Reveromycin A biosynthesis uses RevG and RevJ for stereospecific spiroacetal formation

Proteomics-based metabolic modeling and characterization of the cellulolytic bacterium Thermobifida fusca

Background

Thermobifida fusca is a cellulolytic bacterium with potential to be used as a platform organism for sustainable industrial production of biofuels, pharmaceutical ingredients and other bioprocesses due to its capability of potential to convert plant biomass to value-added chemicals. To best develop T. fusca as a bioprocess organism, it is important to understand its native cellular processes. In the current study, we characterize the metabolic network of T. fusca through reconstruction of a genome-scale metabolic model and proteomics data. The overall goal of this study was to use multiple metabolic models generated by different methods and comparison to experimental data to gain a high-confidence understanding of the T. fusca metabolic network.

Results

We report the generation of three versions of a metabolic model of Thermobifida fusca sp. XY developed using three different approaches (automated, semi-automated, and proteomics-derived). The model closest to in vivo growth was the proteomics-derived model that consists of 975 reactions involving 1382 metabolites and account for 316 EC numbers (296 genes). The model was optimized for biomass production with the optimal flux of 0.48 doublings per hour when grown on cellobiose with a substrate uptake rate of 0.25 mmole/h. In vivo activity of the DXP pathway for terpenoid biosynthesis was also confirmed using real-time PCR.

Conclusions

iTfu296 provides a platform to understand and explore the metabolic capabilities of the actinomycete T. fusca for the potential use in bioprocess industries for the production of biofuel and pharmaceutical ingredients. By comparing different model reconstruction methods, the use of high-throughput proteomics data as a starting point proved to be the most accurate to in vivo growth.

The 7th Japan-Korea chemical biology symposium: chemical biology of natural bioactive molecules

Natural bioactive molecules possess supreme chemical diversity and drug-like properties and are an important source for drug lead compounds. At the seventh Japan-Korea Chemical Biology Symposium at Jeju Island, Korea, chemical biologists from Korea and Japan highlighted the remarkable features of natural products and their significance.

Allosteric regulation of epoxide opening cascades by a pair of epoxide hydrolases in monensin biosynthesis

Multistep catalysis of epoxide hydrolase/cyclase in the epoxide opening cascade is an intriguing issue in polyether biosynthesis. A pair of structurally homologous epoxide hydrolases was found in gene clusters of ionophore polyethers. In the epoxide opening reactions with MonBI and MonBII involved in monensin biosynthesis, we found that MonBII and catalytically inactive MonBI mutant catalyzed two-step reactions of bisepoxide substrate analogue to afford bicyclic product although MonBII alone catalyzed only the first cyclization. The X-ray crystal structure of MonBI dimers suggested the importance of the KSD motif in MonBI/MonBI interaction, which was further supported by gel filtration chromatography of wild-type MonBI and mutant MonBI. The involvement of the KSD motif in heterodimer formation was confirmed by in vitro assay. Direct evidence of MonBI/MonBII interaction was obtained by native mass spectrometry. Its dissociation constant was determined as 2.21 × 10(-5) M by surface plasmon resonance. Our results suggested the involvement of an allosteric regulation mechanism by MonBI/MonBII interaction in monensin skeletal construction.

Mutasynthesis of pyrrole spiroketal compound using calcimycin 3-hydroxy anthranilic acid biosynthetic mutant

The five-membered aromatic nitrogen heterocyclic pyrrole ring is a building block for a wide variety of natural products. Aiming at generating new pyrrole-containing derivatives as well as to identify new candidates that may be of value in designing new anticancer, antiviral, and/or antimicrobial agents, we employed a strategy on pyrrole-containing compound mutasynthesis using the pyrrole-containing calcimycin biosynthetic gene cluster. We blocked the biosynthesis of the calcimycin precursor, 3-hydroxy anthranilic acid, by deletion of calB1-3 and found that two intermediates containing the pyrrole and the spiroketal moiety were accumulated in the culture. We then fed the mutant using the structurally similar compound of 3-hydroxy anthranilic acid. At least four additional new pyrrole spiroketal derivatives were obtained. The structures of the intermediates and the new pyrrole spiroketal derivatives were identified using LC-MS and NMR. One of them shows enhanced antibacterial activity. Our work shows a new way of pyrrole derivative biosynthetic mutasynthesis.

