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Mangiapane G, Pascut D, Dalla E, Antoniali G, Degrassi M, Crocè LS, De Sanctis V, Piazza S, Canarutto G, Tiribelli C, Tell G. Clinical Significance of Apurinic/Apyrimidinic Endodeoxyribonuclease 1 and MicroRNA Axis in Hepatocellular Carcinoma. J Clin Transl Hepatol 2023; 11:1291-1307. [PMID: 37719963 PMCID: PMC10500290 DOI: 10.14218/jcth.2022.00179] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 05/10/2023] [Accepted: 06/07/2023] [Indexed: 09/19/2023] Open
Abstract
Background and Aims Identification of prognostic factors for hepatocellular carcinoma (HCC) opens new perspectives for therapy. Circulating and cellular onco-miRNAs are noncoding RNAs which can control the expression of genes involved in oncogenesis through post-transcriptional mechanisms. These microRNAs (miRNAs) are considered novel prognostic and predictive factors in HCC. The apurinic/apyrimidinic endodeoxyribonuclease 1 (APE1) contributes to the quality control and processing of specific onco-miRNAs and is a negative prognostic factor in several tumors. The present work aims to: a) define APE1 prognostic value in HCC; b) identify miRNAs regulated by APE1 and their relative target genes and c) study their prognostic value. Methods We used The Cancer Genome Atlas (commonly known as TCGA) data analysis to evaluate the expression of APE1 in HCC. To identify differentially-expressed miRNAs (DEmiRNAs) upon APE1 depletion through specific small interfering RNA, we used NGS and nanostring approaches in the JHH-6 HCC tumor cell line. Bioinformatics analyses were performed to identify signaling pathways involving APE1-regulated miRNAs. Microarray analysis was performed to identify miRNAs correlating with serum APE1 expression. Results APE1 is considerably overexpressed in HCC tissues compared to normal liver, according to the TCGA-liver HCC (known as LIHC) dataset. Enrichment analyses showed that APE1-regulated miRNAs are implicated in signaling and metabolic pathways linked to cell proliferation, transformation, and angiogenesis, identifying Cyclin Dependent Kinase 6 and Lysosomal Associated Membrane Protein 2 as targets. miR-33a-5p, miR-769, and miR-877 are related to lower overall survival in HCC patients. Through array profiling, we identified eight circulating DE-miRNAs associated with APE1 overexpression. A training phase identified positive association between sAPE1 and miR-3180-3p and miR-769. Conclusions APE1 regulates specific miRNAs having prognostic value in HCC.
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Affiliation(s)
- Giovanna Mangiapane
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine, University of Udine, Udine, Italy
| | - Devis Pascut
- Fondazione Italiana Fegato - ONLUS, Liver Cancer Unit, Trieste, Italy
| | - Emiliano Dalla
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine, University of Udine, Udine, Italy
| | - Giulia Antoniali
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine, University of Udine, Udine, Italy
| | - Monica Degrassi
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine, University of Udine, Udine, Italy
| | - Lory Saveria Crocè
- Fondazione Italiana Fegato - ONLUS, Liver Cancer Unit, Trieste, Italy
- Department of Medical Sciences, University of Trieste, Trieste, Italy
- Clinica Patologie Fegato, Azienda Sanitaria Universitaria Giuliano Isontina (ASUGI), Trieste, Italy
| | | | - Silvano Piazza
- Computational Biology, International Centre for Genetic Engineering and Biotechnology, ICGEB, Trieste, Italy
| | - Giulia Canarutto
- Computational Biology, International Centre for Genetic Engineering and Biotechnology, ICGEB, Trieste, Italy
| | - Claudio Tiribelli
- Fondazione Italiana Fegato - ONLUS, Liver Cancer Unit, Trieste, Italy
| | - Gianluca Tell
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine, University of Udine, Udine, Italy
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Lirussi L, Nilsen HL. DNA Glycosylases Define the Outcome of Endogenous Base Modifications. Int J Mol Sci 2023; 24:10307. [PMID: 37373453 DOI: 10.3390/ijms241210307] [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: 05/26/2023] [Revised: 06/13/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
Chemically modified nucleic acid bases are sources of genomic instability and mutations but may also regulate gene expression as epigenetic or epitranscriptomic modifications. Depending on the cellular context, they can have vastly diverse impacts on cells, from mutagenesis or cytotoxicity to changing cell fate by regulating chromatin organisation and gene expression. Identical chemical modifications exerting different functions pose a challenge for the cell's DNA repair machinery, as it needs to accurately distinguish between epigenetic marks and DNA damage to ensure proper repair and maintenance of (epi)genomic integrity. The specificity and selectivity of the recognition of these modified bases relies on DNA glycosylases, which acts as DNA damage, or more correctly, as modified bases sensors for the base excision repair (BER) pathway. Here, we will illustrate this duality by summarizing the role of uracil-DNA glycosylases, with particular attention to SMUG1, in the regulation of the epigenetic landscape as active regulators of gene expression and chromatin remodelling. We will also describe how epigenetic marks, with a special focus on 5-hydroxymethyluracil, can affect the damage susceptibility of nucleic acids and conversely how DNA damage can induce changes in the epigenetic landscape by altering the pattern of DNA methylation and chromatin structure.
