Biology subjects

Chiang, Y.-C.

Publications and source records attributed to Chiang, Y.-C..

10 recordsLinked to original sources

bioRxiv2026

Geometry-enhanced protein language modeling enables discovery of novel antibiotic resistance genes

The global antibiotic resistome remains largely unexplored, not because antibiotic resistance genes (ARGs) are rare in the environment, but because many are evolutionarily distant from known ARGs. Current computational approaches primarily rely on sequence homology, and thus miss distant homologues. We develop GeoARG, a geometry-enhanced framework that integrates structural features with protein language models through knowledge distillation, enabling efficient large-scale screening using sequence input alone. Across multiple benchmarks, GeoARG substantially improves the detection of remotely homologous ARGs, particularly under low sequence identity and fragmented conditions. Large-scale metagenomic analysis uncovers 1,485 high-confidence ARG candidates that are highly divergent from known ARGs, expanding the phylogenetic and functional landscape of the resistome. Structural analyses further show that these candidates preserve active-site geometry and maintain stable ligand-binding configurations consistent with known resistance mechanisms. These results demonstrate that geometric constraints enable systematic expansion of the resistome and facilitate the discovery of evolutionarily distant yet functionally conserved genes. A public web server is available at https://ycclab.cuhk.edu.cn/GeoARG/.

bioinformatics↗

bioRxiv2025

Whole chloroplast genomes reveal a complex genetic legacy of lost lineages, past radiations and secondary contacts in the dominant temperate deciduous tree genus Fagus

Background--Major northern temperate tree genera emerged in the Eocene and now have vast ranges across the Northern Hemisphere. Here we undertake a multi-discipline study to provide novel insights into the formation and biogeographic history of a dominant, yet understudied temperate tree genus, Fagus L. Data and methodology--A whole chloroplast genome phylogeny (eighty-two chloroplast genomes) with multi-accessions of most species was determined and contrasted with the timing of lineage diversification inferred from three different nuclear and chloroplast gene time-calibrated phylogenies using 101 fossils as age priors. Main results--Five deeply diverged chloroplast lineages were revealed that, with the exception of a Eurasian lineage, underwent divergence decoupled from speciation predating modern species lineages by up to 28 million years (Ma). The geographic distribution of chloroplast lineages reflects a complex history of genetic admixture during past contact between extinct and modern species including between different subgenera in East Asia and long-term persistence particularly in Japan which is the hotspot of plastome diversity. Conclusion--Modern Fagus forests are the consequence of 62 million years of evolution, migration, genetic exchange and species extinction with most modern species harbouring a mosaic of genetic material, a legacy of multiple admixture events in deep time.

evolutionary biology↗

bioRxiv2025

Impact of Peptide Initial Configuration and Membrane Composition on Melittin's Pore-Forming Ability under Unbiased All-Atom Molecular Dynamics Simulations

The rising challenge of antimicrobial resistance has accelerated the search for alternative therapeutics. Antimicrobial peptides (AMPs), a class of naturally occurring defense molecules found across diverse species, are promising candidates. Despite their potent membrane-disrupting activity, the atomic details of the pore formation process remain insufficiently understood. In this study, we employed all-atom molecular dynamics (MD) simulations to investigate the pore formation process of melittin under different initial configurations. Simulations were conducted using three different membrane systems: a pure POPC bilayer, a mammalian membrane model (DOPC:Cholesterol, 9:1), and a bacterial membrane model (DOPE:DOPG, 3:1). For each system, we examined four different starting configurations, in which six melittin peptides were arranged in a star-like pattern. Our results demonstrated that the pore formation process strongly depends on the initial peptide configuration. In one specific initial arrangement (termed as Conf.I), pore formation consistently occurred within 100 nanoseconds, regardless of membrane composition. Furthermore, the simulations revealed that pore formation was more challenging in the mammalian membrane model and even more so in the bacterial membrane model, in comparison with the pure POPC bilayer. These findings are in line with previously reported minimum inhibitory concentration (MIC) and the 50% hemolysis concentration (HC50) of melittin in the literature. Additionally, we identified lysine-7 (K7) as the key residue in determining whether a stable pore can form. In configurations where the K7 side chain formed electrostatic interactions with the phosphate group of a lipid, melittin were anchored to the membrane surface, thereby preventing pore formation. In contrast, simulations of melittin mutants K7A and K7Q showed no such anchoring effect, and thus pore formation was possible in multiple initial configurations. Notably, the K7Q mutation showed a preference for pore formation in bacterial membranes over mammalian membranes, suggesting that reducing toxicity while maintaining antimicrobial efficacy is possible.

