Professor of Microbiology
264 Aronoff Building
318 W 12th Ave,
Columbus, OH 43210
Areas of Expertise
- Envelope biogenesis in Gram-negative bacteria
- B.A. University of Kansas, 1993
- Ph.D. Washington University, St. Louis, 1998
- Postdoc, Princeton University, 1998-2006
- Research Scientist, Princeton University, 2006-2010
The bacterial cell envelope mediates interactions with the outside world, provides cellular integrity, and serves as a protective permeability barrier. Properly building the cell envelope is therefore critical for bacteria to grow and thrive. Bacteria have evolved several types of cell envelopes that vary in architecture and composition. In the Ruiz laboratory, we use genetic and biochemical approaches to understand envelope biogenesis in Gram-negative bacteria, using Escherichia coli as our model. The Gram-negative cell envelope is composed of two membranes known as the inner and outer membranes, an aqueous compartment known as the periplasm, and a cell wall composed of peptidoglycan. Proper envelope biogenesis requires the coordinated synthesis, transport and assembly of all its components. In our laboratory, we study molecular machines that transport envelope components from their site of synthesis to the envelope compartment where they function.
Understanding peptidoglycan biogenesis
The peptidoglycan cell wall is a glycopeptide polymer composed of glycan chains that are cross-linked through stem peptides. The peptidoglycan cell wall is essential for viability as it protects bacteria from osmotic lysis. In addition, the structure of the peptidoglycan mesh determines cell shape and serves as a scaffold for other envelope structures. Bacteria synthesize a lipid-linked peptidoglycan precursor, known as Lipid II, in the cytoplasmic leaflet of the inner membrane. Then, Lipid II is transported across the membrane so that its disaccharide-peptide moiety is used to build the peptidoglycan structure. Our laboratory studies the function of MurJ, the flippase that transports Lipid II across the inner membrane.
Understanding LPS biogenesis
The cell surface of most Gram-negative bacteria is covered with a large glycolipid known as LPS. LPS molecules form a protective permeability barrier against many antibiotics and toxic molecules present in the environment. LPS is synthesized in the inner membrane and transported to the cell surface by the Lpt trans-envelope complex. Our laboratory investigates how the multi-protein Lpt machine functions to transport LPS across the cell envelope, a complex process that is required for cell growth.
Lundstedt, E.A, Kahne, D., Ruiz, N. (2020). Assembly and maintenance of lipids at the bacterial outer membrane. Chem Rev. doi: 10.1021/acs.chemrev.0c00587 (in press). PMID: 32955879.
Lundstedt, E.A, Simpson, B.W., Ruiz, N. (2020). LptB-LptF coupling mediates closure of the substrate-binding cavity in the LptB2FGC transporter through a rigid-body mechanism to extract LPS. Mol Microbiol. doi: 10.1111/mmi.14506. PMID: 32236984.
Rubino F.A., Mollo, A., Kumar, S., Butler, E.K.; Ruiz, N., Walker, S., Kahne, D. (2020). Detection of transport intermediates in the peptidoglycan flippase MurJ identifies residues essential for conformational cycling. J Am Chem Soc. 142:5482-5486. PMID: 32129990.
Simpson, B.W., Pahil, K.S., Owens, T.W., Lundstedt, E.A., Davis, R.M., Kahne, D., Ruiz, N. (2019). Combining mutations that inhibit two distinct steps of the ATP hydrolysis cycle restores wild-type function in the lipopolysaccharide transporter and shows that ATP binding triggers transport. mBio (4): e01931-19. doi: 10.1128/mBio.01931-19. PMID: 31431556.
Owens, T.W., Taylor, R.J., Pahil, K.S., Bertani, B.R., Ruiz, N., Kruse, A.C., Kahne, D. (2019) Structural basis of unidirectional export of lipopolysaccharide to the cell surface. Nature 567:550-553. PMID: 30894747.
Kumar, S., Rubino F.A., Mendoza, A.G., Ruiz, N. (2019) The bacterial lipid II flippase MurJ functions by an alternating-access mechanism. J Biol Chem 294(3):981-990. PMID: 30482840.
Bertani, B.R. Taylor, R.J, Nagy, E., Kahne, D., Ruiz, N. (2018) A cluster of residues in the lipopolysaccharide exporter that selects substrate variants for transport to the outer membrane. Mol Microbiol 109(4):541-554. PMID: 29995974.
Sham, L. T., Butler, E. K., Lebar, M. D., Kahne, D., Bernhardt, T.G., and Ruiz, N. (2014) MurJ is the flippase of lipid-linked precursors for peptidoglycan biogenesis. Science 345:220-222. PMID: 25013077.
Butler, E.K., Davis, R.M., Bari, V., Nicholson, P.A., and Ruiz, N. (2013) Structure-function analysis of MurJ reveals a solvent-exposed cavity containing residues essential for peptidoglycan biogenesis in Escherichia coli. J Bacteriol 195:4639-4649. PMID:23935042.
Ruiz, N. (2008) Bioinformatics identification of MurJ (MviN) as the peptidoglycan lipid II flippase in Escherichia coli. Proc Natl Acad Sci U S A 105: 15553-15557. PMCID: PMC2563115.