Discovery of a New Bacterial Polyketide Biosynthetic Pathway

Moore, Bradley S.; Hopke, Jörn

doi:10.1002/1439-7633(20010105)2:1<35::aid-cbic35>3.0.co;2-1

Cited by 105 publications

(88 citation statements)

References 17 publications

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“…Structural models were generated using the rotamer library approach of the SCWRL program and the INSIGHT II package (version 2.3.5; Biosym Technologies, San Diego) was used for energy minimization and depiction of structural models. (8). Although none of the type III PKS identified through genome sequencing efforts has been characterized, these results suggest that type III PKS is prevalent in bacteria as well.…”

Section: Methodsmentioning

confidence: 99%

“…The dendrogram based on complete protein sequences had two major branches corresponding to plants and microbial PKSs; further categorization within the plant family was not feasible (8,17). Since protein sequence diversity between plant and bacterial type III PKSs correlates with functional differences between the two systems, it is possible that the active site residues in the catalytic pocket can facilitate more reliable clustering.…”

Section: Homology-basedmentioning

confidence: 99%

“…Type II PKSs are a large multienzyme complex of discrete proteins and resemble type II fatty acid synthases found in bacteria and plants. The type III PKS has been recently discovered in bacteria and belongs to the plant chalcone synthases (CHSs) superfamily of condensing enzymes (8). These are homodimeric proteins and are structurally and mechanistically quite distinct from type I and type II PKSs (9).…”

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confidence: 99%

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A New Family of Type III Polyketide Synthases in Mycobacterium tuberculosis

Saxena

Yadav²,

Mohanty

et al. 2003

Journal of Biological Chemistry

105

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The Mycobacterium tuberculosis genome has revealed a remarkable array of polyketide synthases (PKSs); however, no polyketide product has been isolated thus far. Most of the PKS genes have been implicated in the biosynthesis of complex lipids. We report here the characterization of two novel type III PKSs from M. tuberculosis that are involved in the biosynthesis of long-chain ␣-pyrones. Measurement of steady-state kinetic parameters demonstrated that the catalytic efficiency of PKS18 protein was severalfold higher for long-chain acyl-coenzyme A substrates as compared with the smallchain precursors. The specificity of PKS18 and PKS11 proteins toward long-chain aliphatic acyl-coenzyme A (C 12 to C 20 ) substrates is unprecedented in the chalcone synthase (CHS) family of condensing enzymes. Based on comparative modeling studies, we propose that these proteins might have evolved by fusing the catalytic machinery of CHS and ␤-ketoacyl synthases, the two evolutionarily related members with conserved thiolase fold. The mechanistic and structural importance of several active site residues, as predicted by our structural model, was investigated by performing site-directed mutagenesis. The functional identification of diverse catalytic activity in mycobacterial type III PKSs provide a fascinating example of metabolite divergence in CHSlike proteins.Mycobacteria are classified in the phylogeny of the Actinomycetes, along with the Streptomyces bacteria. Interestingly, these two actinomycete genera have received immense attention due to their contrasting effects on human society. Whereas Streptomyces have provided a rich source of antibiotics and other therapeutic products for human diseases, Mycobacterium tuberculosis and Mycobacterium leprae have been two of humankind's greatest scourges. Although the original phylogenic classifications of Mycobacterium and Streptomyces were based primarily on morphology, the genome sequences of these organisms have further established their common lineage (1, 2). These genome sequences have revealed several families of genes that are common between them, which include an unusually large number of gene clusters that are homologous to polyketide synthases (PKSs). 1 Although a polyketide producthas not yet been isolated from M. tuberculosis, recent studies have implicated some of its PKS genes in the biosynthesis of complex lipids (3). In this report, we have characterized two novel polyketide synthases from M. tuberculosis, which are involved in the biosynthesis of unusual long-chain ␣-pyrones.Polyketides are a diverse class of secondary metabolites that possess a broad range of biological activities (4). Despite structural diversity of these natural products, PKSs synthesize polyketides by a common chemical strategy. Initial priming by a starter molecule is followed by repetitive decarboxylative condensation of coenzyme A (CoA) analogues of simple carboxylic acids. PKS elongates the polyketide chain either by repetitively using a single active site to perform multiple condensation reaction...

