1
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Scaletti ER, Unterlass JE, Almlöf I, Koolmeister T, Vallin KS, Kapsitidou D, Tsuber V, Helleday T, Stenmark P, Jemth AS. Kinetic and structural characterization of NUDT15 and NUDT18 as catalysts of isoprene pyrophosphate hydrolysis. FEBS J 2024. [PMID: 38944687 DOI: 10.1111/febs.17202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/19/2024] [Accepted: 06/06/2024] [Indexed: 07/01/2024]
Abstract
Isoprene pyrophosphates play a crucial role in the synthesis of a diverse array of essential nonsterol and sterol biomolecules and serve as substrates for posttranslational isoprenylation of proteins, enabling specific anchoring to cellular membranes. Hydrolysis of isoprene pyrophosphates would be a means to modulate their levels, downstream products, and protein isoprenylation. While NUDIX hydrolases from plants have been described to catalyze the hydrolysis of isoprene pyrophosphates, homologous enzymes with this function in animals have not yet been reported. In this study, we screened an extensive panel of human NUDIX hydrolases for activity in hydrolyzing isoprene pyrophosphates. We found that human nucleotide triphosphate diphosphatase NUDT15 and 8-oxo-dGDP phosphatase NUDT18 efficiently catalyze the hydrolysis of several physiologically relevant isoprene pyrophosphates. Notably, we demonstrate that geranyl pyrophosphate is an excellent substrate for NUDT18, with a catalytic efficiency of 2.1 × 105 m-1·s-1, thus making it the best substrate identified for NUDT18 to date. Similarly, geranyl pyrophosphate proved to be the best isoprene pyrophosphate substrate for NUDT15, with a catalytic efficiency of 4.0 × 104 M-1·s-1. LC-MS analysis of NUDT15 and NUDT18 catalyzed isoprene pyrophosphate hydrolysis revealed the generation of the corresponding monophosphates and inorganic phosphate. Furthermore, we solved the crystal structure of NUDT15 in complex with the hydrolysis product geranyl phosphate at a resolution of 1.70 Å. This structure revealed that the active site nicely accommodates the hydrophobic isoprenoid moiety and helped identify key binding residues. Our findings imply that isoprene pyrophosphates are endogenous substrates of NUDT15 and NUDT18, suggesting they are involved in animal isoprene pyrophosphate metabolism.
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Affiliation(s)
- Emma R Scaletti
- Department of Biochemistry and Biophysics, Stockholm University, Sweden
| | - Judith E Unterlass
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Ingrid Almlöf
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Tobias Koolmeister
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Karl S Vallin
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Despina Kapsitidou
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Viktoriia Tsuber
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Thomas Helleday
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, 171 77, Sweden
| | - Pål Stenmark
- Department of Biochemistry and Biophysics, Stockholm University, Sweden
| | - Ann-Sofie Jemth
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, 171 77, Sweden
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2
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Benoni B, Potužník J, Škríba A, Benoni R, Trylcova J, Tulpa M, Spustová K, Grab K, Mititelu MB, Pačes J, Weber J, Stanek D, Kowalska J, Bednarova L, Keckesova Z, Vopalensky P, Gahurova L, Cahova H. HIV-1 Infection Reduces NAD Capping of Host Cell snRNA and snoRNA. ACS Chem Biol 2024; 19:1243-1249. [PMID: 38747804 PMCID: PMC11197007 DOI: 10.1021/acschembio.4c00151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 06/22/2024]
Abstract
Nicotinamide adenine dinucleotide (NAD) is a critical component of the cellular metabolism and also serves as an alternative 5' cap on various RNAs. However, the function of the NAD RNA cap is still under investigation. We studied NAD capping of RNAs in HIV-1-infected cells because HIV-1 is responsible for the depletion of the NAD/NADH cellular pool and causing intracellular pellagra. By applying the NAD captureSeq protocol to HIV-1-infected and uninfected cells, we revealed that four snRNAs (e.g., U1) and four snoRNAs lost their NAD cap when infected with HIV-1. Here, we provide evidence that the presence of the NAD cap decreases the stability of the U1/HIV-1 pre-mRNA duplex. Additionally, we demonstrate that reducing the quantity of NAD-capped RNA by overexpressing the NAD RNA decapping enzyme DXO results in an increase in HIV-1 infectivity. This suggests that NAD capping is unfavorable for HIV-1 and plays a role in its infectivity.
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Affiliation(s)
- Barbora Benoni
- Institute
of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí
2, 160 00 Prague
6, Czechia
- First
Faculty of Medicine, Charles University, Kateřinská 32, 121 08 Prague, Czechia
| | - Jiří
František Potužník
- Institute
of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí
2, 160 00 Prague
6, Czechia
- Faculty
of Science, Department of Cell Biology, Charles University, Viničná 7, 121 08 Prague 2, Czechia
| | - Anton Škríba
- Institute
of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí
2, 160 00 Prague
6, Czechia
| | - Roberto Benoni
- Institute
of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí
2, 160 00 Prague
6, Czechia
| | - Jana Trylcova
- Institute
of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí
2, 160 00 Prague
6, Czechia
| | - Matouš Tulpa
- Institute
of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí
2, 160 00 Prague
6, Czechia
- Faculty
of Science, Department of Physical and Macromolecular Chemistry, Charles University, Hlavova 8, 121 08 Prague 2, Czechia
| | - Kristína Spustová
- Institute
of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí
2, 160 00 Prague
6, Czechia
| | - Katarzyna Grab
- Division
of Biophysics, Faculty of Physics, University
of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Maria-Bianca Mititelu
- Institute
of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí
2, 160 00 Prague
6, Czechia
- Faculty
of Science, Department of Cell Biology, Charles University, Viničná 7, 121 08 Prague 2, Czechia
| | - Jan Pačes
- Institute
of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague 4, Czechia
| | - Jan Weber
- Institute
of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí
2, 160 00 Prague
6, Czechia
| | - David Stanek
- Institute
of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague 4, Czechia
| | - Joanna Kowalska
- Division
of Biophysics, Faculty of Physics, University
of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Lucie Bednarova
- Institute
of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí
2, 160 00 Prague
6, Czechia
| | - Zuzana Keckesova
- Institute
of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí
2, 160 00 Prague
6, Czechia
| | - Pavel Vopalensky
- Institute
of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí
2, 160 00 Prague
6, Czechia
| | - Lenka Gahurova
- Institute
of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí
2, 160 00 Prague
6, Czechia
- Department
of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 1760, 37005 České Budějovice, Czechia
| | - Hana Cahova
- Institute
of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí
2, 160 00 Prague
6, Czechia
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3
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Huang Y, Kumar S, Lee J, Lü W, Du J. Coupling enzymatic activity and gating in an ancient TRPM chanzyme and its molecular evolution. Nat Struct Mol Biol 2024:10.1038/s41594-024-01316-4. [PMID: 38773335 DOI: 10.1038/s41594-024-01316-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 04/12/2024] [Indexed: 05/23/2024]
Abstract
Channel enzymes represent a class of ion channels with enzymatic activity directly or indirectly linked to their channel function. We investigated a TRPM2 chanzyme from choanoflagellates that integrates two seemingly incompatible functions into a single peptide: a channel module activated by ADP-ribose with high open probability and an enzyme module (NUDT9-H domain) consuming ADP-ribose at a remarkably slow rate. Using time-resolved cryogenic-electron microscopy, we captured a complete series of structural snapshots of gating and catalytic cycles, revealing the coupling mechanism between channel gating and enzymatic activity. The slow kinetics of the NUDT9-H enzyme module confers a self-regulatory mechanism: ADPR binding triggers NUDT9-H tetramerization, promoting channel opening, while subsequent hydrolysis reduces local ADPR, inducing channel closure. We further demonstrated how the NUDT9-H domain has evolved from a structurally semi-independent ADP-ribose hydrolase module in early species to a fully integrated component of a gating ring essential for channel activation in advanced species.
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Affiliation(s)
- Yihe Huang
- Van Andel Institute, Grand Rapids, MI, USA
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | | | - Junuk Lee
- Van Andel Institute, Grand Rapids, MI, USA
| | - Wei Lü
- Van Andel Institute, Grand Rapids, MI, USA.
| | - Juan Du
- Van Andel Institute, Grand Rapids, MI, USA.
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4
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Balıkçı E, Marques ASMC, Bauer LG, Seupel R, Bennett J, Raux B, Buchan K, Simelis K, Singh U, Rogers C, Ward J, Cheng C, Szommer T, Schützenhofer K, Elkins JM, Sloman DL, Ahel I, Fedorov O, Brennan PE, Huber KVM. Unexpected Noncovalent Off-Target Activity of Clinical BTK Inhibitors Leads to Discovery of a Dual NUDT5/14 Antagonist. J Med Chem 2024; 67:7245-7259. [PMID: 38635563 PMCID: PMC11089510 DOI: 10.1021/acs.jmedchem.4c00072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/20/2024]
Abstract
Cofactor mimicry represents an attractive strategy for the development of enzyme inhibitors but can lead to off-target effects due to the evolutionary conservation of binding sites across the proteome. Here, we uncover the ADP-ribose (ADPr) hydrolase NUDT5 as an unexpected, noncovalent, off-target of clinical BTK inhibitors. Using a combination of biochemical, biophysical, and intact cell NanoBRET assays as well as X-ray crystallography, we confirm catalytic inhibition and cellular target engagement of NUDT5 and reveal an unusual binding mode that is independent of the reactive acrylamide warhead. Further investigation of the prototypical BTK inhibitor ibrutinib also revealed potent inhibition of the largely unstudied NUDIX hydrolase family member NUDT14. By exploring structure-activity relationships (SARs) around the core scaffold, we identify a potent, noncovalent, and cell-active dual NUDT5/14 inhibitor. Cocrystallization experiments yielded new insights into the NUDT14 hydrolase active site architecture and inhibitor binding, thus providing a basis for future chemical probe design.
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Affiliation(s)
- Esra Balıkçı
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Anne-Sophie M. C. Marques
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Ludwig G. Bauer
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Raina Seupel
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - James Bennett
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Brigitt Raux
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Karly Buchan
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Klemensas Simelis
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Usha Singh
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Catherine Rogers
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Jennifer Ward
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Carol Cheng
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Tamas Szommer
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Kira Schützenhofer
- Sir
William Dunn School of Pathology, University
of Oxford, South Parks
Road, Oxford OX1 3RE, U.K.
| | - Jonathan M. Elkins
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - David L. Sloman
- Departments
of Discovery Chemistry, Merck & Co.
Inc., 33 Avenue Louis
Pasteur, Boston, Massachusetts 02115, United States
| | - Ivan Ahel
- Sir
William Dunn School of Pathology, University
of Oxford, South Parks
Road, Oxford OX1 3RE, U.K.
| | - Oleg Fedorov
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Paul E. Brennan
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Alzheimer’s
Research UK Oxford Drug Discovery Institute, Nuffield Department of
Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
| | - Kilian V. M. Huber
- Centre
for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
- Target
Discovery Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7FZ, U.K.
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5
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Khan A, Mallick M, Ladke JS, Bhandari R. The ring rules the chain - inositol pyrophosphates and the regulation of inorganic polyphosphate. Biochem Soc Trans 2024; 52:567-580. [PMID: 38629621 DOI: 10.1042/bst20230256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 03/29/2024] [Accepted: 04/03/2024] [Indexed: 04/25/2024]
Abstract
The maintenance of phosphate homeostasis serves as a foundation for energy metabolism and signal transduction processes in all living organisms. Inositol pyrophosphates (PP-InsPs), composed of an inositol ring decorated with monophosphate and diphosphate moieties, and inorganic polyphosphate (polyP), chains of orthophosphate residues linked by phosphoanhydride bonds, are energy-rich biomolecules that play critical roles in phosphate homeostasis. There is a complex interplay between these two phosphate-rich molecules, and they share an interdependent relationship with cellular adenosine triphosphate (ATP) and inorganic phosphate (Pi). In eukaryotes, the enzymes involved in PP-InsP synthesis show some degree of conservation across species, whereas distinct enzymology exists for polyP synthesis among different organisms. In fact, the mechanism of polyP synthesis in metazoans, including mammals, is still unclear. Early studies on PP-InsP and polyP synthesis were conducted in the slime mould Dictyostelium discoideum, but it is in the budding yeast Saccharomyces cerevisiae that a clear understanding of the interplay between polyP, PP-InsPs, and Pi homeostasis has now been established. Recent research has shed more light on the influence of PP-InsPs on polyP in mammals, and the regulation of both these molecules by cellular ATP and Pi levels. In this review we will discuss the cross-talk between PP-InsPs, polyP, ATP, and Pi in the context of budding yeast, slime mould, and mammals. We will also highlight the similarities and differences in the relationship between these phosphate-rich biomolecules among this group of organisms.
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Affiliation(s)
- Azmi Khan
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500039, India
| | - Manisha Mallick
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500039, India
- Graduate Studies, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Jayashree S Ladke
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500039, India
- Graduate Studies, Regional Centre for Biotechnology, Faridabad 121001, Haryana, India
| | - Rashna Bhandari
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500039, India
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6
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Zhang Z, Samsa WE, Gong Z. NUDT16 regulates CtIP PARylation to dictate homologous recombination repair. Nucleic Acids Res 2024; 52:3761-3777. [PMID: 38324469 PMCID: PMC11039996 DOI: 10.1093/nar/gkae064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/04/2024] [Accepted: 01/22/2024] [Indexed: 02/09/2024] Open
Abstract
CtIP initiates DNA end resection and mediates homologous recombination (HR) repair. However, the underlying mechanisms of CtIP regulation and how the control of its regulation affects DNA repair remain incompletely characterized. In this study, NUDT16 loss decreases CtIP protein levels and impairs CtIP recruitment to double-strand breaks (DSBs). Furthermore, overexpression of a catalytically inactive NUDT16 mutant is unable to rescue decreased CtIP protein and impaired CtIP recruitment to DSBs. In addition, we identified a novel posttranslational modification of CtIP by ADP-ribosylation that is targeted by a PAR-binding E3 ubiquitin ligase, RNF146, leading to CtIP ubiquitination and degradation. These data suggest that the hydrolase activity of NUDT16 plays a major role in controlling CtIP protein levels. Notably, ADP-ribosylation of CtIP is required for its interaction with NUDT16, its localization at DSBs, and for HR repair. Interestingly, NUDT16 can also be ADP-ribosylated. The ADP-ribosylated NUDT16 is critical for CtIP protein stability, CtIP recruitment to DSBs, and HR repair in response to DNA damage. In summary, we demonstrate that NUDT16 and its PARylation regulate CtIP stability and CtIP recruitment to DSBs, providing new insights into our understanding of the regulation of CtIP-mediated DNA end resection in the HR repair pathway.
