Total In Vitro Biosynthesis of the Thioamitide Thioholgamide and Investigation of the Pathway

Thioholgamides are ribosomally synthesized and post-translationally modified peptides (RiPPs) with potent activity against cancerous cell lines and an unprecedented structure. Despite being one of the most structurally and chemically complex RiPPs, very few biosynthetic steps have been elucidated. Here, we report the complete in vitro reconstitution of the biosynthetic pathway. We demonstrate that thioamidation is the first step and acts as a gatekeeper for downstream processing. Thr dehydration follows thioamidation, and our studies reveal that both these modifications require the formation of protein complexes – ThoH/I and ThoC/D. Harnessing the power of AlphaFold we deduce that ThoD acts as a lyase and also propose putative catalytic residues. ThoF catalyzes the oxidative decarboxylation of the terminal Cys and the subsequent macrocyclization is facilitated by ThoE. This is followed by Ser dehydration, which is also carried out by ThoC/D. ThoG is responsible for histidine bis-N-methylation, which is a prerequisite for His β-hydroxylation – a modification carried out by ThoJ. The last step of the pathway is the removal of the leader peptide by ThoK to afford mature thioholgamide.

Studies of Strained Ring Systems: Cyclopropa[1]Phenanthrenes

<p>The aim of the present study has been the synthesis of 1H-cyclo-Propa[1]phenanthrene (16a) and its derivatives, the sole remaining unknown structural type of the cycloproparenes. Established procedures for cycloproparene synthesis are not readily adaptable to this ring system, and routes based upon new bridge-head-substituted 1a,9b-dihydrocyclopropa[1]phenanthrenes are examined. 1, 1-Dichloro-1a-phenylseleno-1a, 9b-dihydrocyclopropa [1] phenanthrene (73) is prepared by the addition of dichlorocarbene to the corresponding phenanthrenyl selenide (72). syn-Selenoxide elimination of PhSeOH from the derived selenoxide (74) gives 1,1-dichloro-1H-cyclopropa[1]phenanthrene (76) which is intercepted by methanolysis. Labelling studies provide convincing evidence for the intermediacy of the 1H-cycloproparene. The viability of an oxidative decarboxylation route to 1,1-dialkyl-1H-cyclopropa[1]phenanthrenes is investigated for the model compound 7,7-dimethylbicyclo[4.1.0]hept-3-ene-1-carboxylic acid (122). A product of formal cyclopropyl-allyl cation rearrangement, is isolated. 1a-Methylseleno-1a,9b-dihydrocyclopropa[1]phenanthrenes (174) is prepared by the unprecedented addition of methylselenide anion to 1aH-cyclopropa[1]phenanthrene (63) (generated by a new route involving the fluoride ion-promoted elimination of the elements of chlorotrimethylsilane from the isomeric 1-chloro-1a-trimethylsilyl-1a, 9b-dihydrocyclopropa[1]phenanthrenes (170) and (171)). Treatment of the drived dimethylselenonium tetra-fluoroborate (179) with base in the presence of furan gives the endo- and exo-furan cycloadducts (180) and (181) of 1H-cyclopropa[1]phenanthrene (16a). The results presented herein provide the first conclusive evidence for the existence of the 1H-cyclopropa[1]phenanthrene ring system, both as the parent hydrocarbon (16a) and the 1,1-dichloro-derivative(76).</p>

