================VARIANT CODES:=================================

1.0 - complete set of de novo agrinine biosynthetic pathway functions, with the presence of both ArgA and ArgJ

1.1 - Arg J fulfils both the first and the fifth catalytic steps of the pathway.

1.2 - instead of ArgF there is an enzyme ArgF1(ArgF')- N-acetylornithine carbamoyltransferase (EC 2.1.3.9)- which catalyzes the carbamylation of N-acetyl-L-ornithine instead of L-ornithine (as in all Xanthomonas);

2.0 - no ArgJ and ArgA - like in all Bacteroides fragilis

3.0 - no ArgJ and ArgE - like in all Campylobacters except Campylobacter fetus subsp. fetus;

-1 - organism apparently does not synthesize agrinine

This is an extended version of de novo arginine biosynthetic pathway (Subsystem: Arginine Biosynthesis, master:RickS) in the light of resent enzymatic and genomic discoveries(see list of referenses).


===============Notes:=============================

ArgJ: Ornithine acetyltransferase (mono or bifunctional) annotated in Seed as: Glutamate N-acetyltransferase (EC 2.3.1.35) / Amino-acid acetyltransferase (EC 2.3.1.1)

ArgJ a is bi-functional protein and can complement absence of ArgA or ArgE.

In the arginine biosynthetic pathway of the vast majority of prokaryotes, the formation of ornithine is catalyzed by an enzyme transferring the acetyl group of N-alpha-acetylornithine to glutamate (ornithine acetyltransferase [OATase]) (argJ encoded). In many bacteria of gamma and delta groups of the class Proteobacteria ornithine is produced from N-alpha-acetylornithine by a deacylase, acetylornithinase (AOase) (argE encoded).

In C. glutamicum ornithine acetyltransferase appears monofunctional.
In E.coli, Salmonellae: Amino-acid acetyltransferase (EC 2.3.1.1) clusters with cell wall lysis related genes, ArgE- clusters with agrinine biosynthetic pathway.

ArgE-homology to dapE: N-succinyl-L,L-diaminopimelate desuccinylase (EC 3.5.1.18)
Protein fig|196164.1.peg.1523: Corynebacterium efficiens YS-314 - substitution for ArgE??-clusters with other arg. biosynthesis genes. Alpha-aminoadopate pathway of lysine biosynthesis is functionally and evolutionarily related to arginine biosynthesis.

======== ArgF1 - ArgE pathway (see diagram and Ref.2)- variant 1.2 ========================

This is a variation found in several eubacteria. While in most of the prokaryotic and eukaryotic organisms N-acetyl-L-ornithine is deacetylate to L-ornithine, which is subsequntly transcarbamylated to form citrulline, in this variant N-acetyl-L-ornithine is not deacetylated. Instead, it is transcarbamylated directly by the enzyme acetylornithine transcarbamylase, resulting in N-acetyl-L-citrulline.
The enzyme acetylornithine deacetylase can accept N-acetyl-L-citrulline as a substrate, and deacetylates it into citrulline.

======== REFERENCES: ===============

1a. Xu Y, Labedan B, Glansdorff N. Surprising arginine biosynthesis: a reappraisal of the enzymology and evolution of the pathway in microorganisms. Microbiol Mol Biol Rev. 2007 Mar;71(1):36-47. Review. PMID: 17347518

1. Xu Y, Glansdorff N, Labedan B. Bioinformatic analysis of an unusual gene-enzyme relationship in the arginine biosynthetic pathway among marine gamma proteobacteria: implications concerning the formation of N-acetylated intermediates in prokaryotes. BMC Genomics. 2006 Jan 12;7(1):4. PMID: 16409639.

2. Martin PR, Mulks MH. Sequence analysis and complementation studies of the argJ gene encoding ornithine acetyltransferase from Neisseria gonorrhoeae.
J Bacteriol. 1992 Apr;174(8):2694-701.

3. H. Morizono, J. Cabrera-Luque, D. Shi, R. Gallegos, S. Yamaguchi, X. Yu, N. M. Allewell, M. H. Malamy, and M. Tuchman. Acetylornithine transcarbamylase: a novel enzyme in arginine biosynthesis. J. Bacteriol., April 1, 2006; 188(8): 2974 - 2982.

4. Baetens M, Legrain C, Boyen A, Glansdorff N. Genes and enzymes of the acetyl cycle of arginine biosynthesis in the extreme thermophilic bacterium Thermus thermophilus HB27.Microbiology. 1998 Feb;144 ( Pt 2):479-92.

5. Sakanyan V, Petrosyan P, Lecocq M, Boyen A, Legrain C, Demarez M, Hallet JN, Glansdorff N.
Genes and enzymes of the acetyl cycle of arginine biosynthesis in Corynebacterium glutamicum: enzyme evolution in the early steps of the arginine pathway.Microbiology. 1996 Jan;142 ( Pt 1):99-108.

6. Ledwidge R, Blanchard JS. The dual biosynthetic capability of N-acetylornithine aminotransferase in arginine and lysine biosynthesis.Biochemistry. 1999 Mar 9;38(10):3019-24. PMID: 10074354.

7. Fernandez-Murga ML, Gil-Ortiz F, Llacer J, Rubio V. Arginine biosynthesis in Thermotoga maritima: characterization of the arginine-sensitive N-acetyl-L-glutamate kinase. J Bacteriol. 2004;186:6142–6149.