Chapter 11 : Nitrogen Metabolism

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Ebook: Choose a downloadable PDF or ePub file. Chapter is a downloadable PDF file. File must be downloaded within 48 hours of purchase

Buy this Chapter
Digital (?) $15.00

Preview this chapter:
Zoom in

Nitrogen Metabolism, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555818005/9781555812133_Chap11-1.gif /docserver/preview/fulltext/10.1128/9781555818005/9781555812133_Chap11-2.gif


The study of nitrogen metabolism in was initially made possible by the development of defined growth media, which permitted (i) the determination of the minimal amino acid requirements of this bacterium and (ii) the following of the fate of amino acids in whole bacteria. The subsequent publication of the complete genomic sequences of two strains, 26695 and J99, has confirmed some of the data obtained and supplied additional genetic information. is auxotrophic for several amino acids, supporting the idea that its growth in vivo is strictly dependent on the gastric environment. Large amounts of amino acids, dipeptides, and polypeptides are present in the gastric juice owing to the activities of enzymes such as pepsin, which break down proteins efficiently. Amino acid utilization by grown in a defined medium has been investigated by nuclear magnetic resonance (NMR) spectroscopy and amino acid analysis. Nitrogen metabolism in generates considerable amounts of free ammonia that either could be incorporated into proteins via the glutamine synthetase (GS-ase) pathway or released into the external environment by diffusion in its NH form. The possibility that has a urea cycle was investigated by assessing the activity of the four enzymes of this cycle: arginase, anabolic ornithine transcarbamoylase (OTC-ase), arginosuccinate synthetase, and arginosuccinase, employing one- and two-dimensional NMR spectroscopy and radioactive tracer analysis.

Citation: De Reuse H, Skouloubris S. 2001. Nitrogen Metabolism, p 125-133. In Mobley H, Mendz G, Hazell S (ed), . ASM Press, Washington, DC. doi: 10.1128/9781555818005.ch11

Key Concept Ranking

Basic Amino Acids
Amino Acids
Highlighted Text: Show | Hide
Loading full text...

Full text loading...


Image of Figure 1
Figure 1

Nitrogen sources for The reactions are catalyzed by the following enzymes: ( ) glutaminase, ( ) L-serine deaminase, ( ) aspartate-ammonia lyase, ( ) L-asparaginase II, ( ) urease, ( ) formamidase, ( ) aliphatic amidase. The products of these deamination and deamidation reactions are also shown.

Citation: De Reuse H, Skouloubris S. 2001. Nitrogen Metabolism, p 125-133. In Mobley H, Mendz G, Hazell S (ed), . ASM Press, Washington, DC. doi: 10.1128/9781555818005.ch11
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 2
Figure 2

Pathways of nitrogen assimilation in and GOGAT-ase corresponds to glutamate synthase, GDH-ase to glutamate dehydrogenase, and GS-ase to glutamine synthetase.

Citation: De Reuse H, Skouloubris S. 2001. Nitrogen Metabolism, p 125-133. In Mobley H, Mendz G, Hazell S (ed), . ASM Press, Washington, DC. doi: 10.1128/9781555818005.ch11
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 3
Figure 3

Enzymatic reactions of the urea cycle. Urea hydrolysis by urease in is indicated, as is the reaction producing carbamoyl phosphate.

Citation: De Reuse H, Skouloubris S. 2001. Nitrogen Metabolism, p 125-133. In Mobley H, Mendz G, Hazell S (ed), . ASM Press, Washington, DC. doi: 10.1128/9781555818005.ch11
Permissions and Reprints Request Permissions
Download as Powerpoint


