Cytochrome P450 Genes Research Articles

Genome-Wide Expression Profiling of Cytochrome P450 Genes in Response to the Oxidative Stress in Saccharum spp.

Genome-Wide Expression Profiling of Cytochrome P450 Genes in Response to the Oxidative Stress in Saccharum spp.

RNA sequencing of Beauveria bassiana JEF-350-infected Thrips palmi reveals change of host defense and homeostasis.

Melon thrips, Thrips palmi, represent a significant threat to plants, inducing necrosis and acting as vectors for numerous plant viruses. Entomopathogenic fungi present a promising avenue for the management of melon thrips populations resistant to conventional chemical treatments. In this work, an adult colony of melon thrips was exposed to Beauveria bassiana strain JEF-350, and the ensuing transcriptional response of the infected thrips was scrutinized to elucidate their reactions during fungal pathogenesis. Utilizing Illumina sequencing, RNA samples were extracted from untreated thrips as well as from thrips continuously infected for 2 and 4days, each with three biological replicates. While no notable alterations in gene expression were observed between the untreated control and thrips infected for 2days, those infected for 4days exhibited a plethora of differentially expressed genes. Specifically, in the thrips infected for the extended period, pathways associated with lysosomal function and insect hormone biosynthesis were notably repressed, while others such as serine and glycine metabolism, Toll and Imd, and circadian rhythm pathways displayed heightened activity. Noteworthy downregulation was observed in numerous lysosomal hydrolase genes encoding glycosidases, sulfatases, and lipases, particularly glycosidases. Furthermore, certain genes related to hydrolase precursors within the Golgi apparatus exhibited heightened expression levels but failed to progress toward hydrolase biosynthesis. Upstream regulation of juvenile hormone biosynthesis was augmented, yet downstream genes were significantly downregulated, leading to a disruption in juvenile hormone production. Similarly, while cytochrome P450 genes in the downstream of ecdysone biosynthesis were upregulated, expressions of cholesterol desaturase and cytochrome P450 genes in the upstream were inhibited, consequently dampening ecdysone biosynthesis. The observed differential targeting of organs or pathways by B. bassiana JEF-350, in contrast to conventional chemicals primarily affecting neurotransmission and energy production, suggests its potential efficacy in managing resistant thrips populations. Consequently, integrating JEF-350 into the chemical spray regimen or incorporating it into tank-mix formulations with chemical insecticides emerges as a pragmatic approach within the realm of integrated pest management strategies. KEY POINTS: • Beauveria treatment inhibited lysosomal function and hormone synthesis in thrips. • Thrips serine/glycine metabolism, Toll and Imd, and circadian rhythm pathways were activated. • Upstream functions of thrips hormone biosynthesis increased, while downstream functions were suppressed. • Regarding biosynthesis of metabolites, this fungus targets other pathways with resistance management.

Predictive modeling of the probability of gynecological complications of tamoxifen therapy: A prospective study

Background. It is well known that adjuvant therapy for breast cancer (BC) with tamoxifen is associated with an increased risk of endometrial hyperplasia (EH). Currently, the problem of hyperplastic processes and endometrial cancer during long-term tamoxifen therapy is particularly relevant since the incidence of endometrial disorders has a direct correlation with the duration of tamoxifen therapy. Follow-up by a gynecologist should be tailored to consider the risk of endometrial cancer in women who survived BC to improve the early detection of endometrial cancer and avoid unnecessary invasive procedures. Aim. To predict adverse drug reactions (ADRs) of tamoxifen, including EH, endometrial polyps, and abnormal uterine bleeding, based on mathematical modeling in relation to the carriage of polymorphic variants of cytochrome P450 enzyme genes and drug transporter proteins. Materials and methods. A prospective pharmacogenetic study of 120 women with stage I–III luminal BC receiving tamoxifen was conducted. The polymerase chain reaction method was used to detect the presence of polymorphisms of cytochrome P450 genes, followed by an assessment of their associations with ADRs of tamoxifen, namely with local gynecological symptoms. Results. Predictive models of ADR occurrence based on the logistic regression function have been created and validated by ROC analysis. We have developed a prognostic model to estimate the probability of developing a composite endpoint (polyp, EH, abnormal uterine bleeding) based on history and genetic risk factors. It was found that the predictors of the combination of local gynecological ADRs (EH, endometrial polyp, and abnormal uterine bleeding) include such factors as weight loss, the presence of asthenia, an increase in the number of births, carriage of the TT genotype of the ABCB1 3435 polymorphic variant and the GG genotype of the CYP2D6*4 polymorphic variant, GG of the CYP3A5 polymorphic variant. The relatively high incidence (43.3%) of local gynecological symptoms requires regular monitoring by obstetrician-gynecologists using instrumental methods (transvaginal ultrasound). Conclusion. This prognostic model has demonstrated high diagnostic effectiveness, which allows it to be implemented in the routine clinical practice of an obstetrician-gynecologist.

