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Stuut Balsam S, Zhong F, Pence N, Levintov L, Andhare D, Hammond JH, Ragusa MJ, Vashisth H, Hogan DA, Pletneva EV. Conserved C-Terminal Tail Is Responsible for Membrane Localization and Function of Pseudomonas aeruginosa Hemerythrin. Biochemistry 2024. [PMID: 38951132 DOI: 10.1021/acs.biochem.4c00174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
Many bacteria have hemerythrin (Hr) proteins that bind O2, including Pseudomonas aeruginosa, in which microoxia-induced Hr (Mhr) provide fitness advantages under microoxic conditions. Mhr has a 23 amino-acid extension at its C-terminus relative to a well-characterized Hr from Methylococcus capsulatus, and similar extensions are also found in Hrs from other bacteria. The last 11 amino acids of this extended, C-terminal tail are highly conserved in gammaproteobacteria and predicted to form a helix with positively charged and hydrophobic faces. In cellular fractionation assays, wild-type (WT) Mhr was found in both membrane and cytosolic fractions, while a MhrW143* variant lacking the last 11 residues was largely in the cytosol and did not complement Mhr function in competition assays. MhrL112Y, a variant that has a much longer-lived O2-bound form, was fully functional and had a similar localization pattern to that of WT Mhr. Both MhrW143* and MhrL112Y had secondary structures, stabilities, and O2-binding kinetics similar to those of WT Mhr. Fluorescence studies revealed that the C-terminal tail, and particularly the fragment corresponding to its last 11 residues, was sufficient and necessary for association with lipid vesicles. Molecular dynamics simulations and subsequent cellular analysis of Mhr variants have demonstrated that conserved, positively charged residues in the tail are important for Mhr interactions with negatively charged membranes and the contribution of this protein to competitive fitness. Together, these data suggest that peripheral interactions of Mhr with membranes are guided by the C-terminal tail and are independent of O2-binding.
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Affiliation(s)
- Stacie Stuut Balsam
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755, United States
| | - Fangfang Zhong
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, United States
| | - Natasha Pence
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, United States
| | - Lev Levintov
- Department of Chemical Engineering and Bioengineering, University of New Hampshire, Durham, New Hampshire 03824, United States
| | - Devika Andhare
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, United States
| | - John H Hammond
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755, United States
| | - Michael J Ragusa
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, United States
| | - Harish Vashisth
- Department of Chemical Engineering and Bioengineering, University of New Hampshire, Durham, New Hampshire 03824, United States
- Department of Chemistry, University of New Hampshire, Durham, New Hampshire 03824, United States
- Integrated Applied Mathematics Program, University of New Hampshire, Durham, New Hampshire 03824, United States
- Molecular and Cellular Biotechnology Program, University of New Hampshire, Durham, New Hampshire 03824, United States
| | - Deborah A Hogan
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755, United States
| | - Ekaterina V Pletneva
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, United States
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2
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Yáñez-Vilches A, Romero AM, Barrientos-Moreno M, Cruz E, González-Prieto R, Sharma S, Vertegaal ACO, Prado F. Physical interactions between specifically regulated subpopulations of the MCM and RNR complexes prevent genetic instability. PLoS Genet 2024; 20:e1011148. [PMID: 38776358 PMCID: PMC11149843 DOI: 10.1371/journal.pgen.1011148] [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: 01/19/2024] [Revised: 06/04/2024] [Accepted: 05/08/2024] [Indexed: 05/24/2024] Open
Abstract
The helicase MCM and the ribonucleotide reductase RNR are the complexes that provide the substrates (ssDNA templates and dNTPs, respectively) for DNA replication. Here, we demonstrate that MCM interacts physically with RNR and some of its regulators, including the kinase Dun1. These physical interactions encompass small subpopulations of MCM and RNR, are independent of the major subcellular locations of these two complexes, augment in response to DNA damage and, in the case of the Rnr2 and Rnr4 subunits of RNR, depend on Dun1. Partial disruption of the MCM/RNR interactions impairs the release of Rad52 -but not RPA-from the DNA repair centers despite the lesions are repaired, a phenotype that is associated with hypermutagenesis but not with alterations in the levels of dNTPs. These results suggest that a specifically regulated pool of MCM and RNR complexes plays non-canonical roles in genetic stability preventing persistent Rad52 centers and hypermutagenesis.
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Affiliation(s)
- Aurora Yáñez-Vilches
- Centro Andaluz de Biología Molecular y Medicina Regenerativa–CABIMER, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Universidad Pablo de Olavide, Seville, Spain
| | - Antonia M. Romero
- Centro Andaluz de Biología Molecular y Medicina Regenerativa–CABIMER, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Universidad Pablo de Olavide, Seville, Spain
| | - Marta Barrientos-Moreno
- Centro Andaluz de Biología Molecular y Medicina Regenerativa–CABIMER, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Universidad Pablo de Olavide, Seville, Spain
| | - Esther Cruz
- Centro Andaluz de Biología Molecular y Medicina Regenerativa–CABIMER, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Universidad Pablo de Olavide, Seville, Spain
| | - Román González-Prieto
- Centro Andaluz de Biología Molecular y Medicina Regenerativa–CABIMER, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Universidad Pablo de Olavide, Seville, Spain
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Sushma Sharma
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Alfred C. O. Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Félix Prado
- Centro Andaluz de Biología Molecular y Medicina Regenerativa–CABIMER, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, Universidad Pablo de Olavide, Seville, Spain
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3
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Song DY, Stubbe J, Nocera DG. Protein engineering a PhotoRNR chimera based on a unifying evolutionary apparatus among the natural classes of ribonucleotide reductases. Proc Natl Acad Sci U S A 2024; 121:e2317291121. [PMID: 38648489 PMCID: PMC11067019 DOI: 10.1073/pnas.2317291121] [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] [Accepted: 03/19/2024] [Indexed: 04/25/2024] Open
Abstract
Ribonucleotide reductases (RNRs) are essential enzymes that catalyze the de novo transformation of nucleoside 5'-di(tri)phosphates [ND(T)Ps, where N is A, U, C, or G] to their corresponding deoxynucleotides. Despite the diversity of factors required for function and the low sequence conservation across RNRs, a unifying apparatus consolidating RNR activity is explored. We combine aspects of the protein subunit simplicity of class II RNR with a modified version of Escherichia coli class la photoRNRs that initiate radical chemistry with light to engineer a mimic of a class II enzyme. The design of this RNR involves fusing a truncated form of the active site containing α subunit with the functionally important C-terminal tail of the radical-generating β subunit to render a chimeric RNR. Inspired by a recent cryo-EM structure, a [Re] photooxidant is located adjacent to Y356[β], which is an essential component of the radical transport pathway in class I RNRs. Combination of this RNR photochimera with cytidine diphosphate (CDP), adenosine triphosphate (ATP), and light resulted in the generation of Y356• along with production of deoxycytidine diphosphate (dCDP) and cytosine. The photoproducts reflect an active site chemistry consistent with both the consensus mechanism of RNR and chemistry observed when RNR is inactivated by mechanism-based inhibitors in the active site. The enzymatic activity of the RNR photochimera in the absence of any β metallocofactor highlights the adaptability of the 10-stranded αβ barrel finger loop to support deoxynucleotide formation and accommodate the design of engineered RNRs.
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Affiliation(s)
- David Y. Song
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA02138
| | - JoAnne Stubbe
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA02138
| | - Daniel G. Nocera
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA02138
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4
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Hellenbrand CN, Stevenson DM, Gromek KA, Amador-Noguez D, Hershey DM. A deoxynucleoside triphosphate triphosphohydrolase promotes cell cycle progression in Caulobacter crescentus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.25.591158. [PMID: 38712277 PMCID: PMC11071499 DOI: 10.1101/2024.04.25.591158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Intracellular pools of deoxynucleoside triphosphates (dNTPs) are strictly maintained throughout the cell cycle to ensure accurate and efficient DNA replication. DNA synthesis requires an abundance of dNTPs, but elevated dNTP concentrations in nonreplicating cells delay entry into S phase. Enzymes known as deoxyguanosine triphosphate triphosphohydrolases (Dgts) hydrolyze dNTPs into deoxynucleosides and triphosphates, and we propose that Dgts restrict dNTP concentrations to promote the G1 to S phase transition. We characterized a Dgt from the bacterium Caulobacter crescentus termed flagellar signaling suppressor C (fssC) to clarify the role of Dgts in cell cycle regulation. Deleting fssC increases dNTP levels and extends the G1 phase of the cell cycle. We determined that the segregation and duplication of the origin of replication (oriC) is delayed in ΔfssC, but the rate of replication elongation is unchanged. We conclude that dNTP hydrolysis by FssC promotes the initiation of DNA replication through a novel nucleotide signaling pathway. This work further establishes Dgts as important regulators of the G1 to S phase transition, and the high conservation of Dgts across all domains of life implies that Dgt-dependent cell cycle control may be widespread in both prokaryotic and eukaryotic organisms.
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Affiliation(s)
| | - David M. Stevenson
- Department of Bacteriology, University of Wisconsin – Madison, Madison, WI 53706, USA
| | - Katarzyna A. Gromek
- Department of Bacteriology, University of Wisconsin – Madison, Madison, WI 53706, USA
| | - Daniel Amador-Noguez
- Department of Bacteriology, University of Wisconsin – Madison, Madison, WI 53706, USA
| | - David M. Hershey
- Department of Bacteriology, University of Wisconsin – Madison, Madison, WI 53706, USA
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5
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Dombi E, Marinaki T, Spingardi P, Millar V, Hadjichristou N, Carver J, Johnston IG, Fratter C, Poulton J. Nucleoside supplements as treatments for mitochondrial DNA depletion syndrome. Front Cell Dev Biol 2024; 12:1260496. [PMID: 38665433 PMCID: PMC11043827 DOI: 10.3389/fcell.2024.1260496] [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: 07/17/2023] [Accepted: 03/11/2024] [Indexed: 04/28/2024] Open
Abstract
Introduction: In mitochondrial DNA (mtDNA) depletion syndrome (MDS), patients cannot maintain sufficient mtDNA for their energy needs. MDS presentations range from infantile encephalopathy with hepatopathy (Alpers syndrome) to adult chronic progressive external ophthalmoplegia. Most are caused by nucleotide imbalance or by defects in the mtDNA replisome. There is currently no curative treatment available. Nucleoside therapy is a promising experimental treatment for TK2 deficiency, where patients are supplemented with exogenous deoxypyrimidines. We aimed to explore the benefits of nucleoside supplementation in POLG and TWNK deficient fibroblasts. Methods: We used high-content fluorescence microscopy with software-based image analysis to assay mtDNA content and membrane potential quantitatively, using vital dyes PicoGreen and MitoTracker Red CMXRos respectively. We tested the effect of 15 combinations (A, T, G, C, AT, AC, AG, CT, CG, GT, ATC, ATG, AGC, TGC, ATGC) of deoxynucleoside supplements on mtDNA content of fibroblasts derived from four patients with MDS (POLG1, POLG2, DGUOK, TWNK) in both a replicating (10% dialysed FCS) and quiescent (0.1% dialysed FCS) state. We used qPCR to measure mtDNA content of supplemented and non-supplemented fibroblasts following mtDNA depletion using 20 µM ddC and after 14- and 21-day recovery in a quiescent state. Results: Nucleoside treatments at 200 µM that significantly increased mtDNA content also significantly reduced the number of cells remaining in culture after 7 days of treatment, as well as mitochondrial membrane potential. These toxic effects were abolished by reducing the concentration of nucleosides to 50 µM. In POLG1 and TWNK cells the combination of ATGC treatment increased mtDNA content the most after 7 days in non-replicating cells. ATGC nucleoside combination significantly increased the rate of mtDNA recovery in quiescent POLG1 cells following mtDNA depletion by ddC. Conclusion: High-content imaging enabled us to link mtDNA copy number with key read-outs linked to patient wellbeing. Elevated G increased mtDNA copy number but severely impaired fibroblast growth, potentially by inhibiting purine synthesis and/or causing replication stress. Combinations of nucleosides ATGC, T, or TC, benefited growth of cells harbouring POLG mutations. These combinations, one of which reflects a commercially available preparation, could be explored further for treatment of POLG patients.
