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 ß-strands, offset by an increase in the helical component.
Subject(s)
AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase , DNA Methylation , Humans , AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase/genetics , Amino Acids , DNA , Ferrous CompoundsABSTRACT
N1-methyladenosine (m1A) is a post-transcriptionally modified RNA molecule that plays a pivotal role in the regulation of various biological functions and activities. Especially in cancer cell invasion, proliferation and cell cycle regulation. Over recent years, there has been a burgeoning interest in investigating the m1A modification of RNA. Most studies have focused on the regulation of m1A in cancer enrichment areas and different regions. This review provides a comprehensive overview of the methodologies employed for the detection of m1A modification. Furthermore, this review delves into the key players in m1A modification, known as the "writers," "erasers," and "readers." m1A modification is modified by the m1A methyltransferases, or writers, such as TRMT6, TRMT61A, TRMT61B, TRMT10C, NML, and, removed by the demethylases, or erasers, including FTO and ALKBH1, ALKBH3. It is recognized by m1A-binding proteins YTHDF1, TYHDF2, TYHDF3, and TYHDC1, also known as "readers". Additionally, we explore the intricate relationship between m1A modification and its regulators and their implications for the development and progression of specific types of cancer, we discuss how m1A modification can potentially facilitate the discovery of novel approaches for cancer diagnosis, treatment, and prognosis. Our summary of m1A methylated adenosine modification detection methods and regulatory mechanisms in various cancers provides useful insights for cancer diagnosis, treatment, and prognosis. Video Abstract.
Subject(s)
Neoplasms , Humans , Neoplasms/diagnosis , Neoplasms/genetics , Neoplasms/metabolism , RNA/genetics , RNA/metabolism , Methyltransferases/genetics , Methyltransferases/metabolism , Methylation , AlkB Homolog 1, Histone H2a Dioxygenase/metabolism , AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase/metabolism , Alpha-Ketoglutarate-Dependent Dioxygenase FTO/metabolismABSTRACT
N1 -methyladenosine (m1 A) is a prevalent post-transcriptional RNA modification, and the distribution and dynamics of the modification play key epitranscriptomic roles in cell development. At present, the human AlkB Fe(II)/α-ketoglutarate-dependent dioxygenase family member ALKBH3 is the only known mRNA m1 A demethylase, but its catalytic mechanism remains unclear. Here, we present the structures of ALKBH3-oligo crosslinked complexes obtained with the assistance of a synthetic antibody crystallization chaperone. Structural and biochemical results showed that ALKBH3 utilized two ß-hairpins (ß4-loop-ß5 and ß'-loop-ß'') and the α2 helix to facilitate single-stranded substrate binding. Moreover, a bubble-like region around Asp194 and a key residue inside the active pocket (Thr133) enabled specific recognition and demethylation of m1 A- and 3-methylcytidine (m3 C)-modified substrates. Mutation of Thr133 to the corresponding residue in the AlkB Fe(II)/α-ketoglutarate-dependent dioxygenase family members FTO or ALKBH5 converted ALKBH3 substrate selectivity from m1 A to N6 -methyladenosine (m6 A), as did Asp194 deletion. Our findings provide a molecular basis for understanding the mechanisms of substrate recognition and m1 A demethylation by ALKBH3. This study is expected to aid structure-guided design of chemical probes for further functional studies and therapeutic applications.
Subject(s)
Alpha-Ketoglutarate-Dependent Dioxygenase FTO , RNA , Humans , RNA/chemistry , Alpha-Ketoglutarate-Dependent Dioxygenase FTO/metabolism , RNA, Messenger/metabolism , Demethylation , Ferrous Compounds , AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase/metabolismABSTRACT
Albeit N1-Methyladenosine (m1A) RNA modification represents an important regulator of RNA metabolism, the role of m1A modification in carcinogenesis remains enigmatic. Herein, we found that histone lactylation enhances ALKBH3 expression and simultaneously attenuates the formation of tumor-suppressive promyelocytic leukemia protein (PML) condensates by removing the m1A methylation of SP100A, promoting the malignant transformation of cancers. First, ALKBH3 is specifically upregulated in high-risk ocular melanoma due to excessive histone lactylation levels, referring to m1A hypomethylation status. Moreover, the multiomics analysis subsequently identified that SP100A, a core component for PML bodies, serves as a downstream candidate target for ALKBH3. Therapeutically, the silencing of ALKBH3 exhibits efficient therapeutic efficacy in melanoma both in vitro and in vivo, which could be reversed by the depletion of SP100A. Mechanistically, we found that YTHDF1 is responsible for recognition of the m1A methylated SP100A transcript, which increases its RNA stability and translational efficacy. Conclusively, we initially demonstrated that m1A modification is necessary for tumor suppressor gene expression, expanding the current understandings of dynamic m1A function during tumor progression. In addition, our results indicate that lactylation-driven ALKBH3 is essential for the formation of PML nuclear condensates, which bridges our knowledge of m1A modification, metabolic reprogramming, and phase-separation events.
