1
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Su L, Wang X, Wang J, Luh F, Yen Y. Impact of N221S missense mutation in human ribonucleotide reductase small subunit b on mitochondrial DNA depletion syndrome. Sci Rep 2023; 13:19899. [PMID: 37964013 PMCID: PMC10645729 DOI: 10.1038/s41598-023-47284-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 11/11/2023] [Indexed: 11/16/2023] Open
Abstract
The impact of N221S mutation in hRRM2B gene, which encodes the small subunit of human ribonucleotide reductase (RNR), on RNR activity and the pathogenesis of mitochondrial DNA depletion syndrome (MDDS) was investigated. Our results demonstrate that N221 mutations significantly reduce RNR activity, suggesting its role in the development of MDDS. We proposed an allosteric regulation pathway involving a chain of three phenylalanine residues on the αE helix of RNR small subunit β. This pathway connects the C-terminal loop of β2, transfers the activation signal from the large catalytic subunit α to β active site, and controls access of oxygen for radical generation. N221 is near this pathway and likely plays a role in regulating RNR activity. Mutagenesis studies on residues involved in the phenylalanine chain and the regulation pathway were conducted to confirm our proposed mechanism. We also performed molecular dynamic simulation and protein contact network analysis to support our findings. This study sheds new light on RNR small subunit regulation and provides insight on the pathogenesis of MDDS.
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Affiliation(s)
- Leila Su
- Sino-American Cancer Foundation, Covina, CA, 91722, USA
| | - Xin Wang
- Sino-American Cancer Foundation, Covina, CA, 91722, USA
| | - Jianghai Wang
- Sino-American Cancer Foundation, Covina, CA, 91722, USA
| | - Frank Luh
- Sino-American Cancer Foundation, Covina, CA, 91722, USA
| | - Yun Yen
- Ph.D. Program for Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, 250 Wu-Hsing Street, Taipei, 110301, Taiwan.
- Center for Cancer Translational Research, Tzu Chi University, Hualien, 970374, Taiwan.
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2
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Alqahtani SS, Koltai T, Ibrahim ME, Bashir AHH, Alhoufie STS, Ahmed SBM, Molfetta DD, Carvalho TMA, Cardone RA, Reshkin SJ, Hifny A, Ahmed ME, Alfarouk KO. Role of pH in Regulating Cancer Pyrimidine Synthesis. J Xenobiot 2022; 12:158-180. [PMID: 35893264 PMCID: PMC9326563 DOI: 10.3390/jox12030014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 06/17/2022] [Accepted: 06/28/2022] [Indexed: 11/18/2022] Open
Abstract
Replication is a fundamental aspect of cancer, and replication is about reproducing all the elements and structures that form a cell. Among them are DNA, RNA, enzymes, and coenzymes. All the DNA is doubled during each S (synthesis) cell cycle phase. This means that six billion nucleic acids must be synthesized in each cycle. Tumor growth, proliferation, and mutations all depend on this synthesis. Cancer cells require a constant supply of nucleotides and other macromolecules. For this reason, they must stimulate de novo nucleotide synthesis to support nucleic acid provision. When deregulated, de novo nucleic acid synthesis is controlled by oncogenes and tumor suppressor genes that enable increased synthesis and cell proliferation. Furthermore, cell duplication must be achieved swiftly (in a few hours) and in the midst of a nutrient-depleted and hypoxic environment. This also means that the enzymes participating in nucleic acid synthesis must work efficiently. pH is a critical factor in enzymatic efficiency and speed. This review will show that the enzymatic machinery working in nucleic acid synthesis requires a pH on the alkaline side in most cases. This coincides with many other pro-tumoral factors, such as the glycolytic phenotype, benefiting from an increased intracellular pH. An increased intracellular pH is a perfect milieu for high de novo nucleic acid production through optimal enzymatic performance.
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Affiliation(s)
- Saad Saeed Alqahtani
- Department of Pharmacy Practice, College of Pharmacy, Jazan University, Jazan 45142, Saudi Arabia;
- Pharmacy Practice Research Unit, College of Pharmacy, Jazan University, Jazan 45142, Saudi Arabia
| | | | - Muntaser E. Ibrahim
- Department of Molecular Biology, Institute of Endemic Diseases, University of Khartoum, Khartoum 11111, Sudan; (M.E.I.); (A.H.H.B.)
| | - Adil H. H. Bashir
- Department of Molecular Biology, Institute of Endemic Diseases, University of Khartoum, Khartoum 11111, Sudan; (M.E.I.); (A.H.H.B.)
| | - Sari T. S. Alhoufie
- Medical Laboratories Technology Department, College of Applied Medical Sciences, Taibah University, Medina 42353, Saudi Arabia;
| | - Samrein B. M. Ahmed
- Department of Biosciences and Chemistry, College of Health, Wellbeing and Life Sciences, Sheffield Hallam University, Sheffield S1 1WB, UK;
| | - Daria Di Molfetta
- Department of Biosciences, Biotechnologies, and Biopharmaceutics, University of Bari, 70126 Bari, Italy; (D.D.M.); (T.M.A.C.); (R.A.C.); (S.J.R.)
| | - Tiago M. A. Carvalho
- Department of Biosciences, Biotechnologies, and Biopharmaceutics, University of Bari, 70126 Bari, Italy; (D.D.M.); (T.M.A.C.); (R.A.C.); (S.J.R.)
| | - Rosa Angela Cardone
- Department of Biosciences, Biotechnologies, and Biopharmaceutics, University of Bari, 70126 Bari, Italy; (D.D.M.); (T.M.A.C.); (R.A.C.); (S.J.R.)
| | - Stephan Joel Reshkin
- Department of Biosciences, Biotechnologies, and Biopharmaceutics, University of Bari, 70126 Bari, Italy; (D.D.M.); (T.M.A.C.); (R.A.C.); (S.J.R.)
| | | | - Mohamed E. Ahmed
- Research Center, Zamzam University College, Khartoum 11123, Sudan;
| | - Khalid Omer Alfarouk
- Research Center, Zamzam University College, Khartoum 11123, Sudan;
- Alfarouk Biomedical Research LLC, Temple Terrace, FL 33617, USA
- Hala Alfarouk Cancer Center, Khartoum 11123, Sudan
- Correspondence:
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3
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Iqbal W, Demidova EV, Serrao S, ValizadehAslani T, Rosen G, Arora S. RRM2B Is Frequently Amplified Across Multiple Tumor Types: Implications for DNA Repair, Cellular Survival, and Cancer Therapy. Front Genet 2021; 12:628758. [PMID: 33868369 PMCID: PMC8045241 DOI: 10.3389/fgene.2021.628758] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 02/23/2021] [Indexed: 01/21/2023] Open
Abstract
RRM2B plays a crucial role in DNA replication, repair and oxidative stress. While germline RRM2B mutations have been implicated in mitochondrial disorders, its relevance to cancer has not been established. Here, using TCGA studies, we investigated RRM2B alterations in cancer. We found that RRM2B is highly amplified in multiple tumor types, particularly in MYC-amplified tumors, and is associated with increased RRM2B mRNA expression. We also observed that the chromosomal region 8q22.3–8q24, is amplified in multiple tumors, and includes RRM2B, MYC along with several other cancer-associated genes. An analysis of genes within this 8q-amplicon showed that cancers that have both RRM2B-amplified along with MYC have a distinct pattern of amplification compared to cancers that are unaltered or those that have amplifications in RRM2B or MYC only. Investigation of curated biological interactions revealed that gene products of the amplified 8q22.3–8q24 region have important roles in DNA repair, DNA damage response, oxygen sensing, and apoptosis pathways and interact functionally. Notably, RRM2B-amplified cancers are characterized by mutation signatures of defective DNA repair and oxidative stress, and at least RRM2B-amplified breast cancers are associated with poor clinical outcome. These data suggest alterations in RR2MB and possibly the interacting 8q-proteins could have a profound effect on regulatory pathways such as DNA repair and cellular survival, highlighting therapeutic opportunities in these cancers.