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Affiliation(s)
- Lisa Lirussi
- Department of Clinical Molecular Biology, Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway
- Section of Clinical Molecular Biology (EpiGen), Akershus University Hospital, 1478 Lørenskog, Norway
- Department of Microbiology, Oslo University Hospital, 0424 Oslo, Norway
| | - Hilde Loge Nilsen
- Department of Clinical Molecular Biology, Institute of Clinical Medicine, University of Oslo, 0318 Oslo, Norway
- Department of Microbiology, Oslo University Hospital, 0424 Oslo, Norway
- Unit for Precision Medicine, Akershus University Hospital, 1478 Lørenskog, Norway
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Molecular Mechanisms Regulating the DNA Repair Protein APE1: A Focus on Its Flexible N-Terminal Tail Domain. Int J Mol Sci 2021; 22:ijms22126308. [PMID: 34208390 PMCID: PMC8231204 DOI: 10.3390/ijms22126308] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/08/2021] [Accepted: 06/09/2021] [Indexed: 02/06/2023] Open
Abstract
APE1 (DNA (apurinic/apyrimidinic site) endonuclease 1) is a key enzyme of one of the major DNA repair routes, the BER (base excision repair) pathway. APE1 fulfils additional functions, acting as a redox regulator of transcription factors and taking part in RNA metabolism. The mechanisms regulating APE1 are still being deciphered. Structurally, human APE1 consists of a well-characterized globular catalytic domain responsible for its endonuclease activity, preceded by a conformationally flexible N-terminal extension, acquired along evolution. This N-terminal tail appears to play a prominent role in the modulation of APE1 and probably in BER coordination. Thus, it is primarily involved in mediating APE1 localization, post-translational modifications, and protein–protein interactions, with all three factors jointly contributing to regulate the enzyme. In this review, recent insights on the regulatory role of the N-terminal region in several aspects of APE1 function are covered. In particular, interaction of this region with nucleophosmin (NPM1) might modulate certain APE1 activities, representing a paradigmatic example of the interconnection between various regulatory factors.
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Malfatti MC, Antoniali G, Codrich M, Burra S, Mangiapane G, Dalla E, Tell G. New perspectives in cancer biology from a study of canonical and non-canonical functions of base excision repair proteins with a focus on early steps. Mutagenesis 2021; 35:129-149. [PMID: 31858150 DOI: 10.1093/mutage/gez051] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 12/05/2019] [Indexed: 12/15/2022] Open
Abstract
Alterations of DNA repair enzymes and consequential triggering of aberrant DNA damage response (DDR) pathways are thought to play a pivotal role in genomic instabilities associated with cancer development, and are further thought to be important predictive biomarkers for therapy using the synthetic lethality paradigm. However, novel unpredicted perspectives are emerging from the identification of several non-canonical roles of DNA repair enzymes, particularly in gene expression regulation, by different molecular mechanisms, such as (i) non-coding RNA regulation of tumour suppressors, (ii) epigenetic and transcriptional regulation of genes involved in genotoxic responses and (iii) paracrine effects of secreted DNA repair enzymes triggering the cell senescence phenotype. The base excision repair (BER) pathway, canonically involved in the repair of non-distorting DNA lesions generated by oxidative stress, ionising radiation, alkylation damage and spontaneous or enzymatic deamination of nucleotide bases, represents a paradigm for the multifaceted roles of complex DDR in human cells. This review will focus on what is known about the canonical and non-canonical functions of BER enzymes related to cancer development, highlighting novel opportunities to understand the biology of cancer and representing future perspectives for designing new anticancer strategies. We will specifically focus on APE1 as an example of a pleiotropic and multifunctional BER protein.
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Affiliation(s)
- Matilde Clarissa Malfatti
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Giulia Antoniali
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Marta Codrich
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Silvia Burra
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Giovanna Mangiapane
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Emiliano Dalla
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Gianluca Tell
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
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Salemi M, Mazzetti S, De Leonardis M, Giampietro F, Medici V, Poloni TE, Cannarella R, Giaccone G, Pezzoli G, Cappelletti G, Ferri R. Poly (ADP-ribose) polymerase 1 and Parkinson's disease: A study in post-mortem human brain. Neurochem Int 2021; 144:104978. [PMID: 33516746 DOI: 10.1016/j.neuint.2021.104978] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 01/06/2021] [Accepted: 01/23/2021] [Indexed: 02/07/2023]
Abstract
Poly (ADP-ribose) polymerase 1 (PARP1) is crucial in both maintenance of genome integrity and cell death. PARP1 activation has been very recently linked to Parkinson's disease (PD) and its role in inducing the pathologic accumulation of α-Synuclein demonstrated in a PD mouse model. The objective of this study was to investigate the presence and localization of PARP1 in PD brain. PARP1 localization was assessed by immunostaining and confocal microscopy in post-mortem human brains obtained from PD patients (Braak stage VI) compared to controls. PARP1 positive nuclei in substantia nigra, mainly in dopaminergic neurons but also in astrocytes and oligodendrocytes, were decreased in PD. The same alteration was observed in several areas that are affected in PD pathology, namely the dorsal motor nucleus of vagus, frontal and cingulate cortex, whereas no changes in PARP1 staining were detectable in the inferior olivary nucleus that is unaffected in PD. In addition, PARP1 co-localizes with α-Synuclein that is accumulated in the cytoplasm and in Lewy bodies of PD tissue sections. Our data reveal previously unknown changes of PARP1 localization in the brain of PD patients, in both neurons and glia, supporting its widespread involvement in this pathology and its potential use as a therapeutic target.
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Affiliation(s)
| | - Samanta Mazzetti
- Fondazione Grigioni per il Morbo di Parkinson, via Zuretti 35, I-20135, Milan, Italy
| | | | | | - Valentina Medici
- Department of Neurology and Neuropathology, Golgi-Cenci Foundation, Abbiategrasso, Milan, Italy
| | - Tino Emanuele Poloni
- Department of Neurology and Neuropathology, Golgi-Cenci Foundation, Abbiategrasso, Milan, Italy
| | - Rossella Cannarella
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Giorgio Giaccone
- Unit of Neuropathology and Neurology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Gianni Pezzoli
- Fondazione Grigioni per il Morbo di Parkinson, via Zuretti 35, I-20135, Milan, Italy
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RNA Metabolism Guided by RNA Modifications: The Role of SMUG1 in rRNA Quality Control. Biomolecules 2021; 11:biom11010076. [PMID: 33430019 PMCID: PMC7826747 DOI: 10.3390/biom11010076] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/29/2020] [Accepted: 01/05/2021] [Indexed: 12/19/2022] Open
Abstract
RNA modifications are essential for proper RNA processing, quality control, and maturation steps. In the last decade, some eukaryotic DNA repair enzymes have been shown to have an ability to recognize and process modified RNA substrates and thereby contribute to RNA surveillance. Single-strand-selective monofunctional uracil-DNA glycosylase 1 (SMUG1) is a base excision repair enzyme that not only recognizes and removes uracil and oxidized pyrimidines from DNA but is also able to process modified RNA substrates. SMUG1 interacts with the pseudouridine synthase dyskerin (DKC1), an enzyme essential for the correct assembly of small nucleolar ribonucleoproteins (snRNPs) and ribosomal RNA (rRNA) processing. Here, we review rRNA modifications and RNA quality control mechanisms in general and discuss the specific function of SMUG1 in rRNA metabolism. Cells lacking SMUG1 have elevated levels of immature rRNA molecules and accumulation of 5-hydroxymethyluridine (5hmU) in mature rRNA. SMUG1 may be required for post-transcriptional regulation and quality control of rRNAs, partly by regulating rRNA and stability.