Studies of Strained Ring Systems: Cyclopropa[1]Phenanthrenes

<p>The aim of the present study has been the synthesis of 1H-cyclo-Propa[1]phenanthrene (16a) and its derivatives, the sole remaining unknown structural type of the cycloproparenes. Established procedures for cycloproparene synthesis are not readily adaptable to this ring system, and routes based upon new bridge-head-substituted 1a,9b-dihydrocyclopropa[1]phenanthrenes are examined. 1, 1-Dichloro-1a-phenylseleno-1a, 9b-dihydrocyclopropa [1] phenanthrene (73) is prepared by the addition of dichlorocarbene to the corresponding phenanthrenyl selenide (72). syn-Selenoxide elimination of PhSeOH from the derived selenoxide (74) gives 1,1-dichloro-1H-cyclopropa[1]phenanthrene (76) which is intercepted by methanolysis. Labelling studies provide convincing evidence for the intermediacy of the 1H-cycloproparene. The viability of an oxidative decarboxylation route to 1,1-dialkyl-1H-cyclopropa[1]phenanthrenes is investigated for the model compound 7,7-dimethylbicyclo[4.1.0]hept-3-ene-1-carboxylic acid (122). A product of formal cyclopropyl-allyl cation rearrangement, is isolated. 1a-Methylseleno-1a,9b-dihydrocyclopropa[1]phenanthrenes (174) is prepared by the unprecedented addition of methylselenide anion to 1aH-cyclopropa[1]phenanthrene (63) (generated by a new route involving the fluoride ion-promoted elimination of the elements of chlorotrimethylsilane from the isomeric 1-chloro-1a-trimethylsilyl-1a, 9b-dihydrocyclopropa[1]phenanthrenes (170) and (171)). Treatment of the drived dimethylselenonium tetra-fluoroborate (179) with base in the presence of furan gives the endo- and exo-furan cycloadducts (180) and (181) of 1H-cyclopropa[1]phenanthrene (16a). The results presented herein provide the first conclusive evidence for the existence of the 1H-cyclopropa[1]phenanthrene ring system, both as the parent hydrocarbon (16a) and the 1,1-dichloro-derivative(76).</p>

Studies of Strained Ring Systems: Cyclopropa[1]Phenanthrenes

<p>The aim of the present study has been the synthesis of 1H-cyclo-Propa[1]phenanthrene (16a) and its derivatives, the sole remaining unknown structural type of the cycloproparenes. Established procedures for cycloproparene synthesis are not readily adaptable to this ring system, and routes based upon new bridge-head-substituted 1a,9b-dihydrocyclopropa[1]phenanthrenes are examined. 1, 1-Dichloro-1a-phenylseleno-1a, 9b-dihydrocyclopropa [1] phenanthrene (73) is prepared by the addition of dichlorocarbene to the corresponding phenanthrenyl selenide (72). syn-Selenoxide elimination of PhSeOH from the derived selenoxide (74) gives 1,1-dichloro-1H-cyclopropa[1]phenanthrene (76) which is intercepted by methanolysis. Labelling studies provide convincing evidence for the intermediacy of the 1H-cycloproparene. The viability of an oxidative decarboxylation route to 1,1-dialkyl-1H-cyclopropa[1]phenanthrenes is investigated for the model compound 7,7-dimethylbicyclo[4.1.0]hept-3-ene-1-carboxylic acid (122). A product of formal cyclopropyl-allyl cation rearrangement, is isolated. 1a-Methylseleno-1a,9b-dihydrocyclopropa[1]phenanthrenes (174) is prepared by the unprecedented addition of methylselenide anion to 1aH-cyclopropa[1]phenanthrene (63) (generated by a new route involving the fluoride ion-promoted elimination of the elements of chlorotrimethylsilane from the isomeric 1-chloro-1a-trimethylsilyl-1a, 9b-dihydrocyclopropa[1]phenanthrenes (170) and (171)). Treatment of the drived dimethylselenonium tetra-fluoroborate (179) with base in the presence of furan gives the endo- and exo-furan cycloadducts (180) and (181) of 1H-cyclopropa[1]phenanthrene (16a). The results presented herein provide the first conclusive evidence for the existence of the 1H-cyclopropa[1]phenanthrene ring system, both as the parent hydrocarbon (16a) and the 1,1-dichloro-derivative(76).</p>