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Affiliation(s)
- Zhen Zhang
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
| | - William E Samsa
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
| | - Zihua Gong
- Department of Cancer Biology, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
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7
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Massey JC, Magagnoli J, Sutton SS, Buckhaults PJ, Wyatt MD. Collateral damage of NUDT15 deficiency in cancer provides a cancer pharmacogenetic therapeutic window with thiopurines. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.08.588560. [PMID: 38645136 PMCID: PMC11030356 DOI: 10.1101/2024.04.08.588560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Genome instability is a hallmark of cancer and are driven by mutations in oncogenes and tumor suppressor genes. Despite successes seen with select targeted therapeutics, this type of personalized medicine is only beneficial for a small subpopulation of cancer patients who have one of a few actionable genetic changes. Most tumors also contain hundreds of passenger mutations that offered no fitness advantage or disadvantage during tumor evolution. Mutations in known pharmacogenetic (PGx) loci for which germline variants encode variability in drug response can cause somatically acquired drug sensitivity. The NUDT15 gene is a known PGx locus that participates in the rate-limiting metabolism of thiopurines. People with two defective germline alleles of NUDT15 are hypersensitive to the toxic effects of thiopurines. NUDT15 is located adjacent to the Retinoblastoma ( RB1 ) tumor suppressor gene, which often undergoes homozygous deletion in retinoblastomas and other epithelial cancers. We observed that RB1 undergoes homozygous deletions in 9.4% of prostate adenocarcinomas and 2.5% of ovarian cancers, and in nearly all of these cases NUDT15 is also lost. Moreover, 44% of prostate adenocarcinomas and over 60% of ovarian cancers have lost one allele of NUDT15, which predicts that a majority of all prostate and ovarian cancers have somatically acquired hypersensitivity to thiopurine treatment. We performed a retrospective analysis of >16,000 patients in the US Veterans Administration health care system and found concurrent xanthine oxidase inhibition (XOi) and thiopurine usage for non-cancer indications is significantly associated with reduced incidence of prostate cancer. The hazard ratio for the development of prostate cancer in patients treated with thiopurines and XOi was 0.562 (0.301-1.051) for the unmatched cohort and 0.389 (0.185-0.819) for the propensity score matched cohort. We experimentally depleted NUDT15 from ovarian and prostate cancer cell lines and observed a dramatic sensitization to thiopurine-induced and DNA damage-dependent toxicity. These results indicate that somatic loss of NUDT15 predicts therapeutic sensitivity to a low cost and well tolerated drug with a broad therapeutic window.
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8
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Viana Neto AM, Guerreiro DD, Martins JAM, Vasconcelos FÁR, Melo RÉBF, Velho ALMCS, Neila-Montero M, Montes-Garrido R, Nagano CS, Araújo AA, Moura AA. Sperm traits and seminal plasma proteome of locally adapted hairy rams subjected to intermittent scrotal insulation. Anim Reprod Sci 2024; 263:107439. [PMID: 38447240 DOI: 10.1016/j.anireprosci.2024.107439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 02/16/2024] [Indexed: 03/08/2024]
Abstract
The present study evaluated the effects of heat stress on reproductive parameters of hairy rams. Six animals were subjected to scrotal insulation during four consecutive nights (6 PM - 6 AM). Day (D) 0 was the first day of insulation. Scrotal circumference increased from 30.5 ± 0.3 cm (at pre-insulation) to 31.8 ± 0.4 cm on D4, decreased 3.9 cm on D28, returning to 30.6 ± 0.6 cm on D57. Sperm concentration decreased from 3.7 ± 0.12 ×109 sperm/mL before insulation to 2.6 ± 0.1 ×109 on D23, returning to normal on D57. Sperm motility averaged 75 ± 2.9% before insulation, was undetectable on D23, and became normal on D77. Sperm with normal morphology reached 5.9 ± 2.6% on D35 but recovered (86.8 ± 2.1%) on D91. Sperm DNA integrity decreased from 86.5 ± 4.7% before insulation to 11.1 ± 3.7% on D63, returning to pre-insulation values on D120. Sperm BSP immunostaining was reduced after scrotal insulation. Variations in seminal protein abundances coincided with changes in sperm parameters. Seminal plasma superoxide dismutase, carboxypeptidase Q-precursor and NPC intracellular cholesterol transporter 2 decreased on D18, returning to normal after D28. Albumin, inhibitor of carbonic anhydrase precursor, EGF-like repeat and discoid I-like domain-containing protein 3 and polymeric immunoglobulin receptor increased after insulation. In summary, intermittent scrotal insulation drastically altered ram sperm attributes and seminal proteins, especially those associated with oxidative stress. Knowledge of animal´s response to thermal stress is vital in the scenario of climate changes.
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Affiliation(s)
| | - Denise D Guerreiro
- Department of Animal Science, Federal University of Ceará, Fortaleza, Brazil
| | - Jorge A M Martins
- School of Veterinary Medicine, Federal University of Cariri, Juazeiro do Norte, Brazil
| | | | - R Évila B F Melo
- Department of Animal Science, Federal University of Ceará, Fortaleza, Brazil
| | | | - Marta Neila-Montero
- Itra-ULE, Animal Reproduction and Obstetrics, Department of Veterinary Medicine, Surgery and Anatomy, University of León, León, Spain
| | - Rafael Montes-Garrido
- Itra-ULE, Animal Reproduction and Obstetrics, Department of Veterinary Medicine, Surgery and Anatomy, University of León, León, Spain
| | - Celso S Nagano
- Department of Fisheries Engineering, Federal University of Ceará, Fortaleza, Brazil
| | - Airton A Araújo
- Department of Animal Science, Federal University of Ceará, Fortaleza, Brazil; School of Veterinary Medicine, Ceará State University, Fortaleza, Brazil
| | - Arlindo A Moura
- Department of Animal Science, Federal University of Ceará, Fortaleza, Brazil.
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9
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František Potužník J, Nešuta O, Škríba A, Voleníková B, Mititelu MB, Mancini F, Serianni V, Fernandez H, Spustová K, Trylčová J, Vopalensky P, Cahová H. Diadenosine Tetraphosphate (Ap 4 A) Serves as a 5' RNA Cap in Mammalian Cells. Angew Chem Int Ed Engl 2024; 63:e202314951. [PMID: 37934413 DOI: 10.1002/anie.202314951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 11/08/2023]
Abstract
The recent expansion of the field of RNA chemical modifications has changed our understanding of post-transcriptional gene regulation. Apart from internal nucleobase modifications, 7-methylguanosine was long thought to be the only eukaryotic RNA cap. However, the discovery of non-canonical RNA caps in eukaryotes revealed a new niche of previously undetected RNA chemical modifications. We are the first to report the existence of a new non-canonical RNA cap, diadenosine tetraphosphate (Ap4 A), in human and rat cell lines. Ap4 A is the most abundant dinucleoside polyphosphate in eukaryotic cells and can be incorporated into RNA by RNA polymerases as a non-canonical initiating nucleotide (NCIN). Using liquid chromatography-mass spectrometry (LC-MS), we show that the amount of capped Ap4 A-RNA is independent of the cellular concentration of Ap4 A. A decapping enzyme screen identifies two enzymes cleaving Ap4 A-RNA,NUDT2 and DXO, both of which also cleave other substrate RNAs in vitro. We further assess the translatability and immunogenicity of Ap4 A-RNA and show that although it is not translated, Ap4 A-RNA is recognized as self by the cell and does not elicit an immune response, making it a natural component of the transcriptome. Our findings open a previously unexplored area of eukaryotic RNA regulation.
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Affiliation(s)
- Jiří František Potužník
- Chemical Biology of Nucleic, Acids, Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, Prague, 6, Czechia
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, Prague, 2, Czechia
| | - Ondřej Nešuta
- Chemical Biology of Nucleic, Acids, Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, Prague, 6, Czechia
| | - Anton Škríba
- Chemical Biology of Nucleic, Acids, Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, Prague, 6, Czechia
| | - Barbora Voleníková
- Chemical Biology of Nucleic, Acids, Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, Prague, 6, Czechia
| | - Maria-Bianca Mititelu
- Chemical Biology of Nucleic, Acids, Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, Prague, 6, Czechia
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, Prague, 2, Czechia
| | - Flaminia Mancini
- Chemical Biology of Nucleic, Acids, Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, Prague, 6, Czechia
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, Prague, 2, Czechia
| | - Valentina Serianni
- Chemical Biology of Nucleic, Acids, Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, Prague, 6, Czechia
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, Prague, 2, Czechia
| | - Henri Fernandez
- Chemical Biology of Nucleic, Acids, Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, Prague, 6, Czechia
| | - Kristína Spustová
- Chemical Biology of Nucleic, Acids, Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, Prague, 6, Czechia
| | - Jana Trylčová
- Chemical Biology of Nucleic, Acids, Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, Prague, 6, Czechia
| | - Pavel Vopalensky
- Chemical Biology of Nucleic, Acids, Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, Prague, 6, Czechia
| | - Hana Cahová
- Chemical Biology of Nucleic, Acids, Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 2, Prague, 6, Czechia
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10
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Huth T, Dreher EC, Lemke S, Fritzsche S, Sugiyanto RN, Castven D, Ibberson D, Sticht C, Eiteneuer E, Jauch A, Pusch S, Albrecht T, Goeppert B, Candia J, Wang XW, Ji J, Marquardt JU, Nahnsen S, Schirmacher P, Roessler S. Chromosome 8p engineering reveals increased metastatic potential targetable by patient-specific synthetic lethality in liver cancer. SCIENCE ADVANCES 2023; 9:eadh1442. [PMID: 38134284 PMCID: PMC10745716 DOI: 10.1126/sciadv.adh1442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023]
Abstract
Large-scale chromosomal aberrations are prevalent in human cancer, but their function remains poorly understood. We established chromosome-engineered hepatocellular carcinoma cell lines using CRISPR-Cas9 genome editing. A 33-mega-base pair region on chromosome 8p (chr8p) was heterozygously deleted, mimicking a frequently observed chromosomal deletion. Using this isogenic model system, we delineated the functional consequences of chr8p loss and its impact on metastatic behavior and patient survival. We found that metastasis-associated genes on chr8p act in concert to induce an aggressive and invasive phenotype characteristic for chr8p-deleted tumors. Genome-wide CRISPR-Cas9 viability screening in isogenic chr8p-deleted cells served as a powerful tool to find previously unidentified synthetic lethal targets and vulnerabilities accompanying patient-specific chromosomal alterations. Using this target identification strategy, we showed that chr8p deletion sensitizes tumor cells to targeting of the reactive oxygen sanitizing enzyme Nudix hydrolase 17. Thus, chromosomal engineering allowed for the identification of novel synthetic lethalities specific to chr8p loss of heterozygosity.
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Affiliation(s)
- Thorben Huth
- Heidelberg University, Medical Faculty, Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Emely C. Dreher
- Heidelberg University, Medical Faculty, Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Steffen Lemke
- Quantitative Biology Center (QBiC), University of Tübingen, 72076 Tübingen, Germany
- Department of Peptide-based Immunotherapy, University and University Hospital Tübingen, 72076 Tübingen, Germany
- Institute for Cell Biology, Department of Immunology, University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, 72076 Tübingen, Germany
| | - Sarah Fritzsche
- Heidelberg University, Medical Faculty, Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Raisatun N. Sugiyanto
- Heidelberg University, Medical Faculty, Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Darko Castven
- Department of Medicine I, University Medical Center Schleswig Holstein, 23538 Lübeck, Germany
| | - David Ibberson
- Deep Sequencing Core Facility, CellNetworks Excellence Cluster, Heidelberg University, 69120 Heidelberg, Germany
| | - Carsten Sticht
- NGS Core Facility, Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany
| | - Eva Eiteneuer
- Heidelberg University, Medical Faculty, Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Anna Jauch
- Institute of Human Genetics, Heidelberg University, 69120 Heidelberg, Germany
| | - Stefan Pusch
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Thomas Albrecht
- Heidelberg University, Medical Faculty, Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Benjamin Goeppert
- Heidelberg University, Medical Faculty, Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Institute of Tissue Medicine and Pathology, University of Bern, 3008 Bern, Switzerland
- Institute of Pathology and Neuropathology, RKH Klinikum Ludwigsburg, 71640 Ludwigsburg, Germany
| | - Julián Candia
- Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Xin Wei Wang
- Laboratory of Human Carcinogenesis and Liver Cancer Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Junfang Ji
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Jens U. Marquardt
- Department of Medicine I, University Medical Center Schleswig Holstein, 23538 Lübeck, Germany
| | - Sven Nahnsen
- Quantitative Biology Center (QBiC), University of Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC2180) “Image-Guided and Functionally Instructed Tumor Therapies”, University of Tübingen, 72076 Tübingen, Germany
- Biomedical Data Science, Department of Computer Science, University of Tübingen, 72076 Tübingen, Germany
- The M3 Research Center, University of Tübingen, 72076 Tübingen, Germany
| | - Peter Schirmacher
- Heidelberg University, Medical Faculty, Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Stephanie Roessler
- Heidelberg University, Medical Faculty, Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
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11
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Gomes-Filho JV, Breuer R, Morales-Filloy HG, Pozhydaieva N, Borst A, Paczia N, Soppa J, Höfer K, Jäschke A, Randau L. Identification of NAD-RNA species and ADPR-RNA decapping in Archaea. Nat Commun 2023; 14:7597. [PMID: 37989750 PMCID: PMC10663502 DOI: 10.1038/s41467-023-43377-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 11/07/2023] [Indexed: 11/23/2023] Open
Abstract
NAD is a coenzyme central to metabolism that also serves as a 5'-terminal cap for bacterial and eukaryotic transcripts. Thermal degradation of NAD can generate nicotinamide and ADP-ribose (ADPR). Here, we use LC-MS/MS and NAD captureSeq to detect and identify NAD-RNAs in the thermophilic model archaeon Sulfolobus acidocaldarius and in the halophilic mesophile Haloferax volcanii. None of the four Nudix proteins of S. acidocaldarius catalyze NAD-RNA decapping in vitro, but one of the proteins (Saci_NudT5) promotes ADPR-RNA decapping. NAD-RNAs are converted into ADPR-RNAs, which we detect in S. acidocaldarius total RNA. Deletion of the gene encoding the 5'-3' exonuclease Saci-aCPSF2 leads to a 4.5-fold increase in NAD-RNA levels. We propose that the incorporation of NAD into RNA acts as a degradation marker for Saci-aCPSF2. In contrast, ADPR-RNA is processed by Saci_NudT5 into 5'-p-RNAs, providing another layer of regulation for RNA turnover in archaeal cells.