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Affiliation(s)
- Waleed Iqbal
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, United States.,School of Biomedical Engineering, Science and Health Systems, Drexel University College of Engineering, Philadelphia, PA, United States
| | - Elena V Demidova
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, United States.,Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Samantha Serrao
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, United States.,Department of Epidemiology and Biostatistics, Dornsife School of Public Health, Drexel University, Philadelphia, PA, United States
| | - Taha ValizadehAslani
- Department of Electrical and Computer Engineering, College of Engineering, Drexel University, Philadelphia, PA, United States
| | - Gail Rosen
- Department of Electrical and Computer Engineering, College of Engineering, Drexel University, Philadelphia, PA, United States
| | - Sanjeevani Arora
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, United States.,Department of Radiation Oncology, Fox Chase Cancer Center, Philadelphia, PA, United States
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4
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Tseng YT, Li SW, HuangFu WC, Yen Y, Liu IH. The single nucleotide variant at c.662A>G in human RRM2B is a loss-of-function mutation. Mol Genet Genomic Med 2020; 8:e1497. [PMID: 32931159 PMCID: PMC7667293 DOI: 10.1002/mgg3.1497] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 08/14/2020] [Accepted: 08/21/2020] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Mitochondrial DNA maintenance defects (MDMDs) is one of the critical pediatric dysfunction. One of the recent report indicated that a severe patient of MDMDs carries the NP_056528.2:p.Asn221Ser (N221S) variation in the RRM2B gene (NM_015713.5). However, there is no direct evidence demonstrating the nature of the N221S variation. MATERIALS AND METHODS This study aimed to utilize zebrafish and morpholino oligomer (MO) knockdown technique to provide direct evidence for the nature of the N221S variation in the RRM2B. RESULTS The results showed that two distinct MOs were both able to perturb the expression of rrm2b in zebrafish and dose-dependently induced morphological defects. Furthermore, co-injection of human wild-type RRM2B mRNA with MO-e4i4 successfully rescued the developmental defects, whereas co-injection of RRM2B/N221S mRNA with MO-e4i4 did not rescue the developmental defects. CONCLUSION In conclusion, the functional assay in this study provided the direct evidence proving that the N221S variation is a loss-of-function mutation and plausibly related to the pathogenic developmental defects found in the infants of previous clinical reports.
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Affiliation(s)
- Yen-Tzu Tseng
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Shang-Wei Li
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan.,Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Wei-Chun HuangFu
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan.,Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Yun Yen
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan.,Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan.,TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei, Taiwan.,Cancer Center, Taipei Municipal WanFang Hospital, Taipei, Taiwan
| | - I-Hsuan Liu
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan.,Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan.,School of Veterinary Medicine, National Taiwan University, Taipei, Taiwan
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5
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Roberts L, Julius S, Dawlat S, Yildiz S, Rebello G, Meldau S, Pillay K, Esterhuizen A, Vorster A, Benefeld G, da Rocha J, Beighton P, Sellars SL, Thandrayen K, Pettifor JM, Ramesar RS. Renal dysfunction, rod-cone dystrophy, and sensorineural hearing loss caused by a mutation in RRM2B. Hum Mutat 2020; 41:1871-1876. [PMID: 32827185 DOI: 10.1002/humu.24094] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 08/03/2020] [Accepted: 08/14/2020] [Indexed: 12/29/2022]
Abstract
More than two decades ago, a recessive syndromic phenotype affecting kidneys, eyes, and ears, was first described in the endogamous Afrikaner population of South Africa. Using whole-exome sequencing of DNA from two affected siblings (and their carrier parents), we identified the novel RRM2B c.786G>T variant as a plausible disease-causing mutation. The RRM2B gene is involved in mitochondrial integrity, and the observed change was not previously reported in any genomic database. The subsequent screening revealed the variant in two newly presenting unrelated patients, as well as two patients in our registry with rod-cone dystrophy, hearing loss, and Fanconi-type renal disease. All patients with the c.786G>T variant share an identical 1.5 Mb haplotype around this gene, suggesting a founder effect in the Afrikaner population. We present ultrastructural evidence of mitochondrial impairment in one patient, to support our thesis that this RRM2B variant is associated with the renal, ophthalmological, and auditory phenotype.
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Affiliation(s)
- Lisa Roberts
- UCT/MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Stephanie Julius
- UCT/MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Shrinav Dawlat
- Department of Human Genetics, National Health Laboratory Servicexs, Groote Schuur Hospital, Cape Town, South Africa
| | - Safiye Yildiz
- UCT/MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - George Rebello
- UCT/MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Surita Meldau
- Department of Human Genetics, National Health Laboratory Servicexs, Groote Schuur Hospital, Cape Town, South Africa.,Division of Chemical Pathology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Komala Pillay
- Division of Anatomical Pathology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Alina Esterhuizen
- UCT/MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Department of Human Genetics, National Health Laboratory Servicexs, Groote Schuur Hospital, Cape Town, South Africa
| | - Alvera Vorster
- UCT/MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Gameda Benefeld
- UCT/MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Jorge da Rocha
- Sydney Brenner Institute for Molecular Bioscience, Division of Human Genetics, National Health Laboratory Service, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Peter Beighton
- UCT/MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Sean L Sellars
- Division of Otorhinolaryngology, Department of Surgery, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Kebashni Thandrayen
- Department of Paediatrics, Chris Hani Baragwanath Academic Hospital and School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - John M Pettifor
- Department of Paediatrics, Chris Hani Baragwanath Academic Hospital and School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Raj S Ramesar
- UCT/MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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6
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Prediction of the Impact of Deleterious Nonsynonymous Single Nucleotide Polymorphisms on the Human RRM2B Gene: A Molecular Modeling Study. BIOMED RESEARCH INTERNATIONAL 2020; 2020:7614634. [PMID: 32775440 PMCID: PMC7399733 DOI: 10.1155/2020/7614634] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/04/2020] [Accepted: 07/06/2020] [Indexed: 01/19/2023]
Abstract
RRM2B gene encodes ribonucleoside-diphosphate reductase subunit M2 B, the p53-inducible small subunit (p53R2) of ribonucleotide reductase (RNR), an enzyme catalyzing dNTP synthesis for mitochondrial DNA. Defects in this gene may cause severe mitochondrial disease affecting mainly the nervous system. This study is aimed at examining the effect of deleterious nonsynonymous SNP (nsSNP) on the structure of the RRM2B protein, using a variety of prediction tools followed by a molecular modeling analysis. After using 13 algorithms, 19 nsSNPs were predicted deleterious. Among these variants, 18 decreased the protein stability and 16 were localized in very highly conserved regions. Protein 3D structure analysis showed that 18 variants changed amino acid interactions. These results concur with what has been found in experimental trials; 7 deleterious nsSNPs were previously reported in patients suffering from genetic disorders affecting the nervous system. Thus, our study will provide useful information to design more efficient and fast genetic tests to find RRM2B gene mutations.
