1
|
Hung SH, Elliott GI, Ramkumar TR, Burtnyak L, McGrenaghan CJ, Alkuzweny S, Quaiyum S, Iwata-Reuyl D, Pan X, Green BD, Kelly VP, de Crécy-Lagard V, Swairjo M. Structural basis of Qng1-mediated salvage of the micronutrient queuine from queuosine-5'-monophosphate as the biological substrate. Nucleic Acids Res 2023; 51:935-951. [PMID: 36610787 PMCID: PMC9881137 DOI: 10.1093/nar/gkac1231] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 12/02/2022] [Accepted: 12/10/2022] [Indexed: 01/09/2023] Open
Abstract
Eukaryotic life benefits from-and ofttimes critically relies upon-the de novo biosynthesis and supply of vitamins and micronutrients from bacteria. The micronutrient queuosine (Q), derived from diet and/or the gut microbiome, is used as a source of the nucleobase queuine, which once incorporated into the anticodon of tRNA contributes to translational efficiency and accuracy. Here, we report high-resolution, substrate-bound crystal structures of the Sphaerobacter thermophilus queuine salvage protein Qng1 (formerly DUF2419) and of its human ortholog QNG1 (C9orf64), which together with biochemical and genetic evidence demonstrate its function as the hydrolase releasing queuine from queuosine-5'-monophosphate as the biological substrate. We also show that QNG1 is highly expressed in the liver, with implications for Q salvage and recycling. The essential role of this family of hydrolases in supplying queuine in eukaryotes places it at the nexus of numerous (patho)physiological processes associated with queuine deficiency, including altered metabolism, proliferation, differentiation and cancer progression.
Collapse
Affiliation(s)
- Shr-Hau Hung
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA, USA
- The Viral Information Institute, San Diego State University, San Diego, CA, USA
| | - Gregory I Elliott
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA, USA
| | - Thakku R Ramkumar
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
| | - Lyubomyr Burtnyak
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Callum J McGrenaghan
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Sana Alkuzweny
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA, USA
| | - Samia Quaiyum
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
| | - Dirk Iwata-Reuyl
- Department of Chemistry, PO Box 751 Portland State University, Portland, OR 97207, USA
| | - Xiaobei Pan
- School of Biological Sciences, Institute for Global Food Security, Queen's University Belfast, Belfast, UK
| | - Brian D Green
- School of Biological Sciences, Institute for Global Food Security, Queen's University Belfast, Belfast, UK
| | - Vincent P Kelly
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
- University of Florida Genetics Institute, Gainesville, FL 32610, USA
| | - Manal A Swairjo
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA, USA
- The Viral Information Institute, San Diego State University, San Diego, CA, USA
| |
Collapse
|
2
|
Katanski CD, Watkins CP, Zhang W, Reyer M, Miller S, Pan T. Analysis of queuosine and 2-thio tRNA modifications by high throughput sequencing. Nucleic Acids Res 2022; 50:e99. [PMID: 35713550 PMCID: PMC9508811 DOI: 10.1093/nar/gkac517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/26/2022] [Accepted: 06/14/2022] [Indexed: 11/30/2022] Open
Abstract
Queuosine (Q) is a conserved tRNA modification at the wobble anticodon position of tRNAs that read the codons of amino acids Tyr, His, Asn, and Asp. Q-modification in tRNA plays important roles in the regulation of translation efficiency and fidelity. Queuosine tRNA modification is synthesized de novo in bacteria, whereas in mammals the substrate for Q-modification in tRNA is queuine, the catabolic product of the Q-base of gut bacteria. This gut microbiome dependent tRNA modification may play pivotal roles in translational regulation in different cellular contexts, but extensive studies of Q-modification biology are hindered by the lack of high throughput sequencing methods for its detection and quantitation. Here, we describe a periodate-treatment method that enables single base resolution profiling of Q-modification in tRNAs by Nextgen sequencing from biological RNA samples. Periodate oxidizes the Q-base, which results in specific deletion signatures in the RNA-seq data. Unexpectedly, we found that periodate-treatment also enables the detection of several 2-thio-modifications including τm5s2U, mcm5s2U, cmnm5s2U, and s2C by sequencing in human and E. coli tRNA. We term this method periodate-dependent analysis of queuosine and sulfur modification sequencing (PAQS-seq). We assess Q- and 2-thio-modifications at the tRNA isodecoder level, and 2-thio modification changes in stress response. PAQS-seq should be widely applicable in the biological studies of Q- and 2-thio-modifications in mammalian and microbial tRNAs.
