Biology subjects

Jia, R.

Publications and source records attributed to Jia, R..

29 records · Page 2Linked to original sources

bioRxiv2022

Integrative HDX-MS enables quantification of the conformational landscape of the sugar transporter XylE

A yet unresolved challenge in structural biology is to quantify conformational states of proteins underpinning function. This challenge is particularly acute for membrane proteins owing to the difficulties in stabilising them for in vitro studies. To address this challenge, we present here an integrative strategy that combines hydrogen-deuterium exchange mass spectrometry (HDX-MS) with ensemble modelling. We benchmark our strategy on wild type and mutant conformers of XylE, a prototypical member of the ubiquitous Major Facilitator Superfamily (MFS) of transporters. Next, we apply our strategy to quantify conformational ensembles of XylE embedded in different lipid environments and identify key lipid contacts that modulate protein conformations. Further application of our integrative strategy to substrate-bound and inhibitor-bound ensembles, allowed us to unravel protein-ligand interactions contributing to the alternating access mechanism of secondary transport in atomistic detail. Overall, our study highlights the potential of integrative HDX-MS modelling to capture, accurately quantify and subsequently visualise co-populated states of membrane proteins in association with mutations and diverse substrates and inhibitors. For Table of Content Only O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=117 SRC="FIGDIR/small/499559v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@cf7b35org.highwire.dtl.DTLVardef@1a1da1eorg.highwire.dtl.DTLVardef@f70627org.highwire.dtl.DTLVardef@1b52b90_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2022

The cytolethal distending toxin modulates cell differentiation and elicits epithelial to mesenchymal transition

We are frequently exposed to bacterial genotoxins, such as cytolethal distending toxin (CDT), a prevalent heterotrimeric toxin whose active moiety is its CdtB subunit. CdtB triggers potent DNA damage, predisposing factors in the development of cancers, in host cells. CDT from Helicobacter hepaticus, a mouse pathogen, was shown to be directly involved in the development of murine hepatocarcinoma. Preliminary studies have shown that CDT induces certain phenotypes reminiscent of epithelial to mesenchymal transition (EMT), a process by which cells lose their epithelial characteristics in favor of mesenchymal ones, conducive to cell motility. In the present study, we investigated the different steps of EMT using liver tissues of mice infected with H. hepaticus, as well as human epithelial cell lines and xenograft mouse models following H. hepaticus CdtB expression. Most of the different steps of the EMT process were reproduced throughout the studied models. Indeed, microarray data showed a CdtB- dependent regulation of EMT-related transcripts. The key transcriptional regulators of EMT (SNAIL1 and ZEB1) and EMT markers (Vimentin, Fibronectin and 5{beta}1 integrin) were upregulated both at RNA and protein levels in response to CdtB. It also induced cell-cell junctions disassembly, causing individualization of cells and acquisition of a spindle-like morphology. CdtB activated the expression and activity of matrix metalloproteases and increased cell motility. This study demonstrated that CDT/CdtB elicits EMT process activation, supporting the idea that infection with genotoxin-producing bacteria can promote malignant transformation. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=96 SRC="FIGDIR/small/487255v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@f94756org.highwire.dtl.DTLVardef@1ba7d59org.highwire.dtl.DTLVardef@7b80ccorg.highwire.dtl.DTLVardef@44d56d_HPS_FORMAT_FIGEXP M_FIG C_FIG Author SummaryWe are frequently exposed to infection with genotoxin--producing bacterial from the gut microbiota, such as cytolethal distending toxin (CDT). CDT, via its active CdtB subunit, causes severe DNA damage in host cells, well-known risk factor of cancer development and progression. Chronic infection with CDT-producing bacteria is thus involved in cancer development. CDT is widespread among many bacteria and its impact in human cancer seems likely underestimated. Despite its major significance, CDT remains little studied. Here, we showed that cells exposed to CdtB are no longer cohesive, become individualized and acquire a spindle-shaped morphology known to be conducive to migration. These cells also express increased level of mesenchymal markers, as well as increased level of SNAIL1 and ZEB1, two key transcription factors orchestrating a crucial mechanism for cancer initiation and progression: epithelial to mesenchymal transition. These effects induced by CdtB were associated with increased matrix metalloproteinases degrading activity and emergence of cellular motility. Collectively, these data showed that CdB activates epithelial to mesenchymal transition, supporting the role of CDT in tumorigenesis.

