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Dodson TA, Nieuwoudt S, Morse CN, Pierre V, Liu C, Senyo SE, Prestwich EG. Ribonucleosides from tRNA in hyperglycemic mammalian cells and diabetic murine cardiac models. Life Sci 2023; 318:121462. [PMID: 36736767 PMCID: PMC9992345 DOI: 10.1016/j.lfs.2023.121462] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 01/24/2023] [Accepted: 01/26/2023] [Indexed: 02/04/2023]
Abstract
AIMS Cardiomyopathy is a diabetic comorbidity with few molecular targets. To address this, we evaluated transfer RNA (tRNA) modifications in the diabetic heart because tRNA modifications have been implicated in diabetic etiologies. MAIN METHODS tRNA was isolated from aorta, apex, and atrial tissue of healthy and diabetic murine hearts and related hyperglycemic cell models. tRNA modifications and canonical ribonucleosides were quantified by liquid-chromatography tandem mass spectrometry (LC-MS/MS) using stable isotope dilution. Correlations between ribonucleosides and diabetic comorbidity pathology were assessed using statistical analyses. KEY FINDINGS Total tRNA ribonucleoside levels were analyzed from cell types and healthy and diabetic murine heart tissue. Each heart structure had characteristic ribonucleoside profiles and quantities. Several ribonucleosides were observed as significantly different in hyperglycemic cells and diabetic tissues. In hyperglycemic models, ribonucleosides N4-acetylcytidine (ac4C), 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U), 5-methylcytidine (m5C), and N1-methylguanosine (m1G) were anomalous. Specific tRNA modifications known to be on murine tRNAIni(CAU) were higher in diabetic heart tissue which suggests that tRNA modifications could be regulating translation in diabetes. SIGNIFICANCE We identified tRNA ribonucleosides and tRNA species associated with hyperglycemia and diabetic etiology.
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Affiliation(s)
- Taylor A Dodson
- Department of Medicinal and Biological Chemistry, College of Pharmacy and Pharmaceutical Sciences, University of Toledo, Toledo, OH, United States
| | - Stephan Nieuwoudt
- Department of Biomedical Engineering, School of Engineering, Case Western Reserve University, Cleveland, OH, United States
| | - Chase N Morse
- Department of Medicinal and Biological Chemistry, College of Pharmacy and Pharmaceutical Sciences, University of Toledo, Toledo, OH, United States
| | - Valinteshley Pierre
- Department of Biomedical Engineering, School of Engineering, Case Western Reserve University, Cleveland, OH, United States
| | - Chao Liu
- Department of Biomedical Engineering, School of Engineering, Case Western Reserve University, Cleveland, OH, United States
| | - Samuel E Senyo
- Department of Biomedical Engineering, School of Engineering, Case Western Reserve University, Cleveland, OH, United States
| | - Erin G Prestwich
- Department of Medicinal and Biological Chemistry, College of Pharmacy and Pharmaceutical Sciences, University of Toledo, Toledo, OH, United States.