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Affiliation(s)
- Eszter Dombi
- Nuffield Department of Women’s and Reproductive Health, University of Oxford, Oxford, United Kingdom
| | - Tony Marinaki
- Purine Research Laboratory, Department of Biochemical Sciences, Guy’s and St Thomas’ Hospitals, London, United Kingdom
| | - Paolo Spingardi
- Ludwig Institute for Cancer Research, Nuffield Department of Medicine, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Val Millar
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Janet Carver
- Nuffield Department of Women’s and Reproductive Health, University of Oxford, Oxford, United Kingdom
| | - Iain G. Johnston
- Department of Mathematics, University of Bergen, Bergen, Norway
- Computational Biology Unit, University of Bergen, Bergen, Norway
| | - Carl Fratter
- Oxford Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Joanna Poulton
- Nuffield Department of Women’s and Reproductive Health, University of Oxford, Oxford, United Kingdom
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6
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Kienbeck K, Malfertheiner L, Zelger-Paulus S, Johannsen S, von Mering C, Sigel RKO. Identification of HDV-like theta ribozymes involved in tRNA-based recoding of gut bacteriophages. Nat Commun 2024; 15:1559. [PMID: 38378708 PMCID: PMC10879173 DOI: 10.1038/s41467-024-45653-w] [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: 07/25/2023] [Accepted: 01/29/2024] [Indexed: 02/22/2024] Open
Abstract
Trillions of microorganisms, collectively known as the microbiome, inhabit our bodies with the gut microbiome being of particular interest in biomedical research. Bacteriophages, the dominant virome constituents, can utilize suppressor tRNAs to switch to alternative genetic codes (e.g., the UAG stop-codon is reassigned to glutamine) while infecting hosts with the standard bacterial code. However, what triggers this switch and how the bacteriophage manipulates its host is poorly understood. Here, we report the discovery of a subgroup of minimal hepatitis delta virus (HDV)-like ribozymes - theta ribozymes - potentially involved in the code switch leading to the expression of recoded lysis and structural phage genes. We demonstrate their HDV-like self-scission behavior in vitro and find them in an unreported context often located with their cleavage site adjacent to tRNAs, indicating a role in viral tRNA maturation and/or regulation. Every fifth associated tRNA is a suppressor tRNA, further strengthening our hypothesis. The vast abundance of tRNA-associated theta ribozymes - we provide 1753 unique examples - highlights the importance of small ribozymes as an alternative to large enzymes that usually process tRNA 3'-ends. Our discovery expands the short list of biological functions of small HDV-like ribozymes and introduces a previously unknown player likely involved in the code switch of certain recoded gut bacteriophages.
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Affiliation(s)
- Kasimir Kienbeck
- Department of Chemistry, University of Zurich, Zurich, CH-8057, Switzerland
| | - Lukas Malfertheiner
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, CH-8057, Switzerland
| | | | - Silke Johannsen
- Department of Chemistry, University of Zurich, Zurich, CH-8057, Switzerland
| | - Christian von Mering
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, CH-8057, Switzerland.
| | - Roland K O Sigel
- Department of Chemistry, University of Zurich, Zurich, CH-8057, Switzerland.
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7
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Zhong J, Soudackov AV, Hammes-Schiffer S. Probing Nonadiabaticity of Proton-Coupled Electron Transfer in Ribonucleotide Reductase. J Phys Chem Lett 2024; 15:1686-1693. [PMID: 38315651 DOI: 10.1021/acs.jpclett.3c03552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
The enzyme ribonucleotide reductase, which is essential for DNA synthesis, initiates the conversion of ribonucleotides to deoxyribonucleotides via radical transfer over a 32 Å pathway composed of proton-coupled electron transfer (PCET) reactions. Previously, the first three PCET reactions in the α subunit were investigated with hybrid quantum mechanical/molecular mechanical (QM/MM) free energy simulations. Herein, the fourth PCET reaction in this subunit between C439 and guanosine diphosphate (GDP) is simulated and found to be slightly exoergic with a relatively high free energy barrier. To further elucidate the mechanisms of all four PCET reactions, we analyzed the vibronic and electron-proton nonadiabaticities. This analysis suggests that interfacial PCET between Y356 and Y731 is vibronically and electronically nonadiabatic, whereas PCET between Y731 and Y730 and between C439 and GDP is fully adiabatic and PCET between Y730 and C439 is in the intermediate regime. These insights provide guidance for selecting suitable rate constant expressions for these PCET reactions.
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Affiliation(s)
- Jiayun Zhong
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Alexander V Soudackov
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Sharon Hammes-Schiffer
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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8
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Nguyen RC, Stagliano C, Liu A. Structural insights into the half-of-sites reactivity in homodimeric and homotetrameric metalloenzymes. Curr Opin Chem Biol 2023; 75:102332. [PMID: 37269676 PMCID: PMC10528533 DOI: 10.1016/j.cbpa.2023.102332] [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: 09/01/2022] [Revised: 04/24/2023] [Accepted: 04/29/2023] [Indexed: 06/05/2023]
Abstract
Half-of-sites reactivity in many homodimeric and homotetrameric metalloenzymes has been known for half a century, yet its benefit remains poorly understood. A recently reported cryo-electron microscopy structure has given some clues on the less optimized reactivity of Escherichia coli ribonucleotide reductase with an asymmetric association of α2β2 subunits during catalysis. Moreover, nonequivalence of enzyme active sites has been reported in many other enzymes, possibly as a means of regulation. They are often induced by substrate binding or caused by a critical component introduced from a neighboring subunit in response to substrate loadings, such as in prostaglandin endoperoxide H synthase, cytidine triphosphate synthase, glyoxalase, tryptophan dioxygenase, and several decarboxylases or dehydrogenases. Overall, half-of-sites reactivity is likely not an act of wasting resources but rather a method devised in nature to accommodate catalytic or regulatory needs.
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Affiliation(s)
- Romie C Nguyen
- Department of Chemistry, University of Texas, San Antonio, TX, 78249, USA
| | - Cassadee Stagliano
- Department of Chemistry, University of Texas, San Antonio, TX, 78249, USA
| | - Aimin Liu
- Department of Chemistry, University of Texas, San Antonio, TX, 78249, USA.
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9
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Zhu Q, Costentin C, Stubbe J, Nocera DG. Disulfide radical anion as a super-reductant in biology and photoredox chemistry. Chem Sci 2023; 14:6876-6881. [PMID: 37389245 PMCID: PMC10306091 DOI: 10.1039/d3sc01867a] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 05/17/2023] [Indexed: 07/01/2023] Open
Abstract
Disulfides are involved in a broad range of radical-based synthetic organic and biochemical transformations. In particular, the reduction of a disulfide to the corresponding radical anion, followed by S-S bond cleavage to yield a thiyl radical and a thiolate anion plays critical roles in radical-based photoredox transformations and the disulfide radical anion in conjunction with a proton donor, mediates the enzymatic synthesis of deoxynucleotides from nucleotides within the active site of the enzyme, ribonucleotide reductase (RNR). To gain fundamental thermodynamic insight into these reactions, we have performed experimental measurements to furnish the transfer coefficient from which the standard E0(RSSR/RSSR˙-) reduction potential has been determined for a homologous series of disulfides. The electrochemical potentials are found to be strongly dependent on the structures and electronic properties of the substituents of the disulfides. In the case of cysteine, a standard potential of E0(RSSR/RSSR˙-) = -1.38 V vs. NHE is determined, making the disulfide radical anion of cysteine one of the most reducing cofactors in biology.
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Affiliation(s)
- Qilei Zhu
- Department of Chemistry and Chemical Biology, Harvard University 12 Oxford Street Cambridge Massachusetts 02138 USA
- Department of Chemistry, University of Utah Salt Lake City Utah 84112 USA
| | | | - JoAnne Stubbe
- Department of Chemistry and Chemical Biology, Harvard University 12 Oxford Street Cambridge Massachusetts 02138 USA
- Departments of Chemistry and Department of Biology, Massachusetts Institute of Technology Cambridge Massachusetts 02139 USA
| | - Daniel G Nocera
- Department of Chemistry and Chemical Biology, Harvard University 12 Oxford Street Cambridge Massachusetts 02138 USA
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10
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Remines M, Schoonover M, Knox Z, Kenwright K, Hoffert KM, Coric A, Mead J, Ampfer J, Seye S, Strome ED. Profiling The Compendium Of Changes In Saccharomyces cerevisiae Due To Mutations That Alter Availability Of The Main Methyl Donor S-Adenosylmethionine. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.09.544294. [PMID: 37333147 PMCID: PMC10274911 DOI: 10.1101/2023.06.09.544294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
The SAM1 and SAM2 genes encode for S-AdenosylMethionine (AdoMet) synthetase enzymes, with AdoMet serving as the main methyl donor. We have previously shown that independent deletion of these genes alters chromosome stability and AdoMet concentrations in opposite ways in S. cerevisiae. To characterize other changes occurring in these mutants, we grew wildtype, sam1∆/sam1∆, and sam2∆/sam2∆ strains in 15 different Phenotypic Microarray plates with different components, equal to 1440 wells, and measured for growth variations. RNA-Sequencing was also carried out on these strains and differential gene expression determined for each mutant. In this study, we explore how the phenotypic growth differences are linked to the altered gene expression, and thereby predict the mechanisms by which loss of the SAM genes and subsequent AdoMet level changes, impact S. cerevisiae pathways and processes. We present six stories, discussing changes in sensitivity or resistance to azoles, cisplatin, oxidative stress, arginine biosynthesis perturbations, DNA synthesis inhibitors, and tamoxifen, to demonstrate the power of this novel methodology to broadly profile changes due to gene mutations. The large number of conditions that result in altered growth, as well as the large number of differentially expressed genes with wide-ranging functionality, speaks to the broad array of impacts that altering methyl donor abundance can impart, even when the conditions tested were not specifically selected as targeting known methyl involving pathways. Our findings demonstrate that some cellular changes are directly related to AdoMet-dependent methyltransferases and AdoMet availability, some are directly linked to the methyl cycle and its role is production of several important cellular components, and others reveal impacts of SAM gene mutations on previously unconnected pathways.
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Affiliation(s)
- McKayla Remines
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099
| | - Makailyn Schoonover
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099
| | - Zoey Knox
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099
| | - Kailee Kenwright
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099
| | - Kellyn M. Hoffert
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099
| | - Amila Coric
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099
| | - James Mead
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099
| | - Joseph Ampfer
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099
| | - Serigne Seye
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099
| | - Erin D. Strome
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY 41099
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11
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Saez-Ayala M, Hoffer L, Abel S, Ben Yaala K, Sicard B, Andrieu GP, Latiri M, Davison EK, Ciufolini MA, Brémond P, Rebuffet E, Roche P, Derviaux C, Voisset E, Montersino C, Castellano R, Collette Y, Asnafi V, Betzi S, Dubreuil P, Combes S, Morelli X. From a drug repositioning to a structure-based drug design approach to tackle acute lymphoblastic leukemia. Nat Commun 2023; 14:3079. [PMID: 37248212 DOI: 10.1038/s41467-023-38668-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 05/11/2023] [Indexed: 05/31/2023] Open
Abstract
Cancer cells utilize the main de novo pathway and the alternative salvage pathway for deoxyribonucleotide biosynthesis to achieve adequate nucleotide pools. Deoxycytidine kinase is the rate-limiting enzyme of the salvage pathway and it has recently emerged as a target for anti-proliferative therapies for cancers where it is essential. Here, we present the development of a potent inhibitor applying an iterative multidisciplinary approach, which relies on computational design coupled with experimental evaluations. This strategy allows an acceleration of the hit-to-lead process by gradually implementing key chemical modifications to increase affinity and activity. Our lead compound, OR0642, is more than 1000 times more potent than its initial parent compound, masitinib, previously identified from a drug repositioning approach. OR0642 in combination with a physiological inhibitor of the de novo pathway doubled the survival rate in a human T-cell acute lymphoblastic leukemia patient-derived xenograft mouse model, demonstrating the proof-of-concept of this drug design strategy.
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Affiliation(s)
- Magali Saez-Ayala
- Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS, INSERM, Aix-Marseille Univ, Institut Paoli-Calmettes, Marseille, France.
| | - Laurent Hoffer
- Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS, INSERM, Aix-Marseille Univ, Institut Paoli-Calmettes, Marseille, France
- Drug Discovery Program, Ontario Institute for Cancer Research (OICR), Toronto, ON, Canada
| | - Sébastien Abel
- Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS, INSERM, Aix-Marseille Univ, Institut Paoli-Calmettes, Marseille, France
| | - Khaoula Ben Yaala
- Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS, INSERM, Aix-Marseille Univ, Institut Paoli-Calmettes, Marseille, France
| | - Benoit Sicard
- Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS, INSERM, Aix-Marseille Univ, Institut Paoli-Calmettes, Marseille, France
| | - Guillaume P Andrieu
- Institut Necker Enfants Malades (INEM), INSERM, Hôpital Necker Enfants-Malades, Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Université de Paris, Paris, France
| | - Mehdi Latiri
- Institut Necker Enfants Malades (INEM), INSERM, Hôpital Necker Enfants-Malades, Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Université de Paris, Paris, France
| | - Emma K Davison
- Department of Chemistry, Faculty of Science, University of British Columbia, Vancouver, BC, Canada
- Department of Chemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Marco A Ciufolini
- Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS, INSERM, Aix-Marseille Univ, Institut Paoli-Calmettes, Marseille, France
- Department of Chemistry, Faculty of Science, University of British Columbia, Vancouver, BC, Canada
| | - Paul Brémond
- Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS, INSERM, Aix-Marseille Univ, Institut Paoli-Calmettes, Marseille, France
| | - Etienne Rebuffet
- Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS, INSERM, Aix-Marseille Univ, Institut Paoli-Calmettes, Marseille, France
| | - Philippe Roche
- Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS, INSERM, Aix-Marseille Univ, Institut Paoli-Calmettes, Marseille, France
| | - Carine Derviaux
- Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS, INSERM, Aix-Marseille Univ, Institut Paoli-Calmettes, Marseille, France
| | - Edwige Voisset
- Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS, INSERM, Aix-Marseille Univ, Institut Paoli-Calmettes, Marseille, France
| | - Camille Montersino
- Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS, INSERM, Aix-Marseille Univ, Institut Paoli-Calmettes, Marseille, France
| | - Remy Castellano
- Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS, INSERM, Aix-Marseille Univ, Institut Paoli-Calmettes, Marseille, France
| | - Yves Collette
- Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS, INSERM, Aix-Marseille Univ, Institut Paoli-Calmettes, Marseille, France
| | - Vahid Asnafi
- Institut Necker Enfants Malades (INEM), INSERM, Hôpital Necker Enfants-Malades, Laboratory of Onco-Hematology, Assistance Publique-Hôpitaux de Paris, Université de Paris, Paris, France
| | - Stéphane Betzi
- Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS, INSERM, Aix-Marseille Univ, Institut Paoli-Calmettes, Marseille, France
| | - Patrice Dubreuil
- Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS, INSERM, Aix-Marseille Univ, Institut Paoli-Calmettes, Marseille, France.
| | - Sébastien Combes
- Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS, INSERM, Aix-Marseille Univ, Institut Paoli-Calmettes, Marseille, France.
| | - Xavier Morelli
- Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS, INSERM, Aix-Marseille Univ, Institut Paoli-Calmettes, Marseille, France.
