Biosynthesis of aromatic polyketides in bacteria

Abstract

Natural products, produced chiefly by microorganisms and plants, can be large and structurally complex molecules. These molecules are manufactured by cellular assembly lines, in which enzymes construct the molecules in a stepwise fashion. The means by which enzymes interact and work together in a modular fashion to create diverse structural features has been an active area of research; the work has provided insight into the fine details of biosynthesis. A number of polycyclic aromatic natural products--including several noteworthy anticancer, antibacterial, antifungal, antiviral, antiparasitic, and other medicinally significant substances--are synthesized by polyketide synthases (PKSs) in soil-borne bacteria called actinomycetes. Concerted biosynthetic, enzymological, and structural biological investigations into these modular enzyme systems have yielded interesting mechanistic insights. A core module called the minimal PKS is responsible for synthesizing a highly reactive, protein-bound poly-beta-ketothioester chain. In the absence of other enzymes, the minimal PKS also catalyzes chain initiation and release, yielding an assortment of polycyclic aromatic compounds. In the presence of an initiation PKS module, polyketide backbones bearing additional alkyl, alkenyl, or aryl primer units are synthesized, whereas a range of auxiliary PKS enzymes and tailoring enzymes convert the product of the minimal PKS into the final natural product. In this Account, we summarize the knowledge that has been gained regarding this family of PKSs through recent investigations into the biosynthetic pathways of two natural products, actinorhodin and R1128 (A-D). We also discuss the practical relevance of these fundamental insights for the engineered biosynthesis of new polycyclic aromatic compounds. With a deeper understanding of the biosynthetic process in hand, we can assert control at various stages of molecular construction and thus introduce unnatural functional groups in the process. The metabolic engineer affords a number of new avenues for creating novel molecular structures that will likely have properties akin to their fully natural cousins.

Figure 1

Structures of selected actinomyces-derived aromatic polyketides [DMAC: 3,8-dihydroxy-1-methylanthraquinone-2-carboxylic acid].

Figure 2

Schematic representation of DMAC (3,8-dihydroxy-1-methylanthraquinone-2-carboxylic acid) biosynthesis by the act PKS. The cysteine thiol of the KS and the pantetheinyl thiol of the ACP are explicitly shown. Chain growth is initiated via decarboxylation of malonyl-ACP, followed by transfer of the resultant acetyl group onto the KS. Following seven rounds of chain elongation, the ACP-bound octaketide is released from the KS-CLF, whereafter it is modified by various auxiliary PKS subunits and tailoring enzymes into DMAC or actinorhodin. The atomic structures of all proteins shown, except for the act ARO/CYC and CYC, have been solved. The relevant PDB coordinate filenames are: 1TQY (act KS-CLF), 1OR5 (ACP), 1NM2 (MAT), 1X7H (act KR). [KS: Ketosynthase; CLF: Chain Length Factor; ACP: Acyl Carrier Protein; MAT: Malonyl-CoA:ACP Transacylase; KR: Ketoreductase; ARO: Aromatase; CYC: Cyclase, NADP: Nicotinamide Adenine Dinucleotide Phosphate]

Figure 3

Schematic representation of the initiation PKS module of the R1128 synthase. The cysteine and pantetheinyl thiols of the two KSs and two ACPs, respectively are explicitly shown. Chain growth is initiated by the initiation module, followed by transfer to the elongation module. Those enzymes whose structures are known are shown as ribbon diagrams; their PDB coordinate file-names are: 1MZJ (ZhuH, KSIII), 2NM0 (β-Ketoacyl-Acyl Carrier Protein Reductase, KR); 1TQY (act KS-CLF), 1OR5 (ACP), 1NM2 (MAT). The ACP cartoons in red and blue refer to the ACP from initiation module and elongation module respectively. [KS: Ketosynthase; CLF: Chain Length Factor; ACP: Acyl Carrier Protein; MAT: Malonyl-CoA:ACP Transacylase; KR: Ketoreductase; DH: Dehydratase; ER: Enoyl Reductase; NADP: Nicotinamide Adenine Dinucleotide Phosphate]

Figure 4

Aromatic Polyketides produced by (A) act Minimal PKS and (B) R1128 Initiation Module and tcm Minimal PKS. The act minimal PKS synthesizes a C₁₆ carbon chain backbone that is primed by acetyl group. The five and six-carbon primer unit in YT127 and YT127b respectively is derived from the initiation module of the R1128 PKS. In conjunction with this initiation module, the tcm minimal PKS therefore synthesizes an octaketide backbone rather than a decaketide backbone, so that the chain length of the resulting polyketide product remains constant.