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Affiliation(s)
| | - Ruth Breuer
- Faculty of Biology, Philipps-Universität Marburg, Marburg, Germany
| | | | | | - Andreas Borst
- Institute for Molecular Biosciences, Biocentre, Goethe-University, Frankfurt am Main, Germany
| | - Nicole Paczia
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Jörg Soppa
- Institute for Molecular Biosciences, Biocentre, Goethe-University, Frankfurt am Main, Germany
| | - Katharina Höfer
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- SYNMIKRO, Center for Synthetic Microbiology, Marburg, Germany
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Heidelberg, Germany
| | - Lennart Randau
- Faculty of Biology, Philipps-Universität Marburg, Marburg, Germany.
- SYNMIKRO, Center for Synthetic Microbiology, Marburg, Germany.
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12
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Sokołowska B, Orłowska M, Okrasińska A, Piłsyk S, Pawłowska J, Muszewska A. What can be lost? Genomic perspective on the lipid metabolism of Mucoromycota. IMA Fungus 2023; 14:22. [PMID: 37932857 PMCID: PMC10629195 DOI: 10.1186/s43008-023-00127-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 10/23/2023] [Indexed: 11/08/2023] Open
Abstract
Mucoromycota is a phylum of early diverging fungal (EDF) lineages, of mostly plant-associated terrestrial fungi. Some strains have been selected as promising biotechnological organisms due to their ability to produce polyunsaturated fatty acids and efficient conversion of nutrients into lipids. Others get their lipids from the host plant and are unable to produce even the essential ones on their own. Following the advancement in EDF genome sequencing, we carried out a systematic survey of lipid metabolism protein families across different EDF lineages. This enabled us to explore the genomic basis of the previously documented ability to produce several types of lipids within the fungal tree of life. The core lipid metabolism genes showed no significant diversity in distribution, however specialized lipid metabolic pathways differed in this regard among different fungal lineages. In total 165 out of 202 genes involved in lipid metabolism were present in all tested fungal lineages, while remaining 37 genes were found to be absent in some of fungal lineages. Duplications were observed for 69 genes. For the first time we demonstrate that ergosterol is not being produced by several independent groups of plant-associated fungi due to the losses of different ERG genes. Instead, they possess an ancestral pathway leading to the synthesis of cholesterol, which is absent in other fungal lineages. The lack of diacylglycerol kinase in both Mortierellomycotina and Blastocladiomycota opens the question on sterol equilibrium regulation in these organisms. Early diverging fungi retained most of beta oxidation components common with animals including Nudt7, Nudt12 and Nudt19 pointing at peroxisome divergence in Dikarya. Finally, Glomeromycotina and Mortierellomycotina representatives have a similar set of desaturases and elongases related to the synthesis of complex, polyunsaturated fatty acids pointing at an ancient expansion of fatty acid metabolism currently being explored by biotechnological studies.
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Affiliation(s)
- Blanka Sokołowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106, Warsaw, Poland
- Faculty of Biology, Biological and Chemical Research Centre, Institute of Evolutionary Biology, University of Warsaw, Zwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Małgorzata Orłowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106, Warsaw, Poland
- Faculty of Biology, Biological and Chemical Research Centre, Institute of Evolutionary Biology, University of Warsaw, Zwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Alicja Okrasińska
- Faculty of Biology, Biological and Chemical Research Centre, Institute of Evolutionary Biology, University of Warsaw, Zwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Sebastian Piłsyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106, Warsaw, Poland
| | - Julia Pawłowska
- Faculty of Biology, Biological and Chemical Research Centre, Institute of Evolutionary Biology, University of Warsaw, Zwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Anna Muszewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106, Warsaw, Poland.
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13
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Li Z, Luo A, Xie B. The Complex Network of ADP-Ribosylation and DNA Repair: Emerging Insights and Implications for Cancer Therapy. Int J Mol Sci 2023; 24:15028. [PMID: 37834477 PMCID: PMC10573881 DOI: 10.3390/ijms241915028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/23/2023] [Accepted: 10/04/2023] [Indexed: 10/15/2023] Open
Abstract
ADP-ribosylation is a post-translational modification of proteins that plays a key role in various cellular processes, including DNA repair. Recently, significant progress has been made in understanding the mechanism and function of ADP-ribosylation in DNA repair. ADP-ribosylation can regulate the recruitment and activity of DNA repair proteins by facilitating protein-protein interactions and regulating protein conformations. Moreover, ADP-ribosylation can influence additional post-translational modifications (PTMs) of proteins involved in DNA repair, such as ubiquitination, methylation, acetylation, phosphorylation, and SUMOylation. The interaction between ADP-ribosylation and these additional PTMs can fine-tune the activity of DNA repair proteins and ensure the proper execution of the DNA repair process. In addition, PARP inhibitors have been developed as a promising cancer therapeutic strategy by exploiting the dependence of certain cancer types on the PARP-mediated DNA repair pathway. In this paper, we review the progress of ADP-ribosylation in DNA repair, discuss the crosstalk of ADP-ribosylation with additional PTMs in DNA repair, and summarize the progress of PARP inhibitors in cancer therapy.
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Affiliation(s)
| | - Aiqin Luo
- Key Laboratory of Molecular Medicine and Biological Diagnosis and Treatment (Ministry of Industry and Information Technology), School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Bingteng Xie
- Key Laboratory of Molecular Medicine and Biological Diagnosis and Treatment (Ministry of Industry and Information Technology), School of Life Science, Beijing Institute of Technology, Beijing 100081, China
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14
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Lukaszewicz M, Ferenc-Mrozek A, Kokosza J, Stefaniuk A, Stepinski J, Bojarska E, Darzynkiewicz E. Mammalian Nudt15 hydrolytic and binding activity on methylated guanosine mononucleotides. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:487-495. [PMID: 37644211 PMCID: PMC10618335 DOI: 10.1007/s00249-023-01678-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/06/2023] [Accepted: 08/14/2023] [Indexed: 08/31/2023]
Abstract
The Nudt15 enzyme of the NUDIX protein family is the subject of extensive study due to its action on thiopurine drugs used in the treatment of cancer and inflammatory diseases. In addition to thiopurines, Nudt15 is enzymatically active in vitro on several nucleotide substrates. It has also been suggested that this enzyme may play a role in 5'RNA turnover by hydrolyzing m7GDP, a product of mRNA decapping. However, no detailed studies on this substrate with Nudt15 are available. Here, we analyzed the enzymatic activity of Nudt15 with m7GDP, its triphosphate form m7GTP, and the trimethylated counterparts (m32,2,7GDP and m32,2,7GTP). Kinetic data revealed a moderate activity of Nudt15 toward these methylated mononucleotides compared to the dGTP substrate. However m7GDP and m32,2,7GDP showed a distinct stabilization of Nudt15 upon ligand binding, in the same range as dGTP, and thus these two mononucleotides may be used as leading structures in the design of small molecule binders of Nudt15.
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Affiliation(s)
- Maciej Lukaszewicz
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland.
| | - Aleksandra Ferenc-Mrozek
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Julia Kokosza
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Anna Stefaniuk
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Janusz Stepinski
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Elzbieta Bojarska
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Edward Darzynkiewicz
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097, Warsaw, Poland
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15
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Broderick K, Moutaoufik MT, Aly KA, Babu M. Sanitation enzymes: Exquisite surveillance of the noncanonical nucleotide pool to safeguard the genetic blueprint. Semin Cancer Biol 2023; 94:11-20. [PMID: 37211293 DOI: 10.1016/j.semcancer.2023.05.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 05/14/2023] [Accepted: 05/17/2023] [Indexed: 05/23/2023]
Abstract
Reactive oxygen species (ROS) are common products of normal cellular metabolism, but their elevated levels can result in nucleotide modifications. These modified or noncanonical nucleotides often integrate into nascent DNA during replication, causing lesions that trigger DNA repair mechanisms such as the mismatch repair machinery and base excision repair. Four superfamilies of sanitization enzymes can effectively hydrolyze noncanonical nucleotides from the precursor pool and eliminate their unintended incorporation into DNA. Notably, we focus on the representative MTH1 NUDIX hydrolase, whose enzymatic activity is ostensibly nonessential under normal physiological conditions. Yet, the sanitization attributes of MTH1 are more prevalent when ROS levels are abnormally high in cancer cells, rendering MTH1 an interesting target for developing anticancer treatments. We discuss multiple MTH1 inhibitory strategies that have emerged in recent years, and the potential of NUDIX hydrolases as plausible targets for the development of anticancer therapeutics.
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Affiliation(s)
- Kirsten Broderick
- Department of Biochemistry, University of Regina, Regina, Saskatchewan, Canada
| | | | - Khaled A Aly
- Department of Biochemistry, University of Regina, Regina, Saskatchewan, Canada
| | - Mohan Babu
- Department of Biochemistry, University of Regina, Regina, Saskatchewan, Canada.
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16
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Debar L, Ishak L, Moretton A, Anoosheh S, Morel F, Jenninger L, Balandier I, Vernet P, Hofer A, van den Wildenberg S, Farge G. NUDT6 and NUDT9, two mitochondrial members of the NUDIX family, have distinct hydrolysis activities. Mitochondrion 2023:S1567-7249(23)00054-5. [PMID: 37343711 DOI: 10.1016/j.mito.2023.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 06/16/2023] [Accepted: 06/17/2023] [Indexed: 06/23/2023]
Abstract
The 22 members of the NUDIX (NUcleoside DIphosphate linked to another moiety, X) hydrolase superfamily can hydrolyze a variety of phosphorylated molecules including (d)NTPs and their oxidized forms, nucleotide sugars, capped mRNAs and dinucleotide coenzymes such as NADH and FADH. Beside this broad range of enzymatic substrates, the NUDIX proteins can also be found in different cellular compartments, mainly in the nucleus and in the cytosol, but also in the peroxisome and in the mitochondria. Here we studied two members of the family, NUDT6 and NUDT9. We showed that NUDT6 is expressed in human cells and localizes exclusively to mitochondria and we confirmed that NUDT9 has a mitochondrial localization. To elucidate their potential role within this organelle, we investigated the functional consequences at the mitochondrial level of NUDT6- and NUDT9-deficiency and found that the depletion of either of the two proteins results in an increased activity of the respiratory chain and an alteration of the mitochondrial respiratory chain complexes expression. We demonstrated that NUDT6 and NUDT9 have distinct substrate specificity in vitro, which is dependent on the cofactor used. They can both hydrolyze a large range of low molecular weight compounds such as NAD+(H), FAD and ADPR, but NUDT6 is mainly active towards NADH, while NUDT9 displays a higher activity towards ADPR.
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Affiliation(s)
- Louis Debar
- Université Clermont Auvergne, CNRS, Laboratoire de Physique de Clermont, F-63000 CLERMONT-FERRAND, France
| | - Layal Ishak
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
| | - Amandine Moretton
- Université Clermont Auvergne, CNRS, Laboratoire de Physique de Clermont, F-63000 CLERMONT-FERRAND, France
| | - Saber Anoosheh
- Umeå University, Department of Medical Biochemistry and Biophysics, SE-90187 Umeå, Sweden
| | - Frederic Morel
- Université Clermont Auvergne, CNRS, Laboratoire de Physique de Clermont, F-63000 CLERMONT-FERRAND, France
| | - Louise Jenninger
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, P.O. Box 440, SE-405 30 Gothenburg, Sweden
| | - Isabelle Balandier
- Université Clermont Auvergne, CNRS, Laboratoire de Physique de Clermont, F-63000 CLERMONT-FERRAND, France
| | - Patrick Vernet
- Université Clermont Auvergne, CNRS, Laboratoire de Physique de Clermont, F-63000 CLERMONT-FERRAND, France
| | - Anders Hofer
- Umeå University, Department of Medical Biochemistry and Biophysics, SE-90187 Umeå, Sweden
| | - Siet van den Wildenberg
- Université Clermont Auvergne, CNRS, Laboratoire de Physique de Clermont, F-63000 CLERMONT-FERRAND, France; Université Clermont Auvergne, CNRS, IRD, Université Jean Monnet Saint Etienne, LMV, F-63000 Clermont-Ferrand, France
| | - Geraldine Farge
- Université Clermont Auvergne, CNRS, Laboratoire de Physique de Clermont, F-63000 CLERMONT-FERRAND, France.
