NITROGEN FIXATION; NITROGEN METABOLISM; NITROGEN UPTAKE; NONHUMAN; NUCLEOTIDE SEQUENCE; TRANSCRIPTION REGULATION; BACTERIAL GENOME; BIOLOGY; COMPARATIVE STUDY; GENETICS; METABOLISM; PHYLOGENY; SYNTENY;

ACTINOBACTERIA (CLASS); CORYNEBACTERINEAE; CORYNEBACTERIUM GLUTAMICUM; MYCOBACTERIUM; MYCOBACTERIUM AVIUM; MYCOBACTERIUM BOVIS; MYCOBACTERIUM LEPRAE; MYCOBACTERIUM SMEGMATIS; MYCOBACTERIUM TUBERCULOSIS; STREPTOMYCES COELICOLOR;

COMPUTATIONAL BIOLOGY; GENES, BACTERIAL; GENOME, BACTERIAL; GENOMICS; METABOLIC NETWORKS AND PATHWAYS; MYCOBACTERIUM; NITROGEN; PHYLOGENY; SYNTENY;

EID: 67649410544     PISSN: 14641801     EISSN: None     Source Type: Journal    
DOI: 10.1159/000159195     Document Type: Article

References (55)

1. Amon J, Bräu T, Grimrath A, Hänßler E, Hasselt K, Höller M, Jeßberger N, Ott L, Szököl J, Titgemeyer F, Burkovski A: Nitrogen control in Mycobacterium smegmatis: Nitrogen-dependent expression of ammonium transport and assimilation proteins depends on OmpR-type regulator GlnR. J Bacteriol 2008, Epub ahead of print.
2. Bange FC, Collins FM, Jacobs WR Jr: Survival of mice infected with Mycobacterium smegmatis containing large DNA fragments from Mycobacterium tuberculosis. Tuber Lung Dis 1999;79:171-180.
3. Baumbach J: CoryneRegNet 4.0 - A reference database for corynebacterial gene regulatory networks. BMC Bioinformatics 2007;8:429.
4. Beckers G, Nolden L, Burkovski A: Glutamate synthase of Corynebacterium glutamicum is not essential for glutamate synthesis and is regulated by the nitrogen status. Microbiology 2001;147:2961-2970.
5. Beckers G, Bendt AK, Krämer R, Burkovski A: Molecular identification of the urea uptake system and transcriptional analysis of urea transporter- and urease-encoding genes in Corynebacterium glutamicum. J Bacteriol 2004;186:7645-7652.
6. Beckers G, Strösser J, Hildebrandt U, Kalinowski J, Farwick M, Krämer R, Burkovski A: Regulation of AmtR-controlled gene expression in Corynebacterium glutamicum: mechanism and characterization of the AmtR regulon. Mol Microbiol 2005;58:580-595.
7. Börmann ER, Eikmanns BJ, Sahm H: Molecular analysis of the Corynebacterium glutamicum gdh gene encoding glutamate dehydrogenase. Mol Microbiol 1992;6:317-326.
8. Burkovski A: I do it my way: Regulation of ammonium uptake and ammonium assimilation in Corynebacterium glutamicum. Arch Microbiol 2003a;179:83-88.
9. Burkovski A: Ammonium assimilation and nitrogen control in Corynebacterium glutamicum and its relatives: an example for new regulatory mechanisms in actinomycetes. FEMS Microbiol Rev 2003b:27:617-628.
10. Burkovski A: Nitrogen metabolism and its regulation; in Bott M, Eggeling L (eds): Handbook of Corynebacterium glutamicum. Boca Raton, CRC Press LLC, 2005, pp 333-349.
11. Burkovski A: Nitrogen control in Corynebacterium glutamicum: proteins, mechanisms, signals. J Microbiol Biotechnol 2007;17:187-194.
12. Carroll P, Pashley CA, Parish T: Functional analysis of GlnE, an essential adenylyl transferase in Mycobacterium tuberculosis. J Bacteriol 2008;DOI:10.1128/JB.00166-08.
13. Clemens DL, Lee BY, Horwitz MA: Purification, characterization, and genetic analysis of Mycobacterium tuberculosis urease, a potentially critical determinant of host-pathogen interaction. J Bacteriol 1995;177:5644-5652.
14. Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C, Harris D, et al: Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 1998;393:537-544.
15. Cole ST, Eiglmeier K, Parkhill J, James KD, Thomson NR, Wheeler PR, et al: Massive gene decay in the leprosy bacillus. Nature 2001;409:1007-1011.
16. Crooks GE, Hon G, Chandonia JM, Brenner SE: WebLogo: a sequence logo generator. Genome Res 2004;14:1188-1190.
17. Detsch C, Stülke J: Ammonium utilization in Bacillus subtilis: transport and regulatory functions of NrgA and NrgB. Microbiology 2003;149:3289-3297.