Subject(s)
AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase , Antigens, Nuclear , Autoantigens , Eye Neoplasms , Histones , Melanoma , Humans , AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase/metabolism , Demethylation , DNA Methylation , Histones/genetics , Histones/metabolism , Promyelocytic Leukemia Protein/genetics , Promyelocytic Leukemia Protein/metabolism , RNA/metabolism , Transcription Factors/metabolism , Antigens, Nuclear/metabolism , Autoantigens/metabolism , Eye Neoplasms/metabolismABSTRACT
Methylation is one of the most prevalent epigenetic modifications in natural organisms, and the processes of methylation and demethylation are closely associated with cell growth, differentiation, gene transcription and expression. Abnormal methylation may lead to various human diseases including cancers. Simultaneous analysis of multiple DNA demethylases remains a huge challenge due to the requirement of diverse substrate probes and scarcity of proper signal transduction strategies. Herein, we propose a sensitive and label-free method for simultaneous monitoring of multiple DNA demethylases on the basis of demethylation-activated light-up dual-color RNA aptamers. The presence of targets AlkB homologue-3 (ALKBH3) and fat mass and obesity-associated enzyme (FTO) erases the methyl group in DNA substrate probes, activating the ligation-mediate bidirectional transcription amplification reaction to produce enormous Spinach and Mango aptamers. The resulting RNA aptamers (i.e., Spinach and Mango aptamers) can bind with their cognate nonfluorescent fluorogens (DFHBI and TO1-biotin) to significantly improve the fluorescence signals. This aptamersensor shows high specificity and sensitivity with a limit of detection (LOD) of 8.50 × 10-14 M for ALKBH3 and 6.80 × 10-14 M for FTO, and it can apply to screen DNA demethylase inhibitors, evaluate DNA demethylase kinetic parameters, and simultaneously measure multiple endogenous DNA demethylases in a single cell. Importantly, this aptamersensor can accurately discriminate the expressions of ALKBH3 and FTO between healthy tissues and non-small cell lung cancer (NSCLC) patient tissues, offering a powerful platform for clinical diagnosis and drug discovery.
Subject(s)
Aptamers, Nucleotide , Biosensing Techniques , Carcinoma, Non-Small-Cell Lung , Lung Neoplasms , Humans , RNA/chemistry , Aptamers, Nucleotide/metabolism , Lung Neoplasms/diagnosis , Lung Neoplasms/genetics , DNA/metabolism , Demethylation , Lung/metabolism , AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase/metabolism , Alpha-Ketoglutarate-Dependent Dioxygenase FTO/chemistry , Alpha-Ketoglutarate-Dependent Dioxygenase FTO/metabolismABSTRACT
Salivary gland tumours (SGTs) are a heterogeneous group of benign tumours of various origins and pathologies, showing a number of DNA modifications. Previously, in malignant head and neck cancer (HNSCC), we found overexpression of ALKBH proteins, the homologs of Escherichia coli AlkB 2-oxoglutarate and Fe(II) dependent dioxygenase. Moreover, we proved the connection of some of these dioxygenases with cancer development. Here, we studied the expression of five of these ALKBH dioxygenases: 1, 3, 4, 5, and FTO in benign SGTs. Using Western blot analysis, we found overexpression of three proteins: ALKBH1, 4, and FTO in SGT as compared to the surrounding, unaffected tissue. ALKBH4 was overexpressed in 76% of patient samples, whereas ALKBH1 and FTO in 65% of the samples. These results differ from those obtained in HNSCC, where FTO overexpression has been observed in 90% of patient samples. We also investigated the relationships between ALKBHs' expression levels in normal and SGT tissues and identified two correlated pairs: ALKBH1-ALKBH3 and ALKBH1-ALKBH5. Additionally, in tumour tissue ALKBHs: ALKBH1, ALKBH3, ALKBH4, and ALKBH5 levels were correlated with each other. Together, these findings show that the ALKBH proteins exhibit pro cancerogenic action in SGT, even though the levels ALKBHs are generally lower in benign SGT than in malignant HNSCC. We suggest that the overexpression of the ALKBHs, especially FTO, may be used as a cancer marker and for its grading.