Genome-wide identification and functional analysis of CYP450 genes in eggplant (Solanum melongena L.) with a focus on anthocyanin accumlation

BackgroundIn plants, Cytochrome P450 (CYP450) constitutes the largest family of metabolic enzymes and plays a crucial role in various physiological processes, including plant growth and development. Eggplants are well-known for their peel’s high concentration of anthocyanin compounds that provide significant health benefits to humans. The accumulation of anthocyanins in eggplant peels is an important process during growth and development. Therefore, it is essential to identify the CYP450 genes in eggplant (SmCYPs) and analyze their expression profiles during the period of anthocyanin accumulation in the peel.ResultsA total of 180 SmCYPs were identified in the eggplant genome and classified into eight subfamilies based on phylogenetic analysis. These SmCYPs exhibited highly conserved gene structure (exon/intron) and protein motifs, especially within their respective subgroup. Sixteen pairs of genes with collinearity were identified through gene duplication analysis. Promoter cis-acting element analysis revealed that SmCYPs are involved in various responses, including growth and development, stress responsiveness, and light responsiveness. Transcriptome data analysis revealed that all SmCYPs were expressed in various eggplant tissues, such as roots, stems, leaves, flowers, and fruits; with diverse expression patterns among members. The expression patterns of SmCYPs in eggplant peel also exhibited diversity during different stages of anthocyanin accumulation. qRT-PCR analysis demonstrated similar expression patterns for 15 selected SmCYPs as observed in the transcriptome data. Metabolomics analysis further suggested that SmCYPs are involved in the biosynthesis of secondary metabolites and metabolic pathways related to flavonoid and flavone/flavonol biosynthesis. Notably, three specific SmCYPs (SmCYP73A1/75A/98A1) play a significant role in flavonoid biosynthesis, particularly in anthocyanin synthesis in eggplant.ConclusionGenome-wide identification, phylogenetic analysis, expression profile analysis, and exploration of metabolic pathways related to SmCYPs provide valuable insights into the roles of these genes in anthocyanin accumulation in various tissues and organs, including eggplant peel. The findings from this study lay a foundation for the functional analysis of SmCYPs involvement in anthocyanin accumulation in eggplant peel, providing a molecular basis for breeders to cultivate novel varieties of eggplants with high levels of anthocyanin content.

Overexpression of a Soybean Cytochrome P450 Gene, GmCYP, Improves Drought and Insect Tolerance in Tobacco

Overexpression of a Soybean Cytochrome P450 Gene, GmCYP, Improves Drought and Insect Tolerance in Tobacco

Varying levels of natural light intensity affect the phyto-biochemical compounds, antioxidant indices and genes involved in the monoterpene biosynthetic pathway of Origanum majorana L.

