Biology subjects

Wu, T.-Y.

Publications and source records attributed to Wu, T.-Y..

14 recordsLinked to original sources

bioRxiv2025

Multigram-scale stereoselective synthesis of neurosteroid isomers by gut microbial isolates using plant biomass-derived medium

Neurosteroids are vital therapeutics for mood disorders, with FDA-approved allopregnanolone (Zulresso) for postpartum depression and zuranolone for major depressive disorder representing breakthrough treatments. However, current production methods rely on costly animal-derived sources or non-stereoselective chemical synthesis that require extensive chiral purification steps. Here, we present a sustainable microbial platform utilizing gut bacteria and a completely plant-based medium for stereoselective neurosteroid biosynthesis. Through bioinformatics- and structural biology-guided screening of more than 3000 bacterial isolates, we identified three anaerobic gut strains exhibiting distinct stereospecificities: Holdemania filiformis produces isopregnanolone (3{beta}-hydroxy-5-pregnan-20-one), Clostridium innocuum generates epipregnanolone (3{beta}-hydroxy-5{beta}-pregnan-20-one), and Hungatella effluvii synthesizes pregnanolone (3-hydroxy-5{beta}-pregnan-20-one). We developed Molasses-Okara Medium (MOM), a fully plant-derived composite medium combining sugarcane molasses with enzymatically hydrolyzed okara devoid of animal-derived components. In multigram batch whole-cell biotransformation trials using MOM, we achieved >95% progesterone conversion into target neurosteroid isomers. The inherent stereoselectivity of these whole-cell biotransformations bypasses downstream chiral chromatographic separation, enabling pharmaceutical-grade product recovery through a simple open-column purification. Compared to using peptone-yeast-glucose media for whole-cell biotransformation, MOM reduced production costs by 90% and carbon footprint by 95% that embodies sustainable bioeconomy principles in pharmaceutical biotechnology. Technology Readiness BoxWe argue that this gut microbiota-derived neurosteroid bioproduction technology has reached a Technology Readiness Level (TRL) of 4, having been validated in laboratory environments with the demonstrated multigram-scale synthesis of high-purity neurosteroids. The platform integrates stereoselective bacterial isolates (Holdemania filiformis, Clostridium innocuum, and Hungatella effluvii) with a sustainable plant-based fermentation medium (molasses-okara medium), achieving >90% progesterone conversion efficiency, >99.9% stereochemical purity, and the successful production of 0.7-0.9 g of neurosteroids per gram of progesterone across multiple 1 L fed-batch fermentations. Compared with conventional chemical synthesis approaches that require expensive chiral catalysts and multi-step purification, this microbial platform offers inherent stereoselectivity while eliminating animal-derived media components. Despite these advantages, several challenges remain for industrial implementation, including scale-up validation beyond laboratory conditions, optimization of anaerobic bioprocess control at pilot scale, and ensuring consistent performance under variable industrial feedstock conditions. Addressing these issues will require pilot-scale demonstration (10-50 L bioreactors), process robustness validation, and supply chain development for plant-based feedstocks. Regulatory pathway development will also be essential for pharmaceutical applications, particularly establishing precedents for gut microbiota-derived therapeutic compounds under existing cGMP frameworks HighlightsO_LIIdentification of gut bacteria for stereoselective synthesis of neurosteroid isomers (isopregnanolone, epipregnanolone, pregnanolone) with >99% chiral purity C_LIO_LISustainable plant biomass-based medium replacing animal-derived components for whole-cell progesterone biotransformation C_LIO_LIMulti-gram scale production of progestogenic neurosteroids and one-step-open-column purification bypassing chiral chromatographic separation C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/671209v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@11147b0org.highwire.dtl.DTLVardef@1799d64org.highwire.dtl.DTLVardef@14c33deorg.highwire.dtl.DTLVardef@1e14e21_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2025