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Mijit M, Caston R, Gampala S, Fishel ML, Fehrenbacher J, Kelley MR. APE1/Ref-1 - One Target with Multiple Indications: Emerging Aspects and New Directions. JOURNAL OF CELLULAR SIGNALING 2021; 2:151-161. [PMID: 34557865 PMCID: PMC8457357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
In the realm of DNA repair, base excision repair (BER) protein, APE1/Ref-1 (Apurinic/Apyrimidinic Endonuclease 1/Redox Effector - 1, also called APE1) has been studied for decades. However, over the past decade, APE1 has been established as a key player in reduction-oxidation (redox) signaling. In the review by Caston et al. (The multifunctional APE1 DNA repair-redox signaling protein as a drug target in human disease), multiple roles of APE1 in cancer and other diseases are summarized. In this Review, we aim to expand on the contributions of APE1 to various diseases and its effect on disease progression. In the scope of cancer, more recent roles for APE1 have been identified in cancer cell metabolism, as well as chemotherapy-induced peripheral neuropathy (CIPN) and inflammation. Outside of cancer, APE1 signaling may be a critical factor in inflammatory bowel disease (IBD) and is also an emergent area of investigation in retinal ocular diseases. The ability of APE1 to regulate multiple transcription factors (TFs) and therefore multiple pathways that have implications outside of cancer, makes it a particularly unique and enticing target. We discuss APE1 redox inhibitors as a means of studying and potentially combating these diseases. Lastly, we examine the role of APE1 in RNA metabolism. Overall, this article builds on our previous review to elaborate on the roles and conceivable regulation of important pathways by APE1 in multiple diseases.
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Affiliation(s)
- Mahmut Mijit
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, 1044 W. Walnut, Indianapolis, IN 46202, USA,Department of Pediatrics, Indiana University School of Medicine, 1044 W. Walnut, Indianapolis, IN 46202, USA
| | - Rachel Caston
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, 1044 W. Walnut, Indianapolis, IN 46202, USA,Department of Pediatrics, Indiana University School of Medicine, 1044 W. Walnut, Indianapolis, IN 46202, USA
| | - Silpa Gampala
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, 1044 W. Walnut, Indianapolis, IN 46202, USA,Department of Pediatrics, Indiana University School of Medicine, 1044 W. Walnut, Indianapolis, IN 46202, USA
| | - Melissa L. Fishel
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, 1044 W. Walnut, Indianapolis, IN 46202, USA,Department of Pediatrics, Indiana University School of Medicine, 1044 W. Walnut, Indianapolis, IN 46202, USA,Department of Pharmacology and Toxicology, Indiana University School of Medicine, 1044 W. Walnut, Indianapolis, IN 46202, USA,Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, 1044 W. Walnut, Indianapolis, IN 46202, USA
| | - Jill Fehrenbacher
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, 1044 W. Walnut, Indianapolis, IN 46202, USA,Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, 1044 W. Walnut, Indianapolis, IN 46202, USA
| | - Mark R. Kelley
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana University School of Medicine, 1044 W. Walnut, Indianapolis, IN 46202, USA,Department of Pediatrics, Indiana University School of Medicine, 1044 W. Walnut, Indianapolis, IN 46202, USA,Department of Pharmacology and Toxicology, Indiana University School of Medicine, 1044 W. Walnut, Indianapolis, IN 46202, USA,Indiana University Simon Comprehensive Cancer Center, Indiana University School of Medicine, 1044 W. Walnut, Indianapolis, IN 46202, USA,Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 1044 W. Walnut, Indianapolis, IN 46202, USA,Correspondence should be addressed to Mark R. Kelley;
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Kowalska M, Piekut T, Prendecki M, Sodel A, Kozubski W, Dorszewska J. Mitochondrial and Nuclear DNA Oxidative Damage in Physiological and Pathological Aging. DNA Cell Biol 2020; 39:1410-1420. [PMID: 32315547 DOI: 10.1089/dna.2019.5347] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Mitochondria play an important role in numerous processes, including energy generation, regulating ion homeostasis, and cell signaling. Mitochondria are also the main source of reactive oxygen species (ROS). Due to the oxidative environment within mitochondria, the macromolecules therein, for example, mtDNA, proteins, and lipids are more susceptible to sustaining damage. During aging, mitochondrial functions decline, partly as a result of an accumulation of mtDNA mutations, decreased mtDNA copy number and protein expression, and a reduction in oxidative capacity. The aim of this study was to summarize the knowledge on DNA oxidative damage in aging and age-related neurodegenerative diseases. It has been hypothesized that various ROS may play an important role not only in physiological senescence but also in the development of neurodegenerative diseases, for example, Alzheimer's disease and Parkinson's disease. Thus, mitochondria seem to be a potential target of novel treatments for neurodegenerative diseases.