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12
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Meher S, Gade CR, Sharma NK. Tropolone-Conjugated DNA: A Fluorescent Thymidine Analogue Exhibits Solvatochromism, Enzymatic Incorporation into DNA and HeLa Cell Internalization. Chembiochem 2023; 24:e202200732. [PMID: 36510378 DOI: 10.1002/cbic.202200732] [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: 12/09/2022] [Accepted: 12/12/2022] [Indexed: 12/14/2022]
Abstract
Tropolone is a non-benzenoid aromatic scaffold with unique photophysical and metal-chelating properties. Recently, it has been conjugated with DNA, and the photophysical properties of this conjugate have been explored. Tropolonyl-deoxyuridine (tr-dU) is a synthetic fluorescent DNA nucleoside analogue that exhibits pH-dependent emissions. However, its solvent-dependent fluorescence properties are unexplored owing to its poor solubility in most organic solvents. It would be interesting to incorporate it into DNA primer enzymatically. This report describes the solvent-dependent fluorescence properties of the silyl-derivative, and enzymatic incorporation of its triphosphate analogue. For practical use, its cell-internalization and cytotoxicity are also explored. tr-dU nucleoside was found to be a potential analogue to design DNA probes and can be explored for various therapeutic applications in the future.
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Affiliation(s)
- Sagarika Meher
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) Bhubaneswar, Jatani, 752050, Odisha, India.,Homi Bhabha National Institute (HBNI), Training School Complex, Anushaktinagar, Mumbai, 400094, India
| | - Chandrasekhar Reddy Gade
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) Bhubaneswar, Jatani, 752050, Odisha, India.,Homi Bhabha National Institute (HBNI), Training School Complex, Anushaktinagar, Mumbai, 400094, India
| | - Nagendra K Sharma
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) Bhubaneswar, Jatani, 752050, Odisha, India.,Homi Bhabha National Institute (HBNI), Training School Complex, Anushaktinagar, Mumbai, 400094, India
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13
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Nagar S, Mehta R, Kaur P, Liliah RT, Vancura A. Tolerance to replication stress requires Dun1p kinase and activation of the electron transport chain. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119382. [PMID: 36283478 PMCID: PMC10329874 DOI: 10.1016/j.bbamcr.2022.119382] [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: 04/22/2022] [Revised: 09/26/2022] [Accepted: 10/12/2022] [Indexed: 11/13/2022]
Abstract
One of the key outcomes of activation of DNA replication checkpoint (DRC) or DNA damage checkpoint (DDC) is the increased synthesis of the deoxyribonucleoside triphosphates (dNTPs), which is a prerequisite for normal progression through the S phase and for effective DNA repair. We have recently shown that DDC increases aerobic metabolism and activates the electron transport chain (ETC) to elevate ATP production and dNTP synthesis by repressing transcription of histone genes, leading to globally altered chromatin architecture and increased transcription of genes encoding enzymes of tricarboxylic acid (TCA) cycle and the ETC. The aim of this study was to determine whether DRC activates ETC. We show here that DRC activates ETC by a checkpoint kinase Dun1p-dependent mechanism. DRC induces transcription of RNR1-4 genes and elevates mtDNA copy number. Inactivation of RRM3 or SGS1, two DNA helicases important for DNA replication, activates DRC but does not render cells dependent on ETC. However, fitness of rrm3Δ and sgs1Δ cells requires Dun1p. The slow growth of rrm3Δdun1Δ and sgs1Δdun1Δ cells can be suppressed by introducing sml1Δ mutation, indicating that the slow growth is due to low levels of dNTPs. Interestingly, inactivation of ETC in dun1Δ cells results in a synthetic growth defect that can be suppressed by sml1Δ mutation, suggesting that ETC is important for dNTP synthesis in the absence of Dun1p function. Together, our results reveal an unexpected connection between ETC, replication stress, and Dun1p kinase.
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Affiliation(s)
- Shreya Nagar
- Department of Biological Sciences, St. John's University, Queens, NY, USA
| | - Riddhi Mehta
- Department of Biological Sciences, St. John's University, Queens, NY, USA
| | - Pritpal Kaur
- Department of Biological Sciences, St. John's University, Queens, NY, USA
| | - Roshini T Liliah
- Department of Biological Sciences, St. John's University, Queens, NY, USA
| | - Ales Vancura
- Department of Biological Sciences, St. John's University, Queens, NY, USA.
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14
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Genomics, Transcriptomics, and Metabolomics Reveal That Minimal Modifications in the Host Are Crucial for the Compensatory Evolution of ColE1-Like Plasmids. mSphere 2022; 7:e0018422. [PMID: 36416553 PMCID: PMC9769657 DOI: 10.1128/msphere.00184-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Plasmid-mediated antimicrobial resistance is one of the major threats to public health worldwide. The mechanisms involved in the plasmid/host coadaptation are still poorly characterized, and their understanding is crucial to comprehend the genesis and evolution of multidrug-resistant bacteria. With this purpose, we designed an experimental evolution using Haemophilus influenzae RdKW20 as the model strain carrying the ColE1-like plasmid pB1000. Five H. influenzae populations adapted previously to the culture conditions were transformed with pB1000 and subsequently evolved to compensate for the plasmid-associated fitness cost. Afterward, we performed an integrative multiomic analysis combining genomics, transcriptomics, and metabolomics to explore the molecular mechanisms involved in the compensatory evolution of the plasmid. Our results demonstrate that minimal modifications in the host are responsible for plasmid adaptation. Among all of them, the most enriched process was amino acid metabolism, especially those pathways related to serine, tryptophan, and arginine, eventually related to the genesis and resolution of plasmid dimers. Additional rearrangements occurred during the plasmid adaptation, such as an overexpression of the ribonucleotide reductases and metabolic modifications within specific membrane phospholipids. All these findings demonstrate that the plasmid compensation occurs through the combination of diverse host-mediated mechanisms, of which some are beyond genomic and transcriptomic modifications. IMPORTANCE The ability of bacteria to horizontally transfer genetic material has turned antimicrobial resistance into one of the major sanitary crises of the 21st century. Plasmid conjugation is considered the main mechanism responsible for the mobilization of resistance genes, and its understanding is crucial to tackle this crisis. It is generally accepted that the acquisition and maintenance of mobile genetic elements entail a fitness cost to its host, which is susceptible to be alleviated through a coadaptation process or compensatory evolution. Notwithstanding, despite recent major efforts, the underlying mechanisms involved in this adaptation remain poorly characterized. Analyzing the plasmid/host coadaptation from a multiomic perspective sheds light on the physiological processes involved in the compensation, providing a new understanding on the genesis and evolution of plasmid-mediated antimicrobial-resistant bacteria.
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15
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Li H, Li L, Wu W, Wang F, Zhou F, Lin Y. SvSTL1 in the large subunit family of ribonucleotide reductases plays a major role in chloroplast development of Setaria viridis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:625-641. [PMID: 35608125 DOI: 10.1111/tpj.15842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 05/04/2022] [Accepted: 05/20/2022] [Indexed: 06/15/2023]
Abstract
Ribonucleotide reductases (RNRs) are essential enzymes in DNA synthesis. However, little is known about the RNRs in plants. Here, we identified a svstl1 mutant from the self-created ethyl methanesulfonate (EMS) mutant library of Setaria viridis. The mutant leaves exhibited a bleaching phenotype at the heading stage. Paraffin section analysis showed the destruction of the C4 Kranz anatomy. Transmission electron microscopy results further demonstrated the severely disturbed development of some chloroplasts. MutMap analysis revealed that the SvSTL1 gene is the primary candidate, encoding a large subunit of RNRs. Complementation experiments confirmed that SvSTL1 is responsible for the phenotype of svstl1. There are two additional RNR large subunit homologs in S. viridis, SvSTL2 and SvSTL3. To further understand the functions of these three RNR large subunit genes, a series of mutants were generated via CRISPR/Cas9 technology. In striking contrast to the finding that all three SvSTLs interact with the RNR small subunit, the phenotype varied along with the copies of chloroplast genome among different svstl single mutants: the svstl1 mutant exhibited pronounced chloroplast development and significantly fewer copies of the chloroplast genome than the svstl2 or svstl3 single mutants. These results suggested that SvSTL1 plays a major role in the optimal function of RNRs and is essential for chloroplast development. Furthermore, through the analysis of double and triple mutants, the study provides new insights into the finely tuned coordination among SvSTLs to maintain normal chloroplast development in the emerging C4 model plant S. viridis.
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Affiliation(s)
- Huanying Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Lin Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Weichen Wu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Fei Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Fei Zhou
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Yongjun Lin
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
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16
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Fietze T, Wilk P, Kabinger F, Anoosheh S, Hofer A, Lundin D, Feiler CG, Weiss MS, Loderer C. HUG Domain Is Responsible for Active Dimer Stabilization in an NrdJd Ribonucleotide Reductase. Biochemistry 2022; 61:1633-1641. [PMID: 35856337 DOI: 10.1021/acs.biochem.2c00173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ribonucleotide reductases (RNRs) catalyze the reduction of ribonucleotides to the corresponding deoxyribonucleotides. The catalytic activity of most RNRs depends on the formation of a dimer of the catalytic subunits. The active site is located at the interface, and part of the substrate binding site and regulatory mechanisms work across the subunit in the dimer. In this study, we describe and characterize a novel domain responsible for forming the catalytic dimer in several class II RNRs. The 3D structure of the class II RNR from Rhodobacter sphaeroides reveals a so far undescribed α-helical domain in the dimer interface, which is embracing the other subunit. Genetic removal of this HUG domain leads to a severe reduction of activity paired with reduced dimerization capability. In comparison with other described RNRs, the enzyme with this domain is less dependent on the presence of nucleotides to act as allosteric effectors in the formation of dimers. The HUG domain appears to serve as an interlock to keep the dimer intact and functional even at low enzyme and/or effector concentrations.
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Affiliation(s)
- Tobias Fietze
- Chair of Molecular Biotechnology, Technische Universität Dresden, Dresden 01217, Germany
| | - Piotr Wilk
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Berlin 12489, Germany.,Malopolska Centre of Biotechnology (MCB), Jagiellonian University, Krakow 31-007, Poland
| | - Florian Kabinger
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen 37077, Germany
| | - Saber Anoosheh
- Department of Medical Biochemistry, Umeå University, Umeå 1965, Sweden
| | - Anders Hofer
- Department of Medical Biochemistry, Umeå University, Umeå 1965, Sweden
| | - Daniel Lundin
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm 114 19, Sweden
| | - Christian G Feiler
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Berlin 12489, Germany
| | - Manfred S Weiss
- Macromolecular Crystallography, Helmholtz-Zentrum Berlin, Berlin 12489, Germany
| | - Christoph Loderer
- Chair of Molecular Biotechnology, Technische Universität Dresden, Dresden 01217, Germany
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17
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Van Stappen C, Deng Y, Liu Y, Heidari H, Wang JX, Zhou Y, Ledray AP, Lu Y. Designing Artificial Metalloenzymes by Tuning of the Environment beyond the Primary Coordination Sphere. Chem Rev 2022; 122:11974-12045. [PMID: 35816578 DOI: 10.1021/acs.chemrev.2c00106] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metalloenzymes catalyze a variety of reactions using a limited number of natural amino acids and metallocofactors. Therefore, the environment beyond the primary coordination sphere must play an important role in both conferring and tuning their phenomenal catalytic properties, enabling active sites with otherwise similar primary coordination environments to perform a diverse array of biological functions. However, since the interactions beyond the primary coordination sphere are numerous and weak, it has been difficult to pinpoint structural features responsible for the tuning of activities of native enzymes. Designing artificial metalloenzymes (ArMs) offers an excellent basis to elucidate the roles of these interactions and to further develop practical biological catalysts. In this review, we highlight how the secondary coordination spheres of ArMs influence metal binding and catalysis, with particular focus on the use of native protein scaffolds as templates for the design of ArMs by either rational design aided by computational modeling, directed evolution, or a combination of both approaches. In describing successes in designing heme, nonheme Fe, and Cu metalloenzymes, heteronuclear metalloenzymes containing heme, and those ArMs containing other metal centers (including those with non-native metal ions and metallocofactors), we have summarized insights gained on how careful controls of the interactions in the secondary coordination sphere, including hydrophobic and hydrogen bonding interactions, allow the generation and tuning of these respective systems to approach, rival, and, in a few cases, exceed those of native enzymes. We have also provided an outlook on the remaining challenges in the field and future directions that will allow for a deeper understanding of the secondary coordination sphere a deeper understanding of the secondary coordintion sphere to be gained, and in turn to guide the design of a broader and more efficient variety of ArMs.
