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Prasad CB, Oo A, Liu Y, Qiu Z, Zhong Y, Li N, Singh D, Xin X, Cho YJ, Li Z, Zhang X, Yan C, Zheng Q, Wang QE, Guo D, Kim B, Zhang J. The thioredoxin system determines CHK1 inhibitor sensitivity via redox-mediated regulation of ribonucleotide reductase activity. Nat Commun 2024; 15:4667. [PMID: 38821952 PMCID: PMC11143221 DOI: 10.1038/s41467-024-48076-9] [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: 04/13/2023] [Accepted: 04/19/2024] [Indexed: 06/02/2024] Open
Abstract
Checkpoint kinase 1 (CHK1) is critical for cell survival under replication stress (RS). CHK1 inhibitors (CHK1i's) in combination with chemotherapy have shown promising results in preclinical studies but have displayed minimal efficacy with substantial toxicity in clinical trials. To explore combinatorial strategies that can overcome these limitations, we perform an unbiased high-throughput screen in a non-small cell lung cancer (NSCLC) cell line and identify thioredoxin1 (Trx1), a major component of the mammalian antioxidant-system, as a determinant of CHK1i sensitivity. We establish a role for redox recycling of RRM1, the larger subunit of ribonucleotide reductase (RNR), and a depletion of the deoxynucleotide pool in this Trx1-mediated CHK1i sensitivity. Further, the TrxR inhibitor auranofin, an approved anti-rheumatoid arthritis drug, shows a synergistic interaction with CHK1i via interruption of the deoxynucleotide pool. Together, we show a pharmacological combination to treat NSCLC that relies on a redox regulatory link between the Trx system and mammalian RNR activity.
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Affiliation(s)
- Chandra Bhushan Prasad
- Department of Radiation Oncology, James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Adrian Oo
- Center for ViroScience and Cure, Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Yujie Liu
- Department of Radiation Oncology, James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Zhaojun Qiu
- Department of Radiation Oncology, James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Yaogang Zhong
- Department of Radiation Oncology, James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University, Columbus, OH, 43210, USA
- The Comprehensive Cancer Center, Center for Cancer Metabolism, The Ohio State University, Columbus, OH, 43210, USA
| | - Na Li
- Department of Radiation Oncology, James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Deepika Singh
- Department of Radiation Oncology, James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Xiwen Xin
- The Ohio State University, Columbus, OH, 43210, USA
| | - Young-Jae Cho
- Center for ViroScience and Cure, Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Zaibo Li
- Department of Pathology, The Ohio State University Wexner Medical Center, College of Medicine, Columbus, OH, 43210, USA
| | - Xiaoli Zhang
- Department of Biomedical Informatics, Wexner Medical Center, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Chunhong Yan
- Georgia Cancer Center, Augusta University, Augusta, GA, 30912, USA
| | - Qingfei Zheng
- Department of Radiation Oncology, James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University, Columbus, OH, 43210, USA
- The Comprehensive Cancer Center, Center for Cancer Metabolism, The Ohio State University, Columbus, OH, 43210, USA
| | - Qi-En Wang
- Department of Radiation Oncology, James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University, Columbus, OH, 43210, USA
| | - Deliang Guo
- Department of Radiation Oncology, James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University, Columbus, OH, 43210, USA
- The Comprehensive Cancer Center, Center for Cancer Metabolism, The Ohio State University, Columbus, OH, 43210, USA
| | - Baek Kim
- Center for ViroScience and Cure, Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Junran Zhang
- Department of Radiation Oncology, James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University, Columbus, OH, 43210, USA.
- The Comprehensive Cancer Center, Center for Cancer Metabolism, The Ohio State University, Columbus, OH, 43210, USA.
- The Comprehensive Cancer Center, Pelotonia Institute for Immuno-Oncology, The Ohio State University, Columbus, OH, 43210, USA.
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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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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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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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Forbes M, Kempa R, Mastrobuoni G, Rayman L, Pietzke M, Bayram S, Arlt B, Spruessel A, Deubzer HE, Kempa S. L-Glyceraldehyde Inhibits Neuroblastoma Cell Growth via a Multi-Modal Mechanism on Metabolism and Signaling. Cancers (Basel) 2024; 16:1664. [PMID: 38730615 PMCID: PMC11083149 DOI: 10.3390/cancers16091664] [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: 03/28/2024] [Revised: 04/18/2024] [Accepted: 04/22/2024] [Indexed: 05/13/2024] Open
Abstract
Glyceraldehyde (GA) is a three-carbon monosaccharide that can be present in cells as a by-product of fructose metabolism. Bruno Mendel and Otto Warburg showed that the application of GA to cancer cells inhibits glycolysis and their growth. However, the molecular mechanism by which this occurred was not clarified. We describe a novel multi-modal mechanism by which the L-isomer of GA (L-GA) inhibits neuroblastoma cell growth. L-GA induces significant changes in the metabolic profile, promotes oxidative stress and hinders nucleotide biosynthesis. GC-MS and 13C-labeling was employed to measure the flow of carbon through glycolytic intermediates under L-GA treatment. It was found that L-GA is a potent inhibitor of glycolysis due to its proposed targeting of NAD(H)-dependent reactions. This results in growth inhibition, apoptosis and a redox crisis in neuroblastoma cells. It was confirmed that the redox mechanisms were modulated via L-GA by proteomic analysis. Analysis of nucleotide pools in L-GA-treated cells depicted a previously unreported observation, in which nucleotide biosynthesis is significantly inhibited. The inhibitory action of L-GA was partially relieved with the co-application of the antioxidant N-acetyl-cysteine. We present novel evidence for a simple sugar that inhibits cancer cell proliferation via dysregulating its fragile homeostatic environment.
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Affiliation(s)
- Martin Forbes
- Integrative Proteomics and Metabolomics, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115 Berlin, Germany
- Department of Pediatric Hematology and Oncology, Charité—Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Richard Kempa
- Integrative Proteomics and Metabolomics, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115 Berlin, Germany
| | - Guido Mastrobuoni
- Integrative Proteomics and Metabolomics, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115 Berlin, Germany
| | - Liam Rayman
- Integrative Proteomics and Metabolomics, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115 Berlin, Germany
| | - Matthias Pietzke
- Integrative Proteomics and Metabolomics, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115 Berlin, Germany
- Mass Spectrometry Facility, MaxPlanck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany
| | - Safak Bayram
- Integrative Proteomics and Metabolomics, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115 Berlin, Germany
| | - Birte Arlt
- Integrative Proteomics and Metabolomics, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115 Berlin, Germany
- Department of Pediatric Hematology and Oncology, Charité—Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
- Berliner Institut für Gesundheitsforschung (BIH), Anna-Louisa-Karsch-Strase 2, 10178 Berlin, Germany
| | - Annika Spruessel
- Berliner Institut für Gesundheitsforschung (BIH), Anna-Louisa-Karsch-Strase 2, 10178 Berlin, Germany
| | - Hedwig E. Deubzer
- Department of Pediatric Hematology and Oncology, Charité—Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
- Berliner Institut für Gesundheitsforschung (BIH), Anna-Louisa-Karsch-Strase 2, 10178 Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, Invalidenstr. 80, 10115 Berlin, Germany
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
- Experimental and Clinical Research Center (ECRC), Charité and Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association, 13125 Berlin, Germany
| | - Stefan Kempa
- Integrative Proteomics and Metabolomics, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine in the Helmholtz Association, Hannoversche Str. 28, 10115 Berlin, Germany
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Wang Y, Hang L, Shou W, Li C, Dong F, Feng X, Jin R, Li B, Xiao S. Case Report: A novel RRM2B variant in a Chinese infant with mitochondrial DNA depletion syndrome and collective analyses of RRM2B variants for disease etiology. Front Pediatr 2024; 12:1363728. [PMID: 38737634 PMCID: PMC11084280 DOI: 10.3389/fped.2024.1363728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 04/10/2024] [Indexed: 05/14/2024] Open
Abstract
Background There are few reports of infantile mitochondrial DNA depletion syndrome (MDDS) caused by variants in RRM2B and the correlation between genotype and phenotype has rarely been analyzed in detail. This study investigated an infantile patient with MDDS, from clinical characteristics to genetic causes. Methods Routine physical examinations, laboratory assays, which included gas chromatography-mass spectrometry of blood and urine, and MRI scans were performed to obtain an exact diagnosis. Whole-exome sequencing was used to pinpoint the abnormal gene and bioinformatic analyses were performed on the identified variant. Results The case presented with progressive neurologic deterioration, failure to thrive, respiratory distress and lactic acidosis. Sequencing revealed that the patient had a homozygous novel missense variant, c.155T>C (p.Ile52Thr), in exon 2 of the RRM2B gene. Multiple lines of bioinformatic evidence suggested that this was a likely detrimental variant. In addition, reported RRM2B variants were compiled from the relevant literature to analyze disease etiology. We found a distinctive distribution of genotypes across disease manifestations of different severity. Pathogenic alleles of RRM2B were significantly enriched in MDDS cases. Conclusion The novel variant is a likely genetic cause of MDDS. It expands our understanding of the pathogenic variant spectrum and the contribution of the RRM2B gene to the disease spectrum of MDDS.
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Affiliation(s)
- Yanjun Wang
- Pediatric Intensive Care Unit, Kunming Children’s Hospital, Children’s Hospital Affiliated to Kunming Medical University, Kunming, China
| | - Ling Hang
- Pediatric Intensive Care Unit, Kunming Children’s Hospital, Children’s Hospital Affiliated to Kunming Medical University, Kunming, China
| | - Weihua Shou
- Kunming Key Laboratory of Children Infection and Immunity, Yunnan Key Laboratory of Children’s Major Disease Research, Yunnan Medical Center for Pediatric Diseases, Yunnan Institute of Pediatrics, Kunming Children’s Hospital, Kunming, China
| | - Cuifen Li
- Pediatric Intensive Care Unit, Kunming Children’s Hospital, Children’s Hospital Affiliated to Kunming Medical University, Kunming, China
| | - Fangling Dong
- Pediatric Intensive Care Unit, Kunming Children’s Hospital, Children’s Hospital Affiliated to Kunming Medical University, Kunming, China
| | - Xingxing Feng
- Department of Clinical Laboratory, Kunming Children’s Hospital, Children’s Hospital Affiliated to Kunming Medical University, Kunming, China
| | - Ruohong Jin
- Pediatric Intensive Care Unit, Kunming Children’s Hospital, Children’s Hospital Affiliated to Kunming Medical University, Kunming, China
| | - Bin Li
- Pediatric Intensive Care Unit, Kunming Children’s Hospital, Children’s Hospital Affiliated to Kunming Medical University, Kunming, China
| | - Shufang Xiao
- Pediatric Intensive Care Unit, Kunming Children’s Hospital, Children’s Hospital Affiliated to Kunming Medical University, Kunming, China
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Dumitru CA, Walter N, Siebert CLR, Schäfer FTA, Rashidi A, Neyazi B, Stein KP, Mawrin C, Sandalcioglu IE. The Roles of AGTRAP, ALKBH3, DIVERSIN, NEDD8 and RRM1 in Glioblastoma Pathophysiology and Prognosis. Biomedicines 2024; 12:926. [PMID: 38672281 PMCID: PMC11048029 DOI: 10.3390/biomedicines12040926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/15/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024] Open
Abstract
This study determined the expression of five novel biomarker candidates in IDH wild-type glioblastoma (GBM) tissues compared to non-malign brain parenchyma, as well as their prognostic relevance for the GBM patients' outcomes. The markers were analysed by immunohistochemistry in tumour tissues (n = 186) and healthy brain tissues (n = 54). The association with the patients' overall survival (OS) and progression-free survival (PFS) was assessed by Kaplan-Meier and log-rank test. The prognostic value of the markers was determined using multivariate Cox proportional hazard models. AGTRAP, DIVERSIN, cytoplasmic NEDD8 (NEDD8c) and RRM1 were significantly overexpressed in tumour tissues compared to the healthy brain, while the opposite was observed for ALKBH3. AGTRAP, ALKBH3, NEDD8c and RRM1 were significantly associated with OS in univariate analysis. AGTRAP and RRM1 were also independent prognostic factors for OS in multivariate analysis. For PFS, only AGTRAP and NEDD8c reached significance in univariate analysis. Additionally, AGTRAP was an independent prognostic factor for PFS in multivariate models. Finally, combined analysis of the markers enhanced their prognostic accuracy. The combination AGTRAP/ALKBH3 had the strongest prognostic value for the OS of GBM patients. These findings contribute to a better understanding of the GBM pathophysiology and may help identify novel therapeutic targets in this type of cancer.