1. Alm, R. A.,, L. S. L. Ling,, D. T. Moir,, B. L. King,, E. D. Brown,, P. C. Doig,, D. R. Smith,, B. Noonan,, B. C. Guild,, B. L. deJonge,, G. Carmel,, P. J. Tummino,, A. Caruso,, M. Uria-Nickelsen,, D. M. Mills,, C. Ives,, R. Gibson,, D. Merberg,, S. D. Mills,, Q. Jiang,, D. E. Taylor,, G. F. Vovis,, and T. J. Trust. 1999. Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori. Nature 397:176180.
2. Chevalier, C.,, J.-M. Thiberge,, R. L. Ferrero,, and A. Labigne. 1999. Essential role of Helicobacter pylori -y-glutamyltrans-peptidase for the colonization of the gastric mucosa of mice. Mol. Microbiol. 31:13591372.
3. Dekigai, H.,, M. Murakami,, and T. Kita. 1995. Mechanism of Helicobacter pylori-associated gastric mucosal injury. Dig. Dis. Sci. 40:13321339.
4. Doig, P.,, B. L. de Jonge,, R. A. Aim,, E. D. Brown,, M. Uria-Nickelsen,, B. Noonan,, S. D. Mills,, P. Tummino,, G. Carmel,, B. C. Guild,, D. T. Moir,, G. F. Vovis,, and T. J. Trust. 1999. Helicobacter pylori physiology predicted from genomic comparison of two strains. Microbiol. Mol. Biol. Rev. 63:675707.
5. Doring, V.,, and P. Marliere. 1998. Reassigning cysteine in the genetic code of Escherichia coli. Genetics 150:543551.
6. Eaton, K. A.,, C. L. Brooks,, D. R. Morgan,, and S. Krakowka. 1991. Essential role of urease in pathogenesis of gastritis induced by Helicobacter pylori in gnotobiotic piglets. Infect. Immun. 59:24702475.
7. Eaton, K. A.,, and S. Krakowka. 1994. Effect of gastric pH on urease-dependent colonization of gnotobiotic piglets by Helicobacter pylori. Infect. Immun. 62:36043607.
8. Ferrero, R. L.,, and A. Lee. 1991. The importance of urease in acid protection for the gastric-colonising bacteria Helicobacter pylori and Helicobacter felis sp. nov. Microb. Ecol. Health Dis. 4:121134.
9. Gardan, R.,, G. Rapoport,, and M. Debarbouille. 1995. Expression of the rocDEF operon involved in arginine catabolism in Bacillus subtilis. J. Mol. Biol. 249:843856.
10. Garner, R. M.,, J. Fulkerson, Jr.,, and H. L. Mobley. 1998. Helicobacter pylori glutamine synthetase lacks features associated with transcriptional and posttranslational regulation. Infect. Immun. 66:18391847.
11. Hu, L. T.,, and H. L. Mobley. 1990. Purification and N-terminal analysis of urease from Helicobacter pylori. Infect. Immun. 58:992998.
12. Kleiner, D.,, A. Traglauer,, and S. Domm. 1998. Does ammonia production by Klebsiella contribute to pathogenesis? Bull. Inst. Pasteur 96:257265.
13. Komorowska, M.,, H. Szafran,, T. Popiela,, and Z. Szafran. 1981. Free amino acids in gastric juice. Acta Physiol. Pol. 32: 559567.
14. Lee, A.,, J. O'Rourke,, M. Corazon De Ungria,, B. Robertson,, G. Daskalopoulos,, and M. F. Dixon. 1997. A standardized mouse model of Helicobacter pylori infection: introducing the Sydney strain. Gastroenterology 112:13861397.
15. Marais, A.,, G. L. Mendz,, S. L. Hazell,, and F. Megraud. 1999. Metabolism and genetics of Helicobacter pylori: the genome era. Microbiol. Mol. Biol. Rev. 63:642674.
16. Marshall, B. J.,, L. Barret,, C. Prakash,, R. McCallum,, and R. Guerrant. 1990. Urea protects Helicobacter (Campylobacter) pylori from the bactericidal effect of acid. Gastroenterology 99:269276.
17. McGee, D. J.,, F. J. Radcliff,, G. L. Mendz,, R. L. Ferrero,, and H. L. Mobley. 1999. Helicobacter pylori rocF is required for arginase activity and acid protection in vitro but is not essential for colonization of mice or for urease activity. J. Bacteriol. 181:73147322.
18. Mendz, G. L.,, and S. L. Hazell. 1995. Amino acid utilization by Helicobacter pylori. Int. J. Biochem. Cell. Biol. 27:10851093.
19. Mendz, G. L.,, and S. L. Hazell. 1996. The urea cycle of Helicobacter pylori. Microbiology 142:29592967.
20. Mendz, G. L.,, and E. M. Holmes,. 1998. Metabolic fate of arginine, an essential amino acid for Helicobacter pylori, p. 193196. In A. J. Lastovica,, D. G. Newell,, and E. E. Lastovica (ed.), Campylobacter, Helicobacter and Related Organisms. Institute of Child Health, Cape Town, South Africa.
21. Mendz, G. L.,, E. M. Holmes,, and R. L. Ferrero. 1998. In situ characterization of Helicobacter pylori arginase. Biochim. Biophys. Acta 1388:465477.