Subject(s)
Dioxygenases , Head and Neck Neoplasms , Salivary Gland Neoplasms , Humans , Dioxygenases/genetics , Dioxygenases/metabolism , Squamous Cell Carcinoma of Head and Neck , Salivary Gland Neoplasms/genetics , AlkB Homolog 1, Histone H2a Dioxygenase/genetics , AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase/genetics , Alpha-Ketoglutarate-Dependent Dioxygenase FTO/genetics , Alpha-Ketoglutarate-Dependent Dioxygenase FTO/metabolismABSTRACT
tRNA-derived fragments (tRFs) are a class of small RNAs that occur when tRNAs are broken down by enzymes due to stress. Increasing reports have shown that tRFs are associated with multiple physiological and pathological processes, especially in cancers; however, very little is known of the effects and mechanisms of tRFs. Therefore, further investigation on the biological roles and clinical value of tRFs is required. In this study, we utilized whole-transcriptome sequencing to profile tRFs expression in the tissues and plasma exosomes of patients with colorectal cancer (CRC). Three tRFs (tRF-3022b, tRF-3030b and tRF-5008b) showed an increasing trend in CRC tissues compared to adjacent normal tissues. They also tended to be elevated in plasma exosomes of CRC patients compared to healthy controls. These results indicated that they may be upregulated in cancer cells and then secreted by exosomes. The knockdown of tRF-regulated factors such as AlkB homolog 3 (ALKBH3), tRNA aspartic acid methyltransferase 1 (DNMT2), angiogenin (ANG), and argonaute RISC catalytic component 2 (AGO2) could affect the expression of tRFs. Notably, we found that the decrease in the three tRFs arrests the progression of the CRC cell cycle and induces cell apoptosis. Silencing tRF-3022b could facilitate M2 macrophage polarization. Mechanistically, we found that tRF-3022b binds to galectin 1 (LGALS1) and macrophage migration inhibitory factor (MIF) in CRC cells and reduces polarization by regulating MIF in M2 macrophages. In conclusion, our study revealed the expression pattern of tRFs in both tissue and plasma exosomes and identified a novel tRF, tRF-3022b, which may affect CRC tumor growth and M2 macrophage polarization by binding to LGALS1 and MIF.
Subject(s)
Colorectal Neoplasms , Galectin 1 , Humans , Cytokines , RNA, Transfer/genetics , RNA, Transfer/metabolism , Apoptosis , Macrophages/metabolism , Colorectal Neoplasms/genetics , AlkB Homolog 3, Alpha-Ketoglutarate-Dependent DioxygenaseABSTRACT
Long noncoding RNAs (lncRNAs) are confirmed as the key regulators of hepatocellular carcinoma (HCC) occurrence and progression, but the role of AlkB homologue 3 antisense RNA 1 (ALKBH3-AS1) in HCC is unclear. We revealed the overexpression of ALKBH3-AS1 in HCC tissues. The upregulated levels of ALKBH3-AS1 were observed in HCC cells. ALKBH3-AS1 was expressed in the nucleus and cytoplasm of HCC cells. The high ALKBH3-AS1 expression was markedly associated with a decreased survival rate of HCC patients. ALKBH3-AS1 knockdown repressed and ALKBH3-AS1 overexpression enhanced HCC cell invasion and proliferation. ALKBH3-AS1 silencing restricted HCC growth in vivo. A significant positive correlation between ALKBH3-AS1 and ALKBH3 mRNA levels was confirmed in HCC specimens. ALKBH3-AS1 silencing reduced ALKBH3 expression by stabilizing its mRNA stability in HCC cells. Notably, the impact of ALKBH3 silencing on HCC cells was similar to that of ALKBH3-AS1 knockdown. ALKBH3 restoration prominently attenuated the suppressive effects resulting from ALKBH3-AS1 silencing in HCCLM3 cells. Hypoxia-inducible factor-1α (HIF-1α) transcriptionally activated ALKBH3-AS1 expression in hypoxic HCC cells. ALKBH3-AS1 knockdown markedly attenuated cell proliferation and invasion in hypoxic Huh7 cells. Collectively, HIF-1α-activated ALKBH3-AS1 exerted an oncogenic role by enhancing ALKBH3 mRNA stability in HCC cells.
