Biology subjects

Singh, D. K.

Publications and source records attributed to Singh, D. K..

At least 19 recordsLinked to original sources

bioRxiv2026

Prenatal cannabis exposure affects human fetal neurodevelopment: anintegrated multi-omics study

Prenatal cannabis use is on the rise, and observational studies suggest that such use results in neurodevelopmental deficits in the offspring. Because observational studies can be confounded by unaccounted factors, we studied the neurodevelopmental consequences, at the molecular level, of prenatal cannabis use. We applied an integrated multi-omics approach, combining transcriptomics and global proteomics, to first trimester (T1) and second trimester (T2) human fetal brains from pregnancies with and without documented maternal cannabis exposure and no use of drugs of abuse. Prenatal cannabis exposure produced minimal molecular effects in female T1 fetal brains but induced pronounced system-level disruption in male T2 fetal brains. These disrupted pathways have molecular signatures linked to neurodevelopmental and neuropsychiatric disorders, including autism spectrum disorder, schizophrenia-related pathology, and disorders of cortical connectivity, raising significant concerns of prenatal cannabis use.

neuroscience↗

bioRxiv2026

Megalin (LRP2), prenatal betamethasone, and injury susceptibility in the developing kidney

Preterm infants undergo postnatal nephrogenesis and are often exposed to gentamicin (gent). Mothers at risk of preterm birth receive betamethasone (beta) to accelerate fetal lung development. Gent cytotoxicity occurs in proximal tubules (PT) after megalin (LRP2)-mediated endocytosis and accumulation. The objective of this study was to evaluate the impact of proximal tubular maturation, impacted by both age and prenatal beta, on injury susceptibility and nephron number in rats. Pups were given toxic gent dosing (100mg/kg) or saline intraperitoneal for 5 days during nephrogenesis (P0-4) or tubular maturation (P6-10). This was repeated with maternal exposure to beta to evaluate impact of beta on injury. Quantitative proteomics analysis revealed significantly higher levels of LRP2 at P10 as compared to P4, correlating with increased injury to gent exposure from P6-10 relative to P0-4. P10 pups exposed to prenatal beta had significantly more LRP2 protein relative to controls, which correlated to more injury after gent exposure at P6-10. Only those exposed to prenatal beta with P6-10 gent demonstrated ~50% nephron reduction. This study supports that tubular maturation is a critical period of vulnerability to gentamicin correlating to LRP2 protein abundance. Prenatal corticosteroids increase the severity of acute and chronic injury in this highest risk exposure group.

developmental biology↗

bioRxiv2026

Bronchus associated lymphoid tissue induced by an attenuated Mycobacterium tuberculosis vaccine prevents tuberculosis from heterologous TB challenge

Tuberculosis (TB) remains a leading cause of death from infectious disease worldwide, underscoring the urgent need for vaccines with greater and more consistent efficacy than Bacille Calmette-Guerin (BCG). We previously showed that mucosal vaccination with an isogenic Mycobacterium tuberculosis (Mtb) mutant lacking the stress-response transcription factor SigH ({Delta}sigH) prevents pulmonary TB in two macaque species. In the absence of SigH, Mtb is unable to effectively counter host oxidative stress. Vaccinated macaques were notably protected from disease, exhibiting an absence of granulomatous pathology together with the formation of lymphoid follicles and robust antigen-specific CD4+ and CD8+ T cell responses, identifying{Delta} sigH as a promising live-attenuated TB vaccine candidate. The{Delta} sigH mutant used in prior studies was generated in the Mtb CDC1551 background, a commonly used laboratory strain for challenge studies. Here, we evaluated whether{Delta} sigH-mediated protection extends to heterologous challenge with the more virulent Mtb Erdman strain. Mucosal{Delta} sigH vaccination conferred significant protection against heterologous challenge, markedly reducing pulmonary bacterial burden and TB-associated pathology. Longitudinal high-resolution PET/CT imaging demonstrated that aerosol{Delta} sigH vaccination induced robust inducible bronchus-associated lymphoid tissue (iBALT) responses in the lung. Unlike granulomas, these iBALT structures resolved over time while remaining associated with protection against subsequent Mtb challenge. Protection of highly susceptible rhesus macaques against virulent heterologous Mtb challenge following aerosol{Delta} sigH vaccination supports the further preclinical development of{Delta} sigH-based live-attenuated TB vaccines and highlights iBALT induction as a potential correlate and mechanistic driver of protective immunity against TB.

