Search Results (75)

The objective of this study was to identify the AlkB family genes in poultry using bioinformatics, and to explore their molecular characteristics, evolutionary relationships, and expression patterns to clarify their potential functions in poultry. (1) Methods: The study utilized the NCBI database to obtain chicken genome data, and screened and validated AlkB family members (ALKBH1-5, ALKBH8, and FTO) by hmmsearch and TBtools. MEGA 11.0 was used for phylogenetic analysis, PHYRE2 and I-TASSER predicted protein structures, and the String database was used to construct an interoperability network. Finally, the tissue expression profiles were analyzed by using The Human Protein Atlas online database and qRT-PCR. (2) Results: Phylogenetic analysis revealed distinct avian and mammalian clusters, with chicken AlkB proteins exhibiting low sequence homology but conserved 3D structures compared to mammals. Chromosomal synteny and conserved domains highlighted evolutionary divergence, with ALKBH4 lacking typical AlkB structural motifs. Protein interaction networks linked ALKBH1/2/3/5/8/FTO, underscoring functional coordination in poultry adaptation. Tissue-specific expression showed high AlkB levels in brain tissues, while ALKBH5 dominated in muscle. During differentiation, ALKBH3, ALKBH5, and FTO expression significantly increased during myoblast differentiation. (3) Conclusions: This study identified seven AlkB family genes in poultry, revealing their phylogenetic classification into two subfamilies, conserved structural domains, chromosomal synteny, and tissue-specific expression patterns. Full article

Background: Isocitrate dehydrogenase 1 and 2 (IDH1 and IDH2) are enzymes that catalyze the oxidative decarboxylation of isocitrate to alpha-ketoglutarate (α-KG), which is essential for many metabolic processes, including some steps in DNA repair. In tumors, notably in gliomas, IDH1 and IDH2 are frequently mutated. The mutation found in different cancers is functionally active, causing, instead of α-KG, the formation of 2-hydroxyglutarate (2-HG), which inhibits α-KG-dependent enzymes. Gliomas harboring mutated IDH1/2 show a better prognosis than IDH1 wild-type (wt) tumors of the same grade, which might result from the inhibition of DNA repair functions. A DNA repair enzyme dependent on α-KG is alkB homolog 2 (ALKBH2), which removes several lesions from DNA. These findings prompted us to investigate the response of glioma cells to artesunate (ART), a plant ingredient with genotoxic and anticancer activity currently used in several trials. Materials and Methods: We used isogenic glioblastoma cell lines that express IDH1 wild-type or, based on a TET-inducible system, the IDH1 mutant (mt) protein, and treated them with increasing doses of artesunate. We also treated glioblastoma cells with 2-HG, generated ALKBH2 knockout cells, and checked their sensitivity to the cytotoxic effects of artesunate. Results: We show that the cell-killing effect of ART is enhanced if the IDH1 mutant (R132H) is expressed in glioblastoma cells. Further, we show that 2-HG imitates the effect of IDH1mt as 2-HG ameliorates the cytotoxicity of ART. Finally, we demonstrate that the knockout of ALKBH2 causes the sensitization of glioblastoma cells to ART. Conclusions: The data indicate that ALKBH2 protects against the anticancer effect of ART, and the mutation of IDH1/2 commonly occurring in low-grade gliomas sensitizes to ART via an ALKBH2-dependent mechanism. The data support the use of ART in the therapy of IDH1/2-mutated cancers both in combination with chemotherapy and adjuvant treatment. Full article

Nipah virus (NiV), a highly lethal zoonotic paramyxovirus, displays strain-specific pathogenicity, yet the molecular basis for this divergence remains elusive. Here, we identify N6-methyladenosine (m6A) modification as a pivotal regulator of NiV replication. Higher m6A methylation levels on viral genomic RNA and mRNAs are associated with the increased virulence observed in the NiV-Malaysia (NiV-M) strain compared to NiV-Bangladesh (NiV-B). Underlying this phenomenon, NiV infection orchestrates a reprogramming of the host m6A machinery by downregulating the methyltransferase METTL3 and the demethylase ALKBH5, while concurrently upregulating m6A reader proteins YTHDF1-3. Both METTL3 and ALKBH5 bind directly to NiV RNA, with METTL3 installing m6A to promote viral replication and ALKBH5 removing them to inhibit it. Strikingly, pharmacological inhibition of m6A modification markedly attenuates NiV replication in vitro and in vivo, underscoring the therapeutic potential of targeting the m6A pathway. Our study establishes m6A as a key determinant of NiV pathogenicity and provides a paradigm for host-directed antiviral strategies against high-risk RNA viruses. Full article