Subject(s)
Carcinoma, Hepatocellular , Liver Neoplasms , MicroRNAs , RNA Stability , RNA, Long Noncoding , AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase/genetics , AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase/metabolism , Carcinoma, Hepatocellular/pathology , Cell Line, Tumor , Cell Movement/genetics , Cell Proliferation/genetics , Gene Expression Regulation, Neoplastic , Humans , Hypoxia-Inducible Factor 1, alpha Subunit/metabolism , Liver Neoplasms/pathology , MicroRNAs/genetics , RNA, Antisense , RNA, Long Noncoding/genetics , RNA, Long Noncoding/metabolism , RNA, Messenger/geneticsABSTRACT
Studies on biological functions of RNA modifications such as N6-methyladenosine (m6A) in mRNA have sprung up in recent years, while the roles of N1-methyladenosine (m1A) in cancer progression remain largely unknown. We find m1A demethylase ALKBH3 can regulate the glycolysis of cancer cells via a demethylation activity dependent manner. Specifically, sequencing and functional studies confirm that ATP5D, one of the most important subunit of adenosine 5'-triphosphate synthase, is involved in m1A demethylase ALKBH3-regulated glycolysis of cancer cells. The m1A modified A71 at the exon 1 of ATP5D negatively regulates its translation elongation via increasing the binding with YTHDF1/eRF1 complex, which facilitates the release of message RNA (mRNA) from ribosome complex. m1A also regulates mRNA stability of E2F1, which directly binds with ATP5D promoter to initiate its transcription. Targeted specific demethylation of ATP5D m1A by dm1ACRISPR system can significantly increase the expression of ATP5D and glycolysis of cancer cells. In vivo data confirm the roles of m1A/ATP5D in tumor growth and cancer progression. Our study reveals a crosstalk of mRNA m1A modification and cell metabolism, which expands the understanding of such interplays that are essential for cancer therapeutic application.
Subject(s)
Glycolysis , Mitochondrial Proton-Translocating ATPases , Neoplasms , RNA, Messenger , AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase/genetics , AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase/metabolism , Glycolysis/genetics , Humans , Methylation , Mitochondrial Proton-Translocating ATPases/metabolism , Neoplasms/enzymology , Neoplasms/genetics , RNA, Messenger/metabolismABSTRACT
Understanding the occurrence, repair, and biological consequences of DNA damage is important in environmental toxicology and risk assessment. The most common way to assess DNA damage elicited by exogenous sources in a laboratory setting is to expose cells or experimental animals with chemicals that modify DNA. Owing to the lack of reaction specificities of DNA damaging agents, the approach frequently does not allow for induction of a specific DNA lesion. Herein, we employed metabolic labeling to selectively incorporate N2-methyl-dG (N2-MedG) and N2-n-butyl-dG (N2-nBudG) into genomic DNA of cultured mammalian cells, and investigated how the levels of the two lesions in cellular DNA are modulated by different DNA repair factors. Our results revealed that nucleotide excision repair (NER) exert moderate effects on the removal of N2-MedG and N2-nBudG from genomic DNA. We also observed that DNA polymerases κ and η contribute to the incorporation of N2-MedG into genomic DNA and modulate its repair in human cells. In addition, loss of ALKBH3 resulted in higher frequencies of N2-MedG and N2-nBuG incorporation into genomic DNA, suggesting a role of oxidative dealkylation in the reversal of these lesions. Together, our study provided new insights into the repair of minor-groove N2-alkyl-dG lesions in mammalian cells.