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Affiliation(s)
| | - Nikolas Walter
- Department of Neurosurgery, Otto-von-Guericke University, 39120 Magdeburg, Germany (I.E.S.)
| | | | | | - Ali Rashidi
- Department of Neurosurgery, Otto-von-Guericke University, 39120 Magdeburg, Germany (I.E.S.)
| | - Belal Neyazi
- Department of Neurosurgery, Otto-von-Guericke University, 39120 Magdeburg, Germany (I.E.S.)
| | - Klaus-Peter Stein
- Department of Neurosurgery, Otto-von-Guericke University, 39120 Magdeburg, Germany (I.E.S.)
| | - Christian Mawrin
- Department of Neuropathology, Otto-von-Guericke University, 39120 Magdeburg, Germany
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Shetty MG, Pai P, Padavu M, Satyamoorthy K, Kampa Sundara B. Synergistic therapeutics: Co-targeting histone deacetylases and ribonucleotide reductase for enhanced cancer treatment. Eur J Med Chem 2024; 269:116324. [PMID: 38520762 DOI: 10.1016/j.ejmech.2024.116324] [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: 01/13/2024] [Revised: 03/06/2024] [Accepted: 03/09/2024] [Indexed: 03/25/2024]
Abstract
The development of cancer is influenced by several variables, including altered protein expression, and signaling pathways. Cancers are inherently heterogeneous and exhibit genetic and epigenetic aberrations; therefore, developing therapies that act on numerous biological targets is encouraged. To achieve this, two approaches are employed: combination therapy and dual/multiple targeting chemotherapeutics. Two enzymes, histone deacetylases (HDACs) and ribonucleotide reductase (RR), are crucial for several biological functions, including replication and repair of DNA, division of cells, transcription of genes, etc. However, it has been noted that different cancers exhibit abnormal functions of these enzymes. Potent inhibitors for each of these proteins have been extensively researched. Many medications based on these inhibitors have been successfully food and drug administration (FDA) approved, and the majority are undergoing various stages of clinical testing. This review discusses various studies of HDAC and RR inhibitors in combination therapy and dual-targeting chemotherapeutics.
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Affiliation(s)
- Manasa Gangadhar Shetty
- Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Padmini Pai
- Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Mythili Padavu
- Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, India
| | - Kapaettu Satyamoorthy
- Shri Dharmasthala Manjunatheshwara (SDM) University, Manjushree Nagar, Sattur, Dharwad, 580009, India
| | - Babitha Kampa Sundara
- Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, India.
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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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10
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Du S, Wu Y, Ying H, Wu Z, Yang M, Chen F, Shao J, Liu H, Zhang Z, Zhao Y. Genome sequences of the first Autographiviridae phages infecting marine Roseobacter. Microb Genom 2024; 10. [PMID: 38630615 DOI: 10.1099/mgen.0.001240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024] Open
Abstract
The ubiquitous and abundant marine phages play critical roles in shaping the composition and function of bacterial communities, impacting biogeochemical cycling in marine ecosystems. Autographiviridae is among the most abundant and ubiquitous phage families in the ocean. However, studies on the diversity and ecology of Autographiviridae phages in marine environments are restricted to isolates that infect SAR11 bacteria and cyanobacteria. In this study, ten new roseophages that infect marine Roseobacter strains were isolated from coastal waters. These new roseophages have a genome size ranging from 38 917 to 42 634 bp and G+C content of 44.6-50 %. Comparative genomics showed that they are similar to known Autographiviridae phages regarding gene content and architecture, thus representing the first Autographiviridae roseophages. Phylogenomic analysis based on concatenated conserved genes showed that the ten roseophages form three distinct subgroups within the Autographiviridae, and sequence analysis revealed that they belong to eight new genera. Finally, viromic read-mapping showed that these new Autographiviridae phages are widely distributed in global oceans, mostly inhabiting polar and estuarine locations. This study has expanded the current understanding of the genomic diversity, evolution and ecology of Autographiviridae phages and roseophages. We suggest that Autographiviridae phages play important roles in the mortality and community structure of roseobacters, and have broad ecological applications.
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Affiliation(s)
- Sen Du
- College of Juncao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou, PR China
| | - Ying Wu
- College of Juncao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou, PR China
| | - Hanqi Ying
- College of Juncao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou, PR China
| | - Zuqing Wu
- College of Juncao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou, PR China
| | - Mingyu Yang
- College of Juncao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou, PR China
| | - Feng Chen
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, USA
| | - Jiabing Shao
- College of Juncao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou, PR China
| | - He Liu
- College of Juncao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou, PR China
| | - Zefeng Zhang
- College of Juncao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou, PR China
| | - Yanlin Zhao
- College of Juncao Science and Ecology, Fujian Agriculture and Forestry University, Fuzhou, PR China
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Fujian Agriculture and Forestry University, Fuzhou, PR China
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11
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Su J, Xie Q, Xie L. Identification and validation of a metabolism-related gene signature for predicting the prognosis of paediatric medulloblastoma. Sci Rep 2024; 14:7540. [PMID: 38553479 PMCID: PMC10980764 DOI: 10.1038/s41598-024-57549-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 03/19/2024] [Indexed: 04/01/2024] Open
Abstract
Medulloblastoma (MB) is a malignant brain tumour that is highly common in children and has a tendency to spread to the brain and spinal cord. MB is thought to be a metabolically driven brain tumour. Understanding tumour cell metabolic patterns and characteristics can provide a promising foundation for understanding MB pathogenesis and developing treatments. Here, by analysing RNA-seq data of MB samples from the Gene Expression Omnibus (GEO) database, 12 differentially expressed metabolic-related genes (DE-MRGs) were chosen for the construction of a predictive risk score model for MB. This model demonstrated outstanding accuracy in predicting the outcomes of MB patients and served as a standalone predictor. An evaluation of functional enrichment revealed that the risk score showed enrichment in pathways related to cancer promotion and the immune response. In addition, a high risk score was an independent poor prognostic factor for MB in patients with different ages, sexes, metastasis stages and subgroups (SHH and Group 4). Consistently, the metabolic enzyme ornithine decarboxylase (ODC1) was upregulated in MB patients with poor survival time. Inhibition of ODC1 in primary and metastatic MB cell lines decreased cell proliferation, migration and invasion but increased immune infiltration. This study could aid in identifying metabolic targets for MB as well as optimizing risk stratification systems and individual treatment plans for MB patients via the use of a metabolism-related gene prognostic risk score signature.
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Affiliation(s)
- Jun Su
- Department of Neurosurgery, The Affiliated Children's Hospital Of Xiangya School of Medicine, Central South University (Hunan children's hospital), No. 86 Ziyuan Road, Changsha, 410007, Hunan, China
| | - Qin Xie
- Department of Neurosurgery, Xiangya Hospital, Central South University, No. 86 Xiangya Road, Changsha, 410008, Hunan, China
| | - Longlong Xie
- Pediatrics Research Institute of Hunan Province, Hunan Provincial Key Laboratory of Pediatric Orthopedics, The Affiliated Children's Hospital Of Xiangya School of Medicine, Central South University (Hunan children's hospital), No. 86 Ziyuan Road, Changsha, 410007, Hunan, China.
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12
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Nithimethachoke T, Boonmak C, Morikawa M. A novel alkane monooxygenase evolved from a broken piece of ribonucleotide reductase in Geobacillus kaustophilus HTA426 isolated from Mariana Trench. Extremophiles 2024; 28:18. [PMID: 38353731 PMCID: PMC10867098 DOI: 10.1007/s00792-024-01332-8] [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: 11/04/2023] [Accepted: 12/30/2023] [Indexed: 02/16/2024]
Abstract
We have accidentally found that a thermophilic Geobacillus kaustophilus HTA426 is capable of degrading alkanes although it has no alkane oxygenating enzyme genes. Our experimental results revealed that a putative ribonucleotide reductase small subunit GkR2loxI (GK2771) gene encodes a novel heterodinuclear Mn-Fe alkane monooxygenase/hydroxylase. GkR2loxI protein can perform two-electron oxidations similar to homonuclear diiron bacterial multicomponent soluble methane monooxygenases. This finding not only answers a long-standing question about the substrate of the R2lox protein clade, but also expands our understanding of the vast diversity and new evolutionary lineage of the bacterial alkane monooxygenase/hydroxylase family.
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Affiliation(s)
- Tanasap Nithimethachoke
- Graduate School of Environmental Science, Hokkaido University, Kita-10 Nishi-5, Kita-ku, Sapporo, 060-0810, Japan
| | - Chanita Boonmak
- Department of Microbiology, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Rd., Lat Yao, Chatuchak, Bangkok, 10900, Thailand
| | - Masaaki Morikawa
- Graduate School of Environmental Science, Hokkaido University, Kita-10 Nishi-5, Kita-ku, Sapporo, 060-0810, Japan.
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13
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Korotenko V, Zipse H. The stability of oxygen-centered radicals and its response to hydrogen bonding interactions. J Comput Chem 2024; 45:101-114. [PMID: 37747356 DOI: 10.1002/jcc.27221] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/10/2023] [Accepted: 08/11/2023] [Indexed: 09/26/2023]
Abstract
The stability of various alkoxy/aryloxy/peroxy radicals, as well as TEMPO and triplet dioxygen (3 O2 ) has been explored at a variety of theoretical levels. Good correlations between RSEtheor and RSEexp are found for hybrid DFT methods, for compound schemes such as G3B3-D3, and also for DLPNO-CCSD(T) calculations. The effects of hydrogen bonding interactions on the stability of oxygen-centered radicals have been probed by addition of a single solvating water molecule. While this water molecule always acts as a H-bond donor to the oxygen-centered radical itself, it can act as a H-bond donor or acceptor to the respective closed-shell parent.
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Affiliation(s)
| | - Hendrik Zipse
- Department of Chemistry, LMU Munich, Munich, Germany
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14
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Chen J, Cui L, Lu S, Xu S. Amino acid metabolism in tumor biology and therapy. Cell Death Dis 2024; 15:42. [PMID: 38218942 PMCID: PMC10787762 DOI: 10.1038/s41419-024-06435-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: 09/27/2023] [Revised: 12/19/2023] [Accepted: 01/04/2024] [Indexed: 01/15/2024]
Abstract
Amino acid metabolism plays important roles in tumor biology and tumor therapy. Accumulating evidence has shown that amino acids contribute to tumorigenesis and tumor immunity by acting as nutrients, signaling molecules, and could also regulate gene transcription and epigenetic modification. Therefore, targeting amino acid metabolism will provide new ideas for tumor treatment and become an important therapeutic approach after surgery, radiotherapy, and chemotherapy. In this review, we systematically summarize the recent progress of amino acid metabolism in malignancy and their interaction with signal pathways as well as their effect on tumor microenvironment and epigenetic modification. Collectively, we also highlight the potential therapeutic application and future expectation.
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Affiliation(s)
- Jie Chen
- National Key Lab of Immunity and Inflammation and Institute of Immunology, Naval Medical University/Second Military Medical University, Shanghai, 200433, China
| | - Likun Cui
- National Key Lab of Immunity and Inflammation and Institute of Immunology, Naval Medical University/Second Military Medical University, Shanghai, 200433, China
| | - Shaoteng Lu
- National Key Lab of Immunity and Inflammation and Institute of Immunology, Naval Medical University/Second Military Medical University, Shanghai, 200433, China
| | - Sheng Xu
- National Key Lab of Immunity and Inflammation and Institute of Immunology, Naval Medical University/Second Military Medical University, Shanghai, 200433, China.
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai, 200120, China.
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15
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Wang ZH, Li J, Liu Q, Qian JC, Li QQ, Wang QY, Zeng LT, Li SJ, Gao X, Pan JX, Gao XF, Wu K, Hu GX, Iwakuma T, Cai JP. A modified nucleoside O6-methyl-2'-deoxyguanosine-5'-triphosphate exhibits anti-glioblastoma activity in a caspase-independent manner. Pharmacol Res 2024; 199:106990. [PMID: 37984506 DOI: 10.1016/j.phrs.2023.106990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/07/2023] [Accepted: 11/13/2023] [Indexed: 11/22/2023]
Abstract
Resistance to temozolomide (TMZ), the frontline chemotherapeutic agent for glioblastoma (GBM), has emerged as a formidable obstacle, underscoring the imperative to identify alternative therapeutic strategies to improve patient outcomes. In this study, we comprehensively evaluated a novel agent, O6-methyl-2'-deoxyguanosine-5'-triphosphate (O6-methyl-dGTP) for its anti-GBM activity both in vitro and in vivo. Notably, O6-methyl-dGTP exhibited pronounced cytotoxicity against GBM cells, including those resistant to TMZ and overexpressing O6-methylguanine-DNA methyltransferase (MGMT). Mechanistic investigations revealed that O6-methyl-dGTP could be incorporated into genomic DNA, disrupting nucleotide pools balance, and inducing replication stress, resulting in S-phase arrest and DNA damage. The compound exerted its anti-tumor properties through the activation of AIF-mediated apoptosis and the parthanatos pathway. In vivo studies using U251 and Ln229 cell xenografts supported the robust tumor-inhibitory capacity of O6-methyl-dGTP. In an orthotopic transplantation model with U87MG cells, O6-methyl-dGTP showcased marginally superior tumor-suppressive activity compared to TMZ. In summary, our research, for the first time, underscores the potential of O6-methyl-dGTP as an effective candidate against GBM, laying a robust scientific groundwork for its potential clinical adoption in GBM treatment regimens.
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Affiliation(s)
- Zi-Hui Wang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, China; Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Jin Li
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, China
| | - Qian Liu
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, China; Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Jian-Chang Qian
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Qing-Qing Li
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Qing-Yu Wang
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, China
| | - Lv-Tao Zeng
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, China
| | - Si-Jia Li
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, China
| | - Xin Gao
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, China
| | - Jia-Xin Pan
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, China
| | - Xu-Fan Gao
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, China; Department of Geriatrics, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Kun Wu
- Wu Xi AppTec (Tianjin) Co., Ltd, China
| | - Guo-Xin Hu
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Tomoo Iwakuma
- Children's Mercy Research Institute, Kansas City, MO 64108, USA
| | - Jian-Ping Cai
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, China; Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.
