Biology subjects

Hua, Z.

Publications and source records attributed to Hua, Z..

9 recordsLinked to original sources

bioRxiv2026

Molecular basis of enfumafungin inhibition and resistance in Candida glabrata β-1,3-Glucan synthase FKS1

{beta}-1,3-Glucan synthase FKS1 is essential for fungal cell wall biogenesis and serves as a validated target of widely prescribed antifungal drugs. However, the molecular mechanism of pathogenic FKS1, its modes of inhibition, and the associated resistance mechanisms remain elusive, hindering the antifungal development. Here, we focus on Candida glabrata FKS1, a clinically relevant target frequently linked to antifungal resistance. We present cryo-EM structures of C. glabrata FKS1 in multiple detergent environments and in complex with the triterpenoid antifungal enfumafungin. Integrated functional studies revealed a key catalytic residue within the conserved ED motif and uncovered structural adaptations to different membrane-mimetic environments, rationalizing FKS1s sensitivity to its surrounding membrane context. Enfumafungin binds at the extracellular membrane leaflet of cgFKS1 transmembrane domain, engaging a convex surface separated from the cytosolic active site, consistent with its role as a non-competitive inhibitor. Further analyses identified key enfumafungin-binding residues from TM5-TM6 and elucidated the molecular basis of drug resistance in C. glabrata. Collectively, these findings establish a mechanistic framework for pathogenic FKS1 function and inhibition and provide a molecular basis for the rational design of next-generation antifungal therapeutics.

microbiology↗

bioRxiv2025

Rapid and Cost-Effective Digital Quantification of RNA Editing and Maturation in Organelle Transcripts

RNA editing and maturation are critical regulatory mechanisms in plant organelles, yet their quantification remains technically challenging. Traditional Sanger sequencing lacks sensitivity and reproducibility, whereas advanced next-generation sequencing (NGS) approaches, such as rRNA-depleted RNA-seq or targeted amplicon-seq, involve high costs, complex workflows, and limited accessibility. To address these limitations, we developed a rapid and cost-effective long-read sequencing approach, termed premium PCR sequencing, for digital quantification of RNA-editing and intron retention events in targeted chloroplast transcripts. This method combines multiplexed high-fidelity PCR amplification with Oxford Nanopore sequencing and custom in-house Perl and Python scripts for streamlined data processing, including barcode-based demultiplexing, strand reorientation, alignment to a pseudo-genome, manual editing-site inspection, and splicing variant identification and comparison. Using this platform, we analyzed the ndhB and ndhD transcripts, two chloroplast NAD(P)H dehydrogenase genes with the highest number of known editing sites, in an inducible CRISPR interference (iCRISPRi) system targeting MORF2, a key RNA-editing factor. Our results revealed MORF2 dosage-dependent reductions in C-to-U editing efficiency, with significant defects observed in the strongly repressed P1-12 line. Moreover, we identified an accumulation of intron-retaining ndhB transcripts, specifically in Dex-treated iCRISPRi lines, indicating impaired chloroplast splicing functions upon MORF2 suppression. The platform achieves single-molecule resolution, robust reproducibility, and high read coverage across biological replicates at a fraction of the cost of lncRNA-seq, making it broadly accessible. This study establishes premium PCR sequencing as a versatile, scalable, and affordable tool for targeted post-transcriptional analysis in plant organelles and expands our understanding of MORF2s role in chloroplast RNA maturation. Significance StatementWe present a rapid, affordable, and reproducible method for digital quantification of RNA editing and intron retention in plant organellar transcripts using nanopore-based long-read sequencing. This platform overcomes key limitations of existing approaches and enables routine, site-specific analysis of post-transcriptional regulation in organelles, including RNA editing and splicing, making it broadly accessible to researchers studying plastid biology, stress responses, and organelle-nucleus communication.

plant biology↗

bioRxiv2024

Arabidopsis GENOMES UNCOUPLED PROTEIN1 binds to plastid RNAs and promotes their maturation

