Research Interests. single molecule biophysics, super-resolution imaging, cell division, gene regulation
Research Description. My laboratory focuses on developing novel single-molecule imaging tools in live cells to probe various dynamic aspects of cellular processes. We develop single-molecule gene expression reporting systems and chromosomal DNA conformation markers to probe the dynamics of gene regulation and transcription in live bacterial cells. We also pioneered the use of superresolution imaging to probe the structure, function and dynamics of the bacterial cell division machinery. Our work is at the frontier of imaging dynamic cellular processes, and has enabled new quantitative understandings of gene regulation and cell division. Recently we are expanding our horizons by collaborating with experts of different fields to map the spatial organization of a single cell’s genome and epigenetic markers, and to develop new single-molecule based technologies for sensitive early detection of cancer markers in blood samples.
Our major research topics are:
Structure, function and dynamics of bacterial cell division complex
In bacteria, cell division is carried out by a highly conserved supramolecular complex, the divisome. Understanding the structure and function of the divisome is important for developing new antibiotics. Central to the divisome is a ring-like structure formed by the essential FtsZ protein, named the Z-ring. However, it has been difficult to probe the in vivo structural organization of the Z-ring because of its small size and highly dynamic nature. We made our first major contribution to the field by illustrating the structural organization of the Z-ring in live E. coli cells using single-molecule based superresolution imaging. The structure provides an important foundation to understand how different components of the divisome are assembled and coordinated to carry out cell division. Next, we showed that there exists a multi-layered protein network residing in the cytoplasm, physically connecting the Z-ring to the chromosome to stabilize the Z-ring and coordinate cell division with chromosome segregation. We also provide substantial evidence to demonstrate that, in contrary to the common belief, the Z-ring is not the major constrictive force generator. Instead, septum closure rate is limited by cell wall growth, and further modulated by nucleoid segregation. Most recently we made the exciting discovery that FtsZ uses its GTP hydrolysis to power treadmilling dynamics to distribute sPG synthase FtsWI evenly along the septum to ensure smooth, symmetric septum formation without affecting their enzymatic activities. Our work redefines the role of the Z-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.
- 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), 2010, PLoS One, 5, e12680, [PMC2938336]
- 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
- Yang X., Lyu Z., Miguel A., McQuillen R., Huang K.C., Xiao J., GTPase activity-coupled treadmilling of the bacterial tubulin FtsZ organizes septal cell-wall synthesis, Science, 2017, 355, 744-747, [PMID: 28209899.
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 significantly 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, 2012, Nat. Struct. Mol. Biol. 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:22587120]
- 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, [PMID:23430319]
- 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, [PMID: 30018349]
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 are developing new 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. We are currently developing new superresolution methods to probe both genome organization and transcription activity simultaneously in the same cells.
- 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, [PMID:23853547]
- Weng X., Xiao J., Spatial organization of transcription in E. coli, 2014, Trends in Genetics, 2014 Jul;30(7):287-297, [PMID: 24862529]
- Coltharp C, Yang X., Xiao J., Quantitative analysis of single-molecule superresolution images, 2014, Curr Opin Struct Biol, Aug 29;28C:112-121, [PMID: 25179006]]
- Weng X, Bohrer, C.H., Bettridge K., Lagda, A.C., Cagliero, C., Jin, D. J., Xiao, J., Spatial organization of RNA polymerase and its relationship with transcription in E. coli, P.N.A.S., 2019, 10.1073/pnas.1903968116
Development of single-molecule imaging and analysis tools
We are the first to establish single-molecule localization based superresolution imaging in small bacterial cells. We develop computational methods and quantitative imaging analyses to counter blinking behaviors of fluorescent labels, correct confinement errors, and identify spatial features of cellular structures. 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.
- Bohrer, C.H., Bettridge, K., and Xiao, J., Reduction of Confinement Error in Single-Molecule Tracking in Live Bacterial Cells Using SPICER. Biophys. J. 2017. 112(4): p. 568-574, [PMID: 28256217]
- Mo, C.H., Ross, B., Hertel, F., Manna, P., Yang, X., Greenwald, E., Booth, C., Plummer, A.M., Tenner, B., Chen, Z., Wang, Y., Kennedy, E.J., Cole, P.A., Flemming, K.G., Palmer, A., Jimenez, R., Xiao, J., Dedecker, P., and Zhang, J., Genetically-Encoded Biosensors for Visualizing Live-cell Biochemical Activity at Superresolution. Nat. Meth, 2017. 14(4):427-434, [PMID: 28288122]
- Sy,u GD, Wang, SC, Ma, G, Liu, S, Pearce, D, Prakash, A, Henson, B, Weng, LC, Ghosh, D, Ramos, P, Eichinger, D, Pino, I, Dong, X, Xiao, J, Wang, S, Tao, N, Kim, KS, Desai, PJ, Zhu, H. Development and application of a high-content virion display human GPCR array. Nat. Commun. 2019, 10(1):1997, [PMID:31040288]
- 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, PMID: 31358945
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/