Acyltransferases as Tools for Polyketide Synthase Engineering

Abstract

Polyketides belong to the most valuable natural products, including diverse bioactive compounds, such as antibiotics, anticancer drugs, antifungal agents, immunosuppressants and others. Their structures are assembled by polyketide synthases (PKSs). Modular PKSs are composed of modules, which involve sets of domains catalysing the stepwise polyketide biosynthesis. The acyltransferase (AT) domains and their “partners”, the acyl carrier proteins (ACPs), thereby play an essential role. The AT loads the building blocks onto the “substrate acceptor”, the ACP. Thus, the AT dictates which building blocks are incorporated into the polyketide structure. The precursor- and occasionally the ACP-specificity of the ATs differ across the polyketide pathways and therefore, the ATs contribute to the structural diversity within this group of complex natural products. Those features make the AT enzymes one of the most promising tools for manipulation of polyketide assembly lines and generation of new polyketide compounds. However, the AT-based PKS engineering is still not straightforward and thus, rational design of functional PKSs requires detailed understanding of the complex machineries. This review summarizes the attempts of PKS engineering by exploiting the AT attributes for the modification of polyketide structures. The article includes 253 references and covers the most relevant literature published until May 2018.

Actinomycete-Derived Polyketides as a Source of Antibiotics and Lead Structures for the Development of New Antimicrobial Drugs

“…In the past, the producers of valuable bioactive compounds were mainly isolated from soil samples and either directly or indirectly, using culture filtrates or extracts, subjected to susceptibility testing (diffusion method) ( Figure 1). Recent advances in different disciplines of science, such as robotics [3], biology [4], chemistry [5][6][7], genetics [8], and/or bioinformatics [9] has extended the spectrum of methodology applied to the isolation and identification of actinomycetes and the produced metabolites. In addition to technical innovations which, for example, enable sampling of unexplored and difficult to access environments, Next Generation Sequencing Technologies (NGST) and genome mining facilitate accurate and cost-effective sequencing of actinomycetes genomes and a fast identification of genes encoding the proteins of the secondary metabolite biosynthetic machineries (biosynthetic gene clusters, BGCs).…”

Biosynthetic engineering of the antifungal, anti-MRSA auroramycin

“…To engineer the extender units that constitute the macrocycle core (Figure 1, 4), we first examined a strategy consisting of complementation of an inactivated cis -acyltransferase with a trans -acting acyltransferase of a different specificity (Figure 4A, [16]). Previous AT complementation examples include complementation of a single module (DEBS Mod6) for the production of 2-desmethyl-6-dEB by malonyltransferase [17] and by a trans -acting AT from bryostatin PKS [18].…”

“…However, these strategies are not trivial and should be undertaken for natural products of high interest. Further diversity for targeted functional groups can be achieved by altering enzyme specificities and swapping enzyme domains [16, 27].…”

Computer-aided re-engineering of nonribosomal peptide and polyketide biosynthetic assembly lines

“…One example is the exchange of module 1 and 2 (load methylmalonyl-CoA) of DEBS by specic malonyl-CoA modules of Streptomyces hygroscopicus ATCC 29253 and the rapamycin module 14 PKS. 68,69 New derivatives were obtained, however, again with strongly decreased yield. It is noteworthy to mention that the drop in production was highly dependent on the swapping position of the PKS assembly line.…”

“…For successful engineering of PKSs, the identication of the interaction regions and the elucidation of the mechanism involved in the communication between the domains or modules is required. 68 For PKS engineering, the studies have been based on two research lines: modication of AT domains and docking domains (DDs). Principally, the engineering of ATs has concentrated on the swapping of solely AT domains or the complete module.…”