Melatonin (MT) has been found to mitigate cadmium (Cd) toxicity with negligible environmental risks. It remains poorly understood as to how MT mitigates Cd-induced growth repression and regulates RNA m⁶A methylation. We aimed to elucidate the effect of MT on growth repression and RNA m⁶A methylation in Arabidopsis (Arabidopsis thaliana) exposed to Cd stress. MT mitigated, on average, 13.96% and 8.42% of growth repression resulting from Cd and mismatch repair (MMR) deficiency. The ameliorative effect on Cd stress was reduced by 70.56% and 34.23% in msh2 and msh6 mutants, respectively. With distinct dose–effect relationships, m⁶A hypermethylation responded to Cd stress rather than Cu stress, which was further elevated in MMR-deficient seedlings. MT reduced m⁶A levels by 22.98% even without stress induction, whereas the depressed m⁶A levels in MMR-deficient seedlings, greatly exceeding those in the WT. The “writer” and “eraser” gene expression responsible for m⁶A methylation was reduced with the concentration of stresses due to MT, but VIR and ALKBH9B no longer responded to Cd stress in msh2 and msh6. Despite the remarkable repression, MMR gene expression was regularly promoted by MT under Cd and Cu stress. Our study provides novel insights into the molecular mechanisms underlying the restorative effects of MT on growth repression and m⁶A methylation regulation, which shed light on Cd phytoremediation. Full article

N6-methyladenosine (m⁶A) is one of the most prevalent methylated modifications of mRNA in eukaryotes. This reversible alteration can directly or indirectly influence biological functions, including RNA degradation, translation, and splicing. This study investigates the impact of chronic morphine administration and varying withdrawal durations (1 day, 1 week, 4 weeks, and 12 weeks) on the m⁶A modification levels in brain regions critical to addiction development and persistence. Our findings indicate that in the prefrontal cortex, the m⁶A levels and METTL3 expression decrease, accompanied by an increase in FTO and ALKBH5 expression, followed by fluctuating, but statistically insignificant changes in methylation-regulating enzymes over prolonged withdrawal. In the striatum, reductions in m⁶A levels and METTL3 expression are observed at 4 weeks of withdrawal, preceded by non-significant fluctuations in enzyme expression and the m⁶A modification levels. In contrast, no changes in the m⁶A modification levels or the expression of related enzymes are detected in the hippocampus and the cerebellum. Our data suggest that m⁶A modification and its regulatory enzymes undergo region-specific and time-dependent changes in response to chronic morphine exposure and subsequent withdrawal. Full article

N6-methyladenosine (m⁶A) methylation functions as a vital post-transcriptional and epigenetic modification in higher plants regulated by α-ketoglutarate-dependent dioxygenases (ALKBH). However, the role of ALKBH genes in oriental melon (Cucumis melo L.) fruit ripening has not been explored. Therefore, we treated oriental melon with an exogenous m⁶A demethylase inhibitor (mechlorfenamic acid) then analyzed endogenous ethylene production and ripening-related indicators to explore the effects of m⁶A methylation on ripening. Bioinformatics and real-time quantitative PCR analyses were used to determine the impact of ALKBH genes on key ethylene synthesis gene expression. Treatment effectively inhibited endogenous ethylene production, firmness changes, and soluble solid contents, thereby extending fruit ripening. Eight ALKBH gene family members belonging to five major groups were identified in the melon genome. All members were expressed in ripening fruits, with different expression patterns during ripening. CmALKBH6, CmALKBH7, and CmALKBH8 expression was inhibited by an ethylene inhibitor (1-methylcyclopropene). The transient overexpression (OE) of CmALKBH8 in oriental melon led to the increased expression of the ethylene synthesis genes CmACS1, CmACS2, and CmACO1. In summary, the ethylene-regulated gene CmALKBH8 may participate in oriental melon fruit ripening regulation by modulating the methylation levels of ethylene synthesis-related genes. These findings help us better understand how m⁶A methylation regulates melon ripening. Full article

