Genome Mining and Evolutionary Analysis Reveal Diverse Type III Polyketide Synthase Pathways in Cyanobacteria

Abstract

Cyanobacteria are prolific producers of natural products, including polyketides and hybrid compounds thereof. Type III polyketide synthases (PKSs) are of particular interest, due to their wide substrate specificity and simple reaction mechanism, compared to both type I and type II PKSs. Surprisingly, only two type III PKS products, hierridins and (7.7)paracyclophanes, have been isolated from cyanobacteria. Here we report the mining of 517 cyanobacterial genomes for type III PKS biosynthesis gene clusters. Approximately 17% of the genomes analysed encoded one or more type III PKSs. Together with already characterised type III PKSs, the phylogeny of this group of enzymes was investigated. Our analysis showed that type III PKSs in cyanobacteria evolved into three major lineages, including enzymes associated with (i) (7.7)paracyclophane-like biosynthesis gene clusters, (ii) hierridin-like biosynthesis gene clusters, and (iii) cytochrome b5 genes. The evolutionary history of these enzymes is complex, with some sequences partitioning primarily according to speciation and others putatively according to their reaction type. Protein modelling showed that cyanobacterial type III PKSs generally have a smaller active site cavity (mean = 109.035 Å3) compared to enzymes from other organisms. The size of the active site did not correlate well with substrate size, however, the ‘Gatekeeper’ amino acid residues within the active site were strongly correlated to enzyme phylogeny. Our study provides unprecedented insight into the distribution, diversity and molecular evolution of cyanobacterial type III PKSs, which could facilitate the discovery, characterisation and exploitation of novel enzymes, biochemical pathways, and specialised metabolites from this biosynthetically talented clade of microorganisms.

Characterization of the Key Bibenzyl Synthase in Dendrobium sinense

“…With the advent of high-throughput sequencing technologies, it has become increasingly feasible to explore a single gene or gene family [ 1 , 13 , 22 ]. To identify the key type III PKS genes involved in bibenzyl biosynthesis, the roots, pseudobulbs, and leaves of D. sinense were individually sequenced by Illumina platform.…”

“…Type III polyketide synthases (PKSs) catalyze cyclization and aromatization of intermediate to form polyketides [ 13 ]. The combinational difference of enzyme bound substrates may cause the functional difference of PKSs [ 14 ].…”

Production, Biosynthesis, and Commercial Applications of Fatty Acids From Oleaginous Fungi

“…The type I has a multidomain architecture whose active sites were distributed on large modules, while the type II is composed of monofunctional enzymes, with catalytic sites separated on different proteins ( 119 ). Type III polyketide synthases (PKSs) produce secondary metabolites with diverse biological activities, including antimicrobials ( 120 , 121 ). In contrast to types I and II, type III PKSs are dimers of ketone synthases that undergo a series of reactions such as initiation of primer substrates, decarboxylation condensation of extended substrates, ring closure of growing polyketide chains and aromatization, and produce a variety of biologically active aromatic compounds ( 122 ).…”

Potential of Producing Flavonoids Using Cyanobacteria As a Sustainable Chassis

“…The reaction then enters the first committed enzyme in flavonoid biosynthesis mediated by chalcone synthase (CHS), the most-widely studied type III prototype polyketide synthase. 136,137 additional catalytic step, which is mediated by the intramolecular lyase chalcone isomerase (CHI), to generate classic flavonoids, referred to as naringenin. Naringenin is the precursor for a variety of flavonoids, and downstream pathways involve enzymes such as flavone synthase (FNS), flavanone hydroxylase (F3H), flavonol synthase (FLS), dihydroflavonol 4-reductase (DFR), and anthocyanidin synthase (ANS) or is further modified through UDP glucosyltransferase, O-methyltransferases, and acyltransferases.…”

“…In the subsequent step, 4-coumarate-CoA ligase (4CL) catalyzes the conversion of p -coumaric acid into an activated CoA thioester format, p -coumaroy-CoA. The reaction then enters the first committed enzyme in flavonoid biosynthesis mediated by chalcone synthase (CHS), the most-widely studied type III prototype polyketide synthase. , CHS catalyzes condensation of the C 6 –C 3 unit of p -coumaroy-CoA with three C 2 units of malonyl-CoA to form chalcone as the central C 15 intermediate, from which structurally diverse flavonoids are derived. Critically, chalcone requires an additional catalytic step, which is mediated by the intramolecular lyase chalcone isomerase (CHI), to generate classic flavonoids, referred to as naringenin.…”