immunology↗

bioRxiv2026

Enforced ZFP281 expression delays breast cancer initiation and can provide lifelong protection against breast cancer metastasis

Breast cancer metastatic reactivation and its links to mammary development are largely unknown. Here, using conditional knockout and overexpression in normal and HER2+ mammary glands, we show that the dormancy regulator ZFP281 promotes branching and dissemination while suppressing growth, and its overexpression can even override HER2-driven cancer initiation. Notably, while ZFP281 does not limit HER2-driven early dissemination, it constrains DCC plasticity, confining cells to a dormant mesenchymal/hybrid-like state and effectively suppressing metastasis throughout the mouse lifespan. ZFP281 is induced by estrogen, progesterone, and glucocorticoid signaling, and RNA sequencing of early lesions revealed that it regulates glutathione metabolism and ferroptosis, potentially supporting fitness during dormancy, while repressing angiogenesis, Th17-like inflammation, innate immune genes, and pro-inflammatory programs that might otherwise trigger awakening. Integrating these findings with human data, we show that DCIS and IBC (invasive breast cancer) lesions that later relapse are selectively enriched for ZFP281-regulated M-like and dormancy signatures and, after pregnancy, depleted for a ZFP281-induced stress-autophagy module, indicating that erosion or imbalance of these programs marks lesions that seed DCCs with higher reactivation potential. We propose that ZFP281 acts as a hormone-regulated dormancy gatekeeper that uncouples dissemination from growth, enforcing a metabolically fit, angiogenesis-low, immune-evasive dormant state in breast DCCs, thereby shaping the timing of metastatic relapse and potentially exploitable for durable prevention of metastasis. STATEMENT OF SIGNIFICANCEZFP281, a hormone-regulated dormancy gatekeeper, uncouples dissemination from growth and constrains DCCs into long-term arrest, defining human gene signatures that distinguish dormancy-prone from awakening-prone lesions and predict breast cancer relapse dynamics.

cancer biology↗

bioRxiv2026

A New Fluorogenic Substrate for CYP1A2 and Its Application in Studying the Effects of Alcohol Exposure on Liver Drug Metabolism

Aiming to develop a high-throughput fluorimetric assay for the activity CYP1A2, we introduced 6-Methoxy-2-naphthoic acid (MONA) as a new fluorogenic substrate for this important metabolizer of antidepressants and psychotropic drugs in human liver. We demonstrated that oxidative demethylation of MONA by liver microsomes results in a red shift and a substantial increase in fluorescence. This effect, which is exceptionally well pronounced at alkaline pH, allowed us to develop a sensitive and robust high-throughput assay of MONA metabolism. Probing the activity of 15 individual recombinant human P450 enzymes, we found that only two P450 species exhibited activity in MONA demethylation: CYP1A2 (kcat=11.9{+/-}2.2 min-1, KM=578{+/-}106 {micro}M) and CYP2A6 (kcat=0.48{+/-}0.07 min-1, KM=54{+/-}15 {micro}M). Since the KM values of the two enzymes are well resolved and the turnover rate observed with CYP2A6 is much lower than that of CYP1A2, this new fluorogenic substrate is useful as a specific probe for CYP1A2 activity in HLM. Importantly, MONA is not metabolized by CYP1A1 and CYP2C19, which distinguishes it from all known CYP1A2 fluorogenic substrates. We then used MONA to investigate the effects of chronic alcohol exposure on CYP1A2 activity using a series of 23 proteomically characterized individual HLM preparations from donors with various levels of alcohol consumption. The substrate saturation profiles (SSP) acquired with these preparations were subjected to global kinetic analysis by approximating them with combinations of two Michaelis-Menten equations with globally optimized KM values of 11 and 553 {micro}M. The amplitudes (Vmax values) of both components showed a pronounced increase with increasing alcohol exposure of the liver donors. The Vmax of the minor high-affinity component was best correlated with the abundance of alcohol-inducible CYP2E1 enzyme. The correlation was further improved by combining it with the abundances of CYP2A6 and CPR. This finding suggests that this minor component reflects the activity of CYP2A6 in the complex with alcohol-inducible CYP2E1 protein. In contrast, the Vmax of the predominant CYP1A2-catalyzed low-affinity component revealed a pronounced correlation with the abundances of CYP1A2 and NADPH cytochrome P450 reductase (CPR). These results suggest a considerable increase in the rate of metabolism of drug substrates of CYP1A2 by chronic alcohol exposure that takes place despite an alcohol-induced decrease in CYP1A2 expression.