Background/Objectives: RNA-modifying proteins play a crucial role in the progression of cancer. The fat mass and obesity-associated protein (FTO) and alkB homolog 5 RNA demethylase (ALKBH5) are RNA-demethylating proteins that have contrasting effects in renal cell carcinoma (RCC) among different populations. This research investigates the genotype and expression levels of FTO and ALKBH5 in RCC patients from the Middle East and Northern Africa (MENA) region. Methods: Formalin-fixed paraffin-embedded samples from the kidney biopsies of RCC patients and controls were examined using targeted DNA sequencing, whole transcriptome profiling, and immunohistochemistry. Results: Our findings show that the rs11075995T variant in FTO is associated with a heightened risk of clear-cell RCC (ccRCC). ALKBH5 and FTO protein expression were significantly lower in ccRCC and chromophobe RCC (chRCC) patients but not in papillary RCC (pRCC) patients. In ccRCC, transcriptomic data revealed a significant downregulation of FTO (log₂FC = −5.2, q < 0.001) and ALKBH5 (log₂FC = −4.7, q < 0.001) compared to controls. A significant negative correlation was found in ccRCC between FTO expression and T allele frequency in rs11075995, suggesting that FTO expression is affected. Conclusions: This is the first demonstration of the association of the dysregulated expression of FTO and ALKBH5 in ccRCC and chRCC patients from the MENA region. FTO variant rs11075995T increased the risk of ccRCC and was negatively associated with FTO protein expression. Full article

Tomato (Solanum lycopersicum L.) is one of the major vegetable crops worldwide. Research on the Janus kinase–signal transducer and activator of transcription (JAK–STAT) signaling pathway in tomatoes and other plant systems is extremely limited. In this study, the roles of STAT, a crucial element of the JAK–STAT signaling pathway in tomato seed germination and low-temperature stress responses are examined, employing gene family analysis and genetic transformation. The results indicate that the S. lycopersicum genome contains only one member of the STAT gene family, SlSTAT. Subcellular localization experiments reveal that SlSTAT is found in both the cytoplasm and nucleus, suggesting its potential involvement in biological functions within these cellular compartments. Among the 26 different tomato tissue/organs tested, SlSTAT exhibited higher expression levels in hypocotyl (8 days past germination; 8 DPG), and low expression of SlSTAT significantly reduced the germination rate and impacted biomass at 8 DPG. In addition, the SlSTAT gene was significantly downregulated during low-temperature treatment. Compared with the wild-type (WT) tomatoes, the SlSTAT-overexpressing plants showed more resistance to low-temperature conditions, whereas the downexpressing tomatoes exhibited increased sensitivity. The expressions of low-temperature marker genes (SlCBF1-3) and N⁶-methyladenosine (m⁶A)-modification-related genes (m⁶A writer, reader, and eraser genes) were detected to explore possible molecular mechanisms by which SlSTAT causes changes in tomato low-temperature stress resistance. The expression changes of SlCBF1-3 in transgenic plants do not merely follow a straightforward linear relationship with the changes in SlSTAT expression, suggesting a more complex molecular mechanism and a non-direct interaction between SlSTAT and the promoters of SlCBFs. On the other hand, SlSTAT also changes the expression levels of RNA m⁶A-modification-related genes, especially SlFIP37 (writer gene), SlYTP8/9 (reader genes), and SlALKBH8 (eraser gene), ultimately leading to changes in the levels of m⁶A modification. These research findings lay the groundwork for exploring functions of JAK–STAT pathway in tomato development and stress responses, expanding the scope of JAK–STAT signaling studies in plant systems. Full article

