Jie Xiao

Research Interests.   single molecule biophysics, super-resolution imaging, cell division, chromosome organization, transcription, gene regulation

Research Description.  My laboratory focuses on developing novel single-molecule imaging and labeling tools in single cells to study the structures, functions and dynamics of macromolecular assemblies. We are broadly interested in understanding how molecular constituents of cellular processes are spatially organized and what essential functions such an organization conveys. For example, we pioneered the use of superresolution imaging and single-molecule tracking in microbiology to study bacterial cell division. We developed single-molecule gene expression reporting systems and chromosomal DNA conformation markers to probe the dynamics of gene regulation, chromosome organization, and transcription in bacterial cells. We also devote significant efforts to develop single-molecule imaging methods with new capacities to aid biological investigations in human cells, fluid and tissues. Our work is at the frontier of single-molecule single-cell biophysics, and has enabled new quantitative understandings of essential cellular processes including gene regulation and cell division.

Our major research topics are:

1. Structure, function, and dynamics of bacterial cell division complex

In bacteria, cell division is carried out by a highly conserved, ring-like supramolecular complex, the divisome. The divisome is formed by the polymerization of the essential cytoskeletal protein FtsZ at the division plane and the subsequent recruitment of more than thirty proteins, many of them being cell wall enzymes and regulators. Understanding how the divisome directs cell wall constriction is essential for identifying new antibiotic targets. However, because of the small size of bacterial cells, it has been challenging to investigate the divisome’s structural organization, dynamics, and functions using traditional imaging approaches.

Most recently, using single-molecule tracking (SMT) and coupled with genetic studies, we discovered that FtsZ uses its GTP hydrolysis to power treadmilling dynamics to distribute septal cell wall synthase complexes evenly along the septum to ensure smooth, symmetric septum formation. The enzymatic activities and processivity of the septal cell wall synthase complex are regulated by the differential coupling of the complex to the treadmilling FtsZ polymers and cell wall synthesis regulators. We further elucidated the molecular mechanism for the activation of the sPG synthase FtsWI complex by their regulators, FtsQLB and FtsN. These discoveries would not be possible without the single- molecule imaging approaches. Our work redefines the role of the FtsZ-ring in bacterial cell division. It opens new directions to study the precise spatial coordination and regulation of the large ensemble of cell division proteins.

4585. Britton BM, Yovanno RA, Costa SF, McCausland J, Lau AY, Xiao J, Hensel Z. Conformational changes in the essential E. coli septal cell wall synthesis complex suggest an activation mechanism. Nat Commun. 2023 Jul 31;14(1):4585. PubMed Central PMCID: PMC10390529.
4586. Lyu Z, Yahashiri A, Yang X, McCausland JW, Kaus GM, McQuillen R, Weiss DS, Xiao J. FtsN maintains active septal cell wall synthesis by forming a processive complex with the septum- specific peptidoglycan synthases in E. coli. Nat Commun. 2022 Sep 30;13(1):5751. PubMed Central PMCID: PMC9525312.
4587. Yang X, McQuillen R, Lyu Z, Phillips-Mason P, De La Cruz A, McCausland JW, Liang H, DeMeester KE, Santiago CC, Grimes CL, de Boer P, Xiao J. A two-track model for the spatiotemporal coordination of bacterial septal cell wall synthesis revealed by single-molecule imaging of FtsW. Nat Microbiol. 2021 May;6(5):584-593. PubMed Central PMCID: PMC8085133.
4588. Yang X, Lyu Z, Miguel A, McQuillen R, Huang KC, Xiao GTPase activity-coupled treadmilling of

the bacterial tubulin FtsZ organizes septal cell wall synthesis. Science. 2017 Feb 17;355(6326):744-747. PubMed Central PMCID: PMC5851775.

1. Spatial organization of transcription and chromosome

Recent studies suggest that the genome is spatially organized; where genes are and how they are organized are important for their transcriptional activities. To test this hypothesis, we developed new single-molecule imaging techniques to visualize chromosomal DNA conformation and transcription activity in individual cells. The first set of DNA localization markers we developed allowed us to probe the dynamics of transcription factor-mediated DNA looping in live E. coli cells and relate to the transcription activity of the gene it controls. In one of our recent works, we probed the spatial organization of RNA polymerase (RNAP) and the chromosome in E. coli cells and showed RNAP was organized into active transcription centers under the rich medium growth condition; their spatial arrangement at the cellular level, however, was not dependent on rRNA synthesis activity and was likely organized by the underlying nucleoid. Most recently, using single-molecule tracking, we discovered that the nucleoid-associated protein HU plays a dual role in maintaining a proper nucleoid volume through its differential interactions with chromosomal DNA. We further collaborated with computational biologists and discovered a significant impact of DNA topological domains on transcription mediated by DNA supercoiling.