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Section: Methodsmentioning

confidence: 99%

Section: Homology-basedmentioning

confidence: 99%

mentioning

confidence: 99%

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A New Family of Type III Polyketide Synthases in Mycobacterium tuberculosis

Saxena

Yadav²,

Mohanty

et al. 2003

Journal of Biological Chemistry

105

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“…Phylogenetic analyses of more bacterial type III PKS from whole-genome sequencing (e.g. S. coelicolor, Bacillus subtilis, and Mycobacterium tuberculosis) have made it clear that these enzymes belong to the CHS/STS superfamily of PKSs previously only found in plants (Schrö der, 1999;Moore and Hö pke, 2001). Some unusual mechanisms of PKS biochemistry have been reported for bacterial type III PKS, e.g.…”

Section: Chalcone Synthases (Chss) and Pkss Are Common In Plants And mentioning

confidence: 99%

Possibility of Bacterial Recruitment of Plant Genes Associated with the Biosynthesis of Secondary Metabolites

Bode¹,

Müller²

2003

Plant Physiology

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“…The type III PKS enzyme family (9 -11), defined by homology to chalcone synthase (CHS) (12)(13)(14)(15), is currently known to include at least 15 functionally divergent (11) ␤-ketosynthases (KSs) of plant (9 -11) and bacterial origin (11,16). As first revealed in the crystal structure of alfalfa CHS (17), each type III PKS monomer utilizes a Cys-His-Asn catalytic triad (Fig.…”

mentioning

confidence: 99%

Crystal Structure of a Bacterial Type III Polyketide Synthase and Enzymatic Control of Reactive Polyketide Intermediates

Austin

Izumikawa

Bowman

et al. 2004

Journal of Biological Chemistry

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162

145

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In bacteria, a structurally simple type III polyketide synthase (PKS) known as 1,3,6,8-tetrahydroxynaphthalene synthase (THNS) catalyzes the iterative condensation of five CoA-linked malonyl units to form a pentaketide intermediate. THNS subsequently catalyzes dual intramolecular Claisen and aldol condensations of this linear intermediate to produce the fused ring tetrahydroxynaphthalene (THN) skeleton. The type III PKScatalyzed polyketide extension mechanism, utilizing a conserved Cys-His-Asn catalytic triad in an internal active site cavity, is fairly well understood. However, the mechanistic basis for the unusual production of THN and dual cyclization of its malonyl-primed pentaketide is obscure. Here we present the first bacterial type III PKS crystal structure, that of Streptomyces coelicolor THNS, and identify by mutagenesis, structural modeling, and chemical analysis the unexpected catalytic participation of an additional THNS-conserved cysteine residue in facilitating malonyl-primed polyketide extension beyond the triketide stage. The resulting new mechanistic model, involving the use of additional cysteines to alter and steer polyketide reactivity, may generally apply to other PKS reaction mechanisms, including those catalyzed by iterative type I and II PKS enzymes. Our crystal structure also reveals an unanticipated novel cavity extending into the "floor" of the traditional active site cavity, providing the first plausible structural and mechanistic explanation for yet another unusual THNS catalytic activity: its previously inexplicable extra polyketide extension step when primed with a long acyl starter. This tunnel allows for selective expansion of available active site cavity volume by sequestration of aliphatic starter-derived polyketide tails, and further suggests another distinct protection mechanism involving maintenance of a linear polyketide conformation.1,3,6,8-Tetrahydroxynaphthalene (THN) 1 is biosynthesized from polyketide intermediates in fungi and bacteria (Fig. 1A). In some fungi, THN is reduced to 1,8-dihydroxynaphthalene and undergoes polymerization to form UV-protective 1,8-dihydroxynaphthalene-melanin (1). Filamentous bacteria of the genus Streptomyces utilize THN not only for melanin production (2) but also incorporate the THN scaffold into pharmacologically active meroterpenoids such as neomarinone (3).Fungi and bacteria use dramatically different enzymatic systems to produce THN from five activated thioester-linked malonyl building blocks. In fungi, THN is synthesized by an iterative type I polyketide synthase (PKS), which functions as a large (ϳ230-kDa) multidomain complex (4). Whereas type I PKSs and their fatty acid synthase ancestors have been intensely studied, their three-dimensional domain organization remains obscure due to their size and complexity. In stark contrast, bacteria use a structurally simple type III PKS architecturally organized as a homodimeric condensing enzyme (ϳ40 kDa) to synthesize THN from five coenzyme A (CoA)-tethered malonyl units, without the use of...

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Discovery of a New Bacterial Polyketide Biosynthetic Pathway

Abstract: Figure 3. Structures of prenylated naphthoquinones from Streptomyces spp. The postulated THN-derived units are depicted in red.

Cited by 105 publications

References 17 publications

A New Family of Type III Polyketide Synthases in Mycobacterium tuberculosis

A New Family of Type III Polyketide Synthases in Mycobacterium tuberculosis

Possibility of Bacterial Recruitment of Plant Genes Associated with the Biosynthesis of Secondary Metabolites

Crystal Structure of a Bacterial Type III Polyketide Synthase and Enzymatic Control of Reactive Polyketide Intermediates

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