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7
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The natural history of infantile mitochondrial DNA depletion syndrome due to RRM2B deficiency. Genet Med 2019; 22:199-209. [DOI: 10.1038/s41436-019-0613-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 07/09/2019] [Indexed: 01/21/2023] Open
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8
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Valdebenito-Maturana B, Reyes-Suarez JA, Henriquez J, Holmes DS, Quatrini R, Pohl E, Arenas-Salinas M. Mutantelec: An In Silico mutation simulation platform for comparative electrostatic potential profiling of proteins. J Comput Chem 2018; 38:467-474. [PMID: 28114729 DOI: 10.1002/jcc.24712] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 12/06/2016] [Accepted: 12/07/2016] [Indexed: 11/07/2022]
Abstract
The electrostatic potential plays a key role in many biological processes like determining the affinity of a ligand to a given protein target, and they are responsible for the catalytic activity of many enzymes. Understanding the effect that amino acid mutations will have on the electrostatic potential of a protein, will allow a thorough understanding of which residues are the most important in a protein. MutantElec, is a friendly web application for in silico generation of site-directed mutagenesis of proteins and the comparison of electrostatic potential between the wild type protein and the mutant(s), based on the three-dimensional structure of the protein. The effect of the mutation is evaluated using different approach to the traditional surface map. MutantElec provides a graphical display of the results that allows the visualization of changes occurring at close distance from the mutation and thus uncovers the local and global impact of a specific change. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Braulio Valdebenito-Maturana
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, Talca, 346 5548, Chile
| | - Jose Antonio Reyes-Suarez
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, Talca, 346 5548, Chile
| | - Jaime Henriquez
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, Talca, 346 5548, Chile
| | - David S Holmes
- Fundación Ciencia & Vida, Santiago, 778 0272, Chile.,Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
| | | | - Ehmke Pohl
- Department of Chemistry, Durham University, Durham, DH1 3LE, United Kingdom.,Department of Biosciences, Durham University, Durham, DH1 3LE, United Kingdom.,Biophysical Sciences Institute, Durham University, Durham, DH1 3LE, United Kingdom
| | - Mauricio Arenas-Salinas
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, Talca, 346 5548, Chile
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9
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Penque BA, Su L, Wang J, Ji W, Bale A, Luh F, Fulbright RK, Sarmast U, Sega AG, Konstantino M, Spencer-Manzon M, Pierce R, Yen Y, Lakhani SA. A homozygous variant in RRM2B is associated with severe metabolic acidosis and early neonatal death. Eur J Med Genet 2018; 62:103574. [PMID: 30439532 DOI: 10.1016/j.ejmg.2018.11.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 10/23/2018] [Accepted: 11/09/2018] [Indexed: 11/26/2022]
Abstract
RRM2B encodes the crucial p53-inducible ribonucleotide reductase small subunit 2 homolog (p53R2), which is required for DNA synthesis throughout the cell cycle. Mutations in this gene have been associated with a lethal mitochondrial depletion syndrome. Here we present the case of an infant with a novel homozygous p.Asn221Ser mutation in RRM2B who developed hypotonia, failure to thrive, sensorineural hearing loss, and severe metabolic lactic acidosis, ultimately progressing to death at 3 months of age. Through molecular modeling using the X-ray crystal structure of p53R2, we demonstrate that this mutation likely causes disruption of a highly conserved helix region of the protein by altering intramolecular interactions. This report expands our knowledge of potential pathogenic RRM2B mutations as well as our understanding of the molecular function of p53R2 and its role in the pathogenesis of mitochondrial DNA depletion.
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Affiliation(s)
- Brent A Penque
- Pediatric Genomics Discovery Program, Department of Pediatrics, Section of Critical Care Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Leila Su
- Department of Cancer Biology and Drug Discovery, College of Medical Technology, Taipei Medical University, Taipei, 110, Taiwan; Sino-American Cancer Foundation, Temple City, CA, USA
| | - Jianghai Wang
- Department of Cancer Biology and Drug Discovery, College of Medical Technology, Taipei Medical University, Taipei, 110, Taiwan; Sino-American Cancer Foundation, Temple City, CA, USA
| | - Weizhen Ji
- Pediatric Genomics Discovery Program, Department of Pediatrics, Section of Critical Care Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Allen Bale
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Frank Luh
- Department of Cancer Biology and Drug Discovery, College of Medical Technology, Taipei Medical University, Taipei, 110, Taiwan; Sino-American Cancer Foundation, Temple City, CA, USA
| | - Robert K Fulbright
- Department of Radiology and Biomedical Imaging, Yale University School of Medicine, New Haven, CT, USA
| | - Uzair Sarmast
- Department of Radiology and Biomedical Imaging, Yale University School of Medicine, New Haven, CT, USA
| | - Annalisa G Sega
- Pediatric Genomics Discovery Program, Department of Pediatrics, Section of Critical Care Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Monica Konstantino
- Pediatric Genomics Discovery Program, Department of Pediatrics, Section of Critical Care Medicine, Yale University School of Medicine, New Haven, CT, USA
| | | | - Richard Pierce
- Pediatric Genomics Discovery Program, Department of Pediatrics, Section of Critical Care Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Yun Yen
- Department of Cancer Biology and Drug Discovery, College of Medical Technology, Taipei Medical University, Taipei, 110, Taiwan; Sino-American Cancer Foundation, Temple City, CA, USA.
| | - Saquib A Lakhani
- Pediatric Genomics Discovery Program, Department of Pediatrics, Section of Critical Care Medicine, Yale University School of Medicine, New Haven, CT, USA.
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10
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Brignole EJ, Tsai KL, Chittuluru J, Li H, Aye Y, Penczek PA, Stubbe J, Drennan CL, Asturias F. 3.3-Å resolution cryo-EM structure of human ribonucleotide reductase with substrate and allosteric regulators bound. eLife 2018; 7:31502. [PMID: 29460780 PMCID: PMC5819950 DOI: 10.7554/elife.31502] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 01/15/2018] [Indexed: 12/31/2022] Open
Abstract
Ribonucleotide reductases (RNRs) convert ribonucleotides into deoxyribonucleotides, a reaction essential for DNA replication and repair. Human RNR requires two subunits for activity, the α subunit contains the active site, and the β subunit houses the radical cofactor. Here, we present a 3.3-Å resolution structure by cryo-electron microscopy (EM) of a dATP-inhibited state of human RNR. This structure, which was determined in the presence of substrate CDP and allosteric regulators ATP and dATP, has three α2 units arranged in an α6 ring. At near-atomic resolution, these data provide insight into the molecular basis for CDP recognition by allosteric specificity effectors dATP/ATP. Additionally, we present lower-resolution EM structures of human α6 in the presence of both the anticancer drug clofarabine triphosphate and β2. Together, these structures support a model for RNR inhibition in which β2 is excluded from binding in a radical transfer competent position when α exists as a stable hexamer. Cells often need to make more DNA, for example when they are about to divide or need to repair their genetic information. The building blocks of DNA – also called deoxyribonucleotides – are created through a series of biochemical reactions. Among the enzymes that accomplish these reactions, ribonucleotide reductases (or RNRs, for short) perform a key irreversible step. One prominent class of RNR contains two basic units, named alpha and beta. The active form of these RNRs is made up of a pair of alpha units (α2), which associates with a pair of beta units (β2) to create an α2β2 structure. α2 captures molecules called ribonucleotides and, with the help of β2, converts them to deoxyribonucleotides that after futher processing will be used to create DNA. As RNR produces deoxyribonucleotides, levels of DNA building blocks in the cell rise. To avoid overstocking the cell, RNR contains an ‘off switch’ that is triggered when levels of one of the DNA building blocks, dATP, is high enough to occupy a particular site on the alpha unit. Binding of dATP to this site results in three pairs of alpha units getting together to form a stable ring of six units (called α6). How the formation of this stable α6 ring actually turns off RNR was an open question. Here, Brignole, Tsai et al. use a microscopy method called cryo-EM to reveal the three-dimensional structure of the inactive human RNR almost down to the level of individual atoms. When the alpha pairs form an α6 ring, the hole in the center of this circle is smaller than β2, keeping β2 away from α2. This inaccessibility leads to RNR being switched off. If RNR is inactive, DNA synthesis is impaired and cells cannot divide. In turn, controlling whether or not cells proliferate is key to fighting diseases like cancer (where ‘rogue’ cells keep replicating) or bacterial infections. Certain cancer treatments already target RNR, and create the inactive α6 ring structure. In addition, in bacteria, the inactive form of RNR is different from the human one and forms an α4β4 ring,rather than an α6 ring. Understanding the structure of the human inactive RNR could help scientists to find both new anticancer and antibacterial drugs.