Mastitis poses a severe threat to the global cattle industry, causing huge economic losses. Environmental mastitis is mainly induced by Escherichia coli (E. coli), and the current treatment is still using antibiotics, with problems such as drug resistance and food safety. ALKBH5 is an RNA m⁶A demethylase that plays an important role in various biological processes, while p65 is a key regulator of inflammatory responses. Therefore, studying the interaction between ALKBH5 and p65 in protecting the mammary epithelial barrier provides new insights into the pathogenesis of mastitis. This study revealed that E. coli-induced acute inflammation activated the NF-κB/p65 signaling pathway and disrupted mammary epithelial cell tight junctions. Knockdown of ALKBH5 promoted p65 phosphorylation and inhibited the expressions of the tight junction proteins TJP1, CDH1, and OCLN. Furthermore, motif analysis, CHIP-PCR, and dual luciferase assay confirmed that phosphorylated p65 inhibited TJP1 promoter activity, thereby inhibiting TJP1 expression. In addition, the mouse experiment further demonstrated that knockdown of ALKBH5 aggravated E. coli-induced acute mastitis and epithelial cell tight junction disruption, and promoted E. coli invasion and proliferation. Significantly, this study is the first to demonstrate the details of the interaction between p65 and TJP1 and to declare the molecular mechanism of ALKBH5 in improving the cell tight junction, which lays a potential target and theoretical foundation for the treatment of mastitis and other infectious diseases. Full article

Tamarix chinensis (T. chinensis), an esteemed salt-tolerant plant, holds significant importance in elucidating mechanisms of plant stress adaptation. The ALKBH genes family, which is involved in RNA N⁶-methyladenosine (m⁶A) demethylation, plays a crucial role in plant growth, development, and stress responses. This study performed a genome-wide identification and analysis of the ALKBH genes family in T. chinensis using bioinformatics methodologies. A total of eight ALKBH genes were identified and named TcALKBH1 to TcALKBH8 based on their chromosomal positions. Phylogenetic analysis divided the TcALKBH genes family into different subgroups, revealing that, in comparison to Arabidopsis and other plants, T. chinensis lacks members of the ALKBH6 and ALKBH10 families. Further analysis of gene structure, conserved domain, and motif analysis elucidated the basic features of the TcALKBH gene family. Gene duplication analysis identified TcALKBH3 and TcALKBH7 as homologous gene pairs, and collinearity analysis indicated a closer relationship between T. chinensis and Populus compared to Arabidopsis. In addition, gene expression analysis revealed tissue-specific expression patterns of the TcALKBH genes, with significant upregulation observed under abiotic stress conditions such as ABA, NaCl, and NaHCO₃. It is noteworthy that the expression of TcALKBH4 increased nearly 30-fold after 6 h of ABA stress, suggesting that TcALKBH4 may play a key regulatory role in the ABA response. These results indicate that the TcALKBH genes might be crucial for stress responses in T. chinensis. This research offers a theoretical foundation for a deeper exploration of the roles and molecular mechanisms of the TcALKBH genes family in stress adaptation. It also presents valuable candidate genes for enhancing stress resistance in plants through breeding programs. Full article

Research exploring involvement of RNA N⁶-methyladenosine (m⁶A) in tomato (Solanum lycopersicum) seed germination remains limited. There is also a lack of direct evidence supporting the interaction among tomato seed germination, microgravity, and m⁶A modification. In this study, Micro-Tom tomatoes are used as the experimental material to conduct tomato genetic transformation, seed germination assay, and m⁶A modification levels identification experiments. During tomato seed germination processes, the m⁶A modification level significantly increases under the mutual influence of various m⁶A methyltransferase subunits and multiple eraser proteins. As a m⁶A reader gene, SlYTP9 expression significantly affects the germination of tomato seeds, with promotion and inhibition in OE (overexpression) and RNAi (RNA interference) transgenic tomato plants, respectively. Microgravity promotes seed germination in the early germination period (0–3 days past germination; 0–3 DPG), but this promoting effect gradually disappears as the seedling grows (8–15 DPG). Further exploration revealed that this promoting effect is correlated with m⁶A modification, manifested as enhanced expression of most m⁶A writer genes; increased expression levels of overall reader genes; altered expression trends of some m⁶A eraser genes, particularly SlALKBH2; and enhanced m⁶A modification levels. The experimental results obtained in this study can provide a theoretical basis and evidence support for elucidating the role of m⁶A in tomato seed germination, as well as for exploring the interactions between seed germination, microgravity, and m⁶A modification. Full article