BackgroundLight is a critical environmental factor in plants, encompassing two vital aspects: intensity and quality. To assess the influence of different light intensities on Origanum majorana L., pots containing the herb were subjected to four levels of light intensity: 20, 50, 70, and 100% natural light. After a 60-day treatment period, the plants were evaluated for metabolite production, including total sugar content, protein, dry weight, antioxidant indices, expression of monoterpenes biosynthesis genes, and essential oil compounds. The experimental design followed a randomized complete blocks format, and statistical analysis of variance was conducted.ResultsThe results indicated a correlation between increased light intensity and elevated total sugar and protein content, which contributed to improved plant dry weight. The highest levels of hydrogen peroxide and malondialdehyde (MDA) were observed under 100% light intensity. Catalase and superoxide dismutase enzymes exhibited increased activity, with a 4.23-fold and 2.14-fold increase, respectively, under full light. In contrast, peroxidase and polyphenol oxidase enzyme activities decreased by 3.29-fold and 3.24-fold, respectively. As light intensity increases, the expression level of the 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR) gene increases. However, beyond a light intensity of 70%, the DXR gene expression level decreased. Furthermore, the expression levels of the cytochrome P450 genes CYP71D178 and CYP71D179 exhibited an increasing trend in response to elevated light intensity. Essential oil content increased from 0.02 to 0.5% until reaching 70% light intensity. However, with further increases in light intensity, the essential oil content decreased by 54 to 0.23%.ConclusionsThese findings emphasize the importance of balancing plant growth promotion and stress management under different light conditions. The research suggests that sweet marjoram plants thrive best in unshaded open spaces, resulting in maximum biomass. However, essential oil production decreases under the same conditions. For farmers in areas with an average light intensity of approximately 1700 µmol m−2s−1, it is recommended to cultivate sweet marjoram in shade-free fields to optimize biomass and essential oil production. Towards the end of the growth cycle, it is advisable to use shades that allow 70% of light to pass through. The specific duration of shade implementation can be further explored in future research.

Assessing Alcohol Genes Targets in Mouse Liver

Background: Alcohol is a risk factor for liver diseases. There is a correlation between alcohol consumption and fatty liver disease. Experiences have shown gene expression alteration in the liver following alcohol consumption. Since the molecular mechanism of connection between alcohol consumption and fatty liver disease needs a clear perspective, this study aims to explore the significant genes that are targeted by alcohol in the liver of mice.Methods: Gene expression profiles of mice livers fed with alcohol were retrieved from the Gene Expression Omnibus (GEO) database and compared with the control samples. Data are pre-evaluated with the GEO2R program, and the significant differentially expressed genes (DEGs) are analyzed via gene expression evaluations and regulatory network assessment. Results: Among the 25619 dysregulated genes, 78 significant DEGs were pointed out. Gene expression analysis showed that most extremely dysregulated genes are up-regulated and belong to the cytochrome P450 genes family. Finally, cytochrome P450 and glutathione S-transferase genes family, as well as hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 4, were introduced as the critical targeted genes.Conclusion: In conclusion, detoxification of xenobiotics, cellular metabolism and homeostasis, the pathogenesis of some liver diseases, synthesis of several prostaglandins and steroid hormones, and inflammation fibrosis in the liver are possibly associated with alcohol consumption.

Adaptive evolution of invasive fall armyworms to maize with potential involvement of Cytochrome P450 genes

BackgroundAn invasion occurs when introduced species establish and maintain stable populations in areas outside of their native habitat. Adaptive evolution has been proposed to contribute to this process. The fall armyworm (Spodoptera frugiperda) is one of the major pest insects infesting maize in both invaded and native areas. The invasion of this species was reported from West Africa in 2016, followed by spreading across the Old World. We tested adaptive evolution to maize using 56 native samples from the USA and 59 invasive samples from Senegal, based on genomic and transcriptomic analyses.ResultsPrincipal component analysis revealed that the Senegalese population originated from corn strain. Three genetic loci were identified as targets of selective sweeps in the Senegalese population. These loci include four Cytochrome P450 genes (CYP321B1, CYP321B3, CYP321B4, and CYP337B5), as well as 12 genes of which the function is unclear. Transcriptomic analysis showed an overexpression of CYP321B1 and CYP321B3 genes in sfC samples compared to sfR samples. Additionally, these two genes were overexpressed when corn strain samples were exposed to maize. In larval feeding assays, the Senegalese population exhibited higher survival rates than a Floridan population across all four tested maize varieties.ConclusionsThese results suggest that the analyzed Senegalese population experienced adaptive evolution involving loci containing CYP genes, potentially associated with an increase in the survival rates on maize. We argue that the invasive success of the fall armyworm is contributed by stabilizing selection to maize.

