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Fitzsimmons CM, Mandler MD, Lunger JC, Chan D, Maligireddy S, Schmiechen A, Gamage S, Link C, Jenkins L, Chan K, Andresson T, Crooks D, Meier J, Linehan W, Batista P. Rewiring of RNA methylation by the oncometabolite fumarate in renal cell carcinoma. NAR Cancer 2024; 6:zcae004. [PMID: 38328795 PMCID: PMC10849186 DOI: 10.1093/narcan/zcae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 01/09/2024] [Accepted: 01/16/2024] [Indexed: 02/09/2024] Open
Abstract
Metabolic reprogramming is a hallmark of cancer that facilitates changes in many adaptive biological processes. Mutations in the tricarboxylic acid cycle enzyme fumarate hydratase (FH) lead to fumarate accumulation and cause hereditary leiomyomatosis and renal cell cancer (HLRCC). HLRCC is a rare, inherited disease characterized by the development of non-cancerous smooth muscle tumors of the uterus and skin, and an increased risk of an aggressive form of kidney cancer. Fumarate has been shown to inhibit 2-oxoglutarate-dependent dioxygenases (2OGDDs) involved in the hydroxylation of HIF1α, as well as in DNA and histone demethylation. However, the link between fumarate accumulation and changes in RNA post-transcriptional modifications has not been defined. Here, we determine the consequences of fumarate accumulation on the activity of different members of the 2OGDD family targeting RNA modifications. By evaluating multiple RNA modifications in patient-derived HLRCC cell lines, we show that mutation of FH selectively affects the levels of N6-methyladenosine (m6A), while the levels of 5-formylcytosine (f5C) in mitochondrial tRNA are unaffected. This supports the hypothesis of a differential impact of fumarate accumulation on distinct RNA demethylases. The observation that metabolites modulate specific subsets of RNA-modifying enzymes offers new insights into the intersection between metabolism and the epitranscriptome.
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Affiliation(s)
- Christina M Fitzsimmons
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mariana D Mandler
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Judith C Lunger
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dalen Chan
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Siddhardha S Maligireddy
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alexandra C Schmiechen
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Supuni Thalalla Gamage
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Courtney Link
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Lisa M Jenkins
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - King Chan
- Protein Characterization Laboratory, Research Technology Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21701, USA
| | - Thorkell Andresson
- Protein Characterization Laboratory, Research Technology Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21701, USA
| | - Daniel R Crooks
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jordan L Meier
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Pedro J Batista
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Yu R, Zhang W, Li Y, Tang J, Kim K, Li B. Functional characterisation of Fe (II) and 2OG-dependent dioxygenase TcALKBH4 in the red flour beetle, Tribolium castaneum. INSECT MOLECULAR BIOLOGY 2023; 32:676-688. [PMID: 37462221 DOI: 10.1111/imb.12865] [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: 03/25/2023] [Accepted: 07/03/2023] [Indexed: 11/08/2023]
Abstract
Alpha-ketoglutarate-dependent dioxygenase ALKB homologue 4 (ALKBH4) is a member of the Fe (II) and 2-oxoglutarate-dependent ALKB homologue family that plays important roles in epigenetic regulation by alkyl lesions removal in mammals. However, the roles of ALKBH4 in insects are not clear. Here, TcALKBH4 was cloned and functionally characterised in Tribolium castaneum. Temporal expression revealed that TcALKBH4 was highly expressed in early embryos and early pupae. Spatial expression showed that TcALKBH4 was highly expressed in the adult testis, and followed by the ovary. RNA interference targeting TcALKBH4 at different developmental stages in T. castaneum led to apparent phenotypes including the failure of development in larvae, the reduction of food intake and the deficiency of fertility in adult. However, further dot blot analyses showed that TcALKBH4 RNAi does not seem to influence 6 mA levels in vivo. qRT-PCR was used to further explore the underlying molecular mechanisms; the result showed that TcALKBH4 mediates the development of larvae possibly through 20E signalling pathway, and the fertility of female and male adult might be regulated by the expression of vitellogenesis and JH signalling pathway, respectively. Altogether, these findings will provide new insights into the potential function of ALKBH4 in insects.
