Search Results (100)

Plant mitochondrial genomes are characterized by their complex compositions and structures, large genomes, rapid recombination and evolution rates, and frequent intracellular gene transfer events. Centipedegrass, known as “Chinese turfgrass”, is a warm-season turfgrass that exhibits excellent tolerance to both biotic and abiotic stresses. The chloroplast genome, with 139,107 bp, and the mitochondrial genome, with 564,432 bp, were both assembled into a single circular structure. We identified 44 gene transfer events between the chloroplast and mitochondrial genomes. The mitochondrial gene cox1 could serve as a marker for distinguishing accessions found at different altitudes. The unique features of the centipedegrass mitochondrial genome, coupled with the comparative genomic analysis of both chloroplast and mitochondrial genomes, have the potential to enrich the Poaceae database and provide crucial perspectives on plant evolution, energy metabolism, and responses to environmental conditions. The markers developed could facilitate the analysis of the genetic diversity of centipedegrass. Full article

Adansonia L. (1753) belongs to the family Malvaceae and is commonly known as the baobab tree. This species holds significant cultural and ecological value and is often referred to as the ‘tree of life.’ Although its nuclear genome has been reported, the mitogenome has not yet been studied. Mitogenome research is crucial for understanding the evolution of the entire genome. In this study, we assembled and analyzed the mitogenomes of four Adansonia species by integrating short-read and long-read data. The results showed that the mitogenomes of all four Adansonia species were resolved as single circular sequences. Their total genome lengths ranged from 507,138 to 607,344 bp and contained a large number of repetitive sequences. Despite extensive and complex rearrangements between the mitogenomes of Adansonia and other Malvaceae species, a phylogenetic tree constructed based on protein-coding genes clearly indicated that Adansonia is more closely related to the Bombax. Selection pressure analysis suggests that the rps4 gene in Adansonia may have undergone positive selection compared to other Malvaceae species, indicating that this gene may play a significant role in the evolution of Adansonia. Additionally, by analyzing intracellular gene transfer between the chloroplast, mitochondria, and nuclear genomes, we found that genes from the chloroplast and mitochondria can successfully transfer to each chromosome of the nuclear genome, and the psbJ gene from the chloroplast remains intact in both the mitochondrial and nuclear genomes. This study enriches the genetic information of Adansonia and provides important evidence for evolutionary research in the family Malvaceae. Full article

Ganoderma lucidum polysaccharides (GLPs) are natural compounds with a broad spectrum of biological activities. β-1,3-glucosyltransferase (GL20535) plays an important role in polysaccharide synthesis by catalyzing the transfer of UDP-glucose to extend sugar chains, but its underlying mechanism remains unclear. In this study, the regulatory mechanism of GL20535 in polysaccharide synthesis was elucidated by overexpressing and silencing gl20535 in G. lucidum. Overexpression of gl20535 resulted in maximum increases of 18.08%, 79.04%, and 18.01% in intracellular polysaccharide (IPS), extracellular polysaccharide (EPS), and β-1,3-glucan contents, respectively. In contrast, silencing gl20535 resulted in maximum reductions of 16.97%, 30.20%, and 23.56% in IPS, EPS, and β-1,3-glucan contents, respectively. These phenomena in the overexpression strains were attributed to gl20535-mediated promotion of UDP-glucose synthesis in the sugar donor pathway and upregulation of the expression of glycoside hydrolase genes. The opposite trend was observed in the silenced strains. In mycelial growth studies, neither overexpression nor silencing of gl20535 affected biomass and cell wall thickness. Furthermore, the GL20535 isozyme gene gl24465 remained unaffected in gl20535-overexpressed strains but was upregulated in gl20535-silenced strains, suggesting a compensatory regulatory relationship. These findings reveal the regulatory role of GL20535 on gene expression in the GLPs synthesis pathway and deepen our understanding of GL20535 function in the polysaccharide network of edible and medicinal fungi. Full article