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Affiliation(s)
- Marta Kowalska
- Laboratory of Neurobiology, Department of Neurology, Poznan University of Medical Sciences, Poznan, Poland
| | - Thomas Piekut
- Laboratory of Neurobiology, Department of Neurology, Poznan University of Medical Sciences, Poznan, Poland
| | - Michal Prendecki
- Laboratory of Neurobiology, Department of Neurology, Poznan University of Medical Sciences, Poznan, Poland
| | - Agnieszka Sodel
- Laboratory of Neurobiology, Department of Neurology, Poznan University of Medical Sciences, Poznan, Poland
| | - Wojciech Kozubski
- Chair and Department of Neurology, Poznan University of Medical Sciences, Poznan, Poland
| | - Jolanta Dorszewska
- Laboratory of Neurobiology, Department of Neurology, Poznan University of Medical Sciences, Poznan, Poland
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Architecture of The Human Ape1 Interactome Defines Novel Cancers Signatures. Sci Rep 2020; 10:28. [PMID: 31913336 PMCID: PMC6949240 DOI: 10.1038/s41598-019-56981-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 12/16/2019] [Indexed: 12/19/2022] Open
Abstract
APE1 is essential in cancer cells due to its central role in the Base Excision Repair pathway of DNA lesions and in the transcriptional regulation of genes involved in tumor progression/chemoresistance. Indeed, APE1 overexpression correlates with chemoresistance in more aggressive cancers, and APE1 protein-protein interactions (PPIs) specifically modulate different protein functions in cancer cells. Although important, a detailed investigation on the nature and function of protein interactors regulating APE1 role in tumor progression and chemoresistance is still lacking. The present work was aimed at analyzing the APE1-PPI network with the goal of defining bad prognosis signatures through systematic bioinformatics analysis. By using a well-characterized HeLa cell model stably expressing a flagged APE1 form, which was subjected to extensive proteomics analyses for immunocaptured complexes from different subcellular compartments, we here demonstrate that APE1 is a central hub connecting different subnetworks largely composed of proteins belonging to cancer-associated communities and/or involved in RNA- and DNA-metabolism. When we performed survival analysis in real cancer datasets, we observed that more than 80% of these APE1-PPI network elements is associated with bad prognosis. Our findings, which are hypothesis generating, strongly support the possibility to infer APE1-interactomic signatures associated with bad prognosis of different cancers; they will be of general interest for the future definition of novel predictive disease biomarkers. Future studies will be needed to assess the function of APE1 in the protein complexes we discovered. Data are available via ProteomeXchange with identifier PXD013368.
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Koliadenko V, Wilanowski T. Additional functions of selected proteins involved in DNA repair. Free Radic Biol Med 2020; 146:1-15. [PMID: 31639437 DOI: 10.1016/j.freeradbiomed.2019.10.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/16/2019] [Accepted: 10/16/2019] [Indexed: 12/30/2022]
Abstract
Protein moonlighting is a phenomenon in which a single polypeptide chain can perform a number of different unrelated functions. Here we present our analysis of moonlighting in the case of selected DNA repair proteins which include G:T mismatch-specific thymine DNA glycosylase (TDG), methyl-CpG-binding domain protein 4 (MBD4), apurinic/apyrimidinic endonuclease 1 (APE1), AlkB homologs, poly (ADP-ribose) polymerase 1 (PARP-1) and single-strand selective monofunctional uracil DNA glycosylase 1 (SMUG1). Most of their additional functions are not accidental and clear patterns are emerging. Participation in RNA metabolism is not surprising as bases occurring in RNA are the same or very similar to those in DNA. Other common additional function involves regulation of transcription. This is not unexpected as these proteins bind to specific DNA regions for DNA repair, hence they can also be recruited to regulate transcription. Participation in demethylation and replication of DNA appears logical as well. Some of the multifunctional DNA repair proteins play major roles in many diseases, including cancer. However, their moonlighting might prove a major difficulty in the development of new therapies because it will not be trivial to target a single protein function without affecting its other functions that are not related to the disease.
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Affiliation(s)
- Vlada Koliadenko
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Ilji Miecznikowa 1, 02-096, Warsaw, Poland
| | - Tomasz Wilanowski
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Ilji Miecznikowa 1, 02-096, Warsaw, Poland.
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Mironova N, Vlassov V. Surveillance of Tumour Development: The Relationship Between Tumour-Associated RNAs and Ribonucleases. Front Pharmacol 2019; 10:1019. [PMID: 31572192 PMCID: PMC6753386 DOI: 10.3389/fphar.2019.01019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 08/09/2019] [Indexed: 12/14/2022] Open
Abstract
Tumour progression is accompanied by rapid cell proliferation, loss of differentiation, the reprogramming of energy metabolism, loss of adhesion, escape of immune surveillance, induction of angiogenesis, and metastasis. Both coding and regulatory RNAs expressed by tumour cells and circulating in the blood are involved in all stages of tumour progression. Among the important tumour-associated RNAs are intracellular coding RNAs that determine the routes of metabolic pathways, cell cycle control, angiogenesis, adhesion, apoptosis and pathways responsible for transformation, and intracellular and extracellular non-coding RNAs involved in regulation of the expression of their proto-oncogenic and oncosuppressing mRNAs. Considering the diversity/variability of biological functions of RNAs, it becomes evident that extracellular RNAs represent important regulators of cell-to-cell communication and intracellular cascades that maintain cell proliferation and differentiation. In connection with the elucidation of such an important role for RNA, a surge in interest in RNA-degrading enzymes has increased. Natural ribonucleases (RNases) participate in various cellular processes including miRNA biogenesis, RNA decay and degradation that has determined their principal role in the sustention of RNA homeostasis in cells. Findings were obtained on the contribution of some endogenous ribonucleases in the maintenance of normal cell RNA homeostasis, which thus prevents cell transformation. These findings directed attention to exogenous ribonucleases as tools to compensate for the malfunction of endogenous ones. Recently a number of proteins with ribonuclease activity were discovered whose intracellular function remains unknown. Thus, the comprehensive investigation of physiological roles of RNases is still required. In this review we focused on the control mechanisms of cell transformation by endogenous ribonucleases, and the possibility of replacing malfunctioning enzymes with exogenous ones.
