Xiaowei Zhang

All Publications

• Post-Transcriptional Modular Synthetic Receptors. bioRxiv : the preprint server for biology Zhang, X., Mille-Fragoso, L. S., Kaseniit, K. E., Call, C. C., Zhang, M., Hu, Y., Xie, Y., Gao, X. J. 2024

  Abstract

  Inspired by the power of transcriptional synthetic receptors and hoping to complement them to expand the toolbox for cell engineering, we establish LIDAR (Ligand-Induced Dimerization Activating RNA editing), a modular post-transcriptional synthetic receptor platform that harnesses RNA editing by ADAR. LIDAR is compatible with various receptor architectures in different cellular contexts, and enables the sensing of diverse ligands and the production of functional outputs. Furthermore, LIDAR can sense orthogonal signals in the same cell and produce synthetic spatial patterns, potentially enabling the programming of complex multicellular behaviors. Finally, LIDAR is compatible with compact encoding and can be delivered by synthetic mRNA. Thus, LIDAR expands the family of synthetic receptors, holding the promise to empower basic research and therapeutic applications.

  View details for DOI 10.1101/2024.05.03.592453

  View details for PubMedID 38746461

  View details for PubMedCentralID PMC11092781

• Sensitive bacterial Vm sensors revealed the excitability of bacterial Vm and its role in antibiotic tolerance. Proceedings of the National Academy of Sciences of the United States of America Jin, X., Zhang, X., Ding, X., Tian, T., Tseng, C. K., Luo, X., Chen, X., Lo, C. J., Leake, M. C., Bai, F. 2023; 120 (3): e2208348120

  Abstract

  As an important free energy source, the membrane voltage (Vm) regulates many essential physiological processes in bacteria. However, in comparison with eukaryotic cells, knowledge of bacterial electrophysiology is very limited. Here, we developed a set of novel genetically encoded bacterial Vm sensors which allow single-cell recording of bacterial Vm dynamics in live cells with high temporal resolution. Using these new sensors, we reveal the electrically "excitable" and "resting" states of bacterial cells dependent on their metabolic status. In the electrically excitable state, frequent hyperpolarization spikes in bacterial Vm are observed, which are regulated by Na+/K+ ratio of the medium and facilitate increased antibiotic tolerance. In the electrically resting state, bacterial Vm displays significant cell-to-cell heterogeneity and is linked to the cell fate after antibiotic treatment. Our findings demonstrate the potential of our newly developed voltage sensors to reveal the underpinning connections between bacterial Vm and antibiotic tolerance.

  View details for DOI 10.1073/pnas.2208348120

  View details for PubMedID 36623202

• Multiplexed genome regulation in vivo with hyper-efficient Cas12a. Nature cell biology Guo, L. Y., Bian, J., Davis, A. E., Liu, P., Kempton, H. R., Zhang, X., Chemparathy, A., Gu, B., Lin, X., Rane, D. A., Xu, X., Jamiolkowski, R. M., Hu, Y., Wang, S., Qi, L. S. 2022

  Abstract

  Multiplexed modulation of endogenous genes is crucial for sophisticated gene therapy and cell engineering. CRISPR-Cas12a systems enable versatile multiple-genomic-loci targeting by processing numerous CRISPR RNAs (crRNAs) from a single transcript; however, their low efficiency has hindered in vivo applications. Through structure-guided protein engineering, we developed a hyper-efficient Lachnospiraceae bacterium Cas12a variant, termed hyperCas12a, with its catalytically dead version hyperdCas12a showing significantly enhanced efficacy for gene activation, particularly at low concentrations of crRNA. We demonstrate that hyperdCas12a has comparable off-target effects compared with the wild-type system and exhibits enhanced activity for gene editing and repression. Delivery of the hyperdCas12a activator and a single crRNA array simultaneously activating the endogenous Oct4, Sox2 and Klf4 genes in the retina of post-natal mice alters the differentiation of retinal progenitor cells. The hyperCas12a system offers a versatile in vivo tool for a broad range of gene-modulation and gene-therapy applications.

  View details for DOI 10.1038/s41556-022-00870-7

  View details for PubMedID 35414015

• Membraneless organelles formed by liquid-liquid phase separation increase bacterial fitness. Science advances Jin, X., Lee, J. E., Schaefer, C., Luo, X., Wollman, A. J., Payne-Dwyer, A. L., Tian, T., Zhang, X., Chen, X., Li, Y., McLeish, T. C., Leake, M. C., Bai, F. 2021; 7 (43): eabh2929

  Abstract

  [Figure: see text].

  View details for DOI 10.1126/sciadv.abh2929

  View details for PubMedID 34669478

  View details for PubMedCentralID PMC8528417