The selective regulation of gene expression at the RNA level represents a rapidly evolving field offering substantial clinical potential. This review examines the molecular mechanisms of intracellular enzymatic systems that utilize single-stranded nucleic acids to downregulate specific RNA targets. The analysis encompasses antisense oligonucleotides and synthetic mimics of small interfering RNA (siRNA), microRNA (miRNA), transfer RNA-derived small RNA (tsRNA), and PIWI-interacting RNA (piRNA), elucidating their intricate interactions with crucial cellular machinery, specifically RNase H1, RNase P, AGO, and PIWI proteins, mediating their biological effects. The functional and structural characteristics of these endonucleases are examined in relation to their mechanisms of action and resultant therapeutic outcomes. This comprehensive analysis illuminates the interactions between single-stranded nucleic acids and their endonuclease partners, covering antisense inhibition pathways as well as RNA interference processes. This field of research has important implications for advancing targeted RNA modulation strategies across various disease contexts. Full article

The mitochondrial genome of Spartina alterniflora, an invasive species with significant ecological and economic impacts, was analyzed to provide a theoretical basis for understanding its phylogenetic relationships and molecular biology. Mitochondrial genome sequences of S. alterniflora and 23 related species from NCBI were utilized for bioinformatics and comparative genomic analyses. A sliding window analysis identified three genes (rps2, atp9, and nad6) as potential DNA barcodes for species identification. Intracellular gene transfer (IGT) events between mitochondrial and chloroplast genome were detected, highlighting the dynamic nature of genomic evolution. A selective pressure analysis revealed that most protein-coding genes (PCGs) underwent purifying selection (K_a/K_s < 1), while the nad2 and ccmB genes showed signs of positive selection pressure (K_a/K_s > 1), indicating their role in adaptation. A phylogenetic analysis demonstrated a close relationship between S. alterniflora and Eleusine indica, supported by a collinearity analysis, which suggests environmental convergence. This study provides novel insights into the structural and evolutionary characteristics of the S. alterniflora mitochondrial genome, offering valuable genomic resources for future research on invasive species management and evolutionary biology. Full article

As a globally distributed perennial Gramineae, Phragmites australis can adapt to harsh ecological environments and has significant economic and environmental values. Here, we performed a complete assembly and annotation of the mitogenome of P. australis using genomic data from the PacBio and BGI platforms. The P. australis mitogenome is a multibranched structure of 501,134 bp, divided into two circular chromosomes of 325,493 bp and 175,641 bp, respectively. A sequence-simplified succinate dehydrogenase 4 gene was identified in this mitogenome, which is often translocated to the nuclear genome in the mitogenomes of gramineous species. We also identified tissue-specific mitochondrial differentially expressed genes using RNAseq data, providing new insights into understanding energy allocation and gene regulatory strategies in the long-term adaptive evolution of P. australis mitochondria. In addition, we studied the mitogenome features of P. australis in more detail, including repetitive sequences, gene Ka/Ks analyses, codon preferences, intracellular gene transfer, RNA editing, and multispecies phylogenetic analyses. Our results provide an essential molecular resource for understanding the genetic characterisation of the mitogenome of P. australis and provide a research basis for population genetics and species evolution in Arundiaceae. Full article

Bacterial and eukaryotic dihydrofolate reductase (DHFR) enzymes are essential for DNA synthesis and are differentially sensitive to the competitive inhibitors trimethoprim and methotrexate. Unexpectedly, trimethoprim did not reduce Wolbachia abundance, and the wStri DHFR homolog contained amino acid substitutions associated with trimethoprim resistance in E. coli. A phylogenetic tree showed good association of DHFR protein sequences with supergroup A and B assignments. In contrast, DHFR is not encoded by wFol (supergroup E) and wBm (supergroup D) or by genomes of the closely related genera Anaplasma, Ehrlichia, Neorickettsia, and possibly Orientia. In E. coli and humans, DHFR participates in a coupled reactions with the conventional thymidylate synthase (TS) encoded by thyA to produce the dTMP required for DNA synthesis. In contrast, Wolbachia and other Rickettsiales express the unconventional FAD-TS enzyme encoded by thyX, even when folA is present. The exclusive use of FAD-TS suggests that Wolbachia DHFR provides a supplementary rather than an essential function for de novo synthesis of dTMP, possibly reflecting the relative availability of, and competing demands for, FAD and NAD coenzymes in the diverse intracellular environments of its hosts. Whether encoded by thyA or thyX, TS produces dTMP by transferring a methyl group from methylene tetrahydrofolate to dUMP. In the Rickettsiales, serine hydroxymethyltransferase (SMHT), encoded by a conserved glyA gene, regenerates methylene tetrahydrofolate. Unlike thyA, thyX lacks a human counterpart and thus provides a potential target for the treatment of infections caused by pathogenic members of the Rickettsiales. Full article

