Investigating the Role of Class I Adenylate-Forming Enzymes in Natural Product Biosynthesis

Abstract

Adenylate-forming enzymes represent one of the most important enzyme classes in biology, responsible for the activation of carboxylate substrates for biosynthetic modifications. The byproduct of the adenylate-forming enzyme acetyl-CoA synthetase, acetyl-CoA, is incorporated into virtually every primary and secondary metabolic pathway. Modification of acetyl-CoA by an array of other adenylate-forming enzymes produces complex classes of natural products including nonribosomal peptides, polyketides, phenylpropanoids, lipopeptides, and terpenes. Adenylation domains possess a variety of unique structural and functional features that provide for such diversification in their resulting metabolites. As the number of organisms with sequenced genomes increases, more adenylate-forming enzymes are being identified, each with roles in metabolite production that have yet to be characterized. In this Review, we explore the broad role of class I adenylate-forming enzymes in the context of natural product biosynthesis and how they contribute to primary and secondary metabolism by focusing on important work conducted in the field. We highlight features of subclasses from this family that facilitate the production of structurally diverse metabolites, including those from noncanonical adenylation domains, and additionally discuss when biological roles for these compounds are known.

Global analysis of adenylate-forming enzymes reveals β-lactone biosynthesis pathway in pathogenic Nocardia

“…Adenylation is a widespread and essential reaction in nature to transform inert carboxylic acid groups into high energy acyl-AMP intermediates. Class I adenylate-forming enzymes catalyze reactions for natural product biosynthesis, firefly bioluminescence, and the activation of fatty acids with coenzyme A (1). The conversion of acetate to acetyl-CoA by a partially purified acetyl-CoA ligase was first described by Lipmann in 1944 (2).…”

Linking Genes to Molecules in Eukaryotic Sources: An Endeavor to Expand Our Biosynthetic Repertoire

“…Remarkably, many of these organisms contain multi-modular type I PKS and FAS genes with unknown metabolites [128,131,132]. While there is not a definitively known function for the polyketide metabolites within these organisms, we [131] and others [133,134] have hypothesized structural roles in oocyst wall formation, analogous to polyketide-derived mycolic acids in Mycobacterium spp. cell walls [135].…”

“…Some secondary metabolites from these organisms have been associated with altering specific life cycle stages, including facilitating egress from the host cell [129] and potentially increasing transmission rates [130]. Remarkably, many of these organisms contain multi-modular type I PKS and FAS genes with unknown metabolites [128,131,132]. While there is not a definitively known function for the polyketide metabolites within these organisms, we [131] and others [133,134] have hypothesized structural roles in oocyst wall formation, analogous to polyketide-derived mycolic acids in Mycobacterium spp.…”

The crystal structure of AjiA1 reveals a novel structural motion mechanism in the adenylate-forming enzyme family

“…Although class I AFE members show divergence in structural features and function, they all catalyze the same general biochemical transformation (Lux et al, 2019;D'Ambrosio & Derbyshire, 2020). AFEs catalyze this reaction in two steps: they first catalyze the ATP-dependent activation of a carboxylic acid substrate as a reactive acyl adenylate (acyl-AMP) intermediate, which is followed by the binding of the enzyme by an acceptor molecule and the consecutive transfer of the acyl adenylate to a nucleophilic O, S or N atom, generating ester, thioester and amide products, respectively (Lux et al, 2019;D'Ambrosio & Derbyshire, 2020;Duckworth et al, 2012).…”

“…Structurally, the active site is at the interface of N-terminal and C-terminal domains, which are connected by a flexible hinge (Schmelz & Naismith, 2009;D'Ambrosio & Derbyshire, 2020). To catalyze the adenylation reaction, the class I AFEs undergo extensive conformational changes during the second half of the reaction (Lux et al, 2019).…”