1
|
Kanazhevskaya LY, Gorbunov AA, Lukina MV, Smyshliaev DA, Zhdanova PV, Lomzov AA, Koval VV. The Role of Key Amino Acids of the Human Fe(II)/2OG-Dependent Dioxygenase ALKBH3 in Structural Dynamics and Repair Activity toward Methylated DNA. Int J Mol Sci 2024; 25:1145. [PMID: 38256217 PMCID: PMC10816986 DOI: 10.3390/ijms25021145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/13/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
Non-heme dioxygenases of the AlkB family hold a unique position among enzymes that repair alkyl lesions in nucleic acids. These enzymes activate the Fe(II) ion and molecular oxygen through the coupled decarboxylation of the 2-oxoglutarate co-substrate to subsequently oxidize the substrate. ALKBH3 is a human homolog of E. coli AlkB, which displays a specific activity toward N1-methyladenine and N3-methylcytosine bases in single-stranded DNA. Due to the lack of a DNA-bound structure of ALKBH3, the basis of its substrate specificity and structure-function relationships requires further exploration. Here we have combined biochemical and biophysical approaches with site-directed mutational analysis to elucidate the role of key amino acids in maintaining the secondary structure and catalytic activity of ALKBH3. Using stopped-flow fluorescence spectroscopy we have shown that conformational dynamics play a crucial role in the catalytic repair process catalyzed by ALKBH3. A transient kinetic mechanism, which comprises the steps of the specific substrate binding, eversion, and anchoring within the DNA-binding cleft, has been described quantitatively by rate and equilibrium constants. Through CD spectroscopy, we demonstrated that replacing side chains of Tyr143, Leu177, and His191 with alanine results in significant alterations in the secondary structure content of ALKBH3 and decreases the stability of mutant proteins. The bulky side chain of Tyr143 is critical for binding the methylated base and stabilizing its flipped-out conformation, while its hydroxyl group is likely involved in facilitating the product release. The removal of the Leu177 and His191 side chains substantially affects the secondary structure content and conformational flexibility, leading to the complete inactivation of the protein. The mutants lacking enzymatic activity exhibit a marked decrease in antiparallel β-strands, offset by an increase in the helical component.
Collapse
Affiliation(s)
- Lyubov Yu. Kanazhevskaya
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), 8 Lavrentiev Ave., Novosibirsk 630090, Russia
| | - Alexey A. Gorbunov
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), 8 Lavrentiev Ave., Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, 1 Pirogova St., Novosibirsk 630090, Russia
| | - Maria V. Lukina
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), 8 Lavrentiev Ave., Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, 1 Pirogova St., Novosibirsk 630090, Russia
| | - Denis A. Smyshliaev
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), 8 Lavrentiev Ave., Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, 1 Pirogova St., Novosibirsk 630090, Russia
| | - Polina V. Zhdanova
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), 8 Lavrentiev Ave., Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, 1 Pirogova St., Novosibirsk 630090, Russia
| | - Alexander A. Lomzov
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), 8 Lavrentiev Ave., Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, 1 Pirogova St., Novosibirsk 630090, Russia
| | - Vladimir V. Koval
- Institute of Chemical Biology and Fundamental Medicine (ICBFM), 8 Lavrentiev Ave., Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, 1 Pirogova St., Novosibirsk 630090, Russia
| |
Collapse
|
2
|
Kuschman HP, Palczewski MB, Hoffman B, Menhart M, Wang X, Glynn S, Islam ABMMK, Benevolenskaya EV, Thomas DD. Nitric oxide inhibits FTO demethylase activity to regulate N 6-methyladenosine mRNA methylation. Redox Biol 2023; 67:102928. [PMID: 37866163 PMCID: PMC10623363 DOI: 10.1016/j.redox.2023.102928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/27/2023] [Accepted: 10/07/2023] [Indexed: 10/24/2023] Open
Abstract
N6-methyladenosine (m6A) is the most abundant internal modification on eukaryotic mRNAs. Demethylation of m6A on mRNA is catalyzed by the enzyme fat mass and obesity-associated protein (FTO), a member of the nonheme Fe(II) and 2-oxoglutarate (2-OG)-dependent family of dioxygenases. FTO activity and m6A-mRNA are dysregulated in multiple diseases including cancers, yet endogenous signaling molecules that modulate FTO activity have not been identified. Here we show that nitric oxide (NO) is a potent inhibitor of FTO demethylase activity by directly binding to the catalytic iron center, which causes global m6A hypermethylation of mRNA in cells and results in gene-specific enrichment of m6A on mRNA of NO-regulated transcripts. Both cell culture and tumor xenograft models demonstrated that endogenous NO synthesis can regulate m6A-mRNA levels and transcriptional changes of m6A-associated genes. These results build a direct link between NO and m6A-mRNA regulation and reveal a novel signaling mechanism of NO as an endogenous regulator of the epitranscriptome.
