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Jun Liu, PhD

Assistant Professor
Pathology & Laboratory Medicine
(713) 500 - 5342
Jun.Liu.1@uth.tmc.edu

High-throughput cryo-electron tomography , 3-D structure/function of molecular machines in cells,
Bacterial motility and flagellar motor,
Bacterial chemotaxis and chemoreceptor array,
Bacteriophage and viral infection,
Lyme-disease spirochete,
E. coli minicell

 

Education: 1998, Chinese Academy of Sciences, Beijing, China 

Research Interests: My laboratory is interested in 3-D structure/function of molecular machines in living cells, which have emerged as one of the major challenges and excitements in Structural Biology. We developed two model systems (Lyme disease spirochete and E. coli minicell) to study bacterial flagellar motor, chemotaxis machinery and bacteriophage infection at native cellular environment. In particular, a high-throughput cryo-electron tomography (cryo-ET) system has been established and effectively utilized to visualize those molecular machines at the nanometer level.

High-throughput Cryo-Electron Tomography

Cryo-Electron Tomography (cryo-ET) is currently the most promising technology to determine 3-D architecture of nano-machines in situ at molecular resolution. We have established and optimized a high-throughput Cryo-ET system (Figure 1), which has been used effectively to collect cryo tomograms of intact B. burgdorferi cells embedded in thin vitreous ice. We have developed the unique procedure to visualize hundreds of cells at molecular resolution within one week, using a combination of automated Cryo-ET data collection and high-throughput image processing. The ability to rapidly produce and process hundreds of tilt series has improved both the throughput and the quality of the resulting 3-D reconstructions. It’s becoming possible to generate a high-resolution 3-D structure of molecular nano-machine in situ within a month.

Figure 1. High-throughput pipeline of Cryo-ET: from sample to high resolution 3-D structure in situ. Preparation of frozen hydrated specimen of viable B. burgdorferi cells (A) and the loading of multiple EM grids into a TEM microscope (B) takes about one hour. Nearly 100 cryo tomography tilt series of intact cells (C) can be generated by FEI batch tomography in three days. In three weeks, we are able to process the resulting data and determine the molecular architecture of the intact flagellar motor in situ (D).

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Molecular Architecture of Chemoreceptor Arrays

The chemoreceptors of Escherichia coli localize to the cell poles and form a highly ordered array in concert with the CheA kinase and the CheW coupling factor. We use cryo-electron tomography of flagellated E. coliminicells to derive a three-dimensional map of the intact array. Docking of high-resolution structures into the electron density map provides a model of the signaling complex, in which a CheA/CheW dimer bridges two adjacent receptor trimers via multiple hydrophobic interactions (Figure 2). An interaction between CheW and the homologous P5 domain of CheA in an adjacent core complex connects the complexes into an extended array (Figure 3). This architecture provides a structural basis for array formation and could explain the high sensitivity and cooperativity of chemotaxis signaling in E. coli.

Figure 2. Molecular architecture of the MCP-CheW-CheA core complex was determined by cryo-electron tomography of intact receptor arrays in E.coli minicells. A core complex with a stoichiometry of 6:2:1 (six MCP dimers and two CheW monomers for each CheA dimer) is shown in two different orientations (Liu et al. PNAS, 2012).

Figure 3. A simplified cartoon model of the receptor array assembly. The initial components, consisting of the P3 and P5 domains of CheA (orange), MCP trimer (blue), and CheW (yellow) form a core signaling complex (step 1). Three complexes are inter-connected by P5/CheW interactions to form a lattice unit (step 2), which can assemble further to form an indefinitely large array (step 3). Rings containing only CheW may play a role in reinforcing the network to achieve optimal cooperativity and sensitivity (step 4). Adapted from Liu et al. PNAS, 2012.

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Massive structural changes facilitate viral infection

Adsorption and genome ejection are fundamental to the bacteriophage life cycle, yet their molecular mechanisms are not well understood. We used cryo-electron tomography to capture T7 virions at successive stages of infection with unprecedented details (Figure 4). The six tail fibers fold against the capsid, extending and orienting symmetrically only after productive adsorption. Receptor binding by the tail triggers massive conformational changes, resulting in the insertion of an extended tail into the cell cytoplasm which functions as the DNA ejection channel. After ejection the extended tail collapses or disassembles, allowing membrane resealing. Our structures reveal the first complete pathway of infection initiation by any phage (Hu et al. Science 2013).