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Affiliation(s)
- Casey Van Stappen
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yunling Deng
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yiwei Liu
- Department of Chemistry, University of Illinois, Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Hirbod Heidari
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Jing-Xiang Wang
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yu Zhou
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Aaron P Ledray
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yi Lu
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States.,Department of Chemistry, University of Illinois, Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
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18
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Klemm BP, Sikkema AP, Hsu AL, Horng JC, Hall TMT, Borgnia MJ, Schaaper RM. High-resolution structures of the SAMHD1 dGTPase homolog from Leeuwenhoekiella blandensis reveal a novel mechanism of allosteric activation by dATP. J Biol Chem 2022; 298:102073. [PMID: 35643313 PMCID: PMC9257424 DOI: 10.1016/j.jbc.2022.102073] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 10/27/2022] Open
Abstract
Deoxynucleoside triphosphate (dNTP) triphosphohydrolases (dNTPases) are important enzymes that may perform multiple functions in the cell, including regulating the dNTP pools and contributing to innate immunity against viruses. Among the homologs that are best studied are human sterile alpha motif and HD domain-containing protein 1 (SAMHD1), a tetrameric dNTPase, and the hexameric Escherichia coli dGTPase; however, it is unclear whether these are representative of all dNTPases given their wide distribution throughout life. Here, we investigated a hexameric homolog from the marine bacterium Leeuwenhoekiella blandensis, revealing that it is a dGTPase that is subject to allosteric activation by dATP, specifically. Allosteric regulation mediated solely by dATP represents a novel regulatory feature among dNTPases that may facilitate maintenance of cellular dNTP pools in L. blandensis. We present high-resolution X-ray crystallographic structures (1.80-2.26 Å) in catalytically important conformations as well as cryo-EM structures (2.1-2.7 Å) of the enzyme bound to dGTP and dATP ligands. The structures, the highest resolution cryo-EM structures of any SAMHD1-like dNTPase to date, reveal an intact metal-binding site with the dGTP substrate coordinated to three metal ions. These structural and biochemical data yield insights into the catalytic mechanism and support a conserved catalytic mechanism for the tetrameric and hexameric dNTPase homologs. We conclude that the allosteric activation by dATP appears to rely on structural connectivity between the allosteric and active sites, as opposed to the changes in oligomeric state upon ligand binding used by SAMHD1.
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Affiliation(s)
- Bradley P Klemm
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, North Carolina, USA
| | - Andrew P Sikkema
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, North Carolina, USA
| | - Allen L Hsu
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, North Carolina, USA
| | - James C Horng
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, North Carolina, USA
| | - Traci M Tanaka Hall
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, North Carolina, USA
| | - Mario J Borgnia
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, North Carolina, USA
| | - Roel M Schaaper
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, North Carolina, USA.
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19
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Wang H, He X, Zhang L, Dong H, Huang F, Xian J, Li M, Chen W, Lu X, Pathak KV, Huang W, Li Z, Zhang L, Nguyen LXT, Yang L, Feng L, Gordon DJ, Zhang J, Pirrotte P, Chen CW, Salhotra A, Kuo YH, Horne D, Marcucci G, Sykes DB, Tiziani S, Jin H, Wang X, Li L. Disruption of dNTP homeostasis by ribonucleotide reductase hyperactivation overcomes AML differentiation blockade. Blood 2022; 139:3752-3770. [PMID: 35439288 PMCID: PMC9247363 DOI: 10.1182/blood.2021015108] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 04/07/2022] [Indexed: 01/09/2023] Open
Abstract
Differentiation blockade is a hallmark of acute myeloid leukemia (AML). A strategy to overcome such a blockade is a promising approach against the disease. The lack of understanding of the underlying mechanisms hampers development of such strategies. Dysregulated ribonucleotide reductase (RNR) is considered a druggable target in proliferative cancers susceptible to deoxynucleoside triphosphate (dNTP) depletion. Herein, we report an unanticipated discovery that hyperactivating RNR enables differentiation and decreases leukemia cell growth. We integrate pharmacogenomics and metabolomics analyses to identify that pharmacologically (eg, nelarabine) or genetically upregulating RNR subunit M2 (RRM2) creates a dNTP pool imbalance and overcomes differentiation arrest. Moreover, R-loop-mediated DNA replication stress signaling is responsible for RRM2 activation by nelarabine treatment. Further aggravating dNTP imbalance by depleting the dNTP hydrolase SAM domain and HD domain-containing protein 1 (SAMHD1) enhances ablation of leukemia stem cells by RRM2 hyperactivation. Mechanistically, excessive activation of extracellular signal-regulated kinase (ERK) signaling downstream of the imbalance contributes to cellular outcomes of RNR hyperactivation. A CRISPR screen identifies a synthetic lethal interaction between loss of DUSP6, an ERK-negative regulator, and nelarabine treatment. These data demonstrate that dNTP homeostasis governs leukemia maintenance, and a combination of DUSP inhibition and nelarabine represents a therapeutic strategy.
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Affiliation(s)
- Hanying Wang
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA
- Department of Medical Oncology and
| | - Xin He
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA
| | - Lei Zhang
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA
| | - Haojie Dong
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA
| | - Feiteng Huang
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA
- Department of Hematology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - Jie Xian
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA
| | - Min Li
- Department of Information Sciences, Beckman Research Institute and
| | - Wei Chen
- Integrative Genomics Core, Beckman Research Institute, City of Hope Medical Center, Duarte, CA
| | - Xiyuan Lu
- Department of Nutritional Sciences, The University of Texas at Austin, Austin, TX
| | - Khyatiben V Pathak
- Cancer & Cell Biology Division, The Translational Genomics Research Institute, Phoenix, AZ
| | - Wenfeng Huang
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA
| | - Zheng Li
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA
- Department of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Lianjun Zhang
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA
| | - Le Xuan Truong Nguyen
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA
| | - Lu Yang
- Department of Systems Biology, Beckman Research Institute, City of Hope Medical Center, Duarte, CA
| | - Lifeng Feng
- Laboratory of Cancer Biology, Provincial Key Laboratory of Biotherapy in Zhejiang, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | - David J Gordon
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Iowa, Iowa City, IA
| | - Jing Zhang
- McArdle Laboratory for Cancer Research and Wisconsin Blood Cancer Research Institute, University of Wisconsin-Madison, Madison, WI
| | - Patrick Pirrotte
- Cancer & Cell Biology Division, The Translational Genomics Research Institute, Phoenix, AZ
- Cancer & Cell Biology Division, The Translational Genomics Research Institute, Phoenix, AZ
| | - Chun-Wei Chen
- Department of Systems Biology, Beckman Research Institute, City of Hope Medical Center, Duarte, CA
| | | | - Ya-Huei Kuo
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA
| | - David Horne
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA
| | - Guido Marcucci
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA
- Department of Hematology and Hematopoietic Cell Transplantation and
| | - David B Sykes
- Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA; and
| | - Stefano Tiziani
- Department of Nutritional Sciences, The University of Texas at Austin, Austin, TX
- Department of Pediatrics and
- Department of Oncology, Dell Medical School, LiveSTRONG Cancer Institutes, The University of Texas at Austin, Austin, TX
| | - Hongchuan Jin
- Laboratory of Cancer Biology, Provincial Key Laboratory of Biotherapy in Zhejiang, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
| | | | - Ling Li
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, Hematologic Malignancies and Stem Cell Transplantation Institute, Beckman Research Institute, City of Hope Medical Center, Duarte, CA
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20
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Kinetic model for reversible radical transfer in ribonucleotide reductase. Proc Natl Acad Sci U S A 2022; 119:e2202022119. [PMID: 35714287 DOI: 10.1073/pnas.2202022119] [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] [Indexed: 11/18/2022] Open
Abstract
The enzyme ribonucleotide reductase (RNR), which catalyzes the reduction of ribonucleotides to deoxynucleotides, is vital for DNA synthesis, replication, and repair in all living organisms. Its mechanism requires long-range radical translocation over ∼32 Å through two protein subunits and the intervening aqueous interface. Herein, a kinetic model is designed to describe reversible radical transfer in Escherichia coli RNR. This model is based on experimentally studied photoRNR systems that allow the photochemical injection of a radical at a specific tyrosine residue, Y356, using a photosensitizer. The radical then transfers across the interface to another tyrosine residue, Y731, and continues until it reaches a cysteine residue, C439, which is primed for catalysis. This kinetic model includes radical injection, an off-pathway sink, radical transfer between pairs of residues along the pathway, and the conformational flipping motion of Y731 at the interface. Most of the input rate constants for this kinetic model are obtained from previous experimental measurements and quantum mechanical/molecular mechanical free-energy simulations. Ranges for the rate constants corresponding to radical transfer across the interface are determined by fitting to the experimentally measured Y356 radical decay times in photoRNR systems. This kinetic model illuminates the time evolution of radical transport along the tyrosine and cysteine residues following radical injection. Further analysis identifies the individual rate constants that may be tuned to alter the timescale and probability of the injected radical reaching C439. The insights gained from this kinetic model are relevant to biochemical understanding and protein-engineering efforts with potential pharmacological implications.
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21
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Lamb NA, Bard JE, Loll-Krippleber R, Brown GW, Surtees JA. Complex mutation profiles in mismatch repair and ribonucleotide reductase mutants reveal novel repair substrate specificity of MutS homolog (MSH) complexes. Genetics 2022; 221:6605222. [PMID: 35686905 PMCID: PMC9339293 DOI: 10.1093/genetics/iyac092] [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: 02/14/2022] [Accepted: 05/24/2022] [Indexed: 12/30/2022] Open
Abstract
Determining mutation signatures is standard for understanding the etiology of human tumors and informing cancer treatment. Multiple determinants of DNA replication fidelity prevent mutagenesis that leads to carcinogenesis, including the regulation of free deoxyribonucleoside triphosphate pools by ribonucleotide reductase and repair of replication errors by the mismatch repair system. We identified genetic interactions between rnr1 alleles that skew and/or elevate deoxyribonucleoside triphosphate levels and mismatch repair gene deletions. These defects indicate that the rnr1 alleles lead to increased mutation loads that are normally acted upon by mismatch repair. We then utilized a targeted deep-sequencing approach to determine mutational profiles associated with mismatch repair pathway defects. By combining rnr1 and msh mutations to alter and/or increase deoxyribonucleoside triphosphate levels and alter the mutational load, we uncovered previously unreported specificities of Msh2-Msh3 and Msh2-Msh6. Msh2-Msh3 is uniquely able to direct the repair of G/C single-base deletions in GC runs, while Msh2-Msh6 specifically directs the repair of substitutions that occur at G/C dinucleotides. We also identified broader sequence contexts that influence variant profiles in different genetic backgrounds. Finally, we observed that the mutation profiles in double mutants were not necessarily an additive relationship of mutation profiles in single mutants. Our results have implications for interpreting mutation signatures from human tumors, particularly when mismatch repair is defective.
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Affiliation(s)
- Natalie A Lamb
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Jonathan E Bard
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY 14203, USA,University at Buffalo Genomics and Bioinformatics Core, State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Raphael Loll-Krippleber
- Department of Biochemistry and Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Grant W Brown
- Department of Biochemistry and Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Jennifer A Surtees
- Corresponding author: Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Rm 4215, 955 Main Street, Buffalo, NY 14203, USA.
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22
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Huff SE, Winter JM, Dealwis CG. Inhibitors of the Cancer Target Ribonucleotide Reductase, Past and Present. Biomolecules 2022; 12:biom12060815. [PMID: 35740940 PMCID: PMC9221315 DOI: 10.3390/biom12060815] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 06/01/2022] [Accepted: 06/07/2022] [Indexed: 01/02/2023] Open
Abstract
Ribonucleotide reductase (RR) is an essential multi-subunit enzyme found in all living organisms; it catalyzes the rate-limiting step in dNTP synthesis, namely, the conversion of ribonucleoside diphosphates to deoxyribonucleoside diphosphates. As expression levels of human RR (hRR) are high during cell replication, hRR has long been considered an attractive drug target for a range of proliferative diseases, including cancer. While there are many excellent reviews regarding the structure, function, and clinical importance of hRR, recent years have seen an increase in novel approaches to inhibiting hRR that merit an updated discussion of the existing inhibitors and strategies to target this enzyme. In this review, we discuss the mechanisms and clinical applications of classic nucleoside analog inhibitors of hRRM1 (large catalytic subunit), including gemcitabine and clofarabine, as well as inhibitors of the hRRM2 (free radical housing small subunit), including triapine and hydroxyurea. Additionally, we discuss novel approaches to targeting RR and the discovery of new classes of hRR inhibitors.