biochemistry↗

bioRxiv2023

Transcriptome and Mutant Analysis of Neuronal Genes for Memory Formation and Retrieval in Caenorhabditis elegans

Although it is generally believed that the formation and retrieval of memory require distinct sets of genes, little is known about the identity and temporal specificity of genes that act at different memory stages. Here we characterize the transcriptomes for the formation and retrieval of stress-induced aversive memory in the nematode Caenorhabditis elegans. Our RNA-sequencing analysis show that neuronal genes for calcium homeostasis, membrane excitability, synaptic function and signaling are progressively activated during the formation of aversive memory. Stage-specific transcriptomes further reveal that memory formation and retrieval display distinct gene activation patterns. We carried out a candidate screen of mutants for these memory genes and verified the temporal requirement of memory function for several of them. Further in-depth characterization of casy-1/calsyntenin show that while the short CASY-1B isoform acts in memory retrieval, the long CASY-1A isoform functions during memory formation, and its shed extracellular N-terminus fragment is likely a critical signal for memory regulation. Our work uncovers gene expression patterns associated with distinct memory stages and provides a foundation for future mechanistic interrogation of memory functions.

neuroscience↗

bioRxiv2020

Crystal structure of steroid reductase SRD5A reveals conserved steroid reduction mechanism

Steroid hormones are essential in stress response, immune system regulation, and reproduction in mammals. Steroids with 3-oxo-{Delta}4 structure, such as testosterone, androstenedione and progesterone, could be catalyzed by steroid 5-reductases (SRD5As) to generate their corresponding 3-oxo-5 steroids, which are essential for multiple physiological and pathological processes. Abnormal activities of SRD5As will lead to benign prostatic hyperplasia, alopecia, prostatic cancer or infertility due to the poor quality of sperms. However, the detailed reduction mechanisms of SRD5As remain elusive. Here we report the crystal structure of PbSRD5A, which shares 60.6% and 51.5% sequence similarities with human SRD5A1 and -2 respectively, from Proteobacteria bacterium in complex with the cofactor NADPH at 2.0 [A] resolution. PbSRD5A exists as a monomer comprised of seven transmembrane segments (TMs). The TM1-4 enclose a hydrophobic cavity for steroids substrates binding, whereas TM5-7 coordinate with cofactor NADPH through extensive hydrogen bonds network. Homology-based structural models of HsSRD5A1 and -2, together with extensive biochemical characterizations, for the first time unveiled the substrate recognition of SRD5As and provide an important framework for further understanding of the mechanism of NADPH mediated steroids 3-oxo-{Delta}4 reduction. Based on these analyses, the design of therapeutic molecules targeting SRD5As with improved specificity and therapeutic efficacy would be possible. One Sentence SummaryStructural and biochemical characterizations decipher the evolutionarily conserved mechanism in steroid 5-reductases catalyzing NADPH mediated steroids reduction.

biochemistry↗

bioRxiv2019

The relative transmissibility of shigellosis among male and female individuals in Hubei Province, China: a modelling study