microbiology↗

bioRxiv2021

A new prognostic model for pancreatic cancer based on pyroptosis-related genes

Pancreatic cancer is one of the most common malignant tumors of the digestive tract. It is known as the "king of cancer" in the field of cancer, and is one of the worst prognosis malignant tumors. Pyroptosis is a kind of programmed cell death, which can promote the inflammatory response of cells. Studies have shown that the effect of pyroptosis-related genes in cancer is significant. However, the role of pyroptosis in pancreatic cancer is not clear. The aim of this study is to establish a prognostic model based on pyroptosis. The gene expression and clinical data of pancreatic cancer patients were obtained from TCGA and verified in GEO. The differential expression of 33 pyroptosis-related genes in pancreatic cancer and normal tissues was analyzed, of which 6 genes were up-regulated and 12 genes were down regulated. Then, it was analyzed that pyroptosis-related genes were mainly enriched in the defense against bacteria and pyroptosis pathways. A concise and reliable model is established by lasso-cox regression analysis. Km curve shows that there are differences between high-risk group and low-risk group. And the nomogram has reliable prediction ability. In conclusion, pyroptosis an important role in pancreatic cancer, which can be used for the prediction of pancreatic cancer and provide a new perspective for the treatment of pancreatic cancer. AUTHOR APPROVALSThe authors have seen and approved the manuscript, and that it hasnt been accepted or published elsewhere. COMPETING INTERESTSThe authors declare no competing interests.

molecular biology↗

bioRxiv2021

Genetic loci of the R. anatipestifer serotype discovered by Pan-GWAS and its application for the development of a multiplex PCR serotyping method

The disease caused by Riemerella anatipestifer (R. anatipestifer) causes large economic losses to the global duck industry every year. Serotype-related genomic variation (such as in O-antigen and capsular polysaccharide gene clusters) has been widely used for the serotyping in many gram-negative bacteria. To date, there have been few studies focused on genetic basis of serotypes in R. anatipestifer. Here, we used pan-genome-wide association studies (Pan-GWAS) to identify the serotype-specific genetic loci of 38 R. anatipestifers strain. Analyses of the loci of 11 serotypes showed that the loci could be well mapped with the serotypes of the corresponding strains. We constructed the knockout strain for the wzy gene at the locus, and the results showed that the mutant lost the agglutination characteristics to positive antisera. Based on the of Pan-GWAS results, we developed a multiple PCR method to identify serotypes 1, 2, and 11 of R. anatipestifer. Our study provides a precedent for systematically analysing the genetic basis of the R anatipestifer serotypes and establishing a complete serotyping system in the future. HighlightsO_LIR. anatipestifer serotype-specific locus was identified by Pan-GWAS for the first time. C_LIO_LIMolecular serotyping multiplex PCR was developed based on O-antigen biosynthesis gene clusters C_LI

genomics↗

bioRxiv2020

Dorsal raphe nuclei to anterior cingulate cortex 5-HTergic neural circuit is implicated in consolation-like behaviors and sociability in mandarin voles

Consolation is a common response to the distress of others in humans and some social animals, but the neural mechanisms underlying this behavior are not well characterized. By using socially monogamous mandarin voles, we found that optogenetic or chemogenetic inhibition of 5-HTergic neurons in the dorsal raphe nucleus (DR) or optogenetic inhibition of 5-HT terminals in the anterior cingulate cortex (ACC) significantly decreased allogrooming time in the consolation test and reduced sociability in the three-chamber test. The release of 5-HT within the ACC and the activity of DR neurons were significantly increased during allogrooming, sniffing and social approaching. Finally, we found that the activation of 5-HT1A receptors in the ACC was sufficient to reverse consolation and sociability deficits induced by the chemogenetic inhibition of 5-HTergic neurons in the DR. Our study provided first direct evidence that DR-ACC 5-HTergic neural circuit is implicated in consolation-like behaviors and sociability.

neuroscience↗

bioRxiv2020

Tracing two causative SNPs reveals SARS-CoV-2 transmission in North America population