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Affiliation(s)
- Sarah E. Huff
- Department of Pediatrics, University of California, San Diego, CA 92093, USA;
| | - Jordan M. Winter
- Department of Surgery, Division of Surgical Oncology, University Hospitals Cleveland Medical Center, Akron, OH 44106, USA;
| | - Chris G. Dealwis
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106, USA
- Department of Chemistry, Case Western Reserve University, Cleveland, OH 44106, USA
- Correspondence:
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23
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Meyer A, Kehl A, Cui C, Reichardt FAK, Hecker F, Funk LM, Pan KT, Urlaub H, Tittmann K, Stubbe J, Bennati M. 19F Electron-Nuclear Double Resonance Reveals Interaction between Redox-Active Tyrosines across the α/β Interface of E. coli Ribonucleotide Reductase. J Am Chem Soc 2022; 144:11270-11282. [PMID: 35652913 PMCID: PMC9248007 DOI: 10.1021/jacs.2c02906] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Ribonucleotide reductases
(RNRs) catalyze the reduction of ribonucleotides
to deoxyribonucleotides, thereby playing a key role in DNA replication
and repair. Escherichia coli class
Ia RNR is an α2β2 enzyme complex
that uses a reversible multistep radical transfer (RT) over 32 Å
across its two subunits, α and β, to initiate, using its
metallo-cofactor in β2, nucleotide reduction in α2. Each step is proposed to involve a distinct proton-coupled
electron-transfer (PCET) process. An unresolved step is the RT involving
Y356(β) and Y731(α) across the α/β
interface. Using 2,3,5-F3Y122-β2 with 3,5-F2Y731-α2, GDP (substrate) and TTP (allosteric effector), a Y356• intermediate was trapped and its identity was
verified by 263 GHz electron paramagnetic resonance (EPR) and 34 GHz
pulse electron–electron double resonance spectroscopies. 94
GHz 19F electron-nuclear double resonance spectroscopy
allowed measuring the interspin distances between Y356• and the 19F nuclei of 3,5-F2Y731 in this RNR mutant. Similar experiments with the
double mutant E52Q/F3Y122-β2 were carried out for comparison to the recently published
cryo-EM structure of a holo RNR complex. For both mutant combinations,
the distance measurements reveal two conformations of 3,5-F2Y731. Remarkably, one conformation is consistent with
3,5-F2Y731 within the H-bond distance to Y356•, whereas the second one is consistent
with the conformation observed in the cryo-EM structure. The observations
unexpectedly suggest the possibility of a colinear PCET, in which
electron and proton are transferred from the same donor to the same
acceptor between Y356 and Y731. The results
highlight the important role of state-of-the-art EPR spectroscopy
to decipher this mechanism.
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Affiliation(s)
- Andreas Meyer
- Research group ESR spectroscopy, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Annemarie Kehl
- Research group ESR spectroscopy, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Chang Cui
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Fehmke A K Reichardt
- Research group ESR spectroscopy, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Fabian Hecker
- Research group ESR spectroscopy, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Lisa-Marie Funk
- Department of structural dynamics, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany.,Department of Molecular Enzymology, Georg-August University, 37077 Göttingen, Germany
| | - Kuan-Ting Pan
- Research group bioanalytical mass spectrometry, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany.,Bioanalytics, University Medical Center, 37075 Göttingen, Germany
| | - Henning Urlaub
- Research group bioanalytical mass spectrometry, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany.,Bioanalytics, University Medical Center, 37075 Göttingen, Germany
| | - Kai Tittmann
- Department of structural dynamics, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany.,Department of Molecular Enzymology, Georg-August University, 37077 Göttingen, Germany
| | - JoAnne Stubbe
- Department of Chemistry and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 20139, United States
| | - Marina Bennati
- Research group ESR spectroscopy, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany.,Department of Chemistry, Georg-August University, 37077 Göttingen, Germany
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24
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Rozman Grinberg I, Martínez-Carranza M, Bimai O, Nouaïria G, Shahid S, Lundin D, Logan DT, Sjöberg BM, Stenmark P. A nucleotide-sensing oligomerization mechanism that controls NrdR-dependent transcription of ribonucleotide reductases. Nat Commun 2022; 13:2700. [PMID: 35577776 PMCID: PMC9110341 DOI: 10.1038/s41467-022-30328-1] [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: 09/20/2021] [Accepted: 04/22/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractRibonucleotide reductase (RNR) is an essential enzyme that catalyzes the synthesis of DNA building blocks in virtually all living cells. NrdR, an RNR-specific repressor, controls the transcription of RNR genes and, often, its own, in most bacteria and some archaea. NrdR senses the concentration of nucleotides through its ATP-cone, an evolutionarily mobile domain that also regulates the enzymatic activity of many RNRs, while a Zn-ribbon domain mediates binding to NrdR boxes upstream of and overlapping the transcription start site of RNR genes. Here, we combine biochemical and cryo-EM studies of NrdR from Streptomyces coelicolor to show, at atomic resolution, how NrdR binds to DNA. The suggested mechanism involves an initial dodecamer loaded with two ATP molecules that cannot bind to DNA. When dATP concentrations increase, an octamer forms that is loaded with one molecule each of dATP and ATP per monomer. A tetramer derived from this octamer then binds to DNA and represses transcription of RNR. In many bacteria — including well-known pathogens such as Mycobacterium tuberculosis — NrdR simultaneously controls multiple RNRs and hence DNA synthesis, making it an excellent target for novel antibiotics development.
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25
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Abstract
Some oxidoreductase enzymes use redox-active tyrosine, tryptophan, cysteine, and/or glycine residues as one-electron, high-potential redox (radical) cofactors. Amino-acid radical cofactors typically perform one of four tasks-they work in concert with a metallocofactor to carry out a multielectron redox process, serve as storage sites for oxidizing equivalents, activate the substrate molecules, or move oxidizing equivalents over long distances. It is challenging to experimentally resolve the thermodynamic and kinetic redox properties of a single-amino-acid residue. The inherently reactive and highly oxidizing properties of amino-acid radicals increase the experimental barriers further still. This review describes a family of stable and well-structured model proteins that was made specifically to study tyrosine and tryptophan oxidation-reduction. The so-called α3X model protein system was combined with very-high-potential protein film voltammetry, transient absorption spectroscopy, and theoretical methods to gain a comprehensive description of the thermodynamic and kinetic properties of protein tyrosine and tryptophan radicals.
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Affiliation(s)
- Cecilia Tommos
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA;
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26
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Shaban NM, Yan R, Shi K, Moraes SN, Cheng AZ, Carpenter MA, McLellan JS, Yu Z, Harris RS. Cryo-EM structure of the EBV ribonucleotide reductase BORF2 and mechanism of APOBEC3B inhibition. SCIENCE ADVANCES 2022; 8:eabm2827. [PMID: 35476445 PMCID: PMC9045721 DOI: 10.1126/sciadv.abm2827] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 02/23/2022] [Indexed: 05/26/2023]
Abstract
Viruses use a plethora of mechanisms to evade immune responses. A recent example is neutralization of the nuclear DNA cytosine deaminase APOBEC3B by the Epstein-Barr virus (EBV) ribonucleotide reductase subunit BORF2. Cryo-EM studies of APOBEC3B-BORF2 complexes reveal a large >1000-Å2 binding surface composed of multiple structural elements from each protein, which effectively blocks the APOBEC3B active site from accessing single-stranded DNA substrates. Evolutionary optimization is suggested by unique insertions in BORF2 absent from other ribonucleotide reductases and preferential binding to APOBEC3B relative to the highly related APOBEC3A and APOBEC3G enzymes. A molecular understanding of this pathogen-host interaction has potential to inform the development of drugs that block the interaction and liberate the natural antiviral activity of APOBEC3B. In addition, given a role for APOBEC3B in cancer mutagenesis, it may also be possible for information from the interaction to be used to develop DNA deaminase inhibitors.
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Affiliation(s)
- Nadine M. Shaban
- Department of Biochemistry, Molecular Biology, and Biophysics, Institute for Molecular Virology, Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Rui Yan
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 55416, USA
| | - Ke Shi
- Department of Biochemistry, Molecular Biology, and Biophysics, Institute for Molecular Virology, Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Sofia N. Moraes
- Department of Biochemistry, Molecular Biology, and Biophysics, Institute for Molecular Virology, Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Adam Z. Cheng
- Department of Biochemistry, Molecular Biology, and Biophysics, Institute for Molecular Virology, Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Michael A. Carpenter
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN 55416, USA
| | - Jason S. McLellan
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Zhiheng Yu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 55416, USA
| | - Reuben S. Harris
- Department of Biochemistry, Molecular Biology, and Biophysics, Institute for Molecular Virology, Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Howard Hughes Medical Institute, University of Minnesota, Minneapolis, MN 55416, USA
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27
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Narasimhan J, Letinski S, Jung SP, Gerasyuto A, Wang J, Arnold M, Chen G, Hedrick J, Dumble M, Ravichandran K, Levitz T, Cui C, Drennan CL, Stubbe J, Karp G, Branstrom A. Ribonucleotide reductase, a novel drug target for gonorrhea. eLife 2022; 11:e67447. [PMID: 35137690 PMCID: PMC8865847 DOI: 10.7554/elife.67447] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 02/08/2022] [Indexed: 11/13/2022] Open
Abstract
Antibiotic-resistant Neisseria gonorrhoeae (Ng) are an emerging public health threat due to increasing numbers of multidrug resistant (MDR) organisms. We identified two novel orally active inhibitors, PTC-847 and PTC-672, that exhibit a narrow spectrum of activity against Ng including MDR isolates. By selecting organisms resistant to the novel inhibitors and sequencing their genomes, we identified a new therapeutic target, the class Ia ribonucleotide reductase (RNR). Resistance mutations in Ng map to the N-terminal cone domain of the α subunit, which we show here is involved in forming an inhibited α4β4 state in the presence of the β subunit and allosteric effector dATP. Enzyme assays confirm that PTC-847 and PTC-672 inhibit Ng RNR and reveal that allosteric effector dATP potentiates the inhibitory effect. Oral administration of PTC-672 reduces Ng infection in a mouse model and may have therapeutic potential for treatment of Ng that is resistant to current drugs.
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Affiliation(s)
| | | | | | | | - Jiashi Wang
- PTC Therapeutics, IncSouth PlainfieldUnited States
| | | | | | - Jean Hedrick
- PTC Therapeutics, IncSouth PlainfieldUnited States
| | | | - Kanchana Ravichandran
- Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Talya Levitz
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Chang Cui
- Department of Chemistry and Chemical Biology, Harvard UniversityCambridgeUnited States
| | - Catherine L Drennan
- Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
- Howard Hughes Medical Institute, Massachusetts Institute of TechnologyCambridgeUnited States
| | - JoAnne Stubbe
- Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
- Department of Biology, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Gary Karp
- PTC Therapeutics, IncSouth PlainfieldUnited States
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28
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Proteomic Response of Deinococcus radiodurans to Short-Term Real Microgravity during Parabolic Flight Reveals Altered Abundance of Proteins Involved in Stress Response and Cell Envelope Functions. Life (Basel) 2021; 12:life12010023. [PMID: 35054415 PMCID: PMC8779699 DOI: 10.3390/life12010023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/17/2021] [Accepted: 12/20/2021] [Indexed: 12/22/2022] Open
Abstract
Rapidly evolving space exploration makes understanding the short- and long- term effects of microgravity on humans, plants, and microorganisms an important task. The ubiquitous presence of the gravitational force has had an influence on the development of all living entities on Earth, and short- and long-term changes in perceived gravitational force can induce notable changes within cells. Deinococcus radiodurans is the Gram-positive bacterium that is best known for its extreme resistance to UV-C and gamma radiation, oxidation stress, and desiccation. Thus increased interest has been placed on this species in the context of space research. The present study aims to elucidate the short-term proteomic response of this species to real microgravity during parabolic flight. Overnight cultures of D. radiodurans were subjected to microgravity during a single parabola, and metabolic activity was quenched using methanol. Proteins were extracted and subsequently measured using HPLC nESI MS/MS. The results, such as the enrichment of the peptidoglycan biosynthesis pathway with differentially abundant proteins and altered S-layer protein abundance, suggested molecular rearrangements in the cell envelope of D. radiodurans. Altered abundance of proteins involved in energy metabolism and DNA repair could be linked with increased endogenous ROS production that contributes to the stress response. Moreover, changes in protein abundance in response to microgravity show similarities with previously reported stress responses. Thus, the present results could be used to further investigate the complex regulation of the remarkable stress management of this bacterium.
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29
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Rehling D, Scaletti ER, Rozman Grinberg I, Lundin D, Sahlin M, Hofer A, Sjöberg BM, Stenmark P. Structural and Biochemical Investigation of Class I Ribonucleotide Reductase from the Hyperthermophile Aquifex aeolicus. Biochemistry 2021; 61:92-106. [PMID: 34941255 PMCID: PMC8772380 DOI: 10.1021/acs.biochem.1c00503] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Ribonucleotide reductase (RNR) is an essential enzyme with a complex mechanism of allosteric regulation found in nearly all living organisms. Class I RNRs are composed of two proteins, a large α-subunit (R1) and a smaller β-subunit (R2) that exist as homodimers, that combine to form an active heterotetramer. Aquifex aeolicus is a hyperthermophilic bacterium with an unusual RNR encoding a 346-residue intein in the DNA sequence encoding its R2 subunit. We present the first structures of the A. aeolicus R1 and R2 (AaR1 and AaR2, respectively) proteins as well as the biophysical and biochemical characterization of active and inactive A. aeolicus RNR. While the active oligomeric state and activity regulation of A. aeolicus RNR are similar to those of other characterized RNRs, the X-ray crystal structures also reveal distinct features and adaptations. Specifically, AaR1 contains a β-hairpin hook structure at the dimer interface, which has an interesting π-stacking interaction absent in other members of the NrdAh subclass, and its ATP cone houses two ATP molecules. We determined structures of two AaR2 proteins: one purified from a construct lacking the intein (AaR2) and a second purified from a construct including the intein sequence (AaR2_genomic). These structures in the context of metal content analysis and activity data indicate that AaR2_genomic displays much higher iron occupancy and activity compared to AaR2, suggesting that the intein is important for facilitating complete iron incorporation, particularly in the Fe2 site of the mature R2 protein, which may be important for the survival of A. aeolicus in low-oxygen environments.