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Dopkins N, Neameh WH, Hall A, Lai Y, Rutkovsky A, Gandy AO, Lu K, Nagarkatti PS, Nagarkatti M. Effects of Acute 2,3,7,8-Tetrachlorodibenzo-p-Dioxin Exposure on the Circulating and Cecal Metabolome Profile. Int J Mol Sci 2021; 22:11801. [PMID: 34769237 PMCID: PMC8583798 DOI: 10.3390/ijms222111801] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 10/28/2021] [Accepted: 10/28/2021] [Indexed: 02/06/2023] Open
Abstract
2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) is a polyhalogenated planar hydrocarbon belonging to a group of highly toxic and persistent environmental contaminants known as "dioxins". TCDD is an animal teratogen and carcinogen that is well characterized for causing immunosuppression through activation of aryl hydrocarbon receptor (AHR). In this study, we investigated the effect of exposure of mice to an acute dose of TCDD on the metabolic profile within the serum and cecal contents to better define the effects of TCDD on host physiology. Our findings demonstrated that within the circulating metabolome following acute TCDD exposure, there was significant dysregulation in the metabolism of bioactive lipids, amino acids, and carbohydrates when compared with the vehicle (VEH)-treated mice. These widespread changes in metabolite abundance were identified to regulate host immunity via modulating nuclear factor-kappa B (NF-κB) and extracellular signal-regulated protein kinase (ERK1/2) activity and work as biomarkers for a variety of organ injuries and dysfunctions that follow TCDD exposure. Within the cecal content of mice exposed to TCDD, we were able to detect changes in inflammatory markers that regulate NF-κB, markers of injury-related inflammation, and changes in lysine degradation, nicotinamide metabolism, and butanoate metabolism, which collectively suggested an immediate suppression of broad-scale metabolic processes in the gastrointestinal tract. Collectively, these results demonstrate that acute TCDD exposure results in immediate irregularities in the circulating and intestinal metabolome, which likely contribute to TCDD toxicity and can be used as biomarkers for the early detection of individual exposure.
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Affiliation(s)
- Nicholas Dopkins
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC 29209, USA; (N.D.); (W.H.N.); (A.H.); (A.R.); (A.O.G.); (P.S.N.)
| | - Wurood Hantoosh Neameh
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC 29209, USA; (N.D.); (W.H.N.); (A.H.); (A.R.); (A.O.G.); (P.S.N.)
| | - Alina Hall
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC 29209, USA; (N.D.); (W.H.N.); (A.H.); (A.R.); (A.O.G.); (P.S.N.)
| | - Yunjia Lai
- Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, NC 27599, USA; (Y.L.); (K.L.)
| | - Alex Rutkovsky
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC 29209, USA; (N.D.); (W.H.N.); (A.H.); (A.R.); (A.O.G.); (P.S.N.)
| | - Alexa Orr Gandy
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC 29209, USA; (N.D.); (W.H.N.); (A.H.); (A.R.); (A.O.G.); (P.S.N.)
| | - Kun Lu
- Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, NC 27599, USA; (Y.L.); (K.L.)
| | - Prakash S. Nagarkatti
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC 29209, USA; (N.D.); (W.H.N.); (A.H.); (A.R.); (A.O.G.); (P.S.N.)
| | - Mitzi Nagarkatti
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC 29209, USA; (N.D.); (W.H.N.); (A.H.); (A.R.); (A.O.G.); (P.S.N.)
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Knutson SD, Arthur RA, Johnston HR, Heemstra JM. Direct Immunodetection of Global A-to-I RNA Editing Activity with a Chemiluminescent Bioassay. Angew Chem Int Ed Engl 2021; 60:17009-17017. [PMID: 33979483 PMCID: PMC8562906 DOI: 10.1002/anie.202102762] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/08/2021] [Indexed: 12/15/2022]
Abstract
Adenosine-to-inosine (A-to-I) editing is a conserved eukaryotic RNA modification that contributes to development, immune response, and overall cellular function. Here, we utilize Endonuclease V (EndoV), which binds specifically to inosine in RNA, to develop an EndoV-linked immunosorbency assay (EndoVLISA) as a rapid, plate-based chemiluminescent method for measuring global A-to-I editing signatures in cellular RNA. We first optimize and validate our assay with chemically synthesized oligonucleotides. We then demonstrate rapid detection of inosine content in treated cell lines, demonstrating equivalent performance against current standard RNA-seq approaches. Lastly, we deploy our EndoVLISA for profiling differential A-to-I RNA editing signatures in normal and diseased human tissue, illustrating the utility of our platform as a diagnostic bioassay. Together, the EndoVLISA method is cost-effective, straightforward, and utilizes common laboratory equipment, offering a highly accessible new approach for studying A-to-I editing. Moreover, the multi-well plate format makes this the first assay amenable for direct high-throughput quantification of A-to-I editing for applications in disease detection and drug development.
