Wei Mi
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Research Summary
Cells are surrounded by the plasma membranes and a variety of cellular processes, such as substance transport and cell signaling, are carried out by proteins embedded in the membrane. Membrane proteins are targets of more than half of all modern pharmaceutical drugs, and they are notorious for structural determination. Recent breakthroughs in the cryo-electron microscopy (cryo-EM) field provide unprecedented tools to study structures of membrane proteins in their native environment and hence greatly improve our mechanistic views. The Mi laboratory exploits structural, biochemical and biophysical approaches to understand the structures and functions of membrane proteins.
Extensive Research Description
Antibiotic resistance is one of the most pressing public health challenges of our time, demanding new druggable targets, especially for Gram-negative bacteria. Compared with Gram-positive bacteria that have only a plasma membrane, Gram-negative bacteria have an additional unique outer membrane (OM). The OM has an asymmetric lipid structure, with phospholipids in the periplasmic leaflet and lipopolysaccharides (LPS) on the cell surface. Tightly packed LPS molecules form a remarkable permeability barrier against many antibiotics, including large polar molecules and hydrophobic agents. Because of the essential roles played by LPS in antibiotic resistance and bacterial viability, its biogenesis is an attractive target for antibacterial agents. Several inhibitors that target LPS synthesis and transport are under development as promising antibacterial candidates. However, proteins involved in the regulation of LPS biogenesis have not received a great deal of attention mainly because little is known about its regulation. Since very high or low amounts of LPS are lethal to cell viability, regulation of LPS biogenesis provides a potential opportunity for developing valuable antibiotics. By focusing on understanding how LPS biogenesis is regulated in Escherichia coli, we will provide new molecular mechanistic insights and identify novel targets and approaches for antibiotic development.
It has been known for more than two decades that LpxC, a key enzyme in LPS synthesis, determines LPS levels and that FtsH-dependent proteolysis in Escherichia coli primarily regulates LpxC cellular concentrations. However, how FtsH adjusts its protease activity to specifically regulate LpxC turnover rate according to cellular status is not clear. Recently, genetic analyses and in vivo studies suggested that two essential membrane proteins LapB (YciM) and YejM regulate FtsH protease activity, but there have been no in vitro studies on the regulatory mechanisms. The Mi lab established the first assays to reconstitute LpxC degradation in vitro. We have recently determined the cryoEM structure of YejM/LapB complex structure, elucidating the functions of these key membrane proteins in regulating LPS synthesis.
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Research Interests
Bacteria; Cell Wall; Lipid A; Lipid Bilayers; Membrane Proteins; Phospholipids; Shock, Septic; Cryoelectron Microscopy; Penicillin-Binding Proteins
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Selected Publications
- Dual function of LapB (YciM) in regulating Escherichia coli lipopolysaccharide synthesis.Shu S, Tsutsui Y, Nathawat R, Mi W. Dual function of LapB (YciM) in regulating Escherichia coli lipopolysaccharide synthesis. Proc Natl Acad Sci U S A 2024, 121: e2321510121. PMID: 38635633, DOI: 10.1073/pnas.2321510121.
- Cryo-EM analyses of KIT and oncogenic mutants reveal structural oncogenic plasticity and a target for therapeutic interventionKrimmer S, Bertoletti N, Suzuki Y, Katic L, Mohanty J, Shu S, Lee S, Lax I, Mi W, Schlessinger J. Cryo-EM analyses of KIT and oncogenic mutants reveal structural oncogenic plasticity and a target for therapeutic intervention. Proceedings Of The National Academy Of Sciences Of The United States Of America 2023, 120: e2300054120. PMID: 36943885, PMCID: PMC10068818, DOI: 10.1073/pnas.2300054120.
- Separating Inner and Outer Membranes of Escherichia coli by EDTA-free Sucrose Gradient CentrifugationShu S, Mi W. Separating Inner and Outer Membranes of Escherichia coli by EDTA-free Sucrose Gradient Centrifugation. Bio-protocol 2023, 13: e4638. PMID: 36968434, PMCID: PMC10031520, DOI: 10.21769/bioprotoc.4638.
- Regulatory mechanisms of lipopolysaccharide synthesis in Escherichia coliShu S, Mi W. Regulatory mechanisms of lipopolysaccharide synthesis in Escherichia coli. Nature Communications 2022, 13: 4576. PMID: 35931690, PMCID: PMC9356133, DOI: 10.1038/s41467-022-32277-1.