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17
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Lukaszewicz M, Mrozek AF, Bojarska E, Stelmach J, Stepinski J, Darzynkiewicz E. Contribution of Nudt12 enzyme to differentially methylated dinucleotides of 5'RNA cap structure. Biochim Biophys Acta Gen Subj 2023:130400. [PMID: 37301333 DOI: 10.1016/j.bbagen.2023.130400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/17/2023] [Accepted: 06/04/2023] [Indexed: 06/12/2023]
Abstract
Recent findings have substantially broadened our knowledge about the diversity of modifications of the 5'end of RNAs, an issue generally attributed to mRNA cap structure (m7GpppN). Nudt12 is one of the recently described new enzymatic activities involved in cap metabolism. However, in contrast to its roles in metabolite-cap turnover (e.g., NAD-cap) and NADH/NAD metabolite hydrolysis, little is known regarding its hydrolytic activity towards dinucleotide cap structures. In order to gain further insight into this Nudt12 activity, comprehensive analysis with a spectrum of cap-like dinucleotides was performed with respect to different nucleotide types adjacent to the (m7)G moiety and its methylation status. Among the tested compounds, GpppA, GpppAm, and Gpppm6Am were identified as novel potent Nudt12 substrates, with KM values in the same range as that of NADH. Interestingly, substrate inhibition of Nudt12 catalytic activity was detected in the case of the GpppG dinucleotide, a phenomenon not reported to date. Finally, comparison of Nudt12 with DcpS and Nud16, two other enzymes with known activity on dinucleotide cap structures, revealed their overlapping and more specific substrates. Altogether, these findings provide a basis for clarifying the role of Nudt12 in cap-like dinucleotide turnover.
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Affiliation(s)
- Maciej Lukaszewicz
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland.
| | - Aleksandra-Ferenc Mrozek
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Elzbieta Bojarska
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Joanna Stelmach
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Janusz Stepinski
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
| | - Edward Darzynkiewicz
- Department of Biophysics, Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland; Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
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18
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Wojtczak BA, Bednarczyk M, Sikorski PJ, Wojtczak A, Surynt P, Kowalska J, Jemielity J. Synthesis and Evaluation of Diguanosine Cap Analogs Modified at the C8-Position by Suzuki-Miyaura Cross-Coupling: Discovery of 7-Methylguanosine-Based Molecular Rotors. J Org Chem 2023. [PMID: 37209102 DOI: 10.1021/acs.joc.3c00126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Chemical modifications of the mRNA cap structure can enhance the stability, translational properties, and half-life of mRNAs, thereby altering the therapeutic properties of synthetic mRNA. However, cap structure modification is challenging because of the instability of the 5'-5'-triphosphate bridge and N7-methylguanosine. The Suzuki-Miyaura cross-coupling reaction between boronic acid and halogen compound is a mild, convenient, and potentially applicable approach for modifying biomolecules. Herein, we describe two methods to synthesize C8-modified cap structures using the Suzuki-Miyaura cross-coupling reaction. Both methods employed phosphorimidazolide chemistry to form the 5',5'-triphosphate bridge. However, in the first method, the introduction of the modification via the Suzuki-Miyaura cross-coupling reaction at the C8 position occurs postsynthetically, at the dinucleotide level, whereas in the second method, the modification was introduced at the level of the nucleoside 5'-monophosphate, and later, the triphosphate bridge was formed. Both methods were successfully applied to incorporate six different groups (methyl, cyclopropyl, phenyl, 4-dimethylaminophenyl, 4-cyanophenyl, and 1-pyrene) into either the m7G or G moieties of the cap structure. Aromatic substituents at the C8-position of guanosine form a push-pull system that exhibits environment-sensitive fluorescence. We demonstrated that this phenomenon can be harnessed to study the interaction with cap-binding proteins, e.g., eIF4E, DcpS, Nudt16, and snurportin.
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Affiliation(s)
- Blazej A Wojtczak
- Centre of New Technologies, University of Warsaw; S. Banacha 2c, 02-097 Warsaw, Poland
| | - Marcelina Bednarczyk
- Centre of New Technologies, University of Warsaw; S. Banacha 2c, 02-097 Warsaw, Poland
- Faculty of Physics, University of Warsaw; L. Pasteura 5, 02-093, Warsaw, Poland
| | - Pawel J Sikorski
- Centre of New Technologies, University of Warsaw; S. Banacha 2c, 02-097 Warsaw, Poland
| | - Anna Wojtczak
- Faculty of Physics, University of Warsaw; L. Pasteura 5, 02-093, Warsaw, Poland
| | - Piotr Surynt
- Centre of New Technologies, University of Warsaw; S. Banacha 2c, 02-097 Warsaw, Poland
- Faculty of Physics, University of Warsaw; L. Pasteura 5, 02-093, Warsaw, Poland
| | - Joanna Kowalska
- Faculty of Physics, University of Warsaw; L. Pasteura 5, 02-093, Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw; S. Banacha 2c, 02-097 Warsaw, Poland
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19
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Banfield MJ. Manipulation of plant immunity via an mRNA decapping pathogen effector. THE NEW PHYTOLOGIST 2023. [PMID: 37096655 DOI: 10.1111/nph.18921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 03/30/2023] [Indexed: 05/03/2023]
Affiliation(s)
- Mark J Banfield
- Department of Biochemistry & Metabolism, John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
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20
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Zegarra V, Mais CN, Freitag J, Bange G. The mysterious diadenosine tetraphosphate (AP4A). MICROLIFE 2023; 4:uqad016. [PMID: 37223742 PMCID: PMC10148737 DOI: 10.1093/femsml/uqad016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 03/15/2023] [Accepted: 04/21/2023] [Indexed: 05/25/2023]
Abstract
Dinucleoside polyphosphates, a class of nucleotides found amongst all the Trees of Life, have been gathering a lot of attention in the past decades due to their putative role as cellular alarmones. In particular, diadenosine tetraphosphate (AP4A) has been widely studied in bacteria facing various environmental challenges and has been proposed to be important for ensuring cellular survivability through harsh conditions. Here, we discuss the current understanding of AP4A synthesis and degradation, protein targets, their molecular structure where possible, and insights into the molecular mechanisms of AP4A action and its physiological consequences. Lastly, we will briefly touch on what is known with regards to AP4A beyond the bacterial kingdom, given its increasing appearance in the eukaryotic world. Altogether, the notion that AP4A is a conserved second messenger in organisms ranging from bacteria to humans and is able to signal and modulate cellular stress regulation seems promising.
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Affiliation(s)
- Victor Zegarra
- Department of Chemistry and Center for Synthetic Microbiology, Philipps University Marburg, Marburg 35043, Germany
| | - Christopher-Nils Mais
- Department of Chemistry and Center for Synthetic Microbiology, Philipps University Marburg, Marburg 35043, Germany
| | - Johannes Freitag
- Department of Biology, Philipps University Marburg, Marburg 35043, Germany
| | - Gert Bange
- Corresponding author. Karl-von-Frisch Strasse 14, 35043 Marburg, Germany. E-mail:
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21
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Walter M, Mayr F, Hanna BMF, Cookson V, Mortusewicz O, Helleday T, Herr P. NUDT22 promotes cancer growth through pyrimidine salvage. Oncogene 2023; 42:1282-1293. [PMID: 36871087 PMCID: PMC10101856 DOI: 10.1038/s41388-023-02643-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 02/15/2023] [Accepted: 02/17/2023] [Indexed: 03/06/2023]
Abstract
The NUDIX hydrolase NUDT22 converts UDP-glucose into glucose-1-phosphate and the pyrimidine nucleotide uridine monophosphate but a biological significance for this biochemical reaction has not yet been established. Glucose-1-phosphate is an important metabolite for energy and biomass production through glycolysis and nucleotides required for DNA replication are produced through energetically expensive de novo or energy-efficient salvage pathways. Here, we describe p53-regulated pyrimidine salvage through NUDT22-dependent hydrolysis of UDP-glucose to maintain cancer cell growth and to prevent replication stress. NUDT22 expression is consistently elevated in cancer tissues and high NUDT22 expression correlates with worse survival outcomes in patients indicating an increased dependency of cancer cells to NUDT22. Furthermore, we show that NUDT22 transcription is induced after inhibition of glycolysis, MYC-mediated oncogenic stress, and DNA damage directly through p53. NUDT22-deficient cancer cells suffer from growth retardation, S-phase delay, and slower DNA replication fork speed. Uridine supplementation rescues replication fork progression and alleviates replication stress and DNA damage. Conversely, NUDT22 deficiency sensitizes cells to de novo pyrimidine synthesis inhibition in vitro and reduces cancer growth in vivo. In conclusion, NUDT22 maintains pyrimidine supply in cancer cells and depletion of NUDT22 leads to genome instability. Targeting NUDT22 therefore has high potential for therapeutic applications in cancer therapy.
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Affiliation(s)
- Melanie Walter
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, S10 2RX, UK
| | - Florian Mayr
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institute, 171 76, Stockholm, Sweden
| | - Bishoy M F Hanna
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institute, 171 76, Stockholm, Sweden
| | - Victoria Cookson
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, S10 2RX, UK
| | - Oliver Mortusewicz
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institute, 171 76, Stockholm, Sweden
| | - Thomas Helleday
- Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institute, 171 76, Stockholm, Sweden
| | - Patrick Herr
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, S10 2RX, UK.
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22
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Huang Y, Lü W, Du J. Coupling enzymatic activity and gating in an ancient TRPM chanzyme and its molecular evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.16.533055. [PMID: 36993210 PMCID: PMC10055075 DOI: 10.1101/2023.03.16.533055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
The canonical ion channels gated by chemical ligands use the free energy of agonist binding to open the channel pore, returning to a closed state upon agonist departure. A unique class of ion channels, known as channel-enzymes (chanzymes), possess additional enzymatic activity that is directly or indirectly linked to their channel function. Here we investigated a TRPM2 chanzyme from choanoflagellates, an evolutionary ancestor of all metazoan TRPM channels, which integrates two seemingly incompatible functions into a single peptide: a channel module activated by ADP ribose (ADPR) with high open probability and an enzyme module (NUDT9-H domain) consuming ADPR at a remarkably slow rate. Using time-resolved cryo- electron microscopy (cryo-EM), we captured a complete series of structural snapshots of the gating and catalytic cycles, revealing the coupling mechanism between channel gating and enzymatic activity. Our results showed that the slow kinetics of the NUDT9-H enzyme module confers a novel self-regulatory mechanism, whereby the enzyme module modulates channel gating in a binary manner. Binding of ADPR to NUDT9-H first triggers tetramerization of the enzyme modules, promoting channel opening, while the subsequent hydrolysis reaction reduces local ADPR availability, inducing channel closure. This coupling enables the ion-conducting pore to alternate rapidly between open and closed states, avoiding Mg 2+ and Ca 2+ overload. We further demonstrated how the NUDT9-H domain has evolved from a structurally semi-independent ADPR hydrolase module in early species TRPM2 to a fully integrated component of a gating ring essential for channel activation in advanced species TRPM2. Our study demonstrated an example of how organisms can adapt to their environments at the molecular level.
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23
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Gómez-Rubio E, Garcia-Marin J. Molecular dynamics simulations reveal the impact of NUDT15 R139C and R139H variants in structural conformation and dynamics. J Biomol Struct Dyn 2023; 41:14812-14821. [PMID: 36907600 DOI: 10.1080/07391102.2023.2187626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 02/22/2023] [Indexed: 03/14/2023]
Abstract
NUDT15, also known as MTH2, is a member of the NUDIX protein family that catalyzes the hydrolysis of nucleotides and deoxynucleotides, as well as thioguanine analogues. NUDT15 has been reported as a DNA sanitizer in humans, and more recent studies have shown that some genetic variants are related to a poor prognosis in neoplastic and immunologic diseases treated with thioguanine drugs. Despite this, the role of NUDT15 in physiology and molecular biology is quite unclear, as is the mechanism of action of this enzyme. The existence of clinically relevant variants has prompted the study of these enzymes, whose capacity to bind and hydrolyze thioguanine nucleotides is still poorly understood. By using a combination of biomolecular modeling techniques and molecular dynamics, we have studied the monomeric wild type NUDT15 as well as two important variants, R139C and R139H. Our findings reveal not only how nucleotide binding stabilizes the enzyme but also how two loops are responsible for keeping the enzyme in a packed, close conformation. Mutations in α2 helix affect a network of hydrophobic and π-interactions that enclose the active site. This knowledge contributes to the understanding of NUDT15 structural dynamics and will be valuable for the design of new chemical probes and drugs targeting this protein.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Elena Gómez-Rubio
- Departamento de Biología Estructural y Química, Centro de Investigaciones Biológicas Margarita Salas, CIB-CSIC, Madrid, Spain
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Spain
| | - Javier Garcia-Marin
- Departamento de Química Orgánica y Química Inorgánica, Instituto de Investigación Química Andrés M. del Río (IQAR), Universidad de Alcalá (IRYCIS), Madrid, Spain
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24
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Duarte-Pereira S, Matos S, Oliveira JL, Silva RM. Study of NAD-interacting proteins highlights the extent of NAD regulatory roles in the cell and its potential as a therapeutic target. J Integr Bioinform 2023:jib-2022-0049. [PMID: 36880517 PMCID: PMC10389049 DOI: 10.1515/jib-2022-0049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 02/08/2023] [Indexed: 03/08/2023] Open
Abstract
Nicotinamide adenine dinucleotide (NAD) levels are essential for the normal physiology of the cell and are strictly regulated to prevent pathological conditions. NAD functions as a coenzyme in redox reactions, as a substrate of regulatory proteins, and as a mediator of protein-protein interactions. The main objectives of this study were to identify the NAD-binding and NAD-interacting proteins, and to uncover novel proteins and functions that could be regulated by this metabolite. It was considered if cancer-associated proteins were potential therapeutic targets. Using multiple experimental databases, we defined datasets of proteins that directly interact with NAD - the NAD-binding proteins (NADBPs) dataset - and of proteins that interact with NADBPs - the NAD-protein-protein interactions (NAD-PPIs) dataset. Pathway enrichment analysis revealed that NADBPs participate in several metabolic pathways, while NAD-PPIs are mostly involved in signalling pathways. These include disease-related pathways, namely, three major neurodegenerative disorders: Alzheimer's disease, Huntington's disease, and Parkinson's disease. Then, the complete human proteome was further analysed to select potential NADBPs. TRPC3 and isoforms of diacylglycerol (DAG) kinases, which are involved in calcium signalling, were identified as new NADBPs. Potential therapeutic targets that interact with NAD were identified, that have regulatory and signalling functions in cancer and neurodegenerative diseases.