Characterization and Expression of the Cytochrome P450 Genes in Daphnia magna Exposed to Cerium Oxide Nanoparticles.

As cerium oxide nanoparticles (nCeO2) continue to infiltrate aquatic environments, the resulting health risks to exposed aquatic organisms are becoming evident. Cytochrome P450 (CYP) enzymes are integral to the detoxification processes in these species. Herein, we conducted a genomic analysis of CYPs in Daphnia magna, encompassing phylogenetic relationships, gene structure, and chromosomal localization. We identified twenty-six CYPs in D. magna, categorizing them into four clans and seven families, distributed across six chromosomes and one unanchored scaffold. The encoded CYP proteins varied in length from 99 to 585 amino acids, with molecular weights ranging from 11.6 kDa to 66.4 kDa. A quantitative real-time PCR analysis demonstrated a significant upregulation of CYP4C1.4, CYP4C1.5, CYP4C1.6, CYP4c3.3, and CYP4c3.6 in D. magna exposed to 150 mg/L nCeO2 for 24 h. The transcript levels of CYP4C1.3, CYP18a1, CYP4C1.1, and CYP4c3.9 were notably downregulated in D. magna exposed to 10 mg/L nCeO2 for 48 h. A further transcriptomic analysis identified differential expression patterns of eight CYP genes, including CYP4C1.3, in response to nCeO2 exposure. The differential regulation observed across most of the 26 CYPs highlights their potential role in xenobiotic detoxification in D. magna, thereby enhancing our understanding of CYP-mediated toxicological responses to metal nanoparticles in aquatic invertebrates.

Di(2-ethylhexyl) phthalate disrupts circadian rhythm associated with changes in metabolites and cytochrome P450 gene expression in Caenorhabditis elegans

The plasticizer di(2-ethylhexyl) phthalate (DEHP) is a widespread environmental pollutant due to its extensive use. While circadian rhythms are inherent in most living organisms, the detrimental effects of DEHP on circadian rhythm and the underlying mechanisms remain largely unknown. This study investigated the influence of early developmental exposure to DEHP on circadian rhythm and explored the possible relationship between circadian disruption and DEHP metabolism in the model organism Caenorhabditis elegans. We observed that DEHP disrupted circadian rhythm in a dose-dependent fashion. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis revealed that DEHP-induced circadian disruption accompanies with altered proportions of DEHP metabolites in C. elegans. RNA sequencing data demonstrated that DEHP-induced circadian rhythm disruption caused differential gene expression. Moreover, DEHP-induced circadian disruption coincided with attenuated inductions of DEHP-induced cytochrome P450 genes, cyp-35A2, cyp-35A3, and cyp-35A4. Notably, cyp-35A2 mRNA exhibited circadian rhythm with entrainment, but DEHP exposure disrupted this rhythm. Our findings suggest that DEHP exposure disrupts circadian rhythm, which is associated with changes in DEHP metabolites and cytochrome P450 gene expression in C. elegans. Given the ubiquitous nature of DEHP pollution and the prevalence of circadian rhythms in living organisms, this study implies a potential negative impact of DEHP on circadian rhythm and DEHP metabolism in organisms.

Assessing the effects of imidacloprid exposure on the microbiota of Binodoxys communis (Hymenoptera: Braconidae) and gene expression