TISCalling: Leveraging Machine Learning to Identify Translational Initiation Sites in Plants and Viruses

The recognition of translational initiation sites (TISs) offers complementary insights into identifying genes encoding novel proteins or small peptides. Conventional computational methods primarily identify Ribo-seq-supported TISs and lack the capacity of systematical and global identification of TIS, especially for non-AUG sites in plants. Additionally, these methods are often unsuitable for evaluating the importance of mRNA sequence features for TIS determination. In this study, we present TISCalling, a robust framework that combines machine learning (ML) models and statistical analysis to identify and rank novel TISs across eukaryotes. TISCalling generalized and ranks important features common to multiple plant and mammalian species while identifying kingdom-specific features such as mRNA secondary structures and G-contents. Furthermore, TISCalling achieved high predictive power for identifying novel viral TISs. Importantly, TISCalling provides prediction scores for putative TIS along plant transcripts, enabling prioritization of those of interest for further validation. We offer TISCalling as a command-line-based package [https://github.com/yenmr/TIScalling], capable of generating prediction models and identifying key sequence features. Additionally, we provide web tools [https://predict.southerngenomics.org/TIScalling] for visualizing pre-computed potential TISs, making it accessible to users without programming experience. The TISCalling framework offers a sequence-aware and interpretable approach for decoding genome sequences and exploring functional proteins in plants and viruses.

bioinformatics↗

bioRxiv2025

Evolutionarily Conserved Heat-Induced Chromatin Dynamics Drive Heat Stress Responses in Plants

Eukaryotic organisms remodel chromatin landscapes to regulate gene expression in response to environmental stress. In plants, heat stress (HS) induces widespread chromatin changes, yet the role of heat-responsive Heat Shock Transcription Factors (HSFs) in chromatin remodeling and their evolutionary conservation remains unclear. Using chromatin accessibility profiling and transcriptomics in Marchantia polymorpha hsf mutants, we identify HSFA1 as a key determinant in positioning cis-regulatory elements (CREs) for HS-induced gene activation, a mechanism conserved across land plants, mice, and human cells. By integrating gene regulatory network modeling, we identify parallel transcription factor subnetworks, with MpWRKY10 and MpABI5B acting as indirect regulators of HS responses via phenylpropanoid pathways and general stress signaling. We further explore crosstalk between HS and abscisic acid (ABA) signaling, showing that while ABA modulates gene expression in an HSFA1-dependent manner, it does not induce broad chromatin remodeling, positioning it as a downstream regulator rather than a primary determinant of chromatin dynamics. To extend these insights, we develop a cross-species and cross-condition machine learning framework that accurately predicts chromatin accessibility and gene expression, demonstrating a conserved regulatory logic of stress-responsive chromatin and transcription dynamics. Our findings provide a conceptual framework for understanding how TFs coordinate chromatin architecture to drive stress adaptation in plants and potentially other eukaryotes.