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Affiliation(s)
- Sara Duarte-Pereira
- IEETA/DETI, University of Aveiro, Aveiro, Portugal.,Department of Medical Sciences, iBiMED - Institute of Biomedicine, University of Aveiro, Aveiro, Portugal
| | - Sérgio Matos
- IEETA/DETI, University of Aveiro, Aveiro, Portugal.,LASI - Intelligent Systems Associate Laboratory, Guimarães, Portugal
| | - José Luís Oliveira
- IEETA/DETI, University of Aveiro, Aveiro, Portugal.,LASI - Intelligent Systems Associate Laboratory, Guimarães, Portugal
| | - Raquel M Silva
- Department of Medical Sciences, iBiMED - Institute of Biomedicine, University of Aveiro, Aveiro, Portugal.,Universidade Católica Portuguesa, Faculty of Dental Medicine, Center for Interdisciplinary Research in Health (CIIS), Viseu, Portugal
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25
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Larson J, Tokmina-Lukaszewska M, Fausset H, Spurzem S, Cox S, Cooper G, Copié V, Bothner B. Arsenic Exposure Causes Global Changes in the Metalloproteome of Escherichia coli. Microorganisms 2023; 11:382. [PMID: 36838347 PMCID: PMC9965246 DOI: 10.3390/microorganisms11020382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/03/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023] Open
Abstract
Arsenic is a toxic metalloid with differential biological effects, depending on speciation and concentration. Trivalent arsenic (arsenite, AsIII) is more toxic at lower concentrations than the pentavalent form (arsenate, AsV). In E. coli, the proteins encoded by the arsRBC operon are the major arsenic detoxification mechanism. Our previous transcriptional analyses indicate broad changes in metal uptake and regulation upon arsenic exposure. Currently, it is not known how arsenic exposure impacts the cellular distribution of other metals. This study examines the metalloproteome of E. coli strains with and without the arsRBC operon in response to sublethal doses of AsIII and AsV. Size exclusion chromatography coupled with inductively coupled plasma mass spectrometry (SEC-ICPMS) was used to investigate the distribution of five metals (56Fe, 24Mg, 66Zn, 75As, and 63Cu) in proteins and protein complexes under native conditions. Parallel analysis by SEC-UV-Vis spectroscopy monitored the presence of protein cofactors. Together, these data reveal global changes in the metalloproteome, proteome, protein cofactors, and soluble intracellular metal pools in response to arsenic stress in E. coli. This work brings to light one outcome of metal exposure and suggests that metal toxicity on the cellular level arises from direct and indirect effects.
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Affiliation(s)
| | | | | | | | | | | | | | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59715, USA
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26
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Helleday T. Mitotic MTH1 Inhibitors in Treatment of Cancer. Cancer Treat Res 2023; 186:223-237. [PMID: 37978139 DOI: 10.1007/978-3-031-30065-3_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
The DNA damage response (DDR) protein MTH1 is sanitising the oxidized dNTP pool and preventing incorporation of oxidative damage into DNA and has an emerging role in mitosis. It is a stress-induced protein and often found to be overexpressed in cancer. Mitotic MTH1 inhibitors arrest cells in mitosis and result in incorporation of oxidative damage into DNA and selective killing of cancer cells. Here, I discuss the leading mitotic MTH1 inhibitor TH1579 (OXC-101, karonudib), now being evaluated in clinical trials, and describe its dual effect on mitosis and incorporation of oxidative DNA damage in cancer cells. I describe why MTH1 inhibitors that solely inhibits the enzyme activity fail to kill cancer cells and discuss if MTH1 is a valid target for cancer treatment. I discuss emerging roles of MTH1 in regulating tubulin polymerisation and mitosis and the necessity of developing the basic science insights along with translational efforts. I also give a perspective on how edgetic perturbation is making target validation difficult in the DDR field.
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Affiliation(s)
- Thomas Helleday
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden.
- Department of Oncology and Metabolism, Weston Park Cancer Centre, University of Sheffield, Sheffield, UK.
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27
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Rack JGM, Ahel I. A Simple Method to Study ADP-Ribosylation Reversal: From Function to Drug Discovery. Methods Mol Biol 2023; 2609:111-132. [PMID: 36515833 DOI: 10.1007/978-1-0716-2891-1_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
ADP-ribosylation is an ancient modification of proteins, nucleic acids, and other biomolecules found in all kingdoms of life as well as in certain viruses. The regulation of fundamental (patho)physiological processes by ADP-ribosylation, including the cellular stress response, inflammation, and immune response to bacterial and viral pathogens, has created a strong interest into the study of modification establishment and removal to explore novel therapeutic approaches. Beyond ADP-ribosylation in humans, direct targeting of factors that alter host ADP-ribosylation signaling (e.g., viral macrodomains) or utilize ADP-ribosylation to manipulate host cell behavior (e.g., bacterial toxins) were shown to reduce virulence and disease severity. However, the realization of these therapeutic potentials is thus far hampered by the unavailability of simple, high-throughput methods to study the modification "writers" and "erasers" and screen for novel inhibitors.Here, we describe a scalable method for the measurement of (ADP-ribosyl)hydrolase activity. The assay relies on the conversion of ADP-ribose released from a modified substrate by the (ADP-ribosyl)hydrolase under investigation into AMP by the phosphodiesterase NudT5 into bioluminescence via a commercially available detection assay. Moreover, this method can be utilized to study the role of nudix- or ENPP-type phosphodiesterases in ADP-ribosylation processing and may also be adapted to investigate the activity of (ADP-ribosyl)transferases. Overall, this method is applicable for both basic biochemical characterization and screening of large drug libraries; hence, it is highly adaptable to diverse project needs.
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Affiliation(s)
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
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28
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Marcos Santos L, da Silveira NJF. Current Fragment-to-lead Approaches Starting from the 7-azaindole: The Pharmacological Versatility of a Privileged Molecular Fragment. Curr Top Med Chem 2023; 23:2116-2130. [PMID: 37461366 DOI: 10.2174/1568026623666230718100541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 06/03/2023] [Accepted: 06/15/2023] [Indexed: 09/09/2023]
Abstract
Fragment-based drug discovery is one of the most powerful paradigms in the recent context of medicinal chemistry and is being widely practiced by academic and industrial researchers. Currently, azaindoles are among the most exploited molecular fragments in pharmaceutical innovation projects inspired by fragment-to-lead strategies. The 7-azaindole is the most prominent representative within this remarkable family of pyrrolopyridine fragments, as it is present in the chemical structure of several approved antitumor drugs and also of numerous therapeutic candidates. In this paper, a brief overview on existing proofs of concept in the literature will be presented, as well as some recent works that corroborate 7-azaindole as a privileged and pharmacologically versatile molecular fragment.
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Affiliation(s)
- Leandro Marcos Santos
- Laboratory of Molecular Modeling and Computer Simulation / MolMod-CS (D311-F), Institute of Chemistry, Federal University of Alfenas / UNIFAL-MG, Alfenas, Minas Gerais, 37130-001, Brazil
- Pharmaceutical Chemistry Research Laboratory / LQFar (D202A), Department of Food and Medicines, Faculty of Pharmaceutical Sciences, Federal University of Alfenas / UNIFAL-MG, Alfenas, Minas Gerais, 37130-001, Brazil
| | - Nelson José Freitas da Silveira
- Laboratory of Molecular Modeling and Computer Simulation / MolMod-CS (D311-F), Institute of Chemistry, Federal University of Alfenas / UNIFAL-MG, Alfenas, Minas Gerais, 37130-001, Brazil
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29
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Qi H, Grace Wright RH, Beato M, Price BD. The ADP-ribose hydrolase NUDT5 is important for DNA repair. Cell Rep 2022; 41:111866. [PMID: 36543120 DOI: 10.1016/j.celrep.2022.111866] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 09/16/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022] Open
Abstract
DNA damage leads to rapid synthesis of poly(ADP-ribose) (pADPr), which is important for damage signaling and repair. pADPr chains are removed by poly(ADP-ribose) glycohydrolase (PARG), releasing free mono(ADP-ribose) (mADPr). Here, we show that the NUDIX hydrolase NUDT5, which can hydrolyze mADPr to ribose-5-phosphate and either AMP or ATP, is recruited to damage sites through interaction with PARG. NUDT5 does not regulate PARP or PARG activity. Instead, loss of NUDT5 reduces basal cellular ATP levels and exacerbates the decrease in cellular ATP that occurs during DNA repair. Further, loss of NUDT5 activity impairs RAD51 recruitment, attenuates the phosphorylation of key DNA-repair proteins, and reduces both H2A.Z exchange at damage sites and repair by homologous recombination. The ability of NUDT5 to hydrolyze mADPr, and/or regulate cellular ATP, may therefore be important for efficient DNA repair. Targeting NUDT5 to disrupt PAR/mADPr and energy metabolism may be an effective anti-cancer strategy.
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Affiliation(s)
- Hongyun Qi
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston MA 02215, USA
| | - Roni Helene Grace Wright
- Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, Sant Cugat del Vallès, 08195 Barcelona, Spain
| | - Miguel Beato
- Centro de Regulación Genòmica (CRG), The Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Brendan D Price
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston MA 02215, USA.
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30
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Hong X, Hu Y, Yuan Z, Fang Z, Zhang X, Yuan Y, Guo C. Oxidatively Damaged Nucleic Acid: Linking Diabetes and Cancer. Antioxid Redox Signal 2022; 37:1153-1167. [PMID: 35946074 DOI: 10.1089/ars.2022.0096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Significance: Our current knowledge of the mechanism between diabetes and cancer is limited. Oxidatively damaged nucleic acid is considered a critical factor to explore the connections between these two diseases. Recent Advances: The link between diabetes mellitus and cancer has attracted increasing attention in recent years. Emerging evidence supports that oxidatively damaged nucleic acid caused by an imbalance between reactive oxygen species generation and elimination is a bridge connecting diabetes and cancer. 8-Oxo-7,8-dihydro-2'-deoxyguanosine and 8-oxo-7,8-dihydroguanosine assume important roles as biomarkers in assessing the relationship between oxidatively damaged nucleic acid and cancer. Critical Issues: The consequences of diabetes are extensive and may lead to the occurrence of cancer by influencing a combination of factors. At present, there is no direct evidence that diabetes causes cancer by affecting a single factor. Furthermore, the difficulty in controlling variables and differences in detection methods lead to poor reliability and repeatability of results, and there are no clear cutoff values for biomarkers to indicate cancer risk. Future Directions: A better understanding of connections as well as mechanisms between diabetes and cancer is still needed. Both diabetes and cancer are currently intractable diseases. Further exploration of the specific mechanism of oxidatively damaged nucleic acid in the connection between diabetes and cancer is urgently needed. In the future, it is necessary to further take oxidatively damaged nucleic acid as an entry point to provide new ideas for the diagnosis and treatment of diabetes and cancer. Experimental drugs targeting the repair process of oxidatively generated damage require an extensive preclinical evaluation and could ultimately provide new treatment strategies for these diseases. Antioxid. Redox Signal. 37, 1153-1167.
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Affiliation(s)
- Xiujuan Hong
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yiqiu Hu
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhijun Yuan
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhihao Fang
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoxiao Zhang
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ying Yuan
- Department of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Cancer Center, Zhejiang University, Hangzhou, China
| | - Cheng Guo
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Cancer Center, Zhejiang University, Hangzhou, China
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31
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BenDavid E, Pfaller CK, Pan Y, Samuel CE, Ma D. Host 5'-3' Exoribonuclease XRN1 Acts as a Proviral Factor for Measles Virus Replication by Downregulating the dsRNA-Activated Kinase PKR. J Virol 2022; 96:e0131922. [PMID: 36300942 PMCID: PMC9683022 DOI: 10.1128/jvi.01319-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 09/22/2022] [Indexed: 11/20/2022] Open
Abstract
Many negative-sense RNA viruses, including measles virus (MeV), are thought to carry out much of their viral replication in cytoplasmic membraneless foci known as inclusion bodies (IBs). The mechanisms by which IBs facilitate efficient viral replication remain largely unknown but may involve an intricate network of regulation at the host-virus interface. Viruses are able to modulate such interactions by a variety of strategies including adaptation of their genomes and "hijacking" of host proteins. The latter possibility broadens the molecular reservoir available for a virus to enhance its replication and/or antagonize host antiviral responses. Here, we show that the cellular 5'-3' exoribonuclease, XRN1, is a host protein hijacked by MeV. We found that upon MeV infection, XRN1 is translocated to cytoplasmic IBs where it acts in a proviral manner by preventing the accumulation of double-stranded RNA (dsRNA) within the IBs. This leads to the suppression of the dsRNA-induced innate immune responses mediated via the protein kinase R (PKR)-integrated stress response (ISR) pathway. IMPORTANCE Measles virus remains a major global health threat due to its high transmissibility and significant morbidity in children and immunocompromised individuals. Although there is an effective vaccine against MeV, a large population in the world remains without access to the vaccine, contributing to more than 7,000,000 measles cases and 60,000 measles deaths in 2020 (CDC). For negative-sense RNA viruses including MeV, one active research area is the exploration of virus-host interactions occurring at cytoplasmic IBs where viral replication takes place. In this study we present evidence suggesting a model in which MeV IBs antagonize host innate immunity by recruiting XRN1 to reduce dsRNA accumulation and subsequent PKR kinase activation/ISR induction. In the absence of XRN1, the increased dsRNA level acts as a potent activator of the antiviral PKR/ISR pathway leading to suppression of global cap-dependent mRNA translation and inhibition of viral replication.
