Biology subjects

Dang, A.

Publications and source records attributed to Dang, A..

13 recordsLinked to original sources

bioRxiv2026

GAPDH is tethered to axonal transport vesicles by S-acylation

Vesicle movement along axonal microtubules in neurons requires the ATP-dependent molecular motors dynein and kinesin. Fast axonal transport is fueled by ATP, provided by vesicle-associated glycolytic enzymes, but how these predicted soluble enzymes attach to vesicles in unclear. One potential mechanism is the protein lipid modification S-acylation, which involves the addition of long chain fatty acids to protein cysteine residues mediated by the ZDHHC (Asp-His-His-Cys) family of protein S-acyltransferases. Among the many effects this lipid modification imparts is an increase in protein localization to membranes. We found that eight of the ten glycolytic enzymes are S-acylated in the brain. Of the 10 glycolytic enzymes, we focused on glyceraldehyde 3-phosphate dehydrogenase (GAPDH) as it is the first enzyme of the payoff phase of glycolysis. GAPDH is S-acylated on cysteine 247 by ZDHHC5 and ZDHHC17. Importantly, C247 point mutation impairs GAPDH association with vesicles in hippocampal neurons. Investigating the role of S-acylation in glycolytic enzyme localization will lead to novel insights into neuronal transport mechanisms and may also shed light on neurodegenerative disease pathology and potential drug targets.

neuroscience↗

bioRxiv2026

SAPPTree: Identification of an S-Acylation Motif Drives a Novel S-Acylation Prediction Program

S-acylation, the reversible addition of fatty acids to proteins, has emerged as an abundant post-translational modification that drives protein localization and function. With no known consensus sequence, current prediction programs rely on machine learning algorithms that use short peptide sequences and large proteomic datasets. However, current prediction programs often suggest incorrect sites of S-acylation, leading to wasted experimental time and effort following site-directed mutagenesis and low-throughput validation experiments. Using only experimentally confirmed sites of S-acylation, we sought to identify primary sequence, secondary structure, and tertiary structure features common amongst S-acylation sites to aid in developing more robust prediction tools. In doing so, we identified an S-acylation motif including a cysteine cluster flanked by a hydrophobic stretch, and a positively charged polybasic region found within a helical stretch. These features were combined with known or AlphaFold-predicted structures and additional features including residue depth and solvent accessibility into a random forest model to generate a new and more accurate S-acylation prediction program (SAPP), named SAPPTree. All the processed datasets and complete model training pipeline are available at https://github.com/neurdyphagy-lab/palm-prediction-model, while the webserver is available at http://martintools.sci.uwaterloo.ca/.

bioinformatics↗

bioRxiv2026

Finite afterload during asymmetrically cycled preload promotes fetal ventricular growth, maturation, and contractile function while suppressing fibrotic remodeling

Myocardial development requires precise modulation of its growth and maturation by the mechanical loads within cardiac cycle, including preload and afterload. However, the mechanisms by which these natural cardiac loads interact to simultaneously govern growth and maturation of the developing myocardium in both cellular and mesoscale levels remain poorly understood. Here, we developed a naturally engineered fetal ventricular tissue (NFVT) platform that enables the application of afterload under dynamic preload using cyclic stretching with an asymmetrical duty cycle (asymmetrically cycled preload) to better replicate the natural cardiac loading in chick NFVT. Our results showed that low afterload (LA) enhanced NFVT contractile function with sustained tissue growth and improved cardiomyocyte maturation while suppressing fibrosis phenotypes. These effects were associated with reduced YAP1 and NOTCH activation in cardiomyocytes and enhanced tissue architecture. In contrast, high afterload (HA) induced contractile impairment with fibrotic remodeling through activation of cardiomyocyte PIEZO1/YAP1 signaling and sustained fibroblast entanglement. TeaserLow afterload under asymmetrically cycled preload promotes NFVTs contractile function with sustained tissue growth and cardiomyocyte maturation while suppressing fibrosis phenotypes through regulation of cellular mechanotransduction, including minimal PIEZO1 expression and inhibited YAP1 and NOTCH activation in cardiomyocytes, and improvement of collective cellular organization.

Cell Biology↗

bioRxiv2026

ZDHHC17 Links S-Acylation, Huntington Disease, VCP-associated Multisystem Proteinopathy, and Amyotrophic Lateral Sclerosis.