plant biology↗

bioRxiv2024

Multi-Omics Mapping of Gut Microbiota's Role in Progesterone Metabolism

5-neurosteroids such as allopregnanolone and isopregnanolone play critical roles in neurological health and mood regulation, yet current therapeutic production faces significant limitations. We demonstrate that specific gut microbes represent a previously unrecognized source of bioavailable 5-neurosteroids that reach the central nervous system via the gut-brain axis. Through integrated metabolomic and genomic analyses of progesterone-amended fecal cultures, we identified Holdemania as a major producer of isopregnanolone via microbial steroid 5-reductase (BaiJ type 2) and 3{beta}-hydroxysteroid dehydrogenase/reductase. Phylogenetic analysis revealed that BaiJ-like sequences cluster predominantly within Firmicutes, with Holdemania species forming a distinct clade. In female C57BL/6 mice administered progesterone and H. filiformis, 5-neurosteroids including isopregnanolone predominated in gut tissues while allopregnanolone was the major hepatic neurosteroid. Critically, using stable isotope tracing with [3,4-{superscript 1}3C2]progesterone, we detected {superscript 1}3C-labeled isopregnanolone in brain tissue, providing direct evidence for gut-to-brain transport of microbiota-derived neurosteroids. High-fat diet significantly enhanced brain 5-neurosteroid accumulation. Global meta-analysis reveals reduced Holdemania abundance in PCOS patients (n = 346) compared to healthy women (n = 321). These findings identify gut microbiota as pharmacologically relevant neurosteroid producers and position H. filiformis as a promising probiotic candidate for enhancing endogenous neurosteroid production to treat mood disorders and other neuropsychiatric conditions. HighlightsO_LIHoldemania was identified as a major producer of 5-neurosteroids, particularly isopregnanolone, in the intestinal tract C_LIO_LIHoldemania 5-reductase (BaiJ type 2) belongs to a distinct phylogenetic clade compared to characterized Clostridium BaiJ (type 1) C_LIO_LI5-neurosteroids occurred predominantly in the cecum of female mice administered H. filiformis, progesterone, and high-fat diet C_LIO_LI{superscript 1}3C-labeled 5-neurosteroids were detected in brain tissue of female mice orally administered [3,4-{superscript 1}3C2]progesterone and H. filiformis, demonstrating gut-to-brain transport C_LIO_LIGut microbes such as H. filiformis represent promising probiotic candidates for enhancing 5-neurosteroid production and circulation via the gut-brain axis C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=146 HEIGHT=200 SRC="FIGDIR/small/628284v3_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@1b85caaorg.highwire.dtl.DTLVardef@cbb352org.highwire.dtl.DTLVardef@169f7fcorg.highwire.dtl.DTLVardef@17c638_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2024

Aromatase-independent estrogenesis: Wood-Ljungdahl pathway likely contributed to the emergence of estrogens in the biosphere

Androgen and estrogen, key sex hormones, were long thought to be exclusively produced by vertebrates. The O2-dependent aromatase that converts androgen to estrogen (estrogenesis) has never been identified in any prokaryotes. Here, we report the discovery of anaerobic estrogenesis in a Peptococcaceae bacterium (strain TUW77) isolated from the gut of the great blue-spotted mudskipper (Boleophthalmus pectinirostris). This strain exhibits unprecedented testosterone fermentation pathways, transforming testosterone into estrogens and androstanediol under anaerobic conditions. Physiological experiments revealed that strain TUW77 grows exclusively on testosterone, utilizing the androgenic C-19 methyl group as both the carbon source and electron donor. The genomic analysis identified three copies of a polycistronic gene cluster, abeABC (anaerobic bacterial estrogenesis), encoding components of a classic cobalamin-dependent methyltransferase system. These genes, highly expressed under testosterone-fed conditions, show up to 57% protein identity to the characterized EmtAB from denitrifying Denitratisoma spp., known for methylating estrogen into androgen (the reverse reaction). Tiered transcriptomic and proteomic analyses suggest that the removed C-19 methyl group is completely oxidized to CO2 via the oxidative Wood-Ljungdahl pathway, while the reducing equivalents (NADH) fully reduce remaining testosterone to androstanediol. Consistently, the addition of anthraquinone-2,6-disulfonate, an extracellular electron acceptor, to testosterone-fed TUW77 cultures enabled complete testosterone conversion into estrogen without androstanediol accumulation (anaerobic testosterone oxidation). This discovery of aromatase-independent estrogenesis in anaerobic bacteria suggests that the ancient Wood-Ljungdahl pathway may have contributed to the emergence of estrogens in the early biosphere. SignificanceUsing a testosterone-grown anaerobic bacterium as a model organism, we characterized this unusual anaerobic estrogenesis at the molecular level. Our findings challenge the long-held belief that estrogen production is exclusive to aromatase-containing vertebrates, expanding our understanding of steroid hormone biosynthesis across domains of life. The involvement of ancient strictly anaerobic Peptococcaceae members and the Wood-Ljungdahl pathway suggests that bacterial estrogenesis may predate O2-dependent estrogenesis in vertebrates. Furthermore, the identification of estrogen-producing bacteria in animal guts opens new avenues for potential microbiome-based hypoestrogenism therapies to supplement estrogen in menopausal or ovariectomized females, offering an innovative alternative to current hormone replacement strategies.

