C-C bond forming radical SAM enzymes involved in the construction of carbon skeletons of cofactors and natural products

Covering: up to the end of 2017 C-C bond formations are frequently the key steps in cofactor and natural product biosynthesis. Historically, C-C bond formations were thought to proceed by two electron mechanisms, represented by Claisen condensation in fatty acids and polyketide biosynthesis. These types of mechanisms require activated substrates to create a nucleophile and an electrophile. More recently, increasing number of C-C bond formations catalyzed by radical SAM enzymes are being identified. These free radical mediated reactions can proceed between almost any sp3 and sp2 carbon centers, allowing introduction of C-C bonds at unconventional positions in metabolites. Therefore, free radical mediated C-C bond formations are frequently found in the construction of structurally unique and complex metabolites. This review discusses our current understanding of the functions and mechanisms of C-C bond forming radical SAM enzymes and highlights their important roles in the biosynthesis of structurally complex, naturally occurring organic molecules. Mechanistic consideration of C-C bond formation by radical SAM enzymes identifies the significance of three key mechanistic factors: radical initiation, acceptor substrate activation and radical quenching. Understanding the functions and mechanisms of these characteristic enzymes will be important not only in promoting our understanding of radical SAM enzymes, but also for understanding natural product and cofactor biosynthesis.

Characterization of the tunicamycin gene cluster unveiling unique steps involved in its biosynthesis

Tunicamycin, a potent reversible translocase I inhibitor, is produced by several Actinomycetes species. The tunicamycin structure is highly unusual, and contains an 11-carbon dialdose sugar and an α, β-1″,11'-glycosidic linkage. Here we report the identification of a gene cluster essential for tunicamycin biosynthesis by high-throughput heterologous expression (HHE) strategy combined with a bioassay. Introduction of the genes into heterologous non-producing Streptomyces hosts results in production of tunicamycin by these strains, demonstrating the role of the genes for the biosynthesis of tunicamycins. Gene disruption experiments coupled with bioinformatic analysis revealed that the tunicamycin gene cluster is minimally composed of 12 genes (tunA-tunL). Amongst these is a putative radical SAM enzyme (Tun B) with a potentially unique role in biosynthetic carbon-carbon bond formation. Hence, a seven-step novel pathway is proposed for tunicamycin biosynthesis. Moreover, two gene clusters for the potential biosynthesis of tunicamycin-like antibiotics were also identified in Streptomyces clavuligerus ATCC 27064 and Actinosynnema mirums DSM 43827. These data provide clarification of the novel mechanisms for tunicamycin biosynthesis, and for the generation of new-designer tunicamycin analogs with selective/enhanced bioactivity via combinatorial biosynthesis strategies.

Biosynthesis of the tunicamycins: a review

Tunicamycins are nucleotide sugar analogs produced by several Streptomyces species. In eukaryotes, tunicamycins inhibit UDP-N-acetylglucosamine: dolichol phosphate GlcNAc-1-P transferase (GPT) that catalyzes the first step in protein glycosylation. In bacteria they inhibit UDP-N-acetylmuramoyl-pentapeptide: undecaprenol phosphate MurNAc-pentapeptide-1-P transtransferase (MraY) that catalyzes an early stage in peptidoglycan cell wall assembly. Tunicamycins are substrate analog of GPT and MraY, such that the alphabeta-1'',11'-linked GlcNAc residue of the tunicamycins mimics the transferred GlcNAc-1-phosphate. The unusual structure of tunicamycins, particularly the unique 11-carbon sugar, tunicamine, and the alphabeta-1'',11'-O-glycosidic linkage, suggest its biosynthesis to be unique. This review discusses potential biosyntheses for tunicamycins via the synthesis and conjugation of uridine-5'-aldehyde and UDP-4-keto-N-acetylgalactosamine-5,6-ene and the subsequent formation of the alpha,beta-1'',11' glycosidic linkage.