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16
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Chang Y, Zhou Y, Zhou J, Li W, Cao J, Jing Y, Zhang S, Shen Y, Lin Q, Fan X, Yang H, Dong X, Zhang S, Yi X, Shuai L, Shi L, Liu Z, Yang J, Ma X, Hao J, Chen K, Li MJ, Wang F, Huang D. Unraveling the causal genes and transcriptomic determinants of human telomere length. Nat Commun 2023; 14:8517. [PMID: 38129441 PMCID: PMC10739845 DOI: 10.1038/s41467-023-44355-z] [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: 01/18/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023] Open
Abstract
Telomere length (TL) shortening is a pivotal indicator of biological aging and is associated with many human diseases. The genetic determinates of human TL have been widely investigated, however, most existing studies were conducted based on adult tissues which are heavily influenced by lifetime exposure. Based on the analyses of terminal restriction fragment (TRF) length of telomere, individual genotypes, and gene expressions on 166 healthy placental tissues, we systematically interrogate TL-modulated genes and their potential functions. We discover that the TL in the placenta is comparatively longer than in other adult tissues, but exhibiting an intra-tissue homogeneity. Trans-ancestral TL genome-wide association studies (GWASs) on 644,553 individuals identify 20 newly discovered genetic associations and provide increased polygenic determination of human TL. Next, we integrate the powerful TL GWAS with placental expression quantitative trait locus (eQTL) mapping to prioritize 23 likely causal genes, among which 4 are functionally validated, including MMUT, RRM1, KIAA1429, and YWHAZ. Finally, modeling transcriptomic signatures and TRF-based TL improve the prediction performance of human TL. This study deepens our understanding of causal genes and transcriptomic determinants of human TL, promoting the mechanistic research on fine-grained TL regulation.
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Affiliation(s)
- Ying Chang
- Tianjin Key Lab of Human Development and Reproductive Regulation, Tianjin Central Hospital of Obstetrics and Gynecology, Nankai University, Tianjin, China
| | - Yao Zhou
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Junrui Zhou
- Department of Genetics and Tianjin Key Laboratory of Cellular and Molecular Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
- Department of Clinical Laboratory, Shanghai Children's Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Wen Li
- Tianjin Key Lab of Human Development and Reproductive Regulation, Tianjin Central Hospital of Obstetrics and Gynecology, Nankai University, Tianjin, China
| | - Jiasong Cao
- Tianjin Key Lab of Human Development and Reproductive Regulation, Tianjin Central Hospital of Obstetrics and Gynecology, Nankai University, Tianjin, China
| | - Yaqing Jing
- Department of Genetics and Tianjin Key Laboratory of Cellular and Molecular Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Shan Zhang
- Department of Genetics and Tianjin Key Laboratory of Cellular and Molecular Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Yongmei Shen
- Tianjin Key Lab of Human Development and Reproductive Regulation, Tianjin Central Hospital of Obstetrics and Gynecology, Nankai University, Tianjin, China
| | - Qimei Lin
- Tianjin Key Lab of Human Development and Reproductive Regulation, Tianjin Central Hospital of Obstetrics and Gynecology, Nankai University, Tianjin, China
| | - Xutong Fan
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Hongxi Yang
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Xiaobao Dong
- Department of Genetics and Tianjin Key Laboratory of Cellular and Molecular Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Shijie Zhang
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Xianfu Yi
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Ling Shuai
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Tianjin Central Hospital of Gynecology Obstetrics/Tianjin Key Laboratory of Human Development and Reproductive Regulation, Nankai University, Tianjin, China
| | - Lei Shi
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Zhe Liu
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Jie Yang
- Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Xin Ma
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Jihui Hao
- Department of Pancreatic Cancer, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Kexin Chen
- Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Mulin Jun Li
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.
- Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China.
| | - Feng Wang
- Department of Genetics and Tianjin Key Laboratory of Cellular and Molecular Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.
- Tianjin Medical University School of Stomatology, Tianjin Medical University, Tianjin, China.
- Department of Geriatrics, Tianjin Medical University General Hospital; Tianjin Geriatrics Institute, Tianjin, China.
| | - Dandan Huang
- Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.
- Wuxi School of Medicine, Jiangnan University, Wuxi, China.
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17
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Singh D, Banerjee G, Verma N, Sinha AK. MAP kinases may mediate regulation of the cell cycle in rice by E2F2 phosphorylation. FEBS Lett 2023; 597:2993-3009. [PMID: 37843487 DOI: 10.1002/1873-3468.14753] [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: 05/21/2023] [Revised: 08/10/2023] [Accepted: 09/06/2023] [Indexed: 10/17/2023]
Abstract
E2F is the key transcription factor that determines the proliferative status of cells by regulating the G1/S phase of the cell cycle. In this study, we show that in rice (Oryza sativa), OsE2F2 is a phosphorylation target of MAP kinases. The MAP kinases OsMPK3, OsMPK4, and OsMPK6 interact with and phosphorylate OsE2F2. Next, we determined the serine and threonine residues that could play a role in the phosphorylation of OsE2F2. Subsequently, our study suggests a possible link between MAP kinase-mediated OsE2F2 phosphorylation and its impact on DNA proliferation in the roots of rice seedlings. Finally, we found positive feedback regulation of OsMPK4 by OsE2F2. Therefore, our study hints at the potential impact of MAP kinase signaling on the cell cycle of rice plants.
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Affiliation(s)
- Dhanraj Singh
- National Institute of Plant Genome Research, Delhi, New Delhi, India
| | - Gopal Banerjee
- National Institute of Plant Genome Research, Delhi, New Delhi, India
| | - Neetu Verma
- National Institute of Plant Genome Research, Delhi, New Delhi, India
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18
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Studstill CJ, Mac M, Moody CA. Interplay between the DNA damage response and the life cycle of DNA tumor viruses. Tumour Virus Res 2023; 16:200272. [PMID: 37918513 PMCID: PMC10685005 DOI: 10.1016/j.tvr.2023.200272] [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: 08/25/2023] [Revised: 10/26/2023] [Accepted: 10/29/2023] [Indexed: 11/04/2023] Open
Abstract
Approximately 20 % of human cancers are associated with virus infection. DNA tumor viruses can induce tumor formation in host cells by disrupting the cell's DNA replication and repair mechanisms. Specifically, these viruses interfere with the host cell's DNA damage response (DDR), which is a complex network of signaling pathways that is essential for maintaining the integrity of the genome. DNA tumor viruses can disrupt these pathways by expressing oncoproteins that mimic or inhibit various DDR components, thereby promoting genomic instability and tumorigenesis. Recent studies have highlighted the molecular mechanisms by which DNA tumor viruses interact with DDR components, as well as the ways in which these interactions contribute to viral replication and tumorigenesis. Understanding the interplay between DNA tumor viruses and the DDR pathway is critical for developing effective strategies to prevent and treat virally associated cancers. In this review, we discuss the current state of knowledge regarding the mechanisms by which human papillomavirus (HPV), merkel cell polyomavirus (MCPyV), Kaposi's sarcoma-associated herpesvirus (KSHV), and Epstein-Barr virus (EBV) interfere with DDR pathways to facilitate their respective life cycles, and the consequences of such interference on genomic stability and cancer development.
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Affiliation(s)
- Caleb J Studstill
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States
| | - Michelle Mac
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States
| | - Cary A Moody
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States.
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19
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McCown C, Yu CH, Ivanov DN. Allosteric substrate activation of SAMHD1 shapes deoxynucleotide triphosphate imbalances by interconnecting the depletion and biosynthesis of different dNTPs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.14.567083. [PMID: 38014186 PMCID: PMC10680743 DOI: 10.1101/2023.11.14.567083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
SAMHD1 is a dNTPase that impedes replication of HIV-1 in myeloid cells and resting T lymphocytes. Here we elucidate the substrate activation mechanism of SAMHD1 that depends on dNTP binding at allosteric sites and the concomitant tetramerization of the enzyme. The study reveals that SAMHD1 activation involves an inactive tetrameric intermediate with partial occupancy of the allosteric sites. The equilibrium between the inactive and active tetrameric states, which is coupled to cooperative binding/dissociation of at least two allosteric dNTP ligands, controls the dNTPase activity of the enzyme, which, in addition, depends on the identity of the dNTPs occupying the four allosteric sites of the active tetramer. We show how such allosteric regulation determines deoxynucleotide triphosphate levels established in the dynamic equilibria between dNTP production and SAMHD1-catalyzed depletion. Notably, the mechanism enables a distinctive functionality of SAMHD1, which we call facilitated dNTP depletion, whereby elevated biosynthesis of some dNTPs results in more efficient depletion of others. The regulatory relationship between the biosynthesis and depletion of different dNTPs sheds light on the emerging role of SAMHD1 in the biology of dNTP homeostasis with implications for HIV/AIDS, innate antiviral immunity, T cell disorders, telomere maintenance and therapeutic efficacy of nucleoside analogs.
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20
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Yue C, Zhang C, Zhang R, Yuan J. Tethered particle motion of the adaptation enzyme CheR in bacterial chemotaxis. iScience 2023; 26:107950. [PMID: 37817931 PMCID: PMC10561060 DOI: 10.1016/j.isci.2023.107950] [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] [Received: 05/09/2023] [Revised: 07/25/2023] [Accepted: 09/14/2023] [Indexed: 10/12/2023] Open
Abstract
Bacteria perform chemotactic adaptation by sequential modification of multiple modifiable sites on chemoreceptors through stochastic action of tethered adaptation enzymes (CheR and CheB). To study the molecular kinetics of this process, we measured the response to different concentrations of MeAsp for the Tar-only Escherichia coli strain. We found a strong dependence of the methylation rate on the methylation level and established a new mechanism of adaptation kinetics due to tethered particle motion of the methylation enzyme CheR. Experiments with various lengths of the C-terminal flexible chain in the Tar receptor further validated this mechanism. The tethered particle motion resulted in a CheR concentration gradient that ensures encounter-rate matching of the sequential modifiable sites. An analytical model of multisite catalytic reaction showed that this enables robustness of methylation to fluctuations in receptor activity or cell-to-cell variations in the expression of adaptation enzymes and reduces the variation in methylation level among individual receptors.
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Affiliation(s)
- Caijuan Yue
- Hefei National Laboratory for Physical Sciences at the Microscale, and Department of Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Chi Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, and Department of Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Rongjing Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, and Department of Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Junhua Yuan
- Hefei National Laboratory for Physical Sciences at the Microscale, and Department of Physics, University of Science and Technology of China, Hefei, Anhui 230026, China
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21
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Fuertes T, Álvarez-Corrales E, Gómez-Escolar C, Ubieto-Capella P, Serrano-Navarro Á, de Molina A, Méndez J, Ramiro AR, de Yébenes VG. miR-28-based combination therapy impairs aggressive B cell lymphoma growth by rewiring DNA replication. Cell Death Dis 2023; 14:687. [PMID: 37852959 PMCID: PMC10585006 DOI: 10.1038/s41419-023-06178-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 09/07/2023] [Accepted: 09/26/2023] [Indexed: 10/20/2023]
Abstract
Diffuse large B cell lymphoma (DLBCL) is the most common aggressive B cell lymphoma and accounts for nearly 40% of cases of B cell non-Hodgkin lymphoma. DLBCL is generally treated with R-CHOP chemotherapy, but many patients do not respond or relapse after treatment. Here, we analyzed the therapeutic potential of the tumor suppressor microRNA-28 (miR-28) for DLBCL, alone and in combination with the Bruton's tyrosine kinase inhibitor ibrutinib. Combination therapy with miR-28 plus ibrutinib potentiated the anti-tumor effects of monotherapy with either agent by inducing a specific transcriptional cell-cycle arrest program that impairs DNA replication. The molecular actions of miR-28 and ibrutinib synergistically impair DNA replication by simultaneous inhibition of origin activation and fork progression. Moreover, we found that downregulation of the miR-28-plus-ibrutinib gene signature correlates with better survival of ABC-DLBCL patients. These results provide evidence for the effectiveness of a new miRNA-based ibrutinib combination therapy for DLBCL and unveil the miR-28-plus-ibrutinib gene signature as a new predictor of outcome in ABC-DLBCL patients.
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Affiliation(s)
- Teresa Fuertes
- B Cell Biology Laboratory Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Emigdio Álvarez-Corrales
- Department of Immunology, Ophthalmology and ENT, Universidad Complutense de Madrid; Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid, Spain
| | - Carmen Gómez-Escolar
- B Cell Biology Laboratory Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | | | - Álvaro Serrano-Navarro
- B Cell Biology Laboratory Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Antonio de Molina
- Comparative Medicine Unit. Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Juan Méndez
- DNA replication Group. Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid, Spain
| | - Almudena R Ramiro
- B Cell Biology Laboratory Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain.
| | - Virginia G de Yébenes
- Department of Immunology, Ophthalmology and ENT, Universidad Complutense de Madrid; Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), Madrid, Spain.