microbiology↗

bioRxiv2024

Label-Free Optical Mapping for Large-Area Biomechanical Dynamics of Multicellular Systems

Mapping cellular activities over large areas is crucial for understanding the collective behaviors of multicellular systems. Biomechanical properties, such as cellular traction force, serve as critical regulators of physiological states and molecular configurations. However, existing technologies for mapping large-area biomechanical dynamics are limited by the small field of view and scanning nature. To address this, we propose a novel platform that utilizes a vast number of optical diffractive elements for mapping large-area biomechanical dynamics. This platform achieves a field-of-view of 10.6 mm X 10.6 mm, a three-orders-of-magnitude improvement over traditional traction force microscopy. Transient mechanical waves generated by monolayer neonatal rat ventricular myocytes were captured with high spatiotemporal resolution (130 fps and 20 {micro}m for temporal and spatial resolution, respectively). Furthermore, its label-free nature allows for long-term observations extended to a week, with minimal disruption of cellular functions. Finally, simultaneous measurements of calcium ions concentrations and biomechanical dynamics are demonstrated.

bioengineering↗

bioRxiv2024

PREDICT: Advancing Accurate Gene Expression Prediction and Motif Identification in Plant Stress Responses

Cells respond to environmental stimuli through transcriptional responses, orchestrated by transcription factors (TFs) that interpret the gene cis-regulatory DNA sequences, determining gene expression dynamics timing and locations. Diversification in TFs and cis-regulatory element (CRE) interactions result in unique gene regulatory networks (GRNs) that underpin plant adaptation. A primary challenge is identifying Transcription Factor Binding Motifs (TFBMs) for temporal and condition-specific gene expressions in plants. While the Multiple EM for Motif Elicitation (MEME) suite identifies stress-responsive CREs in Arabidopsis, its predictive power for gene expression remains uncertain. Alternatively, the k-mer approach identifies CRE sites and consensus TF motifs, thereby improving gene expression prediction models. In this study, we harnessed the power of a k-mer pipeline to address sequence-to-expression prediction problems across diverse abiotic stresses, in both bryophytic and vascular plants, including monocots and dicots. Moreover, we characterized both un-gapped and gapped CREs and, coupled with GRN analyses, pinpointed key TFs within transcriptional cascades. Lastly, we developed the Predictive Regulatory Element Database for Identifying Cis-regulatory elements and Transcription factors (PREDICT), a web tool for efficient k-mer identification. This advancement will enrich our understanding of the cis-regulatory code landscape that shapes gene regulation in plant adaptation. PREDICT web tool is available at [http://predict.southerngenomics.org/kmers/kmers.php].

bioinformatics↗

bioRxiv2024

Clostridium innocuum, an opportunistic gut pathogen, inactivates host gut progesterone and arrests ovarian follicular development