biochemistry↗

bioRxiv2026

The role of CYP3A-CYP2E1 interactions in activation of CYP3A enzymes by chronic alcohol exposure

Aiming to examine the effect of chronic alcohol exposure on the activity of CYP3A enzymes in human liver, we studied the metabolism of two CYP3A-specific substrates, 7-benzyloxyquinoline (7-BQ) and ivermectin, in 23 preparations of human liver microsomes (HLM) obtained from donors with documented alcohol exposure, graded from non-drinkers to heavy alcoholics. All HLM samples were characterized for the composition of the cytochrome P450 pool and the abundances of other drug-metabolizing and endoplasmic reticulum-stress-related enzymes by global proteomics. Our studies revealed a striking increase in the activities of CYP3A enzymes caused by chronic alcohol exposure. This effect is not associated with CYP3A enzyme levels, which do not correlate with alcohol exposure. Instead, the rates of 7-BQ and ivermectin metabolism correlate with the content of alcohol-inducible CYP2E1. However, this enzyme does not metabolize ivermectin, and its activity with 7-BQ is negligible. These results suggest that the observed acceleration of the elimination of drugs metabolized by CYP3A enzymes by alcohol exposure is due to functional effects of the interaction between CYP3A and CYP2E1. To elucidate the potential mechanism of this effect, we studied the formation of CYP2E1-CYP3A4 complexes in CYP3A4-containing Supersomes with co-incorporated CYP2E1 using tag-transfer chemical crosslinking mass spectrometry (CX-MS). These experiments confirmed physical interactions between the proteins and allowed the identification of CYP3A4 residues at the sites of contact. This information was used to build structural models of the CYP2E1-CYP3A4 complex and to propose possible mechanisms for the observed effects.

biochemistry↗

bioRxiv2026

A crucial role for PIH1D1 in modulating p53 stability via the R2TP complex

The R2TP is a multimeric protein complex consists of RUVBL1, RUVBL2, PIH1D1, and RPAP3, and it is known to functions as a specialized co-chaperone. We hypothesize that PIH1D1 recognizes p53 and stabilizes it via R2TP complex. Upon successful completion of this study, innovative mechanism has been found for the interaction and stabilization of p53 and hence govern the cell cycle. Upon interaction between p53 and PIH1D1 protein, p53 is stabilized by PIH1D1 protein, without affecting its C-terminal domain. We have also observed that p53 protein levels were affected after the alteration in expression levels of PIH1D1. Based on the finding, we suggest that the R2TP complex stabilizes and regulates P53. Therefore, this novel method will work as a flashpoint to restore the function of p53 in cancer cells, controlling cancer and cell cycle progression.

biochemistry↗

bioRxiv2026

Reprogramming BCMA-Targeted CAR-T Cells through γ-Secretase Modulation Blocks Antigen Shedding and Extends CAR-T Longevity