737. Fu Z, Guo MS, Zhou W, Xiao J. Differential roles of positive and negative supercoiling in organizing the E. coli genome. Nucleic Acids Res. 2024 Jan 25;52(2):724-737. PubMed Central PMCID: PMC10810199.
738. Bettridge K, Verma S, Weng X, Adhya S, Xiao J. Single-molecule tracking reveals that the nucleoid-associated protein HU plays a dual role in maintaining proper nucleoid volume through differential interactions with chromosomal DNA. Mol Microbiol. 2021 Jan;115(1):12-27. PubMed Central PMCID: PMC8655832.
739. Weng X, Bohrer CH, Bettridge K, Lagda AC, Cagliero C, Jin DJ, Xiao J. Spatial organization of RNA polymerase and its relationship with transcription in Escherichia coli. Proc Natl Acad Sci U S A. 2019 Oct 1;116(40):20115-20123. PubMed Central PMCID:
740. Hensel Z, Weng X, Lagda AC, Xiao J. Transcription-factor-mediated DNA looping probed by high- resolution, single-molecule imaging in live E. coli cells. PLoS Biol. 2013;11(6):e1001591. PubMed Central PMCID: PMC3708714.

• Stochastic gene expression

Gene expression is inherently stochastic. How cells battle noise in gene expression to achieve robust growth and development has been the subject of intense studies. To find out how cells repress intrinsic noise using autoregulatory transcription factors, we developed a single-molecule gene expression reporter to monitor the stochastic expression of a transcription factor and its autoregulatory actions. We discovered that intrinsic noise has a negligible effect on the overall gene expression noise. Instead, extrinsic noise, or fluctuations caused by different compositions of cellular factors in other cells, dominates noise in gene expression. These findings advance our understanding of the operational principle of gene regulatory networks and signal a significant change in the field of stochastic gene expression. In one of our new studies, we discovered that, surprisingly, a classic bacterial bistable switch exhibits four instead of two stable states, uncovering new cell fate potentials beyond the classic picture. Along the same line, we also developed new computational methods to facilitate the inference of gene regulatory network operational details.

84. Shachaf LI, Roberts E, Cahan P, Xiao J. Gene regulation network inference using k-nearest neighbor-based mutual information estimation: revisiting an old DREAM. BMC Bioinformatics. 2023 Mar 6;24(1):84. PubMed Central PMCID: PMC9990267.
85. Fang X, Liu Q, Bohrer C, Hensel Z, Han W, Wang J, Xiao Cell fate potentials and switching

kinetics uncovered in a classic bistable genetic switch. Nat Commun. 2018 Jul 17;9(1):2787. PubMed Central PMCID: PMC6050291.

802. Hensel Z, Feng H, Han B, Hatem C, Wang J, Xiao J. Stochastic expression dynamics of a transcription factor revealed by single-molecule noise analysis. Nat Struct Mol Biol. 2012 Aug;19(8):797-802. PubMed PMID: 22751020.
803. Feng H, Hensel Z, Xiao J, Wang J. Analytical calculation of protein production distributions in models of clustered protein expression. Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Mar;85(3 Pt 1):031904. PubMed PMID: 22587120.

• Development of single-molecule imaging and analysis tools

Technology advancement often drives scientific breakthroughs. We are dedicated to developing cutting-edge single-molecule imaging and analysis tools to facilitate scientific discovery. We are among the first to establish single-molecule localization-based superresolution imaging in small bacterial cells. We develop computational methods and quantitative imaging analyses to identify spatial features of cellular structures, correct confinement errors, and counter-blinking behaviors of fluorescent labels. Recently, we collaborated with experts in mammalian systems to develop new single-molecule-based technologies for sensitive early detection of cancer markers in blood samples and multiplexed protein and nucleic acids detection in human and animal tissues.

314. Ha T, Kaiser C, Myong S, Wu B, Xiao J. Next generation single-molecule techniques: Imaging, labeling, and manipulation in vitro and in cellulo. Mol Cell. 2022 Jan 20;82(2):304-314. PubMed PMID: 35063098.
315. Mao CP, Wang SC, Su YP, Tseng SH, He L, Wu AA, Roden RBS, Xiao J, Hung CF. Protein detection in blood with single-molecule imaging. Sci Adv. 2021 Aug;7(33) PubMed Central PMCID: PMC8357237.
316. Bohrer CH, Yang X, Thakur S, Weng X, Tenner B, McQuillen R, Ross B, Wooten M, Chen X, Zhang J, Roberts E, Lakadamyali M, Xiao J. A pairwise distance distribution correction (DDC) algorithm to eliminate blinking-caused artifacts in SMLM. Nat Methods. 2021 Jun;18(6):669-677. PubMed Central PMCID: PMC9040192.
317. Fu G, Huang T, Buss J, Coltharp C, Hensel Z, Xiao J. In vivo structure of the E. coli FtsZ-ring revealed by photoactivated localization microscopy (PALM). PLoS One. 2010 Sep 13;5(9):e12682. PubMed Central PMCID: PMC2938336.

A complete list of publications, excluding chapters and articles not accessed by PubMed, can be found at: https://www.ncbi.nlm.nih.gov/myncbi/jie.xiao.1/bibliography/public/