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Li Q, Zallot R, MacTavish BS, Montoya A, Payan DJ, Hu Y, Gerlt JA, Angerhofer A, de Crécy-Lagard V, Bruner SD. Epoxyqueuosine Reductase QueH in the Biosynthetic Pathway to tRNA Queuosine Is a Unique Metalloenzyme. Biochemistry 2021; 60:3152-3161. [PMID: 34652139 DOI: 10.1021/acs.biochem.1c00164] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Queuosine is a structurally unique and functionally important tRNA modification, widely distributed in eukaryotes and bacteria. The final step of queuosine biosynthesis is the reduction/deoxygenation of epoxyqueuosine to form the cyclopentene motif of the nucleobase. The chemistry is performed by the structurally and functionally characterized cobalamin-dependent QueG. However, the queG gene is absent from several bacteria that otherwise retain queuosine biosynthesis machinery. Members of the IPR003828 family (previously known as DUF208) have been recently identified as nonorthologous replacements of QueG, and this family was renamed QueH. Here, we present the structural characterization of QueH from Thermotoga maritima. The structure reveals an unusual active site architecture with a [4Fe-4S] metallocluster along with an adjacent coordinated iron metal. The juxtaposition of the cofactor and coordinated metal ion predicts a unique mechanism for a two-electron reduction/deoxygenation of epoxyqueuosine. To support the structural characterization, in vitro biochemical and genomic analyses are presented. Overall, this work reveals new diversity in the chemistry of iron/sulfur-dependent enzymes and novel insight into the last step of this widely conserved tRNA modification.
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Affiliation(s)
- Qiang Li
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Rémi Zallot
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Brian S MacTavish
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Alvaro Montoya
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Daniel J Payan
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - You Hu
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - John A Gerlt
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Departments of Biochemistry and Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Alexander Angerhofer
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611, United States.,University of Florida Genetics Institute, Gainesville, Florida 32611, United States
| | - Steven D Bruner
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
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Yuan Y, Zallot R, Grove TL, Payan DJ, Martin-Verstraete I, Šepić S, Balamkundu S, Neelakandan R, Gadi VK, Liu CF, Swairjo MA, Dedon PC, Almo SC, Gerlt JA, de Crécy-Lagard V. Discovery of novel bacterial queuine salvage enzymes and pathways in human pathogens. Proc Natl Acad Sci U S A 2019; 116:19126-19135. [PMID: 31481610 PMCID: PMC6754566 DOI: 10.1073/pnas.1909604116] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
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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Affiliation(s)
- Yifeng Yuan
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611
| | - Rémi Zallot
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Tyler L Grove
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461
| | - Daniel J Payan
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Isabelle Martin-Verstraete
- Laboratoire de Pathogénèse des Bactéries Anaérobies, Institut Pasteur et Université de Paris, F-75015 Paris, France
| | - Sara Šepić
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611
| | - Seetharamsingh Balamkundu
- Singapore-MIT Alliance for Research and Technology, Infectious Disease Interdisciplinary Research Group, 138602 Singapore, Singapore
| | - Ramesh Neelakandan
- Singapore-MIT Alliance for Research and Technology, Infectious Disease Interdisciplinary Research Group, 138602 Singapore, Singapore
| | - Vinod K Gadi
- Singapore-MIT Alliance for Research and Technology, Infectious Disease Interdisciplinary Research Group, 138602 Singapore, Singapore
| | - Chuan-Fa Liu
- Singapore-MIT Alliance for Research and Technology, Infectious Disease Interdisciplinary Research Group, 138602 Singapore, Singapore
| | - Manal A Swairjo
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182
- The Viral Information Institute, San Diego State University, San Diego, CA 92182
| | - Peter C Dedon
- Singapore-MIT Alliance for Research and Technology, Infectious Disease Interdisciplinary Research Group, 138602 Singapore, Singapore
- Department of Biological Engineering and Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Steven C Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461
| | - John A Gerlt
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611;
- University of Florida Genetics Institute, Gainesville, FL 32610
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