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Affiliation(s)
- Steve D Knutson
- Department of Chemistry, Emory University, 1515 Dickey Dr., Atlanta, GA, 30322, USA
| | - Robert A Arthur
- Emory Integrated Computational Core, Emory University, 101 Woodruff Cir., Atlanta, GA, 30322, USA
- Department of Human Genetics, Emory University, 1365 Clifton Rd, Atlanta, GA, 30322, USA
| | - H Richard Johnston
- Emory Integrated Computational Core, Emory University, 101 Woodruff Cir., Atlanta, GA, 30322, USA
- Department of Human Genetics, Emory University, 1365 Clifton Rd, Atlanta, GA, 30322, USA
| | - Jennifer M Heemstra
- Department of Chemistry, Emory University, 1515 Dickey Dr., Atlanta, GA, 30322, USA
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Direct Immunodetection of Global A‐to‐I RNA Editing Activity with a Chemiluminescent Bioassay. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Srinivasan S, Torres AG, Ribas de Pouplana L. Inosine in Biology and Disease. Genes (Basel) 2021; 12:600. [PMID: 33921764 PMCID: PMC8072771 DOI: 10.3390/genes12040600] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/13/2021] [Accepted: 04/15/2021] [Indexed: 02/06/2023] Open
Abstract
The nucleoside inosine plays an important role in purine biosynthesis, gene translation, and modulation of the fate of RNAs. The editing of adenosine to inosine is a widespread post-transcriptional modification in transfer RNAs (tRNAs) and messenger RNAs (mRNAs). At the wobble position of tRNA anticodons, inosine profoundly modifies codon recognition, while in mRNA, inosines can modify the sequence of the translated polypeptide or modulate the stability, localization, and splicing of transcripts. Inosine is also found in non-coding and exogenous RNAs, where it plays key structural and functional roles. In addition, molecular inosine is an important secondary metabolite in purine metabolism that also acts as a molecular messenger in cell signaling pathways. Here, we review the functional roles of inosine in biology and their connections to human health.
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Affiliation(s)
- Sundaramoorthy Srinivasan
- Institute for Research in Biomedicine, Barcelona Institute of Science and Technology, 08028 Barcelona, Catalonia, Spain; (S.S.); (A.G.T.)
| | - Adrian Gabriel Torres
- Institute for Research in Biomedicine, Barcelona Institute of Science and Technology, 08028 Barcelona, Catalonia, Spain; (S.S.); (A.G.T.)
| | - Lluís Ribas de Pouplana
- Institute for Research in Biomedicine, Barcelona Institute of Science and Technology, 08028 Barcelona, Catalonia, Spain; (S.S.); (A.G.T.)