Biosynthesis of tunicamycin and metabolic origin of the 11-carbon dialdose sugar, tunicamine

Tunicamycin is a reversible inhibitor of polyprenol-phosphate: N-acetylhexosamine-1-phosphate translocases and is produced by several Streptomyces species. We have examined tunicamycin biosynthesis, an important but poorly characterized biosynthetic pathway. Biosynthetic precursors have been identified by incorporating radioactive and stable isotopes, and by determining the labeling pattern using electrospray ionization-collision induced dissociation-mass spectrometry (ESI-CID-MS), and proton, deuterium, and C-13 nuclear magnetic resonance (NMR) spectroscopy. Preparation and analysis of [uracil-5-(2)H]-labeled tunicamycin established the complete ESI-CID-MS fragmentation pathway for the major components of the tunicamycin complex. Competitive metabolic experiments indicate that 7 deuteriums incorporate into tunicamycin from [6,6'-(2)H,(2)H]-labeled D-glucose, 6 of which arise from D-GlcNAc and 1 from uridine and/or D-ribose. Inverse correlation NMR experiments (heteronuclear single-quantum coherence (HSQC)) of (13)C-labeled tunicamycin enriched from D-[1-(13)C]glucose suggest that the unique tunicamine 11-carbon dialdose sugar backbone arises from a 5-carbon furanose precursor derived from uridine and a 6-carbon N-acetylamino-pyranose precursor derived from UDP-D-N-acetylglucosamine. The equivalent incorporation of (13)C into both the alpha-1" and beta-11' anomeric carbons of tunicamycin supports a direct biosynthesis via 6-carbon metabolism. It also indicates that the tunicamine motif and the alpha-1"-linked GlcNAc residue are both derived from the same metabolic pool of UDP-GlcNAc, without significant differential metabolic processing. A biosynthetic pathway is therefore proposed for tunicamycin for the first time: an initial formation of the 11-carbon tunicamine sugar motif from uridine and UDP-GlcNAc via uridine-5'-aldehyde and UDP-4-keto-6-ene-N-acetylhexosamine, respectively, and subsequent formation of the anomeric-to-anomeric alpha, beta-1",11'-glycosidic bond.

Glycosylation and secretion of human tissue plasminogen activator in recombinant baculovirus-infected insect cells

Cell lines established from the lepidopteran insect Spodoptera frugiperda (fall armyworm; Sf9) are used routinely as hosts for the expression of foreign proteins by recombinant baculovirus vectors. We have examined the pathway of protein glycosylation and secretion in these cells, using human tissue plasminogen activator (t-PA) as a model. t-PA expressed in Sf9 cells was both N glycosylated and secreted. At least a subset of the N-linked oligosaccharides in extracellular t-PA was resistant to endo-beta-N-acetyl-D-glucosaminidase H, which removes immature, high-mannose-type oligosaccharides. This refutes the general conclusion from previous studies that Sf9 cells cannot process immature N-linked oligosaccharides to an endo-beta-N-acetyl-D-glucosaminidase H-resistant form. A nonglycosylated t-PA precursor was not detected in Sf9 cells, even with very short pulse-labeling times. This suggests that the mammalian signal sequence of t-PA is efficiently recognized in Sf9 cells and that it can mediate rapid translocation across the membrane of the rough endoplasmic reticulum, where cotranslational N glycosylation takes place. However, t-PA was secreted rather slowly, with a half-time of about 1.6 h. Thus, a rate-limiting step(s) in secretion occurs subsequent to translocation and N glycosylation of the t-PA polypeptide. Treatment of Sf9 cells with tunicamycin, but not with inhibitors of oligosaccharide processing, prevented the appearance of t-PA in the extracellular medium. This suggests that N glycosylation per se, but not processing of the N-linked oligosaccharides, is required directly or indirectly in baculovirus-infected Sf9 cells for the secretion of t-PA. Finally, the relative efficiency of secretion decreased dramatically with time of infection, suggesting that the Sf9 host cell secretory pathway is compromised during the later stages of baculovirus infection.

Minor modifications to the structure of tunicamycin lead to loss of the biological activity of the antibiotic

Three analogues of tunicamycin, each with minor alterations in structure in different regions of the molecule, have been employed to study the effects of such modifications upon the biological activity of the antibiotic. The data indicate that any modification of structure results in loss of the ability of the antibiotic to inhibit N-glycosylation of proteins. In contrast to tunicamycin itself, none of the analogues had any deleterious effects upon cellular macromolecule synthesis, nor upon the kinetics of export of de novo synthesised IgM or IgG molecules from treated rat hybridoma cells. In addition, the incorporation of tritiated sugars into acid-precipitable macromolecules was not inhibited. Endoglycosidase H digestion of isolated IgG molecules further suggested that the analogues employed did not interfere with qualitative glycosylation at the level of N-acetylglucosamine transferases I and II in the golgi apparatus. The data are consistent with the interpretation that tunicamycin has very precise structural requirements for expression of inhibitory effects upon protein glycosylation, and that small variations of structure can lead to loss of its inhibitory effects.