HighlightsO_LIWe identified Clostridium innocuum as a key player in gut progesterone metabolism. C_LIO_LIProgesterone is converted into epipregnanolone with negligible progestogenic activity. C_LIO_LIWe identified the enzyme and mechanisms of microbial epipregnanolone production. C_LIO_LIC. innocuum caused decreased serum progesterone and follicular arrest in female mice. C_LIO_LIC. innocuum is a causal factor of progesterone resistance in women taking progesterone. C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=93 SRC="FIGDIR/small/585140v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@14cceaborg.highwire.dtl.DTLVardef@1946432org.highwire.dtl.DTLVardef@13e46d2org.highwire.dtl.DTLVardef@19b9a25_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG In briefChen et al. identified Clostridium innocuum as a major species involved in gut progesterone metabolism, with epipregnanolone as the main product, and elucidated the molecular mechanisms. C. innocuum inactivates gut progesterone in female mice, leading to decreased circulating progesterone levels. C. innocuum is also a causal factor of follicular arrest. Levels of progesterone, an endogenous female hormone, increase after ovulation; progesterone is crucial in the luteal phase to maintain successful pregnancy and prevent early miscarriage. Both endogenous and exogenous progesterone are recycled between the liver and gut; thus, the gut microbiota regulate host progesterone levels by inhibiting enterohepatic progesterone circulation. Our data indicated Clostridium innocuum as a major species involved in gut progesterone metabolism in women with infertility. C. innocuum converts progesterone into the neurosteroid epipregnanolone (with negligible progestogenic activity). We purified and characterized the corresponding enzyme, namely NADPH-dependent 5{beta}-dihydroprogesterone reductase, which is highly oxygen sensitive and whose corresponding genes are prevalent in C. innocuum. Moreover, C. innocuum-administered female C57BL/6 mice (aged 7 weeks) exhibited decreased serum progesterone levels ([~]35%). Clostridium-specific antibiotics (metronidazole) restored low serum progesterone levels in these mice. Furthermore, prolonged C. innocuum administration (12 weeks) arrested ovarian follicular development in female mice. Cytological and histological analyses indicated that C. innocuum may cause luteal phase insufficiency and affect menstrual regularity. Our findings suggest C. innocuum as a causal factor of progesterone resistance in women taking progesterone.

microbiology↗

bioRxiv2023

Modeling alternative translation initiation sites in plants reveals evolutionarily conserved cis-regulatory codes in eukaryotes

mRNA translation relies on identifying translation initiation sites (TISs) in mRNAs. Alternative TISs are prevalent across plant transcriptomes, but the mechanisms for their recognition are unclear. Using ribosome profiling and machine learning, we developed models for predicting alternative TISs in Arabidopsis thaliana and tomato (Solanum lycopersicum). Distinct feature sets were predictive of AUG and non-AUG TISs in 5' untranslated regions and coding sequences, including a novel CU-rich sequence that promoted plant TIS activity, a translational enhancer found across dicots and monocots and also in humans and viruses. Our results elucidate the mechanistic and evolutionary basis of TIS recognition, whereby cis-regulatory RNA signatures affect start site selection. The TIS prediction model provides global estimates of TISs to discover neglected protein-coding genes across plant genomes. The prevalence of cis-regulatory signatures across eukaryotes and viruses suggests their broad, critical roles in reprogramming the translational landscape in the plant-virus arms race. TeaserNew insights into how plant ribosomes distinguish AUG and non-AUG triplets for protein synthesis via a conserved eukaryotic cis-regulatory strategy.

systems biology↗

bioRxiv2023

scTIE: data integration and inference of gene regulation using single-cell temporal multimodal data

Single-cell technologies offer unprecedented opportunities to dissect gene regulatory mecha-nisms in context-specific ways. Although there are computational methods for extracting gene regulatory relationships from scRNA-seq and scATAC-seq data, the data integration problem, essential for accurate cell type identification, has been mostly treated as a standalone challenge. Here we present scTIE, a unified method that integrates temporal multimodal data and infers regulatory relationships predictive of cellular state changes. scTIE uses an autoencoder to embed cells from all time points into a common space using iterative optimal transport, followed by extracting interpretable information to predict cell trajectories. Using a variety of synthetic and real temporal multimodal datasets, we demonstrate scTIE achieves effective data integration while preserving more biological signals than existing methods, particularly in the presence of batch effects and noise. Furthermore, on the exemplar multiome dataset we generated from differentiating mouse embryonic stem cells over time, we demonstrate scTIE captures regulatory elements highly predictive of cell transition probabilities, providing new potentials to understand the regulatory landscape driving developmental processes.