Protein mislocalization is an important contributor to neurodegeneration. We have identified disrupted S-acylation as a driver of mislocalization. S11acylation, the addition of long-chain fatty acids to cysteine residues, is mediated by the ZDHHC family of S-acyltransferases, and regulates protein localization by modulating protein hydrophobicity. Among these enzymes, we have identified ZDHHC17 as a central node in neurodegenerative disease. Although decreased ZDHHC17 activity is correlated with Huntington disease (HD) pathology, its broader contributions to neurodegeneration remain poorly defined. Here, we present new evidence that ZDHHC17 S-acylates or interacts with multiple proteins implicated in amyotrophic lateral sclerosis (ALS), including Valosin-containing protein (VCP) and TAR DNA Binding Protein (TDP1143). We further confirm that VCP, TDP-43, FUS, C9ORF72, and SQSTM1 are S-acylated across rodent models of multiple neurodegenerative diseases, including HD, VCP-associated multisystem proteinopathy, and ALS. Using biochemical S-acylation assays and confocal microscopy, we show that ZDHHC17 S-acylates VCP, depletes the nuclear localization of both VCP and TDP-43, and modulates VCP-dependent toxicity via ER-stress. We additionally demonstrate that TDP-43 is S-acylated by ZDHHC9. Motivated by these findings, we investigated the functional significance of motor-neuronal (MN) ZDHHC17 by studying dHip14 (the fly analog of ZDHHC17) in Drosophila melanogaster. Here, we found that motor neuron-specific dHip14 knockdown (KD) in flies resulted in impaired motor function, whereas ubiquitous depletion led to pharate-adult lethality. Together, these results highlight a shared mechanism across neurodegenerative diseases. Collectively, our findings position ZDHHC17 as a critical enzyme that links fatty acylation, protein homeostasis, and neurodegeneration. Understanding how ZDHHC17 orchestrates S-acylation across different cellular pathways may reveal new therapeutic strategies to restore proteostasis in neurodegenerative disease.

molecular biology↗

bioRxiv2026

Vorinostat Rescues SQSTM1 Palmitoylation and Restores Dysfunctional Autophagy in Huntington Disease

Protein mislocalization, dysfunctional autophagy, and protein aggregation are key features of Huntington disease (HD). Accordingly, a central focus of our work has been identifying and correcting the protein mislocalization that drives the underlying autophagic defects which exacerbates protein aggregation. We previously demonstrated that palmitoylation, or S-acylation, of the autophagy receptor sequestosome 1 (SQSTM1; p62) is significantly reduced in the brains of HD patients and the YAC128 HD mouse model, thereby providing a possible mechanism for the cargo-loading failure observed in HD. Here, we identify the FDA-approved small molecule Vorinostat (suberoylanilide hydroxamic acid, SAHA) as a modulator of this pathway and show that it rescues SQSTM1 palmitoylation and restores autophagic function in HD models. Importantly, we demonstrate that Vorinostat crosses the blood-brain-barrier and significantly increases SQSTM1 palmitoylation in the cortices of YAC128 mice using acyl-biotin exchange and click chemistry assays. We further show that Vorinostat enhances autophagic flux, as evidenced by significant changes in autophagy marker levels and a marked increase in the colocalization of huntingtin with SQSTM1 and lysosomes. Finally, we investigate the mechanism of Vorinostat and propose a dual mode of action involving inhibition of depalmitoylating enzymes and transcriptional regulation of key pathway components. Collectively, these findings underscore SQSTM1 palmitoylation as a promising therapeutic target and support Vorinostat as a strong therapeutic candidate in HD.

neuroscience↗

bioRxiv2025

Evolution of opsin genes in closely-related species of butterflies specialized in different microhabitats.

How do adaptive processes acting on the coevolution of opsin genes shape the evolution of colour vision in animals? At large phylogenetic scales, natural selection due to the contrasted light environments has been found to impact the evolution of photoreceptor genes. However, in closely-related species, species interactions due to sexual selection or competition may also influence opsin evolution. Here, we investigate the diversification of opsin sequences and their expression in closely-related blue Morpho butterfly species, living in different vertical strata within tropical forests, to shed light on the biotic and abiotic selective pressures shaping the coordinated evolution of opsin genes. We combined comparative genomics, transcriptomics, and immunochemistry to characterize the expression and the spatial distribution of the opsin proteins found in the eyes of Morpho helenor. We detected a double duplication of the LW opsin and found unique ommatidial types compared to other butterfly species. We then investigated the evolution of opsin genes among 21 Morpho species, found signatures of positive selection on two opsin genes (LW3Rh and BRh), and identified key co-evolving amino-acids within and among these two opsin genes. We showed that such opsin evolution was correlated with both light environment and wing coloration, highlighting the joint effect of several selective pressures in the coordinated evolution of proteins.

evolutionary biology↗

bioRxiv2023

Reduced S-acylation of SQSTM1/p62 in Huntington disease is associated with impaired autophagy