18. Dye C, Watt CJ, Bleed DM, Hosseini SM, Raviglione MC: Evolution of tuberculosis control and prospects for reducing tuberculosis incidence, prevalence, and deaths globally. JAMA 2005;293:2767-2775.
19. Fink D, Weisschuh N, Reuther J, Wohlleben W, Engels A: Two transcriptional regulators GlnR and GlnRII are involved in regulation of nitrogen metabolism in Streptomyces coelicolor A3(2). Mol Microbiol 2002;46:331-347.
20. Garnier T, Eiglmeier K, Camus JC, Medina N, Mansoor H, Pryor M, et al: The complete genome sequence of Mycobacterium bovis. Proc Natl Acad Sci USA 2003;100:7877-7882.
21. Gómez-Valero L, Rocha EPC, Latorre A, Silva FJ: Reconstructing the ancestor of Mycobacterium leprae: The dynamics of gene loss and genome reduction. Genome Res 2007;17:1178-1185.
22. Hänßler E, Burkovski A: Molecular mechanisms of nitrogen control in corynebacteria; in Burkovski A (ed): Corynebacteria: Genomics and Molecular Biology. Wymondham, Caister Academic Press, 2008, pp 183-201.
23. Harth G, Clemens DL, Horwitz AA: Glutamine synthetase of Mycobacterium tuberculosis: extracellular release and characterization of its enzymatic activity. Proc Natl Acad Sci USA 1994;91: 9342-9346.
24. Harth G, Maslesa-Galic S, Tullius MV, Horwitz AA: All four Mycobacterium tuberculosis glnA genes encode glutamine synthetase activities but only GlnA1 is abundantly expressed and essential for bacterial homeostasis. Mol Microbiol 2005;58:1157-1172.
25. Hesketh A, Fink D, Gust B, Rexer H-U, Scheel B, Chater K, Wohlleben W, Engels A: The GlnD and GlnK homologues of Streptomyces coelicolor A3(2) are functionally dissimilar to their nitrogen regulatory system counterparts from enteric bacteria. Mol Microbiol 2002;46:319-330.
26. Hiard S, Maree R, Colson S, Hoskisson PA, Titgemeyer F, van Wezel G, Joris B, Wehenkel L, Rigali S: PREDetector: a new tool to identify regulatory elements in bacterial genomes. Biochem Biophys Res Commun 2007;357:861-864.
27. Hotter GS, Mouat P, Collins DM: Independent transcription of glutamine synthetase (glnA2) and glutamine synthetase adenylyl-transferase (glnE) in Mycobacterium bovis and Mycobacterium tuberculosis. Tuberculosis DOI:10.1016/j.tube.2008.02.006.
28. Jakoby M, Krämer R, Burkovski A: Nitrogen regulation in Corynebacterium glutamicum: Isolation of genes involved and biochemical characterization of the corresponding proteins. FEMS Microbiol Lett 1999;173:303-310.
29. Jakoby M, Nolden L, Meier-Wagner J, Krämer R, Burkovski A: AmtR, a global repressor in the nitrogen regulation system of Corynebacterium glutamicum. Mol Microbiol 2000;37:964-977.
30. Khan A, Akhtar S, Ahmad J, Sarkar D: Presence of a functional nitrate pathway in Mycobacterium smegmatis. Microb Pathog 2008;44:71-77.
31. Li L, Bannantine JP, Zhang Q, Amonsin A, Max BJ, Alt D, Banerji N, Kanjilal S, Kapur V: The complete genome sequence of Mycobacterium avium subspecies paratuberculosis. Proc Natl Acad Sci USA 2005;102:12344-12349.
32. Meier-Wagner J, Nolden L, Jakoby M, Siewe R, Krämer R, Burkovski A: Multiplicity of ammonium uptake systems in Corynebacterium glutamicum: role of Amt and AmtB. Microbiology 2001;147:135-143.
33. Nolden L, Beckers G, Burkovski A: Nitrogen assimilation in Corynebacterium diphtheriae: pathways and regulatory cascades. FEMS Microbiol Lett 2002;208:287-293.
34. Nordqvist A, Nilsson MT, Röttger S, Odell LR, Krajewski WW, Andersson CE, Larhed M, Mowbray SL, Karlén A: Evaluation of the amino acid binding site of Mycobacterium tuberculosis glutamine synthetase for drug discovery. Bioorg Med Chem 2008;6:5501-5513.
35. Parish T, Stoker NG: glnE is an essential gene in Mycobacterium tuberculosis. J Bacteriol 2000;182:5715-5720.