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Affiliation(s)
- Edward J Brignole
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
| | - Kuang-Lei Tsai
- Department of Integrative Computational and Structural Biology, The Scripps Research Institute, La Jolla, United States
| | - Johnathan Chittuluru
- Department of Integrative Computational and Structural Biology, The Scripps Research Institute, La Jolla, United States
| | - Haoran Li
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
| | - Yimon Aye
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
| | - Pawel A Penczek
- Department of Biochemistry and Molecular Biology, The University of Texas-Houston Medical School, Houston, United States
| | - JoAnne Stubbe
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
| | - Catherine L Drennan
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
| | - Francisco Asturias
- Department of Integrative Computational and Structural Biology, The Scripps Research Institute, La Jolla, United States
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11
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Foskolou IP, Jorgensen C, Leszczynska KB, Olcina MM, Tarhonskaya H, Haisma B, D'Angiolella V, Myers WK, Domene C, Flashman E, Hammond EM. Ribonucleotide Reductase Requires Subunit Switching in Hypoxia to Maintain DNA Replication. Mol Cell 2017; 66:206-220.e9. [PMID: 28416140 PMCID: PMC5405111 DOI: 10.1016/j.molcel.2017.03.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 02/13/2017] [Accepted: 03/07/2017] [Indexed: 02/07/2023]
Abstract
Cells exposed to hypoxia experience replication stress but do not accumulate DNA damage, suggesting sustained DNA replication. Ribonucleotide reductase (RNR) is the only enzyme capable of de novo synthesis of deoxyribonucleotide triphosphates (dNTPs). However, oxygen is an essential cofactor for mammalian RNR (RRM1/RRM2 and RRM1/RRM2B), leading us to question the source of dNTPs in hypoxia. Here, we show that the RRM1/RRM2B enzyme is capable of retaining activity in hypoxia and therefore is favored over RRM1/RRM2 in order to preserve ongoing replication and avoid the accumulation of DNA damage. We found two distinct mechanisms by which RRM2B maintains hypoxic activity and identified responsible residues in RRM2B. The importance of RRM2B in the response to tumor hypoxia is further illustrated by correlation of its expression with a hypoxic signature in patient samples and its roles in tumor growth and radioresistance. Our data provide mechanistic insight into RNR biology, highlighting RRM2B as a hypoxic-specific, anti-cancer therapeutic target. RRM2B is induced in response to hypoxia in both cell models and patient datasets RRM2B retains activity in hypoxic conditions and is the favored RNR subunit in hypoxia Loss of RRM2B has detrimental consequences for cell fate, specifically in hypoxia RRM2B depletion enhanced hypoxic-specific apoptosis and increased radiosensitivity
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Affiliation(s)
- Iosifina P Foskolou
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Christian Jorgensen
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK
| | - Katarzyna B Leszczynska
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Monica M Olcina
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Hanna Tarhonskaya
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Bauke Haisma
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Vincenzo D'Angiolella
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - William K Myers
- Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, UK
| | - Carmen Domene
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, UK; Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Emily Flashman
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Ester M Hammond
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK.
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12
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Cho E, Yen Y. Novel regulators and molecular mechanisms of p53R2 and its disease relevance. Biochimie 2016; 123:81-4. [DOI: 10.1016/j.biochi.2016.01.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 01/16/2016] [Indexed: 10/22/2022]
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13
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Pagba CV, McCaslin TG, Veglia G, Porcelli F, Yohannan J, Guo Z, McDaniel M, Barry BA. A tyrosine-tryptophan dyad and radical-based charge transfer in a ribonucleotide reductase-inspired maquette. Nat Commun 2015; 6:10010. [PMID: 26627888 PMCID: PMC4686667 DOI: 10.1038/ncomms10010] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 10/23/2015] [Indexed: 01/29/2023] Open
Abstract
In class 1a ribonucleotide reductase (RNR), a substrate-based radical is generated in the α2 subunit by long-distance electron transfer involving an essential tyrosyl radical (Y122O·) in the β2 subunit. The conserved W48 β2 is ∼10 Å from Y122OH; mutations at W48 inactivate RNR. Here, we design a beta hairpin peptide, which contains such an interacting tyrosine–tryptophan dyad. The NMR structure of the peptide establishes that there is no direct hydrogen bond between the phenol and the indole rings. However, electronic coupling between the tyrosine and tryptophan occurs in the peptide. In addition, downshifted ultraviolet resonance Raman (UVRR) frequencies are observed for the radical state, reproducing spectral downshifts observed for β2. The frequency downshifts of the ring and CO bands are consistent with charge transfer from YO· to W or another residue. Such a charge transfer mechanism implies a role for the β2 Y-W dyad in electron transfer. Tyrosine-tryptophan dyads are known to mediate electron transfer reactions in a range of different proteins. Here, the authors study a beta hairpin peptide, probing the tyrosine-tryptophan interaction and showing no hydrogen bonding but rather charge transfer between the tyrosyl radical and tryptophan'.
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Affiliation(s)
- Cynthia V Pagba
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.,Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Tyler G McCaslin
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.,Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Gianluigi Veglia
- Department of Biochemistry, Biophysics and Molecular Biology, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Fernando Porcelli
- Department of Biochemistry, Biophysics and Molecular Biology, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA.,Department for Innovation in Biological, Agro-food and Forest Systems, University of Tuscia, Viterbo 01100, Italy
| | - Jiby Yohannan
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.,Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Zhanjun Guo
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.,Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Miranda McDaniel
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.,Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Bridgette A Barry
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.,Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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14
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Chen X, Zhu L, Xin L, Du K, Ran X, Cui X, Xiang Q, Zhang H, Xu P, Wu X. Rice stripe1-2 and stripe1-3 Mutants Encoding the Small Subunit of Ribonucleotide Reductase Are Temperature Sensitive and Are Required for Chlorophyll Biosynthesis. PLoS One 2015; 10:e0130172. [PMID: 26102588 PMCID: PMC4478038 DOI: 10.1371/journal.pone.0130172] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 05/18/2015] [Indexed: 11/19/2022] Open
Abstract
We induced mutants, stripe1-2 (st1-2) and stripe1-3 (st1-3), from rice (Oryza sativa L.) Indica 9311 using Ethyl methanesulfonate (EMS). Both st1-2 and st1-3 mutants encoded the small subunit of ribonucleotide reductase 1 (RNRS1), differed in the location of the mutated base, and displayed white-stripe from the L2 stage through maturity. The mutants were sensitive to temperature, and their chlorophyll content increased with the increase in temperature; however, they did not revert to normal green leaf phenotype under field conditions. The mutant st1-2 showed loosely arranged thylakoid lamellar structure as compared with wild-type (WT) plants. Contrastingly, st1-3 displayed normal thylakoid lamellar structure, good agronomic traits, and higher yield than st1-2 but lower yield than WT. Three-dimensional structure prediction for RNRS1 indicated that the mutation in Val-171 residue in st1-2 influenced the connection of RNRS1 to iron, causing abnormal development of chloroplasts. Real-time PCR analysis showed that the expression levels associated with chlorophyll biosynthetic pathway and photosynthesis were affected in st1-2 and st1-3 at different temperatures and different developmental stages.