Collapse
Affiliation(s)
- Christopher D Katanski
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Christopher P Watkins
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Wen Zhang
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Matthew Reyer
- Program of Biophysics, University of Chicago, Chicago, IL 60637, USA
| | - Samuel Miller
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Tao Pan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| |
Collapse
|
3
|
Richard P, Kozlowski L, Guillorit H, Garnier P, McKnight NC, Danchin A, Manière X. Queuine, a bacterial-derived hypermodified nucleobase, shows protection in in vitro models of neurodegeneration. PLoS One 2021; 16:e0253216. [PMID: 34379627 PMCID: PMC8357117 DOI: 10.1371/journal.pone.0253216] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 05/29/2021] [Indexed: 11/26/2022] Open
Abstract
Growing evidence suggests that human gut bacteria, which comprise the microbiome, are linked to several neurodegenerative disorders. An imbalance in the bacterial population in the gut of Parkinson's disease (PD) and Alzheimer's disease (AD) patients has been detected in several studies. This dysbiosis very likely decreases or increases microbiome-derived molecules that are protective or detrimental, respectively, to the human body and those changes are communicated to the brain through the so-called 'gut-brain-axis'. The microbiome-derived molecule queuine is a hypermodified nucleobase enriched in the brain and is exclusively produced by bacteria and salvaged by humans through their gut epithelium. Queuine replaces guanine at the wobble position (position 34) of tRNAs with GUN anticodons and promotes efficient cytoplasmic and mitochondrial mRNA translation. Queuine depletion leads to protein misfolding and activation of the endoplasmic reticulum stress and unfolded protein response pathways in mice and human cells. Protein aggregation and mitochondrial impairment are often associated with neural dysfunction and neurodegeneration. To elucidate whether queuine could facilitate protein folding and prevent aggregation and mitochondrial defects that lead to proteinopathy, we tested the effect of chemically synthesized queuine, STL-101, in several in vitro models of neurodegeneration. After neurons were pretreated with STL-101 we observed a significant decrease in hyperphosphorylated alpha-synuclein, a marker of alpha-synuclein aggregation in a PD model of synucleinopathy, as well as a decrease in tau hyperphosphorylation in an acute and a chronic model of AD. Additionally, an associated increase in neuronal survival was found in cells pretreated with STL-101 in both AD models as well as in a neurotoxic model of PD. Measurement of queuine in the plasma of 180 neurologically healthy individuals suggests that healthy humans maintain protective levels of queuine. Our work has identified a new role for queuine in neuroprotection uncovering a therapeutic potential for STL-101 in neurological disorders.
Collapse
Affiliation(s)
- Patricia Richard
- Stellate Therapeutics Inc., JLABS @ NYC, New York, New York, United States of America
| | | | - Hélène Guillorit
- Stellate Therapeutics SAS, Paris, France
- Institut de Génomique Fonctionnelle, Montpellier, France
| | | | - Nicole C. McKnight
- Stellate Therapeutics Inc., JLABS @ NYC, New York, New York, United States of America
| | | | | |
Collapse
|
4
|
Brandmayr C, Wagner M, Brückl T, Globisch D, Pearson D, Kneuttinger AC, Reiter V, Hienzsch A, Koch S, Thoma I, Thumbs P, Michalakis S, Müller M, Biel M, Carell T. Isotope-based analysis of modified tRNA nucleosides correlates modification density with translational efficiency. Angew Chem Int Ed Engl 2012; 51:11162-5. [PMID: 23037940 PMCID: PMC3533783 DOI: 10.1002/anie.201203769] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 07/26/2012] [Indexed: 11/09/2022]
Abstract
Useful diversity: Quantification of modified tRNA nucleobases in different murine and porcine tissues reveals a tissue-specific overall modification content. The modification content correlates with rates of protein synthesis in vitro, suggesting a direct link between tRNA modification levels and tissue-specific translational efficiency.
Collapse
Affiliation(s)
- Caterina Brandmayr
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität MünchenButenandtstrasse 5–13, 81377 Munich (Germany) E-mail: Homepage: http://www.carellgroup.de
| | - Mirko Wagner
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität MünchenButenandtstrasse 5–13, 81377 Munich (Germany) E-mail: Homepage: http://www.carellgroup.de
| | - Tobias Brückl
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität MünchenButenandtstrasse 5–13, 81377 Munich (Germany) E-mail: Homepage: http://www.carellgroup.de
| | - Daniel Globisch
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität MünchenButenandtstrasse 5–13, 81377 Munich (Germany) E-mail: Homepage: http://www.carellgroup.de
| | - David Pearson
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität MünchenButenandtstrasse 5–13, 81377 Munich (Germany) E-mail: Homepage: http://www.carellgroup.de
| | - Andrea Christa Kneuttinger
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität MünchenButenandtstrasse 5–13, 81377 Munich (Germany) E-mail: Homepage: http://www.carellgroup.de
| | - Veronika Reiter
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität MünchenButenandtstrasse 5–13, 81377 Munich (Germany) E-mail: Homepage: http://www.carellgroup.de
| | - Antje Hienzsch
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität MünchenButenandtstrasse 5–13, 81377 Munich (Germany) E-mail: Homepage: http://www.carellgroup.de
| | - Susanne Koch
- Center for Integrated Protein Science at the Department of Pharmacy, Ludwig-Maximilians-Universität MünchenButenandtstrasse 5–13, 81377 Munich (Germany)
| | - Ines Thoma
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität MünchenButenandtstrasse 5–13, 81377 Munich (Germany) E-mail: Homepage: http://www.carellgroup.de
| | - Peter Thumbs
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität MünchenButenandtstrasse 5–13, 81377 Munich (Germany) E-mail: Homepage: http://www.carellgroup.de
| | - Stylianos Michalakis
- Center for Integrated Protein Science at the Department of Pharmacy, Ludwig-Maximilians-Universität MünchenButenandtstrasse 5–13, 81377 Munich (Germany)
| | - Markus Müller
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität MünchenButenandtstrasse 5–13, 81377 Munich (Germany) E-mail: Homepage: http://www.carellgroup.de
| | - Martin Biel
- Center for Integrated Protein Science at the Department of Pharmacy, Ludwig-Maximilians-Universität MünchenButenandtstrasse 5–13, 81377 Munich (Germany)
| | - Thomas Carell
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität MünchenButenandtstrasse 5–13, 81377 Munich (Germany) E-mail: Homepage: http://www.carellgroup.de
| |
Collapse
|
5
|
Brandmayr C, Wagner M, Brückl T, Globisch D, Pearson D, Kneuttinger AC, Reiter V, Hienzsch A, Koch S, Thoma I, Thumbs P, Michalakis S, Müller M, Biel M, Carell T. Eine isotopenbasierte Analyse modifizierter tRNA-Nukleoside korreliert die Modifikationsdichte mit der Translationseffizienz. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201203769] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|