22. Mobley, H. L.,, M. D. Island,, and R. P. Hausinger. 1995. Molecular biology of microbial ureases. Microbiol. Rev. 59: 451480.
23. Nedenskov, P. 1994. Nutritional requirements for growth of Helicobacter pylori. Appl. Environ. Microbiol. 60: 34503453.
24. Quintero, M. J.,, A. M. Muro-Pastor,, A. Herrero,, and E. Flores. 2000. Arginine catabolism in the cyanobacterium Synechocystis sp. strain PCC6803 involves the urea cycle and arginase pathway. J. Bacteriol. 182:10081015.
25. Reitzer, L. J., 1996. Ammonia assimilation and the biosynthesis of glutamine, glutamate, asparate, asparagine, L-alanine and D-alanine, p. 301407. In F. C. Neidhardt (ed.), Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd ed. ASM Press, Washington, D.C..
26. Reynolds, D. J.,, and C. W. Penn. 1994. Characteristics of Helicobacter pylori growth in a defined medium and determination of its amino acid requirements. Microbiology 140:26492656.
27. Skouloubris, S.,, A. Labigne,, and H. De Reuse. The AmiE aliphatic amidase and AmiF formamidase of Helicobacter pylori: natural evolution of two enzyme paralogs. Mol. Microbiol, in press.
28. Skouloubris, S.,, A. Labigne,, and H. De Reuse. 1997. Identification and characterization of an aliphatic amidase in Helicobacter pylori. Mol. Microbiol. 25:989998.
29. Skouloubris, S.,, J. M. Thiberge,, A. Labigne,, and H. De Reuse. 1998. The Helicobacter pylori Urel protein is not involved in urease activity but is essential for bacterial survival in vivo. Infect. Immun. 66:45174521.
30. Smoot, D. T.,, H. L. Mobley,, G. R. Chippendale,, J. F. Lewison,, and J. H. Resau. 1990. Helicobacter pylori urease activity is toxic to human gastric epithelial cells. Infect. Immun. 58:19921994.
31. Spohn, G.,, and V. Scarlato. 1999. Motility of Helicobacter pylori is coordinately regulated by the transcriptional activator FlgR, an NtrC homolog. J. Bacteriol. 181:593599.
32. Stark, R. M.,, M. S. Suleiman,, I. J. Hassan,, J. Greenman,, and M. R. Millar. 1997. Amino acid utilisation and deamination of glutamine and asparagine by Helicobacter pylori. J. Med. Microbiol. 46:793800.
33. Suzuki, M.,, S. Miura,, M. Suematsu,, D. Fukumura,, I. Kurose,, H. Suzuki,, A. Kai,, Y. Kudoh,, M. Ohashi,, and M. Tsuchiya. 1992. Helicobacter pylori-associated ammonia production enhances neutrophil-dependent gastric mucosas cell injury. Am. J. Physiol. 263:G719G725.
34. Tomb, J.-F.,, O. White,, A. R. Kerlavage,, R. A. Clayton,, G. G. Sutton,, R. D. Fleischmann,, K. A. Ketchum,, H. P. Klenk,, S. Gill,, B. A. Dougherty,, K. Nelson,, J. Quackenbush,, L. Zhou,, E. F. Kirkness,, S. Peterson,, B. Loftus,, D. Richardson,, R. Dodson,, H. G. Khalak,, A. Glodek,, K. McKenney,, L. M. Fitzegerald,, N. Lee,, M. D. Adams,, E. K. Hickey,, D. E. Berg,, J. D. Gocayne,, T. R. Utterback,, J. D. Peterson,, J. M. Kelley,, M. D. Cotton,, J. M. Weidman,, C. Fuji,, C. Bowman,, L. Watthey,, E. Wallin,, W. S. Hayes,, M. Borodovsky,, P. D. Karp,, H. O. Smith,, C. M. Fraser,, and J. C. Venter. 1997. The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature 388:539547.
35. Tsuda, M.,, M. Karita,, M. G. Morshed,, K. Okita,, and T. Nakazawa. 1994. A urease-negative mutant of Helicobacter pylori constructed by allelic exchange lacks the ability to colonize the nude mouse stomach. Infect. Immun. 1994:35863589.
36. Weeks, D. L.,, S. Eskandari,, D. R. Scott,, and G. Sachs. 2000. A H+-gated urea channel: the link between Helicobacter pylori urease and gastric colonization. Science 287:482485.
37. Williams, C. L.,, T. Preston,, M. Hossack,, C. Slater,, and K. E. McColl. 1996. Helicobacter pylori utilises urea for amino acid synthesis. FEMS Immunol. Med. Microbiol. 13:8794.
38. Wilson, S. A.,, R. J. Williams,, L. H. Pearl,, and R. E. Drew. 1995. Identification of two new genes in the Pseudomonas aeruginosa amidase operon, encoding an ATPase (AmiB) and a putative integral membrane protein (AmiS). J. Biol. Chem. 270:1881818824.
39. Wirth, H. P.,, M. H. Beins,, M. Yang,, K. T. Tham,, and M. J. Blaser. 1998. Experimental infection of Mongolian gerbils with wild-type and mutant Helicobacter pylori strains. Infect. Immun. 66:48564866.

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error