Background/Objectives: Pathogen inactivation and harmful gene destruction from water just before drinking is the last line of defense to protect people from waterborne diseases. However, commonly used disinfection methods, such as chlorination, ultraviolet irradiation, and membrane filtration, experience several challenges such as continuous chemical dosing, the spread of antibiotic resistance genes (ARGs), and intensive energy consumption. Methods: Here, we perform a simultaneous elimination of pathogens and ARGs in drinking water using local electric fields and in-situ generated trace copper ions (LEF-Cu) without external chemical dosing. A 100-μm thin copper wire placed in the center of a household water pipe can generate local electric fields and trace copper ions near its surface after an external low voltage is applied. Results: The local electric field rapidly damages the outer structure of microorganisms through electroporation, and the trace copper ions can effectively permeate the electroporated microorganisms, successfully damaging their nucleic acids. The LEF-Cu disinfection system achieved complete inactivation (>6 log removal) of Escherichia coli O157:H7, Pseudomonas aeruginosa PAO1, and bacteriophage MS2 in drinking water at 2 V for 2 min, with low energy consumption (10⁻² kWh/m³). Meanwhile, the system effectively damages both intracellular (0.54~0.64 log) and extracellular (0.5~1.09 log) ARGs and blocks horizontal gene transfer. Conclusions: LEF-Cu disinfection holds promise for preventing horizontal gene transfer and providing safe drinking water for household applications. Full article

Vesicle transport is a fundamental mechanism for intracellular substance transfer and signal transduction, involving the formation, transport, fusion with target membranes, and release of vesicle contents within cells. Issues such as disruption of water balance, difficulty in regulating osmotic pressure, and oxidative stress caused by salt stress can lead to disturbances in the secretion system of plants, thus affecting plant growth and development. Cyclocarya paliurus (C. paliurus), widely used in traditional Chinese medicine, has not been previously reported in terms of how the vesicle transport P24 gene regulates its adaptation to salt stress. In this research project, a total of eight CpP24 genes were successfully identified. Upon examination of gene architecture and conserved sequence elements, the CpP24 genes exhibited a variation in exon count, ranging from 4 to 6. Moreover, the CpP24 gene family’s reaction to salt stress and specific stressors including methyl jasmonate (MeJA), sodium hydrosulfide (NaHS), and sodium nitroprusside (SNP) was further explored in our study. Comprehensive analysis of the expression patterns of CpP24 genes under various conditions showed that salt stress induced the expression of these genes, and the combined treatment of salt stress with specific stresses caused changes in their expression. This study lays a theoretical foundation for further probing into the physiological functions of C. paliurus and the underlying mechanisms regarding its response to environmental stress. Full article

The epidermis, the outer layer of the skin, relies on a delicate balance of cell growth and keratinocyte differentiation for its function and renewal. Recent research has shed light on exosomes’ role in facilitating skin communication by transferring molecules like miRNAs, which regulate gene expression post-transcriptionally. Additionally, these factors lead to skin aging through oxidative stress caused by reactive oxygen species (ROS). In this research project, experiments were conducted to study the impact of Sun2000 solar simulator irradiation on exosomal miRNA profiles in HEKa cells. We hypothesized that acute oxidative stress induced by solar simulator irradiation would alter the expression profile of exosomal miRNAs in HEKa cells. The cells were exposed to different durations of irradiation to induce oxidative stress, and the levels of reactive ROS were measured using the CellROX Deep Red flow cytometry assay kit. Exosomes were isolated from both control and irradiated cells, characterized using DLS and SEM techniques, and their miRNAs were extracted and analyzed using qPCR. Solar simulator irradiation led to a time-dependent increase in intracellular ROS and a decrease in cell viability. Exosomal size increased in irradiated cells. Fifty-nine exosomal miRNAs were differentially expressed in irradiated HEKa cells, including hsa-miR-425-5p, hsa-miR-181b-5p, hsa-miR-196b-5p, hsa-miR-376c-3p, and hsa-miR-15a-5p. This study highlights the significant impact of solar radiation on exosomal miRNA expression in keratinocytes, suggesting their potential role in the cellular response to oxidative stress. Full article