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22
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Wu LY, Piedade GJ, Moore RM, Harrison AO, Martins AM, Bidle KD, Polson SW, Sakowski EG, Nissimov JI, Dums JT, Ferrell BD, Wommack KE. Ubiquitous, B 12-dependent virioplankton utilizing ribonucleotide-triphosphate reductase demonstrate interseasonal dynamics and associate with a diverse range of bacterial hosts in the pelagic ocean. ISME COMMUNICATIONS 2023; 3:108. [PMID: 37789093 PMCID: PMC10547690 DOI: 10.1038/s43705-023-00306-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 08/31/2023] [Accepted: 09/06/2023] [Indexed: 10/05/2023]
Abstract
Through infection and lysis of their coexisting bacterial hosts, viruses impact the biogeochemical cycles sustaining globally significant pelagic oceanic ecosystems. Currently, little is known of the ecological interactions between lytic viruses and their bacterial hosts underlying these biogeochemical impacts at ecosystem scales. This study focused on populations of lytic viruses carrying the B12-dependent Class II monomeric ribonucleotide reductase (RNR) gene, ribonucleotide-triphosphate reductase (Class II RTPR), documenting seasonal changes in pelagic virioplankton and bacterioplankton using amplicon sequences of Class II RTPR and the 16S rRNA gene, respectively. Amplicon sequence libraries were analyzed using compositional data analysis tools that account for the compositional nature of these data. Both virio- and bacterioplankton communities responded to environmental changes typically seen across seasonal cycles as well as shorter term upwelling-downwelling events. Defining Class II RTPR-carrying viral populations according to major phylogenetic clades proved a more robust means of exploring virioplankton ecology than operational taxonomic units defined by percent sequence homology. Virioplankton Class II RTPR populations showed positive associations with a broad phylogenetic diversity of bacterioplankton including dominant taxa within pelagic oceanic ecosystems such as Prochlorococcus and SAR11. Temporal changes in Class II RTPR virioplankton, occurring as both free viruses and within infected cells, indicated possible viral-host pairs undergoing sustained infection and lysis cycles throughout the seasonal study. Phylogenetic relationships inferred from Class II RTPR sequences mirrored ecological patterns in virio- and bacterioplankton populations demonstrating possible genome to phenome associations for an essential viral replication gene.
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Affiliation(s)
- Ling-Yi Wu
- Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, Padualaan 8, Utrecht, 3584 CH, the Netherlands
| | - Gonçalo J Piedade
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, 1797 SZ, t'Horntje, The Netherlands
- Department of Oceanography and Fisheries and Ocean Sciences Institute-OKEANOS, University of the Azores, 9901-862 Horta, Faial, Azores, Portugal
| | - Ryan M Moore
- Delaware Biotechnology Institute, University of Delaware, 590 Avenue 1743, Newark, DE, 19713, USA
| | - Amelia O Harrison
- Delaware Biotechnology Institute, University of Delaware, 590 Avenue 1743, Newark, DE, 19713, USA
| | - Ana M Martins
- Department of Oceanography and Fisheries and Ocean Sciences Institute-OKEANOS, University of the Azores, 9901-862 Horta, Faial, Azores, Portugal
| | - Kay D Bidle
- Department of Marine and Coastal Sciences, Rutgers University, 71 Dudley Rd., New Brunswick, NJ, 08901, USA
| | - Shawn W Polson
- Delaware Biotechnology Institute, University of Delaware, 590 Avenue 1743, Newark, DE, 19713, USA
| | - Eric G Sakowski
- Department of Earth Sciences, Johns Hopkins University, Baltimore, MD, USA
| | - Jozef I Nissimov
- Department of Biology, University of Waterloo, 200 University Ave. West, Waterloo, ON, N2L 3G1, Canada
| | - Jacob T Dums
- Delaware Biotechnology Institute, University of Delaware, 590 Avenue 1743, Newark, DE, 19713, USA
- Biotechnology Program, North Carolina State University, 2800 Faucette Dr, Raleigh, NC, 27695, USA
| | - Barbra D Ferrell
- Delaware Biotechnology Institute, University of Delaware, 590 Avenue 1743, Newark, DE, 19713, USA
| | - K Eric Wommack
- Delaware Biotechnology Institute, University of Delaware, 590 Avenue 1743, Newark, DE, 19713, USA.
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23
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Chen C, Xue N, Liu K, He Q, Wang C, Guo Y, Tian J, Liu X, Pan Y, Chen G. USP12 promotes nonsmall cell lung cancer progression through deubiquitinating and stabilizing RRM2. Mol Carcinog 2023; 62:1518-1530. [PMID: 37341611 DOI: 10.1002/mc.23593] [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: 03/18/2023] [Revised: 05/16/2023] [Accepted: 06/05/2023] [Indexed: 06/22/2023]
Abstract
RRM2 is the catalytic subunit of ribonucleotide reductase (RNR), which catalyzes de novo synthesis of deoxyribonucleotide triphosphates (dNTPs) and plays critical roles in cancer cell proliferation. RRM2 protein level is controlled by ubiquitination mediated protein degradation system; however, its deubiquitinase has not been identified yet. Here we showed that ubiquitin-specific peptidase 12 (USP12) directly interacts with and deubiquitinates RRM2 in non-small cell lung cancer (NSCLC) cells. Knockdown of USP12 causes DNA replication stress and retards tumor growth in vivo and in vitro. Meanwhile, USP12 protein levels were positively correlated to RRM2 protein levels in human NSCLC tissues. In addition, high expression of USP12 was associated with poor prognosis in NSCLC patients. Therefore, our study reveals that USP12 is a RRM2 regulator and targeting USP12 could be considered as a potential therapeutical strategy for NSCLC treatment.
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Affiliation(s)
- Congcong Chen
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, P.R. China
- Department of Medical Biochemistry and Molecular Biology, School of Medicine, Jinan University, Guangzhou, P.R. China
| | - Ning Xue
- Department of Acupuncture, Jurong Hospital Affiliated to Jiangsu University, Zhenjiang, P.R. China
| | - Kangshou Liu
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, P.R. China
- Department of Medical Biochemistry and Molecular Biology, School of Medicine, Jinan University, Guangzhou, P.R. China
| | - Qiang He
- Department of Medical Biochemistry and Molecular Biology, School of Medicine, Jinan University, Guangzhou, P.R. China
| | - Cong Wang
- School of Biopharmacy, China Pharmaceutical University, Nanjing, P.R. China
| | - Yanguan Guo
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, P.R. China
- Department of Medical Biochemistry and Molecular Biology, School of Medicine, Jinan University, Guangzhou, P.R. China
| | - Jiaxin Tian
- Department of Medical Biochemistry and Molecular Biology, School of Medicine, Jinan University, Guangzhou, P.R. China
| | - Xinjian Liu
- Department of Pathogen Biology, Key Laboratory of Antibody Technique of National Health Commission of China, Nanjing Medical University, Nanjing, P.R. China
| | - Yunlong Pan
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, P.R. China
| | - Guo Chen
- Department of Medical Biochemistry and Molecular Biology, School of Medicine, Jinan University, Guangzhou, P.R. China
- School of Biopharmacy, China Pharmaceutical University, Nanjing, P.R. China
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24
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Zhan Y, Tao Q, Lang Z, Lin L, Li X, Yu S, Yu Z, Zhou G, Wu K, Zhou Z, Yu Z, Zheng J. Serum ribonucleotide reductase M2 is a potential biomarker for diagnosing and monitoring liver fibrosis in chronic hepatitis B patients. J Med Virol 2023; 95:e29157. [PMID: 37814947 DOI: 10.1002/jmv.29157] [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: 06/11/2023] [Revised: 09/14/2023] [Accepted: 09/25/2023] [Indexed: 10/11/2023]
Abstract
It is known that ribonucleotide reductase M2 (RRM2) could be induced by hepatitis B virus (HBV) via DNA damage response. However, whether RRM2 is a potential biomarker for diagnosing and monitoring liver fibrosis in chronic hepatitis B (CHB) patients is still unclear. In this study, CHB patients from GSE84044 (a transcriptome data from GEO data set) were downloaded and RRM2 was selected as a hub gene. Interestingly, a positive correlation was found between serum RRM2 and liver fibrosis stage. The similar results were found in CHB patients with normal alanine aminotransferase (ALT). Notably, RRM2 could effectively differentiate preliminary fibrosis from advanced fibrosis in CHB patients with/without normal ALT. In addition, RRM2 had a better performance in diagnosing liver fibrosis than two commonly used noninvasive methods (aspartate aminotransferase-to-platelet ratio index and fibrosis index based on the four factors), two classic fibrotic biomarkers (hyaluronic acid and type IV collagen) as well as Mac-2 binding protein glycosylation isomer, a known serum fibrosis marker. Moreover, CHB patients with high RRM2, who were associated with advanced fibrosis, had higher expressions of immune checkpoints. Overall, serum RRM2 may be a promising biomarker for diagnosing and monitoring liver fibrosis in CHB patients.
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Affiliation(s)
- Yating Zhan
- Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Qiqi Tao
- Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Zhichao Lang
- Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Lifan Lin
- Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xinmiao Li
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Suhui Yu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Zhengping Yu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Guangyao Zhou
- Department of Infectious Diseases, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Kaifeng Wu
- Department of Laboratory Medicine, The First People's Hospital of Zunyi, Zunyi, China
| | - Zhenxu Zhou
- Department of Hernia and Abdominal Wall Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Zhixian Yu
- Department of Urology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Jianjian Zheng
- Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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25
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Hess SS, Coppola F, Dang VT, Tran PN, Mickel PJ, Oktawiec J, Ren Z, Král P, Nguyen AI. Noncovalent Peptide Assembly Enables Crystalline, Permutable, and Reactive Thiol Frameworks. J Am Chem Soc 2023; 145:19588-19600. [PMID: 37639365 DOI: 10.1021/jacs.3c03645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Though thiols are exceptionally versatile, their high reactivity has also hindered the synthesis and characterization of well-defined thiol-containing porous materials. Leveraging the mild conditions of the noncovalent peptide assembly, we readily synthesized and characterized a number of frameworks with thiols displayed at many unique positions and in several permutations. Importantly, nearly all assemblies were structurally determined using single-crystal X-ray diffraction to reveal their rich sequence-structure landscape and the cooperative noncovalent interactions underlying their assembly. These observations and supporting molecular dynamics calculations enabled rational engineering by the positive and negative design of noncovalent interactions. Furthermore, the thiol-containing frameworks undergo diverse single-crystal-to-single-crystal reactions, including toxic metal ion coordination (e.g., Cd2+, Pb2+, and Hg2+), selective uptake of Hg2+ ions, and redox transformations. Notably, we find a framework that supports thiol-nitrosothiol interconversion, which is applicable for biocompatible nitric oxide delivery. The modularity, ease of synthesis, functionality, and well-defined nature of these peptide-based thiol frameworks are expected to accelerate the design of complex materials with reactive active sites.
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Affiliation(s)
- Selina S Hess
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, United States
| | - Francesco Coppola
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, United States
| | - Viet Thuc Dang
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, United States
| | - Phuong Nguyen Tran
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, United States
| | - Philip J Mickel
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, United States
| | - Julia Oktawiec
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Zhong Ren
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, United States
| | - Petr Král
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, United States
| | - Andy I Nguyen
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, United States
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26
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Tsybizova A, Fritsche L, Miloglyadova L, Kräutler B, Chen P. Cryogenic Ion Vibrational Predissociation (CIVP) Spectroscopy of Aryl Cobinamides in the Gas Phase: How Good Are the Calculations for Vitamin B 12 Derivatives? J Am Chem Soc 2023; 145:19561-19570. [PMID: 37656981 PMCID: PMC10510309 DOI: 10.1021/jacs.3c03001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Indexed: 09/03/2023]
Abstract
Aryl corrins represent a novel class of designed B12 derivatives with biological properties of "antivitamins B12". In our previous study, we experimentally determined bond strength in a series of aryl-corrins by the threshold collision-induced dissociation experiments (T-CID) and compared the measured bond dissociation energies (BDEs) with those calculated with density functional theory (DFT). We found that the BDEs are modulated by the side chains around the periphery of the corrin unit. Given that aryl cobinamides have many side chains that increase their conformational space and that the question of a specific structure, measured in the gas phase, was important for further evaluation of our T-CID experiment, we proceeded to analyze structural properties of aryl cobinamides using cryogenic ion vibrational predissociation (CIVP) spectroscopy, static DFT, and Born-Oppenheimer molecular dynamic (BOMD) simulations. We found that none of the examined DFT models could reproduce the CIVP spectra convincingly; both "static" DFT calculations and "dynamic" BOMD simulations provide a surprisingly poor representation of the vibrational spectra, specifically of the number, position, and intensity of bands assigned to hydrogen-bonded versus non-hydrogen-bonded NH and OH moieties. We conclude that, for a flexible molecule with ca. 150 atoms, more accurate approaches are needed before definitive conclusions about computed properties, specifically the structure of the ground-state conformer, may be made.
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Affiliation(s)
- Alexandra Tsybizova
- Laboratorium
für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
| | - Lukas Fritsche
- Laboratorium
für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
| | - Larisa Miloglyadova
- Laboratorium
für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
| | - Bernhard Kräutler
- Institute
of Organic Chemistry, University of Innsbruck, Innrain 80/82, 6020 Innsbruck, Austria
| | - Peter Chen
- Laboratorium
für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 2, CH-8093 Zurich, Switzerland
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27
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Tang S, Leng M, Tan C, Zhu L, Pang Y, Zhang X, Chang YF, Lin W. Critical role for ribonucleoside-diphosphate reductase subunit M2 in ALV-J-induced activation of Wnt/β-catenin signaling via interaction with P27. J Virol 2023; 97:e0026723. [PMID: 37582207 PMCID: PMC10506463 DOI: 10.1128/jvi.00267-23] [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: 02/19/2023] [Accepted: 06/20/2023] [Indexed: 08/17/2023] Open
Abstract
Avian leukemia virus subgroup J (ALV-J) causes various diseases associated with tumor formation and decreased fertility and induced immunosuppressive disease, resulting in significant economic losses in the poultry industry globally. Virus usually exploits the host cellular machinery for their replication. Although there are increasing evidences for the cellular proteins involving viral replication, the interaction between ALV-J and host proteins leading to the pivotal steps of viral life cycle are still unclear. Here, we reported that ribonucleoside-diphosphate reductase subunit M2 (RRM2) plays a critical role during ALV-J infection by interacting with capsid protein P27 and activating Wnt/β-catenin signaling. We found that the expression of RRM2 is effectively increased during ALV-J infection, and that RRM2 facilitates ALV-J replication by interacting with viral capsid protein P27. Furthermore, ALV-J P27 activated Wnt/β-catenin signaling by promoting β-catenin entry into the nucleus, and RRM2 activated Wnt/β-catenin signaling by enhancing its phosphorylation at Ser18 during ALV-J infection. These data suggest that the upregulation of RRM2 expression by ALV-J infection favors viral replication in host cells via activating Wnt/β-catenin signaling. IMPORTANCE Our results revealed a novel mechanism by which RRM2 facilitates ALV-J growth. That is, the upregulation of RRM2 expression by ALV-J infection favors viral replication by interacting with capsid protein P27 and activating Wnt/β-catenin pathway in host cells. Furthermore, the phosphorylation of serine at position 18 of RRM2 was verified to be the important factor regulating the activation of Wnt/β-catenin signaling. This study provides insights for further studies of the molecular mechanism of ALV-J infection.