B-cell maturation antigen (BCMA) shedding by {gamma}-secretase generates soluble BCMA (sBCMA), which diminishes membrane antigen density, and limits the durability of BCMA-directed immunotherapies in multiple myeloma (MM). Here, using AI-driven diffusion modeling, we identify peptide inhibitors that selectively block {gamma}-secretase-mediated BCMA cleavage, stabilizing membrane-bound BCMA (mBCMA) without compromising cellular viability. The lead peptide, P5, suppresses sBCMA and restores mBCMA in vitro and in xenograft models. To create sustained, cell-intrinsic inhibition, we engineered Shedding Deterrent Locked-in (SHEDLOCK) CAR-T cells that locally secrete {gamma}-secretase-modulatory peptides. SHEDLOCK-1 CAR-T cells secreting P5 exhibits enhanced cytotoxicity and persistence relative to conventional CAR-T cells. Building on this, SHEDLOCK-2 CAR-T cells were generated, which secrete a modified, naturally derived peptide (nxP) that directly engages the {gamma}-secretase catalytic site, concurrently preventing BCMA shedding, and surprisingly enhancing CAR-T cell longevity by preserving telomere integrity and metabolic fitness. In MM xenograft and patient-derived models, SHEDLOCK-2 CAR-T cells demonstrate durable antitumor activity with a favorable safety profile. Together, these findings establish SHEDLOCK as a next-generation CAR-T platform and provide a strong preclinical foundation for Phase I clinical evaluation. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=128 SRC="FIGDIR/small/700575v1_ufig1.gif" ALT="Figure 1"> View larger version (69K): org.highwire.dtl.DTLVardef@3cd38aorg.highwire.dtl.DTLVardef@164167borg.highwire.dtl.DTLVardef@1ffed21org.highwire.dtl.DTLVardef@1294d06_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

CDM1 is required for meiotic progression and genome integrity during male meiosis in Arabidopsis

Microsporogenesis involves the integration of meiosis with the developmental program leading to formation of microspores from meiocytes. The CALLOSE DEFICIENT MICROSPORE 1 (CDM1) gene of Arabidopsis has been previously characterized as being required for callose metabolism and its loss results in defects in microspore wall development, degeneration of meiotic products, and male sterility. We report here that CDM1 is required for normal meiosis I progression, meiotic chromosome organization, and maintenance of DNA integrity. CDM1 is part of the ATM dependent DNA damage response in dividing vegetative tissues. The cdm1 mutant shows defects in meiotic chromosome condensation, arrest at metaphase I, susceptibility to chromosome breakage in rDNA regions, defects in positioning of the products of meiosis, and increased expression of recombination related genes. However, fidelity of chromosome segregation is not affected. Furthermore, the meiotic phenotype of cdm1 is independent of SPO11 induced meiotic double strand breaks. CDM1 protein displays granular localization in meiosis throughout the cytoplasm that resembles that of mRNP granules. The results show that CDM1 is required for maintenance of proper chromosome organization and DNA integrity in the course of male meiosis. The chromosomal defects in cdm1 may originate from regions of defective or incomplete replication. HighlightCDM1 expression is DNA damage inducible in Arabidopsis mitotic cells. CDM1 is required for genome integrity in male meiosis independent of SPO11-induced DNA breaks, suggesting a role in regulation of premeiotic replication repair.

plant biology↗

bioRxiv2025

Unlocking meiotic crossovers near plant centromeres

Crossovers (COs) ensure proper chromosome segregation during meiosis and generate genetic diversity. COs are non-uniformly distributed along chromosomes and almost universally suppressed in centromere-proximal regions, notably creating a significant bottleneck for plant breeding. The mechanism of this CO suppression is elusive, but chromatin state is a contributing factor. Here, we identify three factors that actively limit proximal CO in Arabidopsis, the cohesion establishment factor CTF18, the centromeric cohesin protector SGO2, and the deSUMOylase SPF2. The mutation of these factors allows both the formation of CO in centromere-proximal region where they were completely absent in the wild-type, and enhance their frequency where they were rare. COs can be further increased by combining these mutations together or with mutation in the DNA methylase CMT3, suggesting that multiple mechanism prevent proximal CO in parallel. The identification of the very conserved CTF18, SGO2 and SPF2 as suppressors of centromere-proximal CO highlights the importance of cohesin turnover in this process and opens up new possibilities for plant breeding.

genetics↗

bioRxiv2025

Monopolar orientation of kinetochores at meiosis is enforced by COHESINS and their regulators, CENP-C, and the deSUMOylase SPF2