Imidacloprid is a potent neonicotinoid insecticide that exerts control over cotton aphids. Binodoxys communis is the predominant parasitic threat to cotton aphids, serving as a crucial biological means to control cotton aphids. Imidacloprid has been Sprayed to control cotton aphids, but it also causes toxic effects on the natural enemies of cotton aphids, such as parasitic wasps, Binodoxys communis. However, the sublethal impact of imidacloprid on parasitic antagonists has remained unclear. This study sought to investigate the sublethal effects of imidacloprid on B. communis at the biological phenotype and transcriptional level, as well as the impact of imidacloprid on the microbial composition in the B. communis. Our research indicated that the sublethal dosages of imidacloprid imparted significant biologic adverse impacts on B. communis, including extended larval and pupal stages, as well as reduced parasitism and emergence rates. Following treatment with imidacloprid, transcriptomic analysis identified 1263 significantly differentially expressed genes. These differentially expressed genes were predominantly annotated in metabolic routes, and the annotated genes mainly belong to the fatty acid metabolism pathway, the carbon metabolism pathway, and protein processing in the endoplasmic reticulum pathway. 16S rDNA sequencing results showed significant changes in the composition of the microbial community in B. communis after exposure to imidacloprid. A total of 14 bacteria exhibiting the highest abundance in parasitic wasps were found, and the microbiota abundance of Akkermansia, Bacteroides, Streptomyces, Helicobacter, and Prevotellaceae UCG_001 was noticeably reduced, while Lactobacillus, Escherichia Shigella, Ligilactobacillus, Lachnospiraceae, Rikenellaceae RC9_gut_group, Erysipelatoclostridium, Acinetobacter, Enterococcus, and Aquabacterium were significantly elevated. By evaluating the enrichment pathways of microbial functions, it was found that the microbial functions with significant changes in proportion were mainly annotated to the carbon, fatty acid, and amino acid (aa) metabolic pathways, which was consistent with the transcriptome sequencing results. This finding mirrored transcriptome analysis results. According to transcriptomics analysis and 16S rDNA sequencing data, imidacloprid limits changes in metabolic pathways of B. communis, including fatty acid metabolism, impacting the development and parasitic competence of B. communis. Accordingly, the gene expression linked to detoxification and the cytochrome P450 gene family was significantly elevated at 1 h and significantly declined after three days.

A chromosome-level genome assembly of the legume pod borer, Maruca vitrata Fabricius (Lepidoptera: Crambidae)

Maruca vitrata, a significant pest of legumes, impacts food security in Asia and Africa. This study presents a high-quality genome assembly of M. vitrata, utilizing advanced sequencing technologies including Nanopore long-read, MGI short-read, and Hi-C. The genome, totaling 482.3 Mb with a contig N50 of 2.91 Mb, features 41.58% repetitive sequences and encompasses 13,320 protein-coding genes. We performed comparative genomic analyses to affirm the accuracy and completeness of the protein sequences assembled, ensuring the assembly’s integrity. Additionally, the annotation of 83 Cytochrome P450 (CYP) genes further confirms the comprehensive nature of the genome assembly and its annotations. This genome assembly not only deepens our understanding of M. vitrata biology but also supports the development of sustainable pest management strategies. This research highlights the importance of genomics in advancing sustainable agricultural solutions through innovative pest management approaches.

Comprehensive genomic analysis and expression profiling of the cytochrome P450 genes during abiotic stress and flavonoid biosynthesis in potato (Solanum tuberosum)

The research focused on the cytochrome P450 (CYP) superfamily, a prominent enzyme family involved in plant metabolism. A total of 253 StCYP genes from the potato genome were investigated and characterized through various methods, including phylogentic analysis, physical and chemical characterization, chromosome localization, gene structure and conserved protein domain classification, gene duplication occurrences, collinearity and expression pattern analysis. The 253 StCYPs were classified into seven clans and 33 families, distributed unevenly across 12 chromosomes. Collinearity analysis revealed 28 pairs of orthologous genes between potato StCYPs and Arabidopsis AtCYPs. Moreover, the expression of the StCYPs in various tissue parts of doubled haploid (DM) potatoes under abiotic stress and exogenous hormone treatment was investigated by using RNA-seq data from the PGSC database. It was discovered that one StCYP gene likely contributes to drought stress response through the ABA-dependent pathway. Furthermore, RNA-seq analysis of pigmented tuber flesh from three potato clones at three developmental stages enabled the identification of StCYPs potentially implicated in the flavonoid biosynthesis in potato tubers. In particular, StCYP705A-like was further validated for its potential role in this process. Employing Gfanno software in conjunction with RNA-seq data, seven StCYP genes (Two StC4H, three StF3′H, one StFNS Ⅱ and one StF3′5′H) were identified as flavonoid biosynthetic pathway genes in potato. Additionally, five StCYPs in CYP 71 clan demonstrated a strong association with flavonoid biosynthesis. These findings lay a groundwork for a more comprehensive understanding of the StCYP gene family and further exploration of the functions of StCYP genes in potato abiotic stress tolerance and flavonoids biosynthesis.