Studies of Strained Ring Systems: Cyclopropa[1]Phenanthrenes

<p>The aim of the present study has been the synthesis of 1H-cyclo-Propa[1]phenanthrene (16a) and its derivatives, the sole remaining unknown structural type of the cycloproparenes. Established procedures for cycloproparene synthesis are not readily adaptable to this ring system, and routes based upon new bridge-head-substituted 1a,9b-dihydrocyclopropa[1]phenanthrenes are examined. 1, 1-Dichloro-1a-phenylseleno-1a, 9b-dihydrocyclopropa [1] phenanthrene (73) is prepared by the addition of dichlorocarbene to the corresponding phenanthrenyl selenide (72). syn-Selenoxide elimination of PhSeOH from the derived selenoxide (74) gives 1,1-dichloro-1H-cyclopropa[1]phenanthrene (76) which is intercepted by methanolysis. Labelling studies provide convincing evidence for the intermediacy of the 1H-cycloproparene. The viability of an oxidative decarboxylation route to 1,1-dialkyl-1H-cyclopropa[1]phenanthrenes is investigated for the model compound 7,7-dimethylbicyclo[4.1.0]hept-3-ene-1-carboxylic acid (122). A product of formal cyclopropyl-allyl cation rearrangement, is isolated. 1a-Methylseleno-1a,9b-dihydrocyclopropa[1]phenanthrenes (174) is prepared by the unprecedented addition of methylselenide anion to 1aH-cyclopropa[1]phenanthrene (63) (generated by a new route involving the fluoride ion-promoted elimination of the elements of chlorotrimethylsilane from the isomeric 1-chloro-1a-trimethylsilyl-1a, 9b-dihydrocyclopropa[1]phenanthrenes (170) and (171)). Treatment of the drived dimethylselenonium tetra-fluoroborate (179) with base in the presence of furan gives the endo- and exo-furan cycloadducts (180) and (181) of 1H-cyclopropa[1]phenanthrene (16a). The results presented herein provide the first conclusive evidence for the existence of the 1H-cyclopropa[1]phenanthrene ring system, both as the parent hydrocarbon (16a) and the 1,1-dichloro-derivative(76).</p>

Energy Conservation in Fermentations of Anaerobic Bacteria

Anaerobic bacteria ferment carbohydrates and amino acids to obtain energy for growth. Due to the absence of oxygen and other inorganic electron acceptors, the substrate of a fermentation has to serve as electron donor as well as acceptor, which results in low free energies as compared to that of aerobic oxidations. Until about 10 years ago, anaerobes were thought to exclusively use substrate level phosphorylation (SLP), by which only part of the available energy could be conserved. Therefore, anaerobes were regarded as unproductive and inefficient energy conservers. The discovery of electrochemical Na+ gradients generated by biotin-dependent decarboxylations or by reduction of NAD+ with ferredoxin changed this view. Reduced ferredoxin is provided by oxidative decarboxylation of 2-oxoacids and the recently discovered flavin based electron bifurcation (FBEB). In this review, the two different fermentation pathways of glutamate to ammonia, CO2, acetate, butyrate and H2 via 3-methylaspartate or via 2-hydroxyglutarate by members of the Firmicutes are discussed as prototypical examples in which all processes characteristic for fermentations occur. Though the fermentations proceed on two entirely different pathways, the maximum theoretical amount of ATP is conserved in each pathway. The occurrence of the 3-methylaspartate pathway in clostridia from soil and the 2-hydroxyglutarate pathway in the human microbiome of the large intestine is traced back to the oxygen-sensitivity of the radical enzymes. The coenzyme B12-dependent glutamate mutase in the 3-methylaspartate pathway tolerates oxygen, whereas 2-hydroxyglutaryl-CoA dehydratase is extremely oxygen-sensitive and can only survive in the gut, where the combustion of butyrate produced by the microbiome consumes the oxygen and provides a strict anaerobic environment. Examples of coenzyme B12-dependent eliminases are given, which in the gut are replaced by simpler extremely oxygen sensitive glycyl radical enzymes.

Characterization of 3-isopropylmalate dehydrogenase from extremely halophilic archaeon Haloarcula japonica

3-Isopropylmalate dehydrogenase (IPMDH) catalyzes oxidative decarboxylation of (2R, 3S)-3-isopropylmalate to 2-oxoisocaproate in leucine biosynthesis. In this study, recombinant IPMDH (HjIPMDH) from an extremely halophilic archaeon, Haloarcula japonica TR-1, was characterized. Activity of HjIPMDH increased as KCl concentration increased, and the maximum activity was observed at 3.0 M KCl. Analytical ultracentrifugation revealed that HjIPMDH formed a homotetramer at high KCl concentrations, and it dissociated to a monomer at low KCl concentrations. Additionally, HjIPMDH was thermally stabilized by higher KCl concentrations. This is the first report on haloarchaeal IPMDH.