The first division of meiosis is unique in its capacity to halve the ploidy of the future gametes. To this end, one key innovation compared to mitosis is the monopolar orientation of the pairs of sister kinetochores required for the proper separation of homologs at meiosis I. How monopolar orientation is imposed is unclear and seems to vary in eukaryotes. Here we performed a forward genetic screen in Arabidopsis thaliana, specifically designed to identify the molecular components imposing monopolar orientation, based on mutants ability to restore fertility in spo11 osd1 haploid plants. We show that monopolar orientation involves all four cohesin subunits (REC8, SCC3, SMC1, SMC3), the cohesion establishment factors CTF18 and DCC1, and the cohesin protectors SGO1/2 and PANS1, the inner kinetochore protein CENP-C, and the desumoylase SPF2. The mutants show bipolar orientation of achiasmatic chromosomes, but monopolar orientation is maintained in the presence of crossovers despite splitting of sister kinetochores at metaphase I and reduced levels of cohesin. Taken together, the findings demonstrate that cohesion establishment and protection, kinetochore function, and deSUMOylation, together with crossovers, enforce monopolar orientation in plants and support a cohesion-driven model of kinetochore orientation at meiosis I that is conserved across kingdoms.

cell biology↗

bioRxiv2025

From discovery to translation: Endogenous substrates of OAT1 and OAT3 as clinical biomarkers for renal secretory function

The recent ICH M12 guidance on Drug Interaction Studies encourages the use of alternate approaches for predicting drug-drug interaction (DDI) potential of new chemical entities. One approach involves biomarkers, which are endogenous substrates of drug metabolizing enzymes and transporters (DMET) and can be used to assess the inhibitory potential of new chemical entities during Phase 1 clinical studies. Thus, biomarkers could potentially eliminate the need for dedicated DDI studies with exogenous probe substrates. Metabolomics, in conjunction with in vitro and/or in vivo preclinical models or clinical studies, can be used for biomarker discovery. We developed and applied a novel metabolomics-based DMET biomarker discovery (MDBD) approach to identify and qualify biomarkers of renal organic anion transporter 1 (OAT1) and OAT3. Untargeted metabolomics of pooled plasma and urine samples from a pharmacokinetic DDI study using the OAT1/3 inhibitor, probenecid, yielded 153 features identified as putative OAT1/3 biomarkers. Subsequently, in vitro transporter uptake assays using processed urine samples confirmed 57 of these features as OAT1 and/or OAT3 substrates. Finally, 23 features were clinically validated as OAT1/3 biomarkers through a detailed pharmacokinetic analysis (0-24 h) of plasma and urine samples. These biomarkers, either alone or as part of a panel, can predict OAT1/3-mediated DDIs and interindividual variability in the renal secretory clearance of organic anions across different populations, thereby enabling translational utility in clinical settings. The novel MDBD approach can be extended to discover biomarkers of other transporters and enzymes. SUMMARYUsing clinical and mechanistic in vitro approaches, 23 endogenous substrates of OAT1/3 were identified as potential clinical biomarkers of renal secretary elimination of organic anions.

pharmacology and toxicology↗

bioRxiv2024

Quantitative contributions of hepatic and renal organic cation transporters to the clinical pharmacokinetic cimetidine-metformin interaction

The widely prescribed oral anti-diabetic drug metformin is eliminated unchanged in the urine primarily through active tubular secretion. This process is mediated by organic cation transporter 2 (OCT2), an uptake transporter expressed on the basolateral membrane of renal proximal tubule cells. Metformin uptake into the liver, the site of action, is mediated by OCT1, which is expressed on the sinusoidal membrane of hepatocytes. Sixteen healthy adults participated in a clinical pharmacokinetic drug-drug interaction study in which they were orally administered metformin (50 mg) as a dual OCT1/2 substrate alone (baseline) and with cimetidine (400 mg) as an OCT inhibitor. Relative to baseline, metformin systemic plasma exposure increased by 24% (p<0.05) in the presence of cimetidine, which was accompanied by a disproportional decrease (8%) in metformin renal clearance (p=0.005). Genetic variants of OCT1 and OCT2 moderately impacted the significance and magnitude of the interaction. Collectively, we hypothesized that the cimetidine-metformin interaction involves inhibition of hepatic OCT1 as well as renal OCT2. We tested this hypothesis by developing a physiologically based pharmacokinetic (PBPK) model and assessing potential OCT biomarkers in plasma and urine to gain mechanistic insight into the transporters involved in this interaction. The PBPK model predicted that cimetidine primarily inhibits hepatic OCT1 and, to a lesser extent, renal OCT2. The unchanged renal clearance of potential OCT2 biomarkers following cimetidine exposure supports a minimal role for renal OCT2 in this interaction.