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Affiliation(s)
- Shuang Tang
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangdong Provincial Animal Virus Vector Vaccine Engineering Technology Research Center, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Mei Leng
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangdong Provincial Animal Virus Vector Vaccine Engineering Technology Research Center, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Chen Tan
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangdong Provincial Animal Virus Vector Vaccine Engineering Technology Research Center, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Lin Zhu
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangdong Provincial Animal Virus Vector Vaccine Engineering Technology Research Center, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yanling Pang
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangdong Provincial Animal Virus Vector Vaccine Engineering Technology Research Center, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Xinheng Zhang
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangdong Provincial Animal Virus Vector Vaccine Engineering Technology Research Center, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Yung-Fu Chang
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Wencheng Lin
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangdong Provincial Animal Virus Vector Vaccine Engineering Technology Research Center, College of Animal Science, South China Agricultural University, Guangzhou, China
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28
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Cui Y, He M, Liu J, Wang S, Zhang J, Xie S, Hu Z, Guo S, Yan D. Maize LOST SUBSIDIARY CELL encoding a large subunit of ribonucleotide reductase is required for subsidiary cell development and plant growth. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4449-4460. [PMID: 37103989 PMCID: PMC10433938 DOI: 10.1093/jxb/erad153] [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: 12/13/2022] [Accepted: 04/26/2023] [Indexed: 06/19/2023]
Abstract
The four-celled stomatal complex consists of a pair of guard cells (GCs) and two subsidiary cells (SCs) in grasses, which supports a fast adjustment of stomatal aperture. The formation and development of SCs are thus important for stomatal functionality. Here, we report a maize lost subsidiary cells (lsc) mutant, with many stomata lacking one or two SCs. The loss of SCs is supposed to have resulted from impeded subsidiary mother cell (SMC) polarization and asymmetrical division. Besides the defect in SCs, the lsc mutant also displays a dwarf morphology and pale and striped newly-grown leaves. LSC encodes a large subunit of ribonucleotide reductase (RNR), an enzyme involved in deoxyribonucleotides (dNTPs) synthesis. Consistently, the concentration of dNTPs and expression of genes involved in DNA replication, cell cycle progression, and SC development were significantly reduced in the lsc mutant compared with the wild-type B73 inbred line. Conversely, overexpression of maize LSC increased dNTP synthesis and promoted plant growth in both maize and Arabidopsis. Our data indicate that LSC regulates dNTP production and is required for SMC polarization, SC differentiation, and growth of maize.
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Affiliation(s)
- Yongqi Cui
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng 475004, China
| | - Meiqing He
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng 475004, China
| | - Jie Liu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng 475004, China
| | - Shuang Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng 475004, China
| | - Junli Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng 475004, China
| | - Shiyi Xie
- Maize Engineering and Technology Research Center of Hunan Province, College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Zhubing Hu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng 475004, China
| | - Siyi Guo
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng 475004, China
| | - Dawei Yan
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng 475004, China
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29
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Zhang P, Wang X, Wang X, Huang C, James TD, Sun X, Qian X. Chemoselective Fluorogenic Bioconjugation of Vicinal Dithiol-Containing Proteins for Live Cellular Imaging via Small Molecular Conjugate Acceptors. Anal Chem 2023; 95:11953-11959. [PMID: 37490273 DOI: 10.1021/acs.analchem.3c01518] [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: 07/26/2023]
Abstract
To develop small molecular fluorogenic tools for the chemoselective labeling of vicinal dithiol-containing proteins (VDPs) in live cells is important for studying intracellular redox homeostasis. With this research, we developed small molecule-based fluorescent probes, achieving selective labeling of VDPs through thiol-thiol substitutions on bisvinylogous thioester conjugated acceptors (IDAs). Initially, IDAs demonstrated its ability to bridge vicinal cysteine-sulfhydryls on a peptide as a mimic. Then, the peptide complex could be decoupled to recover the original peptide-SH in the presence of dithiothreitol. Furthermore, fluorometric signal amplification of the fluorescent probes occurred with high sensitivity, low limit of detection, and selectivity toward vicinal dithiols on reduced bovine serum albumin, as an example of real world VDPs. More importantly, the probes were utilized successfully for labeling of endogenous VDPs at different redox states in live cells. Thus, the bisvinylogous thioester-based receptor as a functional probe represents a new platform for uncovering the function of VDPs in live cells.
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Affiliation(s)
- Peng Zhang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, No. 28, West Xianning Road, Xi'an 710049, People's Republic of China
| | - Xuechuan Wang
- College of Chemistry and Chemical Engineering, Shaanxi University of Science & Technology, Xi'an 710021, People's Republic of China
| | - Xiao Wang
- College of Chemistry and Chemical Engineering, Shaanxi University of Science & Technology, Xi'an 710021, People's Republic of China
| | - Chusen Huang
- The Education Ministry Key Laboratory of Resource Chemistry, Shanghai Normal University, No. 100 Guilin Road, Shanghai 200234, People's Republic of China
| | - Tony D James
- Department of Chemistry, University of Bath, Bath BA2 7AY, United Kingdom
| | - Xiaolong Sun
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, No. 28, West Xianning Road, Xi'an 710049, People's Republic of China
| | - Xuhong Qian
- State Key Laboratory of Bioreactor Engineering; Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, No. 130 Meilong Road, Shanghai 200237, People's Republic of China
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Nakatani T, Torres-Padilla ME. Regulation of mammalian totipotency: a molecular perspective from in vivo and in vitro studies. Curr Opin Genet Dev 2023; 81:102083. [PMID: 37421903 DOI: 10.1016/j.gde.2023.102083] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 06/03/2023] [Accepted: 06/11/2023] [Indexed: 07/10/2023]
Abstract
In mammals, cells acquire totipotency at fertilization. Embryonic genome activation (EGA), which occurs at the 2-cell stage in the mouse and 4- to 8-cell stage in humans, occurs during the time window at which embryonic cells are totipotent and thus it is thought that EGA is mechanistically linked to the foundations of totipotency. The molecular mechanisms that lead to the establishment of totipotency and EGA had been elusive for a long time, however, recent advances have been achieved with the establishment of new cell lines with greater developmental potential and the application of novel low-input high-throughput techniques in embryos. These have unveiled several principles of totipotency related to its epigenetic makeup but also to characteristic features of totipotent cells. In this review, we summarize and discuss current views exploring some of the key drivers of totipotency from both in vitro cell culture models and embryogenesis in vivo.
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Affiliation(s)
- Tsunetoshi Nakatani
- Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München, D-81377 München, Germany
| | - Maria-Elena Torres-Padilla
- Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München, D-81377 München, Germany; Faculty of Biology, Ludwig-Maximilians Universität, München, Germany.
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31
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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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Lin JC, Liu TP, Chen YB, Huang TS, Chen TY, Yang PM. Inhibition of CDK9 exhibits anticancer activity in hepatocellular carcinoma cells via targeting ribonucleotide reductase. Toxicol Appl Pharmacol 2023; 471:116568. [PMID: 37245555 DOI: 10.1016/j.taap.2023.116568] [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: 02/23/2023] [Revised: 05/12/2023] [Accepted: 05/23/2023] [Indexed: 05/30/2023]
Abstract
Cyclin-dependent kinase 9 (CDK9) inhibitors are a novel category of anticancer treatment for cancers. However, their effects on hepatocellular carcinoma (HCC) are rarely investigated. Human ribonucleotide reductase (RR, which consists of RRM1 and RRM2 subunits) catalyzes the conversion of ribonucleoside diphosphate into 2'-deoxyribonucleoside diphosphate to maintain the homeostasis of nucleotide pools, which play essential roles in DNA synthesis and DNA repair. In this study, we identified that CDK9 protein expression in adjacent non-tumor tissues predicted HCC patients' overall and progression-free survivals. The anticancer activity of a CDK9-selective inhibitor, LDC000067, on HCC cells was positively associated with its ability to inhibit the expression of RRM1 and RRM2. LDC000067 downregulated RRM1 and RRM2 expression through post-transcriptional pathway. Specifically, LDC000067 triggered RRM2 protein degradation via multiple pathways, including proteasome-, lysosome-, and calcium-dependent pathways. Furthermore, CDK9 positively correlates with RRM1 or RRM2 expression in HCC patients, and the expressions of these three genes were associated with the higher infiltration of immune cells in HCC. Taken together, this study identified the prognostic relevance of CDK9 in HCC and the molecular mechanism for the anticancer effect of CDK9 inhibitors on HCC.
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Affiliation(s)
- Jiunn-Chang Lin
- Department of Surgery, MacKay Memorial Hospital, Taipei 10449, Taiwan; MacKay Junior College of Medicine, Nursing, and Management, New Taipei City 11260, Taiwan; Department of Medicine, MacKay Medical College, New Taipei City 25245, Taiwan; Liver Medical Center, MacKay Memorial Hospital, Taipei 10449, Taiwan; PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan
| | - Tsang-Pai Liu
- Department of Surgery, MacKay Memorial Hospital, Taipei 10449, Taiwan; MacKay Junior College of Medicine, Nursing, and Management, New Taipei City 11260, Taiwan; Department of Medicine, MacKay Medical College, New Taipei City 25245, Taiwan; Liver Medical Center, MacKay Memorial Hospital, Taipei 10449, Taiwan; PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan
| | - Yan-Bin Chen
- Department of Surgery, MacKay Memorial Hospital, Taipei 10449, Taiwan
| | - Tun-Sung Huang
- Department of Surgery, MacKay Memorial Hospital, Taipei 10449, Taiwan; Department of Medicine, MacKay Medical College, New Taipei City 25245, Taiwan; Liver Medical Center, MacKay Memorial Hospital, Taipei 10449, Taiwan
| | - Tung-Ying Chen
- Department of Medicine, MacKay Medical College, New Taipei City 25245, Taiwan; Department of Pathology, MacKay Memorial Hospital, Taipei 10449, Taiwan
| | - Pei-Ming Yang
- Liver Medical Center, MacKay Memorial Hospital, Taipei 10449, Taiwan; PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan; Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; TMU Research Center of Cancer Translational Medicine, Taipei 11031, Taiwan; Cancer Center, Wan Fang Hospital, Taipei Medical University, Taipei 11696, Taiwan; TMU and Affiliated Hospitals Pancreatic Cancer Groups, Taipei Medical University, Taipei 11031, Taiwan.
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Bao W, Zhang W, Huang Y, Zhao Y, Wu C, Duan L, Wang L, Yan S. Protein kinase ATR inhibits E3 ubiquitin ligase CRL4 PRL1 to stabilize ribonucleotide reductase in response to replication stress. Cell Rep 2023; 42:112685. [PMID: 37354461 DOI: 10.1016/j.celrep.2023.112685] [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: 10/13/2022] [Revised: 03/14/2023] [Accepted: 06/07/2023] [Indexed: 06/26/2023] Open
Abstract
The protein kinase ATR is essential for replication stress responses in all eukaryotes. Ribonucleotide reductase (RNR) catalyzes the formation of deoxyribonucleotide (dNTP), the universal building block for DNA replication and repair. However, the relationship between ATR and RNR is not well understood. Here, we show that ATR promotes the protein stability of RNR in Arabidopsis. Through an activation tagging-based genetic screen, we found that overexpression of TSO2, a small subunit of RNR, partially suppresses the hypersensitivity of the atr mutant to replication stress. Biochemically, TSO2 interacts with PRL1, a central subunit of the Cullin4-based E3 ubiquitin ligase CRL4PRL1, which polyubiquitinates TSO2 and promotes its degradation. ATR inhibits CRL4PRL1 to attenuate TSO2 degradation. Our work provides an important insight into the replication stress responses and a post-translational regulatory mechanism for RNR. Given the evolutionary conservation of the proteins involved, the ATR-PRL1-RNR module may act across eukaryotes.
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Affiliation(s)
- Weiyi Bao
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen 518000, China; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Weijia Zhang
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen 518000, China; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Yongchi Huang
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen 518000, China; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Yan Zhao
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen 518000, China; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Cong Wu
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen 518000, China; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Leilei Duan
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen 518000, China; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Lili Wang
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen 518000, China; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China.
| | - Shunping Yan
- Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen 518000, China; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China.
