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Background  The N-acetylation of L-glutamate is regarded as a universal metabolic strategy to commit glutamate towards arginine biosynthesis. Until recently, this reaction was thought to be catalyzed by either of two enzymes: (i) the classical N-acetylglutamate synthase (NAGS, gene  argA ) first characterized in  Escherichia coli  and  Pseudomonas aeruginosa  several decades ago and also present in vertebrates, or (ii) the bifunctional version of ornithine acetyltransferase (OAT, gene  argJ ) present in Bacteria, Archaea and many Eukaryotes. This paper focuses on a new and surprising aspect of glutamate acetylation. We recently showed that in  Moritella abyssi  and  M. profunda , two marine gamma proteobacteria, the gene for the last enzyme in arginine biosynthesis ( argH ) is fused to a short sequence that corresponds to the C-terminal, N-acetyltransferase-encoding domain of NAGS and is able to complement an  argA  mutant of  E. coli . Very recently, other authors identified in  Mycobacterium tuberculosis  an independent gene corresponding to this short C-terminal domain and coding for a new type of NAGS. We have investigated the two prokaryotic Domains for patterns of gene-enzyme relationships in the first committed step of arginine biosynthesis.    Results  The  argH-A  fusion, designated  argH(A) , and discovered in  Moritella  was found to be present in (and confined to) marine gamma proteobacteria of the  Alteromonas-  and  Vibrio- like group. Most of them have a classical NAGS with the exception of  Idiomarina loihiensis  and  Pseudoalteromonas haloplanktis  which nevertheless can grow in the absence of arginine and therefore appear to rely on the  arg(A)  sequence for arginine biosynthesis. Screening prokaryotic genomes for virtual  argH-X  'fusions' where  X  stands for a homologue of  arg(A) , we retrieved a large number of Bacteria and several Archaea, all of them devoid of a classical NAGS. In the case of  Thermus thermophilus  and  Deinococcus radiodurans , the  arg(A )-like sequence clusters with  argH  in an operon-like fashion. In this group of sequences, we find the short novel NAGS of the type identified in  M. tuberculosis . Among these organisms, at least  Thermus ,  Mycobacterium  and  Streptomyces  species appear to rely on this short NAGS version for arginine biosynthesis.    Conclusion  The gene-enzyme relationship for the first committed step of arginine biosynthesis should now be considered in a new perspective. In addition to bifunctional OAT, nature appears to implement at least three alternatives for the acetylation of glutamate. It is possible to propose evolutionary relationships between them starting from the same ancestral N-acetyltransferase domain. In  M. tuberculosis  and many other bacteria, this domain evolved as an independent enzyme, whereas it fused either with a carbamate kinase fold to give the classical NAGS (as in  E. coli)  or with  argH  as in marine gamma proteobacteria. Moreover, there is an urgent need to clarify the current nomenclature since the same gene name  argA  has been used to designate structurally different entities. Clarifying the confusion would help to prevent erroneous genomic annotation.

bmc genomics

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