bioinformatics↗

bioRxiv2022

Circulating androgen regulation by androgen-catabolizing gut bacteria in male mouse gut

Abnormally high circulating androgen levels have been considered a causative factor for benign prostatic hypertrophy and prostate cancer. Recent studies suggested that gut bacteria can alter sex steroid profile of host; however, the underlying mechanisms and bacterial taxa remain elusive. Thauera sp. strain GDN1 is an unusual betaproteobacterium capable of aerobic and anaerobic androgen catabolism in environmental conditions (37{degrees}C) resembling the mammalian gut. The strain GDN1 administration to C57BL/6J mice through oral gavage profoundly affected gut bacterial community, along with an approximately 50% reduction in serum androgen level in male mice. Our RT-qPCR results revealed the differential expression of aerobic and anaerobic androgen catabolic genes in the mouse ileum (microaerobic) and caecum (anaerobic), respectively. Furthermore, androgenic ring-cleaved metabolites were detected in the mouse fecal extract. This study discovered that androgen serves as a carbon source of gut microbes and that androgen-catabolizing gut bacteria can modulate host circulating androgen levels. HighlightsO_LIThauera sp. strain GDN1 administration through oral gavage regulated mouse serum androgen levels. C_LIO_LIThe biochemical, genetic, and metabolite profile analyses revealed the occurrence of bacterial androgen catabolism in the mouse gut. C_LIO_LIAndrogen catabolism proceeds through the O2-dependent and O2-independent catabolic pathways in mouse ileum and caecum, respectively. C_LIO_LIA possibility to harness Thauera sp. strain GDN1 as a functional probiotic to treat hyperandrogenism. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=89 SRC="FIGDIR/small/500890v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@515126org.highwire.dtl.DTLVardef@a696faorg.highwire.dtl.DTLVardef@1020beforg.highwire.dtl.DTLVardef@15da175_HPS_FORMAT_FIGEXP M_FIG C_FIG In briefHsiao et al. found that oral administration of androgen-catabolizing Thauera species regulated mouse serum androgen level. They characterized the gut microbe-mediated androgen catabolism through genetic and biochemical analyses. Their discovery portends a possibility of harnessing androgen-catabolic gut bacteria as functional probiotics to treat hyperandrogenism.

microbiology↗

bioRxiv2021

Integrated multi-omics investigations reveal the key role of synergistic microbial networks in removing plasticizer di-(2-ethylhexyl) phthalate from estuarine sediments