Disruption of macroautophagy/autophagy has emerged as a common feature in many neurodegenerative diseases. Autophagy is a membrane-dependent pathway that requires many key regulators to quickly localize on and off membranes during induction promoting membrane fusion. Previously, our bioinformatic approaches have shown that autophagy and Huntington disease (HD) are enriched in S-acylated proteins. S-acylation involves the reversible addition of long chain fatty acids to promote membrane binding. Herein, we show that inhibition of S-acylation regulates the abundance of several key regulators of autophagy and leads to a partial block of autophagic flux. We show that the autophagy receptor SQSTM1/p62 (sequestosome 1) is S-acylated and directed to the lysosome. Importantly, we see that SQSTM1 S-acylation is significantly reduced in HD patient and mouse model brains, thus providing a novel mechanism for the generation of empty autophagosomes previously seen in HD models and patient cells.

neuroscience↗

bioRxiv2023

Mimetic butterfly wings through mimetic butterfly eyes: Evidence that brightness vision helps Adelpha fessonia identify potential mates

Color vision is thought to play a key role in the evolution of animal coloration, while achromatic vision is rarely considered as a mechanism for species recognition. Here we test the hypothesis that brightness vision rather than color vision helps Adelpha fessonia butterflies identify potential mates while their co-mimetic wing coloration is indiscriminable to avian predators. We examine the trichromatic visual system of A. fessonia and characterize its photoreceptors using RNA-seq, eyeshine, epi- microspectrophotometry and optophysiology. We model the discriminability of its wing color patches in relation to those of its co-mimic, A. basiloides, through A. fessonia and avian eyes. Visual modeling suggests that neither A. fessonia nor avian predators can readily distinguish the co-mimics coloration using chromatic or achromatic vision under natural conditions. These results suggest that mimetic colors are well-matched to visual systems to maintain mimicry, and that mate avoidance between these two look-alike species relies on other cues.

evolutionary biology↗

bioRxiv2022

Sex-linked gene traffic underlies the acquisition of sexually dimorphic UV color vision in Heliconius butterflies

Butterflies have photoreceptor cells that are sensitive to the ultraviolet part of the spectrum due to ultraviolet-sensitive rhodopsin (UVRh), a gene that has been duplicated in the Heliconius genus. In individuals expressing UVRh1 and UVRh2, electrophysiological and behavioral studies demonstrate that these opsin proteins enable discrimination of UV wavelengths. This behavioral trait varies between species, being absent in H. melpomene and limited to females in H. erato. To identify the evolutionary origins of this trait, we first examined UV color vision in H. charithonia, a species related to H. erato in the sara/sapho group. We found that this species also has sexually dimorphic UV color vision. To identify the genetic basis of this trait, we built a reference-grade genome assembly of H. charithonia. We discovered that one duplicate, UVRh1, is present on the W chromosome, making it obligately female-specific. We employed gDNA PCR assays of UVRh1 across the Heliconius genus. In species with sexually dimorphic UVRh1 mRNA expression, UVRh1 gDNA is absent in males, whereas in species with sexually monomorphic UVRh1 mRNA expression, UVRh1 gDNA is found in both sexes. The presence or absence of male UVRh1 expression across the Heliconius phylogeny supports a model where sexual dimorphism was acquired early via movement of a gene duplication to the W-chromosome. We used CRISPR-Cas9 to engineer a deletion in the UVRh1 locus in female H. charithonia and use immunohistochemistry to show that UVRh1 protein expression is absent in mutant tissue, similar to that of males. Our results show that a rare behavioral phenotype, sex-specific UV color vision, was acquired via sex chromosome gene traffic of a duplicated UV rhodopsin.

evolutionary biology↗

bioRxiv2021

Plant-associate interactions and diversification across trophic levels

Interactions between species are widely understood to have promoted the diversification of life on Earth, but how interactions spur the formation of new species remains unclear. Interacting species often become locally adapted to each other, but they may also be subject to shared dispersal limitations and environmental conditions. Moreover, theory predicts that different kinds of interactions have different effects on diversification. To better understand how species interactions promote diversification, we compiled population genetic studies of host plants and intimately associated herbivores, parasites, and mutualists. We used Bayesian multiple regressions and the BEDASSLE modeling framework to test whether host and associate population structures were correlated over and above the potentially confounding effects of geography and shared environmental variation. We found that associates population structure often paralleled their hosts population structure, and that this effect is robust to accounting for geographic distance and climate. Associate genetic structure was significantly explained by plant genetic structure somewhat more often in antagonistic interactions than in mutualistic ones. This aligns with a key prediction of coevolutionary theory, that antagonistic interactions promote diversity through local adaptation of antagonists to hosts, while mutualistic interactions more often promote diversity via the effect of hosts geographic distribution on mutualists dispersal.

evolutionary biology↗

bioRxiv2021

Sub-millisecond conformational transitions of short single-stranded DNA lattices by photon correlation single-molecule FRET