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Affiliation(s)
- Daniel Rehling
- Department of Biochemistry and Biophysics, Stockholm University, S-106 91 Stockholm, Sweden
| | - Emma Rose Scaletti
- Department of Biochemistry and Biophysics, Stockholm University, S-106 91 Stockholm, Sweden
| | - Inna Rozman Grinberg
- Department of Biochemistry and Biophysics, Stockholm University, S-106 91 Stockholm, Sweden
| | - Daniel Lundin
- Department of Biochemistry and Biophysics, Stockholm University, S-106 91 Stockholm, Sweden
| | - Margareta Sahlin
- Department of Biochemistry and Biophysics, Stockholm University, S-106 91 Stockholm, Sweden
| | - Anders Hofer
- Department of Biochemistry and Biophysics, Umeå University, SE-907 36 Umeå, Sweden
| | - Britt-Marie Sjöberg
- Department of Biochemistry and Biophysics, Stockholm University, S-106 91 Stockholm, Sweden
| | - Pål Stenmark
- Department of Biochemistry and Biophysics, Stockholm University, S-106 91 Stockholm, Sweden.,Department of Experimental Medical Science, Lund University, 221 00 Lund, Sweden
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30
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Roberts I, Wright Muelas M, Taylor JM, Davison AS, Xu Y, Grixti JM, Gotts N, Sorokin A, Goodacre R, Kell DB. Untargeted metabolomics of COVID-19 patient serum reveals potential prognostic markers of both severity and outcome. Metabolomics 2021; 18:6. [PMID: 34928464 PMCID: PMC8686810 DOI: 10.1007/s11306-021-01859-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 11/29/2021] [Indexed: 12/15/2022]
Abstract
INTRODUCTION The diagnosis of COVID-19 is normally based on the qualitative detection of viral nucleic acid sequences. Properties of the host response are not measured but are key in determining outcome. Although metabolic profiles are well suited to capture host state, most metabolomics studies are either underpowered, measure only a restricted subset of metabolites, compare infected individuals against uninfected control cohorts that are not suitably matched, or do not provide a compact predictive model. OBJECTIVES Here we provide a well-powered, untargeted metabolomics assessment of 120 COVID-19 patient samples acquired at hospital admission. The study aims to predict the patient's infection severity (i.e., mild or severe) and potential outcome (i.e., discharged or deceased). METHODS High resolution untargeted UHPLC-MS/MS analysis was performed on patient serum using both positive and negative ionization modes. A subset of 20 intermediary metabolites predictive of severity or outcome were selected based on univariate statistical significance and a multiple predictor Bayesian logistic regression model was created. RESULTS The predictors were selected for their relevant biological function and include deoxycytidine and ureidopropionate (indirectly reflecting viral load), kynurenine (reflecting host inflammatory response), and multiple short chain acylcarnitines (energy metabolism) among others. Currently, this approach predicts outcome and severity with a Monte Carlo cross validated area under the ROC curve of 0.792 (SD 0.09) and 0.793 (SD 0.08), respectively. A blind validation study on an additional 90 patients predicted outcome and severity at ROC AUC of 0.83 (CI 0.74-0.91) and 0.76 (CI 0.67-0.86). CONCLUSION Prognostic tests based on the markers discussed in this paper could allow improvement in the planning of COVID-19 patient treatment.
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Affiliation(s)
- Ivayla Roberts
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Marina Wright Muelas
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.
| | - Joseph M Taylor
- Department of Clinical Biochemistry and Metabolic Medicine, Liverpool Clinical Laboratories, Royal Liverpool University Hospitals Trust, Liverpool, UK
| | - Andrew S Davison
- Department of Clinical Biochemistry and Metabolic Medicine, Liverpool Clinical Laboratories, Royal Liverpool University Hospitals Trust, Liverpool, UK
| | - Yun Xu
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
- Centre for Metabolomics Research (CMR), Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Justine M Grixti
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Nigel Gotts
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
- Centre for Metabolomics Research (CMR), Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Anatolii Sorokin
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Royston Goodacre
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
- Centre for Metabolomics Research (CMR), Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Douglas B Kell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.
- Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Building 220, Chemitorvet, 2000, Kgs Lyngby, Denmark.
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31
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Jayachandran M, Yoon J, Wu J, Cipurko D, Quon J, Makhlynets O. Mechanistic studies of the cofactor assembly in class Ib ribonucleotide reductases and protein affinity for MnII and FeII. Metallomics 2021; 13:6413552. [PMID: 34718709 DOI: 10.1093/mtomcs/mfab062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 10/21/2021] [Indexed: 11/14/2022]
Abstract
Ribonucleotide reductase (RNR) is an essential enzyme found in all organisms. The function of RNR is to catalyze the conversion of nucleotides to deoxynucleotides. RNRs rely on metallocofactors to oxidize a conserved cysteine in the active site of the enzyme into a thiyl radical, which then initiates nucleotide reduction. The proteins required for MnIII2-Y• cluster formation in class Ib RNRs are NrdF (β-subunit) and NrdI (flavodoxin). An oxidant is channeled from the FMN cofactor in NrdI to the dimanganese center in NrdF, where it oxidizes the dimanganese center and a tyrosyl radical (Y•) is formed. Both Streptococcus sanguinis and Escherichia coli MnII2-NrdF structures have a constriction in the channel immediately above the metal site. In E. coli, the constriction is formed by the side chain of S159, whereas in the S. sanguinis system it involves T158. This serine-to-threonine substitution was investigated using S. sanguinis and Streptococcus pneumoniae class Ib RNRs but it is also present in other pathogenic streptococci. Using stopped-flow kinetics, we investigate the role of this substitution in the mechanism of MnIII2-Y• cluster formation. In addition to different kinetics observed in the studied streptococci, we found that affinity constants of NrdF for MnII and FeII are about 1 µM and the previously reported preference for MnII could not be explained by affinity only.
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Affiliation(s)
- Megha Jayachandran
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
| | - Jennifer Yoon
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
| | - Jacky Wu
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
| | - Denis Cipurko
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
| | - Joyce Quon
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
| | - Olga Makhlynets
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
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Strengths and Weaknesses of Cell Synchronization Protocols Based on Inhibition of DNA Synthesis. Int J Mol Sci 2021; 22:ijms221910759. [PMID: 34639098 PMCID: PMC8509769 DOI: 10.3390/ijms221910759] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/01/2021] [Accepted: 10/02/2021] [Indexed: 01/01/2023] Open
Abstract
Synchronous cell populations are commonly used for the analysis of various aspects of cellular metabolism at specific stages of the cell cycle. Cell synchronization at a chosen cell cycle stage is most frequently achieved by inhibition of specific metabolic pathway(s). In this respect, various protocols have been developed to synchronize cells in particular cell cycle stages. In this review, we provide an overview of the protocols for cell synchronization of mammalian cells based on the inhibition of synthesis of DNA building blocks-deoxynucleotides and/or inhibition of DNA synthesis. The mechanism of action, examples of their use, and advantages and disadvantages are described with the aim of providing a guide for the selection of suitable protocol for different studied situations.
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Safiarian MS, Watson RA, Lieberman RL, Barry BA, Offenbacher AR. E. coli Ribonucleotide Reductase β2 Subunit Inactivation by Triapine Occurs through Binding of a Triapine-Fe(II) Adduct. J Phys Chem Lett 2021; 12:9020-9025. [PMID: 34516127 DOI: 10.1021/acs.jpclett.1c02103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Ribonucleotide reductase (RNR), which supplies the building blocks for DNA biosynthesis and its repair, has been linked to human diseases and is emerging as a therapeutic target. Here, we present a mechanistic investigation of triapine (3AP), a clinically relevant small molecule that inhibits the tyrosyl radical within the RNR β2 subunit. Solvent kinetic isotope effects reveal that proton transfer is not rate-limiting for inhibition of Y122· of E. coli RNR β2 by the pertinent 3AP-Fe(II) adduct. Vibrational spectroscopy further demonstrates that unlike inhibition of the β2 tyrosyl radical by hydroxyurea, a carboxylate containing proton wire is not at play. Binding measurements reveal a low nanomolar affinity (Kd ∼ 6 nM) of 3AP-Fe(II) for β2. Taken together, these data should prompt further development of RNR inactivators based on the triapine scaffold for therapeutic applications.
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Affiliation(s)
- Mohammad S Safiarian
- Department of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - R Atlee Watson
- Department of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Raquel L Lieberman
- Department of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Bridgette A Barry
- Department of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Adam R Offenbacher
- Department of Chemistry, East Carolina University, Greenville, North Carolina 27858, United States
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34
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Nucleotide Pool Imbalance and Antibody Gene Diversification. Vaccines (Basel) 2021; 9:vaccines9101050. [PMID: 34696158 PMCID: PMC8538681 DOI: 10.3390/vaccines9101050] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/13/2021] [Accepted: 09/17/2021] [Indexed: 01/10/2023] Open
Abstract
The availability and adequate balance of deoxyribonucleoside triphosphate (dNTP) is an important determinant of both the fidelity and the processivity of DNA polymerases. Therefore, maintaining an optimal balance of the dNTP pool is critical for genomic stability in replicating and quiescent cells. Since DNA synthesis is required not only in genomic replication but also in DNA damage repair and recombination, the abnormalities in the dNTP pool affect a wide range of chromosomal activities. The generation of antibody diversity relies on antigen-independent V(D)J recombination, as well as antigen-dependent somatic hypermutation and class switch recombination. These processes involve diverse sets of DNA polymerases, which are affected by the dNTP pool imbalances. This review discusses the role of the optimal dNTP pool balance in the diversification of antibody encoding genes.
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Abstract
Radicals in biology, once thought to all be bad actors, are now known to play a central role in many enzymatic reactions. Of the known radical-based enzymes, ribonucleotide reductases (RNRs) are pre-eminent as they are essential in the biology of all organisms by providing the building blocks and controlling the fidelity of DNA replication and repair. Intense examination of RNRs has led to the development of new tools and a guiding framework for the study of radicals in biology, pointing the way to future frontiers in radical enzymology.
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Affiliation(s)
- JoAnne Stubbe
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 20139 USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 20139 USA
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138 USA
| | - Daniel G. Nocera
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138 USA
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36
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Ruskoski TB, Boal AK. The periodic table of ribonucleotide reductases. J Biol Chem 2021; 297:101137. [PMID: 34461093 PMCID: PMC8463856 DOI: 10.1016/j.jbc.2021.101137] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 08/20/2021] [Accepted: 08/26/2021] [Indexed: 12/30/2022] Open
Abstract
In most organisms, transition metal ions are necessary cofactors of ribonucleotide reductase (RNR), the enzyme responsible for biosynthesis of the 2'-deoxynucleotide building blocks of DNA. The metal ion generates an oxidant for an active site cysteine (Cys), yielding a thiyl radical that is necessary for initiation of catalysis in all RNRs. Class I enzymes, widespread in eukaryotes and aerobic microbes, share a common requirement for dioxygen in assembly of the active Cys oxidant and a unique quaternary structure, in which the metallo- or radical-cofactor is found in a separate subunit, β, from the catalytic α subunit. The first class I RNRs, the class Ia enzymes, discovered and characterized more than 30 years ago, were found to use a diiron(III)-tyrosyl-radical Cys oxidant. Although class Ia RNRs have historically served as the model for understanding enzyme mechanism and function, more recently, remarkably diverse bioinorganic and radical cofactors have been discovered in class I RNRs from pathogenic microbes. These enzymes use alternative transition metal ions, such as manganese, or posttranslationally installed tyrosyl radicals for initiation of ribonucleotide reduction. Here we summarize the recent progress in discovery and characterization of novel class I RNR radical-initiating cofactors, their mechanisms of assembly, and how they might function in the context of the active class I holoenzyme complex.
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Affiliation(s)
- Terry B Ruskoski
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Amie K Boal
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA; Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA.
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Schell E, Nouairia G, Steiner E, Weber N, Lundin D, Loderer C. Structural determinants and distribution of phosphate specificity in ribonucleotide reductases. J Biol Chem 2021; 297:101008. [PMID: 34314684 PMCID: PMC8365446 DOI: 10.1016/j.jbc.2021.101008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 11/24/2022] Open
Abstract
Ribonucleotide reductases (RNRs) catalyze the reduction of ribonucleotides to the corresponding deoxyribonucleotides, the building blocks of DNA. RNRs are specific for either ribonucleoside diphosphates or triphosphates as substrates. As far as is known, oxygen-dependent class I RNRs (NrdAB) all reduce ribonucleoside diphosphates, and oxygen-sensitive class III RNRs (NrdD) are all ribonucleoside triphosphate reducers, whereas the adenosylcobalamin-dependent class II (NrdJ) contains both ribonucleoside diphosphate and triphosphate reducers. However, it is unknown how this specificity is conveyed by the active site of the enzymes and how this feature developed in RNR evolution. By structural comparison of the active sites in different RNRs, we identified the apical loop of the phosphate-binding site as a potential structural determinant of substrate specificity. Grafting two residues from this loop from a diphosphate- to a triphosphate-specific RNR caused a change in preference from ribonucleoside triphosphate to diphosphate substrates in a class II model enzyme, confirming them as the structural determinants of phosphate specificity. The investigation of the phylogenetic distribution of this motif in class II RNRs yielded a likely monophyletic clade with the diphosphate-defining motif. This indicates a single evolutionary-split event early in NrdJ evolution in which diphosphate specificity developed from the earlier triphosphate specificity. For those interesting cases where organisms contain more than one nrdJ gene, we observed a preference for encoding enzymes with diverse phosphate specificities, suggesting that this varying phosphate specificity confers a selective advantage.