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Tong Y, Wu X, Liu Y, Chen H, Zhou Y, Jiang L, Li M, Zhao S, Zhang Y. Alternative Z-genome biosynthesis pathway shows evolutionary progression from Archaea to phage. Nat Microbiol 2023:10.1038/s41564-023-01410-1. [PMID: 37308591 DOI: 10.1038/s41564-023-01410-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 05/11/2023] [Indexed: 06/14/2023]
Abstract
Many bacteriophages evade bacterial immune recognition by substituting adenine with 2,6-diaminopurine (Z) in their genomes. The Z-genome biosynthetic pathway involves PurZ that belongs to the PurA (adenylosuccinate synthetase) family and bears particular similarity to archaeal PurA. However, how the transition of PurA to PurZ occurred during evolution is not clear; recapturing this process may shed light on the origin of Z-containing phages. Here we describe the computer-guided identification and biochemical characterization of a naturally existing PurZ variant, PurZ0, which uses guanosine triphosphate as the phosphate donor rather than the ATP used by PurZ. The atomic resolution structure of PurZ0 reveals a guanine nucleotide binding pocket highly analogous to that of archaeal PurA. Phylogenetic analyses suggest PurZ0 as an intermediate during the evolution of archaeal PurA to phage PurZ. Maintaining the balance of different purines necessitates further evolvement of guanosine triphosphate-using PurZ0 to ATP-using PurZ in adaptation to Z-genome life.
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Affiliation(s)
- Yang Tong
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
- Frontiers Science Center for Synthetic Biology, Ministry of Education, Tianjin University, Tianjin, China
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- Department of Chemistry, Tianjin University, Tianjin, China
| | - Xinying Wu
- iHuman Institute, ShanghaiTech University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yang Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Huiyu Chen
- iHuman Institute, ShanghaiTech University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yan Zhou
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Li Jiang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China.
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China.
| | - Suwen Zhao
- iHuman Institute, ShanghaiTech University, Shanghai, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
| | - Yan Zhang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China.
- Frontiers Science Center for Synthetic Biology, Ministry of Education, Tianjin University, Tianjin, China.
- Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.
- Department of Chemistry, Tianjin University, Tianjin, China.
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Yuan F, Su B, Yu Y, Wang J. Study and design of amino acid-based radical enzymes using unnatural amino acids. RSC Chem Biol 2023; 4:431-446. [PMID: 37292061 PMCID: PMC10246556 DOI: 10.1039/d2cb00250g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 05/17/2023] [Indexed: 06/10/2023] Open
Abstract
Radical enzymes harness the power of reactive radical species by placing them in a protein scaffold, and they are capable of catalysing many important reactions. New native radical enzymes, especially those with amino acid-based radicals, in the category of non-heme iron enzymes (including ribonucleotide reductases), heme enzymes, copper enzymes, and FAD-radical enzymes have been discovered and characterized. We discussed recent research efforts to discover new native amino acid-based radical enzymes, and to study the roles of radicals in processes such as enzyme catalysis and electron transfer. Furthermore, design of radical enzymes in a small and simple scaffold not only allows us to study the radical in a well-controlled system and test our understanding of the native enzymes, but also allows us to create powerful enzymes. In the study and design of amino acid-based radical enzymes, the use of unnatural amino acids allows precise control of pKa values and reduction potentials of the residue, as well as probing the location of the radical through spectroscopic methods, making it a powerful research tool. Our understanding of amino acid-based radical enzymes will allow us to tailor them to create powerful catalysts and better therapeutics.
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Affiliation(s)
- Feiyan Yuan
- Institute of Biochemical Engineering, Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology Beijing 102488 China
| | - Binbin Su
- Institute of Biochemical Engineering, Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology Beijing 102488 China
| | - Yang Yu
- Institute of Biochemical Engineering, Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology Beijing 102488 China
| | - Jiangyun Wang
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences Beijing 100101 China
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Virgous C, Lyons L, Sakwe A, Nayyar T, Goodwin S, Hildreth J, Osteen K, Bruner-Tran K, Alawode O, Bourne P, Hills ER, Archibong AE. Resumption of Spermatogenesis and Fertility Post Withdrawal of Hydroxyurea Treatment. Int J Mol Sci 2023; 24:ijms24119374. [PMID: 37298325 DOI: 10.3390/ijms24119374] [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: 03/08/2023] [Revised: 04/11/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
Hydroxyurea (HU), a drug for treating cancers of the blood and the management of sickle cell anemia, induces hypogonadism in males. However, the impact of HU on testicular architecture and function, as well as its effects on the resumption of male fertility following treatment withdrawal, remain poorly understood. We used adult male mice to determine whether HU-induced hypogonadism is reversible. Fertility indices of mice treated with HU daily for ~1 sperm cycle (2 months) were compared with those of their control counterparts. All indices of fertility were significantly reduced among mice treated with HU compared to controls. Interestingly, significant improvements in fertility indices were apparent after a 4-month withdrawal from HU treatment (testis weight: month 1 post-HU withdrawal (M1): HU, 0.09 ± 0.01 vs. control, 0.33 ± 0.03; M4: HU, 0.26 ± 0.03 vs. control, 0.37 ± 0.04 g); sperm motility (M1: HU,12 vs. 59; M4: HU, 45 vs. control, 61%; sperm density (M1: HU, 1.3 ± 0.3 vs. control, 15.7 ± 0.9; M4: HU, 8.1 ± 2.5 vs. control, 16.8 ± 1.9 million). Further, circulating testosterone increased in the 4th month following HU withdrawal and was comparable to that of controls. When a mating experiment was conducted, recovering males sired viable offspring with untreated females albeit at a lower rate than control males (p < 0.05); therefore, qualifying HU as a potential candidate for male contraception.
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Affiliation(s)
- Carlos Virgous
- Animal Care Facility, Meharry Medical College, 1005 D.B. Todd Blvd, Nashville, TN 37209, USA
| | - Letitia Lyons
- Department of Obstetrics and Gynecology, Meharry Medical College, 1005 D.B. Todd Blvd, Nashville, TN 37208, USA
| | - Amos Sakwe
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College, 1005 D.B. Todd Blvd, Nashville, TN 37208, USA
| | - Tultul Nayyar
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College, 1005 D.B. Todd Blvd, Nashville, TN 37208, USA
| | - Shawn Goodwin
- Department of Biochemistry, Cancer Biology, Neuroscience and Pharmacology, Meharry Medical College, 1005 D.B. Todd Blvd, Nashville, TN 37208, USA
| | - James Hildreth
- Department of Microbiology, Immunology and Physiology, Meharry Medical College, 1005 D.B. Todd Blvd, Nashville, TN 37208, USA
| | - Kevin Osteen
- Women's Reproductive Health Research Center, Department of Obstetrics and Gynecology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Kaylon Bruner-Tran
- Women's Reproductive Health Research Center, Department of Obstetrics and Gynecology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Oluwatobi Alawode
- Department of Obstetrics and Gynecology, Meharry Medical College, 1005 D.B. Todd Blvd, Nashville, TN 37208, USA
| | - Phillip Bourne
- Department of Obstetrics and Gynecology, Meharry Medical College, 1005 D.B. Todd Blvd, Nashville, TN 37208, USA
| | - Edward Richard Hills
- Department of Obstetrics and Gynecology, Meharry Medical College, 1005 D.B. Todd Blvd, Nashville, TN 37208, USA
| | - Anthony E Archibong
- Department of Obstetrics and Gynecology, Meharry Medical College, 1005 D.B. Todd Blvd, Nashville, TN 37208, USA
- Department of Microbiology, Immunology and Physiology, Meharry Medical College, 1005 D.B. Todd Blvd, Nashville, TN 37208, USA
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Bharathi S, Mahendiran D, Ahmed S, Rahiman AK. In vitro anti-proliferative, and in silico ribonucleotide reductase and pharmacokinetics studies of heteroleptic silver(I), nickel(II) and copper(II) complexes of 4-methyl-3-thiosemicarbazones and ibuprofen. J Trace Elem Med Biol 2023; 79:127211. [PMID: 37263062 DOI: 10.1016/j.jtemb.2023.127211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 11/10/2022] [Accepted: 05/17/2023] [Indexed: 06/03/2023]
Abstract
OBJECTIVES The present research focuses on the in vitro anti-proliferative, and in silico ribonucleotide reductase and pharmacokinetics studies of twelve heteroleptic metal complexes of the general formulae [Ag(L1-4)(ibu)] (1-4) and [M(L1-4)(ibu)2] (5-12), where L1-4 = 2-(1-(4-substitutedphenyl)ethylidene)-N-methylhydrazinecarbothioamide, ibu = non-steroidal anti-inflammatory drug (ibuprofen), and M = Cu(II) and Ni(II). METHODS Various spectroscopic techniques were used to authenticate the structure of the synthesized complexes. UV-Vis and cyclic voltammetry techniques were used to analyse the stability and the reducing ability of the complexes. In vitro anti-proliferative studies by MTT assay, apoptotic behaviour and cellular uptake studies were investigated followed by the in silico interaction with ribonucleotide reductase (RNR) enzyme. RESULTS The spectral studies predicted distorted tetrahedral geometry around silver(I) ion and distorted octahedral geometry around nickel(II) and copper(II) ions. The reducing ability of the copper(II) complexes was analysed using ascorbic acid by UV-Vis and cyclic voltammetry techniques, which authenticate the reducing ability of the complexes and the possible interactions within the cells. The in vitro anti-proliferative activity of the synthesized complexes against three cancerous (estrogen positive (MCF-7), estrogen negative (MDA-MB-231) and pancreatic (PANC-1)) and one normal (MCF-10a) cell lines by MTT assay showed enhanced activity for copper(II) complexes 11 and 12 containing the hydrophobic substituents. The apoptotic and cellular uptake studies showed that the complex 12 is readily taken up by PANC-1 cell lines and induces ROS-mediated mitochondrial and caspase-dependent apoptosis. The in silico studies indicated hydrogen bonding, hydrophobic and π-pair (π-π, π-σ and π-cation) interactions between the complexes and the ribonucleotide reductase (RNR) enzyme. The in silico pharmacokinetics studies of the complexes predicted the drug-likeness characteristics of the complexes. CONCLUSION The synthesized complexes are found to be less toxic to normal cells and inhibit the growth of cancerous cells by inducing mitochondrial-mediated and caspase dependent apoptotic pathway in PANC-1 cells.
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Affiliation(s)
- Sundaram Bharathi
- Post-Graduate and Research Department of Chemistry, The New College (Autonomous), University of Madras, Chennai 600 014, India; Department of Chemistry, School of Basic Sciences, Vels Institute of Science, Technology and Advanced Studies, Chennai 600 117, India
| | - Dharmasivam Mahendiran
- Post-Graduate and Research Department of Chemistry, The New College (Autonomous), University of Madras, Chennai 600 014, India; Griffith Institute for Drug Discovery, Griffith University, Nathan, Brisbane, Queensland, Australia
| | - Sumeer Ahmed
- Post-Graduate and Research Department of Chemistry, The New College (Autonomous), University of Madras, Chennai 600 014, India
| | - Aziz Kalilur Rahiman
- Post-Graduate and Research Department of Chemistry, The New College (Autonomous), University of Madras, Chennai 600 014, India.
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Purhonen J, Banerjee R, Wanne V, Sipari N, Mörgelin M, Fellman V, Kallijärvi J. Mitochondrial complex III deficiency drives c-MYC overexpression and illicit cell cycle entry leading to senescence and segmental progeria. Nat Commun 2023; 14:2356. [PMID: 37095097 PMCID: PMC10126100 DOI: 10.1038/s41467-023-38027-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 04/12/2023] [Indexed: 04/26/2023] Open
Abstract
Accumulating evidence suggests mitochondria as key modulators of normal and premature aging, yet whether primary oxidative phosphorylation (OXPHOS) deficiency can cause progeroid disease remains unclear. Here, we show that mice with severe isolated respiratory complex III (CIII) deficiency display nuclear DNA damage, cell cycle arrest, aberrant mitoses, and cellular senescence in the affected organs such as liver and kidney, and a systemic phenotype resembling juvenile-onset progeroid syndromes. Mechanistically, CIII deficiency triggers presymptomatic cancer-like c-MYC upregulation followed by excessive anabolic metabolism and illicit cell proliferation against lack of energy and biosynthetic precursors. Transgenic alternative oxidase dampens mitochondrial integrated stress response and the c-MYC induction, suppresses the illicit proliferation, and prevents juvenile lethality despite that canonical OXPHOS-linked functions remain uncorrected. Inhibition of c-MYC with the dominant-negative Omomyc protein relieves the DNA damage in CIII-deficient hepatocytes in vivo. Our results connect primary OXPHOS deficiency to genomic instability and progeroid pathogenesis and suggest that targeting c-MYC and aberrant cell proliferation may be therapeutic in mitochondrial diseases.
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Affiliation(s)
- Janne Purhonen
- Folkhälsan Research Center, Haartmaninkatu 8, 00290, Helsinki, Finland
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, P.O.Box 63, 00014, Helsinki, Finland
| | - Rishi Banerjee
- Folkhälsan Research Center, Haartmaninkatu 8, 00290, Helsinki, Finland
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, P.O.Box 63, 00014, Helsinki, Finland
| | - Vilma Wanne
- Folkhälsan Research Center, Haartmaninkatu 8, 00290, Helsinki, Finland
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, P.O.Box 63, 00014, Helsinki, Finland
| | - Nina Sipari
- Viikki Metabolomics Unit, University of Helsinki, P.O.Box 65, Helsinki, Finland
| | - Matthias Mörgelin
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, P.O.Box 117, 221 00, Lund, Sweden
- Colzyx AB, Scheelevägen 2, 22381, Lund, Sweden
| | - Vineta Fellman
- Folkhälsan Research Center, Haartmaninkatu 8, 00290, Helsinki, Finland
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, P.O.Box 63, 00014, Helsinki, Finland
- Department of Clinical Sciences, Lund, Pediatrics, Lund University, P.O.Box 117, 221 00, Lund, Sweden
- Children's Hospital, Clinicum, University of Helsinki, P.O. Box 22, 00014, Helsinki, Finland
| | - Jukka Kallijärvi
- Folkhälsan Research Center, Haartmaninkatu 8, 00290, Helsinki, Finland.
