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discounted EARLY registration ends Dec 31, 2014
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Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
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MetaCyc Pathway: arginine degradation V (arginine deiminase pathway)

Enzyme View:

This view shows enzymes only for those organisms listed below, in the list of taxa known to possess the pathway. If an enzyme name is shown in bold, there is experimental evidence for this enzymatic activity.

Synonyms: arginine dihydrolase pathway, arginine deiminase degradation

Superclasses: Degradation/Utilization/Assimilation Amino Acids Degradation Arginine Degradation
Superpathways

Some taxa known to possess this pathway include ? : Aeromonas caviae , Aphanocapsa , Arabidopsis thaliana col , Giardia intestinalis , Halobacterium salinarum , Hexamita inflata , Lactobacillus hilgardii , Mycoplasma hominis , Mycoplasma pneumoniae M129 , Pseudomonas aeruginosa , Spiroplasma citri , Streptococcus ratti , Treponema denticola , Trichomonas vaginalis , Tritrichomonas suis , [Clostridium] sticklandii

Expected Taxonomic Range: Archaea , Bacteria , Eukaryota

Summary:
The arginine deiminase (ADI) pathway is widely distributed among prokaryotic organisms. It has been detected in many organisms, including lactic bacteria [Arena99, Arena99a, Arena05], Bacilii [Ottow74, Broman78], Pseudomonas species [Vander84, Stalon87], Aeromonas species [Stalon82], Clostridia [Schmidt52, Mitruka67], Mycoplasma secies [Schimke66, Tyldesley75, Vander84, Lin86], Sterptococci [CasianoColon88, Dong02], Spiroplasma secies [Igwebe78], Spirochaetes [Blakemore76], and cyanobacteria [Weathers78]. It was also demonstrated in the halophylic archaeon Halobacterium salinarum [Dundas66]. In addition, the pathway is also present in some primitive eukaryotic protozoans, including Trichomonas vaginalis [Linstead83], Tritrichomonas suis [Yarlett94], Hexamita inflata [Biagini03], and Giardia intestinalis, in which it plays a significant role in energy metabolism, providing a route for anaerobic substrate level phosphorylation [Schofield90].

The enzymes of this pathway have also been found in Arabidopsis thaliana col, and it was shown that Arabidopsis chloroplasts can metabolize arginine and citrulline all the way to CO2. However, since Arabidopsis rarely encounters exogenous arginine or citrulline, it is assumed that in this organism this pathway may serve as a means for extracting nitrogen from endogenous sources [Ludwig93].

Organisms that employ this pathway use the enzyme arginine deiminase to convert arginine to L-citrulline and ammonia. Citrulline is degraded further (see citrulline degradation), forming ATP, CO2, and L-ornithine [Ruepp96, Arena99a]. The arginine deiminase pathway provides the organisms with energy, carbon, and nitrogen. In addition, it has been suggested that the pathway can also protect some bacteria from acidic conditions, by the production of ammonia. Indeed, the arginine deiminase system can function at very low pH. For example, in Spiroplasma citri FA-1, the pH at which arginolysis was reduced to 10% of the maximum was between 2.1 and 2.6, or more than 1 full pH unit below the minimum for glycolysis (pH 3.7), and more than 2 units below the minimum for growth in complex medium (pH 4.7) [CasianoColon88]. The arginine deiminase pathway is thought to be a critical factor in oral biofilm pH homeostasis that may inhibit the emergence of a cariogenic flora [Burne00a].

The genes encoding the enzymes of this pathway are often found in an operon, which may also include the arcD gene, encoding a membrane-bound arginine-ornithine antiporter, as well as a putative aminopeptidase-encoding arcT gene and a regulator-encoding arcR gene [Verhoogt92, Zuniga98, Zuniga02a].

