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|
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
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 [Burne00].
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, Zuniga02].
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
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
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
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
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
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
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
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
Zuniga02: 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
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
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
Chen05a: 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
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
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
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
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