Collapse
Affiliation(s)
| | - Marianne B Palczewski
- University of Illinois Chicago, College of Pharmacy, Department of Pharmaceutical Sciences, USA
| | - Brian Hoffman
- Weinberg College of Arts and Sciences, Northwestern University, Department of Chemistry, USA
| | - Mary Menhart
- College of Medicine, Departments of Pharmacology and Bioengineering, USA
| | - Xiaowei Wang
- College of Medicine, Departments of Pharmacology and Bioengineering, USA
| | - Sharon Glynn
- University of Galway, College of Medicine, Nursing and Health Sciences, School of Medicine, D. of Pathology, USA
| | | | | | - Douglas D Thomas
- University of Illinois Chicago, College of Pharmacy, Department of Pharmaceutical Sciences, USA.
| |
Collapse
|
3
|
Wang ZY, Li DL, Tian X, Li Y, Zhang CY. Single-Molecule Counting of FTO in Human Breast Tissues Based on a Rolling Circle Transcription Amplification-Driven Clustered Regularly Interspaced Short Palindromic Repeat─Cas12a. Anal Chem 2022; 94:11425-11432. [PMID: 35916620 DOI: 10.1021/acs.analchem.2c02578] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
N6-methyladenosine modification as an mRNA modification in mammalian cells is dynamically reversible, regulated by RNA demethylase [e.g., fat mass and obesity-associated protein (FTO)]. The abnormal expression of FTO is closely related to numerous diseases (e.g., various cancers and obesity). Herein, we demonstrate the single-molecule counting of FTO in human cancer cells and breast tissues based on a T7 RNA polymerase-mediated rolling circle transcription (RCT) amplification-driven clustered regularly interspaced short palindromic repeat (CRISPR)─Cas12a. When FTO is present, it demethylates the DNA substrate, initiating the DpnII-mediated cleavage reaction. After magnetic separation, the cleaved DNA fragments trigger the T7 RNA polymerase-mediated RCT amplification, activating CRISPR-/Cas12a-mediated cleavage of signal probes and releasing abundant FAM molecules that are simply counted via single-molecule detection. In this assay, only target FTO can generate CRISPR RNAs, efficiently improving detection specificity. Moreover, the integration of single-molecule detection with magnetic separation achieves zero background and effectively enhances detection sensitivity. This method can specifically and sensitively monitor FTO activity with a limit of detection of 1.20 × 10-13 M, and it may measure FTO at the single-cell level. Furthermore, it may accurately discriminate the FTO expression level in breast tissues between healthy persons and breast cancer patients and screen the FTO inhibitors as well, with great potential in clinical diagnosis and drug discovery.
Collapse
Affiliation(s)
- Zi-Yue Wang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Dong-Ling Li
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Xiaorui Tian
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Yueying Li
- Institute of Immunity and Infectious Diseases, School of Medicine and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450000, China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| |
Collapse
|