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Affiliation(s)
- Eugen Schell
- Institute for Microbiology, Technische Universität Dresden, Dresden, Saxony, Germany
| | - Ghada Nouairia
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Elisabeth Steiner
- Institute for Microbiology, Technische Universität Dresden, Dresden, Saxony, Germany
| | - Niclas Weber
- Institute for Microbiology, Technische Universität Dresden, Dresden, Saxony, Germany
| | - Daniel Lundin
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Christoph Loderer
- Institute for Microbiology, Technische Universität Dresden, Dresden, Saxony, Germany.
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38
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Hasan M, Banerjee I, Rozman Grinberg I, Sjöberg BM, Logan DT. Solution Structure of the dATP-Inactivated Class I Ribonucleotide Reductase From Leeuwenhoekiella blandensis by SAXS and Cryo-Electron Microscopy. Front Mol Biosci 2021; 8:713608. [PMID: 34381817 PMCID: PMC8350387 DOI: 10.3389/fmolb.2021.713608] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 06/21/2021] [Indexed: 01/14/2023] Open
Abstract
The essential enzyme ribonucleotide reductase (RNR) is highly regulated both at the level of overall activity and substrate specificity. Studies of class I, aerobic RNRs have shown that overall activity is downregulated by the binding of dATP to a small domain known as the ATP-cone often found at the N-terminus of RNR subunits, causing oligomerization that prevents formation of a necessary α2β2 complex between the catalytic (α2) and radical generating (β2) subunits. In some relatively rare organisms with RNRs of the subclass NrdAi, the ATP-cone is found at the N-terminus of the β subunit rather than more commonly the α subunit. Binding of dATP to the ATP-cone in β results in formation of an unusual β4 tetramer. However, the structural basis for how the formation of the active complex is hindered by such oligomerization has not been studied. Here we analyse the low-resolution three-dimensional structures of the separate subunits of an RNR from subclass NrdAi, as well as the α4β4 octamer that forms in the presence of dATP. The results reveal a type of oligomer not previously seen for any class of RNR and suggest a mechanism for how binding of dATP to the ATP-cone switches off catalysis by sterically preventing formation of the asymmetrical α2β2 complex.
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Affiliation(s)
- Mahmudul Hasan
- Biochemistry and Structural Biology, Dept. of Chemistry, Lund University, Lund, Sweden
| | - Ipsita Banerjee
- Biochemistry and Structural Biology, Dept. of Chemistry, Lund University, Lund, Sweden
| | | | - Britt-Marie Sjöberg
- Dept. of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Derek T Logan
- Biochemistry and Structural Biology, Dept. of Chemistry, Lund University, Lund, Sweden
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39
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Watson RA, Offenbacher AR, Barry BA. Detection of Catalytically Linked Conformational Changes in Wild-Type Class Ia Ribonucleotide Reductase Using Reaction-Induced FTIR Spectroscopy. J Phys Chem B 2021; 125:8362-8372. [PMID: 34289692 DOI: 10.1021/acs.jpcb.1c03038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The enzyme, ribonucleotide reductase (RNR), is essential for DNA synthesis in all cells. The class Ia Escherichia coli RNR consists of two dimeric subunits, α2 and β2, which form an active but unstable heterodimer of dimers, α2β2. The structure of the wild-type form of the enzyme has been challenging to study due to the instability of the catalytic complex. A long-range proton-coupled electron-transfer (PCET) pathway facilitates radical migration from the Y122 radical-diiron cofactor in the β subunit to an active site cysteine, C439, in the α subunit to initiate the RNR chemistry. The PCET reactions and active site chemistry are spectroscopically masked by a rate-limiting, conformational gate. Here, we present a reaction-induced Fourier transform infrared (RIFTIR) spectroscopic method to monitor the mechanism of the active, wild-type RNR α2β2 complex. This method is employed to obtain new information about conformational changes accompanying RNR catalysis, including the role of carboxylate interactions, deprotonation, and oxidation of active site cysteines, and a detailed description of reversible secondary structural changes. Labeling of tyrosine revealed a conformationally active tyrosine in the β subunit, assigned to Y356β, which is part of the intersubunit PCET pathway. New insights into the roles of the inhibitors, azidoUDP and dATP, and the sensitivity of RIFTIR spectroscopy to detect subtle conformational motions arising from protein allostery are also presented.
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Affiliation(s)
- Ryan Atlee Watson
- Department of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States
| | - Adam R Offenbacher
- Department of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States.,Department of Chemistry, East Carolina University, Greenville, North Carolina, United States
| | - Bridgette A Barry
- Department of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States
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40
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Hydroxyurea-The Good, the Bad and the Ugly. Genes (Basel) 2021; 12:genes12071096. [PMID: 34356112 PMCID: PMC8304116 DOI: 10.3390/genes12071096] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/13/2021] [Accepted: 07/16/2021] [Indexed: 01/23/2023] Open
Abstract
Hydroxyurea (HU) is mostly referred to as an inhibitor of ribonucleotide reductase (RNR) and as the agent that is commonly used to arrest cells in the S-phase of the cycle by inducing replication stress. It is a well-known and widely used drug, one which has proved to be effective in treating chronic myeloproliferative disorders and which is considered a staple agent in sickle anemia therapy and—recently—a promising factor in preventing cognitive decline in Alzheimer’s disease. The reversibility of HU-induced replication inhibition also makes it a common laboratory ingredient used to synchronize cell cycles. On the other hand, prolonged treatment or higher dosage of hydroxyurea causes cell death due to accumulation of DNA damage and oxidative stress. Hydroxyurea treatments are also still far from perfect and it has been suggested that it facilitates skin cancer progression. Also, recent studies have shown that hydroxyurea may affect a larger number of enzymes due to its less specific interaction mechanism, which may contribute to further as-yet unspecified factors affecting cell response. In this review, we examine the actual state of knowledge about hydroxyurea and the mechanisms behind its cytotoxic effects. The practical applications of the recent findings may prove to enhance the already existing use of the drug in new and promising ways.
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41
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Hoetzinger M, Nilsson E, Arabi R, Osbeck CMG, Pontiller B, Hutinet G, Bayfield OW, Traving S, Kisand V, Lundin D, Pinhassi J, Middelboe M, Holmfeldt K. Dynamics of Baltic Sea phages driven by environmental changes. Environ Microbiol 2021; 23:4576-4594. [PMID: 34190387 DOI: 10.1111/1462-2920.15651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 06/11/2021] [Indexed: 11/29/2022]
Abstract
Phage predation constitutes a major mortality factor for bacteria in aquatic ecosystems, and thus, directly impacts nutrient cycling and microbial community dynamics. Yet, the population dynamics of specific phages across time scales from days to months remain largely unexplored, which limits our understanding of their influence on microbial succession. To investigate temporal changes in diversity and abundance of phages infecting particular host strains, we isolated 121 phage strains that infected three bacterial hosts during a Baltic Sea mesocosm experiment. Genome analysis revealed a novel Flavobacterium phage genus harboring gene sets putatively coding for synthesis of modified nucleotides and glycosylation of bacterial cell surface components. Another novel phage genus revealed a microdiversity of phage species that was largely maintained during the experiment and across mesocosms amended with different nutrients. In contrast to the newly described Flavobacterium phages, phages isolated from a Rheinheimera strain were highly similar to previously isolated genotypes, pointing to genomic consistency in this population. In the mesocosm experiment, the investigated phages were mainly detected after a phytoplankton bloom peak. This concurred with recurrent detection of the phages in the Baltic Proper during summer months, suggesting an influence on the succession of heterotrophic bacteria associated with phytoplankton blooms.
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Affiliation(s)
- Matthias Hoetzinger
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Emelie Nilsson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Rahaf Arabi
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Christofer M G Osbeck
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Benjamin Pontiller
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Geoffrey Hutinet
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
| | - Oliver W Bayfield
- York Structural Biology Laboratory, Department of Chemistry, University of York, York, UK
| | - Sachia Traving
- Nordcee and HADAL, Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Veljo Kisand
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Daniel Lundin
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Mathias Middelboe
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Karin Holmfeldt
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
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42
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Desrosiers V, Barat C, Breton Y, Ouellet M, Tremblay MJ. Thymidylate synthase is essential for efficient HIV-1 replication in macrophages. Virology 2021; 561:47-57. [PMID: 34146963 DOI: 10.1016/j.virol.2021.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/09/2021] [Accepted: 05/05/2021] [Indexed: 11/18/2022]
Abstract
Thymidylate synthase (TS) is a key enzyme in nucleotide biosynthesis. A study performed by our group on human monocyte-derived macrophages (MDMs) infected with HIV-1 showed that many enzymes related to the folate cycle pathway, such as TS, are upregulated in productively infected cells. Here, we suggest that TS is essential for an effective HIV-1 infection in MDMs. Indeed, a TS specific small interfering RNA (siRNA) as well as the TS specific inhibitor Raltitrexed (RTX) caused a reduction in productively infected cells. Quantitative PCR analysis showed that this treatment decreased the efficacy of the early steps of the viral cycle. The RTX inhibitory effect was counteracted by dNTP addition. These results suggest that TS is essential for the early stages of HIV-1 infection by providing optimal dNTP concentrations in MDMs. TS and its related pathway may thus be considered as a potential therapeutic target for HIV-1 treatment.
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Affiliation(s)
- Vincent Desrosiers
- Axe des Maladies Infectieuses et Immunitaires, Centre de Recherche Du CHU de Québec-Université Laval, Pavillon CHUL, Québec, QC, G1V 4G2, Canada
| | - Corinne Barat
- Axe des Maladies Infectieuses et Immunitaires, Centre de Recherche Du CHU de Québec-Université Laval, Pavillon CHUL, Québec, QC, G1V 4G2, Canada
| | - Yann Breton
- Axe des Maladies Infectieuses et Immunitaires, Centre de Recherche Du CHU de Québec-Université Laval, Pavillon CHUL, Québec, QC, G1V 4G2, Canada
| | - Michel Ouellet
- Axe des Maladies Infectieuses et Immunitaires, Centre de Recherche Du CHU de Québec-Université Laval, Pavillon CHUL, Québec, QC, G1V 4G2, Canada
| | - Michel J Tremblay
- Axe des Maladies Infectieuses et Immunitaires, Centre de Recherche Du CHU de Québec-Université Laval, Pavillon CHUL, Québec, QC, G1V 4G2, Canada; Département de Microbiologie-infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, QC, G1V 0A6, Canada.
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43
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Ravindranath BS, Vishnu Vinayak S, Chandra Mohan V. RNR inhibitor binding studies of Chlamydia felis: insights from in silico molecular modeling, docking, and simulation studies. J Biomol Struct Dyn 2021; 40:9416-9428. [PMID: 34032189 DOI: 10.1080/07391102.2021.1930160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Chlamydia felis is the primary cause of chronic conjunctivitis without respiratory infections in cats, making conjunctiva as its primary target. It is a Gram-negative obligate intracellular bacterium that cannot survive outside the host cell. C. felis can be found worldwide and its zoonotic potential is a known phenomenon. The scope of zoonoses, its scale, and their impact experiencing today has no historical precedence. Among the identified 1415 human pathogens 868 have a zoonotic origin making it to 61%. Although with appropriate drug administration there are instances of re-occurrence of chlamydial infections, the emergence of heterotypic antimicrobial resistance to antibiotics targeting rRNA due to mutations has further complicated the diagnosis and treatment of chlamydial infections. Ribonucleotide-diphosphate reductase subunit beta (RNR) is one of the crucial target proteins of the bacterial pathogens essential in the synthesis of deoxyribonucleotides. Our current study primarily focuses on modeling the target structure through homology modeling. Further, the validated model is complexed with the specific inhibitor Cladribine through sequence-based ligand search. Docking of the identified ligand was performed to identify the different modes of interactions with amino acids present in the prioritized binding pockets. Validation of the binding modes is carried out through molecular dynamics (MD) simulations for the best binding pose with a high binding score. MD simulation study demonstrated the stability of the docked complex considered in this study. The findings from this study may be helpful in drug repurposing and novel drug research in the scenario of resistance to currently practiced antibiotics.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- B S Ravindranath
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - S Vishnu Vinayak
- Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Vivek Chandra Mohan
- Department of Biotechnology, Siddaganga Institute of Technology, Tumkur, Karnataka, India
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44
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Alqurashi A, Alfs L, Swann J, Butt JN, Kelly DJ. The flavodoxin FldA activates the class Ia ribonucleotide reductase of Campylobacter jejuni. Mol Microbiol 2021; 116:343-358. [PMID: 33721378 DOI: 10.1111/mmi.14715] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 03/11/2021] [Indexed: 11/30/2022]
Abstract
Campylobacter jejuni is a microaerophilic zoonotic pathogen with an atypical respiratory Complex I that oxidizes a flavodoxin (FldA) instead of NADH. FldA is essential for viability and is reduced via pyruvate and 2-oxoglutarate oxidoreductases (POR/OOR). Here, we show that FldA can also be reduced by FqrB (Cj0559), an NADPH:FldA reductase. An fqrB deletion mutant was viable but displayed a significant growth defect. FqrB is related to flavoprotein reductases from Gram-positive bacteria that can reduce NrdI, a specialized flavodoxin that is needed for tyrosyl radical formation in NrdF, the beta subunit of class 1b-type (Mn) ribonucleotide reductase (RNR). However, C. jejuni possesses a single class Ia-type (Fe) RNR (NrdAB) that would be expected to be ferredoxin dependent. We show that CjFldA is an unusually high potential flavodoxin unrelated to NrdI, yet growth of the fqrB mutant, but not the wild-type or a complemented strain, was stimulated by low deoxyribonucleoside (dRNS) concentrations, suggesting FldA links FqrB and RNR activity. Using purified proteins, we confirmed the NrdB tyrosyl radical could be regenerated in an NADPH, FqrB, and FldA dependent manner, as evidenced by both optical and electron paramagnetic resonance (EPR) spectroscopy. Thus, FldA activates RNR in C. jejuni, partly explaining its essentiality.
