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

2019 ◽  
Vol 116 (38) ◽  
pp. 19126-19135 ◽  
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.

scholarly journals A Novel Class of Modular Transporters for Vitamins in Prokaryotes

2008 ◽  
Vol 191 (1) ◽  
pp. 42-51 ◽  
Author(s):  
Dmitry A. Rodionov ◽  
Peter Hebbeln ◽  
Aymerick Eudes ◽  
Josy ter Beek ◽  
Irina A. Rodionova ◽  
...  
Keyword(s):  
Abc Transporters ◽  
Transmembrane Protein ◽  
Energy Coupling ◽  
Coupling Factor ◽  
Human Pathogens ◽  
Gram Positive Bacteria ◽  
New Class ◽  
Vitamin Uptake ◽  
Genome Context ◽  
Nucleotide Binding Proteins

ABSTRACT The specific and tightly controlled transport of numerous nutrients and metabolites across cellular membranes is crucial to all forms of life. However, many of the transporter proteins involved have yet to be identified, including the vitamin transporters in various human pathogens, whose growth depends strictly on vitamin uptake. Comparative analysis of the ever-growing collection of microbial genomes coupled with experimental validation enables the discovery of such transporters. Here, we used this approach to discover an abundant class of vitamin transporters in prokaryotes with an unprecedented architecture. These transporters have energy-coupling modules comprised of a conserved transmembrane protein and two nucleotide binding proteins similar to those of ATP binding cassette (ABC) transporters, but unlike ABC transporters, they use small integral membrane proteins to capture specific substrates. We identified 21 families of these substrate capture proteins, each with a different specificity predicted by genome context analyses. Roughly half of the substrate capture proteins (335 cases) have a dedicated energizing module, but in 459 cases distributed among almost 100 gram-positive bacteria, including numerous human pathogens, different and unrelated substrate capture proteins share the same energy-coupling module. The shared use of energy-coupling modules was experimentally confirmed for folate, thiamine, and riboflavin transporters. We propose the name energy-coupling factor transporters for the new class of membrane transporters.

scholarly journals 5-Deoxyadenosine Metabolism: More than “Waste Disposal”

2021 ◽  
pp. 1-12
Author(s):  
Johanna Rapp ◽  
Karl Forchhammer
Keyword(s):  
Current Knowledge ◽  
Shikimate Pathway ◽  
Central Carbon Metabolism ◽  
Competitive Growth ◽  
Radical Sam ◽  
Radical Sam Enzymes ◽  
Central Carbon ◽  
Domains Of Life ◽  
Radical Sam Enzyme ◽  
Salvage Pathways

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.

Discovery of Antibacterial Agents Inhibiting the Energy-Coupling Factor (ECF) Transporters by Structure-Based Virtual Screening

2020 ◽  
Author(s):  
Eleonora Diamanti ◽  
Inda Setyawati ◽  
Spyridon Bousis ◽  
leticia mojas ◽  
lotteke Swier ◽  
...  
Keyword(s):  
Virtual Screening ◽  
Antibacterial Agents ◽  
Antimicrobial Agents ◽  
Energy Coupling ◽  
Coupling Factor ◽  
Design Synthesis ◽  
Screening Design ◽  
Starting Point ◽  
Wide Range ◽  
Vitamin Uptake

Here, we report on the virtual screening, design, synthesis and structure–activity relationships (SARs) of the first class of selective, antibacterial agents against the energy-coupling factor (ECF) transporters. The ECF transporters are a family of transmembrane proteins involved in the uptake of vitamins in a wide range of bacteria. Inhibition of the activity of these proteins could reduce the viability of pathogens that depend on vitamin uptake. Because of their central role in the metabolism of bacteria and their absence in humans, ECF transporters are novel potential antimicrobial targets to tackle infection. The hit compound’s metabolic and plasma stability, the potency (20, MIC Streptococcus pneumoniae = 2 µg/mL), the absence of cytotoxicity and a lack of resistance development under the conditions tested here suggest that this scaffold may represent a promising starting point for the development of novel antimicrobial agents with an unprecedented mechanism of action.<br>