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Affiliation(s)
- Nadezhda Mironova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Valentin Vlassov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
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Serum AP-endonuclease 1 (sAPE1) as novel biomarker for hepatocellular carcinoma. Oncotarget 2019; 10:383-394. [PMID: 30719231 PMCID: PMC6349448 DOI: 10.18632/oncotarget.26555] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 12/27/2018] [Indexed: 12/24/2022] Open
Abstract
Late diagnosis for Hepatocellular Carcinoma (HCC) remains one of the leading causes for the high mortality rate. The apurinic/apyrimidinic endonuclease 1 (APE1), an essential member of the base excision DNA repair (BER) pathway, contributes to cell response to oxidative stress and has other non-repair activities. In this study, we evaluate the role of serum APE1 (sAPE1) as a new diagnostic biomarker and we investigate the biological role for extracellular APE1 in HCC. sAPE1 level was quantified in 99 HCC patients, 50 non-HCC cirrhotic and 100 healthy controls. The expression level was significantly high in HCC (75.8 [67.3–87.9] pg/mL) compared to cirrhosis (29.8 [18.3–36.5] pg/mL] and controls (10.8 [7.5–13.2] pg/mL) (p < 0.001). The sAPE1 level corresponded with its protein expression in HCC tissue. sAPE1 had high diagnostic accuracy to differentiate HCC from cirrhotic (AUC = 0.87, sensitivity 88%, specificity 71%, cut-off of 36.3 pg/mL) and healthy subjects (AUC 0.98, sensibility 98% and specificity 83%, cut-off of 19.0 pg/mL). Recombinant APE1, exogenously added to JHH6 cells, significantly promotes IL-6 and IL-8 expression, suggesting a role of sAPE1 as a paracrine pro-inflammatory molecule, which may modulate the inflammatory status in cancer microenvironment. We described herein, for the first time to our knowledge, that sAPE1 might be considered as a promising diagnostic biomarker for HCC.
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Herbert C, Dzowo YK, Urban A, Kiggins CN, Resendiz MJE. Reactivity and Specificity of RNase T 1, RNase A, and RNase H toward Oligonucleotides of RNA Containing 8-Oxo-7,8-dihydroguanosine. Biochemistry 2018; 57:2971-2983. [PMID: 29683663 DOI: 10.1021/acs.biochem.8b00277] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Understanding how oxidatively damaged RNA interacts with ribonucleases is important because of its proposed role in the development and progression of disease. Thus, understanding structural aspects of RNA containing lesions generated under oxidative stress, as well as its interactions with other biopolymers, is fundamental. We explored the reactivity of RNase A, RNase T1, and RNase H toward oligonucleotides of RNA containing 8-oxo-7,8-dihydroguanosine (8oxoG). This is the first example that addresses this relationship and will be useful for understanding (1) how these RNases can be used to characterize the structural impact that this lesion has on RNA and (2) how oxidatively modified RNA may be handled intracellularly. 8-OxoG was incorporated into 10-16-mers of RNA, and its reactivity with each ribonuclease was assessed via electrophoretic analyses, circular dichroism, and the use of other C8-purine-modified analogues (8-bromoguanosine, 8-methoxyguanosine, and 8-oxoadenosine). RNase T1 does not recognize sites containing 8-oxoG, while RNase A recognizes and cleaves RNA at positions containing this lesion while differentiating if it is involved in H-bonding. The selectivity of RNase A followed the order C > 8-oxoG ≈ U. In addition, isothermal titration calorimetry showed that an 8-oxoG-C3'-methylphosphate derivative can inhibit RNase A activity. Cleavage patterns obtained from RNase H displayed changes in reactivity in a sequence- and concentration-dependent manner and displayed recognition at sites containing the modification in some cases. These data will aid in understanding how this modification affects reactivity with ribonucleases and will enable the characterization of global and local structural changes in oxidatively damaged RNA.
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Affiliation(s)
- Cassandra Herbert
- Department of Chemistry , University of Colorado Denver , Science Building, 1151 Arapahoe Street , Denver , Colorado 80204 , United States
| | - Yannick Kokouvi Dzowo
- Department of Chemistry , University of Colorado Denver , Science Building, 1151 Arapahoe Street , Denver , Colorado 80204 , United States
| | - Anthony Urban
- Department of Chemistry , University of Colorado Denver , Science Building, 1151 Arapahoe Street , Denver , Colorado 80204 , United States
| | - Courtney N Kiggins
- Department of Chemistry , University of Colorado Denver , Science Building, 1151 Arapahoe Street , Denver , Colorado 80204 , United States
| | - Marino J E Resendiz
- Department of Chemistry , University of Colorado Denver , Science Building, 1151 Arapahoe Street , Denver , Colorado 80204 , United States
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APE1 polymorphic variants cause persistent genomic stress and affect cancer cell proliferation. Oncotarget 2018; 7:26293-306. [PMID: 27050370 PMCID: PMC5041981 DOI: 10.18632/oncotarget.8477] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 03/12/2016] [Indexed: 01/15/2023] Open
Abstract
Apurinic/apyrimidinic endonuclease 1 (APE1) is the main mammalian AP-endonuclease responsible for the repair of endogenous DNA damage through the base excision repair (BER) pathway. Molecular epidemiological studies have identified several genetic variants associated with human diseases, but a well-defined functional connection between mutations in APE1 and disease development is lacking. In order to understand the biological consequences of APE1 genetic mutations, we examined the molecular and cellular consequences of the selective expression of four non-synonymous APE1 variants (L104R, R237C, D148E and D283G) in human cells. We found that D283G, L104R and R237C variants have reduced endonuclease activity and impaired ability to associate with XRCC1 and DNA polymerase β, which are enzymes acting downstream of APE1 in the BER pathway. Complementation experiments performed in cells, where endogenous APE1 had been silenced by shRNA, showed that the expression of these variants resulted in increased phosphorylation of histone H2Ax and augmented levels of poly(ADP-ribosyl)ated (PAR) proteins. Persistent activation of DNA damage response markers was accompanied by growth defects likely due to combined apoptotic and autophagic processes. These phenotypes were observed in the absence of exogenous stressors, suggesting that chronic replication stress elicited by the BER defect may lead to a chronic activation of the DNA damage response. Hence, our data reinforce the concept that non-synonymous APE1 variants present in the human population may act as cancer susceptibility alleles.