Oenobiol Sun Expert, a food formulation designed to enhance skin health prior to sun exposure, has been optimized by incorporating the OenoGrape Advanced Complex, which includes grape pomace extract, increased selenium content and 10% lycopene-rich tomato extract, with these constituents exhibiting high antioxidant potential. To evaluate the effects of these individual ingredients and the overall formulation at the cellular level, the AOP1 cell antioxidant efficacy assay was employed to measure the intracellular free radical scavenging activity, while the Cell Antioxidant Assay (CAA or DCFH-DA) assay was used to assess peroxidation scavenging at the plasma membrane level. The indirect antioxidant activity was examined using stably transfected cell lines containing a luciferase reporter gene controlled by the Antioxidant Response Element (ARE), which activates the endogenous antioxidant system via the Nrf2/Keap1-ARE pathway. Our results indicate that among the individual components, grape pomace extract and sodium selenite possess high and complementary antioxidant properties. Grape pomace extract was particularly effective in inhibiting free radicals (AOP1 EC₅₀ = 6.80 μg/mL) and activating the ARE pathway (ARE EC₅₀ = 231.1 μg/mL), whereas sodium selenite exerted its effects through potent ARE activation at sub-microgram levels (EC₅₀ = 0.367 μg/mL). In contrast, the lycopene-rich tomato extract did not show a notable contribution to the antioxidant effects. The antiradical activity of the OenoGrape Advanced Complex, comprising these three ingredients, was very efficient and consistent with the results obtained for the individual components (AOP1 EC₅₀ = 15.78 µg/mL and ARE EC₅₀ of 707.7 μg/mL). Similarly, the free radical scavenging activity still persisted in the Oenobiol Sun Expert formulation (AOP1 EC₅₀ = 36.63 µg/mL). Next, in vitro intestinal transepithelial transfer experiments were performed. The basolateral compartments of cells exposed to the ingredients were collected and assessed using the same antioxidant cell assays. The direct and indirect antioxidant activities were measured on both hepatocytes and keratinocytes, demonstrating the bioavailability and bioactivity of grape pomace extract and sodium selenite. These finding suggest that the ingredients of this food supplement contribute to enhanced cytoprotection following ingestion. Full article

Abstract: The metabolism of zinc and manganese plays a pivotal role in cancer progression by mediating cancer cell growth and metastasis. The SLC30A family proteins SLC30A3 and SLC30A10 mediate the efflux of zinc, manganese, and probably other transition element ions outside the cytoplasm to the extracellular space or into intracellular membrane compartments. The SLC39A family members SLC39A8 and SLC39A14 are their functional antagonists that transfer these ions into the cytoplasm. Recently, the SLC30A10 gene was suggested as a promising methylation biomarker of colorectal cancer. Here, we investigated whether forced overexpression or inactivation of SLC30A and SLC39A family genes has an impact on the phenotype of cancer cells and their sensitivity to cancer therapeutics. In the human colon adenocarcinoma HCT-15 and duodenal adenocarcinoma HuTu80 cell lines, we generated clones with knockouts of the SLC39A8 and SLC39A14 genes and forced overexpression of the SLC30A3, SLC30A10, and SLC39A8 genes. Gene expression in the mutant and control cells was assessed by RNA sequencing. The cell growth rate, mitochondrial activity, zinc accumulation, and sensitivity to the drugs cetuximab and cisplatin were investigated in functional tests. Overexpression or depletion of SLC30A or SLC39A family genes resulted in the deep reshaping of intracellular signaling and provoked hyperactivation of mitochondrial respiration. Variation in the expression of the SLC30A/SLC39A genes did not increase the sensitivity to cetuximab but significantly altered the sensitivity to cisplatin: overexpression of SLC30A10 resulted in an ~2.7–4 times increased IC50 of cisplatin, and overexpression of SLC30A3 resulted in an ~3.3 times decreased IC50 of cisplatin. The SLC30A/SLC39A genes should be considered as potential cancer drug resistance biomarkers and putative therapeutic targets. Full article