- Catalan Institution for Research and Advanced Studies, 08010 Barcelona, Catalonia, Spain
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6
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Translesion synthesis by AMV, HIV, and MMLVreverse transcriptases using RNA templates containing inosine, guanosine, and their 8-oxo-7,8-dihydropurine derivatives. PLoS One 2020; 15:e0235102. [PMID: 32857764 PMCID: PMC7455023 DOI: 10.1371/journal.pone.0235102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 08/07/2020] [Indexed: 12/31/2022] Open
Abstract
Inosine is ubiquitous and essential in many biological processes, including RNA-editing. In addition, oxidative stress on RNA has been a topic of increasing interest due, in part, to its potential role in the development/progression of disease. In this work we probed the ability of three reverse transcriptases (RTs) to catalyze the synthesis of cDNA in the presence of RNA templates containing inosine (I), 8-oxo-7,8-dihydroinosine (8oxo-I), guanosine (G), or 8-oxo-7,8-dihydroguanosine (8-oxoG), and explored the impact that these purine derivatives have as a function of position. To this end, we used 29-mers of RNA (as template) containing the modifications at position-18 and reverse transcribed DNA using 17-mers, 18-mers, or 19-mers (as primers). Generally reactivity of the viral RTs, AMV / HIV / MMLV, towards cDNA synthesis was similar for templates containing G or I as well as for those with 8-oxoG or 8-oxoI. Notable differences are: 1) the use of 18-mers of DNA (to explore cDNA synthesis past the lesion/modification) led to inhibition of DNA elongation in cases where a G:dA wobble pair was present, while the presence of I, 8-oxoI, or 8-oxoG led to full synthesis of the corresponding cDNA, with the latter two displaying a more efficient process; 2) HIV RT is more sensitive to modified base pairs in the vicinity of cDNA synthesis; and 3) the presence of a modification two positions away from transcription initiation has an adverse impact on the overall process. Steady-state kinetics were established using AMV RT to determine substrate specificities towards canonical dNTPs (N = G, C, T, A). Overall we found evidence that RNA templates containing inosine are likely to incorporate dC > dT > > dA, where reactivity in the presence of dA was found to be pH dependent (process abolished at pH 7.3); and that the absence of the C2-exocyclic amine, as displayed with templates containing 8-oxoI, leads to increased selectivity towards incorporation of dA over dC. The data will be useful in assessing the impact that the presence of inosine and/or oxidatively generated lesions have on viral processes and adds to previous reports where I codes exclusively like G. Similar results were obtained upon comparison of AMV and MMLV RTs.
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Clendinen CS, Gaul DA, Monge ME, Arnold RS, Edison AS, Petros JA, Fernández FM. Preoperative Metabolic Signatures of Prostate Cancer Recurrence Following Radical Prostatectomy. J Proteome Res 2019; 18:1316-1327. [PMID: 30758971 DOI: 10.1021/acs.jproteome.8b00926] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Technological advances in mass spectrometry (MS), liquid chromatography (LC) separations, nuclear magnetic resonance (NMR) spectroscopy, and big data analytics have made possible studying metabolism at an "omics" or systems level. Here, we applied a multiplatform (NMR + LC-MS) metabolomics approach to the study of preoperative metabolic alterations associated with prostate cancer recurrence. Thus far, predicting which patients will recur even after radical prostatectomy has not been possible. Correlation analysis on metabolite abundances detected on serum samples collected prior to surgery from prostate cancer patients ( n = 40 remission vs n = 40 recurrence) showed significant alterations in a number of pathways, including amino acid metabolism, purine and pyrimidine synthesis, tricarboxylic acid cycle, tryptophan catabolism, glucose, and lactate. Lipidomics experiments indicated higher lipid abundances on recurrent patients for a number of classes that included triglycerides, lysophosphatidylcholines, phosphatidylethanolamines, phosphatidylinositols, diglycerides, acyl carnitines, and ceramides. Machine learning approaches led to the selection of a 20-metabolite panel from a single preoperative blood sample that enabled prediction of recurrence with 92.6% accuracy, 94.4% sensitivity, and 91.9% specificity under cross-validation conditions.