Plastid biogenesis and the coordination of plastid and nuclear genome expression through anterograde and retrograde signaling are essential for plant development. GENOMES UNCOUPLED1 (GUN1) plays a central role in retrograde signaling during early plant development. The putative function of GUN1 has been extensively studied, but its molecular function remains controversial. Here, we evaluate published transcriptome data and generate our own data from gun1 mutants grown under signaling relevant conditions to show that editing and splicing are not relevant for GUN1-dependent retrograde signaling. Our study of the plastid (post)-transcriptome of gun1 seedlings with white and pale cotyledons demonstrates that GUN1 deficiency significantly alters the entire plastid transcriptome. By combining this result with a PPR code-based prediction and experimental validation by RNA immunoprecipitation experiments, several targets of GUN1 were identified, including 23S rRNA, tRNAs and RNAs derived from ycf1.2 and the ndhH-ndhA-ndhI-ndhG-ndhE-psaC-ndhD gene cluster. The absence of plastid rRNAs and the significant reduction of almost all plastid transcripts in white gun1 mutants account for the cotyledon phenotype. Our study identifies RNA binding and maturation as the long-sought molecular function of GUN1 and resolves long-standing controversies. We anticipate that our findings will serve as a basis for subsequent studies investigating the mechanism of plastid gene expression and will facilitate the elucidation of GUN1s function in retrograde signaling.

plant biology↗

bioRxiv2023

Metabolic interactions of a minimal bacterial consortium drive robust nitritation at acidic pH

Microbial communities efficiently mediate aerobic ammonia oxidation even at acidic pH. However, little is known about the adaptations and interactions that allow these communities to withstand challenges such as acidic stress, reactive nitrogen species, and resource deprivation under such conditions. Here we combined metagenomic analysis and biogeochemical measurements to infer the composition, metabolic interactions, and stress adaptation mechanisms of microbial consortia in three acidic nitritation bioreactors, operating at pH 5 to 2. This resulted in the recovery of 70 high-quality and mostly novel metagenome-assembled genomes (MAGs). The dominant ammonia oxidiser across all three bioreactors was a novel proteobacterium, herein named Candidatus (Ca.) Nitrosoglobus kelleri, that we enriched to a relative abundance of 55%. Also present were several heterotrophic bacteria that are predicted to engage in metabolically cross-feeding with the Nitrosoglobus. Particularly abundant were mycobacteria, including the novel actinobacterium Ca. Mycobacterium cookii, which are predicted to use organic carbon, hydrogen, carbon monoxide, sulfide and possibly nitrite as energy sources to drive aerobic respiration and denitrification. Remarkably, we observed efficient conversion of ammonia to nitrate even at pH 2, by a minimalistic community comprising the Nitrosoglobus and Mycobacterium as its only core members. Genomic analysis suggests these bacteria each use multiple strategies to maintain intracellular pH homeostasis, detoxify reactive nitrogen species, and scavenge nutrients at this pH. Altogether, these findings reveal that minimal communities can drive a key biogeochemical process even at acidic pH, and have implications for understanding nitrogen cycling and enhancing wastewater treatment.

ecology↗

bioRxiv2022

Regulation of adventitial interstitial fluid circulation by heartbeat and respiration