Renin and CYP P450 gene variations significantly associated with essential hypertension: A prospective pharmacogenomics study

ObjectiveThis study aims to investigate the association between Renin-angiotensin aldosterone system (RAAS) and Cytochrome P450 gene polymorphisms in hypertension patients of the South Indian population using pharmacogenomics profile. MethodsHypertension cases (N = 147) and control subjects (n = 150) were collected from Tamil Nadu, India. A case-control association study was conducted to assess the involvement of RAAS gene polymorphisms (REN rs397514691, REN rs544315427, REN rs567667202) and CYP gene polymorphisms (CYP2D6 rs754164689, CYP2D6 rs1058172, CYP3A4 rs765598920) in essential hypertensive patients. Genotyping was performed using the PCR-RFLP method, and significant results were validated through RT-PCR analysis. ResultsThe genotype and allele distribution of REN rs397514691 and rs544315427 variants significantly associated with hypertensive patients (Variant Allele Frequency (VAF) = 0.11; VAF = 0.27, respectively). CYP2D6 polymorphisms rs754164689 and rs1058172 variant alleles were significantly associated with female hypertensive patients, suggesting a potential risk allele for essential hypertension in the South Indian population. REN and CYP3A4 variants, highly connected in pharmacology action, were validated through RT-PCR amplification studies, providing new insights into their role in the development of hypertension. Association confirmation was achieved through multifactor dimensionality reduction analysis. ConclusionThe genes associated with specific variants, particularly REN and CYP2D6, may serve as potential markers for the early diagnosis of hypertension and as new drug targets, particularly in the female population.

ScRNA-seq reveals the spatiotemporal distribution of camptothecin pathway and transposon activity in Camptotheca acuminata shoot apexes and leaves.

Camptotheca acuminata Decne., a significant natural source of the anticancer drug camptothecin (CPT), synthesizes CPT through the monoterpene indole alkaloid (MIA) pathway. In this study, we used single-cell RNA sequencing (scRNA-seq) to generate datasets encompassing over 60,000 cells from C. acuminata shoot apexes and leaves. After cell clustering and annotation, we identified five major cell types in shoot apexes and four in leaves. Analysis of MIA pathway gene expression revealed that most of them exhibited heightened expression in proliferating cells (PCs) and vascular cells (VCs). In contrast to MIA biosynthesis in Catharanthus roseus, CPT biosynthesis in C. acuminata did not exhibit multicellular compartmentalization. Some putative genes encoding enzymes and transcription factors (TFs) related to the biosynthesis of CPT and its derivatives were identified through co-expression analysis. These include 19 cytochrome P450 genes, 8 O-methyltransferase (OMT) genes, and 62 TFs. Additionally, these pathway genes exhibited dynamic expression patterns during VC and EC development. Furthermore, by integrating gene and transposable element (TE) expression data, we constructed novel single-cell transcriptome atlases for C. acuminata. This approach significantly facilitated the identification of rare cell types, including peripheral zone cells (PZs). Some TE families displayed cell type specific, tissue specific, or developmental stage-specific expression patterns, suggesting crucial roles for these TEs in cell differentiation and development. Overall, this study not only provides novel insights into CPT biosynthesis and spatial-temporal TE expression characteristics in C. acuminata, but also serves as a valuable resource for further comprehensive investigations into the development and physiology of this species.

Genome-wide identification of Cytochrome P450 gene in Fall Armyworm (Spodoptera frugiperda) in response to insecticide resistance