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15
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Malfatti MC, Balachander S, Antoniali G, Koh KD, Saint-Pierre C, Gasparutto D, Chon H, Crouch RJ, Storici F, Tell G. Abasic and oxidized ribonucleotides embedded in DNA are processed by human APE1 and not by RNase H2. Nucleic Acids Res 2017; 45:11193-11212. [PMID: 28977421 PMCID: PMC5737539 DOI: 10.1093/nar/gkx723] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 08/11/2017] [Indexed: 12/13/2022] Open
Abstract
Ribonucleoside 5′-monophosphates (rNMPs) are the most common non-standard nucleotides found in DNA of eukaryotic cells, with over 100 million rNMPs transiently incorporated in the mammalian genome per cell cycle. Human ribonuclease (RNase) H2 is the principal enzyme able to cleave rNMPs in DNA. Whether RNase H2 may process abasic or oxidized rNMPs incorporated in DNA is unknown. The base excision repair (BER) pathway is mainly responsible for repairing oxidized and abasic sites into DNA. Here we show that human RNase H2 is unable to process an abasic rNMP (rAP site) or a ribose 8oxoG (r8oxoG) site embedded in DNA. On the contrary, we found that recombinant purified human apurinic/apyrimidinic endonuclease-1 (APE1) and APE1 from human cell extracts efficiently process an rAP site in DNA and have weak endoribonuclease and 3′-exonuclease activities on r8oxoG substrate. Using biochemical assays, our results provide evidence of a human enzyme able to recognize and process abasic and oxidized ribonucleotides embedded in DNA.
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Affiliation(s)
- Matilde Clarissa Malfatti
- Laboratory of Molecular Biology and DNA repair, Department of Medicine, University of Udine, Udine, Italy
| | - Sathya Balachander
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Giulia Antoniali
- Laboratory of Molecular Biology and DNA repair, Department of Medicine, University of Udine, Udine, Italy
| | - Kyung Duk Koh
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.,University of California, San Francisco, UCSF, School of Medicine, San Francisco, CA, USA
| | - Christine Saint-Pierre
- Chimie Reconnaissance & Etude Assemblages Biologiques, Université Grenoble Alpes, SPrAM UMR5819 CEA CNRS UGA, INAC/CEA, Grenoble, France
| | - Didier Gasparutto
- Chimie Reconnaissance & Etude Assemblages Biologiques, Université Grenoble Alpes, SPrAM UMR5819 CEA CNRS UGA, INAC/CEA, Grenoble, France
| | - Hyongi Chon
- Developmental Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Robert J Crouch
- Developmental Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Francesca Storici
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Gianluca Tell
- Laboratory of Molecular Biology and DNA repair, Department of Medicine, University of Udine, Udine, Italy
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16
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DNA versus RNA oxidation in Parkinson's disease: Which is more important? Neurosci Lett 2017; 662:22-28. [PMID: 28963060 DOI: 10.1016/j.neulet.2017.09.048] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 09/22/2017] [Accepted: 09/25/2017] [Indexed: 11/21/2022]
Abstract
BACKROUND 8-hydroxy-2 deoxyguanosine (8-OHdG) and the 8-hydroxyguanosine (8-OHG) are the most widely used biomarkers of nucleoside oxidation affecting DNA and RNA and are considered reliable markers of oxidative stress. Increased levels of these markers are found in the various biological fluids of patients with neurodegenerative disorders. OBJECTIVE The primary aim of our study was to assess the differences of investigated markers between patient groups and subsequently study the influence of clinical factors that might modify the levels of investigated markers during the disease progression. METHODS In this study, we analysed the 8-OHdG and 8-OHG levels in the cerebrospinal fluid (CSF) and serum from 44 patients with Parkinson's disease (PD) and 32 controls using an ELISA. RESULTS There were significantly higher CSF levels of both investigated markers in Parkinson's disease patients as compared to controls (p=0.02 and p=0.04). Significantly higher CSF values of 8-OHdG were found in PD patients without dementia (p=0.05), whereas patients with dementia recorded lower 8-OHG CSF levels compared to controls (p=0.04). The disease duration and age influenced the levels of both markers within investigated groups. CONCLUSION Oxidative DNA damage plays an important role in the early stages of PD, whereas during the progression of the disease the process is more complex, and other mechanisms are in the foreground. The measurement of 8-OHdG might be used as an "early-stage marker", whereas the decrease of 8-OHG in CSF might reflect the degree of neurodegeneration during the disease progression, suggesting its utility as a prognostic marker of advanced PD stages.
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17
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Lualdi S, Del Zotto G, Zegarra-Moran O, Pedemonte N, Corsolini F, Bruschi M, Tomati V, Amico G, Candiano G, Dardis A, Cooper DN, Filocamo M. In vitro recapitulation of the site-specific editing (to wild-type) of mutant IDS mRNA transcripts, and the characterization of IDS protein translated from the edited mRNAs. Hum Mutat 2017; 38:849-862. [PMID: 28477385 DOI: 10.1002/humu.23243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 04/05/2017] [Accepted: 04/22/2017] [Indexed: 11/06/2022]
Abstract
The transfer of genomic information into the primary RNA sequence can be altered by RNA editing. We have previously shown that genomic variants can be RNA-edited to wild-type. The presence of distinct "edited" iduronate 2-sulfatase (IDS) mRNA transcripts ex vivo evidenced the correction of a nonsense and frameshift variant, respectively, in three unrelated Hunter syndrome patients. This phenomenon was confirmed in various patient samples by a variety of techniques, and was quantified by single-nucleotide primer extension. Western blotting also confirmed the presence of IDS protein similar in size to the wild-type. Since preliminary experimental evidence suggested that the "corrected" IDS proteins produced by the patients were similar in molecular weight and net charge to their wild-type counterparts, an in vitro system employing different cell types was established to recapitulate the site-specific editing of IDS RNA (uridine to cytidine conversion and uridine deletion), and to confirm the findings previously observed ex vivo in the three patients. In addition, confocal microscopy and flow cytometry analyses demonstrated the expression and lysosomal localization in HEK293 cells of GFP-labeled proteins translated from edited IDS mRNAs. Confocal high-content analysis of the two patients' cells expressing wild-type or mutated IDS confirmed lysosomal localization and showed no accumulation in the Golgi or early endosomes.