Citations: [Zuniga02b]

Superpathways: arginine, ornithine and proline interconversion

Subpathways: citrulline degradation

Variants: arginine degradation I (arginase pathway) , arginine degradation II (AST pathway) , arginine degradation III (arginine decarboxylase/agmatinase pathway) , arginine degradation IV (arginine decarboxylase/agmatine deiminase pathway) , arginine degradation VI (arginase 2 pathway) , arginine degradation VII (arginase 3 pathway) , arginine degradation VIII (arginine oxidase pathway) , arginine degradation IX (arginine:pyruvate transaminase pathway) , arginine degradation X (arginine monooxygenase pathway) , arginine degradation XI , arginine degradation XII , citrulline-nitric oxide cycle , D-arginine degradation , superpathway of arginine and ornithine degradation , superpathway of arginine, putrescine, and 4-aminobutyrate degradation

Unification Links: AraCyc:ARGDEGRAD-PWY

Credits:
Created 21-Sep-1998 by Wagg J , SRI International
Revised 22-Sep-2005 by Caspi R , SRI International


References

Arena05: Arena ME, Manca de Nadra MC (2005). "Influence of ethanol and low pH on arginine and citrulline metabolism in lactic acid bacteria from wine." Res Microbiol NIL. PMID: 15939575

Arena99: Arena ME, Saguir FM, Manca de Nadra MC (1999). "Arginine dihydrolase pathway in Lactobacillus plantarum from orange." Int J Food Microbiol 47(3);203-9. PMID: 10359490

Arena99a: Arena ME, Saguir FM, Manca de Nadra MC (1999). "Arginine, citrulline and ornithine metabolism by lactic acid bacteria from wine." Int J Food Microbiol 52(3);155-61. PMID: 10733246

Biagini03: Biagini GA, Yarlett N, Ball GE, Billetz AC, Lindmark DG, Martinez MP, Lloyd D, Edwards MR (2003). "Bacterial-like energy metabolism in the amitochondriate protozoon Hexamita inflata." Mol Biochem Parasitol 128(1);11-9. PMID: 12706792

Blakemore76: Blakemore RP, Canale-Parola E (1976). "Arginine catabolism by Treponema denticola." J Bacteriol 128(2);616-22. PMID: 977548

Broman78: Broman K, Lauwers N, Stalon V, Wiame JM (1978). "Oxygen and nitrate in utilization by Bacillus licheniformis of the arginase and arginine deiminase routes of arginine catabolism and other factors affecting their syntheses." J Bacteriol 135(3);920-7. PMID: 690081

Burne00a: Burne RA, Marquis RE (2000). "Alkali production by oral bacteria and protection against dental caries." FEMS Microbiol Lett 193(1);1-6. PMID: 11094270

CasianoColon88: Casiano-Colon A, Marquis RE (1988). "Role of the arginine deiminase system in protecting oral bacteria and an enzymatic basis for acid tolerance." Appl Environ Microbiol 54(6);1318-24. PMID: 2843090

Cunin86: Cunin R, Glansdorff N, Pierard A, Stalon V (1986). "Biosynthesis and metabolism of arginine in bacteria." Microbiol Rev 1986;50(3);314-52. PMID: 3534538

Dong02: Dong Y, Chen YY, Snyder JA, Burne RA (2002). "Isolation and molecular analysis of the gene cluster for the arginine deiminase system from Streptococcus gordonii DL1." Appl Environ Microbiol 68(11);5549-53. PMID: 12406748

Dundas66: Dundas IE, Halvorson HO (1966). "Arginine metabolism in Halobacterium salinarium, an obligately halophilic bacterium." J Bacteriol 91(1);113-9. PMID: 5903088

Igwebe78: Igwebe, E. C. K., Thomas, C. (1978). "Occurrence of enzymes of arginine dihydrolase pathway in Spiroplasma citri." J. Gen. Appl. Microbiol. 84:261-269.

Lin86: Lin JS (1986). "Arginine deiminase of Mycoplasma hominis: cytoplasmic and membrane-associated forms." J Gen Microbiol 132(6);1467-74. PMID: 3806049

Linstead83: Linstead D, Cranshaw MA (1983). "The pathway of arginine catabolism in the parasitic flagellate Trichomonas vaginalis." Mol Biochem Parasitol 8(3);241-52. PMID: 6312311

Ludwig93: Ludwig RA (1993). "Arabidopsis chloroplasts dissimilate L-arginine and L-citrulline for use as N source." Plant Physiol 101(2);429-34. PMID: 8278506

Mitruka67: Mitruka BM, Costilow RN (1967). "Arginine and ornithine catabolism by Clostridium botulinum." J Bacteriol 93(1);295-301. PMID: 5335895

Ottow74: Ottow JC (1974). "Arginine dihydrolase activity in species of the genus Bacillus revealed by thin-layer chromatography." J Gen Microbiol 84(1);209-13. PMID: 4436643