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Affiliation(s)
- Chaevien S Clendinen
- School of Chemistry and Biochemistry , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States
| | - David A Gaul
- School of Chemistry and Biochemistry , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States
| | - María Eugenia Monge
- Centro de Investigaciones en Bionanociencias (CIBION) , Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) , Godoy Cruz 2390 , C1425FQD, Ciudad de Buenos Aires , Argentina
| | - Rebecca S Arnold
- Department of Urology , Emory University , Atlanta , Georgia 30308 , United States
| | - Arthur S Edison
- Department of Genetics and Biochemistry and Molecular Biology, Complex Carbohydrate Research Center , University of Georgia , Athens , Georgia 30602 , United States
| | - John A Petros
- Department of Urology , Emory University , Atlanta , Georgia 30308 , United States.,Atlanta VA Medical Center , Atlanta , Georgia 30033 , United States
| | - Facundo M Fernández
- School of Chemistry and Biochemistry , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States
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Hsu WH, Shen YC, Shiao YJ, Kuo CH, Lu CK, Lin TY, Ku WC, Lin YL. Combined proteomic and metabolomic analyses of cerebrospinal fluid from mice with ischemic stroke reveals the effects of a Buyang Huanwu decoction in neurodegenerative disease. PLoS One 2019; 14:e0209184. [PMID: 30645580 PMCID: PMC6333407 DOI: 10.1371/journal.pone.0209184] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 12/01/2018] [Indexed: 01/11/2023] Open
Abstract
Ischemic stroke is one of the most common causes of death worldwide and is a major cause of acquired disability in adults. However, there is still a need for an effective drug for its treatment. Buyang Huanwu decoction (BHD), a traditional Chinese medicine (TCM) prescription, has long been used clinically to aid neurological recovery after stroke. To establish potential clinical indicators of BHD efficacy in stroke treatment and prognosis, we conducted a combined proteomic and metabolomic analysis of cerebrospinal fluid (CSF) samples in a mouse stroke model. CSF samples were obtained from male mice with acute ischemic stroke induced by middle cerebral ischemic/reperfusion (CI/R) injury, some of which were then treated with BHD. Label-free quantitative proteomics was conducted using nano-LC-MS/MS on an LTQ Orbitrap mass and metabolomic analysis was performed using nanoprobe NMR and UHPLC-QTOF-MS. The results showed that several proteins and metabolites were present at significantly different concentrations in the CSF samples from mice with CI/R alone and those treated with BHD. These belonged to pathways related to energy demand, inflammatory signaling, cytoskeletal regulation, Wnt signaling, and neuroprotection against neurodegenerative diseases. In conclusion, our in silico data suggest that BHD treatment is not only protective but can also ameliorate defects in pathways affected by neurological disorders. These data shed light on the mechanism whereby BHD may be effective in the treatment and prevention of stroke-related neurodegenerative disease.
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Affiliation(s)
- Wei-Hsiang Hsu
- Department of Chinese Pharmaceutical Sciences and Chinese Medicine Resources, China Medical University, Taichung, Taiwan
| | - Yuh-Chiang Shen
- National Research Institute of Chinese Medicine, Ministry of Health and Welfare, Taipei, Taiwan
| | - Young-Ji Shiao
- National Research Institute of Chinese Medicine, Ministry of Health and Welfare, Taipei, Taiwan
| | - Ching-Hua Kuo
- Department of Pharmacy, National Taiwan University, Taipei, Taiwan
| | - Chung-Kuang Lu
- National Research Institute of Chinese Medicine, Ministry of Health and Welfare, Taipei, Taiwan
| | - Tai-Yuan Lin
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei, Taiwan
| | - Wei-Chi Ku
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei, Taiwan
- * E-mail: (YLL); (WCK)
| | - Yun-Lian Lin
- Department of Chinese Pharmaceutical Sciences and Chinese Medicine Resources, China Medical University, Taichung, Taiwan
- Department of Pharmacy, National Taiwan University, Taipei, Taiwan
- * E-mail: (YLL); (WCK)
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Filippova JA, Semenov DV, Juravlev ES, Komissarov AB, Richter VA, Stepanov GA. Modern Approaches for Identification of Modified Nucleotides in RNA. BIOCHEMISTRY (MOSCOW) 2018; 82:1217-1233. [PMID: 29223150 DOI: 10.1134/s0006297917110013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
This review considers approaches for detection of modified monomers in the RNA structure of living organisms. Recently, some data on dynamic alterations in the pool of modifications of the key RNA species that depend on external factors affecting the cells and physiological conditions of the whole organism have been accumulated. The recent studies have presented experimental data on relationship between the mechanisms of formation of modified/minor nucleotides of RNA in mammalian cells and the development of various pathologies. The development of novel methods for detection of chemical modifications of RNA nucleotides in the cells of living organisms and accumulation of knowledge on the contribution of modified monomers to metabolism and functioning of individual RNA species establish the basis for creation of novel diagnostic and therapeutic approaches. This review includes a short description of routine methods for determination of modified nucleotides in RNA and considers in detail modern approaches that enable not only detection but also quantitative assessment of the modification level of various nucleotides in individual RNA species.