N6-methyladenosine (m6A) is the most common and abundant internal co-transcriptional modification in eukaryotic RNAs. This modification is catalyzed by m6A methyltransferases, known as “writers”, including METTL3/14 and WTAP, and removed by demethylases, or “erasers”, such as FTO and ALKBH5. It is recognized by m6A-binding proteins, or “readers”, such as YTHDF1/2/3, YTHDC1/2, IGF2BP1/2/3, and HNRNPA2B1. Cardiovascular diseases (CVDs) are the leading cause of morbidity and mortality worldwide. Recent studies indicate that m6A RNA modification plays a critical role in both the physiological and pathological processes involved in the initiation and progression of CVDs. In this review, we will explore how m6A RNA methylation impacts both the normal and disease states of the cardiovascular system. Our focus will be on recent advancements in understanding the biological functions, molecular mechanisms, and regulatory factors of m6A RNA methylation, along with its downstream target genes in various CVDs, such as atherosclerosis, ischemic diseases, metabolic disorders, and heart failure. We propose that the m6A RNA methylation pathway holds promise as a potential therapeutic target in cardiovascular disease. Full article

N6-methyladenosine (m6A) is the most abundant, dynamically reversible, and evolutionarily conserved internal chemical modification in eukaryotic RNA. It is emerging as critical for regulating gene expression at the post-transcriptional level by affecting RNA metabolism through, for example, pre-mRNA processing, mRNA decay, and translation. ALKBH5 has recently been identified as an endogenous m6A demethylase implicated in a multitude of biological processes. This review provides an overview of the structural and functional characteristics of ALKBH5 and the involvement of ALKBH5 in diverse human diseases, including metabolic, immune, reproductive, and nervous system disorders, as well as the development of inhibitors. In summation, this review highlights the current understanding of the structure, functions, and detailed mechanisms of ALKBH5 in various physiological and pathological processes and provides valuable insights for clinical applications and foundational research within related fields. Full article

Members of the m⁶A gene family are involved in key biological processes such as plant growth, development, stress responses, and light signal transduction. However, the function of m⁶A genes in peanuts has been understudied. Our analysis identified 61 m⁶A family members in the peanut genome, including 21 writer genes, 22 eraser genes, and 18 reader genes, distributed across 20 chromosomes. Phylogenetic analysis revealed that ALKBH proteins are categorized into six subfamilies, while YTH family proteins form nine subfamilies. Promoter cis-element analysis indicated that m⁶A gene promoters contain light-responsive, hormone-responsive, growth-related, low-temperature defense, and other stress-related elements. Expression studies of AhALKBH8Ba and AhALKBH8Bb in various peanut tissues suggest that these genes play vital roles in peanut fruit needle development. Furthermore, AhETC1a and AhETC1b were significantly upregulated following the loss of mechanical pressure in peanut pods. This study identifies several key genes involved in light and mechanical stress response during peanut pod development. Full article

Mechanical asphyxia presents a challenging diagnostic issue in forensic medicine due to its often covert nature, and the signs visible during an autopsy are usually not specific. Despite some progress in understanding hypoxia’s effects, traditional methods’ inherent limitations might overlook new biomarkers in mechanical asphyxia. This study employed 4D-DIA proteomics to explore the protein expression profiles of cardiac samples under conditions of mechanical asphyxia. Proteomic analysis identified 271 and 371 differentially expressed proteins in the strangulation and suffocation groups, respectively, compared to the control group. Seventy-eight differentially expressed proteins were identified across different mechanical asphyxia groups compared to the control group. GO and KEGG analysis showed enrichment in pathways, including complement and coagulation cascades, cAMP and cGMP-PKG signaling pathways, inflammatory mediator regulation of TRP channels, and phagosomes. Through stringent selection based on protein interactions, ALKBH5, NAA10, and CLPB were identified as potential diagnostic biomarkers. ALKBH5 showed increased expression in asphyxia models, while NAA10 and CLPB were downregulated; these biomarker changes were validated in both animal models and human cardiac samples. This study highlights the potential of proteomics in discovering reliable biomarkers, which can enhance the specificity of mechanical asphyxia diagnosis in forensic practice, provide new insights into the pathophysiological mechanisms of mechanical asphyxia, and offer new perspectives for diagnosing mechanical asphyxia. Full article