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Affiliation(s)
- Ethan BenDavid
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, California, USA
| | | | - Yue Pan
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, California, USA
| | - Charles E. Samuel
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, California, USA
- Neuroscience Research Institute, University of California, Santa Barbara, California, USA
| | - Dzwokai Ma
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, California, USA
- Neuroscience Research Institute, University of California, Santa Barbara, California, USA
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Mattay J. Noncanonical metabolite RNA caps: Classification, quantification, (de)capping, and function. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1730. [PMID: 35675554 DOI: 10.1002/wrna.1730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 03/11/2022] [Accepted: 03/15/2022] [Indexed: 06/15/2023]
Abstract
The 5' cap of eukaryotic mRNA is a hallmark for cellular functions from mRNA stability to translation. However, the discovery of novel 5'-terminal RNA caps derived from cellular metabolites has challenged this long-standing singularity in both eukaryotes and prokaryotes. Reminiscent of the 7-methylguanosine (m7G) cap structure, these noncanonical caps originate from abundant coenzymes such as NAD, FAD, or CoA and from metabolites like dinucleoside polyphosphates (NpnN). As of now, the significance of noncanonical RNA caps is elusive: they differ for individual transcripts, occur in distinct types of RNA, and change in response to environmental stimuli. A thorough comparison of their prevalence, quantity, and characteristics is indispensable to define the distinct classes of metabolite-capped RNAs. This is achieved by a structured analysis of all present studies covering functional, quantitative, and sequencing data which help to uncover their biological impact. The biosynthetic strategies of noncanonical RNA capping and the elaborate decapping machinery reveal the regulation and turnover of metabolite-capped RNAs. With noncanonical capping being a universal and ancient phenomenon, organisms have developed diverging strategies to adapt metabolite-derived caps to their metabolic needs, but ultimately to establish noncanonical RNA caps as another intriguing layer of RNA regulation. This article is categorized under: RNA Processing > Capping and 5' End Modifications RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA Turnover and Surveillance > Regulation of RNA Stability.
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Affiliation(s)
- Johanna Mattay
- Institute of Biochemistry, University of Münster, Münster, Germany
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Helleday T, Rudd SG. Targeting the DNA damage response and repair in cancer through nucleotide metabolism. Mol Oncol 2022; 16:3792-3810. [PMID: 35583750 PMCID: PMC9627788 DOI: 10.1002/1878-0261.13227] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/05/2022] [Accepted: 05/17/2022] [Indexed: 12/24/2022] Open
Abstract
The exploitation of the DNA damage response and DNA repair proficiency of cancer cells is an important anticancer strategy. The replication and repair of DNA are dependent upon the supply of deoxynucleoside triphosphate (dNTP) building blocks, which are produced and maintained by nucleotide metabolic pathways. Enzymes within these pathways can be promising targets to selectively induce toxic DNA lesions in cancer cells. These same pathways also activate antimetabolites, an important group of chemotherapies that disrupt both nucleotide and DNA metabolism to induce DNA damage in cancer cells. Thus, dNTP metabolic enzymes can also be targeted to refine the use of these chemotherapeutics, many of which remain standard of care in common cancers. In this review article, we will discuss both these approaches exemplified by the enzymes MTH1, MTHFD2 and SAMHD1. © 2022 The Authors. Molecular Oncology published by John Wiley & Sons Ltd on behalf of Federation of European Biochemical Societies.
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Affiliation(s)
- Thomas Helleday
- Science for Life LaboratoryDepartment of Oncology‐PathologyKarolinska InstitutetStockholmSweden,Department of Oncology and Metabolism, Weston Park Cancer CentreUniversity of SheffieldUK
| | - Sean G. Rudd
- Science for Life LaboratoryDepartment of Oncology‐PathologyKarolinska InstitutetStockholmSweden
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Inaba Y, Iwamoto S, Nakayama K. Genome-wide DNA methylation status of Mongolians exhibits signs of cellular stress response related to their nomadic lifestyle. J Physiol Anthropol 2022; 41:30. [PMID: 35986394 PMCID: PMC9388360 DOI: 10.1186/s40101-022-00305-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 08/10/2022] [Indexed: 11/29/2022] Open
Abstract
Background Epigenetics is crucial for connecting environmental stresses with physiological responses in humans. Mongolia, where nomadic livestock pastoralism has been the primal livelihood, has a higher prevalence of various chronic diseases than the surrounding East Asian regions, which are more suitable for crop farming. The genes related to dietary stress and pathogenesis of related disorders may have varying epigenetic statuses among the human populations with diverse dietary cultures. Hence, to understand such epigenetic differences, we conducted a comparative analysis of genome-wide DNA methylation of Mongolians and crop-farming East Asians. Methods Genome-wide DNA methylation status of peripheral blood cells (PBCs) from 23 Mongolian adults and 24 Thai adults was determined using the Infinium Human Methylation 450K arrays and analyzed in combination with previously published 450K data of 20 Japanese and 8 Chinese adults. CpG sites/regions differentially methylated between Mongolians and crop-farming East Asians were detected using a linear model adjusted for sex, age, ethnicity, and immune cell heterogeneity on RnBeads software. Results Of the quality-controlled 389,454 autosomal CpG sites, 223 CpG sites were significantly differentially methylated among Mongolians and the four crop farming East Asian populations (false discovery rate < 0.05). Analyses focused on gene promoter regions revealed that PM20D1 (peptidase M20 domain containing 1), which is involved in mitochondrial uncoupling and various processes, including cellular protection from reactive oxygen species (ROS) and thermogenesis, was the top differentially methylated gene. Moreover, gene ontology enrichment analysis revealed that biological processes related to ROS metabolism were overrepresented among the top 1% differentially methylated genes. The promoter regions of these genes were generally hypermethylated in Mongolians, suggesting that the metabolic pathway detoxifying ROS might be globally suppressed in Mongolians, resulting in the high susceptibility of this population to various chronic diseases. Conclusions This study showed a significantly diverse DNA methylation status among Mongolians and crop-farming East Asians. Further, we found an association between the differentially methylated genes and various metabolic and neurodegenerative diseases. Knowledge of the epigenetic regulators might help in proper understanding, treatment, and control of such disorders, and physiological adaptation in the future. Supplementary Information The online version contains supplementary material available at 10.1186/s40101-022-00305-0.
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Jemth AS, Scaletti ER, Homan E, Stenmark P, Helleday T, Michel M. Nudix hydrolase 18 catalyzes the hydrolysis of active triphosphate metabolites of the antivirals remdesivir, ribavirin, and molnupiravir. J Biol Chem 2022; 298:102169. [PMID: 35732208 PMCID: PMC9212496 DOI: 10.1016/j.jbc.2022.102169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 12/28/2022] Open
Abstract
Remdesivir and molnupiravir have gained considerable interest because of their demonstrated activity against SARS-CoV-2. These antivirals are converted intracellularly to their active triphosphate forms remdesivir-TP and molnupiravir-TP. Cellular hydrolysis of these active metabolites would consequently decrease the efficiency of these drugs; however, whether endogenous enzymes that can catalyze this hydrolysis exist is unknown. Here, we tested remdesivir-TP as a substrate against a panel of human hydrolases and found that only Nudix hydrolase (NUDT) 18 catalyzed the hydrolysis of remdesivir-TP with notable activity. The kcat/Km value of NUDT18 for remdesivir-TP was determined to be 17,700 s-1M-1, suggesting that NUDT18-catalyzed hydrolysis of remdesivir-TP may occur in cells. Moreover, we demonstrate that the triphosphates of the antivirals ribavirin and molnupiravir are also hydrolyzed by NUDT18, albeit with lower efficiency than Remdesivir-TP. Low activity was also observed with the triphosphate forms of sofosbuvir and aciclovir. This is the first report showing that NUDT18 hydrolyzes triphosphates of nucleoside analogs of exogenous origin, suggesting that NUDT18 can act as a cellular sanitizer of modified nucleotides and may influence the antiviral efficacy of remdesivir, molnupiravir, and ribavirin. As NUDT18 is expressed in respiratory epithelial cells, it may limit the antiviral efficacy of remdesivir and molnupiravir against SARS-CoV-2 replication by decreasing the intracellular concentration of their active metabolites at their intended site of action.
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Affiliation(s)
- Ann-Sofie Jemth
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden.
| | - Emma Rose Scaletti
- Department of Biochemistry & Biophysics, Stockholm University, Stockholm, Sweden
| | - Evert Homan
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden
| | - Pål Stenmark
- Department of Biochemistry & Biophysics, Stockholm University, Stockholm, Sweden
| | - Thomas Helleday
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden; Weston Park Cancer Centre, Department of Oncology & Metabolism, Medical School, University of Sheffield, Sheffield, United Kingdom
| | - Maurice Michel
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden.
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Doamekpor SK, Sharma S, Kiledjian M, Tong L. Recent insights into noncanonical 5' capping and decapping of RNA. J Biol Chem 2022; 298:102171. [PMID: 35750211 PMCID: PMC9283932 DOI: 10.1016/j.jbc.2022.102171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 11/30/2022] Open
Abstract
The 5' N7-methylguanosine cap is a critical modification for mRNAs and many other RNAs in eukaryotic cells. Recent studies have uncovered an RNA 5' capping quality surveillance mechanism, with DXO/Rai1 decapping enzymes removing incomplete caps and enabling the degradation of the RNAs, in a process we also refer to as "no-cap decay." It has also been discovered recently that RNAs in eukaryotes, bacteria, and archaea can have noncanonical caps (NCCs), which are mostly derived from metabolites and cofactors such as NAD, FAD, dephospho-CoA, UDP-glucose, UDP-N-acetylglucosamine, and dinucleotide polyphosphates. These NCCs can affect RNA stability, mitochondrial functions, and possibly mRNA translation. The DXO/Rai1 enzymes and selected Nudix (nucleotide diphosphate linked to X) hydrolases have been shown to remove NCCs from RNAs through their deNADding, deFADding, deCoAping, and related activities, permitting the degradation of the RNAs. In this review, we summarize the recent discoveries made in this exciting new area of RNA biology.
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Affiliation(s)
- Selom K. Doamekpor
- Department of Biological Sciences, Columbia University, New York, New York, USA
| | - Sunny Sharma
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey, USA
| | - Megerditch Kiledjian
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey, USA.
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, New York, USA.
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Speijer D. Molecular characteristics of the multi-functional FAO enzyme ACAD9 illustrate the importance of FADH 2 /NADH ratios for mitochondrial ROS formation. Bioessays 2022; 44:e2200056. [PMID: 35708204 DOI: 10.1002/bies.202200056] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 06/04/2022] [Accepted: 06/07/2022] [Indexed: 11/10/2022]
Abstract
A decade ago I postulated that ROS formation in mitochondria was influenced by different FADH2 /NADH (F/N) ratios of catabolic substrates. Thus, fatty acid oxidation (FAO) would give higher ROS formation than glucose oxidation. Both the emergence of peroxisomes and neurons not using FAO, could be explained thus. ROS formation in NADH:ubiquinone oxidoreductase (Complex I) comes about by reverse electron transport (RET) due to high QH2 levels, and scarcity of its electron-acceptor (Q) during FAO. The then new, unexpected, finding of an FAO enzyme, ACAD9, being involved in complex I biogenesis, hinted at connections in line with the hypothesis. Recent findings about ACAD9's role in regulation of respiration fit with predictions the model makes: cementing connections between ROS production and F/N ratios. I describe how ACAD9 might be central to reversing the oxidative damage in complex I resulting from FAO. This seems to involve two distinct, but intimately connected, ACAD9 characteristics: (i) its upregulation of complex I biogenesis, and (ii) releasing FADH2 , with possible conversion into FMN, the crucial prosthetic group of complex I.
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Affiliation(s)
- Dave Speijer
- Amsterdam UMC location University of Amsterdam, Medical Biochemistry, Amsterdam, The Netherlands
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38
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Hughes DL, Willenbrock F, Soonawalla Z, Mukherjee S, O’Neill E. Predicting Early Disease Recurrence of Pancreatic Cancer following Surgery: Determining the Role of NUDT15 as a Prognostic Biomarker. Curr Oncol 2022; 29:2516-2529. [PMID: 35448180 PMCID: PMC9032287 DOI: 10.3390/curroncol29040206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/15/2022] [Accepted: 03/28/2022] [Indexed: 11/21/2022] Open
Abstract
Surgical resection remains the only curative treatment strategy for Pancreatic Ductal Adenocarcinoma (PDAC). A proportion of patients succumb to early disease recurrence post-operatively despite receiving adjuvant chemotherapy. The ability to identify these high-risk individuals at their initial diagnosis, prior to surgery, could potentially alter their treatment algorithm. This unique patient cohort may benefit from neo-adjuvant chemotherapy, even in the context of resectable disease, as this may secure systemic control over their disease burden. It may also improve patient selection for surgery. Using the Cancer Genome Atlas dataset, we first confirmed the poor overall survival associated with early disease recurrence (p < 0.0001). The transcriptomic profiles of these tumours were analysed, and we identified key aberrant signalling pathways involved in early disease relapse; downregulation across several immune signalling pathways was noted. Differentially expressed genes that could serve as biomarkers were identified (BPI, C6orf58, CD177, MCM7 and NUDT15). Receiver operating characteristic curves were constructed in order to identify biomarkers with a high diagnostic ability to identify patients who developed early disease recurrence. NUDT15 expression had the highest discriminatory capability as a biomarker (AUC 80.8%). Its expression was confirmed and validated in an independent cohort of patients with resected PDAC (n = 13). Patients who developed an early recurrence had a statistically higher tumour expression of NUDT15 when compared to patients who did not recur early (p < 0.01). Our results suggest that NUDT15 can be used as a prognostic biomarker that can stratify patients according to their risk of developing early disease recurrence.
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Affiliation(s)
- Daniel Llwyd Hughes
- Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK; (F.W.); (S.M.); (E.O.)
- Department of Hepatobiliary and Pancreatic Surgery, Oxford University Hospitals NHS, Oxford OX3 7LE, UK;
| | - Frances Willenbrock
- Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK; (F.W.); (S.M.); (E.O.)
| | - Zahir Soonawalla
- Department of Hepatobiliary and Pancreatic Surgery, Oxford University Hospitals NHS, Oxford OX3 7LE, UK;
| | - Somnath Mukherjee
- Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK; (F.W.); (S.M.); (E.O.)
| | - Eric O’Neill
- Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK; (F.W.); (S.M.); (E.O.)