36. Pashley CA, Brown AC, Robertson D, Parish T: Identification of the Mycobacterium tuberculosis glnE promoter and its response to nitrogen avai lability. Microbiology 2006;152:2727-2734.
37. Pelicic V, Reyrat JM, Gicquel B: Genetic advances for studying Mycobacterium tuberculosis pathogenicity. Mol Microbiol 1998;28:413-420.
38. Read R, Pashley CA, Smith D, Parish T: The role of GlnD in ammonium assimilation in Mycobacterium tuberculosis. Tuberculosis 2007;87:384-390.
39. Reuther J, Wohlleben W: Nitrogen metabolism in Streptomyces coelicolor: Transcriptional and post-translational regulation. J Mol Microbiol Biotechnol 2007;12:139-146.
40. Rexer HU, Schäberle T, Wohlleben W, Engels A: Investigation of the functional properties and regulation of three glutamine synthetase-like genes in Streptomyces coelicolor A3(2). Arch Microbiol 2006;186:447-458.
41. Sassetti CM, Boyd DH, Rubin EJ: Genes required for mycobacterial growth defined by high density mutagenesis. Mol Microbiol 2003;48:77-84.
42. Schulz AA, Collett HJ, Reid SJ: Regulation of glutamine synthetase and glutamate synthase in Corynebacterium glutamicum ATCC 13032. FEMS Microbiol Lett 2001;205:361-367.
43. Sohaskey CD: Nitrate enhances the survival of Mycobacterium tuberculosis during inhibition of respiration. J Bacteriol 2008;190:2981-2986.
44. Sohaskey CD, Wayne LG: Role of narK2X and narGHJI in hypoxic upregulation of nitrate reduction by Mycobacterium tuberculosis. J Bacteriol 2003;185:7247-7256.
45. Strösser J, Lüdke A, Schaffer S, Krämer R, Burkovski A: Regulation of GlnK activity: modification, membrane sequestration, and proteolysis as regulatory principles in the network of nitrogen control in Corynebacterium glutamicum. Mol Microbiol 2004;54:132-147.
46. Tiffert Y, Supra P, Wurm R, Wohlleben W, Wagner R, Reuther J: The Streptomyces coelicolor GlnR regulon: identification of new GlnR targets and evidence for a central role of GlnR in nitrogen metabolism in actinomycetes. Mol Microbiol 2008;67:436-446.
47. Titgemeyer F, Parche S, Mahfoud M, Amon J, Bail J, Schlicht M, Hillmann D, Rehm N, Stephan J, Walter B, Burkovski A, Niederweis M: Sugar transport in Mycobacterium smegmatis and Mycobacterium tuberculosis. J Bacteriol 2007;189:5903-5915.
48. Tullius MV, Harth G, Horwitz AA: Glutamine synthetase GlnA1 is essential for growth of Mycobacterium tuberculosis in human THP-1 macrophages and guinea pigs. Infect Immun 2003;71:3927-3936.
49. Vissa VD, Brennan PJ: The genome of Mycobacterium leprae: a minimal mycobacterial genome set. Genome Biol 2001;2:1023.1-1023.8.
50. Walter B, Hänßler E, Kalinowski J, Burkovski A: Nitrogen metabolism and nitrogen control in corynebacteria: variations of a common theme. J Mol Microbiol Biotechnol 2007;12:131-138.
51. Walter B, Küspert M, Ansorge A, Krämer R, Burkovski A: Dissection of ammonium uptake systems in Corynebacterium glutamicum: mechanism and energetics of AmtA and AmtB. J Bacteriol 2008;190:2611-2614.
52. Wang H, Gunsalus RP: The nrfA and nirB nitrite reductase operons in Escherichia coli are expressed differently in response to nitrate than to nitrite. J Bacteriol 2000;182:5813-5822.
53. Wray LV, Atkinson MR, Fisher SH: Identification and cloning of the glnR locus, which is required for transcription of the glnA gene in Streptomyces coelicolor A3(2). J Bacteriol 1991;173:7351-7360.
54. Wray LV, Fisher SH: The Streptomyces coelicolor glnR gene encodes a protein similar to other bacterial response regulators. Gene 1993;130:145-150.
55. Yu H, Peng W, Liu Y, Wu T, Yao Y, Cui M, Jiang W, Zhao G-P: Identification and characterization of glnA promoter and its corresponding trans-regulating protein GlnR in the rifamycin SV producing actinomycete, Amycolatopsis mediterranei U32. Acta Biochim Biophys Sin 2006;38:831-843.