Biology subjects

ZHANG, T.

Publications and source records attributed to ZHANG, T..

5 recordsLinked to original sources

bioRxiv2025

Integral Synthesis and Clearance Analysis via DIA (ISDia) Reveals Coordinated Protein Dynamics Regulation during Endoplasmic Reticulum Stress

Endoplasmic Reticulum (ER) stress disrupts protein homeostasis, driving cellular responses critical for survival, development and disease. However, systematic proteome-wide analyses of protein synthesis and clearance during ER stress remain limited. In this study, we developed Integral Synthesis and clearance analysis via DIA (ISDia), a robust mass spectrometry (MS)-based workflow that integrates multiple pulsed-SILAC labeling timepoints under one condition into a single sample and utilize data-independent acquisition (DIA) to quantify heavy and light peptide changes across conditions. It enables proteome-wide tracking of protein synthesis and clearance with high coverage by directly comparing light and heavy peptides in pSILAC-DIA experiments across multiple conditions. Using ISDia, we uncover diverse regulatory mechanisms by which protein synthesis and clearance are modulated to regulate protein abundances during ER stress, revealing PERK dependent and independent regulatory mechanisms across subcellular compartments, complexes and isoforms. These findings highlight the potential of ISDia as a powerful and widely applicable workflow for revealing protein abundance regulatory mechanisms.

systems biology↗

bioRxiv2025

Molecular Mechanism of pH Sensing and Activation in GPR4 Reveals Proton-Mediated GPCR Signaling

Maintaining pH homeostasis is critical for cellular function across all living organisms. Proton-sensing G protein-coupled receptors (GPCRs), particularly GPR4, play a pivotal role in cellular responses to pH changes, yet the molecular mechanisms underlying their proton sensing and activation remain incompletely understood. Here we present high-resolution cryo-electron microscopy structures of GPR4 in complex with G proteins under physiological and acidic pH conditions. Our structures expose an intricate proton-sensing mechanism driven by a sophisticated histidine network in the receptors extracellular domain. Upon protonation of key histidines under acidic conditions, a remarkable conformational cascade is initiated, propagating from the extracellular region to the intracellular G protein-coupling interface. This dynamic process involves precise transmembrane helix rearrangements and conformational shifts of conserved motifs, mediated by strategically positioned water molecules. Notably, we discovered a bound bioactive lipid, lysophosphatidylcholine, which has positive allosteric effects on GPR4 activation. These findings provide a comprehensive framework for understanding proton sensing in GPCRs and the interplay between pH sensing and lipid regulation, offering insights into cellular pH homeostasis and potential therapies for pH-related disorders.

molecular biology↗

bioRxiv2023

Circulating Microparticles: Optimization and Standardization of Isolation Protocols and Reassessment of Their Characteristics and Functions

Microparticles (MPs) are convenient for clinical diagnosis, and have functional roles in signal transduction. Although the importance of MPs is being increasingly recognized, the diversity of isolated protocols for MPs results in a heterogeneous population of their unknown origins, even expands to uncertain functions. Here we systematically studied the composition of MPs at different centrifugal speed intervals, and found that 3000g was a critical centrifugation speed in determining new MPs composition. The platelet-derived particles accounted for more than 80% under 3000g, while only about 20% in MPs obtained over 3000g. Furthermore, we found that the function of new MPs was significantly different from that of traditional ones, such as procoagulation activity, anti-inflammation and clinical diagnosis etc. Thus, our work optimized the method of MPs isolation, clarified some characteristics and physiological functions that should belong to platelets rather than MPs, which will derive new conceptual MPs for its composition and function.

cell biology↗

bioRxiv2020

Mammalian ATG9s drive the autophagosome formation by binding to LC3

The autophagosome is a membranous organelle that executes macroautophagy (call autophagy hereafter for the sake of brevity). Although the biogenesis of autophagosome depends on continuous acquirement of necessary membrane components to support its growth, the underlying mechanism has remained uncertain. Herein, we report that the mammalian ATG9 family members (maATG9s) play master roles in this process. We show that maATG9s directly localize to the growing autophagosomal membrane through their Ubiquitin-interacting motives (UIMs), which interact with the UIM docking site (UDS) on LC3, a component of the autophagosomal membrane. Interrupting the UIM-UDS interaction abrogates the maATG9s-LC3 binding, the localization of maATG9s to the growing autophagosome, and the autophagosome formation. Collectively, our findings show the first evidence that maATG9s act as primary autophagosomal membrane components to drive the autophagosome formation. As autophagy has been implicated in many human diseases, the identified maATG9s-LC3 interaction may serve as a target for manipulating pathological autophagosome formation.

cell biology↗

bioRxiv2019

Paired design of ATP bioluminescence method and colony counting method: whether it is suitable for evaluating the disinfection effect of environmental surface?

ATP bioluminescence method has been used as a on-site rapid detection method in nosocomial infections control more and more. In this study, a paired design between four methods/detectors were performed to detect the environmental surface after disinfection. Two methods were ATP bioluminescence method and colony counting method (C), and ATP bioluminescence method included three kinds of detectors (B, P and N). Every surface was performed by two methods/detectors. ATP content per surface from ICU had no statistically significant difference with internal medicine wards of B and P, of which p was 0.435 and 0.260. By Spearman rank correlation coefficients, with the exception of better correlation between ATP content detected by B and P, the correlation between the remaining methods/detectors was poor or had no correlation. And the differences between detectors are statistically significant. Therefor, ATP bioluminescence method may not be suitable for the evaluation of disinfection effect, but be more appropriate for evaluating the cleanliness of environmental surface.

microbiology↗