pharmacology and toxicology↗

bioRxiv2024

Sodium Chloride Promotes the Growth of Bacterial Soil Isolate and Antimicrobial Activity of Polymixin B

The decomposition of organic matter in the soil, soil salinity, and soil acidity are influenced by soil microbiology, which also controls the recycling and processing of nutrients in the soil. These factors affect soil fertility and ecological stability. This manuscript is focused on the isolation of seven gram-negative bacteria found in the agricultural soil of The Neotia University campus, West Bengal, India. These isolates have been found to be mesophilic based on their study of their growth profiles, which revealed that under the same incubation conditions, the isolates displayed rising development patterns between 24 and 120 hours. The presence of sodium and potassium chloride modulates the growth and development of bacterial strains (DNI1, DNI2, DNI3, DNI4, DNI5, DNI6, and DNI7) during laboratory set up. The sodium and potassium chloride composition of culture media that effectively regulates the development of bacterial isolates has been determined using the combinational method of salt treatment. The ideal physical factor required for the growth and development of microorganisms has been demonstrated by the pH and temperature titration during this study. The powerful antibiotics known as polymyxin B, which are nonribosomal lipopeptides produced by Paenibacillus polymyxa, are especially effective against Gram-negative bacteria. Because multidrug-resistant Gram-negative bacteria have few other choices for treating infections, the use of polymyxins in clinical settings has increased despite their toxicity in the past. This study offers an update on the most current findings about the bioactivity of soil isolates and their significant relationships to temperature, pH, salt, and polymixin B sensitivity. The toxicity impact may be reduced by enhancing polymixin Bs antibacterial activity with salt treatment in clinical research.

microbiology↗

bioRxiv2024

Non-additivity of the functional properties of individual P450 species and its manifestation in the effects of alcohol consumption on the metabolism of ketamine and amitriptyline

To explore functional interconnections between multiple P450 enzymes and their manifestation in alcohol-induced changes in drug metabolism, we implemented a high-throughput study of correlations between the composition of the P450 pool and the substrate saturation profiles (SSP) of amitriptyline and ketamine in a series of 23 individual human liver microsomes preparations from donors with a known history of alcohol consumption. The SSPs were approximated with linear combinations of three Michaelis-Menten equations with globally optimized KM (substrate affinity) values. This analysis revealed a strong correlation between the rate of ketamine metabolism and alcohol exposure. For both substrates, alcohol consumption caused a significant increase in the role of the low-affinity enzymes. The amplitudes of the kinetic components and the total rate were further analyzed for correlations with the abundance of 11 major P450 enzymes assessed by global proteomics. The maximal rate of metabolism of both substrates correlated with the abundance of CYP3A4, their predicted principal metabolizer. However, except for CYP2D6 and CYP2E1, responsible for the low-affinity metabolism of ketamine and amitriptyline, respectively, none of the other potent metabolizers of the drugs revealed a positive correlation. Instead, in the case of ketamine, we observed negative correlations with the abundances of CYP1A2, CYP2C9, and CYP3A5. For amitriptyline, the data suggest inhibitory effects of CYP1A2 and CYP2A6. Our results demonstrate the importance of functional interactions between multiple P450 species and their decisive role in the effects of alcohol exposure on drug metabolism.

biochemistry↗

bioRxiv2024

Effects of alcohol consumption and tobacco smoking on the composition of the ensemble of drug metabolizing enzymes and transporters in human liver