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Affiliation(s)
- Xiaoqiong Chen
- Rice Research Institute of Sichuan Agricultural University, Key Laboratory of Southwest Crop Genetic Resources and Improvement Ministry of Education, 211 Huimin Road, 611130 Wenjiang, Sichuan, China
| | - Ling Zhu
- Rice Research Institute of Sichuan Agricultural University, Key Laboratory of Southwest Crop Genetic Resources and Improvement Ministry of Education, 211 Huimin Road, 611130 Wenjiang, Sichuan, China
| | - Long Xin
- Rice Research Institute of Sichuan Agricultural University, Key Laboratory of Southwest Crop Genetic Resources and Improvement Ministry of Education, 211 Huimin Road, 611130 Wenjiang, Sichuan, China
| | - Kangxi Du
- Rice Research Institute of Sichuan Agricultural University, Key Laboratory of Southwest Crop Genetic Resources and Improvement Ministry of Education, 211 Huimin Road, 611130 Wenjiang, Sichuan, China
| | - Xiuhua Ran
- Rice Research Institute of Sichuan Agricultural University, Key Laboratory of Southwest Crop Genetic Resources and Improvement Ministry of Education, 211 Huimin Road, 611130 Wenjiang, Sichuan, China
| | - Xiaoyun Cui
- Rice Research Institute of Sichuan Agricultural University, Key Laboratory of Southwest Crop Genetic Resources and Improvement Ministry of Education, 211 Huimin Road, 611130 Wenjiang, Sichuan, China
| | - Quanju Xiang
- College of Resources, Sichuan Agricultural University, 211 Huimin Road, 611130 Wenjiang, Sichuan, China
| | - Hongyu Zhang
- Rice Research Institute of Sichuan Agricultural University, Key Laboratory of Southwest Crop Genetic Resources and Improvement Ministry of Education, 211 Huimin Road, 611130 Wenjiang, Sichuan, China
| | - Peizhou Xu
- Rice Research Institute of Sichuan Agricultural University, Key Laboratory of Southwest Crop Genetic Resources and Improvement Ministry of Education, 211 Huimin Road, 611130 Wenjiang, Sichuan, China
| | - Xianjun Wu
- Rice Research Institute of Sichuan Agricultural University, Key Laboratory of Southwest Crop Genetic Resources and Improvement Ministry of Education, 211 Huimin Road, 611130 Wenjiang, Sichuan, China
- * E-mail:
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15
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RRM2B-Mediated Regulation of Mitochondrial Activity and Inflammation under Oxidative Stress. Mediators Inflamm 2015; 2015:287345. [PMID: 26089597 PMCID: PMC4451759 DOI: 10.1155/2015/287345] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Revised: 03/25/2015] [Accepted: 03/25/2015] [Indexed: 11/29/2022] Open
Abstract
RRM2B is a critical ribonucleotide reductase (RR) subunit that exists as p53-inducible and p53-dependent molecule. The p53-independent regulation of RRM2B has been recently studied, and FOXO3 was identified as a novel regulator of RRM2B. However, the p53-independent regulation of RRM2B, particularly under oxidative stress, remains largely unknown. In this study, we investigated the role of RRM2B underoxidative stress-induced DNA damage and further examined the regulation of mitochondrial and inflammatory genes by RRM2B. Our study is the first to report the critical role of RRM2B in mitochondrial homeostasis and the inflammation signaling pathway in a p53-independent manner. Furthermore, our study provides novel insights into the role of the RR in inflammatory diseases.
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16
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Tebbi A, Guittet O, Tuphile K, Cabrié A, Lepoivre M. Caspase-dependent Proteolysis of Human Ribonucleotide Reductase Small Subunits R2 and p53R2 during Apoptosis. J Biol Chem 2015; 290:14077-90. [PMID: 25878246 DOI: 10.1074/jbc.m115.649640] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Indexed: 11/06/2022] Open
Abstract
Ribonucleotide reductase (RnR) is a key enzyme synthesizing deoxyribonucleotides for DNA replication and repair. In mammals, the R1 catalytic subunit forms an active complex with either one of the two small subunits R2 and p53R2. Expression of R2 is S phase-specific and required for DNA replication. The p53R2 protein is expressed throughout the cell cycle and in quiescent cells where it provides dNTPs for mitochondrial DNA synthesis. Participation of R2 and p53R2 in DNA repair has also been suggested. In this study, we investigated the fate of the RnR subunits during apoptosis. The p53R2 protein was cleaved in a caspase-dependent manner in K-562 cells treated with inhibitors of the Bcr-Abl oncogenic kinase and in HeLa 229 cells incubated with TNF-α and cycloheximide. The cleavage site was mapped between Asp(342) and Asn(343). Caspase attack released a C-terminal p53R2 peptide of nine residues containing the conserved heptapeptide essential for R1 binding. As a consequence, the cleaved p53R2 protein was inactive. In vitro, purified caspase-3 and -8 could release the C-terminal tail of p53R2. Knocking down these caspases, but not caspase-2, -7, and -10, also inhibited p53R2 cleavage in cells committed to die via the extrinsic death receptor pathway. The R2 subunit was subjected to caspase- and proteasome-dependent proteolysis, which was prevented by siRNA targeting caspase-8. Knocking down caspase-3 was ineffective. Protein R1 was not subjected to degradation. Adding deoxyribonucleosides to restore dNTP pools transiently protected cells from apoptosis. These data identify RnR activity as a prosurvival function inactivated by proteolysis during apoptosis.
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Affiliation(s)
- Ali Tebbi
- From the Université Paris Sud, Institute of Molecular and Cellular Biochemistry and Biophysics, UMR 8619, 91405 Orsay, France, CNRS, 91405 Orsay, France, and Department of Virology, Institut Pasteur, Pathogenesis of Hepatitis B Virus, 75015 Paris, France
| | - Olivier Guittet
- From the Université Paris Sud, Institute of Molecular and Cellular Biochemistry and Biophysics, UMR 8619, 91405 Orsay, France, CNRS, 91405 Orsay, France, and
| | - Karine Tuphile
- From the Université Paris Sud, Institute of Molecular and Cellular Biochemistry and Biophysics, UMR 8619, 91405 Orsay, France, CNRS, 91405 Orsay, France, and
| | - Aimeric Cabrié
- From the Université Paris Sud, Institute of Molecular and Cellular Biochemistry and Biophysics, UMR 8619, 91405 Orsay, France, CNRS, 91405 Orsay, France, and
| | - Michel Lepoivre
- From the Université Paris Sud, Institute of Molecular and Cellular Biochemistry and Biophysics, UMR 8619, 91405 Orsay, France, CNRS, 91405 Orsay, France, and
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17
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Carnio S, Novello S, Papotti M, Loiacono M, Scagliotti GV. Prognostic and predictive biomarkers in early stage non-small cell lung cancer: tumor based approaches including gene signatures. Transl Lung Cancer Res 2015; 2:372-81. [PMID: 25806256 DOI: 10.3978/j.issn.2218-6751.2013.10.05] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2013] [Accepted: 10/10/2013] [Indexed: 12/26/2022]
Abstract
In early stage non-small cell lung cancer (NSCLC) large randomized trials have demonstrated that in patients with radically resected disease adjuvant chemotherapy improves 5-year survival rates. However, a customization of systemic treatment is needed to avoid treatments in patients cured by surgery alone or to justify the use of adjuvant chemotherapy in high risk patients, including those in stage IA. Recently, the possibility of identifying prognostic and predictive factors related to the genetic signatures of the tumor that could affect adjuvant and neo-adjuvant treatment choices for resectable non-small cell lung cancer (NSCLC) has been of interest. This review summarizes the current status and future opportunities for clinical application of genotyping and genomic tests in early NSCLC.