Subject(s)
Deoxyguanosine , Tandem Mass Spectrometry , AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase/genetics , Animals , Chromatography, Liquid , DNA , DNA Damage , DNA Repair , DNA-Directed DNA Polymerase/metabolism , Deoxyguanosine/metabolism , Genomics , Humans , Mammals/genetics , Mammals/metabolismABSTRACT
Resumen El antígeno prostático específico (PSA) en circulación se encuentra ligado a la alfa-1-quimiotripsina y una pequeña fracción circula de manera libre (PSAl). Se valoró la utilidad clínica del PSA total (PSAt) y el índice de PSA libre para la detección de cáncer prostático en pacientes asintomáticos. Se cuantificó el PSAt, el PSAl y el índice de PSAl en 364 pacientes estratificados por grupo de edad. La frecuencia de valores anormales de PSAt fue del 8,79% (32/364). El grupo de 50-59 años presentó la mayor incidencia de resultados anormales (19/32). No hubo diferencia estadísticamente significativa entre PSAt y el índice de PSAl (p<0,05). El índice PSAl puede potencializar el valor del PSAt para determinar la presencia o ausencia de cáncer prostático. Un índice superior a 0,24 ng/mL puede ayudar a evitar o posponer la indicación de biopsia, principalmente cuando los valores de PSAt están entre 4 y 10 ng/mL.
Abstract Circulating prostate-specific antigen (PSA) is bound to alpha-1-chymotrypsin and a small fraction is free (PSAl). The clinical utility of the total PSA (PSAt) and the PSAl index for prostate cancer screening in asymptomatic patients was assessed. PSAt, PSAl and the PSAl index were quantified in 364 patients stratified by age group. The frequency of abnormal PSAt values was 8.79% (32/364). The 50-59 year-old group presented the highest incidence of abnormal results (19/32). There was no statistically significant difference between PSAt and the PSAl index (p<0.05). The PSAl index can potentiate the PSAt value to determine the presence or absence of prostate cancer. An index greater than 0.24 ng/mL can help to avoid or postpone the indication for a biopsy, especially when the PSAt values are between 4 and 10 ng/mL.
Resumo O antígeno prostático específico (PSA) em circulação é ligado à alfa-1-quimotripsina e a uma pequena fração circula livremente (PSAl). A utilidade clínica do PSA total (PSAt) e do índice de PSAl livre para o rastreamento do câncer de próstata em pacientes assintomáticos foi avaliada. PSAt, PSAl e o índice de PSAl foram quantificados em 364 pacientes estratificados por faixa etária. A frequência de valores anormais de PSAt foi de 8,79% (32/364). O grupo de 50-59 anos apresentou a maior incidência de resultados anormais (19/32). Não houve diferença estatisticamente significativa entre o PSAt e o índice PSAl (p<0,05). O índice PSAl pode potencializar o valor do PSAt para determinar a presença ou ausência de câncer de próstata. Um índice superior a 0,24 ng/mL pode ajudar a evitar ou adiar a indicação de biópsia, principalmente quando os valores de PSAt estão entre 4 e 10 ng/mL.
Subject(s)
Male , Adult , Middle Aged , Aged , Prostatic Hyperplasia , Prostatic Neoplasms , Prostate-Specific Antigen , Serine Peptidase Inhibitor Kazal-Type 5 , Patients , Biopsy , Chymotrypsin , Mass Screening , Incidence , Morbidity , Diagnosis , Absenteeism , AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase , Age GroupsABSTRACT
Alkylation of DNA and RNA is a potentially toxic lesion that can result in mutations and even cell death. In response to alkylation damage, K63-linked polyubiquitin chains are assembled that localize the Alpha-ketoglutarate-dependent dioxygenase alkB homolog 3-Activating Signal Cointegrator 1 Complex Subunit (ASCC) repair complex to damage sites in the nucleus. The protein ASCC2, a subunit of the ASCC complex, selectively binds K63-linked polyubiquitin chains via its coupling of ubiquitin conjugation to ER degradation (CUE) domain. The basis for polyubiquitin-binding specificity was unclear, because CUE domains in other proteins typically bind a single ubiquitin and do not discriminate among different polyubiquitin linkage types. We report here that the ASCC2 CUE domain selectively binds K63-linked diubiquitin by contacting both the distal and proximal ubiquitin. The ASCC2 CUE domain binds the distal ubiquitin in a manner similar to that reported for other CUE domains bound to a single ubiquitin, whereas the contacts with the proximal ubiquitin are unique to ASCC2. Residues in the N-terminal portion of the ASCC2 α1 helix contribute to the binding interaction with the proximal ubiquitin of K63-linked diubiquitin. Mutation of residues within the N-terminal portion of the ASCC2 α1 helix decreases ASCC2 recruitment in response to DNA alkylation, supporting the functional significance of these interactions during the alkylation damage response. Our study reveals the versatility of CUE domains in ubiquitin recognition.