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, P.O.Box 63, 00014, Helsinki, Finland.
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Shen W, Sun J, Xiao Z, Feng P, Zhang T, He G, Sang X. Narrow and Stripe Leaf 2 Regulates Leaf Width by Modulating Cell Cycle Progression in Rice. RICE (NEW YORK, N.Y.) 2023; 16:20. [PMID: 37071312 PMCID: PMC10113404 DOI: 10.1186/s12284-023-00634-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 03/26/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Leaf morphology is an important component of the idea plant architecture that extensively influences photosynthesis, transpiration, and ultimately grain yield in crops. However, the genetic and molecular mechanisms regulating this morphology remain largely unclear. RESULTS In this study, a mutant showing a narrow and stripe leaf phonotype, designated nsl2, was obtained. Histological analysis revealed defects in the vascular system and reduced epidermal cell number in the nsl2, while the cell size remained unchanged. Map-based cloning and genetic complementation experiments revealed that NSL2, which encodes a small subunit of ribonucleotide reductases (RNRs), is a null allelic with ST1 and SDL. The NSL2 was expressed in variety of tissues, with the highest levels detected in leaves, and its protein was localized in the nucleus and cytoplasm. The dNTPs level was altered in the nsl2 mutant, and thereby affecting the dNTPs pool balance. In addition, flow cytometric analysis and the altered transcript level of genes related to cell cycle indicated that NSL2 affects cell cycle progression. CONCLUSIONS Our findings here suggest that NSL2 function in the synthesis of dNTP, the deficient of which leads to DNA synthesis block and in turn affects cell cycle progression, and ultimately decreased cell number and narrow leaf in the nsl2 plant.
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Affiliation(s)
- Wenqiang Shen
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Engineering Research Center of South Upland Agriculture, Ministry of Education, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715 China
| | - Jiajie Sun
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Engineering Research Center of South Upland Agriculture, Ministry of Education, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715 China
| | - Zan Xiao
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Engineering Research Center of South Upland Agriculture, Ministry of Education, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715 China
| | - Ping Feng
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Engineering Research Center of South Upland Agriculture, Ministry of Education, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715 China
| | - Ting Zhang
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Engineering Research Center of South Upland Agriculture, Ministry of Education, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715 China
| | - Guanghua He
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Engineering Research Center of South Upland Agriculture, Ministry of Education, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715 China
| | - Xianchun Sang
- Rice Research Institute, Key Laboratory of Application and Safety Control of Genetically Modified Crops, Engineering Research Center of South Upland Agriculture, Ministry of Education, Academy of Agricultural Sciences, Southwest University, Chongqing, 400715 China
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D'Aronco G, Ferraro P, Sassano V, Dagostino C, Biancotto M, Palumbo E, Presot E, Russo A, Bianchi V, Rampazzo C. SAMHD1 restricts the deoxyguanosine triphosphate pool contributing to telomere stability in telomerase-positive cells. FASEB J 2023; 37:e22883. [PMID: 36934410 DOI: 10.1096/fj.202300122r] [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: 01/23/2023] [Revised: 02/26/2023] [Accepted: 03/07/2023] [Indexed: 03/20/2023]
Abstract
SAMHD1 (Sterile alpha motif and histidine/aspartic acid domain-containing protein 1) is a dNTP triphosphohydrolase crucial in the maintenance of balanced cellular dNTP pools, which support genome integrity. In SAMHD1 deficient fibroblasts isolated from Aicardi-Goutières Syndrome (AGS) patients, all four DNA precursors are increased and markedly imbalanced with the largest effect on dGTP, a key player in the modulation of telomerase processivity. Here, we present data showing that SAMHD1, by restricting the dGTP pool, contributes to telomere maintenance in hTERT-immortalized human fibroblasts from AGS patients as well as in telomerase positive cancer cell lines. Only in cells expressing telomerase, the lack of SAMHD1 causes excessive lengthening of telomeres and telomere fragility, whereas primary fibroblasts lacking both SAMHD1 and telomerase enter normally into senescence. Telomere lengthening observed in SAMHD1 deficient but telomerase proficient cells is a gradual process, in accordance with the intrinsic property of telomerase of adding only a few tens of nucleotides for each cycle. Therefore, only a prolonged exposure to high dGTP content causes telomere over-elongation. hTERT-immortalized AGS fibroblasts display also high fragility of chromosome ends, a marker of telomere replication stress. These results not only demonstrate the functional importance of dGTP cellular level but also reveal the critical role played by SAMHD1 in restraining telomerase processivity and safeguarding telomere stability.
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Affiliation(s)
| | - Paola Ferraro
- Department of Biology, University of Padova, Padova, Italy
| | | | | | | | - Elisa Palumbo
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Ettore Presot
- Department of Biology, University of Padova, Padova, Italy
| | - Antonella Russo
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Vera Bianchi
- Department of Biology, University of Padova, Padova, Italy
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41
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Barua D, Sultana A, Islam MN, Cox F, Gupta A, Gupta S. RRM2 and CDC6 are novel effectors of XBP1-mediated endocrine resistance and predictive markers of tamoxifen sensitivity. BMC Cancer 2023; 23:288. [PMID: 36997866 PMCID: PMC10061897 DOI: 10.1186/s12885-023-10745-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 03/16/2023] [Indexed: 04/01/2023] Open
Abstract
BACKGROUND Endocrine-resistant breast cancers have elevated expression of XBP1, where it drives endocrine resistance by controlling the expression of its target genes. Despite the in-depth understanding of the biological functions of XBP1 in ER-positive breast cancer, effectors of endocrine resistance downstream of XBP1 are poorly understood. The aim of this study was to identify the XBP1-regulated genes contributing to endocrine resistance in breast cancer. METHODS XBP1 deficient sub-clones in MCF7 cells were generated using the CRISPR-Cas9 gene knockout strategy and were validated using western blot and RT-PCR. Cell viability and cell proliferation were evaluated using the MTS assay and colony formation assay, respectively. Cell death and cell cycle analysis were determined using flow cytometry. Transcriptomic data was analysed to identify XBP1-regulated targets and differential expression of target genes was evaluated using western blot and qRT-PCR. Lentivirus and retrovirus transfection were used to generate RRM2 and CDC6 overexpressing clones, respectively. The prognostic value of the XBP1-gene signature was analysed using Kaplan-Meier survival analysis. RESULTS Deletion of XBP1 compromised the upregulation of UPR-target genes during conditions of endoplasmic reticulum (EnR) stress and sensitized cells to EnR stress-induced cell death. Loss of XBP1 in MCF7 cells decreased cell growth, attenuated the induction of estrogen-responsive genes and sensitized them to anti-estrogen agents. The expression of cell cycle associated genes RRM2, CDC6, and TOP2A was significantly reduced upon XBP1 deletion/inhibition in several ER-positive breast cancer cells. Expression of RRM2, CDC6, and TOP2A was increased upon estrogen stimulation and in cells harbouring point-mutants (Y537S, D538G) of ESR1 in steroid free conditions. Ectopic expression of RRM2 and CDC6 increased cell growth and reversed the hypersensitivity of XBP1 KO cells towards tamoxifen conferring endocrine resistance. Importantly, increased expression of XBP1-gene signature was associated with poor outcome and reduced efficacy of tamoxifen treatment in ER-positive breast cancer. CONCLUSIONS Our results suggest that RRM2 and CDC6 downstream of XBP1 contribute to endocrine resistance in ER-positive breast cancer. XBP1-gene signature is associated with poor outcome and response to tamoxifen in ER-positive breast cancer.
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Affiliation(s)
- David Barua
- Discipline of Pathology, Cancer Progression and Treatment Research Group, Lambe Institute for Translational Research, School of Medicine, University of Galway, Galway, Ireland
| | - Afrin Sultana
- Discipline of Pathology, Cancer Progression and Treatment Research Group, Lambe Institute for Translational Research, School of Medicine, University of Galway, Galway, Ireland
| | - Md Nahidul Islam
- Discipline of Biochemistry, School of Medicine, University of Galway, Galway, Ireland
| | - Fergus Cox
- Discipline of Pathology, Cancer Progression and Treatment Research Group, Lambe Institute for Translational Research, School of Medicine, University of Galway, Galway, Ireland
| | - Ananya Gupta
- Discipline of Physiology, Human Biology Building, School of Medicine, University of Galway, Galway, Ireland
| | - Sanjeev Gupta
- Discipline of Pathology, Cancer Progression and Treatment Research Group, Lambe Institute for Translational Research, School of Medicine, University of Galway, Galway, Ireland.
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Restrepo-Vera JL, Rovira-Moreno E, Ramón J, Codina-Sola M, Llauradó A, Salvadó M, Sánchez-Tejerina D, Sotoca J, Martínez-Sáez E, Martí R, García-Arumí E, Juntas-Morales R. Identification of two novel RRM2B variants associated with autosomal recessive progressive external ophthalmoplegia in a family with pseudodominant inheritance pattern. J Hum Genet 2023:10.1038/s10038-023-01144-2. [PMID: 36959467 DOI: 10.1038/s10038-023-01144-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 02/07/2023] [Accepted: 02/28/2023] [Indexed: 03/25/2023]
Abstract
RRM2B encodes the p53-inducible small subunit (p53R2) of ribonucleotide reductase, a key protein for mitochondrial DNA (mtDNA) synthesis. Pathogenic variants in this gene result in familial mitochondrial disease in adults and children, secondary to a maintenance disorder of mtDNA. This study describes two patients, mother and son, with early-onset chronic progressive external ophthalmoplegia (PEO). Skeletal muscle biopsy from the latter was examined: cytochrome c oxidase (COX)-negative fibres were shown, and molecular studies revealed multiple mtDNA deletions. A next-generation sequencing gene panel for nuclear-encoded mitochondrial maintenance genes identified two unreported heterozygous missense variants (c.514 G > A and c.682 G > A) in the clinically affected son. The clinically affected mother harboured the first variant in homozygous state, and the clinically unaffected father harboured the remaining variant in heterozygous state. In silico analyses predicted both variants as deleterious. Cell culture studies revealed that patients' skin fibroblasts, but not fibroblasts from healthy controls, responded to nucleoside supplementation with enhanced mtDNA repopulation, thus suggesting an in vitro functional difference in patients' cells. Our results support the pathogenicity of two novel RRM2B variants found in two patients with autosomal recessive PEO with multiple mtDNA deletions inherited with a pseudodominant pattern.
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Affiliation(s)
- Juan Luis Restrepo-Vera
- Neuromuscular Diseases Unit, European Reference Network on Rare Neuromuscular Diseases, Department of Neurology, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Eulàlia Rovira-Moreno
- Department of Clinical and Molecular Genetics, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
- Medicine Genetics Group, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Javier Ramón
- Research Group on Neuromuscular and Mitochondrial Diseases, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Marta Codina-Sola
- Department of Clinical and Molecular Genetics, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
- Medicine Genetics Group, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Arnau Llauradó
- Neuromuscular Diseases Unit, European Reference Network on Rare Neuromuscular Diseases, Department of Neurology, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Maria Salvadó
- Neuromuscular Diseases Unit, European Reference Network on Rare Neuromuscular Diseases, Department of Neurology, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Daniel Sánchez-Tejerina
- Neuromuscular Diseases Unit, European Reference Network on Rare Neuromuscular Diseases, Department of Neurology, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Javier Sotoca
- Neuromuscular Diseases Unit, European Reference Network on Rare Neuromuscular Diseases, Department of Neurology, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Elena Martínez-Sáez
- Department of Pathology, Hospital Vall d'Hebron, Universitat Autònoma Barcelona, 08035, Barcelona, Spain
| | - Ramon Martí
- Research Group on Neuromuscular and Mitochondrial Diseases, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Elena García-Arumí
- Department of Clinical and Molecular Genetics, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain.
- Research Group on Neuromuscular and Mitochondrial Diseases, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain.
- Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.
| | - Raul Juntas-Morales
- Neuromuscular Diseases Unit, European Reference Network on Rare Neuromuscular Diseases, Department of Neurology, Hospital Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain.
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43
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Poptic AL, Chen YP, Chang T, Chen YS, Moore CE, Zhang S. Site-Differentiated Mn IIFe II Complex Reproducing the Selective Assembly of Biological Heterobimetallic Mn/Fe Cofactors. J Am Chem Soc 2023; 145:3491-3498. [PMID: 36749207 DOI: 10.1021/jacs.2c11930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Class Ic ribonucleotide reductases (RNRIc) and R2-like ligand-binding oxidases (R2lox) are known to contain heterobimetallic MnIIFeII cofactors. How these enzymes assemble MnIIFeII cofactors has been a long-standing puzzle due to the weaker binding affinity of MnII versus FeII. In addition, the heterobimetallic selectivity of RNRIc and R2lox has yet to be reproduced with coordination complexes, leading to the hypothesis that RNRIc and R2lox overcome the thermodynamic preference for coordination of FeII over MnII with their carefully constructed three-dimensional protein structures. Herein, we report the selective formation of a heterobimetallic MnIIFeII complex accomplished in the absence of a protein scaffold. Treatment of the ligand Py4DMcT (L) with equimolar amounts of FeII and MnII along with two equivalents of acetate (OAc) affords [LMnIIFeII (OAc)2(OTf)]+ (MnIIFeII) in 80% yield, while the diiron complex [LFeIIFeII(OAc)2(OTf)]+ (FeIIFeII) is produced in only 8% yield. The formation of MnIIFeII is favored regardless of the order of addition of FeII and MnII sources. X-ray diffraction (XRD) of single crystals of MnIIFeII reveals an unsymmetrically coordinated carboxylate ligand─a primary coordination sphere feature shared by both RNRIc and R2lox that differentiates the two metal binding sites. Anomalous XRD studies confirm that MnIIFeII exhibits the same site selectivity as R2lox and RNRIc, with the FeII (d6) center preferentially occupying the distorted octahedral site. We conclude that the successful assembly of MnIIFeII originates from (1) Fe-deficient conditions, (2) site differentiation, and (3) the inability of ligand L to house a dimanganese complex.