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Tan D, Zhang Y. Silencing of Nudix type 5 represses proliferation and invasion and enhances chemosensitivity of gastric carcinoma cells by affecting the AKT/GSK-3β/β-catenin pathway. Toxicol Appl Pharmacol 2022; 441:115968. [PMID: 35247377 DOI: 10.1016/j.taap.2022.115968] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 02/22/2022] [Accepted: 02/27/2022] [Indexed: 01/01/2023]
Abstract
Nudix type 5 (NUDT5) has been recently identified as a new cancer-associated protein that is involved in numerous cancers. To date, the relationship between NUDT5 and gastric carcinoma has not been addressed. In the current research, we focused on exploring the potential relevance of NUDT5 in gastric carcinoma. The initial analysis of NUDT5 expression in gastric carcinoma by TCGA data revealed a clear increase in NUDT5 expression in tumor versus normal tissue. The increased expression of NUDT5 was also validated in the clinical specimens of gastric carcinoma by immunoblotting detection. Moreover, high NUDT5 levels predicted a poorer overall survival in gastric carcinoma patients. A series of cellular functional assays demonstrated that gastric carcinoma cells with silenced NUDT5 exhibited decreased proliferative and invasive ability, increased cell cycle arrest at the G0/G1 phase, and enhanced chemosensitivity. In-depth research showed that the silencing of NUDT5 led to a reduction in the activation of AKT and β-catenin. The reactivation of AKT blocked the repressive effect of NUDT5 silencing on β-catenin activation. The forced expression of β-catenin also reversed NUDT5-silencing-mediated anticancer effects. A Xenograft tumor assay confirmed the anticancer role of NUDT5 in gastric carcinoma in vivo. In short, these findings reveal elevated NUDT5 levels in gastric carcinoma and demonstrate that the inhibition of NUDT5 displays promising anticancer effects by affecting the AKT/β-catenin pathway. Thus, our work unveils a vital role of NUDT5 in gastric carcinoma and indicates it as a viable candidate target for anticancer drug discovery.
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Affiliation(s)
- Dong Tan
- Department of General Surgery, No. 215 Hospital of Shaanxi Nuclear Industry, No. 52 Weiyang West Road, Xianyang, Shaanxi 712000, PR China
| | - Yafei Zhang
- Department of Endoscopy, No. 215 Hospital of Shaanxi Nuclear Industry, No. 52 Weiyang West Road, Xianyang, Shaanxi 712000, China.
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Wei C, Niu Y, Chen B, Qin P, Wang Y, Hou D, Li T, Li R, Wang C, Yin H, Han R, Xu H, Tian Y, Liu X, Kang X, Li Z. Genetic effect of an InDel in the promoter region of the NUDT15 and its effect on myoblast proliferation in chickens. BMC Genomics 2022; 23:138. [PMID: 35168561 PMCID: PMC8848950 DOI: 10.1186/s12864-022-08362-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 01/25/2022] [Indexed: 12/14/2022] Open
Abstract
Background Molecular breeding accelerates the speed of animal breeding. Screening molecular markers that can affect economic traits through genome-wide association studies (GWAS) can provide a theoretical basis for molecular breeding. At present, a large number of molecular markers have been screened in poultry research, but few reports on how molecular markers affect economic traits exist. It is particularly important to reveal the action mechanisms of molecular markers, which can provide more accurate information for molecular breeding. Results The aim of this study was to investigate the relationships between two indels (NUDT15-indel-2777 and NUDT15-indel-1673) in the promoter region of NUDT15 and growth and carcass traits in chickens and to explore the regulatory mechanism of NUDT15. Significant differences were found in genotype and allele frequencies among commercial broilers, commercial laying hens and dual-purpose chickens. The results of association analyses showed that these two indel loci could significantly affect growth traits, such as body weight, and carcass traits. Tissue expression profiling at E12 showed that the expression of NUDT15 was significantly higher in skeletal muscle, and time-expression profiling of leg muscle showed that the expression of NUDT15 in myoblasts was significantly higher in the E10 and E12 proliferation stages than in other stages. Promoter activity analysis showed that pro-1673-I and pro-1673-D significantly inhibited promoter activity, and the promoter activity of pro-1673-D was significantly lower than that of pro-1673-I. In addition, when NUDT15 was overexpressed or underwent interference in chicken primary myoblasts (CPMs), NUDT15 could inhibit the proliferation of CPMs. Conclusion The results suggest that the studied indels in the promoter region of NUDT15 may regulate the proliferation of CPMs by affecting NUDT15 expression, ultimately affecting the growth and carcass traits of chickens. These indel polymorphisms may be used together as molecular markers for improving economic traits in chickens. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08362-6.
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Affiliation(s)
- Chengjie Wei
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources, Zhengzhou, 450046, China
| | - Yufang Niu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources, Zhengzhou, 450046, China
| | - Bingjie Chen
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources, Zhengzhou, 450046, China
| | - Panpan Qin
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources, Zhengzhou, 450046, China
| | - Yanxing Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources, Zhengzhou, 450046, China
| | - Dan Hou
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources, Zhengzhou, 450046, China
| | - Tong Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources, Zhengzhou, 450046, China
| | - Ruiting Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources, Zhengzhou, 450046, China
| | - Chunxiu Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources, Zhengzhou, 450046, China
| | - Huadong Yin
- Farm Animal genetic resources exploration and innovation key laboratory of sichuan province, sichuan agricultural university, Chengdu, China
| | - Ruili Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources, Zhengzhou, 450046, China
| | - Huifen Xu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources, Zhengzhou, 450046, China
| | - Yadong Tian
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources, Zhengzhou, 450046, China
| | - Xiaojun Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources, Zhengzhou, 450046, China
| | - Xiangtao Kang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China.,Henan Key laboratory for innovation and utilization of chicken germplasm resources, Zhengzhou, 450046, China
| | - Zhuanjian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China. .,Henan Key laboratory for innovation and utilization of chicken germplasm resources, Zhengzhou, 450046, China.
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Curtabbi A, Enríquez JA. The ins and outs of the flavin mononucleotide cofactor of respiratory complex I. IUBMB Life 2022; 74:629-644. [PMID: 35166025 DOI: 10.1002/iub.2600] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 01/23/2022] [Accepted: 01/24/2022] [Indexed: 12/12/2022]
Abstract
The flavin mononucleotide (FMN) cofactor of respiratory complex I occupies a key position in the electron transport chain. Here, the electrons coming from NADH start the sequence of oxidoreduction reactions, which drives the generation of the proton-motive force necessary for ATP synthesis. The overall architecture and the general catalytic proprieties of the FMN site are mostly well established. However, several aspects regarding the complex I flavin cofactor are still unknown. For example, the flavin binding to the N-module, the NADH-oxidizing portion of complex I, lacks a molecular description. The dissociation of FMN from the enzyme is beginning to emerge as an important regulatory mechanism of complex I activity and ROS production. Finally, how mitochondria import and metabolize FMN is still uncertain. This review summarizes the current knowledge on complex I flavin cofactor and discusses the open questions for future research.
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Affiliation(s)
- Andrea Curtabbi
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
| | - José Antonio Enríquez
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain.,Centro de Investigación Biomédica en Red en Fragilidad y Envejecimiento Saludable (CIBERFES), Instituto de Salud Carlos III, Madrid, Spain
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42
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Aluru N, Engelhardt J. OUP accepted manuscript. Toxicol Sci 2022; 188:75-87. [PMID: 35477799 PMCID: PMC9237993 DOI: 10.1093/toxsci/kfac044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Exposure to environmental toxicants during preconception has been shown to affect offspring health and epigenetic mechanisms such as DNA methylation are hypothesized to be involved in adverse outcomes. However, studies addressing the effects of exposure to environmental toxicants during preconception on epigenetic changes in gametes are limited. The objective of this study is to determine the effect of preconceptional exposure to a dioxin-like polychlorinated biphenyl (3,3',4,4',5-pentachlorobiphenyl [PCB126]) on DNA methylation and gene expression in testis. Adult zebrafish were exposed to 3 and 10 nM PCB126 for 24 h and testis tissue was sampled at 7 days postexposure for histology, DNA methylation, and gene expression profiling. Reduced representation bisulfite sequencing revealed 37 and 92 differentially methylated regions (DMRs) in response to 3 and 10 nM PCB126 exposures, respectively. Among them, 19 DMRs were found to be common between both PCB126 treatment groups. Gene ontology (GO) analysis of DMRs revealed that enrichment of terms such as RNA processing, iron-sulfur cluster assembly, and gluconeogenesis. Gene expression profiling showed differential expression of 40 and 1621 genes in response to 3 and 10 nM PCB126 exposures, respectively. GO analysis of differentially expressed genes revealed enrichment of terms related to xenobiotic metabolism, oxidative stress, and immune function. There is no overlap in the GO terms or individual genes between DNA methylation and RNA sequencing results, but functionally many of the altered pathways have been shown to cause spermatogenic defects.
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Affiliation(s)
| | - Jan Engelhardt
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig D-04107, Germany
- Department of Evolutionary Biology, University of Vienna, Vienna A-1030, Austria
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43
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The effects of Acyclovir administration to NCI-H1975 non-small cell lung cancer cells. Toxicol In Vitro 2021; 79:105301. [PMID: 34923092 DOI: 10.1016/j.tiv.2021.105301] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 12/12/2022]
Abstract
The biochemical mechanisms by which the antiviral drug Acyclovir (ACV) may induce anticancer effects even without detecting human herpesviruses (HHVs) are still poorly understood. Herein, we investigated for the first time how NCI-H1975 non-small cell lung cancer cells responded in vitro to ACV administration by exploring mitochondrial damage and apoptosis induction. We confirmed ACV ability to cause the inhibition of cancer cell growth even without detecting intracellular HHVs; the drug also significantly inhibited the colony formation capacity of NCI-H1975 cells. Cell cycle analysis revealed an increase of the sub-G1 hypodiploid peak after ACV treatment; the activation of caspase-3 and the presence of DNA laddering sustained the capacity of the drug to induce apoptotic cell death. Regarding mitochondrial toxicity, a reduction of mitochondrial membrane potential, altered mitochondrial size and shape, and mtDNA damage were found after ACV administration. Furthermore, an increment of intracellular reactive oxygen species levels as well as the upregulation of NudT3 involved in DNA repair mechanisms were observed. Altogether, these findings suggest that mitochondria may be possible initial targets and/or sites of ACV cytotoxicity within cancer cells in the absence of intracellular HHVs.
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Ishibashi Y, Matsushima N, Ito T, Hemmi H. Isopentenyl diphosphate/dimethylallyl diphosphate-specific Nudix hydrolase from the methanogenic archaeon Methanosarcina mazei. Biosci Biotechnol Biochem 2021; 86:246-253. [PMID: 34864834 DOI: 10.1093/bbb/zbab205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 11/25/2021] [Indexed: 11/12/2022]
Abstract
Nudix hydrolases typically catalyze the hydrolysis of nucleoside diphosphate linked to moiety X and yield nucleoside monophosphate and X-phosphate, while some of them hydrolyze a terminal diphosphate group of non-nucleosidic compounds and convert it into a phosphate group. Although the number of Nudix hydrolases is usually limited in archaea comparing with those in bacteria and eukaryotes, the physiological functions of most archaeal Nudix hydrolases remain unknown. In this study, a Nudix hydrolase family protein, MM_2582, from the methanogenic archaeon Methanosarcina mazei was recombinantly expressed in Escherichia coli, purified, and characterized. This recombinant protein shows higher hydrolase activity toward isopentenyl diphosphate and short-chain prenyl diphosphates than that toward nucleosidic compounds. Kinetic studies demonstrated that the archaeal enzyme prefers isopentenyl diphosphate and dimethylallyl diphosphate, which suggests its role in the biosynthesis of prenylated flavin mononucleotide, a recently discovered coenzyme that is required, for example, in the archaea-specific modified mevalonate pathway.
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Affiliation(s)
- Yumi Ishibashi
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 460-8601, Japan
| | - Natsumi Matsushima
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 460-8601, Japan
| | - Tomokazu Ito
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 460-8601, Japan
| | - Hisashi Hemmi
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 460-8601, Japan
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45
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NUDT2 initiates viral RNA degradation by removal of 5'-phosphates. Nat Commun 2021; 12:6918. [PMID: 34824277 PMCID: PMC8616924 DOI: 10.1038/s41467-021-27239-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 11/08/2021] [Indexed: 12/22/2022] Open
Abstract
While viral replication processes are largely understood, comparably little is known on cellular mechanisms degrading viral RNA. Some viral RNAs bear a 5′-triphosphate (PPP-) group that impairs degradation by the canonical 5′-3′ degradation pathway. Here we show that the Nudix hydrolase 2 (NUDT2) trims viral PPP-RNA into monophosphorylated (P)-RNA, which serves as a substrate for the 5′-3′ exonuclease XRN1. NUDT2 removes 5′-phosphates from PPP-RNA in an RNA sequence- and overhang-independent manner and its ablation in cells increases growth of PPP-RNA viruses, suggesting an involvement in antiviral immunity. NUDT2 is highly homologous to bacterial RNA pyrophosphatase H (RppH), a protein involved in the metabolism of bacterial mRNA, which is 5′-tri- or diphosphorylated. Our results show a conserved function between bacterial RppH and mammalian NUDT2, indicating that the function may have adapted from a protein responsible for RNA turnover in bacteria into a protein involved in the immune defense in mammals. RNA of some viruses is protected from degradation by a 5′ triphosphate group. Here the authors identify nudix hydrolase 2 (NUDT2) as novel antiviral defense protein that dephosphorylates viral RNA and thereby enables its degradation.