We examined the effect of alcohol consumption and smoking on the abundance of drug-metabolizing enzymes and transporters (DMET) in human liver microsomes (HLM) isolated from liver tissues of 94 donors. Global proteomics analysis was performed and DMET protein levels were analyzed in relation to alcohol consumption levels, smoking history, and sex using non-parametric tests (p-value [≤] 0.05; cutoff of 1.25-fold change, FC). The examination of the alcohol-induced changes was further enforced by correlational analysis, where we used arbitrary alcohol consumption grade (ACG) scaling from 0 to 4 to establish a set of protein markers. We elaborated a provisional index of alcohol exposure (PIAE) based on a combination of relative abundances of four proteins (ER chaperone HSPA5, protein disulfide isomerases PDIA3 and P4HB, and cocaine esterase CES2) best correlating with ACG. The PIAE index was then used to find its correlations with the abundances of DMET proteins. Our results demonstrate considerable alcohol-induced changes in composition of the pool of cytochrome P450 enzymes in HLM. We observed significantly increased abundances of CYP2E1, CYP2B6, CYP2J2, and NADPH-cytochrome P450 reductase. In contrast, CYP1A2, CYP2C8, CYP2C9, CYP4A11, and cytochrome b5 protein levels were downregulated. Significant alteration in abundances of UDP-glucuronosyltransferase (UGT) were also detected, comprising of elevated UGT1A6, UGT1A9, and UGT2A1, and reduced UGT1A3, UGT1A4, UGT2B7, UGT2B10, and UGT2B15 levels. Important alcohol-induced changes were also observed in the expression of non-CYP and non-UGT DMET. Additionally, tobacco smoke was associated with elevated CYP1A2, UGT1A6, UGT2A1, and UGT2B4 and decreased FMO3, FMO4, and FMO5 levels.

pharmacology and toxicology↗

bioRxiv2023

The gut commensal Blautia maintains colonic mucus function under low fiber consumption through short-chain fatty acid-mediated activation of Ffar2

Beneficial gut bacteria are indispensable for developing colonic mucus and fully establishing its protective function against intestinal microorganisms. Low-fiber diet consumption alters the gut bacterial configuration and disturbs this microbe-mucus interaction, but the specific bacteria and microbial metabolites responsible for maintaining mucus function remain poorly understood. By using human-to-mouse microbiota transplantation and ex vivo analysis of colonic mucus function, our proof-of-concept study demonstrates that individuals who increase their daily dietary fiber intake can improve the capacity of their gut microbiota to prevent diet-mediated mucus defects. Mucus growth, a critical feature of intact colonic mucus, correlated with the abundance of the gut commensal Blautia, and supplementation of Blautia coccoides to mice confirmed its mucus-stimulating capacity. Mechanistically, B. coccoides stimulated mucus growth through the production of the short-chain fatty acids propionate and acetate via activation of the short-chain fatty acid receptor Ffar2, which could serve as a new target to restore mucus growth during mucus-associated lifestyle diseases.

microbiology↗

bioRxiv2023

Archaeal origin translation proofreader imparts multialdehyde stress tolerance to land plants

Aldehydes, being an integral part of carbon metabolism, energy generation and signalling pathways, are ingrained in plant physiology. Land plants have developed intricate metabolic pathways which involve production of reactive aldehydes and its detoxification to survive harsh terrestrial environments. Here, we show that physiologically produced aldehydes i.e., formaldehyde and methylglyoxal in addition to acetaldehyde, generate adducts with aminoacyl-tRNAs, a substrate for protein synthesis. Plants are unique in possessing two distinct chiral proofreading systems, D-aminoacyl-tRNA deacylase1 (DTD1) and DTD2, of bacterial and archaeal origins, respectively. Extensive biochemical analysis revealed that only archaeal DTD2 can remove the stable D-aminoacyl adducts on tRNA thereby shielding archaea and plants from these system-generated aldehydes. Using Arabidopsis as a model system, we have shown that the loss of DTD2 gene renders plants susceptible to these toxic aldehydes as they generate stable alkyl modification on D-aminoacyl-tRNAs, which are recycled only by DTD2. Bioinformatic analysis identifies the expansion of aldehyde metabolising repertoire in land plant ancestors which strongly correlates with the recruitment of archaeal DTD2. Finally, we demonstrate that the overexpression of DTD2 offers better protection against aldehydes than in wild-type Arabidopsis highlighting its role as a multi-aldehyde detoxifier that can be explored as a transgenic crop development strategy.

plant biology↗