- Structural basis of ER-associated protein degradation mediated by the Hrd1 ubiquitin ligase complexWu X, Siggel M, Ovchinnikov S, Mi W, Svetlov V, Nudler E, Liao M, Hummer G, Rapoport TA. Structural basis of ER-associated protein degradation mediated by the Hrd1 ubiquitin ligase complex. Science 2020, 368 PMID: 32327568, PMCID: PMC7380553, DOI: 10.1126/science.aaz2449.
- DNA melting initiates the RAG catalytic pathwayRu H, Mi W, Zhang P, Alt FW, Schatz DG, Liao M, Wu H. DNA melting initiates the RAG catalytic pathway. Nature Structural & Molecular Biology 2018, 25: 732-742. PMID: 30061602, PMCID: PMC6080600, DOI: 10.1038/s41594-018-0098-5.
- Structural basis of MsbA-mediated lipopolysaccharide transportMi W, Li Y, Yoon SH, Ernst RK, Walz T, Liao M. Structural basis of MsbA-mediated lipopolysaccharide transport. Nature 2017, 549: 233-237. PMID: 28869968, PMCID: PMC5759761, DOI: 10.1038/nature23649.
- Cryo-EM structure of the protein-conducting ERAD channel Hrd1 in complex with Hrd3Schoebel S, Mi W, Stein A, Ovchinnikov S, Pavlovicz R, DiMaio F, Baker D, Chambers MG, Su H, Li D, Rapoport TA, Liao M. Cryo-EM structure of the protein-conducting ERAD channel Hrd1 in complex with Hrd3. Nature 2017, 548: 352-355. PMID: 28682307, PMCID: PMC5736104, DOI: 10.1038/nature23314.
- Single-particle electron microscopy in the study of membrane protein structureDe Zorzi R, Mi W, Liao M, Walz T. Single-particle electron microscopy in the study of membrane protein structure. Microscopy 2015, 65: 81-96. PMID: 26470917, PMCID: PMC4749050, DOI: 10.1093/jmicro/dfv058.
- Crystallization and preliminary X‐ray analysis of tubulin‐folding cofactor A from Arabidopsis thalianaLu L, Nan J, Mi W, Wei C, Li L, Li Y. Crystallization and preliminary X‐ray analysis of tubulin‐folding cofactor A from Arabidopsis thaliana. Acta Crystallographica Section F: Structural Biology Communications 2010, 66: 954-956. PMID: 20693679, PMCID: PMC2917302, DOI: 10.1107/s1744309110023900.
- CLIC2-RyR1 Interaction and Structural Characterization by Cryo-electron MicroscopyMeng X, Wang G, Viero C, Wang Q, Mi W, Su XD, Wagenknecht T, Williams AJ, Liu Z, Yin CC. CLIC2-RyR1 Interaction and Structural Characterization by Cryo-electron Microscopy. Journal Of Molecular Biology 2009, 387: 320-334. PMID: 19356589, PMCID: PMC2667806, DOI: 10.1016/j.jmb.2009.01.059.
- 5,5′-Dithio-bis(2-nitrobenzoic acid) modification of cysteine improves the crystal quality of human chloride intracellular channel protein 2Mi W, Li L, Su XD. 5,5′-Dithio-bis(2-nitrobenzoic acid) modification of cysteine improves the crystal quality of human chloride intracellular channel protein 2. Biochemical And Biophysical Research Communications 2008, 368: 919-922. PMID: 18280248, DOI: 10.1016/j.bbrc.2008.02.021.
- The crystal structure of human chloride intracellular channel protein 2: A disulfide bond with functional implicationsMi W, Liang Y, Li L, Su X. The crystal structure of human chloride intracellular channel protein 2: A disulfide bond with functional implications. Proteins Structure Function And Bioinformatics 2008, 71: 509-513. PMID: 18186468, DOI: 10.1002/prot.21922.
- Protein preparation, crystallization and preliminary X-ray crystallographic analysis of Smu.1475c from caries pathogen Streptococcus mutansZhou Y, Mi W, Li L, Zhang X, Liang Y, Su X, Wei S. Protein preparation, crystallization and preliminary X-ray crystallographic analysis of Smu.1475c from caries pathogen Streptococcus mutans. Biochimica Et Biophysica Acta 2005, 1764: 324-326. PMID: 16427820, DOI: 10.1016/j.bbapap.2005.11.022.