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Affiliation(s)
- J A Filippova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
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DeVito S, Woodrick J, Song L, Roy R. Mutagenic potential of hypoxanthine in live human cells. Mutat Res 2017; 803-805:9-16. [PMID: 28704682 DOI: 10.1016/j.mrfmmm.2017.06.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Revised: 06/06/2017] [Accepted: 06/20/2017] [Indexed: 01/08/2023]
Abstract
Hypoxanthine (Hx) is a major DNA lesion generated by deamination of adenine during chronic inflammatory conditions, which is an underlying cause of various diseases including cancer of colon, liver, pancreas, bladder and stomach. There is evidence that deamination of DNA bases induces mutations, but no study has directly linked Hx accumulation to mutagenesis and strand-specific mutations yet in human cells. Using a site-specific mutagenesis approach, we report the first direct evidence of mutation potential and pattern of Hx in live human cells. We investigated Hx-induced mutations in human nonmalignant HEK293 and cancer HCT116 cell lines and found that Hx is mutagenic in both HEK293 and HCT116 cell lines. There is a strand bias for Hx-mediated mutations in both the cell lines; the Hx in lagging strand is more mutagenic than in leading strand. There is also some difference in cell types regarding the strand bias for mutation types; HEK293 cells showed largely deletion (>80%) mutations in both leading and lagging strand and the rest were insertions and A:T→G:C transition mutations in leading and lagging strands, respectively, whereas in HCT116 cells we observed 60% A:T→G:C transition mutations in the leading strand and 100% deletions in the lagging strand. Overall, Hx is a highly mutagenic lesion capable of generating A:T→G:C transitions and large deletions with a significant variation in leading and lagging strands in human cells. In recent meta-analysis study A→G (T→C) mutations were found to be a prominent signature in a variety of cancers, including a majority types that are induced by inflammation. The deletions are known to be a major cause of copy-number variations or CNVs, which is a major underlying cause of many human diseases including mental illness, developmental disorders and cancer. Thus, Hx, a major DNA lesion induced by different deamination mechanisms, has potential to initiate inflammation-driven carcinogenesis in addition to various human pathophysiological consequences.
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Affiliation(s)
- Stephen DeVito
- Department of Oncology, Georgetown Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, United States
| | - Jordan Woodrick
- Department of Oncology, Georgetown Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, United States
| | - Linze Song
- Department of Oncology, Georgetown Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, United States
| | - Rabindra Roy
- Department of Oncology, Georgetown Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, United States.
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Yoneshima Y, Abolhassani N, Iyama T, Sakumi K, Shiomi N, Mori M, Shiomi T, Noda T, Tsuchimoto D, Nakabeppu Y. Deoxyinosine triphosphate induces MLH1/PMS2- and p53-dependent cell growth arrest and DNA instability in mammalian cells. Sci Rep 2016; 6:32849. [PMID: 27618981 PMCID: PMC5020429 DOI: 10.1038/srep32849] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 08/16/2016] [Indexed: 12/30/2022] Open
Abstract
Deoxyinosine (dI) occurs in DNA either by oxidative deamination of a previously incorporated deoxyadenosine residue or by misincorporation of deoxyinosine triphosphate (dITP) from the nucleotide pool during replication. To exclude dITP from the pool, mammals possess specific hydrolysing enzymes, such as inosine triphosphatase (ITPA). Previous studies have shown that deficiency in ITPA results in cell growth suppression and DNA instability. To explore the mechanisms of these phenotypes, we analysed ITPA-deficient human and mouse cells. We found that both growth suppression and accumulation of single-strand breaks in nuclear DNA of ITPA-deficient cells depended on MLH1/PMS2. The cell growth suppression of ITPA-deficient cells also depended on p53, but not on MPG, ENDOV or MSH2. ITPA deficiency significantly increased the levels of p53 protein and p21 mRNA/protein, a well-known target of p53, in an MLH1-dependent manner. Furthermore, MLH1 may also contribute to cell growth arrest by increasing the basal level of p53 activity.