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Affiliation(s)
- Simona Carnio
- University of Torino, Department of Oncology, Torino, Italy
| | - Silvia Novello
- University of Torino, Department of Oncology, Torino, Italy
| | - Mauro Papotti
- University of Torino, Department of Oncology, Torino, Italy
| | - Marco Loiacono
- University of Torino, Department of Oncology, Torino, Italy
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18
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Yu F, Cangelosi VM, Zastrow ML, Tegoni M, Plegaria JS, Tebo AG, Mocny CS, Ruckthong L, Qayyum H, Pecoraro VL. Protein design: toward functional metalloenzymes. Chem Rev 2014; 114:3495-578. [PMID: 24661096 PMCID: PMC4300145 DOI: 10.1021/cr400458x] [Citation(s) in RCA: 340] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Fangting Yu
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | | | | | | | - Alison G. Tebo
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Leela Ruckthong
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hira Qayyum
- University of Michigan, Ann Arbor, Michigan 48109, United States
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19
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Hammerstad M, Hersleth HP, Tomter AB, Røhr ÅK, Andersson KK. Crystal structure of Bacillus cereus class Ib ribonucleotide reductase di-iron NrdF in complex with NrdI. ACS Chem Biol 2014; 9:526-37. [PMID: 24295378 DOI: 10.1021/cb400757h] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Class Ib ribonucleotide reductases (RNRs) use a dimetal-tyrosyl radical (Y•) cofactor in their NrdF (β2) subunit to initiate ribonucleotide reduction in the NrdE (α2) subunit. Contrary to the diferric tyrosyl radical (Fe(III)2-Y•) cofactor, which can self-assemble from Fe(II)2-NrdF and O2, generation of the Mn(III)2-Y• cofactor requires the reduced form of a flavoprotein, NrdIhq, and O2 for its assembly. Here we report the 1.8 Å resolution crystal structure of Bacillus cereus Fe2-NrdF in complex with NrdI. Compared to the previously solved Escherichia coli NrdI-Mn(II)2-NrdF structure, NrdI and NrdF binds similarly in Bacillus cereus through conserved core interactions. This protein-protein association seems to be unaffected by metal ion type bound in the NrdF subunit. The Bacillus cereus Mn(II)2-NrdF and Fe2-NrdF structures, also presented here, show conformational flexibility of residues surrounding the NrdF metal ion site. The movement of one of the metal-coordinating carboxylates is linked to the metal type present at the dimetal site and not associated with NrdI-NrdF binding. This carboxylate conformation seems to be vital for the water network connecting the NrdF dimetal site and the flavin in NrdI. From these observations, we suggest that metal-dependent variations in carboxylate coordination geometries are important for active Y• cofactor generation in class Ib RNRs. Additionally, we show that binding of NrdI to NrdF would structurally interfere with the suggested α2β2 (NrdE-NrdF) holoenzyme formation, suggesting the potential requirement for NrdI dissociation before NrdE-NrdF assembly after NrdI-activation. The mode of interactions between the proteins involved in the class Ib RNR system is, however, not fully resolved.
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Affiliation(s)
- Marta Hammerstad
- Department of Biosciences, University of Oslo, P.O.
Box 1066, Blindern, NO-0316 Oslo, Norway
| | - Hans-Petter Hersleth
- Department of Biosciences, University of Oslo, P.O.
Box 1066, Blindern, NO-0316 Oslo, Norway
| | - Ane B. Tomter
- Department of Biosciences, University of Oslo, P.O.
Box 1066, Blindern, NO-0316 Oslo, Norway
| | - Åsmund K. Røhr
- Department of Biosciences, University of Oslo, P.O.
Box 1066, Blindern, NO-0316 Oslo, Norway
| | - K. Kristoffer Andersson
- Department of Biosciences, University of Oslo, P.O.
Box 1066, Blindern, NO-0316 Oslo, Norway
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20
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Shao J, Liu X, Zhu L, Yen Y. Targeting ribonucleotide reductase for cancer therapy. Expert Opin Ther Targets 2013; 17:1423-37. [PMID: 24083455 DOI: 10.1517/14728222.2013.840293] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Ribonucleotide reductase (RR) is a unique enzyme, because it is responsible for reducing ribonucleotides to their corresponding deoxyribonucleotides, which are the building blocks required for DNA replication and repair. Dysregulated RR activity is associated with genomic instability, malignant transformation and cancer development. The use of RR inhibitors, either as a single agent or combined with other therapies, has proven to be a promising approach for treating solid tumors and hematological malignancies. AREAS COVERED This review covers recent publications in the area of RR, which include: i) the structure, function and regulation of RR; ii) the roles of RR in cancer development; iii) the classification, mechanisms and clinical application of RR inhibitors for cancer therapy and iv) strategies for developing novel RR inhibitors in the future. EXPERT OPINION Exploring the possible nonenzymatic roles of RR subunit proteins in carcinogenesis may lead to new rationales for developing novel anticancer drugs. Updated information about the structure and holoenzyme models of RR will help in identifying potential sites in the protein that could be targets for novel RR inhibitors. Determining RR activity and subunit levels in clinical samples will provide a rational platform for developing personalized cancer therapies that use RR inhibitors.
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Affiliation(s)
- Jimin Shao
- Zhejiang University, School of Medicine, Department of Pathology and Pathophysiology , Hangzhou 310058 , China
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21
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Abstract
Iron is an essential nutrient that facilitates cell proliferation and growth. However, iron also has the capacity to engage in redox cycling and free radical formation. Therefore, iron can contribute to both tumour initiation and tumour growth; recent work has also shown that iron has a role in the tumour microenvironment and in metastasis. Pathways of iron acquisition, efflux, storage and regulation are all perturbed in cancer, suggesting that reprogramming of iron metabolism is a central aspect of tumour cell survival. Signalling through hypoxia-inducible factor (HIF) and WNT pathways may contribute to altered iron metabolism in cancer. Targeting iron metabolic pathways may provide new tools for cancer prognosis and therapy.
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Affiliation(s)
- Suzy V Torti
- Departments of Molecular, Microbial and Structural Biology, University of Connecticut Health Center, Farmington, Connecticut 06030, USA.
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22
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Abstract
The quest for markers of sensitivity to cytotoxic agents has been ongoing for decades. In non-small-cell lung cancer, platinum compounds represent the cornerstone of systemic therapy. They target DNA and induce damage that cancer cells struggle to overcome. Somatic excision repair cross-complementing rodent repair deficiency, complementation group 1 (ERCC1), and ribonucleotide reductase M1 (RRM1) expression levels have been extensively explored as markers of DNA repair capacity in tumor cells. Although low ERCC1 and/or RRM1 expression is generally associated with sensitivity to platinum, the results published in retrospective and prospective studies are not always consistent. Against this background, we will examine in this review the function of these two biomarkers as well as the tools available for their assessment and the associated technical issues. Their prognostic and predictive values will be summarized and considered in terms of customizing systemic therapy according to biomarker (ERCC1 and RRM1) expression levels. We will also discuss why the use of both markers should at this point be restricted to clinical research and underline that functional readouts of DNA repair will help boost future strategies for biomarker discovery in the field.