Subject(s)
AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase , DNA Repair , Nuclear Proteins , Polyubiquitin , Ubiquitin , Ubiquitins , AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase/genetics , AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase/metabolism , DNA/metabolism , Models, Molecular , Nuclear Proteins/genetics , Nuclear Proteins/metabolism , Polyubiquitin/genetics , Polyubiquitin/metabolism , Protein Binding , Ubiquitin/genetics , Ubiquitin/metabolism , Ubiquitins/genetics , Ubiquitins/metabolismABSTRACT
Central to genotoxic responses is their ability to sense highly specific signals to activate the appropriate repair response. We previously reported that the activation of the ASCC-ALKBH3 repair pathway is exquisitely specific to alkylation damage in human cells. Yet the mechanistic basis for the selectivity of this pathway was not immediately obvious. Here, we demonstrate that RNA but not DNA alkylation is the initiating signal for this process. Aberrantly methylated RNA is sufficient to recruit ASCC, while an RNA dealkylase suppresses ASCC recruitment during chemical alkylation. In turn, recruitment of ASCC during alkylation damage, which is mediated by the E3 ubiquitin ligase RNF113A, suppresses transcription and R-loop formation. We further show that alkylated pre-mRNA is sufficient to activate RNF113A E3 ligase in vitro in a manner dependent on its RNA binding Zn-finger domain. Together, our work identifies an unexpected role for RNA damage in eliciting a specific response to genotoxins.
Subject(s)
AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase/metabolism , Cell Nucleus/enzymology , DNA Helicases/metabolism , DNA-Binding Proteins/metabolism , Neoplasms/enzymology , Nuclear Proteins/metabolism , RNA Processing, Post-Transcriptional , RNA, Neoplasm/metabolism , AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase/genetics , Cell Nucleus/genetics , DNA Helicases/genetics , DNA Methylation , DNA-Binding Proteins/genetics , HEK293 Cells , HeLa Cells , Humans , Methylation , Neoplasms/genetics , Nuclear Proteins/genetics , R-Loop Structures , RNA, Neoplasm/genetics , Spliceosomes/genetics , Spliceosomes/metabolism , Transcription, Genetic , UbiquitinationABSTRACT
BACKGROUND: Reversible enzymatic methylation of mammalian mRNA is widespread and serves crucial regulatory functions, but little is known to what degree chemical alkylators mediate overlapping modifications and whether cells distinguish aberrant from canonical methylations. METHODS: Here we use quantitative mass spectrometry to determine the fate of chemically induced methylbases in the mRNA of human cells. Concomitant alteration in the mRNA binding proteome was analyzed by SILAC mass spectrometry. RESULTS: MMS induced prominent direct mRNA methylations that were chemically identical to endogenous methylbases. Transient loss of 40S ribosomal proteins from isolated mRNA suggests that aberrant methylbases mediate arrested translational initiation and potentially also no-go decay of the affected mRNA. Four proteins (ASCC3, YTHDC2, TRIM25 and GEMIN5) displayed increased mRNA binding after MMS treatment. ASCC3 is a binding partner of the DNA/RNA demethylase ALKBH3 and was recently shown to promote disassembly of collided ribosomes as part of the ribosome quality control (RQC) trigger complex. We find that ASCC3-deficient cells display delayed removal of MMS-induced 1-methyladenosine (m1A) and 3-methylcytosine (m3C) from mRNA and impaired formation of MMS-induced P-bodies. CONCLUSIONS: Our findings conform to a model in which ASCC3-mediated disassembly of collided ribosomes allows demethylation of aberrant m1A and m3C by ALKBH3. Our findings constitute first evidence of selective sanitation of aberrant mRNA methylbases over their endogenous counterparts and warrant further studies on RNA-mediated effects of chemical alkylators commonly used in the clinic.