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Affiliation(s)
- Runnan Yu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Wenjing Zhang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Yanxiao Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Jing Tang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - KumChol Kim
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
- Department of Life-Science, University of Science, Pyongyang, Democratic People's Republic of Korea
| | - Bin Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
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Li Q, Zhu Q. The role of demethylase AlkB homologs in cancer. Front Oncol 2023; 13:1153463. [PMID: 37007161 PMCID: PMC10060643 DOI: 10.3389/fonc.2023.1153463] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 03/03/2023] [Indexed: 03/18/2023] Open
Abstract
The AlkB family (ALKBH1-8 and FTO), a member of the Fe (II)- and α-ketoglutarate-dependent dioxygenase superfamily, has shown the ability to catalyze the demethylation of a variety of substrates, including DNA, RNA, and histones. Methylation is one of the natural organisms’ most prevalent forms of epigenetic modifications. Methylation and demethylation processes on genetic material regulate gene transcription and expression. A wide variety of enzymes are involved in these processes. The methylation levels of DNA, RNA, and histones are highly conserved. Stable methylation levels at different stages can coordinate the regulation of gene expression, DNA repair, and DNA replication. Dynamic methylation changes are essential for the abilities of cell growth, differentiation, and division. In some malignancies, the methylation of DNA, RNA, and histones is frequently altered. To date, nine AlkB homologs as demethylases have been identified in numerous cancers’ biological processes. In this review, we summarize the latest advances in the research of the structures, enzymatic activities, and substrates of the AlkB homologs and the role of these nine homologs as demethylases in cancer genesis, progression, metastasis, and invasion. We provide some new directions for the AlkB homologs in cancer research. In addition, the AlkB family is expected to be a new target for tumor diagnosis and treatment.
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Affiliation(s)
- Qiao Li
- Department of Orthopedic Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
- Department of Spine Surgery, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Qingsan Zhu
- Department of Orthopedic Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
- *Correspondence: Qingsan Zhu,
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Xu X, Yang E, Chen Y. Progress in the Study of Optical Probes for the Detection of Formaldehyde. Crit Rev Anal Chem 2022:1-27. [PMID: 35939357 DOI: 10.1080/10408347.2022.2107870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
Formaldehyde, one of the simplest reactive carbonyl substances, is involved in many physiological and pathological processes in living organisms. There is a large amount of data showing that abnormal elevation of formaldehyde is associated with a variety of diseases in the body, such as neurodegenerative diseases, Alzheimer's disease, cardiovascular diseases and cancer, and is also a representative carcinogen, so monitoring formaldehyde is of great importance for disease diagnosis and treatment. In this review, In this paper, we summarize and classify the last ten years of probes for the detection of formaldehyde according to different reaction mechanisms and discuss the structures and applications of the probes. Finally, we briefly describe the challenges and possible solutions in this field. We believe that more new probes provide powerful tools to study the function of formaldehyde in living systems.
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Affiliation(s)
- Xuexuan Xu
- The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Anhui Public Health Clinical Center, Hefei, China
| | - Erpei Yang
- The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Anhui Public Health Clinical Center, Hefei, China
| | - Yanyan Chen
- The First Affiliated Hospital of Anhui Medical University, Hefei, China
- Anhui Public Health Clinical Center, Hefei, China
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Yang H, Zhu J, Guo H, Tang A, Chen S, Zhang D, Yuan L, Liu G. Molecular cloning, characterization, and functional analysis of the uncharacterized C11orf96 gene. BMC Vet Res 2022; 18:170. [PMID: 35538492 PMCID: PMC9086667 DOI: 10.1186/s12917-022-03224-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 03/22/2022] [Indexed: 11/10/2022] Open
Abstract
Background The mammalian genome encodes millions of proteins. Although many proteins have been discovered and identified, a large part of proteins encoded by genes are yet to be discovered or fully characterized. In the present study, we successfully identified a host protein C11orf96 that was significantly upregulated after viral infection. Results First, we successfully cloned the coding sequence (CDS) region of the cat, human, and mouse C11orf96 gene. The CDS region of the C11orf96 gene is 372 bp long, encodes 124 amino acids, and is relatively conserved in different mammals. From bioinformatics analysis, we found that C11orf96 is rich in Ser and has multiple predicted phosphorylation sites. Moreover, protein interaction prediction analysis revealed that the protein is associated with several transmembrane family proteins and zinc finger proteins. Subsequently, we found that C11orf96 is strictly distributed in the cytoplasm. According to the tissue distribution characteristics, C11orf96 is distributed in all tissues and organs, with the highest expression levels in the kidney. These results indicate that C11orf96 may play a specific biological role in the kidney. Conclusions Summarizing, these data lay the foundation for studying the biological functions of C11orf96 and for exploring its role in viral replication. Supplementary Information The online version contains supplementary material available at 10.1186/s12917-022-03224-5.
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Affiliation(s)
- Hongzao Yang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China.,Innovation Team of Small Animal Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, People's Republic of China
| | - Jie Zhu
- Innovation Team of Small Animal Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, People's Republic of China
| | - Hongyuan Guo
- Innovation Team of Small Animal Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, People's Republic of China
| | - Aoxing Tang
- Innovation Team of Small Animal Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, People's Republic of China
| | - Shaoyu Chen
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China
| | - Da Zhang
- Innovation Team of Small Animal Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, People's Republic of China
| | - Ligang Yuan
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730070, People's Republic of China.
| | - Guangqing Liu
- Innovation Team of Small Animal Infectious Disease, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, People's Republic of China.