Spiroketal formation and modification in avermectin biosynthesis involves a dual activity of AveC

Avermectins (AVEs), which are widely used for the treatment of agricultural parasitic diseases, belong to a family of 6,6-spiroketal moiety-containing, macrolide natural products. AVE biosynthesis is known to employ a type I polyketide synthase (PKS) system to assemble the molecular skeleton for further functionalization. It remains unknown how and when spiroketal formation proceeds, particularly regarding the role of AveC, a unique protein in the pathway that shares no sequence homology to any enzyme of known function. Here, we report the unprecedented, dual function of AveC by correlating its activity with spiroketal formation and modification during the AVE biosynthetic process. The findings in this study were supported by characterizing extremely unstable intermediates, products and their spontaneous derivative products from the simplified chemical profile and by comparative analysis of in vitro biotransformations and in vivo complementations mediated by AveC and MeiC (the counterpart in biosynthesizing the naturally occurring, AVE-like meilingmycins). AveC catalyzes the stereospecific spiroketalization of a dihydroxy-ketone polyketide intermediate and the optional dehydration to determine the regiospecific saturation characteristics of spiroketal diversity. These reactions take place between the closures of the hexene ring and 16-membered macrolide and the formation of the hexahydrobenzofuran unit. MeiC can replace the spirocyclase activity of AveC, but it lacks the independent dehydratase activity. Elucidation of the generality and specificity of AveC-type proteins allows for the rationalization of previously published results that were not completely understood, suggesting that enzyme-mediated spiroketal formation was initially underestimated, but is, in fact, widespread in nature for the control of stereoselectivity.

The status of type I polyketide synthase ketoreductases

The functional dissection of type I polyketide synthases has established that ketoreductases most commonly set the orientations of the hydroxyl and alkyl substituents of complex polyketides. Here we review the biochemical, structural biology, and engineering studies that have helped elucidate how stereocontrol is enforced by these enzymes.

Stereoselective synthesis of acortatarins A and B

Acortatarins A and B have been synthesized via stereoselective spirocyclizations of glycals. Mercury-mediated spirocyclization of a pyrrole monoalcohol side chain leads to acortatarin A. Glycal epoxidation and reductive spirocyclization of a pyrrole dialdehyde side chain leads to acortatarin B. Acid equilibration and crystallographic analysis indicate that acortatarin B is a contrathermodynamic spiroketal with distinct ring conformations compared to acortatarin A.

Complexity generation during natural product biosynthesis using redox enzymes

Redox enzymes such as FAD-dependent and cytochrome P450 oxygenases play indispensible roles in generating structural complexity during natural product biosynthesis. In the pre-assembly steps, redox enzymes can convert garden variety primary metabolites into unique starter and extender building blocks. In the post-assembly tailoring steps, redox cascades can transform nascent scaffolds into structurally complex final products. In this review, we will discuss several recently characterized redox enzymes in the biosynthesis of polyketides and nonribosomal peptides.

Beyond ethylmalonyl-CoA: the functional role of crotonyl-CoA carboxylase/reductase homologs in expanding polyketide diversity

This review covers the emerging biosynthetic role of crotonyl-CoA carboxylase/reductase (CCR) homologs in extending the structural and functional diversity of polyketide natural products. CCRs catalyze the reductive carboxylation of α,β-unsaturated acyl-CoA substrates to produce a variety of substituted malonyl-CoA derivatives employed as polyketide synthase extender units. Here we discuss the history of CCRs in both primary and secondary metabolism, the mechanism by which they function, examples of new polyketide diversity from pathway specific CCRs, and the role of CCRs in facilitating the bioengineering novel polyketides.