Fungi inhabiting deep subseafloor sediments have been shown to possess anaerobic methane (CH₄) production capabilities under atmospheric conditions. However, their ability to produce CH₄ under in situ conditions with high hydrostatic pressure (HHP) remains unclear. Here, Schizophyllum commune 20R-7-F01, isolated from ~2 km below the seafloor, was cultured in Seawater Medium (SM) in culture bottles fitted with sterile syringes for pressure equilibration. Subsequently, these culture bottles were transferred into 1 L stainless steel pressure vessels at 30 °C for 5 days to simulate in situ HHP and anaerobic environments. Our comprehensive analysis of bioactivity, biomass, and transcriptomics revealed that the S. commune not only survived but significantly enhanced CH₄ production, reaching approximately 2.5 times higher levels under 35 MPa HHP compared to 0.1 MPa standard atmospheric pressure. Pathways associated with carbohydrate metabolism, methylation, hydrolase activity, cysteine and methionine metabolism, and oxidoreductase activity were notably activated under HHP. Specifically, key genes involved in fungal anaerobic CH₄ synthesis, including methyltransferase mct1 and dehalogenase dh3, were upregulated 7.9- and 12.5-fold, respectively, under HHP. Enhanced CH₄ production under HHP was primarily attributed to oxidative stress induced by pressure, supported by intracellular reactive oxygen species (ROS) levels and comparative treatments with cadmium chloride and hydrogen peroxide. These results may provide a strong theoretical basis and practical guidance for future studies on the contribution of fungi to global CH₄ flux. Full article

Gentiana rigescens, an alpine plant with significant medicinal value, possesses a complex genetic background. However, comprehensive genomic research on G. rigescens is still lacking, particularly concerning its organelle genome. In this study, G. rigescens was studied to sequence the mitochondrial genome (mitogenome) and ascertain the assembly, informational content, and developmental expression of the mitogenome. The mitogenome of G. rigescens was 393,595 bp in length and comprised four circular chromosomes ranging in size from 6646 bp to 362,358 bp. The GC content was 43.73%. The mitogenome featured 30 distinct protein-coding genes, 26 tRNA genes, and 3 rRNA genes. The mitogenome of G. rigescens also revealed 70 SSRs, which were mostly tetra-nucleotides. In addition, 48 homologous fragments were found between the mitogenome and the chloroplast genome, with the longest measuring 23,330 bp. The documentation of the mitochondrial genome of G. rigescens is instrumental in advancing the understanding of its physiological development. Decoding the G. rigescens mitogenome will offer valuable genetic material for phylogenetic research on Gentianaceae and enhance the use of species germplasm resources. Full article

Background/Objectives: The study of oxidative stress in cells and ways to prevent it attract increasing attention. Antioxidant defense of cells can be activated by releasing the transcription factor Nrf2 from a complex with Keap1, its inhibitor protein. The aim of the work was to study the effect of the modular nanotransporter (MNT) carrying an R1 anti-Keap1 monobody (MNT_R1) on cell homeostasis. Methods: The murine hepatocyte AML12 cells were used for the study. The interaction of fluorescently labeled MNT_R1 with Keap1 fused to hrGFP was studied using the Fluorescence-Lifetime Imaging Microscopy–Förster Resonance Energy Transfer (FLIM-FRET) technique on living AML12 cells transfected with the Keap1-hrGFP gene. The release of Nrf2 from the complex with Keap1 and its levels in the cytoplasm and nuclei of the AML12 cells were examined using a cellular thermal shift assay (CETSA) and confocal laser scanning microscopy, respectively. The effect of MNT on the formation of reactive oxygen species was studied by flow cytometry using 6-carboxy-2′,7′-dichlorodihydrofluorescein diacetate. Results: MNT_R1 is able to interact with Keap1 in the cytoplasm, leading to the release of Nrf2 from the complex with Keap1 and a rapid rise in Nrf2 levels both in the cytoplasm and nuclei, ultimately causing protection of cells from the action of hydrogen peroxide. The possibility of cleavage of the monobody in endosomes leads to an increase in the observed effects. Conclusions: These findings open up a new approach to specifically modulating the interaction of intracellular proteins, as demonstrated by the example of the Keap1-Nrf2 system. Full article