Ruepp96: Ruepp A, Soppa J (1996). "Fermentative arginine degradation in Halobacterium salinarium (formerly Halobacterium halobium): genes, gene products, and transcripts of the arcRACB gene cluster." J Bacteriol 1996;178(16);4942-7. PMID: 8759859

Schimke66: Schimke RT, Berlin CM, Sweeney EW, Carroll WR (1966). "The generation of energy by the arginine dihydrolase pathway in Mycoplasma hominis 07." J Biol Chem 241(10);2228-36. PMID: 5911610

Schmidt52: Schmidt, G.C., Logan, M.A., Tytell, A.A. (1952). "The degradation of arginine by Clostridium perfringens (BP6K)." J Biol Chem 198(2);771-83. PMID: 12999794

Schofield90: Schofield PJ, Costello M, Edwards MR, O'Sullivan WJ (1990). "The arginine dihydrolase pathway is present in Giardia intestinalis." Int J Parasitol 20(5);697-9. PMID: 2228433

Stalon82: Stalon V, Simon JP, Mercenier A (1982). "Enzymes of arginine utilization and their formation in Aeromonas formicans NCIB 9232." Arch Microbiol 133(4);295-9. PMID: 6303241

Stalon87: Stalon V, Vander Wauven C, Momin P, Legrain C (1987). "Catabolism of arginine, citrulline and ornithine by Pseudomonas and related bacteria." J Gen Microbiol 133(9);2487-95. PMID: 3129535

Tyldesley75: Tyldesley WR, Kempson SA (1975). "Ultrastructure of the oral epithelium in leukoplakia associated with tylosis and esophageal carcinoma." J Oral Pathol 4(2);49-58. PMID: 126306

Vander84: Vander Wauven C, Pierard A, Kley-Raymann M, Haas D (1984). "Pseudomonas aeruginosa mutants affected in anaerobic growth on arginine: evidence for a four-gene cluster encoding the arginine deiminase pathway." J Bacteriol 160(3);928-34. PMID: 6438064

Verhoogt92: Verhoogt HJ, Smit H, Abee T, Gamper M, Driessen AJ, Haas D, Konings WN (1992). "arcD, the first gene of the arc operon for anaerobic arginine catabolism in Pseudomonas aeruginosa, encodes an arginine-ornithine exchanger." J Bacteriol 174(5);1568-73. PMID: 1311296

Weathers78: Weathers PJ, Chee HL, Allen MM (1978). "Arginine catabolism in Aphanocapsa 6308." Arch Microbiol 118(1);1-6. PMID: 100070

Yarlett94: Yarlett N, Lindmark DG, Goldberg B, Moharrami MA, Bacchi CJ (1994). "Subcellular localization of the enzymes of the arginine dihydrolase pathway in Trichomonas vaginalis and Tritrichomonas foetus." J Eukaryot Microbiol 41(6);554-9. PMID: 7866382

Zuniga02a: Zuniga M, Miralles Md Mdel C, Perez-Martinez G (2002). "The Product of arcR, the sixth gene of the arc operon of Lactobacillus sakei, is essential for expression of the arginine deiminase pathway." Appl Environ Microbiol 68(12);6051-8. PMID: 12450828

Zuniga02b: Zuniga M, Perez G, Gonzalez-Candelas F (2002). "Evolution of arginine deiminase (ADI) pathway genes." Mol Phylogenet Evol 25(3);429-44. PMID: 12450748

Zuniga98: Zuniga M, Champomier-Verges M, Zagorec M, Perez-Martinez G (1998). "Structural and functional analysis of the gene cluster encoding the enzymes of the arginine deiminase pathway of Lactobacillus sake." J Bacteriol 180(16);4154-9. PMID: 9696763

Other References Related to Enzymes, Genes, Subpathways, and Substrates of this Pathway

Bairoch93a: Bairoch A, Boeckmann B (1993). "The SWISS-PROT protein sequence data bank, recent developments." Nucleic Acids Res. 21:3093-3096. PMID: 8332529

Baur87: Baur H, Stalon V, Falmagne P, Luethi E, Haas D (1987). "Primary and quaternary structure of the catabolic ornithine carbamoyltransferase from Pseudomonas aeruginosa. Extensive sequence homology with the anabolic ornithine carbamoyltransferases of Escherichia coli." Eur J Biochem 166(1);111-7. PMID: 3109911