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Affiliation(s)
- Yasuto Yoneshima
- Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8581, Japan
- Research Institute for Diseases of the Chest, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8581, Japan
| | - Nona Abolhassani
- Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8581, Japan
| | - Teruaki Iyama
- Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8581, Japan
| | - Kunihiko Sakumi
- Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8581, Japan
- Research Center for Nucleotide Pool, Kyushu University, Fukuoka 812-8581, Japan
| | - Naoko Shiomi
- National Institute of Radiological Sciences, Chiba 263-8555, Japan
| | - Masahiko Mori
- National Institute of Radiological Sciences, Chiba 263-8555, Japan
| | - Tadahiro Shiomi
- National Institute of Radiological Sciences, Chiba 263-8555, Japan
| | - Tetsuo Noda
- Cancer Institute, Japanese Foundation for Cancer Research, Tokyo 135-8550, Japan
| | - Daisuke Tsuchimoto
- Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8581, Japan
- Research Center for Nucleotide Pool, Kyushu University, Fukuoka 812-8581, Japan
| | - Yusaku Nakabeppu
- Division of Neurofunctional Genomics, Department of Immunobiology and Neuroscience, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8581, Japan
- Research Center for Nucleotide Pool, Kyushu University, Fukuoka 812-8581, Japan
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12
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Nawaz MS, Vik ES, Berges N, Fladeby C, Bjørås M, Dalhus B, Alseth I. Regulation of Human Endonuclease V Activity and Relocalization to Cytoplasmic Stress Granules. J Biol Chem 2016; 291:21786-21801. [PMID: 27573237 DOI: 10.1074/jbc.m116.730911] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 08/29/2016] [Indexed: 01/01/2023] Open
Abstract
Endonuclease V (EndoV) is an enzyme with specificity for inosines in nucleic acids. Whereas the bacterial homologs are active on both DNA and RNA, the mammalian variants only cleave RNA, at least when assayed with recombinant proteins. Here we show that ectopically expressed, as well as endogenously expressed human (h)EndoV, share the same enzymatic properties as the recombinant protein and cleaves RNA with inosine but not DNA. In search for proteins interacting with hEndoV, polyadenylate-binding protein C1 (PABPC1) was identified. The association between PABPC1 and hEndoV is RNA dependent and furthermore, PABPC1 stimulates hEndoV activity and affinity for inosine-containing RNA. Upon cellular stress, PABPC1 relocates to cytoplasmic stress granules that are multimolecular aggregates of stalled translation initiation complexes formed to aid cell recovery. Arsenite, as well as other agents, triggered relocalization also of hEndoV to cytoplasmic stress granules. As inosines in RNA are highly abundant, hEndoV activity is likely regulated in cells to avoid aberrant cleavage of inosine-containing transcripts. Indeed, we find that hEndoV cleavage is inhibited by normal intracellular ATP concentrations. The ATP stores inside a cell do not overlay stress granules and we suggest that hEndoV is redistributed to stress granules as a strategy to create a local environment low in ATP to permit hEndoV activity.