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Affiliation(s)
- Susanna Lualdi
- UOSD Centro di Diagnostica Genetica e Biochimica delle Malattie Metaboliche, Istituto Giannina Gaslini, Genova, Italy
| | | | | | | | - Fabio Corsolini
- UOSD Centro di Diagnostica Genetica e Biochimica delle Malattie Metaboliche, Istituto Giannina Gaslini, Genova, Italy
| | - Maurizio Bruschi
- Laboratory on Physiopathology of Uremia, Istituto Giannina Gaslini, Genova, Italy
| | - Valeria Tomati
- UOC Genetica Medica, Istituto Giannina Gaslini, Genova, Italy
| | - Giulia Amico
- UOSD Centro di Diagnostica Genetica e Biochimica delle Malattie Metaboliche, Istituto Giannina Gaslini, Genova, Italy
| | - Giovanni Candiano
- Laboratory on Physiopathology of Uremia, Istituto Giannina Gaslini, Genova, Italy
| | - Andrea Dardis
- Regional Coordinator Centre for Rare Diseases, University Hospital Santa Maria della Misericordia, Udine, Italy
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Mirella Filocamo
- UOSD Centro di Diagnostica Genetica e Biochimica delle Malattie Metaboliche, Istituto Giannina Gaslini, Genova, Italy
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18
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Burger G, Moreira S, Valach M. Genes in Hiding. Trends Genet 2016; 32:553-565. [PMID: 27460648 DOI: 10.1016/j.tig.2016.06.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 06/23/2016] [Accepted: 06/24/2016] [Indexed: 12/25/2022]
Abstract
Unrecognizable genes are an unsettling problem in genomics. Here, we survey the various types of cryptic genes and the corresponding deciphering strategies employed by cells. Encryption that renders genes substantially different from homologs in other species includes sequence substitution, insertion, deletion, fragmentation plus scrambling, and invasion by mobile genetic elements. Cells decode cryptic genes at the DNA, RNA or protein level. We will focus on a recently discovered case of unparalleled encryption involving massive gene fragmentation and nucleotide deletions and substitutions, occurring in the mitochondrial genome of a poorly understood protist group, the diplonemids. This example illustrates that comprehensive gene detection requires not only auxiliary sequence information - transcriptome and proteome data - but also knowledge about a cell's deciphering arsenal.
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Affiliation(s)
- Gertraud Burger
- Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Canada.
| | - Sandrine Moreira
- Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Canada
| | - Matus Valach
- Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Canada
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19
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Simms CL, Zaher HS. Quality control of chemically damaged RNA. Cell Mol Life Sci 2016; 73:3639-53. [PMID: 27155660 DOI: 10.1007/s00018-016-2261-7] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Revised: 04/15/2016] [Accepted: 04/29/2016] [Indexed: 01/10/2023]
Abstract
The "central dogma" of molecular biology describes how information contained in DNA is transformed into RNA and finally into proteins. In order for proteins to maintain their functionality in both the parent cell and subsequent generations, it is essential that the information encoded in DNA and RNA remains unaltered. DNA and RNA are constantly exposed to damaging agents, which can modify nucleic acids and change the information they encode. While much is known about how cells respond to damaged DNA, the importance of protecting RNA has only become appreciated over the past decade. Modification of the nucleobase through oxidation and alkylation has long been known to affect its base-pairing properties during DNA replication. Similarly, recent studies have begun to highlight some of the unwanted consequences of chemical damage on mRNA decoding during translation. Oxidation and alkylation of mRNA appear to have drastic effects on the speed and fidelity of protein synthesis. As some mRNAs can persist for days in certain tissues, it is not surprising that it has recently emerged that mRNA-surveillance and RNA-repair pathways have evolved to clear or correct damaged mRNA.
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Affiliation(s)
- Carrie L Simms
- Department of Biology, Washington University in St. Louis, One Brookings Drive, Campus Box 1137, St. Louis, MO, 63130, USA
| | - Hani S Zaher
- Department of Biology, Washington University in St. Louis, One Brookings Drive, Campus Box 1137, St. Louis, MO, 63130, USA.