Baur90: Baur H, Tricot C, Stalon V, Haas D (1990). "Converting catabolic ornithine carbamoyltransferase to an anabolic enzyme." J Biol Chem 265(25);14728-31. PMID: 2118516

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

Chen05: Chen L, Brugger K, Skovgaard M, Redder P, She Q, Torarinsson E, Greve B, Awayez M, Zibat A, Klenk HP, Garrett RA (2005). "The genome of Sulfolobus acidocaldarius, a model organism of the Crenarchaeota." J Bacteriol 187(14);4992-9. PMID: 15995215

Editors93: Editors: Abraham L. Sonenshein, James A. Hoch, Richard Losick (1993). "Bacillus subtilis and Other Gram-Positive Bacteria: Biochemistry, Physiology, and Molecular Genetics." American Society For Microbiology, Washington, DC 20005.

Goodyear04: Goodyear CS, Silverman GJ (2004). "Staphylococcal toxin induced preferential and prolonged in vivo deletion of innate-like B lymphocytes." Proc Natl Acad Sci U S A 101(31);11392-7. PMID: 15273292

Hata86: Hata A, Tsuzuki T, Shimada K, Takiguchi M, Mori M, Matsuda I (1986). "Isolation and characterization of the human ornithine transcarbamylase gene: structure of the 5'-end region." J Biochem (Tokyo) 100(3);717-25. PMID: 3782067

Hill67: Hill DL, Chambers P (1967). "The biosynthesis of proline by Tetrahymena pyriformis." Biochim Biophys Acta 148(2);435-47. PMID: 6075416

Himmelreich96: Himmelreich R, Hilbert H, Plagens H, Pirkl E, Li BC, Herrmann R (1996). "Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae." Nucleic Acids Res 1996;24(22);4420-49. PMID: 8948633

Issaly74: Issaly IM, Issaly AS (1974). "Control of ornithine carbamoyltransferase activityby arginase in Bacillus subtilis." Eur J Biochem 1974;49(3);485-95. PMID: 4216455

Kenklies99: Kenklies J, Ziehn R, Fritsche K, Pich A, Andreesen JR (1999). "Proline biosynthesis from L-ornithine in Clostridium sticklandii: purification of delta1-pyrroline-5-carboxylate reductase, and sequence and expression of the encoding gene, proC." Microbiology 1999;145 ( Pt 4);819-26. PMID: 10220161

Knodler98: Knodler LA, Sekyere EO, Stewart TS, Schofield PJ, Edwards MR (1998). "Cloning and expression of a prokaryotic enzyme, arginine deiminase, from a primitive eukaryote Giardia intestinalis." J Biol Chem 273(8);4470-7. PMID: 9468500

Kuo82: Kuo LC, Lipscomb WN, Kantrowitz ER (1982). "Zn(II)-induced cooperativity of Escherichia coli ornithine transcarbamoylase." Proc Natl Acad Sci U S A 1982;79(7);2250-4. PMID: 7048313

Kuo83: Kuo LC "Allosteric cofactor-mediated enzyme cooperativity: A theoretical treatment." Proc Natl Acad Sci USA 1983;80:3243-3247.

Kuo85: Kuo LC, Herzberg W, Lipscomb WN (1985). "Substrate specificity and protonation state of ornithine transcarbamoylase as determined by pH studies." Biochemistry 24(18);4754-61. PMID: 3907689

Kuo88: Kuo LC, Miller AW, Lee S, Kozuma C (1988). "Site-directed mutagenesis of Escherichia coli ornithine transcarbamoylase: role of arginine-57 in substrate binding and catalysis." Biochemistry 1988;27(24);8823-32. PMID: 3072022

Kuo89: Kuo LC, Seaton BA (1989). "X-ray diffraction analysis on single crystals of recombinant Escherichia coli ornithine transcarbamoylase." J Biol Chem 1989;264(27);16246-8. PMID: 2674127

Latendresse13: Latendresse M. (2013). "Computing Gibbs Free Energy of Compounds and Reactions in MetaCyc."

Lee00a: Lee Y, Yoo SK, Lee JS, Kwon YM (2000). "Genomic structure of ornithine carbamoyltransferase gene from Canavalia lineata." Mol Cells 10(4);480-5. PMID: 10987149

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Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 18.5 on Mon Dec 22, 2014, biocyc13.