The pksX gene cluster from Bacillus subtilis is predicted to encode the biosynthesis of an as yet uncharacterized hybrid nonribosomal peptide͞polyketide secondary metabolite. We used a combination of biochemical and mass spectrometric techniques to assign functional roles to the proteins AcpK, PksC, PksL, PksF, PksG, PksH, and PksI, and we conclude that they act to incorporate an acetate-derived ␤-methyl branch on an acetoacetyl-S-carrier protein and ultimately generate a ⌬ 2 -isoprenyl-S-carrier protein. This work highlights the power of mass spectrometry to elucidate the functions of orphan biosynthetic enzymes, and it details a mechanism by which single-carbon ␤-branches can be inserted into polyketide-like structures. This pathway represents a noncanonical route to the construction of prenyl units and serves as a prototype for the intersection of isoprenoid and polyketide biosynthetic manifolds in other natural product biosynthetic pathways.mass spectrometry ͉ orphan gene cluster ͉ hybrid nonribosomal peptide͞polyketide ͉ polyketide methylation P olyketides and nonribosomal peptides are classes of secondary metabolites that are synthesized by the iterative coupling of malonyl (Mal) derivatives and amino acids, respectively. The catalytic machinery responsible for the biosynthesis of these natural products comprises modular synthases that incorporate, and often subsequently tailor, monomer units into the growing small molecule by a thiotemplated mechanism. Often, the sequence of protein domains and modules is colinear with respect to the sequence of biosynthetic reactions catalyzed by the polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) machinery (1-3). Because of their highly modular nature, the small-molecule products of PKSs, NRPSs, and hybrid NRPS-PKS systems can often be predicted by bioinformatic approaches, and there have been recent experimental validations of such predictions (4-6). However, for many cases in which the biosynthetic product encoded by a given gene cluster is unknown, functional characterization of the synthase by bioinformatic methods alone is difficult or impossible.One such orphan cluster for which the product structure is unknown is the hybrid NRPS-PKS pksX cluster from Bacillus subtilis (7-9). Although the pksX cluster has been proposed to encode the biosynthesis of difficidin (7,9,10), recent work has demonstrated that the NRPS portion of the gene cluster is active, disqualifying difficidin, which does not contain any amines, as a candidate for the biosynthetic product of this cluster (11). Long thought to be cryptic, there is now evidence that it is responsible for the biosynthesis of a product that kills streptomycetes (P. D. Straight, M. A. Fischbach, C.T.W., and R. Kolter, unpublished results). Additionally, this cluster does not follow the usual NRPS-PKS colinearity rules because it has only three trans-acting acyltransferases that may load up to 17 of the 20 predicted thiolation domains of the cluster.We were intrigued by a series of predicted ORFs withi...

With the emergence of drug resistance and the genomic revolution there has been a renewed interest in the genes that are responsible for the generation of bioactive natural products. Secondary metabolites of one major class are biosynthesized at one or more sites by ultra large enzymes that carry covalent intermediates on phosphopantetheine arms. Because such intermediates are difficult to characterize in vitro, we have developed a new approach for streamlined detection of substrates, intermediates and products attached to a phosphopantetheinyl arm of the carrier site. During vibrational activation of gas phase carrier domains, facile elimination occurs in benchtop and FourierTransform mass spectrometers alike. Phosphopantetheinyl ejections quickly reduce >100 kDa megaenzymes to <1000 Da ions for structural assignment of intermediates at <0.007 Da mass accuracy without proteolytic digestion. This "Top Down" approach quickly illuminated diverse acylintermediates on the carrier domains of the nonribosomal peptide synthetases (NRPSs) or polyketide synthases (PKSs) found in the biosynthetic pathways of prodigiosin, pyoluteorin, mycosubtilin, nikkomycin, enterobactin, gramicidin and several proteins from the orphan pksX gene cluster from Bacillus subtilis. By focusing on just those regions undergoing covalent chemistry, the method delivered clean proof for the reversible dehydration of hydroxymethylglutaryl-S-PksL via incorporation of 2 H or 18 O from the buffer. The facile nature of this revised assay will allow diverse laboratories to spearhead their NRPS/PKS projects with benchtop mass spectrometers.About 50% of today's drugs and 75% of today's antimicrobials are derived from secondary metabolites (1,2). Many of those secondary metabolites are of polyketide or nonribosomal peptide origin. With the emergence of resistance and the genomic revolution there is a "renaissance" ongoing in the discovery of bioactive natural products and the characterization of the genes responsible for their production (1). Non-ribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs) are large enzymes often >>100 kDa that biosynthesize their natural products (e.g., the antibiotics penicillin, vancomycin) via covalent intermediates on phosphopantetheine arms (3). Currently, even when NRPS and PKS proteins can be overproduced their direct interrogation by mass spectrometry (MS) is difficult and timeconsuming, with reports from relatively few laboratories appearing in the primary literature (4-6). Therefore it would be of great benefit for the NRPS and PKS community if new MSbased methods to characterize these proteins were developed and easier to implement. This paper describes such a method.The purpose of this paper is four-fold: 1) the paper introduces a new and efficient method that utilizes a gas phase elimination reaction that takes place during tandem mass spectrometry (MS/MS) to quickly characterize substrates, intermediates and products that are loaded onto the phosphopantetheinyl arm on carrier domains of NRPS...

Attempts to quantify binding interactions of noncovalent complexes in aqueous solution have been stymied by complications arising from enthalpy-entropy compensation and cooperativity. We have extended work detailing the relationship between noncovalent structure and free energy of binding to include the roles of enthalpy and entropy of association. On the basis of van't Hoff measurements of the dimerization of vancomycin type antibiotics, we demonstrate that positive cooperativity manifests itself in a more favorable enthalpy of association and a partially compensating less favorable entropy of association. Finally, we extend these results to rationalize thermodynamic observations in unrelated systems.

Polyketides are secondary metabolites biosynthesized by the iterative Claisen condensation of malonate units. Despite utilizing only a small set of biochemical transformations, the polyketide biosynthetic machinery yields products of striking structural complexity and diversity. Recently, a new polyketide alkylation pathway was characterized that allows access to "beta-branched" structures. This Highlight will describe this alkylation sequence, with special emphasis on its parallels to isoprenoid biosynthesis from primary metabolism and the scope of structures accessible via this pathway.