Converging studies showed interstitial fluid (ISF) adjacent to blood vessels flows along adventitia of vasculature into heart and lungs. We aim to reveal circulatory pathways and regulatory mechanism of such adventitial ISF flow in rat model. By MRI, real-time fluorescent imaging, micro-CT and histological analysis, ISF was found to flow in adventitial matrix surrounded by fascia and along systemic vessels into heart, then flow into lungs via pulmonary arteries and back to heart via pulmonary veins, which was neither perivascular tissues nor blood or lymphatic vessels. Under physiological conditions, speckle-like adventitial ISF flow rate was positively correlated with heart rate, increased when holding breath, became pulsative during heavy breathing. During cardiac or respiratory cycle, each dilation or contraction of heart or lungs can generate to-and-fro adventitial ISF flow along femoral veins. Discovered regulatory mechanisms of adventitial ISF flow along vasculature by heart and lungs will revolutionize understanding of cardiovascular system. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=159 SRC="FIGDIR/small/512678v3_ufig1.gif" ALT="Figure 1"> View larger version (68K): org.highwire.dtl.DTLVardef@1d29c16org.highwire.dtl.DTLVardef@583f5org.highwire.dtl.DTLVardef@1a551eorg.highwire.dtl.DTLVardef@ca4780_HPS_FORMAT_FIGEXP M_FIG Graphic abstract of adventitial interstitial fluid cycle by heartbeat and respiration.The heart and lungs can work together to regulate the ISF (green arrow) adjacent to blood vessels to flow centripetally in an adventitial pathway along the major arteries and veins of the systemic vasculature to the epicardium and myocardium, then flow into the lungs via the pulmonary arteries and back to the heart via the pulmonary veins, forming an adventitial ISF circulatory network. Under physiological conditions, the speckle-like adventitial ISF flow rate was positively correlated with heart rate, increased when holding breath, and became pulsative during heavy breathing. During respiratory cycle, each expansion of the lungs during inflation generates a centrifugal flow of adventitial ISF along the systemic veins, while each contraction of the lungs during deflation generates a centripetal adventitial ISF flow. During cardiac cycle, each dilation of atria or ventricles generates a centripetal flow of adventitial ISF along the systemic veins, while each contraction of atria or ventricles generates a centrifugal adventitial ISF flow. C_FIG

physiology↗

bioRxiv2021

B1L regulates lateral root development by exocytic vesicular trafficking-mediated polar auxin transport

Auxin and auxin-mediated signaling pathways involved in the regulation of lateral root development are well documented. Although exocytic vesicle trafficking plays an important role in auxin efflux carriers PIN recycling, and polar auxin transport during lateral root formation, however, the mechanistic details of these processes are not well understood. Here, we demonstrate that BYPASS1-LIKE (B1L) regulate lateral root development via exocytic vesicular trafficking-mediated polar auxin transport in Arabidopsis. In b1l mutants, the number of lateral roots increased significantly, and the phenotypes were mainly attributed to lateral root primordium initiation but not to the defects in lateral root primordium development. Furthermore, the auxin signal was stronger in the lateral root primordium of the b1l mutant at stage I than those observed in the wild-type (WT). Moreover, exogenous auxin and auxin transport inhibitory treatments indicated that the phenotype of lateral roots in b1l mutants can be attributed to higher auxin levels and that B1L regulates auxin efflux. Consistently, auxin efflux carriers PIN1-GFP and PIN3-GFP were expressed at higher levels in the lateral root primordium of the b1l mutants. Interestingly, we found that B1L interacted with the exocyst and b1l mutant showed a defect in PIN2 exocytosis. Finally, we found that B1L cooperated with EXO70B1 to regulate lateral root formation. Our findings reveal an essential regulatory mechanism of B1L that interacts with the exocyst to regulate PIN-mediated polar auxin transport and lateral root initiation.

plant biology↗

bioRxiv2020

Nutrient supplementation experiments on saltern microbial communities support utilization of DNA as a source of phosphorus

All environments including hypersaline ones harbor measurable concentrations of dissolved extracellular DNA (eDNA) that can be utilized by microbes as a nutrient. However, it remains poorly understood which eDNA components are used, and who in a community utilizes it. For this study, we incubated a saltern microbial community with combinations of carbon, nitrogen, phosphorus, and DNA, and tracked the community response in each microcosm treatment via 16S rRNA and rpoB gene sequencing. We show that microbial communities used DNA only as a phosphorus source, and provision of other sources of carbon and nitrogen was needed to exhibit a substantial growth. The taxonomic composition of eDNA in the water column changed with the availability of inorganic phosphorus or supplied DNA, hinting at preferential uptake of eDNA from specific organismal sources. Especially favored for growth was eDNA from the most abundant taxa, suggesting some haloarchaea prefer eDNA from closely related taxa. Additionally, microcosms composition shifted substantially depending on the provided nutrient combinations. These shifts allowed us to predict supplemented nutrients from microbial composition with high accuracy, suggesting that nutrient availability in an environment could be assessed from a taxonomic survey of its microbial community.