Figure. 4. Cryo-electron tomography captures T7 virions at successive stages of infection (Hu et al. Science 2013).

A T7 virus "walking" across a cell

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Lyme Disease Spirochete: Borrelia burgdorferi

B. burgdorferi belongs to a group of bacteria, called spirochetes, which are medically significant, but poorly understood. These organisms cause several major diseases in humans: syphilis (T. pallidum), Lyme disease (B. burgdorferi), and leptospirosis (L. interrogans). Syphilis is a major health problem in the world. Leptospirosis is the most common worldwide waterborne zoonosis. Lyme disease is the most common vector-borne infection in the United States, and has shown a steady increase in incidence since its discovery in 1975. Motility is an essential component of the pathogenesis of these and other bacteria and the flagellar motor is considered to be a proficient biological machine for this purpose.

We have focused on B. burgdorferi and its periplasmic flagella as a model system to study the flagellar structure and motility in situ. In collaboration with Dr. Steven Norris, we were able to visualize the three-dimensional structures of intact B. burgdorferi cells with unprecedented detail (as shown in Fig. 2), by using high-throughput cryo-ET.

Video: Surface views of flagellar motor are colored in light blue (stator and C ring), and beige (export apparatus)

By averaging the 3-D images of ~1280 flagellar motors, a ~3.5 nm resolution model of the stator and rotor structures was obtained (see video above). The results indicate an inherent flexibility in the rotor-stator interaction. The FliG switching and energizing component likely provides much of the flexibility needed to maintain the interaction between the curved stator and the relatively symmetrical rotor/C ring assembly during flagellar rotation. Transposon mutants of flgI lacked a torus-shaped structure attached to the flagellar rod, establishing the structural location of the spirochetal P ring. Therefore, combining genetics with our advanced imaging methods will permit a thorough analysis of the structure and assembly of the flagellar motor in situ at the molecular level.

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Structural basis of HIV viral entry and antibody neutralization

Interaction between HIV/SIV and broadly neutralizing antibodies revealed by cryo-ET

 

 

 

 

 

 

 

The envelope glycoproteins (Envs) of HIV/SIV mediate binding to CD4 and co-receptors on target cells to initiate viral entry and infection. The Envs comprise the functional trimeric spikes on the surface of the viral membrane and is composed of a transmembrane glycoprotein (gp41) and a surface glycoprotein (gp120). Although several crystal structures of gp120 monomer are known, the crystal structure of the HIV-1 Env trimer has not yet been determined. Our main goal is to provide molecular understanding of the mechanisms of HIV-1 antibody neutralization at its most fundamental level – the three-dimensional structures of native Envs and their interaction with broadly neutralizing antibodies, by using an approach outlined in Fig.3. A deeper understanding of how broad neutralization is accomplished could provide significant insights on the development of mimics of the viral envelope spike and the rational design of novel immunogen specifically tailored to elicit broadly neutralizing antibody responses against HIV.

CD4 binding results in a major opening of Env trimer of HIV revealed by Cryo-ET. These changes promote viral entry into host cell. [Liu et al. 2008 Nature]

Recently we determined the molecular architecture of native HIV-1 gp120 trimers on the envelope of virions [Liu et al. 2008 Nature], by using high-throughput cryo-ET. For the first time, we were able to demonstrate the structural and conformational changes that occur upon the binding of the Env spikes of HIV to its host cell surface receptor (CD4) (Fig.4) at 2.0nm resolution. The binding of Env to CD4 results in a major reorganization of the Env trimer and a close contact between the virus and target cell co-receptor, thus facilitating viral entry.
In addition, the novel techniques utilized in the projects will foster an in-depth understanding of a variety of human pathogens and offer a wide spectrum of important biomedical information at molecular resolution in living organisms.

Positions Available

We currently welcome applications from individuals with experience in Structural Biology or Microbiology
Please send your resume and statement of research interest to Jun.Liu.1@uth.tmc.edu