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23
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Tomter AB, Zoppellaro G, Andersen NH, Hersleth HP, Hammerstad M, Røhr ÅK, Sandvik GK, Strand KR, Nilsson GE, Bell CB, Barra AL, Blasco E, Le Pape L, Solomon EI, Andersson KK. Ribonucleotide reductase class I with different radical generating clusters. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2012.05.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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24
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Pitceathly RDS, Smith C, Fratter C, Alston CL, He L, Craig K, Blakely EL, Evans JC, Taylor J, Shabbir Z, Deschauer M, Pohl U, Roberts ME, Jackson MC, Halfpenny CA, Turnpenny PD, Lunt PW, Hanna MG, Schaefer AM, McFarland R, Horvath R, Chinnery PF, Turnbull DM, Poulton J, Taylor RW, Gorman GS. Adults with RRM2B-related mitochondrial disease have distinct clinical and molecular characteristics. ACTA ACUST UNITED AC 2012; 135:3392-403. [PMID: 23107649 PMCID: PMC3501970 DOI: 10.1093/brain/aws231] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Mutations in the nuclear-encoded mitochondrial maintenance gene RRM2B are an important cause of familial mitochondrial disease in both adults and children and represent the third most common cause of multiple mitochondrial DNA deletions in adults, following POLG [polymerase (DNA directed), gamma] and PEO1 (now called C10ORF2, encoding the Twinkle helicase) mutations. However, the clinico-pathological and molecular features of adults with RRM2B-related disease have not been clearly defined. In this multicentre study of 26 adult patients from 22 independent families, including five additional cases published in the literature, we show that extra-ocular neurological complications are common in adults with genetically confirmed RRM2B mutations. We also demonstrate a clear correlation between the clinical phenotype and the underlying genetic defect. Myopathy was a prominent manifestation, followed by bulbar dysfunction and fatigue. Sensorineural hearing loss and gastrointestinal disturbance were also important findings. Severe multisystem neurological disease was associated with recessively inherited compound heterozygous mutations with a mean age of disease onset at 7 years. Dominantly inherited heterozygous mutations were associated with a milder predominantly myopathic phenotype with a later mean age of disease onset at 46 years. Skeletal muscle biopsies revealed subsarcolemmal accumulation of mitochondria and/or cytochrome c oxidase-deficient fibres. Multiple mitochondrial DNA deletions were universally present in patients who underwent a muscle biopsy. We identified 18 different heterozygous RRM2B mutations within our cohort of patients, including five novel mutations that have not previously been reported. Despite marked clinical overlap between the mitochondrial maintenance genes, key clinical features such as bulbar dysfunction, hearing loss and gastrointestinal disturbance should help prioritize genetic testing towards RRM2B analysis, and sequencing of the gene may preclude performance of a muscle biopsy.
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Affiliation(s)
- Robert D S Pitceathly
- MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology and National Hospital for Neurology and Neurosurgery, Queen Square, London WC1N 3BG, UK
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25
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Andersson CS, Berthold CL, Högbom M. A Dynamic C‐Terminal Segment in the
Mycobacterium tuberculosis
Mn/Fe R2lox Protein Can Adopt a Helical Structure with Possible Functional Consequences. Chem Biodivers 2012; 9:1981-8. [DOI: 10.1002/cbdv.201100428] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Charlotta S. Andersson
- Stockholm Center for Biomembrane Research, Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE‐10691 Stockholm, (phone: +46 8 16 21 10; fax: +46 8 15 36 79)
| | - Catrine L. Berthold
- Stockholm Center for Biomembrane Research, Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE‐10691 Stockholm, (phone: +46 8 16 21 10; fax: +46 8 15 36 79)
| | - Martin Högbom
- Stockholm Center for Biomembrane Research, Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE‐10691 Stockholm, (phone: +46 8 16 21 10; fax: +46 8 15 36 79)
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26
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Basu A, Sinha BN. Understanding the molecular interactions of different radical scavengers with ribonucleotide reductase M2 (hRRM2) domain: opening the gates and gaining access. J Comput Aided Mol Des 2012; 26:865-81. [PMID: 22639080 DOI: 10.1007/s10822-012-9581-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2012] [Accepted: 05/09/2012] [Indexed: 10/28/2022]
Abstract
We employed a combination of molecular docking and dynamics to understand the interaction of three different radical scavengers (SB-HSC21, ABNM13 and trimidox) with ribonucleotide reductase M2 (hRRM2) domain. On the basis of the observed results, we can propose how these ligands interact with the enzyme, and cease the radical transfer step from the di-iron center to TYR176. All the ligands alter the electron density over TYR176, -OH group by forming an extremely stable H-bond with either -NHOH group, or with phenolic hydroxyl group of the ligands. This change in electronic density disrupts the water bridge between TYR176, -OH and the di-iron center, which stops the single electron transfer process from TYR176, -OH to iron. As a consequence the enzyme is inhibited. Another interesting observation that we are reporting is the two stage gate keeping mechanism of the RR active site tunnel. We describe these as the outer Gate-1 controlled by ARG330, and the inner Gate-2 controlled by SER263, PHE240, and PHE236. We also observed a dynamic conformational shift in these residues, the incoming ligands can go through, and interact with the underlying TYR176, -OH group. From the study we found the active-site of hRRM2 is extremely flexible and shows a significant induced fit.
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Affiliation(s)
- Arijit Basu
- Department of Pharmaceutical Sciences, Birla Institute of Technology, Mesra, Ranchi 835 215, Jharkhand, India.
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27
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Barry BA, Chen J, Keough J, Jenson D, Offenbacher A, Pagba C. Proton Coupled Electron Transfer and Redox Active Tyrosines: Structure and Function of the Tyrosyl Radicals in Ribonucleotide Reductase and Photosystem II. J Phys Chem Lett 2012; 3:543-554. [PMID: 22662289 PMCID: PMC3362996 DOI: 10.1021/jz2014117] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Proton coupled electron transfer (PCET) reactions are important in many biological processes. Tyrosine oxidation/reduction can play a critical role in facilitating these reactions. Two examples are photosystem II (PSII) and ribonucleotide reductase (RNR). RNR is essential in DNA synthesis in all organisms. In E. coli RNR, a tyrosyl radical, Y122(•), is required as a radical initiator. Photosystem II (PSII) generates molecular oxygen from water. In PSII, an essential tyrosyl radical, YZ(•), oxidizes the oxygen evolving center. However, the mechanisms, by which the extraordinary oxidizing power of the tyrosyl radical is controlled, are not well understood. This is due to the difficulty in acquiring high-resolution structural information about the radical state. Spectroscopic approaches, such as EPR and UV resonance Raman (UVRR), can give new information. Here, we discuss EPR studies of PCET and the PSII YZ radical. We also present UVRR results, which support the conclusion that Y122 undergoes an alteration in ring and backbone dihedral angle when it is oxidized. This conformational change results in a loss of hydrogen bonding to the phenolic oxygen. Our analysis suggests that access of water is an important factor in determining tyrosyl radical lifetime and function. TOC graphic.
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28
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Tomter AB, Zoppellaro G, Schmitzberger F, Andersen NH, Barra AL, Engman H, Nordlund P, Andersson KK. HF-EPR, Raman, UV/VIS light spectroscopic, and DFT studies of the ribonucleotide reductase R2 tyrosyl radical from Epstein-Barr virus. PLoS One 2011; 6:e25022. [PMID: 21980375 PMCID: PMC3181257 DOI: 10.1371/journal.pone.0025022] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Accepted: 08/22/2011] [Indexed: 11/19/2022] Open
Abstract
Epstein-Barr virus (EBV) belongs to the gamma subfamily of herpes viruses, among the most common pathogenic viruses in humans worldwide. The viral ribonucleotide reductase small subunit (RNR R2) is involved in the biosynthesis of nucleotides, the DNA precursors necessary for viral replication, and is an important drug target for EBV. RNR R2 generates a stable tyrosyl radical required for enzymatic turnover. Here, the electronic and magnetic properties of the tyrosyl radical in EBV R2 have been determined by X-band and high-field/high-frequency electron paramagnetic resonance (EPR) spectroscopy recorded at cryogenic temperatures. The radical exhibits an unusually low g₁-tensor component at 2.0080, indicative of a positive charge in the vicinity of the radical. Consistent with these EPR results a relatively high C-O stretching frequency associated with the phenoxyl radical (at 1508 cm⁻¹) is observed with resonance Raman spectroscopy. In contrast to mouse R2, EBV R2 does not show a deuterium shift in the resonance Raman spectra. Thus, the presence of a water molecule as a hydrogen bond donor moiety could not be identified unequivocally. Theoretical simulations showed that a water molecule placed at a distance of 2.6 Å from the tyrosyl-oxygen does not result in a detectable deuterium shift in the calculated Raman spectra. UV/VIS light spectroscopic studies with metal chelators and tyrosyl radical scavengers are consistent with a more accessible dimetal binding/radical site and a lower affinity for Fe²⁺ in EBV R2 than in Escherichia coli R2. Comparison with previous studies of RNR R2s from mouse, bacteria, and herpes viruses, demonstrates that finely tuned electronic properties of the radical exist within the same RNR R2 Ia class.