Subject(s)
Cytosine , Ribosomes , Adenosine/analogs & derivatives , AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase , Animals , Cytosine/analogs & derivatives , DNA Helicases , Humans , RNA Helicases , RNA, Messenger/genetics , Transcription Factors , Tripartite Motif Proteins , Ubiquitin-Protein LigasesABSTRACT
N1 -methyladenosine (m1 A) is a prevalent and reversible RNA modification, which plays a crucial role in the regulation of RNA fate and gene expression. However, the lack of tools to precisely manipulate m1 A sites in specific transcripts has hindered efforts to clarify the association between a specific m1 A-modified transcript and its phenotypic outcomes. Here we develop a CRISPR-Cas13d-based tool called reengineered m1 A modification valid eraser (termed "REMOVER") for targeted m1 A demethylation of a specific transcript. The catalytically inactive RfxCas13d (dCasRx) is fused to the m1 A demethylase ALKBH3, and the dCasRx-ALKBH3 fusion protein can mediate potent demethylation of m1 A-modified RNAs. We further find that REMOVER can specifically demethylate m1 A of MALAT1 and PRUNE1 RNAs, thereby significantly increasing their stability. Our study establishes REMOVER as a tool for targeted RNA demethylation of specific m1 A-modified transcripts, which enables further elucidation of the relationship between m1 A modification of specific transcripts and their phenotypic outcomes.
Subject(s)
Adenosine/metabolism , AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase/metabolism , RNA/metabolism , Adenosine/analogs & derivatives , Adenosine/chemistry , AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase/chemistry , Demethylation , Humans , RNA/chemistryABSTRACT
BACKGROUND: tRNA-derived small RNAs (tDRs), which are widely distributed in human tissues including blood and urine, play an important role in the progression of cancer. However, the expression of tDRs in colorectal cancer (CRC) plasma and their potential diagnostic values have not been systematically explored. METHODS: The expression profiles of tDRs in plasma of CRC and health controls (HCs) are investigated by small RNA sequencing. The level and diagnostic value of 5'-tRF-GlyGCC are evaluated by quantitative PCR in plasma samples from 105 CRC patients and 90 HCs. The mechanisms responsible for biogenesis of 5'-tRF-GlyGCC are checked by in vitro and in vivo models. RESULTS: 5'-tRF-GlyGCC is dramatically increased in plasma of CRC patients compared to that of HCs. The area under curve (AUC) for 5'-tRF-GlyGCC in CRC group is 0.882. The combination of carcinoembryonic antigen (CEA) and carbohydrate antigen 199 (CA199) with 5'-tRF-GlyGCC improves the AUC to 0.926. Consistently, the expression levels of 5'-tRF-GlyGCC in CRC cells and xenograft tissues are significantly greater than that in their corresponding controls. Blood cells co-cultured with CRC cells or mice xenografted with CRC tumors show increased levels of 5'-tRF-GlyGCC. In addition, we find that the increased expression of 5'-tRF-GlyGCC is dependent on the upregulation of AlkB homolog 3 (ALKBH3), a tRNA demethylase which can promote tRNA cleaving to generate tDRs. CONCLUSIONS: The level of 5'-tRF-GlyGCC in plasma is a promising diagnostic biomarker for CRC diagnosis.