Di-(2-ethylhexyl) phthalate (DEHP) is the most widely used plasticizer worldwide with an annual global production of over eight million tons. Because of its improper disposal, endocrine-disrupting DEHP often accumulates in estuarine sediments in industrialized countries at sub-millimolar levels, resulting in adverse effects on both ecosystems and human beings. The microbial degraders and biodegradation pathways of DEHP in O2-limited estuarine sediments remain elusive. Here, we employed an integrated meta-omics approach to identify the DEHP degradation pathway and major degraders in this ecosystem. Estuarine sediments were treated with DEHP or its derived metabolites, o-phthalic acid and benzoic acid. The rate of DEHP degradation in denitrifying mesocosms was two times slower than that of o-phthalic acid, suggesting that side-chain hydrolysis of DEHP is the rate-limiting step of anaerobic DEHP degradation. On the basis of microbial community structures, functional gene expression, and metabolite profile analysis, we proposed that DEHP biodegradation in estuarine sediments is mainly achieved through synergistic networks between denitrifying proteobacteria. Acidovorax and Sedimenticola are the major degraders of DEHP side-chains; the resulting o-phthalic acid is mainly degraded by Aestuariibacter through the UbiD-dependent benzoyl-CoA pathway. We isolated and characterized Acidovorax sp. strain 210-6 and its extracellular hydrolase, which hydrolyzes both alkyl side-chains of DEHP. Interestingly, genes encoding DEHP/MEHP hydrolase and phthaloyl-CoA decarboxylase--key enzymes for side-chain hydrolysis and o-phthalic acid degradation, respectively--are flanked by transposases in these proteobacterial genomes, indicating that DEHP degradation capacity is likely transferred horizontally in microbial communities. ImportanceXenobiotic phthalate esters (PAE) have been produced on a considerably large scale for only 70 years. The occurrence of endocrine-disrupting di-(2-ethylhexyl) phthalate (DEHP) in environments has raised public concern, and estuarine sediments are major DEHP reservoirs. Our multi-omics analyses indicated that complete DEHP degradation in O2-limited estuarine sediments depends on synergistic microbial networks between diverse denitrifying proteobacteria and uncultured candidates. Our data also suggest that the side-chain hydrolysis of DEHP, rather than o-phthalic acid activation, is the rate-limiting step in DEHP biodegradation within O2-limited estuarine sediments. Therefore, deciphering the bacterial ecophysiology and related biochemical mechanisms can help facilitate the practice of bioremediation in O2-limited environments. Furthermore, the DEHP hydrolase genes of active DEHP degraders can be used as molecular markers to monitor environmental DEHP degradation. Finally, future studies on the directed evolution of identified DEHP/MEHP hydrolase would bring a more catalytically efficient DEHP/MEHP hydrolase into practice.

microbiology↗

bioRxiv2021

scJoint: transfer learning for data integration of single-cell RNA-seq and ATAC-seq

Single-cell multi-omics data continues to grow at an unprecedented pace, and effectively integrating different modalities holds the promise for better characterization of cell identities. Although a number of methods have demonstrated promising results in integrating multiple modalities from the same tissue, the complexity and scale of data compositions typically present in cell atlases still pose a significant challenge for existing methods. Here we present scJoint, a transfer learning method to integrate atlas-scale, heterogeneous collections of scRNA-seq and scATAC-seq data. scJoint leverages information from annotated scRNA-seq data in a semi-supervised framework and uses a neural network to simultaneously train labeled and unlabeled data, enabling label transfer and joint visualization in an integrative framework. Using multiple atlas data and a biologically varying multi-modal data, we demonstrate scJoint is computationally efficient and consistently achieves significantly higher cell type label accuracy than existing methods while providing meaningful joint visualizations. This suggests scJoint is effective in overcoming the heterogeneity in different modalities towards a more comprehensive understanding of cellular phenotypes.

bioinformatics↗

bioRxiv2019

Retroconversion of estrogens into androgens by bacteria via a cobalamin-mediated methylation

Steroid estrogens modulate physiology and development of vertebrates. Biosynthesis of C18 estrogens from C19 androgens by the O2-dependent aromatase is thought to be irreversible. Here, we report a denitrifying Denitratisoma sp. strain DHT3 capable of catabolizing estrogens or androgens anaerobically. Strain DHT3 genome contains a polycistronic gene cluster emtABCD differentially transcribed under estrogen-fed conditions. emtABCD encodes a cobalamin-dependent methyltransferase system conserved among estrogen-utilizing anaerobes; emtA-disrupted strain DHT3 can catabolize androgens but not estrogens. These data, along with the observed androgen production in estrogen-fed strain DHT3 cultures, indicate the occurrence of a cobalamin-mediated estrogen methylation to form androgens. Consistently, the estrogen conversion into androgens in strain DHT3 cell-extracts requires methylcobalamin and is inhibited by propyl-iodide, a specific inhibitor of cobalamin-dependent enzymes. The identification of the cobalamin-mediated estrogen methylation thus represents an unprecedented metabolic link between cobalamin and steroid metabolism and suggests that retroconversion of estrogens into androgens occurs in the biosphere.

microbiology↗