During the COVID-19 pandemic, precisely tracing the route of the SARS-CoV-2 transmission in human population remains challenging. Because this RNA virus can mutate massively without a specifically tracing maker. Herein, using a geographic stratified genome-wide association study (GWAS) of 2599 full-genome sequences, we identified that two SNPs (i.e., 1059.C>T and 25563.G>T) of linkage disequilibrium were presented in approximately half of North America SARS-CoV-2 population (p = 2.44 x 10-212 and p = 2.98 x 10-261), resulting two missense mutations (i.e., Thr 265 Ile and Gln 57 His) in ORF1ab and ORF3a, respectively. Interestingly, these two SNPs exclusively occurred in the North America dominated clade 1, accumulated during mid to late March, 2020. We did not find any of these two SNPs by retrospectively tracing the two SNPs in bat and pangolin related SARS-CoV-2 and human SARS-CoV-2 from the first epicenter Wuhan or other regions of China mainland. This suggested that the SARS-CoV-2 population of Chinese mainland were different from the prevalent strains of North America. Time-dependently, we found that these two SNPs first occurred in Europe SARS-CoV-2 (26-Feb-2020) which was 3 days early than the occurring date of North America isolates and 17 days early for Asia isolates (Taiwan China dominated). Collectively, this population genetic analysis highlights a well-confidential transmission route of the North America isolates and the two SNPs we newly identified are possibly novel diagnosable or druggable targets for surveillance and treatment.

microbiology↗

bioRxiv2020

Spectrin-based Membrane Mechanics Is Asymmetric and Remodels during Neural Development

Perturbation of spectrin-based membrane mechanics causes hereditary elliptocytosis and spinocerebellar ataxia, but the underlying cellular basis of pathogenesis remains unclear. Here, we introduced the conserved disease-associated spectrin mutations into the C. elegans genome and studied the contribution of spectrin to neuronal migration and dendrite formation in developing larvae. The loss of spectrin generates an ectopic actin polymerization outside of the existing front and secondary membrane protrusions, leading to defective neuronal positioning and dendrite morphology in adult animals. Spectrin accumulates in the lateral and the rear of migrating neuroblasts and redistributes from the soma into the newly formed dendrites, indicating that the spectrin-based membrane skeleton is asymmetric and remodels to regulate actin assembly and cell shape during development. We affinity-purified spectrin from C. elegans and showed that its binding partner ankyrin functions with spectrin. Asymmetry and remodeling of membrane skeleton may enable spatiotemporal modulation of membrane mechanics for distinct developmental events. Significance StatementThe biomechanical regulation of neural development is largely unknown. The spectrin-based membrane skeleton is essential for the structural integrity of the plasma membrane. This study addresses the function and behavior of spectrin in neuroblast migration and dendrite formation. The loss of spectrin generates an ectopic actin polymerization outside of the existing front, leading to defective neuronal positioning and dendrite morphology. Spectrin is absent from the leading edge but accumulates in the posterior of migrating neuroblasts and redistributes from the soma into the nascent dendrites, indicating that the membrane skeleton is asymmetric and remodels. Asymmetry and remodeling of the membrane skeleton may enable spatiotemporal modulation of membrane mechanics for distinct developmental events.

developmental biology↗

bioRxiv2020

A Shift from Value- to Saliency- Neural Encoding of Subjective Value in Combat Veterans with PTSD during Decision Making under Uncertainty

Military personnel engaged in combat are vulnerable to Posttraumatic Stress Disorder (PTSD), following traumatic experiences in the battlefield. Prior research has mostly employed fear-related paradigms to unravel neural underpinnings of fear dysregulation in individuals with PTSD. The ability to acquire and update fear responses depends critically on the individuals ability to cope with uncertainty, yet the role of individual uncertainty attitudes in the development of trauma-related psychopathology has hardly been examined. Here, we investigated the association between PTSD-related alterations and the subjective valuation of uncertain outcomes during decision-making. We used a monetary gambling paradigm inspired by behavioral economics in conjunction with fMRI and explored neural markers of both vulnerability and resilience to PTSD in a group of combat veterans. Behaviorally, PTSD symptom severity was associated with increased aversion to uncertainty. Neurally, activity in the ventromedial prefrontal cortex (vmPFC) during valuation of uncertain options was associated with PTSD symptoms, an effect which was specifically driven by numbing symptoms. Moreover, the neural encoding of the subjective value of those uncertain options was markedly different in the brains of veterans diagnosed with PTSD, compared to veterans who experienced trauma but did not develop PTSD. Most notably, veterans with PTSD exhibited enhanced representations of the saliency of rewards and punishments in the neural valuation system, especially in ventral striatum, compared with trauma-exposed controls. Our results point to a link between the function of the valuation system under uncertainty and the development and maintenance of PTSD symptoms, and stress the significance of studying reward processes in PTSD.