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Affiliation(s)
- Anna L Poptic
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Ying-Pin Chen
- ChemMatCARS, University of Chicago, Argonne, Illinois 60439, United States
| | - Tieyan Chang
- ChemMatCARS, University of Chicago, Argonne, Illinois 60439, United States
| | - Yu-Sheng Chen
- ChemMatCARS, University of Chicago, Argonne, Illinois 60439, United States
| | - Curtis E Moore
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Shiyu Zhang
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
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Kulsh J. Biochemistry-Not Oncogenes-May Demystify and Defeat Cancer. Oncol Ther 2023:10.1007/s40487-023-00221-y. [PMID: 36781712 DOI: 10.1007/s40487-023-00221-y] [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: 12/12/2022] [Accepted: 01/24/2023] [Indexed: 02/15/2023] Open
Abstract
The presence of mutated genes strongly correlates with the incidence of cancer. Decades of research, however, has not yielded any specific causative gene or set of genes for the vast majority of cancers. The Cancer Genome Atlas program was supposed to provide clarity, but it only gave much more data without any accompanying insight into how the disease begins and progresses. It may be time to notice that epidemiological studies consistently show that the environment, not genes, has the principal role in causing cancer. Since carcinogenic chemicals in our food, drink, air, and water are the primary culprits, we need to look at the biochemistry of cancer, with a focus on enzymes that invariably facilitate transformations in a cell. In particular, attention should be paid to the rate-limiting enzyme in DNA synthesis, ribonucleotide reductase (RnR), whose activity is tightly linked to tumor growth. Besides circumstantial evidence that cancer is induced at this enzyme's vulnerable free-radical-containing active site by various carcinogens, its role in initiating retinoblastoma and human papillomavirus (HPV)-related cervical cancers has been well documented in recent years. Blocking the activity of malignant RnR is a certain way to arrest cancer.
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Affiliation(s)
- Jay Kulsh
- Independent Scientist, Los Angeles, CA, USA.
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Zou J, Yang L, Feng W. Mechanism of Radical Initiation and Transfer in Class Id Ribonucleotide Reductase Based on Density Functional Theory. Inorg Chem 2023; 62:2561-2575. [PMID: 36721875 DOI: 10.1021/acs.inorgchem.2c02926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Class Id ribonucleotide reductase (RNR) is a newly discovered enzyme, which employs the dimanganese cofactor in the superoxidized state (MnIII/MnIV) as the radical initiator. The dimanganese cofactor of class Id RNR in the reduced state (inactive) is clearly based on the crystal structure of the Fj-β subunit. However, the state of the dimanganese cofactor of class Id RNR in the oxidized state (active) is not known. The X-band EPR spectra have shown that the activated Fj-β subunit exists in two distinct complexes, 1 and 2. In this work, quantum mechanical/molecular mechanical calculations were carried out to study class Id RNR. First, we have determined that complex 2 contains a MnIII-(μ-oxo)2-MnIV cluster, and complex 1 contains a MnIII-(μ-hydroxo/μ-oxo)-MnIV cluster. Then, based on the determined dimanganese cofactors, the mechanism of radical initiation and transfer in class Id RNR is revealed. The MnIII-(μ-oxo)2-MnIV cluster in complex 2 has not enough reduction potential to initiate radical transfer directly. Instead, it needs to be monoprotonated into MnIII-(μ-hydroxo/μ-oxo)-MnIV (complex 1) before the radical transfer. The protonation state of μ-oxo can be regulated by changing the protein microenvironment, which is induced by the protein aggregation and separation of β subunits with α subunits. The radical transfer between the cluster of MnIII-(μ-hydroxo/μ-oxo)-MnIV and Trp30 in the radical-transfer chain of the Fj-β subunit (MnIII/MnIV ↔ His100 ↔ Asp194 ↔ Trp30 ↔ Arg99) is a water-mediated tri-proton-coupled electron transfer, which transfers proton from the ε-amino group of Lys71 to the carboxyl group of Glu97 via the water molecule Wat551 and the bridging μ-hydroxo ligand through a three-step reaction. This newly discovered proton-coupled electron-transfer mechanism in class Id RNR is different from those reported in the known Ia-Ic RNRs. The ε-amino group of Lys71, which serves as a proton donor, plays an important role in the radical transfer.
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Affiliation(s)
- Jinxin Zou
- Department of Biological Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Lu Yang
- Department of Biological Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Wei Feng
- Department of Biological Engineering, Beijing University of Chemical Technology, Beijing 100029, China
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Abstract
Significance: Thioredoxin (Trx) is a powerful antioxidant that reduces protein disulfides to maintain redox stability in cells and is involved in regulating multiple redox-dependent signaling pathways. Recent Advance: The current accumulation of findings suggests that Trx participates in signaling pathways that interact with various proteins to manipulate their dynamic regulation of structure and function. These network pathways are critical for cancer pathogenesis and therapy. Promising clinical advances have been presented by most anticancer agents targeting such signaling pathways. Critical Issues: We herein link the signaling pathways regulated by the Trx system to potential cancer therapeutic opportunities, focusing on the coordination and strengths of the Trx signaling pathways in apoptosis, ferroptosis, immunomodulation, and drug resistance. We also provide a mechanistic network for the exploitation of therapeutic small molecules targeting the Trx signaling pathways. Future Directions: As research data accumulate, future complex networks of Trx-related signaling pathways will gain in detail. In-depth exploration and establishment of these signaling pathways, including Trx upstream and downstream regulatory proteins, will be critical to advancing novel cancer therapeutics. Antioxid. Redox Signal. 38, 403-424.
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Affiliation(s)
- Junmin Zhang
- State Key Laboratory of Applied Organic Chemistry, School of Pharmacy, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, China
| | - Xinming Li
- State Key Laboratory of Applied Organic Chemistry, School of Pharmacy, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, China.,State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Zhengjia Zhao
- State Key Laboratory of Applied Organic Chemistry, School of Pharmacy, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, China
| | | | - Jianguo Fang
- State Key Laboratory of Applied Organic Chemistry, School of Pharmacy, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, China.,School of Chemistry and Chemical Engineering, Nanjing University of Science & Technology, Nanjing, China
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Kitab B, Tsukiyama-Kohara K. Regulatory Role of Ribonucleotide Reductase Subunit M2 in Hepatocyte Growth and Pathogenesis of Hepatitis C Virus. Int J Mol Sci 2023; 24:ijms24032619. [PMID: 36768940 PMCID: PMC9916403 DOI: 10.3390/ijms24032619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/27/2023] [Accepted: 01/27/2023] [Indexed: 01/31/2023] Open
Abstract
Hepatitis C virus (HCV) frequently causes chronic infection in the human liver, which may progress to advanced hepatic fibrosis, cirrhosis, and hepatocellular carcinoma. HCV primarily infects highly differentiated quiescent hepatocytes and can modulate cell cycle-regulatory genes and proliferation pathways, which ultimately contribute to persistent infection and pathogenesis. On the other hand, several studies have shown differential regulation of HCV RNA and viral protein expression levels, depending on the proliferation state of hepatocytes and the phase of the cell cycle. HCV typically requires factors provided by host cells for efficient and persistent viral replication. Previously, we found that HCV infection upregulates the expression of ribonucleotide reductase subunit M2 (RRM2) in quiescent hepatocytes. RRM2 is a rate-limiting protein that catalyzes de novo synthesis of deoxyribonucleotide triphosphates, and its expression is highly regulated during various phases of the cell cycle. RRM2 functions as a pro-viral factor essential for HCV RNA synthesis, but its functional role in HCV-induced liver diseases remains unknown. Here, we present a comprehensive review of the role of the hepatocyte cell cycle, in correlation with RRM2 expression, in the regulation of HCV replication. We also discuss the potential relevance of this protein in the pathogenesis of HCV, particularly in the development of hepatocellular carcinoma.
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48
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Xia J, Zhang L, Gu T, Liu Q, Wang Q. Identification of ferroptosis related markers by integrated bioinformatics analysis and In vitro model experiments in rheumatoid arthritis. BMC Med Genomics 2023; 16:18. [PMID: 36717858 PMCID: PMC9887825 DOI: 10.1186/s12920-023-01445-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 01/25/2023] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Rheumatoid arthritis (RA) is an autoimmune disease characterized by destructive and symmetrical joint diseases and synovitis. This research attempted to explore the mechanisms involving ferroptosis in RA, and find the biological markers by integrated analysis. METHODS Gene expression data (GSE55235 and GSE55457) of synovial tissues from healthy and RA individuals were downloaded. By filtering the differentially expressed genes (DEGs) and intersecting them with the 484 ferroptosis-related genes (FRGs), the overlapping genes were identified. After the enrichment analysis, the machine learning-based approaches were introduced to screen the potential biomarkers, which were further validated in other two datasets (GSE77298 and GSE93272) and cell samples. Besides, we also analyze the infiltrating immune cells in RA and their correlation with the biomarkers. RESULTS With the criteria, 635 DEGs in RA were included, and 29 of them overlapped in the reported 484 FRGs. The enrichments of the 29 differentially expressed ferroptosis-related genes indicated that they may involve in the FoxO signaling pathway and inherited metabolic disorder. RRM2, validating by the external datasets and western blot, were identified as the biomarker with the high diagnostic value, whose associated immune cells, such as Neutrophils and Macrophages M1, were also further evaluated. CONCLUSION We preliminary explored the mechanisms between ferroptosis and RA. These results may help us better comprehend the pathophysiological changes of RA in basic research, and provide new evidences for the clinical transformation.
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Affiliation(s)
- Jinjun Xia
- grid.263761.70000 0001 0198 0694Department of Clinical Laboratory, Wuxi 9Th People’s Hospital Affiliated to Soochow University, No. 999 Liang Xi Road, Binhu District, Wuxi, 214000 Jiangsu China
| | - Lulu Zhang
- grid.263761.70000 0001 0198 0694Department of Clinical Laboratory, Wuxi 9Th People’s Hospital Affiliated to Soochow University, No. 999 Liang Xi Road, Binhu District, Wuxi, 214000 Jiangsu China
| | - Tao Gu
- grid.263761.70000 0001 0198 0694Department of Clinical Laboratory, Wuxi 9Th People’s Hospital Affiliated to Soochow University, No. 999 Liang Xi Road, Binhu District, Wuxi, 214000 Jiangsu China
| | - Qingyang Liu
- grid.263761.70000 0001 0198 0694Department of Clinical Laboratory, Wuxi 9Th People’s Hospital Affiliated to Soochow University, No. 999 Liang Xi Road, Binhu District, Wuxi, 214000 Jiangsu China
| | - Qiubo Wang
- grid.263761.70000 0001 0198 0694Department of Clinical Laboratory, Wuxi 9Th People’s Hospital Affiliated to Soochow University, No. 999 Liang Xi Road, Binhu District, Wuxi, 214000 Jiangsu China
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Prognostic and Immunological Potential of Ribonucleotide Reductase Subunits in Liver Cancer. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2023; 2023:3878796. [PMID: 36713030 PMCID: PMC9883104 DOI: 10.1155/2023/3878796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 11/08/2022] [Accepted: 11/30/2022] [Indexed: 01/21/2023]
Abstract
Background Ribonucleotide reductase (RR) consists of two subunits, the large subunit RRM1 and the small subunit (RRM2 or RRM2B), which is essential for DNA replication. Dysregulations of RR were implicated in multiple types of cancer. However, the abnormal expressions and biologic functions of RR subunits in liver cancer remain to be elucidated. Methods TCGA, HCCDB, CCLE, HPA, cBioPortal, and GeneMANIA were utilized to perform bioinformatics analysis of RR subunits in the liver cancer. GO, KEGG, and GSEA were used for enrichment analysis. Results The expressions of RRM1, RRM2, and RRM2B were remarkably upregulated among liver cancer tissue both in mRNA and protein levels. High expression of RRM1 and RRM2 was notably associated with high tumor grade, high stage, short overall survival, and disease-specific survival. Enrichment analyses indicated that RRM1 and RRM2 were related to DNA replication, cell cycle, regulation of nuclear division, DNA repair, and DNA recombination. Correlation analysis indicated that RRM1 and RRM2 were significantly associated with several subsets of immune cell, including Th2 cells, cytotoxic cells, and neutrophils. RRM2B expression was positively associated with immune score and stromal score. Chemosensitivity analysis revealed that sensitivity of nelarabine was positively associated with high expressions of RRM1 and RRM2. The sensitivity of rapamycin was positively associated with high expressions of RRM2B. Conclusion Our findings demonstrated high expression profiles of RR subunits in liver cancer, which may provide novel insights for predicting the poor prognosis and increased chemosensitivity of liver cancer in clinic.
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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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