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Laverde EE, Polyzos AA, Tsegay PP, Shaver M, Hutcheson JD, Balakrishnan L, McMurray CT, Liu Y. Flap Endonuclease 1 Endonucleolytically Processes RNA to Resolve R-Loops through DNA Base Excision Repair. Genes (Basel) 2022; 14:genes14010098. [PMID: 36672839 PMCID: PMC9859040 DOI: 10.3390/genes14010098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 12/30/2022] Open
Abstract
Flap endonuclease 1 (FEN1) is an essential enzyme that removes RNA primers and base lesions during DNA lagging strand maturation and long-patch base excision repair (BER). It plays a crucial role in maintaining genome stability and integrity. FEN1 is also implicated in RNA processing and biogenesis. A recent study from our group has shown that FEN1 is involved in trinucleotide repeat deletion by processing the RNA strand in R-loops through BER, further suggesting that the enzyme can modulate genome stability by facilitating the resolution of R-loops. However, it remains unknown how FEN1 can process RNA to resolve an R-loop. In this study, we examined the FEN1 cleavage activity on the RNA:DNA hybrid intermediates generated during DNA lagging strand processing and BER in R-loops. We found that both human and yeast FEN1 efficiently cleaved an RNA flap in the intermediates using its endonuclease activity. We further demonstrated that FEN1 was recruited to R-loops in normal human fibroblasts and senataxin-deficient (AOA2) fibroblasts, and its R-loop recruitment was significantly increased by oxidative DNA damage. We showed that FEN1 specifically employed its endonucleolytic cleavage activity to remove the RNA strand in an R-loop during BER. We found that FEN1 coordinated its DNA and RNA endonucleolytic cleavage activity with the 3'-5' exonuclease of APE1 to resolve the R-loop. Our results further suggest that FEN1 employed its unique tracking mechanism to endonucleolytically cleave the RNA strand in an R-loop by coordinating with other BER enzymes and cofactors during BER. Our study provides the first evidence that FEN1 endonucleolytic cleavage can result in the resolution of R-loops via the BER pathway, thereby maintaining genome integrity.
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Affiliation(s)
- Eduardo E. Laverde
- Biochemistry Ph.D. Program, Florida International University, Miami, FL 33199, USA
| | - Aris A. Polyzos
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Pawlos P. Tsegay
- Biochemistry Ph.D. Program, Florida International University, Miami, FL 33199, USA
| | - Mohammad Shaver
- Department of Biomedical Engineering, Florida International University, Miami, FL 33199, USA
| | - Joshua D. Hutcheson
- Department of Biomedical Engineering, Florida International University, Miami, FL 33199, USA
| | - Lata Balakrishnan
- Department of Biology, Indiana-Purdue University, Indianapolis, IN 46202, USA
| | - Cynthia T. McMurray
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yuan Liu
- Biochemistry Ph.D. Program, Florida International University, Miami, FL 33199, USA
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
- Correspondence:
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Tang Q, Liu Y, Liu Y, Zhu F, Yu Q, Chen H, Chen L, Ma S, Xu H, Chen K, Li G. Bombyx mori Flap endonuclease 1 correlates with the repair of ultraviolet-induced DNA damage. JOURNAL OF INSECT PHYSIOLOGY 2022; 142:104424. [PMID: 35878701 DOI: 10.1016/j.jinsphys.2022.104424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Solar ultraviolet radiation (UV) can cause DNA damage in microorganisms. Flap endonuclease 1 (FEN1) is a structure-specific nuclease and plays important roles in DNA replication and repair. At present, the properties and functions of FEN1 have not been characterized in detail in invertebrates such as Bombyx mori. In this study, Bombyx mori FEN1 (BmFEN1) was expressed in E. coli, and was shown to have nuclease activity that nonspecifically cleaved DNA in vitro. However, inside the cell, BmFEN1 did not cleave DNA randomly. Truncated BmFEN1 missing the nuclear localization signal (346-380 aa) still had the nuclease activity, but was no longer precisely localized to the sites of UV-induced DNA damage. It was further found that BmFEN1 favored the faster repair of UV-damaged DNA. The present study will provide a reference for further understanding the functions of BmFEN1 and UV-induced DNA damage repair mechanisms in insects.
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Affiliation(s)
- Qi Tang
- School of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, China
| | - Yue Liu
- School of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, China
| | - Yutong Liu
- School of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, China
| | - Feifei Zhu
- School of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, China
| | - Qian Yu
- School of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, China
| | - Huiqing Chen
- School of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, China
| | - Liang Chen
- School of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, China
| | - Shangshang Ma
- School of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, China
| | - Huixin Xu
- School of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, China
| | - Keping Chen
- School of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, China.
| | - Guohui Li
- School of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, China.
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Pan-cancer analysis reveals that CTC1-STN1-TEN1 (CST) complex may have a key position in oncology. Cancer Genet 2022; 262-263:80-90. [DOI: 10.1016/j.cancergen.2022.01.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/07/2022] [Accepted: 01/30/2022] [Indexed: 12/14/2022]
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Lung cancer: progression of heat shock protein 70 in association with flap endonuclease 1 protein. 3 Biotech 2021; 11:141. [PMID: 33708464 DOI: 10.1007/s13205-020-02598-3] [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: 09/29/2020] [Accepted: 12/17/2020] [Indexed: 12/24/2022] Open
Abstract
Lung cancer is one of the leading causes of cancer deaths worldwide and existing approaches are not enough to manage, and hence, it is important to concentrate on new drug strategies. This study was aimed to identify the interacting partner of Flap endonuclease 1 (FEN1) and its role in cancer treatment. We identified a new FEN1 interacting partner confirmed it as Heat Shock Protein 70 (HSP 70), and its effect on FEN1 expression, in vitro. Additionally, we found that the 5-Fluorouracil's (5-FU) function was significantly improved when used in combination with HSP 70 inhibitor (KNK 437). The findings are interesting, elucidating the synergistic mechanism between two compounds which helps to develop a novel management strategy for over-expressed FEN1 in the lung. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-020-02598-3.
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