microbiology↗

bioRxiv2019

DeltaNeTS+: Elucidating the mechanism of drugs and diseases using gene expression and transcriptional regulatory networks

BackgroundKnowledge on the molecular targets of diseases and drugs is crucial for elucidating disease pathogenesis and mechanism of action of drugs, and for driving drug discovery and treatment formulation. In this regard, high-throughput gene transcriptional profiling has become a leading technology, generating whole-genome data on the transcriptional alterations caused by diseases or drug compounds. However, identifying direct gene targets, especially in the background of indirect (downstream) effects, based on differential gene expressions is difficult due to the complexity of gene regulatory network governing the gene transcriptional processes.\n\nResultsIn this work, we developed a network analysis method, called DeltaNeTS+, for inferring direct gene targets of drugs and diseases from gene transcriptional profiles. DeltaNeTS+ relies on a gene regulatory network model to identify direct perturbations to the transcription of genes. Importantly, DeltaNeTS+ is able to combine both steady-state and time-course gene expression profiles, as well as to leverage information on the gene network structure that is increasingly becoming available for a multitude of organisms, including human. We demonstrated the power of DeltaNeTS+ in predicting gene targets using gene expression data in complex organisms, including Caenorhabditis elegans and human cell lines (T-cell and Calu-3). More specifically, in an application to time-course gene expression profiles of influenza A H1N1 (swine flu) and H5N1 (avian flu) infection, DeltaNeTS+ shed light on the key differences of dynamic cellular perturbations caused by the two influenza strains.\n\nConclusionDeltaNeTS+ is an enabling tool to infer gene transcriptional perturbations caused by diseases and drugs from gene transcriptional profiles. By incorporating available information on gene network structure, DeltaNeTS+ produces accurate predictions of direct gene targets from a small sample size (~10s). DeltaNeTS+ can freely downloaded from http://www.github.com/cabsel/deltanetsplus.

bioinformatics↗

bioRxiv2018

Closing Target Trimming: a Perl Package for Discovering Hidden Superfamily Loci in Genomes

The contemporary capacity of genome sequence analysis significantly lags behind the rapidly evolving sequencing technologies. Retrieving biological meaningful information from an ever-increasing amount of genome data would be significantly beneficial for functional genomic studies. For example, the duplication, organization, evolution, and function of superfamily genes are arguably important in many aspects of life. However, the incompleteness of annotations in many sequenced genomes often results in biased conclusions in comparative genomic studies of superfamilies. Here, we present a Perl software, called Closing Target Trimming, for automatically identifying most, if not all, members of a gene family in any sequenced genomes. Our test data on the F-box gene superfamily showed 78.2 and 79% gene finding accuracies in two well annotated plant genomes, Arabidopsis thaliana and rice, respectively. This annotation performance is clearly higher than the best ab initio methods that are currently available. To further demonstrate the effectiveness of this program, we ran it through 18 plant genomes and five non-plant genomes to compare the expansion of the F-box and the BTB superfamilies. The program discovered that on average 12.7 and 9.3% of the total F-box and BTB members, respectively, are new loci in plant genomes while it only found a small number of new members in vertebrate genomes. Therefore, different evolutionary and regulatory mechanisms of cullin-RING ubiquitin ligases may be present in the plant and the animal kingdoms. Further studies may shed light on new discoveries in the ubiquitin-26S proteasome system-mediated regulatory pathways in eukaryotic organisms. With a detailed compiling instruction and a simple running operation, we expect that this software will assist many biological scientists with little programming experience to smoothly obtain a comprehensive dataset of a gene superfamily in any sequenced eukaryotic genomes.

bioinformatics↗