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Affiliation(s)
- Meh Sameen Nawaz
- From the Department of Microbiology, Oslo University Hospital HF, Rikshospitalet, and University of Oslo, NO-0424 Oslo
| | - Erik Sebastian Vik
- From the Department of Microbiology, Oslo University Hospital HF, Rikshospitalet, and University of Oslo, NO-0424 Oslo
| | - Natalia Berges
- From the Department of Microbiology, Oslo University Hospital HF, Rikshospitalet, and University of Oslo, NO-0424 Oslo
| | - Cathrine Fladeby
- From the Department of Microbiology, Oslo University Hospital HF, Rikshospitalet, and University of Oslo, NO-0424 Oslo
| | - Magnar Bjørås
- From the Department of Microbiology, Oslo University Hospital HF, Rikshospitalet, and University of Oslo, NO-0424 Oslo.,the Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NO-7491 Trondheim, and
| | - Bjørn Dalhus
- From the Department of Microbiology, Oslo University Hospital HF, Rikshospitalet, and University of Oslo, NO-0424 Oslo.,the Department of Medical Biochemistry, Institute for Clinical Medicine, University of Oslo, NO-0424 Oslo, Norway
| | - Ingrun Alseth
- From the Department of Microbiology, Oslo University Hospital HF, Rikshospitalet, and University of Oslo, NO-0424 Oslo,
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Wang J, Dong H, Chionh YH, McBee ME, Sirirungruang S, Cunningham RP, Shi PY, Dedon PC. The role of sequence context, nucleotide pool balance and stress in 2'-deoxynucleotide misincorporation in viral, bacterial and mammalian RNA. Nucleic Acids Res 2016; 44:8962-8975. [PMID: 27365049 PMCID: PMC5062971 DOI: 10.1093/nar/gkw572] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 06/06/2016] [Indexed: 11/16/2022] Open
Abstract
The misincorporation of 2′-deoxyribonucleotides (dNs) into RNA has important implications for the function of non-coding RNAs, the translational fidelity of coding RNAs and the mutagenic evolution of viral RNA genomes. However, quantitative appreciation for the degree to which dN misincorporation occurs is limited by the lack of analytical tools. Here, we report a method to hydrolyze RNA to release 2′-deoxyribonucleotide-ribonucleotide pairs (dNrN) that are then quantified by chromatography-coupled mass spectrometry (LC-MS). Using this platform, we found misincorporated dNs occurring at 1 per 103 to 105 ribonucleotide (nt) in mRNA, rRNAs and tRNA in human cells, Escherichia coli, Saccharomyces cerevisiae and, most abundantly, in the RNA genome of dengue virus. The frequency of dNs varied widely among organisms and sequence contexts, and partly reflected the in vitro discrimination efficiencies of different RNA polymerases against 2′-deoxyribonucleoside 5′-triphosphates (dNTPs). Further, we demonstrate a strong link between dN frequencies in RNA and the balance of dNTPs and ribonucleoside 5′-triphosphates (rNTPs) in the cellular pool, with significant stress-induced variation of dN incorporation. Potential implications of dNs in RNA are discussed, including the possibilities of dN incorporation in RNA as a contributing factor in viral evolution and human disease, and as a host immune defense mechanism against viral infections.
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Affiliation(s)
- Jin Wang
- Infectious Disease Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore 138602
| | - Hongping Dong
- Novartis Institute for Tropical Diseases, Singapore 138670
| | - Yok Hian Chionh
- Infectious Disease Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore 138602 Department of Microbiology & Immunology Programme, Center for Life Sciences, National University of Singapore, Singapore 117545
| | - Megan E McBee
- Infectious Disease Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore 138602
| | - Sasilada Sirirungruang
- Infectious Disease Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore 138602
| | - Richard P Cunningham
- Department of Biological Sciences, The University at Albany, Albany, NY 12222, USA
| | - Pei-Yong Shi
- Departments of Biochemistry & Molecular Biology and Phamarcology & Toxicology, and Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Peter C Dedon
- Infectious Disease Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore 138602 Department of Biological Engineering & Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139-4307, USA
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