Surprising Arginine Biosynthesis: a Reappraisal of the Enzymology and Evolution of the Pathway in Microorganisms

Abstract

SUMMARY Major aspects of the pathway of de novo arginine biosynthesis via acetylated intermediates in microorganisms must be revised in light of recent enzymatic and genomic investigations. The enzyme N-acetylglutamate synthase (NAGS), which used to be considered responsible for the first committed step of the pathway, is present in a limited number of bacterial phyla only and is absent from Archaea. In many Bacteria, shorter proteins related to the Gcn5-related N-acetyltransferase family appear to acetylate l-glutamate; some are clearly similar to the C-terminal, acetyl-coenzyme A (CoA) binding domain of classical NAGS, while others are more distantly related. Short NAGSs can be single gene products, as in Mycobacterium spp. and Thermus spp., or fused to the enzyme catalyzing the last step of the pathway (argininosuccinase), as in members of the Alteromonas-Vibrio group. How these proteins bind glutamate remains to be determined. In some Bacteria, a bifunctional ornithine acetyltransferase (i.e., using both acetylornithine and acetyl-CoA as donors of the acetyl group) accounts for glutamate acetylation. In many Archaea, the enzyme responsible for glutamate acetylation remains elusive, but possible connections with a novel lysine biosynthetic pathway arose recently from genomic investigations. In some Proteobacteria (notably Xanthomonadaceae) and Bacteroidetes, the carbamoylation step of the pathway appears to involve N-acetylornithine or N-succinylornithine rather than ornithine. The product N-acetylcitrulline is deacetylated by an enzyme that is also involved in the provision of ornithine from acetylornithine; this is an important metabolic function, as ornithine itself can become essential as a source of other metabolites. This review insists on the biochemical and evolutionary implications of these findings.

The Crystal Structure of N-Acetyl-L-glutamate Synthase from Neisseria gonorrhoeae Provides Insights into Mechanisms of Catalysis and Regulation

“…This assertion is consistent with the observations in various NAGS enzymes indicating that the NAT domain is essential for catalysis, whereas the AAK domain may be missing, or if present may or may not have NAGK activity or may even be part of an argH encoded argininosuccinate lyase (49). Based on the above results, the AAK domain in N. gonorrhoeae NAGS does not participate in the glutamate binding contrary to previous hypotheses (12,50). This observation is reminiscent of aspartate transcarbamylase in which the essential catalytic trimer can function alone, complexed with active or inactive dihydroorotase, or regulatory units or even fused to other proteins such as carbamylphosphate synthetase and dihydroorotase (51).…”

Genetic and biochemical characterization of arginine biosynthesis in Sinorhizobium meliloti 1021

“…Most bacteria have only ArgE or ArgJ, and can thus be unambiguously classified as having the linear or recycling pathway, respectively. While the co-occurrence of both enzymes in the same organism is rare, it occurs in the model laboratory organisms Pseudomonas aeruginosa and Corynebacterium glutamicum (Xu et al, 2007).…”

“…Strain 1021 encodes several arg(A) candidates but individual inactivation of these genes did not cause arginine auxotrophy (Madrid, 2013). The presumed presence of a bifunctional ArgJ would make the activity of an Arg(A) unnecessary or purely anaplerotic (Xu et al, 2007).…”

“…Several variations in the enzymic steps converting glutamate to arginine exist in bacteria, making it an attractive model for studying genetic and biochemical regulation (Cunin et al, 1986;Xu et al, 2007). Arginine biosynthesis begins with the transfer of the acetyl group from acetyl-coenzyme A (acetyl-CoA) to glutamate, forming N-acetylglutamate (NAG).…”

“…In bacteria with the recycling pathway, arginine allosterically inhibits ArgB (a homohexamer). In the linear pathway, the target of arginine inhibition is ArgA, and the ArgB (a homodimer) is arginine insensitive (Xu et al, 2007).…”