The fall armyworm (FAW), Spodoptera frugiperda, poses a significant threat to maize, sorghum, and cotton crops, leading to substantial economic losses of up to 80 % in severe infestations. Despite its economic impact, the characterization of Cytochrome P450 (Cyp) genes, pivotal in regulatory metabolic processes, remains unexplored. This study identifies and investigates 33 Cyp-genes involved in critical metabolic pathways. These include fatty acid metabolism, resistance mechanisms, hormone regulation affecting moulting and developmental stages, response to phytotoxins, and detoxification of insecticides.Utilizing in-silico gene expression profiling, we pinpoint key Cyp-genes—Cyp306a1-like, Cyp9e2-like, Cyp6l1-like, Cyp12b1, and Cyp6B2-like—playing critical roles in conferring resistance against four commonly used insecticides: emamectin benzoate, tetrazolium, cyantraniliprole, and spinetoram. Our findings reveal that these identified genes are essential in detoxifying chemical treatments, thus contributing to the development of resistance in fall armyworm populations. In this investigation, key genes such as Cyp306a1-like, Cyp9e2-like, and Cyp6l1-like emerge as important regulatory genes. These genes play a role in resistance and detoxification when exposed to chemical stress. This in-silico study provides insights into the genetic mechanisms underlying resistance and regulatory genes in the fall armyworm, shedding light on potential targets for controlling the notorious agricultural pest. However, further comprehensive investigations are needed to elucidate the intricate resistance mechanisms governed by these key genes, paving the way for developing novel and effective strategies for fall armyworm management in agricultural ecosystems.

Metabolism of isodecyl diphenyl phosphate in rice and microbiome system: Differential metabolic pathways and underlying mechanisms

Isodecyl diphenyl phosphate (IDDP) is among the emerging aromatic organophosphate esters (aryl-OPEs) that pose risks to both human beings and other organisms. This study aims to investigate the translocation and biotransformation behavior of IDDP in rice and the rhizosphere microbiome through hydroponic exposure (the duration of hydroponic exposure was 10 days). The rhizosphere microbiome 9-FY was found to efficiently eliminate IDDP, thereby reducing its uptake in rice tissues and mitigating the negative impact of IDDP on rice growth. Furthermore, this study proposed the first-ever transformation pathways of IDDP, identifying hydrolysis, hydroxylation, methylation, methoxylation, carboxylation, and glucuronidation products. Notably, the methylation and glycosylation pathways were exclusively observed in rice, indicating that the transformation of IDDP in rice may be more complex than in microbiome 9-FY. Additionally, the presence of the product COOH-IDDP in rice suggested that there might be an exchange of degradation products between rice and rhizobacteria, implying their potential interaction. This finding highlights the significance of rhizobacteria's role which cannot be overlooked in the accumulation and transformation of organic pollutants in grain crops. The study revealed active members in 9-FY during IDDP degradation, and metagenomic analysis indicated that most of the active populations contained IDDP-degrading genes. Moreover, transcriptome sequencing showed that cytochrome P450, acid phosphatase, glucosyltransferase, and methyltransferases genes in rice were up-regulated, which was further confirmed by RT-qPCR. This provides insight into the intermediate products identified in rice, such as hydrolysis, hydroxylated, glycosylated, and methylated products. These results significantly contribute to our understanding of the translocation and transformation of organophosphate esters (OPEs) in plants and the rhizosphere microbiome, and reveal the fate of OPEs in rice and microbiome system to ensure the paddy yield and rice safety.

High Expression of AhR and Environmental Pollution as AhR-Linked Ligands Impact on Oncogenic Signaling Pathways in Western Patients with Gastric Cancer-A Pilot Study.

The vast majority of gastric cancer (GC) cases are adenocarcinomas including intestinal and diffuse GC. The incidence of diffuse GC, often associated with poor overall survival, has constantly increased in Western countries. Epidemiological studies have reported increased mortality from GC after occupational exposure to pro-carcinogens that are metabolically activated by cytochrome P450 enzymes through aryl hydrocarbon receptor (AhR). However, little is known about the role of AhR and environmental AhR ligands in diffuse GC as compared to intestinal GC in Western patients. In a cohort of 29, we demonstrated a significant increase in AhR protein and mRNA expression levels in GCs independently of their subtypes and clinical parameters. AhR and RHOA mRNA expression were correlated in diffuse GC. Further, our study aimed to characterize in GC how AhR and the AhR-related genes cytochrome P450 1A1 (CYP1A1) and P450 1B1 (CYP1B1) affect the mRNA expression of a panel of genes involved in cancer development and progression. In diffuse GC, CYP1A1 expression correlated with genes involved in IGF signaling, epithelial-mesenchymal transition (Vimentin), and migration (MMP2). Using the poorly differentiated KATO III epithelial cell line, two well-known AhR pollutant ligands, namely 2-3-7-8 tetrachlorodibenzo-p-dioxin (TCDD) and benzo[a]pyrene (BaP), strongly increased the expression of CYP1A1 and Interleukin1β (IL1B), and to a lesser extend UGT1, NQO1, and AhR Repressor (AhRR). Moreover, the increased expression of CYP1B1 was seen in diffuse GC, and IHC staining indicated that CYP1B1 is mainly expressed in stromal cells. TCDD treatment increased CYP1B1 expression in KATO III cells, although at lower levels as compared to CYP1A1. In intestinal GC, CYP1B1 expression is inversely correlated with several cancer-related genes such as IDO1, a gene involved in the early steps of tryptophan metabolism that contributes to the endogenous AhR ligand kynurenine expression. Altogether, our data provide evidence for a major role of AhR in GC, as an environmental xenobiotic receptor, through different mechanisms and pathways in diffuse and intestinal GC. Our results support the continued efforts to clarify the identity of exogenous AhR ligands in diffuse GC in order to define new therapeutic strategies.