Subject(s)
Biomarkers, Tumor/genetics , Colorectal Neoplasms/diagnosis , Colorectal Neoplasms/genetics , RNA, Transfer/genetics , AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase/blood , AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase/genetics , Animals , Biomarkers, Tumor/blood , Cell Line, Tumor , Colorectal Neoplasms/blood , Female , Gene Expression Profiling , Gene Expression Regulation, Neoplastic , Humans , Male , Mice, Inbred BALB C , RNA, Transfer/blood , RNA, Transfer/metabolism , Xenograft Model Antitumor AssaysSubject(s)
AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase/deficiency , Collagen Type I/biosynthesis , DNA Methylation , Hodgkin Disease/enzymology , Neoplasm Proteins/metabolism , RNA Interference , RNA Processing, Post-Transcriptional , RNA, Neoplasm/metabolism , AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase/genetics , AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase/metabolism , Base Sequence , Cell Line, Tumor , Collagen Type I/genetics , Collagen Type I, alpha 1 Chain , CpG Islands/genetics , DNA Methylation/drug effects , DNA, Neoplasm/genetics , DNA, Neoplasm/metabolism , Datasets as Topic , Decitabine/pharmacology , Hodgkin Disease/genetics , Hodgkin Disease/metabolism , Humans , Leukocytes, Mononuclear/metabolism , Lymphocytes/metabolism , Methylation/drug effects , Neoplasm Proteins/genetics , Promoter Regions, Genetic/genetics , RNA Processing, Post-Transcriptional/drug effects , Sequence Alignment , tRNA Methyltransferases/metabolismABSTRACT
AlkB is a bacterial Fe(II)- and 2-oxoglutarate-dependent dioxygenase that repairs a wide range of alkylated nucleobases in DNA and RNA as part of the adaptive response to exogenous nucleic acid-alkylating agents. Although there has been longstanding interest in the structure and specificity of Escherichia coli AlkB and its homologs, difficulties in assaying their repair activities have limited our understanding of their substrate specificities and kinetic mechanisms. Here, we used quantitative kinetic approaches to determine the transient kinetics of recognition and repair of alkylated DNA by AlkB. These experiments revealed that AlkB is a much faster alkylation repair enzyme than previously reported and that it is significantly faster than DNA repair glycosylases that recognize and excise some of the same base lesions. We observed that whereas 1,N6-ethenoadenine can be repaired by AlkB with similar efficiencies in both single- and double-stranded DNA, 1-methyladenine is preferentially repaired in single-stranded DNA. Our results lay the groundwork for future studies of AlkB and its human homologs ALKBH2 and ALKBH3.
Subject(s)
AlkB Enzymes/chemistry , DNA Repair , DNA, Bacterial/chemistry , Escherichia coli Proteins/chemistry , Escherichia coli/enzymology , AlkB Enzymes/genetics , AlkB Homolog 2, Alpha-Ketoglutarate-Dependent Dioxygenase/chemistry , AlkB Homolog 2, Alpha-Ketoglutarate-Dependent Dioxygenase/genetics , AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase/chemistry , AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase/genetics , DNA/chemistry , DNA/genetics , DNA, Bacterial/genetics , DNA, Single-Stranded/chemistry , DNA, Single-Stranded/genetics , Escherichia coli/genetics , Escherichia coli Proteins/genetics , HumansABSTRACT
Cellular processes, such as DNA replication, recombination and transcription, require DNA strands separation and single-stranded DNA is formation. The single-stranded DNA is promptly wrapped by human single-stranded DNA binding proteins, replication protein A (RPA) complex. RPA binding not only prevent nuclease degradation and annealing, but it also coordinates cell-cycle checkpoint activation and DNA repair. However, RPA binding offers little protection against the chemical modification of DNA bases. This review focuses on the type of DNA base damage that occurs in single-stranded DNA and how the damage is rectified in human cells. The discovery of DNA repair proteins, such as ALKBH3, AGT, UNG2, NEIL3, being able to repair the damaged base in the single-stranded DNA, renewed the interest to study single-stranded DNA repair. These mechanistically different proteins work independently from each other with the overarching goal of increasing fidelity of recombination and promoting error-free replication.
Subject(s)
AlkB Homolog 2, Alpha-Ketoglutarate-Dependent Dioxygenase/metabolism , AlkB Homolog 3, Alpha-Ketoglutarate-Dependent Dioxygenase/metabolism , DNA Damage , DNA, Single-Stranded/genetics , DNA Repair , DNA Replication , DNA, Single-Stranded/drug effects , Humans , Recombination, Genetic , Replication Protein A/metabolismABSTRACT
The integrity of our DNA is challenged daily by a variety of chemicals that cause DNA base alkylation. DNA alkylation repair is an essential cellular defence mechanism to prevent the cytotoxicity or mutagenesis from DNA alkylating chemicals. Human oxidative demethylase ALKBH3 is a central component of alkylation repair, especially from single-stranded DNA. However, the molecular mechanism of ALKBH3-mediated damage recognition and repair is less understood. We report that ALKBH3 has a direct protein-protein interaction with human RAD51 paralogue RAD51C. We also provide evidence that RAD51C-ALKBH3 interaction stimulates ALKBH3-mediated repair of methyl-adduct located within 3'-tailed DNA, which serves as a substrate for the RAD51 recombinase. We further show that the lack of RAD51C-ALKBH3 interaction affects ALKBH3 function in vitro and in vivo. Our data provide a molecular mechanism underlying upstream events of alkyl adduct recognition and repair by ALKBH3.