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20
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Vohhodina J, Harkin DP, Savage KI. Dual roles of DNA repair enzymes in RNA biology/post-transcriptional control. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:604-19. [PMID: 27126972 DOI: 10.1002/wrna.1353] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 03/17/2016] [Accepted: 03/18/2016] [Indexed: 12/12/2022]
Abstract
Despite consistent research into the molecular principles of the DNA damage repair pathway for almost two decades, it has only recently been found that RNA metabolism is very tightly related to this pathway, and the two ancient biochemical mechanisms act in alliance to maintain cellular genomic integrity. The close links between these pathways are well exemplified by examining the base excision repair pathway, which is now well known for dual roles of many of its members in DNA repair and RNA surveillance, including APE1, SMUG1, and PARP1. With additional links between these pathways steadily emerging, this review aims to provide a summary of the emerging roles for DNA repair proteins in the post-transcriptional regulation of RNAs. WIREs RNA 2016, 7:604-619. doi: 10.1002/wrna.1353 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Jekaterina Vohhodina
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - D Paul Harkin
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | - Kienan I Savage
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
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21
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Effect of Depurination on Cellular and Viral RNA. MODIFIED NUCLEIC ACIDS IN BIOLOGY AND MEDICINE 2016. [DOI: 10.1007/978-3-319-34175-0_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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22
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Betat H, Mörl M. The CCA-adding enzyme: A central scrutinizer in tRNA quality control. Bioessays 2015; 37:975-82. [DOI: 10.1002/bies.201500043] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Heike Betat
- Institute for Biochemistry; University of Leipzig; Leipzig Germany
| | - Mario Mörl
- Institute for Biochemistry; University of Leipzig; Leipzig Germany
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23
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Prasad R, Dyrkheeva N, Williams J, Wilson SH. Mammalian Base Excision Repair: Functional Partnership between PARP-1 and APE1 in AP-Site Repair. PLoS One 2015; 10:e0124269. [PMID: 26020771 PMCID: PMC4447435 DOI: 10.1371/journal.pone.0124269] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 03/11/2015] [Indexed: 01/09/2023] Open
Abstract
The apurinic/apyrimidinic- (AP-) site in genomic DNA arises through spontaneous base loss and base removal by DNA glycosylases and is considered an abundant DNA lesion in mammalian cells. The base excision repair (BER) pathway repairs the AP-site lesion by excising and replacing the site with a normal nucleotide via template directed gap-filling DNA synthesis. The BER pathway is mediated by a specialized group of proteins, some of which can be found in multiprotein complexes in cultured mouse fibroblasts. Using a DNA polymerase (pol) β immunoaffinity-capture technique to isolate such a complex, we identified five tightly associated and abundant BER factors in the complex: PARP-1, XRCC1, DNA ligase III, PNKP, and Tdp1. AP endonuclease 1 (APE1), however, was not present. Nevertheless, the complex was capable of BER activity, since repair was initiated by PARP-1’s AP lyase strand incision activity. Addition of purified APE1 increased the BER activity of the pol β complex. Surprisingly, the pol β complex stimulated the strand incision activity of APE1. Our results suggested that PARP-1 was responsible for this effect, whereas other proteins in the complex had no effect on APE1 strand incision activity. Studies of purified PARP-1 and APE1 revealed that PARP-1 was able to stimulate APE1 strand incision activity. These results illustrate roles of PARP-1 in BER including a functional partnership with APE1.
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Affiliation(s)
- Rajendra Prasad
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina, United States of America
| | - Nadezhda Dyrkheeva
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina, United States of America
| | - Jason Williams
- Epigenetics and Stem Cell Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina, United States of America
| | - Samuel H. Wilson
- Genome Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina, United States of America
- * E-mail:
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24
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Chohan M, Mackedenski S, Li WM, Lee CH. Human apurinic/apyrimidinic endonuclease 1 (APE1) has 3' RNA phosphatase and 3' exoribonuclease activities. J Mol Biol 2014; 427:298-311. [PMID: 25498387 DOI: 10.1016/j.jmb.2014.12.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 12/02/2014] [Accepted: 12/02/2014] [Indexed: 10/24/2022]
Abstract
Apurinic/apyrimidinic endonuclease 1 (APE1) is the predominant mammalian enzyme in DNA base excision repair pathway that cleaves the DNA backbone immediately 5' to abasic sites. In addition to its abasic endonuclease activity, APE1 has 3' phosphatase and 3'-5' exonuclease activities against DNA. We recently identified APE1 as an endoribonuclease that preferentially cleaves at UA, UG, and CA sites in single-stranded regions of RNAs and can regulate c-myc mRNA level and half-life in cells. APE1 can also endonucleolytically cleave abasic single-stranded RNA. Here, we show for the first time that the human APE1 has 3' RNA phosphatase and 3' exoribonuclease activities. Using three distinct RNA substrates, we show that APE1, but not RNase A, can remove the phosphoryl group from the 3' end of RNA decay products. Studies using various site-directed APE1 mutant proteins (H309N, H309S, D283N, N68A, D210N, Y171F, D308A, F266A, and D70A) suggest that the 3' RNA phosphatase activity shares the same active center as its other known nuclease activities. A number of APE1 variants previously identified in the human population, including the most common D148E variant, have greater than 80% reduction in the 3' RNA phosphatase activity. APE1 can remove a ribonucleotide from the 3' overhang of RNA decay product, but its 3'-5' exoribonuclease activity against unstructured poly(A), poly(C), and poly(U) RNAs is relatively weak. This study further underscores the significance of understanding the role of APE1 in RNA metabolism in vivo.
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Affiliation(s)
- Manbir Chohan
- Chemistry Program, University of Northern British Columbia, 3333 University Way, Prince George, British Columbia, V2N 4Z9, Canada
| | - Sebastian Mackedenski
- Chemistry Program, University of Northern British Columbia, 3333 University Way, Prince George, British Columbia, V2N 4Z9, Canada
| | - Wai-Ming Li
- Chemistry Program, University of Northern British Columbia, 3333 University Way, Prince George, British Columbia, V2N 4Z9, Canada
| | - Chow H Lee
- Chemistry Program, University of Northern British Columbia, 3333 University Way, Prince George, British Columbia, V2N 4Z9, Canada.
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Base excision repair in Archaea: back to the future in DNA repair. DNA Repair (Amst) 2014; 21:148-57. [PMID: 25012975 DOI: 10.1016/j.dnarep.2014.05.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 05/24/2014] [Indexed: 11/22/2022]
Abstract
Together with Bacteria and Eukarya, Archaea represents one of the three domain of life. In contrast with the morphological difference existing between Archaea and Eukarya, these two domains are closely related. Phylogenetic analyses confirm this evolutionary relationship showing that most of the proteins involved in DNA transcription and replication are highly conserved. On the contrary, information is scanty about DNA repair pathways and their mechanisms. In the present review the most important proteins involved in base excision repair, namely glycosylases, AP lyases, AP endonucleases, polymerases, sliding clamps, flap endonucleases, and ligases, will be discussed and compared with bacterial and eukaryotic ones. Finally, possible applications and future perspectives derived from studies on Archaea and their repair pathways, will be taken into account.
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