De Novo Transcriptome Assembly of Cedar (Cedrela odorata L.) and Differential Gene Expression Involved in Herbivore Resistance.

Timber trees are targets of herbivorous attacks. The identification of genes associated with pest resistance can be accomplished through differential expression analysis using transcriptomes. We reported the de novo assembly of cedar (Cedrela odorata L.) transcriptome and the differential expression of genes involved in herbivore resistance. The assembly and annotation of the transcriptome were obtained using RNAseq from healthy cedar plants and those infested with Chrysobothris yucatanensis. A total of 325.6 million reads were obtained, and 127,031 (97.47%) sequences were successfully assembled. A total of 220 herbivory-related genes were detected, of which 170 genes were annotated using GO terms, and 161 genes with 245 functions were identified-165, 75, and 5 were molecular functions, biological processes, and cellular components, respectively. To protect against herbivorous infestation, trees produce toxins and volatile compounds which are modulated by signaling pathways and gene expression related to molecular functions and biological processes. The limited number of genes identified as cellular components suggests that there are minimal alterations in cellular structure in response to borer attack. The chitin recognition protein, jasmonate ZIM-domain (JAZ) motifs, and response regulator receiver domain were found to be overexpressed, whereas the terpene synthase, cytochrome P450, and protein kinase domain gene families were underexpressed. This is the first report of a cedar transcriptome focusing on genes that are overexpressed in healthy plants and underexpressed in infested plants. This method may be a viable option for identifying genes associated with herbivore resistance.

Harnessing Porphyrin Accumulation in Liver Cancer: Combining Genomic Data and Drug Targeting.

The liver, a pivotal organ in human metabolism, serves as a primary site for heme biosynthesis, alongside bone marrow. Maintaining precise control over heme production is paramount in healthy livers to meet high metabolic demands while averting potential toxicity from intermediate metabolites, notably protoporphyrin IX. Intriguingly, our recent research uncovers a disrupted heme biosynthesis process termed 'porphyrin overdrive' in cancers that fosters the accumulation of heme intermediates, potentially bolstering tumor survival. Here, we investigate heme and porphyrin metabolism in both healthy and oncogenic human livers, utilizing primary human liver transcriptomics and single-cell RNA sequencing (scRNAseq). Our investigations unveil robust gene expression patterns in heme biosynthesis in healthy livers, supporting electron transport chain (ETC) and cytochrome P450 function without intermediate accumulation. Conversely, liver cancers exhibit rewired heme biosynthesis and a massive downregulation of cytochrome P450 gene expression. Notably, despite diminished drug metabolism, gene expression analysis shows that heme supply to the ETC remains largely unaltered or even elevated with patient cancer progression, suggesting a metabolic priority shift. Liver cancers selectively accumulate intermediates, which are absent in normal tissues, implicating their role in disease advancement as inferred by expression analysis. Furthermore, our findings in genomics establish a link between the aberrant gene expression of porphyrin metabolism and inferior overall survival in aggressive cancers, indicating potential targets for clinical therapy development. We provide in vitro proof-of-concept data on targeting porphyrin overdrive with a drug synergy strategy.