Characterization and Mechanistic Study of the Radical SAM Enzyme ArsS Involved in Arsenosugar Biosynthesis

2021 ◽  
Author(s):  
Jinduo Cheng ◽  
Wenjuan Ji ◽  
Suze Ma ◽  
Xinjian Ji ◽  
Zixin Deng ◽  
...  
Keyword(s):  
Mechanistic Study ◽  
Radical Sam ◽  
Radical Sam Enzyme

Characterization of the DNA repair spore photoproduct lyase enzyme from Clostridium acetobutylicum: A radical-SAM enzyme

2007 ◽  
Vol 10 (8) ◽  
pp. 756-765 ◽  
Author(s):  
Alexia Chandor ◽  
Thierry Douki ◽  
Didier Gasparutto ◽  
Serge Gambarelli ◽  
Yannis Sanakis ◽  
...  
Keyword(s):  
Dna Repair ◽  
Clostridium Acetobutylicum ◽  
Radical Sam ◽  
Spore Photoproduct Lyase ◽  
Radical Sam Enzyme ◽  
Spore Photoproduct

Evidence for the synthesis of an unusual high spin (S = 7/2) [Cu–3Fe–4S] cluster in the radical-SAM enzyme RSAD2 (viperin)

2018 ◽  
Vol 54 (62) ◽  
pp. 8614-8617 ◽  
Author(s):  
K. Honarmand Ebrahimi ◽  
C. Silveira ◽  
S. Todorovic
Keyword(s):  
High Spin ◽  
Radical Sam ◽  
Radical Sam Enzyme

We demonstrate the synthesis of an unusual high spin [Cu–3Fe–4S] cluster in the radical S-adenosylmethionine enzyme RSAD2 (also known as viperin).

scholarly journals Bacteriomimetic Liposomes Improve Antibiotic Activity of a Novel Energy-Coupling Factor Transporter Inhibitor

Pharmaceutics ◽  
2021 ◽  
Vol 14 (1) ◽  
pp. 4
Author(s):  
Menka Drost ◽  
Eleonora Diamanti ◽  
Kathrin Fuhrmann ◽  
Adriely Goes ◽  
Atanaz Shams ◽  
...  
Keyword(s):  
Model Organism ◽  
Energy Coupling ◽  
Coupling Factor ◽  
Free Drug ◽  
Drug Formulation ◽  
Phosphatidylcholine Liposomes ◽  
Loading Method ◽  
Fold Reduction ◽  
Hydrophobic Compound ◽  
Bacterial Growth Inhibition

Liposomes have been studied for decades as nanoparticulate drug delivery systems for cytostatics, and more recently, for antibiotics. Such nanoantibiotics show improved antibacterial efficacy compared to the free drug and can be effective despite bacterial recalcitrance. In this work, we present a loading method of bacteriomimetic liposomes for a novel, hydrophobic compound (HIPS5031) inhibiting energy-coupling factor transporters (ECF transporters), an underexplored antimicrobial target. The liposomes were composed of DOPG (18:1 (Δ9-cis) phosphatidylglycerol) and CL (cardiolipin), resembling the cell membrane of Gram-positive Staphylococcus aureus and Streptococcus pneumoniae, and enriched with cholesterol (Chol). The size and polydispersity of the DOPG/CL/± Chol liposomes remained stable over 8 weeks when stored at 4 °C. Loading of the ECF transporter inhibitor was achieved by thin film hydration and led to a high encapsulation efficiency of 33.19% ± 9.5% into the DOPG/CL/Chol liposomes compared to the phosphatidylcholine liposomes (DMPC/DPPC). Bacterial growth inhibition assays on the model organism Bacillus subtilis revealed liposomal HIPS5031 as superior to the free drug, showing a 3.5-fold reduction in CFU/mL at a concentration of 9.64 µM. Liposomal HIPS5031 was also shown to reduce B. subtilis biofilm. Our findings present an explorative basis for bacteriomimetic liposomes as a strategy against drug-resistant pathogens by surpassing the drug-formulation barriers of innovative, yet unfavorably hydrophobic, antibiotics.

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