neuroscience↗

bioRxiv2020

Hydrogen-deuterium exchange mass spectrometry captures distinct dynamics upon substrate and inhibitor binding to a transporter

Proton-coupled transporters use transmembrane proton gradients to power active transport of nutrients inside the cell. High-resolution structures often fail to capture the coupling between proton and ligand binding, and conformational changes associated with transport. We combine HDX-MS with mutagenesis and MD simulations to dissect the molecular mechanism of the prototypical transporter XylE. We show that protonation of a conserved aspartate triggers conformational transition from outward-facing to inward-facing state. This transition only occurs in the presence of substrate xylose, while the inhibitor glucose locks the transporter in the outward-facing state. MD simulations corroborate the experiments by showing that only the combination of protonation and xylose binding, and not glucose, sets up the transporter for conformational switch. Overall, we demonstrate the unique ability of HDX-MS to distinguish between the conformational dynamics of inhibitor and substrate binding, and show that a specific allosteric coupling between substrate binding and protonation is a key step to initiate transport.

biochemistry↗

bioRxiv2019

Negative Regulation of Autophagy by UBA6-BIRC6-Mediated Ubiquitination of LC3

Although the process of autophagy has been extensively studied, the mechanisms that regulate it remain insufficiently understood. The ability to manipulate autophagy is important not only for addressing fundamental biological questions, but also for its possible application to the treatment of various human diseases. To identify novel regulators of autophagy, we performed a whole-genome CRISPR/Cas9 knockout screen in H4 human neuroblastoma cells gene-edited to express the endogenous autophagy effector LC3B fused to a tandem of GFP and mCherry. Using this methodology, we identified the ubiquitin-activating (E1) enzyme UBA6 and the hybrid ubiquitin-conjugating (E2)/ubiquitin-ligase (E3) enzyme BIRC6 as important autophagy regulators. We found that these two enzymes cooperate to monoubiquitinate LC3B on lysine-51, targeting it for degradation by the proteasome. Knockout of UBA6 or BIRC6 increased the levels of LC3B as well as autophagic flux under conditions of nutrient deprivation or protein synthesis inhibition. Moreover, depletion of UBA6 or BIRC6 KO decreased the formation of aggresome-like induced structures in H4 cells, and aggregates of an -synuclein mutant in the axon of rat hippocampal neurons. These findings demonstrate that UBA6 and BIRC6 negatively regulate autophagy by limiting the availability of LC3B, possibly to prevent the deleterious effects of excessive autophagy. Inhibition of UBA6 or BIRC6, on the other hand, could be used to enhance autophagic clearance of protein aggregates in neurodegenerative disorders.

cell biology↗

bioRxiv2017

Increased anxiety and decreased sociability in adulthood following paternal deprivation involve oxytocin in the mPFC

Early adverse experiences often have devastating consequences on adult emotional and social behavior. However, whether paternal deprivation (PD) during the pre-weaning period affects brain and behavioral development remains unexplored in socially mandarin vole (Microtus mandarinus). We found that PD increased anxiety-like behavior and attenuated social preference in adult males and females; decreased prelimbic cortex OT-immunoreactive fibers and paraventricular nucleus OT positive neurons; reduced levels of medial prefrontal cortex (mPFC) OT receptor protein in females and OT receptor and V1a receptor protein in males. Intra-prelimbic cortical OT injections reversed anxiety-like behavior and social preferences affected by PD, whereas injections of OT and OT receptor antagonist blocked this reversal. These findings demonstrate that PD leads to increased anxiety-like behavior and attenuated social preferences with involvement of the mPFC OT system. The prelimbic cortex OT system may be an important target for the treatment of disorders related to early adverse experiences.

neuroscience↗