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Sheng Y, Zhou M, You C, Dai X. Dynamics and biological relevance of epigenetic N6-methyladenine DNA modification in eukaryotic cells. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2021.08.109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Evolutionary History of RNA Modifications at N6-Adenosine Originating from the R-M System in Eukaryotes and Prokaryotes. BIOLOGY 2022; 11:biology11020214. [PMID: 35205080 PMCID: PMC8868631 DOI: 10.3390/biology11020214] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 01/13/2022] [Accepted: 01/24/2022] [Indexed: 12/11/2022]
Abstract
Simple Summary The m6A is the most abundant and well-studied modification of mRNA, and plays an important role in transcription and translation. It is known to be evolutionarily conserved machinery present in the last eukaryotic common ancestor (LECA). The writers and erasers responsible for adding or removing m6A belong to specific protein families, respectively, suggesting that these members are evolutionarily related. However, only some of these mRNA m6A modification-associated proteins have been studied from an evolutionary perspective, while there has been no comprehensive and systematic analysis of the distributions and evolutionary history of N6mA-associated proteins in the three kingdoms of life. In this study, we identified orthologues of all the reported N6mA-associated proteins in 88 organisms from three kingdoms of life and comprehensively reconstructed the evolutionary history of the RNA N6mA modification machinery. The results demonstrate that RNA N6mA-MTases are derived from at least two different types of prokaryotic DNA MTases (class α and β MTases). As the m6A reader, YTH proteins may be acquired by LECA from an individual prokaryotic YTH-domain protein that evolved from the N-terminals of an R-M system endonuclease. In addition, the origin of eukaryotic ALKBH family proteins is inferred to be driven by at least two occasions of independent HTG from the bacterial ALKB family. Abstract Methylation at the N6-position of adenosine (N6mA) on mRNA (m6A) is one of the most widespread, highly selective and dynamically regulated RNA modifications and plays an important role in transcription and translation. In the present study, a comprehensive analysis of phylogenetic relationships, conserved domain sequence characteristics and protein structure comparisons were employed to explore the distribution of RNA N6mA modification (m6A, m6,6A, m6Am, m6, 6Am and m6t6A)-associated proteins (writers, readers and erasers) in three kingdoms of life and reveal the evolutionary history of these modifications. These findings further confirmed that the restriction-modification (R-M) system is the origin of DNA and RNA N6mA modifications. Among them, the existing mRNA m6A modification system derived from the last eukaryotic common ancestor (LECA) is the evolutionary product of elements from the last universal common ancestor (LUCA) or driven by horizontal gene transfer (HGT) from bacterial elements. The subsequent massive gene gains and losses contribute to the development of unique and diverse functions in distinct species. Particularly, RNA methyltransferases (MTases) as the writer responsible for adding N6mA marks on mRNA and ncRNAs may have evolved from class α and β prokaryotic “orphan” MTases originating from the R-M system. The reader, YTH proteins that specifically recognize the m6A deposit, may be acquired by LECA from an individual prokaryotic YTH-domain protein that evolved from N-terminals of an R-M system endonuclease. The eraser, which emerged from the ALKB family (ALKBH5 and FTO) in eukaryotes, may be driven by independent HTG from bacterial ALKB proteins. The evolutionary history of RNA N6mA modifications was inferred in the present study, which will deepen our understanding of these modifications in different species.
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Plessers S, Van Deuren V, Lavigne R, Robben J. High-Throughput Sequencing of Phage Display Libraries Reveals Parasitic Enrichment of Indel Mutants Caused by Amplification Bias. Int J Mol Sci 2021; 22:5513. [PMID: 34073702 PMCID: PMC8197208 DOI: 10.3390/ijms22115513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/18/2021] [Accepted: 05/20/2021] [Indexed: 01/23/2023] Open
Abstract
The combination of phage display technology with high-throughput sequencing enables in-depth analysis of library diversity and selection-driven dynamics. We applied short-read sequencing of the mutagenized region on focused display libraries of two homologous nucleic acid modification eraser proteins-AlkB and FTO-biopanned against methylated DNA. This revealed enriched genotypes with small indels and concomitant doubtful amino acid motifs within the FTO library. Nanopore sequencing of the entire display vector showed additional enrichment of large deletions overlooked by region-specific sequencing, and further impacted the interpretation of the obtained amino acid motifs. We could attribute enrichment of these corrupted clones to amplification bias due to arduous FTO display slowing down host cell growth as well as phage production. This amplification bias appeared to be stronger than affinity-based target selection. Recommendations are provided for proper sequence analysis of phage display data, which can improve motive discovery in libraries of proteins that are difficult to display.
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Affiliation(s)
- Sander Plessers
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G, B-3001 Heverlee, Belgium; (S.P.); (V.V.D.)
| | - Vincent Van Deuren
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G, B-3001 Heverlee, Belgium; (S.P.); (V.V.D.)
| | - Rob Lavigne
- Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21, B-3001 Heverlee, Belgium;
| | - Johan Robben
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G, B-3001 Heverlee, Belgium; (S.P.); (V.V.D.)
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