5-Deoxyadenosine Metabolism: More than “Waste Disposal”

5-Deoxyadenosine (5dAdo) is a by-product of many radical SAM enzyme reactions in all domains of life, and an inhibitor of the radical SAM enzymes themselves. Hence, pathways to recycle or dispose of this toxic by-product must exist but remain largely unexplored. In this review, we discuss the current knowledge about canonical and atypical 5dAdo salvage pathways that have been characterized in the last years. We highlight studies that report on how, in certain organisms, the salvage of 5dAdo via specific pathways can confer a growth advantage by providing either intermediates for the synthesis of secondary metabolites or a carbon source for the synthesis of metabolites of the central carbon metabolism. Yet, an alternative recycling route exists in organisms that use 5dAdo as a substrate to synthesize and excrete 7-deoxysedoheptulose, an allelopathic inhibitor of one enzyme of the shikimate pathway, thereby competing for their own niche. Remarkably, most steps of 5dAdo salvage are the result of the activity of promiscuous enzymes. This strategy enables even organisms with a small genome to synthesize bioactive compounds which they can deploy under certain conditions to gain a competitive growth advantage. We conclude emphasizing that, unexpectedly, 5dAdo salvage pathways seem not to be ubiquitously present, raising questions about the fate of such a toxic by-product in those species. This observation also suggests that additional 5dAdo salvage pathways, possibly relying on the activity of promiscuous enzymes, may exist. The future challenge will be to bring to light these “cryptic” 5dAdo recycling pathways.

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Thioether bond formation by SPASM domain radical SAM enzymes: Cα H-atom abstraction in subtilosin A biosynthesis

Chemical Communications ◽

10.1039/c6cc01317a ◽

2016 ◽

Vol 52 (37) ◽

pp. 6249-6252 ◽

Cited By ~ 31

Author(s):

Alhosna Benjdia ◽

Alain Guillot ◽

Benjamin Lefranc ◽

Hubert Vaudry ◽

Jérôme Leprince ◽

...

Keyword(s):

Bond Formation ◽

Radical Sam ◽

Radical Sam Enzymes ◽

Radical Sam Enzyme ◽

Synthetic Approaches

The radical SAM enzyme AlbA has been reported to catalyze the formation of a thioether bond in the antibiotic subtilosin A. By modeling, biochemical and synthetic approaches, we propose novel mechanistic perspectives on this emerging group of enzymes.

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Discovery of novel bacterial queuine salvage enzymes and pathways in human pathogens

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1909604116 ◽

2019 ◽

Vol 116 (38) ◽

pp. 19126-19135 ◽

Cited By ~ 3

Author(s):

Yifeng Yuan ◽

Rémi Zallot ◽

Tyler L. Grove ◽

Daniel J. Payan ◽

Isabelle Martin-Verstraete ◽

...

Keyword(s):

De Novo ◽

Energy Coupling ◽

Coupling Factor ◽

Intracellular Pathogen ◽

Human Pathogens ◽

Radical Sam ◽

Clostridioides Difficile ◽

Radical Sam Enzyme ◽

Salvage Pathways ◽

Hydrolysis Of

Queuosine (Q) is a complex tRNA modification widespread in eukaryotes and bacteria that contributes to the efficiency and accuracy of protein synthesis. Eukaryotes are not capable of Q synthesis and rely on salvage of the queuine base (q) as a Q precursor. While many bacteria are capable of Q de novo synthesis, salvage of the prokaryotic Q precursors preQ0 and preQ1 also occurs. With the exception of Escherichia coli YhhQ, shown to transport preQ0 and preQ1, the enzymes and transporters involved in Q salvage and recycling have not been well described. We discovered and characterized 2 Q salvage pathways present in many pathogenic and commensal bacteria. The first, found in the intracellular pathogen Chlamydia trachomatis, uses YhhQ and tRNA guanine transglycosylase (TGT) homologs that have changed substrate specificities to directly salvage q, mimicking the eukaryotic pathway. The second, found in bacteria from the gut flora such as Clostridioides difficile, salvages preQ1 from q through an unprecedented reaction catalyzed by a newly defined subgroup of the radical-SAM enzyme family. The source of q can be external through transport by members of the energy-coupling factor (ECF) family or internal through hydrolysis of Q by a dedicated nucleosidase. This work reinforces the concept that hosts and members of their associated microbiota compete for the salvage of Q precursors micronutrients.

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Accumulation of an unprecedented 5′-deoxyadenos-4′-yl radical unmasks the kinetics of the radical-mediated C-C bond formation step in MoaA catalysis

10.1101/2020.01.16.909697 ◽

2020 ◽

Author(s):

Haoran Pang ◽

Edward A. Lilla ◽

Pan Zhang ◽

Du Zhang ◽

Thomas P. Shields ◽

...

Keyword(s):

Biochemical Characterization ◽

Bond Formation ◽

Kinetic Characterization ◽

Amino Acid Residues ◽

Radical Sam ◽

Radical Sam Enzymes ◽

Rate Acceleration ◽

Radical Sam Enzyme ◽

Radical Catalysis

AbstractRadical S-adenosyl-L-methionine (SAM) enzymes catalyze various free radical-mediated reactions. In these enzymes, the rate-determining SAM cleavage kinetically masks all the subsequent steps. Due to this kinetic masking, detailed mechanistic characterization of radical transformations catalyzed by these enzymes is very difficult. Here, we report a successful kinetic characterization of the radical C-C bond formation catalyzed by a MoaA radical SAM enzyme. MoaA catalyzes an unprecedented 3′,8-cyclization of GTP into 3′,8-cyclo-7,8-dihydro-GTP (3′,8-cH2GTP) during the molybdenum cofactor (Moco) biosynthesis. Through a series of EPR and biochemical characterization, we found that MoaA accumulates a 5′-deoxyadenos-4′-yl radical (5′-dA-C4′•) under the turnover conditions, and forms (4′S)-5′-deoxyadenosine ((4′S)-5′-dA), which is a C-4′ epimer of the naturally occurring (4′R)-5′-dA. Together with kinetic characterizations, these observations revealed the presence of a shunt pathway in which an on-pathway intermediate, GTP C-3′ radical, abstracts H-4′ atom from 5′-dA to transiently generate 5′-dA-C4′• that is subsequently reduced stereospecifically to yield (4′S)-5′-dA. Detailed kinetic characterization of the shunt and the main pathways provided the comprehensive view of MoaA kinetics, and determined the rate of the on-pathway 3′,8-cyclization step as 2.7 ± 0.7 s−1. Together with DFT calculations, this observation suggested that the 3′,8-cyclization is accelerated by 6 ∼ 9 orders of magnitude by MoaA. Potential contributions of the active-site amino acid residues, and their potential relationships with human Moco deficiency disease are discussed. This is the first determination of the magnitude of catalytic rate acceleration by a radical SAM enzyme, and provides the foundation for understanding how radical SAM enzymes achieve highly specific radical catalysis.

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