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46
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Samper-Martín B, Sarrias A, Lázaro B, Pérez-Montero M, Rodríguez-Rodríguez R, Ribeiro MPC, Bañón A, Wolfgeher D, Jessen HJ, Alsina B, Clotet J, Kron SJ, Saiardi A, Jiménez J, Bru S. Polyphosphate degradation by Nudt3-Zn 2+ mediates oxidative stress response. Cell Rep 2021; 37:110004. [PMID: 34788624 DOI: 10.1016/j.celrep.2021.110004] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 10/08/2021] [Accepted: 10/22/2021] [Indexed: 02/06/2023] Open
Abstract
Polyphosphate (polyP) is a polymer of hundreds of phosphate residues present in all organisms. In mammals, polyP is involved in crucial physiological processes, including coagulation, inflammation, and stress response. However, after decades of research, the metabolic enzymes are still unknown. Here, we purify and identify Nudt3, a NUDIX family member, as the enzyme responsible for polyP phosphatase activity in mammalian cells. We show that Nudt3 shifts its substrate specificity depending on the cation; specifically, Nudt3 is active on polyP when Zn2+ is present. Nudt3 has in vivo polyP phosphatase activity in human cells, and importantly, we show that cells with altered polyP levels by modifying Nudt3 protein amount present reduced viability upon oxidative stress and increased DNA damage, suggesting that polyP and Nudt3 play a role in oxidative stress protection. Finally, we show that Nudt3 is involved in the early stages of embryo development in zebrafish.
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Affiliation(s)
- Bàrbara Samper-Martín
- Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, 08195 Sant Cugat del Vallès, Barcelona, Spain
| | - Ana Sarrias
- Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, 08195 Sant Cugat del Vallès, Barcelona, Spain
| | - Blanca Lázaro
- Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, 08195 Sant Cugat del Vallès, Barcelona, Spain
| | - Marta Pérez-Montero
- Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, 08195 Sant Cugat del Vallès, Barcelona, Spain
| | - Rosalía Rodríguez-Rodríguez
- Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, 08195 Sant Cugat del Vallès, Barcelona, Spain
| | - Mariana P C Ribeiro
- Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, 08195 Sant Cugat del Vallès, Barcelona, Spain
| | - Aitor Bañón
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra-Parc de Recerca Biomèdica, 08003 Barcelona, Spain
| | - Don Wolfgeher
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Henning J Jessen
- Institute of Organic Chemistry, University of Freiburg, 79104 Freiburg, Germany; CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Berta Alsina
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra-Parc de Recerca Biomèdica, 08003 Barcelona, Spain
| | - Josep Clotet
- Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, 08195 Sant Cugat del Vallès, Barcelona, Spain
| | - Stephen J Kron
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Adolfo Saiardi
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London WC1E6BT, UK
| | - Javier Jiménez
- Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, 08195 Sant Cugat del Vallès, Barcelona, Spain.
| | - Samuel Bru
- Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya, 08195 Sant Cugat del Vallès, Barcelona, Spain; Institut de Neurociències, Universitat Autònoma de Barcelona, 08193 Bellaterra, Cerdanyola del Vallès, Spain.
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47
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Insight into the Binding and Hydrolytic Preferences of hNudt16 Based on Nucleotide Diphosphate Substrates. Int J Mol Sci 2021; 22:ijms222010929. [PMID: 34681586 PMCID: PMC8535469 DOI: 10.3390/ijms222010929] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/28/2021] [Accepted: 10/05/2021] [Indexed: 11/29/2022] Open
Abstract
Nudt16 is a member of the NUDIX family of hydrolases that show specificity towards substrates consisting of a nucleoside diphosphate linked to another moiety X. Several substrates for hNudt16 and various possible biological functions have been reported. However, some of these reports contradict each other and studies comparing the substrate specificity of the hNudt16 protein are limited. Therefore, we quantitatively compared the affinity of hNudt16 towards a set of previously published substrates, as well as identified novel potential substrates. Here, we show that hNudt16 has the highest affinity towards IDP and GppG, with Kd below 100 nM. Other tested ligands exhibited a weaker affinity of several orders of magnitude. Among the investigated compounds, only IDP, GppG, m7GppG, AppA, dpCoA, and NADH were hydrolyzed by hNudt16 with a strong substrate preference for inosine or guanosine containing compounds. A new identified substrate for hNudt16, GppG, which binds the enzyme with an affinity comparable to that of IDP, suggests another potential regulatory role of this protein. Molecular docking of hNudt16-ligand binding inside the hNudt16 pocket revealed two binding modes for representative substrates. Nucleobase stabilization by Π stacking interactions with His24 has been associated with strong binding of hNudt16 substrates.
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48
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Nishii R, Mizuno T, Rehling D, Smith C, Clark BL, Zhao X, Brown SA, Smart B, Moriyama T, Yamada Y, Ichinohe T, Onizuka M, Atsuta Y, Yang L, Yang W, Thomas PG, Stenmark P, Kato M, Yang JJ. NUDT15 polymorphism influences the metabolism and therapeutic effects of acyclovir and ganciclovir. Nat Commun 2021; 12:4181. [PMID: 34234136 PMCID: PMC8263746 DOI: 10.1038/s41467-021-24509-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 06/14/2021] [Indexed: 02/05/2023] Open
Abstract
Nucleobase and nucleoside analogs (NNA) are widely used as anti-viral and anti-cancer agents, and NNA phosphorylation is essential for the activity of this class of drugs. Recently, diphosphatase NUDT15 was linked to thiopurine metabolism with NUDT15 polymorphism associated with drug toxicity in patients. Profiling NNA drugs, we identify acyclovir (ACV) and ganciclovir (GCV) as two new NNAs metabolized by NUDT15. NUDT15 hydrolyzes ACV and GCV triphosphate metabolites, reducing their effects against cytomegalovirus (CMV) in vitro. Loss of NUDT15 potentiates cytotoxicity of ACV and GCV in host cells. In hematopoietic stem cell transplant patients, the risk of CMV viremia following ACV prophylaxis is associated with NUDT15 genotype (P = 0.015). Donor NUDT15 deficiency is linked to graft failure in patients receiving CMV-seropositive stem cells (P = 0.047). In conclusion, NUDT15 is an important metabolizing enzyme for ACV and GCV, and NUDT15 variation contributes to inter-patient variability in their therapeutic effects.
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Affiliation(s)
- Rina Nishii
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Takanori Mizuno
- Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Daniel Rehling
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden
| | - Colton Smith
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Brandi L Clark
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Xujie Zhao
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Scott A Brown
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Brandon Smart
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Takaya Moriyama
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yuji Yamada
- Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Tatsuo Ichinohe
- Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | | | - Yoshiko Atsuta
- Japanese Data Center for Hematopoietic Cell Transplantation, Aichi, Japan
| | - Lei Yang
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Wenjian Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Pål Stenmark
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden. .,Department of Experimental Medical Science, Lund University, Lund, Sweden.
| | - Motohiro Kato
- Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan.
| | - Jun J Yang
- Department of Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA. .,Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, USA. .,Hematological Malignancies Program, Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN, USA.
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49
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Gattkowski E, Rutherford TJ, Möckl F, Bauche A, Sander S, Fliegert R, Tidow H. Analysis of ligand binding and resulting conformational changes in pyrophosphatase NUDT9. FEBS J 2021; 288:6769-6782. [PMID: 34189846 PMCID: PMC7612441 DOI: 10.1111/febs.16097] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 06/04/2021] [Accepted: 06/29/2021] [Indexed: 11/29/2022]
Abstract
Nudix hydrolase 9 (NUDT9) is a member of the nucleoside linked to another moiety X (NUDIX) protein superfamily, which hydrolyses a broad spectrum of organic pyrophosphates from metabolic processes. ADP‐ribose (ADPR) has been the only known endogenous substrate accepted by NUDT9 so far. The Ca2+‐permeable transient receptor potential melastatin subfamily 2 (TRPM2) channel contains a homologous NUDT9‐homology (NUDT9H) domain and is activated by ADPR. Sustained Ca2+ influx via ADPR‐activated TRPM2 triggers apoptotic mechanisms. Thus, a precise regulation of cellular ADPR levels by NUDT9 is essential. A detailed characterization of the enzyme‐substrate interaction would help to understand the high substrate specificity of NUDT9. Here, we analysed ligand binding to NUDT9 using a variety of biophysical techniques. We identified 2′‐deoxy‐ADPR as an additional substrate for NUDT9. Similar enzyme kinetics and binding affinities were determined for the two ligands. The high‐affinity binding was preserved in NUDT9 containing the mutated NUDIX box derived from the human NUDT9H domain. NMR spectroscopy indicated that ADPR and 2′‐deoxy‐ADPR bind to the same binding site of NUDT9. Backbone resonance assignment and subsequent molecular docking allowed further characterization of the binding pocket. Substantial conformational changes of NUDT9 upon ligand binding were observed which might allow for the development of NUDT9‐based ADPR fluorescence resonance energy transfer sensors that may help with the analysis of ADPR signalling processes in cells in the future.
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Affiliation(s)
- Ellen Gattkowski
- The Hamburg Advanced Research Center for Bioorganic Chemistry (HARBOR) & Department of Chemistry, Institute for Biochemistry and Molecular Biology, University of Hamburg, Germany
| | | | - Franziska Möckl
- Department of Biochemistry and Molecular Cell Biology, University Medical Centre Hamburg-Eppendorf, Germany
| | - Andreas Bauche
- Department of Biochemistry and Molecular Cell Biology, University Medical Centre Hamburg-Eppendorf, Germany
| | - Simon Sander
- The Hamburg Advanced Research Center for Bioorganic Chemistry (HARBOR) & Department of Chemistry, Institute for Biochemistry and Molecular Biology, University of Hamburg, Germany
| | - Ralf Fliegert
- Department of Biochemistry and Molecular Cell Biology, University Medical Centre Hamburg-Eppendorf, Germany
| | - Henning Tidow
- The Hamburg Advanced Research Center for Bioorganic Chemistry (HARBOR) & Department of Chemistry, Institute for Biochemistry and Molecular Biology, University of Hamburg, Germany
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50
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Peng S, Guo P, Lin X, An Y, Sze KH, Lau MHY, Chen ZS, Wang Q, Li W, Sun JKL, Ma SY, Chan TF, Lau KF, Ngo JCK, Kwan KM, Wong CH, Lam SL, Zimmerman SC, Tuccinardi T, Zuo Z, Au-Yeung HY, Chow HM, Chan HYE. CAG RNAs induce DNA damage and apoptosis by silencing NUDT16 expression in polyglutamine degeneration. Proc Natl Acad Sci U S A 2021; 118:e2022940118. [PMID: 33947817 PMCID: PMC8126783 DOI: 10.1073/pnas.2022940118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
DNA damage plays a central role in the cellular pathogenesis of polyglutamine (polyQ) diseases, including Huntington's disease (HD). In this study, we showed that the expression of untranslatable expanded CAG RNA per se induced the cellular DNA damage response pathway. By means of RNA sequencing (RNA-seq), we found that expression of the Nudix hydrolase 16 (NUDT16) gene was down-regulated in mutant CAG RNA-expressing cells. The loss of NUDT16 function results in a misincorporation of damaging nucleotides into DNAs and leads to DNA damage. We showed that small CAG (sCAG) RNAs, species generated from expanded CAG transcripts, hybridize with CUG-containing NUDT16 mRNA and form a CAG-CUG RNA heteroduplex, resulting in gene silencing of NUDT16 and leading to the DNA damage and cellular apoptosis. These results were further validated using expanded CAG RNA-expressing mouse primary neurons and in vivo R6/2 HD transgenic mice. Moreover, we identified a bisamidinium compound, DB213, that interacts specifically with the major groove of the CAG RNA homoduplex and disfavors the CAG-CUG heteroduplex formation. This action subsequently mitigated RNA-induced silencing complex (RISC)-dependent NUDT16 silencing in both in vitro cell and in vivo mouse disease models. After DB213 treatment, DNA damage, apoptosis, and locomotor defects were rescued in HD mice. This work establishes NUDT16 deficiency by CAG repeat RNAs as a pathogenic mechanism of polyQ diseases and as a potential therapeutic direction for HD and other polyQ diseases.
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Affiliation(s)
- Shaohong Peng
- Laboratory of Drosophila Research, The Chinese University of Hong Kong, Hong Kong, China
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Pei Guo
- Department of Chemistry, The Chinese University of Hong Kong, Hong Kong, China
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Xiao Lin
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Ying An
- Laboratory of Drosophila Research, The Chinese University of Hong Kong, Hong Kong, China
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Kong Hung Sze
- Department of Microbiology, The University of Hong Kong, Hong Kong, China
| | - Matthew Ho Yan Lau
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong, China
| | - Zhefan Stephen Chen
- Laboratory of Drosophila Research, The Chinese University of Hong Kong, Hong Kong, China
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Qianwen Wang
- School of Pharmacy, The Chinese University of Hong Kong, Hong Kong, China
| | - Wen Li
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | | | - Sum Yi Ma
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Ting-Fung Chan
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
- Gerald Choa Neuroscience Centre, The Chinese University of Hong Kong, Hong Kong, China
- Nexus of Rare Neurodegenerative Diseases, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Kwok-Fai Lau
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Nexus of Rare Neurodegenerative Diseases, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Jacky Chi Ki Ngo
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
- Nexus of Rare Neurodegenerative Diseases, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Kin Ming Kwan
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
- Centre for Cell and Developmental Biology, The Chinese University of Hong Kong, Hong Kong, China
- Nexus of Rare Neurodegenerative Diseases, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Chun-Ho Wong
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Sik Lok Lam
- Department of Chemistry, The Chinese University of Hong Kong, Hong Kong, China
- Nexus of Rare Neurodegenerative Diseases, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Steven C Zimmerman
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | | | - Zhong Zuo
- School of Pharmacy, The Chinese University of Hong Kong, Hong Kong, China
- Nexus of Rare Neurodegenerative Diseases, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Ho Yu Au-Yeung
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong, China
- Nexus of Rare Neurodegenerative Diseases, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Hei-Man Chow
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Nexus of Rare Neurodegenerative Diseases, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Ho Yin Edwin Chan
- Laboratory of Drosophila Research, The Chinese University of Hong Kong, Hong Kong, China;
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
- Gerald Choa Neuroscience Centre, The Chinese University of Hong Kong, Hong Kong, China
- Nexus of Rare Neurodegenerative Diseases, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
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