Thermally-driven conformational fluctuations (or breathing) of DNA plays important roles in the function and regulation of the macromolecular machinery of genome expression. Fluctuations in double-stranded (ds) DNA are involved in the transient exposure of pathways to protein binding sites within the DNA framework, leading to the binding of regulatory proteins to single-stranded (ss) DNA templates. These interactions often require that the ssDNA sequences, as well as the proteins involved, assume transient conformations critical for successful binding. Here we use microsecond-resolved single-molecule Forster Resonance Energy Transfer (smFRET) experiments to investigate the backbone fluctuations of short oligothymidine [oligo(dT)n] templates within DNA constructs that can also serve as models for ss-dsDNA junctions. Such junctions, as well as the attached ssDNA sequences, are involved in the binding of ssDNA binding (ssb) proteins that control and integrate the mechanisms of DNA replication complexes. We have used these data to determine multi-order time-correlation functions (TCFs) and probability distribution functions (PDFs) that characterize the kinetic and thermodynamic behavior of the system. We find that the oligo(dT)n tails of ss-dsDNA constructs inter-convert, on sub-millisecond time-scales, between three macrostates with distinctly different end-to-end distances. These are: (i) a compact macrostate that represents the dominant species at equilibrium; (ii) a partially extended macrostate that exists as a minority species; and (iii) a highly extended macrostate that is present in trace amounts. We propose a model for ssDNA secondary structure that advances our understanding of how spontaneously formed nucleic acid conformations may facilitate the activities of ssDNA associating proteins. Significance StatementThe genetic information of living organisms is encoded as sequences of nucleic acid bases in DNA, and is protected by the thermodynamically stable secondary structure of the Watson-Crick double helix. The processing and manipulation of gene sequences by macromolecular machines requires that stable segments of duplex DNA be disrupted, and that single-stranded (ss) DNA templates be transiently exposed to the binding sites of DNA associating proteins within the cellular environment. Here we elucidate some of the defining features that control the stability and dynamics of ssDNA secondary structure, using time-resolved methods to detect the presence of transient unstable conformations. Understanding the nature of these instabilities is central to elucidating the mechanisms by which ssDNA templates facilitate protein binding and function.

biophysics↗

bioRxiv2019

Suppressed Osteocyte Perilacunar / Canalicular RemodelingPlays a Causal Role in Osteoarthritis

Osteoarthritis (OA), long considered a primary disorder of articular cartilage, is commonly associated with subchondral bone sclerosis. However, the cellular mechanisms responsible for changes to subchondral bone in OA, and the extent to which these changes are drivers of or a secondary reaction to cartilage degeneration, remain unclear. In knee joints from human patients with end-stage OA, we found evidence of profound defects in osteocyte function. Suppression of osteocyte perilacunar/canalicular remodeling (PLR) was most severe in OA subchondral bone, with lower protease expression, diminished canalicular networks, and disorganized and hypermineralized extracellular matrix. To determine if PLR suppression plays a causal role in OA, we ablated the PLR enzyme MMP13 in osteocytes, while leaving chondrocytic MMP13 intact. Not only did osteocytic MMP13 deficiency suppress PLR in cortical and subchondral bone, but it also compromised cartilage. Even in the absence of injury, this osteocyte-intrinsic PLR defect was sufficient to reduce cartilage proteoglycan content and increase the incidence of cartilage lesions, consistent with early OA. Thus, in humans and mice, osteocyte PLR is a critical regulator of cartilage homeostasis. Together, these findings implicate osteocytes in bone-cartilage crosstalk in the joint and identify the causal role of suppressed perilacunar/canalicular remodeling in osteoarthritis.

physiology↗

bioRxiv2018

IFN-γ induces epithelial-to-mesenchymal transition of cancer cells via an unique microRNA processing

Interferon-{gamma} (IFN{gamma}) is a potent cytokine in modulating tumor immunity and tumoricidal effects. We demonstrate a new function of IFN{gamma} in inducing epithelial-to-mesenchymal transition (EMT) in normal and cancer cells from different cell types. IFN{gamma} activates JAK-STAT signaling pathway leading to the transcription of IFN-stimulated genes (ISGs), such as interferon-induced tetratricopeptide repeat 5 (IFIT5). We unveil a new function of IFIT5 complex in degrading precursor microRNAs (pre-miRNA) that include pre-miR-363 from the miR-106a-363 cluster, as well as pre-miR-101 and pre-miR-128 with a similar 5-end structure with pre-miR-363. Noticeably, these suppressive miRNAs have similar functions by targeting EMT transcription factors in prostate cancer (PCa) cells. We further demonstrated that IFIT5 plays a critical role in IFN{gamma}-induced cell invasiveness in vitro and lung metastasis in vivo. Clinically, IFIT5 is highly elevated in high-grade PCa and its expression inversely correlates with these suppressive miRNAs. Altogether, this study unveils pro-tumorigenic role of the IFN pathway via a new mechanism of action, which certainly raises concern about its clinical application.

cancer biology↗