ObjectiveShigellosis has been a heavy burden in China. However, its relative transmissibility in male and female individuals remains unclear.\n\nMethodA sex-based Susceptible-Exposed-Infectious/Asymptomatic-Recovered (SEIAR) model was applied to explore the dataset of reported shigellosis cases built by Hubei Province from 2005 to 2017. Two indicators, secondary attack rate (SAR) and relative ratio of SAR between males and females, were developed to assess the relative transmissibility in males and females.\n\nResultsThe number of cases and reported incidences in males and females demonstrated a significant decreasing trend (Male trend:{chi} 2 = 11.268, P = 0.001, Female trend:{chi} 2 = 11.144, P = 0.001). SEIAR model had a great fitting effect with the data of shigellosis (P < 0.001). Our simulation revealed that, when parameter {beta}fm = 0, the greatest decrease in cases were obtained for different genders. The median value for SARmm was 2.3225 x 10-8 (Range: 1.7574 x 10-8 - 3.8565 x 10-8), SARmf was 2.5729 x 10-8 (Range: 1.3772 x 10-8 - 3.2773 x 10-8), SARfm was 2.7630 x 10-8 (Range: 1.8387 x 10-8 - 4.2638 x 10-8) and SARff was 2.1061 x 10-8 (Range: 1.0201 x 10-8 - 3.2140 x 10-8). The median value of relative ratio calculated by SAR in mm versus (vs) mf was 0.93 (Range: 0.75 - 1.47), mm vs fm was 0.90 (Range: 0.41 - 1.81), mm vs ff was 1.07 (Range: 0.55 - 2.93), mf vs fm was 0.99 (Range: 0.32 - 1.25), mf vs ff was 1.17 (Range: 0.43 - 3.21) and ff vs fm was 0.75 (Range: 0.35 - 1.06).\n\nConclusionTransmissibility of shigellosis is different among male and female individuals. Shigellosis seems to be more transmissible in males than in females.\n\nAuthor summaryShigellosis, also known as bacillary dysentery, is an infectious disease caused by the genus Shigella spp. Developing countries have high disease burden of shigellosis. However, its relative transmissibility in male and female individuals remains unclear. In this study, we employed a mathematical model to explore the dataset of reported shigellosis cases built by Hubei Province, China from 2005 to 2017. Two indicators, secondary attack rate (SAR) and relative ratio of SAR between males and females, were developed to assess the relative transmissibility in males and females. We found that shigellosis has medium transmissibility among male and female individuals. The disease seems to be more transmissible in males than in females.

epidemiology↗

bioRxiv2019

Sonogenetic modulation of cellular activities using an engineered auditory-sensing protein

Biomolecules that respond to different external stimuli enable the remote control of genetically modified cells. Chemogenetics and optogenetics, two tools that can control cellular activities via synthetic chemicals or photons, respectively, have been widely used to elucidate underlying physiological processes. These methods are, however, very invasive, have poor penetrability, or low spatiotemporal precision, attributes that hinder their use in therapeutic applications. We report herein a sonogenetic approach that can manipulate target cell activities by focused ultrasound stimulation. This system requires an ultrasound-responsive protein derived from an engineered auditory-sensing protein prestin. Heterogeneous expression of mouse prestin containing two parallel amino acid substitutions, N7T and N308S, that frequently exist in prestins from echolocating species endowed transfected mammalian cells with the ability to sense ultrasound. An ultrasound pulse of low frequency and low pressure efficiently evoked cellular calcium responses after transfecting with prestin(N7T, N308S). Moreover, pulsed ultrasound can also non-invasively stimulate target neurons expressing prestin(N7T, N308S) in deep regions of mice brains. Our study delineates how an engineered auditory-sensing protein can cause mammalian cells to sense ultrasound stimulation. Moreover, owing to the great penetration of low-frequency ultrasound ([~]400 mm in depth), our sonogenetic tools will serve as new strategies for non-invasive therapy in deep tissues of large animals like primates.

bioengineering↗

bioRxiv2018

Mechanistic basis for the evolution of chalcone synthase catalytic cysteine reactivity in land plants

Flavonoids are important polyphenolic natural products, ubiquitous in land plants, that play diverse functions in plants survival in their ecological niches, including UV protection, pigmentation for attracting pollinators, symbiotic nitrogen fixation, and defense against herbivores. Chalcone synthase (CHS) catalyzes the first committed step in plant flavonoid biosynthesis and is highly conserved in all land plants. In several previously reported crystal structures of flowering plant CHSs, the catalytic cysteine is oxidized to sulfinic acid, indicating enhanced nucleophilicity in this residue associated with its increased susceptibility to oxidation. In this study, we report a set of new crystal structures of CHSs representing all five major lineages of land plants. We reveal that the structures of CHS from a lycophyte and a moss species preserve the catalytic cysteine in a reduced state, in contrast to the cysteine sulfinic acid seen in all euphyllophyte CHS structures. In vivo complementation, in vitro biochemical and mutagenesis analyses, as well as molecular dynamics simulations identify a set of residues that differ between basal-plant and euphyllophyte CHSs and modulate catalytic cysteine reactivity. We propose that the CHS active-site environment has evolved in euphyllophytes to further enhance the nucleophilicity of the catalytic cysteine since the divergence of euphyllophytes from other vascular plant lineages 400 million years ago. These changes in CHS could have contributed to the diversification of flavonoid biosynthesis in euphyllophytes, which in turn contributed to their dominance in terrestrial ecosystems.

