Research Interests. single molecule biophysics, super-resolution imaging, cell division, 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. 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 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:
I. 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 important for identifying new antibiotic targets. However, because of the small size of bacterial cells, it has been challenging to investigate the structural organization, dynamics and functions of the divisome using traditional imaging approaches.
We pioneered the use of single-molecule localization microscopy (SMLM) based superresolution imaging for microbiology and illustrated the spatial organization of the FtsZ-ring in live E. coli cells for the first time. Using three-dimensional (3D) SMLM imaging, we further demonstrated an elaborate, multi-layered protein network connecting the FtsZ-ring to the chromosome to stabilize the divisome and coordinate cell division with chromosome segregation . Next, we provided substantial evidence to show that, in contrary to the long-standing dogma of the field, the FtsZ-ring is not the major constrictive force generator. Instead, inward septal cell wall growth dictates cell division speed and this process is further modulated by nucleoid segregation .
Most recently, using single-molecule tracking (SMT) and coupled with genetic studies, we made the exciting discovery 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 processtivity 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 . 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 and opens new directions to study the precise spatial coordination and regulation of the large ensemble of cell division proteins.
- Buss J, Coltharp C, Shtengel G, Yang X, Hess H and Xiao J, A multi-layered protein network maintains the stability of the FtsZ-ring and modulate constriction dynamics in E.coli, PLoS Genetics, 2015, Apr 7;11(4):e1005128, PMID: 2584771.
- Coltharp C, Buss J, Plumer T, Shtengel G, Hess H, Xiao J, Defining the rate-limiting processes in bacterial cytokinesis, P.N.A.S., 2016, Feb 23, 113(8):E1044-53, PMCID: PMC4776500.
- Yang X, Lyu Z, Miguel A, McQuillen R, Huang KC, Xiao J, GTPase activity-coupled treadmilling of the bacterial tubulin FtsZ organizes septal cell-wall synthesis, Science, 2017, 355, 744-747, PMCID: PMC5851775.
- Yang X, McQuillen R, Lyu Z, Phillips-Mason P, De La Cruz A, McCausland JW, Liang H, DeMeester KE, 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. Microbio., 2021 May;6(5):584-593. PMCID: PMC8085133.
II. Stochastic gene expression
Gene expression is inherently stochastic. How cells battle noise in gene expression in order 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 negligible effect on the overall gene expression noise. Instead, extrinsic noise, or fluctuations caused by different compositions of cellular factors in different cells, dominates noise in gene expression . These findings advance our understanding of the operational principle of gene regulatory networks and signal a major 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. This study opens a new window to explore the genetic and environmental origins of cell fate decision-making process in gene regulatory networks.
- Hensel Z, Feng H, Han B, Hatem C, Wang J, Xiao J, Stochastic expression dynamics of transcription factor revealed by single-molecule noise analysis, Nat. Struct. Mol. Biol. 2012, 19(8):797-802, PMID:22751020.
- Feng H, Hensel Z, Xiao J, Wang J. Analytical calculation of protein production distributions in models of clustered protein expression, Phys Rev Lett E, 2012, 85(3), PMID:2258712/li/li>
- Hensel Z, Xiao J, Single molecule methods for studying gene regulation in vivo, Pflügers Arch-European Journal of Physiology, 2013, Mar;465(3):383-95, PMCID: PMC3595547.
- Fang, X, Liu, Q, Bohrer, C, Hensel Z, Han W, Wang J, Xiao J, New cell fate potentials and switching kinetics uncovered in a classic bistable switch, Nat. Commun, 2018, 2018, 9(1), 2787, PMCID: PMC6050291.
III. 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 transcription activity of the gene it controls . In one of our recent work 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 are currently developing new superresolution methods to probe both genome organization and transcription activity simultaneously in the same cells.
- Weng X, Xiao J, Spatial organization of transcription in E. coli, 2014, Trends in Genetics, 2014 Jul;30(7):287-297, PMCID: PMC6778201.
- Hensel Z, Weng X, Lagda A, Xiao J, Transcription factor mediated DNA looping probed by high-resolution, single-molecule imaging in live E. coli cells, 2013, PLoS Biology, 11(6):e1001591, PMCID: PMC3708714.
- 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 E. coli, P.N.A.S., 2019, 10.1073 /pnas.1903968116, PMCID: PMC6778201.
- 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. 2020 Jul 8;. doi: 10.1111/mmi.14572. PMID: 32640056.
IV. Development of single-molecule imaging and analysis tools
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 started collaborating 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 [3, 4].
- Fu, G., Huang T, Buss J, Coltharp C, Hensel Z, and Xiao J, In vivo structure of the E. coli FtsZ-ring revealed by photoactivated localization microscopy (PALM). PLoS One, 2010. 5(9): p. e12682. PMC2938336.
- Bohrer C.H, Yang X, Weng X, Tenner B, Thakur S, cQuillen R, Ross B, Wooten M, Chen X, Lakadamyali M, Zhang J, Roberts E, Xiao J. A Pairwise Distance Distribution Correction (DDC) algorithm to eliminate blinking-caused artifacts in super-resolution microscopy. Nat. Method, 2021, 18, pages 669–677 (2021).
- Wooten M, Snedeker J, Nizami ZF, Yang X, Ranjan R, Urban E, Kim JM, Gall J, Xiao J, Chen X. Asymmetric histone inheritance via strand-specific incorporation and biased replication fork movement. Nat. Struct. Mol. Biol. 2019 Aug;26(8):732-743, PMCID: PMC6684448.
- Mao CP, Wang SC, Su YP, Tseng SH, He L, Wu A, Roden R, Xiao, J, Hung CF. Protein detection in blood with single-molecule imaging. Sci. Rep., accepted, 2021.
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/