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Affiliation(s)
- Abdulmajeed Alqurashi
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, UK
| | - Laura Alfs
- School of Chemistry, University of East Anglia, Norwich, UK
| | - Jordan Swann
- School of Chemistry, University of East Anglia, Norwich, UK
| | - Julea N Butt
- School of Chemistry, University of East Anglia, Norwich, UK
| | - David J Kelly
- Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield, UK
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45
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Cui C, Greene BL, Kang G, Drennan CL, Stubbe J, Nocera DG. Gated Proton Release during Radical Transfer at the Subunit Interface of Ribonucleotide Reductase. J Am Chem Soc 2020; 143:176-183. [PMID: 33353307 DOI: 10.1021/jacs.0c07879] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The class Ia ribonucleotide reductase of Escherichia coli requires strict regulation of long-range radical transfer between two subunits, α and β, through a series of redox-active amino acids (Y122•[β] ↔ W48?[β] ↔ Y356[β] ↔ Y731[α] ↔ Y730[α] ↔ C439[α]). Nowhere is this more precarious than at the subunit interface. Here, we show that the oxidation of Y356 is regulated by proton release involving a specific residue, E52[β], which is part of a water channel at the subunit interface for rapid proton transfer to the bulk solvent. An E52Q variant is incapable of Y356 oxidation via the native radical transfer pathway or non-native photochemical oxidation, following photosensitization by covalent attachment of a photo-oxidant at position 355[β]. Substitution of Y356 for various FnY analogues in an E52Q-photoβ2, where the side chain remains deprotonated, recovered photochemical enzymatic turnover. Transient absorption and emission data support the conclusion that Y356 oxidation requires E52 for proton management, suggesting its essential role in gating radical transport across the protein-protein interface.
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Affiliation(s)
- Chang Cui
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Brandon L Greene
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Gyunghoon Kang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 20139, United States.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 20139, United States
| | - Catherine L Drennan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 20139, United States.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 20139, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 20139, United States.,Fellow, Bio-inspired Solar Energy Program, Canadian Institute for Advanced Research, Toronto, Ontario M5G 1M1, Canada
| | - JoAnne Stubbe
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 20139, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 20139, United States
| | - Daniel G Nocera
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, United States
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46
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Hemmadi V, Biswas M. An overview of moonlighting proteins in Staphylococcus aureus infection. Arch Microbiol 2020; 203:481-498. [PMID: 33048189 PMCID: PMC7551524 DOI: 10.1007/s00203-020-02071-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 09/29/2020] [Accepted: 10/01/2020] [Indexed: 01/01/2023]
Abstract
Staphylococcus aureus is responsible for numerous instances of superficial, toxin-mediated, and invasive infections. The emergence of methicillin-resistant (MRSA), as well as vancomycin-resistant (VRSA) strains of S. aureus, poses a massive threat to human health. The tenacity of S. aureus to acquire resistance against numerous antibiotics in a very short duration makes the effort towards developing new antibiotics almost futile. S. aureus owes its destructive pathogenicity to the plethora of virulent factors it produces among which a majority of them are moonlighting proteins. Moonlighting proteins are the multifunctional proteins in which a single protein, with different oligomeric conformations, perform multiple independent functions in different cell compartments. Peculiarly, proteins involved in key ancestral functions and metabolic pathways typically exhibit moonlighting functions. Pathogens mainly employ those proteins as virulent factors which exhibit high structural conservation towards their host counterparts. Consequentially, the host immune system counteracts these invading bacterial virulent factors with minimal protective action. Additionally, many moonlighting proteins also play multiple roles in various stages of pathogenicity while augmenting the virulence of the bacterium. This has necessitated elaborative studies to be conducted on moonlighting proteins of S. aureus that can serve as drug targets. This review is a small effort towards understanding the role of various moonlighting proteins in the pathogenicity of S. aureus.
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Affiliation(s)
- Vijay Hemmadi
- Department of Biological Sciences, Birla Institute of Technology and Science, BITS-Pilani, K. K. Birla Goa Campus, NH17B, Zuarinagar, Goa, 403726, India
| | - Malabika Biswas
- Department of Biological Sciences, Birla Institute of Technology and Science, BITS-Pilani, K. K. Birla Goa Campus, NH17B, Zuarinagar, Goa, 403726, India.
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47
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Berndt C, Christ L, Rouhier N, Mühlenhoff U. Glutaredoxins with iron-sulphur clusters in eukaryotes - Structure, function and impact on disease. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1862:148317. [PMID: 32980338 DOI: 10.1016/j.bbabio.2020.148317] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 09/07/2020] [Accepted: 09/18/2020] [Indexed: 12/12/2022]
Abstract
Among the thioredoxin superfamily of proteins, the observation that numerous glutaredoxins bind iron-sulphur (Fe/S) clusters is one of the more recent and major developments concerning their functional properties. Glutaredoxins are present in most organisms. All members of the class II subfamily (including most monothiol glutaredoxins), but also some members of the class I (mostly dithiol glutaredoxins) and class III (land plant-specific monothiol or dithiol glutaredoxins) are Fe/S proteins. In glutaredoxins characterised so far, the [2Fe2S] cluster is coordinated by two active-site cysteine residues and two molecules of non-covalently bound glutathione in homo-dimeric complexes bridged by the cluster. In contrast to dithiol glutaredoxins, monothiol glutaredoxins possess no or very little oxidoreductase activity, but have emerged as important players in cellular iron metabolism. In this review we summarise the recent developments of the most prominent Fe/S glutaredoxins in eukaryotes, the mitochondrial single domain monothiol glutaredoxin 5, the chloroplastic single domain monothiol glutaredoxin S14 and S16, the nuclear/cytosolic multi-domain monothiol glutaredoxin 3, and the mitochondrial/cytosolic dithiol glutaredoxin 2.
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Affiliation(s)
- Carsten Berndt
- Department of Neurology, Medical Faculty, Heinrich-Heine University, Merowingerplatz1a, 40225 Düsseldorf, Germany
| | - Loïck Christ
- Université de Lorraine, INRAE, IAM, F-54000 Nancy, France
| | | | - Ulrich Mühlenhoff
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität Marburg, Robert-Koch Str. 6, 35032 Marburg, Germany.
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48
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Martínez-Carranza M, Jonna VR, Lundin D, Sahlin M, Carlson LA, Jemal N, Högbom M, Sjöberg BM, Stenmark P, Hofer A. A ribonucleotide reductase from Clostridium botulinum reveals distinct evolutionary pathways to regulation via the overall activity site. J Biol Chem 2020; 295:15576-15587. [PMID: 32883811 DOI: 10.1074/jbc.ra120.014895] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/02/2020] [Indexed: 01/05/2023] Open
Abstract
Ribonucleotide reductase (RNR) is a central enzyme for the synthesis of DNA building blocks. Most aerobic organisms, including nearly all eukaryotes, have class I RNRs consisting of R1 and R2 subunits. The catalytic R1 subunit contains an overall activity site that can allosterically turn the enzyme on or off by the binding of ATP or dATP, respectively. The mechanism behind the ability to turn the enzyme off via the R1 subunit involves the formation of different types of R1 oligomers in most studied species and R1-R2 octamers in Escherichia coli To better understand the distribution of different oligomerization mechanisms, we characterized the enzyme from Clostridium botulinum, which belongs to a subclass of class I RNRs not studied before. The recombinantly expressed enzyme was analyzed by size-exclusion chromatography, gas-phase electrophoretic mobility macromolecular analysis, EM, X-ray crystallography, and enzyme assays. Interestingly, it shares the ability of the E. coli RNR to form inhibited R1-R2 octamers in the presence of dATP but, unlike the E. coli enzyme, cannot be turned off by combinations of ATP and dGTP/dTTP. A phylogenetic analysis of class I RNRs suggests that activity regulation is not ancestral but was gained after the first subclasses diverged and that RNR subclasses with inhibition mechanisms involving R1 oligomerization belong to a clade separated from the two subclasses forming R1-R2 octamers. These results give further insight into activity regulation in class I RNRs as an evolutionarily dynamic process.
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Affiliation(s)
| | | | - Daniel Lundin
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Margareta Sahlin
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Lars-Anders Carlson
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden; Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Newal Jemal
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Britt-Marie Sjöberg
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Pål Stenmark
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden; Department of Experimental Medical Science, Lund University, Lund, Sweden.
| | - Anders Hofer
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden.
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49
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Song Y, Shvartsman SY. Chemical Embryology Redux: Metabolic Control of Development. Trends Genet 2020; 36:577-586. [PMID: 32532533 PMCID: PMC10947471 DOI: 10.1016/j.tig.2020.05.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 05/14/2020] [Accepted: 05/18/2020] [Indexed: 11/16/2022]
Abstract
New studies of metabolic reactions and networks in embryos are making important additions to regulatory models of development, so far dominated by genes and signals. Metabolic control of development is not a new idea and can be traced back to Joseph Needham's 'Chemical Embryology', published in the 1930s. Even though Needham's ideas fell by the wayside with the advent of genetic studies of embryogenesis, they demonstrated that embryos provide convenient models for addressing fundamental questions in biochemistry and are now experiencing a comeback, enabled by the powerful merger of detailed mechanistic studies and systems-level techniques. Here we review recent results from studies that quantified the energy budget of embryogenesis in Drosophila and started to untangle the intricate connections between core anabolic processes and developmental transitions. Dynamic coordination of metabolic, genetic, and signaling networks appears to be essential for seamless progression of development.
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Affiliation(s)
- Yonghyun Song
- Computational Sciences Department, Korea Institute for Advanced Study, Seoul 02455, Republic of Korea
| | - Stanislav Y Shvartsman
- The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA; Center for Computational Biology, Flatiron Institute - Simons Foundation, New York, NY 10010, USA.
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50
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Reinhardt CR, Li P, Kang G, Stubbe J, Drennan CL, Hammes-Schiffer S. Conformational Motions and Water Networks at the α/β Interface in E. coli Ribonucleotide Reductase. J Am Chem Soc 2020; 142:13768-13778. [PMID: 32631052 DOI: 10.1021/jacs.0c04325] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Ribonucleotide reductases (RNRs) catalyze the conversion of all four ribonucleotides to deoxyribonucleotides and are essential for DNA synthesis in all organisms. The active form of E. coli Ia RNR is composed of two homodimers that form the active α2β2 complex. Catalysis is initiated by long-range radical translocation over a ∼32 Å proton-coupled electron transfer (PCET) pathway involving Y356β and Y731α at the interface. Resolving the PCET pathway at the α/β interface has been a long-standing challenge due to the lack of structural data. Herein, molecular dynamics simulations based on a recently solved cryogenic-electron microscopy structure of an active α2β2 complex are performed to examine the structure and fluctuations of interfacial water, as well as the hydrogen-bonding interactions and conformational motions of interfacial residues along the PCET pathway. Our free energy simulations reveal that Y731 is able to sample both a flipped-out conformation, where it points toward the interface to facilitate interfacial PCET with Y356, and a stacked conformation with Y730 to enable collinear PCET with this residue. Y356 and Y731 exhibit hydrogen-bonding interactions with interfacial water molecules and, in some conformations, share a bridging water molecule, suggesting that the primary proton acceptor for PCET from Y356 and from Y731 is interfacial water. The conformational flexibility of Y731 and the hydrogen-bonding interactions of both Y731 and Y356 with interfacial water and hydrogen-bonded water chains appear critical for effective radical translocation along the PCET pathway. These simulations are consistent with biochemical and spectroscopic data and provide previously unattainable atomic-level insights into the fundamental mechanism of RNR.
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Affiliation(s)
- Clorice R Reinhardt
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven Connecticut 06520, United States
| | - Pengfei Li
- Department of Chemistry, Yale University, New Haven Connecticut 06520, United States
| | - Gyunghoon Kang
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States
| | - JoAnne Stubbe
- Department of Biology, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States
| | - Catherine L Drennan
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States.,Fellow, Bio-inspired Solar Energy Program, Canadian Institute for Advanced Research (CIFAR), Toronto, ON M5G 1M1, Canada
| | - Sharon Hammes-Schiffer
- Department of Chemistry, Yale University, New Haven Connecticut 06520, United States.,Fellow, Bio-inspired Solar Energy Program, Canadian Institute for Advanced Research (CIFAR), Toronto, ON M5G 1M1, Canada
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