biochemistry↗

bioRxiv2018

Structural basis for independent origins of new catalytic machineries in plant AAAD proteins

Radiation of the plant pyridoxal 5-phosphate (PLP)-dependent aromatic L-amino acid decarboxylase (AAAD) family has yielded an array of paralogous enzymes exhibiting divergent substrate preferences and catalytic mechanisms. Plant AAADs catalyze either the decarboxylation or decarboxylation-dependent oxidative deamination of aromatic L-amino acids to produce aromatic monoamines or aromatic acetaldehydes, respectively. These compounds serve as key precursors for the biosynthesis of several important classes of plant natural products, including indole alkaloids, benzylisoquinoline alkaloids, hydroxycinnamic acid amides, phenylacetaldehyde-derived floral volatiles, and tyrosol derivatives. Here, we present the crystal structures of four functionally distinct plant AAAD paralogs. Through structural and functional analyses, we identify variable structural features of the substrate-binding pocket that underlie the divergent evolution of substrate selectivity toward indole, phenyl, or hydroxyphenyl amino acids in plant AAADs. Moreover, we describe two mechanistic classes of independently arising mutations in AAAD paralogs leading to the convergent evolution of the derived aldehyde synthase activity. Applying knowledge learned from this study, we successfully engineered a shortened benzylisoquinoline alkaloid pathway to produce (S)-norcoclaurine in yeast. This work highlights the pliability of the AAAD fold that allows change of substrate selectivity and access to alternative catalytic mechanisms with only a few mutations. SignificancePlants biosynthesize their own proteinogenic aromatic L-amino acids, namely L-phenylalanine, L-tyrosine and L-tryptophan, not only for building proteins but also for the production of a plethora of aromatic-amino-acid-derived natural products. Pyridoxal 5-phosphate (PLP)-dependent aromatic L-amino acid decarboxylase (AAAD) family enzymes play important roles in channeling various aromatic L-amino acids into diverse downstream specialized metabolic pathways. Through comparative structural analysis of four functionally divergent plant AAAD proteins together with biochemical characterization and molecular dynamics simulations, we reveal the structural and mechanistic basis for the rich divergent and convergent evolutionary development within the plant AAAD family. Knowledge learned from this study aids our ability to engineer high-value aromatic-L-amino-acid-derived natural product biosynthesis in heterologous chassis organisms.

biochemistry↗

bioRxiv2018

Spatiotemporal manipulation of ciliary glutamylation reveals its roles in intraciliary trafficking and Hedgehog signaling

Tubulin post-translational modifications (PTMs) occur spatiotemporally throughout cells and are suggested to be involved in a wide range of cellular activities. However, the complexity and dynamic distribution of tubulin PTMs within cells have hindered the understanding of their physiological roles in specific subcellular compartments. Here we develop a method to rapidly deplete tubulin glutamlyation inside the primary cilia, a microtubule-based sensory organelle protruding on the cell surface, by targeting an engineered deglutamylase to the cilia in minutes. This rapid deglutamylation quickly leads to altered ciliary functions such as kinesin-2-mediated anterograde intraflagellar transport and Hedgehog signaling, along with no apparent crosstalk to other PTMs such as acetylation and detyrosination. Our study offers a feasible approach to spatiotemporally manipulate tubulin PTMs in living cells. Future expansion of the repertoire of actuators that regulate PTMs may facilitate a comprehensive understanding of how diverse tubulin PTMs encode ciliary as well as cellular functions.

cell biology↗