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Affiliation(s)
- Ane B. Tomter
- Department of Molecular Biosciences, University of Oslo, Oslo, Norway
| | | | - Florian Schmitzberger
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Niels H. Andersen
- Department of Molecular Biosciences, University of Oslo, Oslo, Norway
| | - Anne-Laure Barra
- Laboratoire National des Champs Magnétiques Intenses, LNCMI-G, UPR 3228, CNRS, Grenoble, France
| | - Henrik Engman
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Pär Nordlund
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
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29
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Shang H, Li Q, Feng G, Cui Z. Molecular analysis and functions of p53R2 in zebrafish. Gene 2010; 475:30-8. [PMID: 21194559 DOI: 10.1016/j.gene.2010.12.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2010] [Revised: 12/15/2010] [Accepted: 12/20/2010] [Indexed: 02/07/2023]
Abstract
p53R2 is a newly identified small subunit of ribonucleotide reductase and plays a pivotal role in the supply of dNTPs for genomic DNA repair and mitochondrial DNA synthesis, but little is known about its functions in zebrafish. Herein, we obtained the cDNA of zebrafish p53R2 that shares 72.8% and 72.5% amino acid identities with human p53R2 and zebrafish R2, respectively. Residues crucial for enzymatic activity are highly conserved among p53R2 proteins from different species. p53R2 in zebrafish was maternally expressed, its transcripts were detected in developing embryos and all adult tissues examined. A 250-bp minimal promoter upstream of the translational initiation site was identified to drive basal expression of p53R2 in a p53-independent manner. Expression of p53R2 was induced by DNA-damaging reagents CPT or MMS, but suppressed by p53-knockdown in zebrafish embryos. Moreover, p53R2 was mainly distributed in the cytoplasm of cells under normal condition and upon DNA damage. Furthermore, overexpression of p53R2 attenuated apoptosis of embryonic cells caused by CPT or MMS treatment and protected developing embryos from death. Therefore, functions of p53R2 in zebrafish are closely associated with its activity in DNA repair and synthesis.
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Affiliation(s)
- Hanqiao Shang
- Key Laboratory of Biodiversity and Conservation of Aquatic Organism; Institute of Hydrobiology, Chinese Academy of Sciences, 7 Donghu Rd., Wuhan, Hubei, PR China
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30
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Holmgren A, Sengupta R. The use of thiols by ribonucleotide reductase. Free Radic Biol Med 2010; 49:1617-28. [PMID: 20851762 DOI: 10.1016/j.freeradbiomed.2010.09.005] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Revised: 08/17/2010] [Accepted: 09/03/2010] [Indexed: 12/22/2022]
Abstract
Ribonucleotide reductase (RNR) catalyzes the rate-limiting de novo synthesis of 2'-deoxyribonucleotides from the corresponding ribonucleotides and thereby provides balanced deoxyribonucleotide pools required for error-free DNA replication and repair. The essential role of RNR in DNA synthesis and the use of DNA as genetic material has made it an important target for the development of anticancer and antiviral agents. The most well known feature of the universal RNR reaction in all kingdoms of life is the involvement of protein free radicals. Redox-active cysteines, thiyl radicals, and thiol redox proteins of the thioredoxin superfamily play major roles in the catalytic mechanism. The involvement of cysteine residues in catalysis is common to all three classes of RNR. Taking account of the recent progress in this field of research, this review focuses on the use of thiols in the redox mechanism of RNR enzymes.
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Affiliation(s)
- Arne Holmgren
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden.
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31
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Gurmu D, Dahlroth SL, Haas J, Nordlund P, Erlandsen H. Expression, purification, crystallization and preliminary X-ray analysis of ORF60, the small subunit (R2) of ribonucleotide reductase from Kaposi's sarcoma-associated herpesvirus (KSHV). Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:734-7. [PMID: 20516613 PMCID: PMC2882783 DOI: 10.1107/s1744309110016052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2010] [Accepted: 04/30/2010] [Indexed: 11/10/2022]
Abstract
Ribonucleotide reductase (RNR) is responsible for converting ribonucleotides to deoxyribonucleotides, which are the building blocks of DNA. The enzyme is present in all life forms as well as in some large DNA viruses such as herpesviruses. The alpha-herpesviruses and gamma-herpesviruses encode two class Ia RNR subunits, R1 and R2, while the beta-herpesvirus subfamily only encode an inactive R1 subunit. Here, the crystallization of the R2 subunit of RNR encoded by the ORF60 gene from the oncovirus Kaposi's sarcoma-associated gamma-herpesvirus (KSHV) is reported. These are the first crystals of a viral R2 subunit; the use of in situ proteolysis with chymotrypsin and the addition of hexamine cobalt(III) chloride that were necessary to obtain crystals are described. Optimization of the crystallization conditions yielded crystals that diffracted to 2.0 A resolution. The crystals belonged to space group P2(1), with unit-cell parameters a = 63.9, b = 71.2, c = 71.8 A, alpha = 90, beta = 106.7, gamma = 90 degrees. The data set collected was 95.3% complete, with an R(merge) of 9.6%. There are two molecules in the asymmetric unit, corresponding to a solvent content of 43.4%.
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Affiliation(s)
- Daniel Gurmu
- Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles Väg 2, SE-171 77 Stockholm, Sweden
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Sue-Li Dahlroth
- Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles Väg 2, SE-171 77 Stockholm, Sweden
- Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Juergen Haas
- Max von Pettenkofer Institut, Ludvig Maximillian Universität, Pettenkoferstrasse 9a, D-80336 München, Germany
- Division of Pathway Medicine, University of Edinburgh, 49 Little France Crescent, Edinburgh EH16 4SB, Scotland
| | - Pär Nordlund
- Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles Väg 2, SE-171 77 Stockholm, Sweden
| | - Heidi Erlandsen
- University of Alabama at Birmingham, School of Dentistry, Institute of Oral Health Research, 1919 7th Avenue South, Birmingham, Alabama 35294, USA
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32
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Zhou B, Su L, Yuan YC, Un F, Wang N, Patel M, Xi B, Hu S, Yen Y. Structural basis on the dityrosyl-diiron radical cluster and the functional differences of human ribonucleotide reductase small subunits hp53R2 and hRRM2. Mol Cancer Ther 2010; 9:1669-79. [PMID: 20484015 DOI: 10.1158/1535-7163.mct-10-0023] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Ribonucleotide reductase (RNR) is an enzyme for the de novo conversion of ribonucleotides to deoxyribonucleotides. The two human RNR small subunits hRRM2 and hp53R2 share 83% sequence homology but show distinct expression patterns and function. Structural analyses of the oxidized form of hRRM2 and hp53R2 indicate that both proteins contain a conserved Gln127-hp53R2/Gln165-hRRM2 close to the dinuclear iron center and the essential tyrosine residue Tyr124-hp53R2/Tyr162-hRRM2 forms hydrogen bonds with the tyrosine and iron ligands, implying a critical role for the glutamine residue in assembling the dityrosyl-diiron radical cofactor. The present work also showed that Tyr221 in hRRM2, which is replaced by Phe183 in hp53R2, forms a hydrogen bond with Tyr162 to extend the hydrogen bond network from Gln165-hRRM2. Mutagenesis and spectroscopic experiments suggested that the tyrosine-to-phenylalanine switch at Phe183-hp53R2/Tyr221-hRRM2 could lead to differences in radical generation or enzymatic activity for hp53R2 and hRRM2. This study correlates the distinct catalytic mechanisms of the small subunits hp53R2 and hRRM2 with a hydrogen-bonding network and provides novel directions for designing and developing subunit-specific therapeutic agents for human RNR enzymes.
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Affiliation(s)
- Bingsen Zhou
- Department of Molecular Pharmacology, City of Hope National Medical Center, Duarte, California 91010, USA
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