B.A. Univ. of Kansas, 1993
Ph.D. Washington Univ. - St. Louis, 1998
Postdoc. Princeton Univ., 1998-2006
Research Scientist, Princeton Univ., 2006-2010
The cell envelope of Gram-negative bacteria is typically composed of the inner and outer membranes (IM and OM, respectively), an aqueous compartment known as the periplasm, and a mesh-like layer known as peptidoglycan (PG). Proper envelope biogenesis is crucial for the bacterium and it requires the coordinated synthesis, transport and assemblage of all its components. In our laboratory, we use genetic and biochemical approaches to understand envelope biogenesis in the Gram-negative bacterium Escherichia coli.
Understanding PG biogenesis
PG is a glycopeptide polymer composed of glycan chains that are cross-linked through their stem peptides. PG is conserved among most bacteria and protects such cells from osmotic lysis. In addition, the PG mesh determines cell shape and serves as a scaffold for other envelope structures.
In order to build the PG layer, the cell first synthesizes the PG precursor lipid II in the cytoplasm. Then, lipid II is transported across the IM so that its disaccharide component is polymerized into glycan chains by transglycosylases and its peptide is cross-linked to others by transpeptidases in the periplasm. We have proposed a model where the IM protein MurJ flips lipid II across the IM. One of the main focuses of our research is to understand the essential role that MurJ has in PG biogenesis.
Understanding LPS biogenesis
In E. coli, the OM serves as the main protective barrier against toxic molecules present in the environment. Because of the impermeability of its OM, E. coli is naturally resistant to many antibiotics. The main component of the OM responsible for providing this barrier-like quality to the OM is LPS, a lipopolysaccharide that is located at the cell surface.
LPS is synthesized in the cytoplasmic leaflet of the IM. Therefore, it must be transported across the cell envelope before it is assembled at the cell surface. We know that the ABC transporter MsbA flips LPS across the IM and that once it is in the periplasmic leaflet of the IM, LPS is transported to the cell surface by the Lpt trans-envelope complex. This Lpt complex is composed of seven different proteins that are essential for LPS transport and viability of E. coli. In our laboratory, we are interested in understanding how the Lpt transport machine functions.
- Butler EK, Davis RM, Bari V, Nicholson PA & 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
- Yao Z, Davis RM, Kishony R, Kahne D & Ruiz N. (2012) Regulation of cell size in response to nutrient availability by fatty acid biosynthesis in Escherichia coli. Proc Natl Acad Sci U S A Epub August 20. PMID:22908292
- Freinkman E, Okuda S, Ruiz N & Kahne D. (2012) Regulated assembly of the transenvelope protein complex required for lipopolysaccharide export. Biochemistry 51:4800-4806. PMID:22668317
- Karoamoto M, Cline S, Redding K, Ruiz N & Hamel PP. (2011) Lumen Thiol Oxidoreductase1, a disulfide bond-forming catalyst, is required for the assembly of photosystem II in Arabidopsis. Plant Cell 23:4446-4461. PMID: 22209765
- Ruiz N, Chng SS, Hiniker A, Kahne D & Silhavy TJ. (2010) Nonconsecutive disulfide bond formation in an essential integral outer membrane protein. Proc Natl Acad Sci U S A. 107:12245-50.
- Chng SS, Ruiz N, Chimalakonda G, Silhavy TJ & Kahne D. (2010) Characterization of the two-protein complex in Escherichia coli responsible for lipopolysaccharide assembly at the outer membrane. Proc Natl Acad Sci U S A. 107: 5363-8.
- Ruiz N, Kahne D & Silhavy TJ. (2009) Transport of lipopolysaccharide across the cell envelope: the long road of discovery. Nature Rev Microbiol. 7: 677-83.
- Ruiz N (2009) Streptococcus pyogenes YtgP (Spy_0390) complements Escherichia coli strains depleted of the putative peptidoglycan flippase MurJ. Antimicrob Agents Chemother. 53: 3604-5.
- Vertommen D, Ruiz N, Leverrier P, Silhavy TJ & Collet JF. (2009) Characterization of the role of the Escherichia coli periplasmic chaperone SurA using differential proteomics. Proteomics 9: 2432-43.
- 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: 15553-7.
- Ruiz N, Gronenberg LS, Kahne D & Silhavy TJ. (2008) Identification of two inner-membrane proteins required for the transport of lipopolysaccharide to the outer membrane of Escherichia coli. Proc Natl Acad Sci U S A. 105: 5537-42.
- Ruiz N, Wu T, Kahne D & Silhavy TJ. (2006) Probing the barrier function of the outer membrane with chemical conditionality. ACS Chem Biol. 1: 385-95.
- Ruiz N, Kahne D & Silhavy TJ. (2006) Advances in understanding bacterial outer membrane biogenesis. Nature Rev Microbiol. 4: 57-66.
- Ruiz N, Falcone B, Kahne D & Silhavy TJ. (2005) Chemical conditionality: A genetic strategy to probe organelle assembly. Cell. 121: 307-17.
- Wu T, Malinverni J, Ruiz N, Kim S, Silhavy TJ & Kahne D. (2005) Identification of a multi-component complex required for outer membrane biogenesis in Escherichia coli. Cell. 121: 235-45.