Hiroshi Nikaido

Professor of the Graduate School Division of Biochemistry, Biophysics and Structural Biology

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Research Interests

We are interested in the biochemical and molecular genetic analysis of the structure and functions of bacterial membranes. Topics currently pursued include the specific and non-specific channel-forming proteins of the outer membrane, the diffusion of lipophilic compounds (inhibitors and antibiotics) across the unusually impermeable bilayer domain of the outer membrane, as well as the mechanism and regulation of multidrug efflux transport systems that pump out an incredibly wide range of compounds from bacterial cells.

Current Projects

The most fundamental function of biological membrane is to serve as a general permeation barrier and at the same time to allow the selective permeation of certain types of molecules. We are trying to understand the molecular mechanisms underlying this function by using several systems.

All Gram-negative bacteria, including Escherichia coli, produce an extra membrane layer, called outer membrane, which is located outside the cytoplasmic membrane and the peptidoglycan (cell wall) layer. This is an ideal model for studies of this type, because sources of energy are not available at this location, and therefore the membrane allows only the passive and facilitated diffusion processes. In this system, we discovered one of the first examples of the proteins forming non-specific diffusion channels, and named it "porin." This was followed by our identification of the phage lambda receptor protein as the protein that produces channels specific for maltose and maltodextrins. We are studying the structure-function relationships in these channel-forming proteins by a variety of approaches. We believe these studies are of potential significance, not only because these channels can serve as models for other channels with more complex functions, but also because, from the practical point of view, most antibiotics have to pass through these outer membrane channels in order to be effective against Gram-negative bacteria.

Another example of an effective permeability barrier on cell surface is the cell wall of mycobacteria. We discovered that this is a bilayer of very unusual composition, with the parallel arrangement of extremely long fatty acid chains producing a structure of exceptionally low fluidity, which prevents the rapid influx of antibiotics and chemotherapeutic agents and thus contributes to the intrinsic resistance of these bacteria.

We became aware, however, during the course of these studies that permeability barriers by themselves are not sufficient to produce high levels of drug resistance. Search for additional mechanisms led to the discovery that most bacteria produce active efflux pumps that display extremely wide range of substrate specificity, a range that had not been suspected to exist earlier. For example, the AcrAB efflux pump of E. coli pumps out not only dyes and detergents but also practically all commercially important classes of antibiotics, with the sole exception of aminoglycosides, and in addition, even simple solvent molecules.

Furthermore, most Gram-negative pumps can excrete drugs directly into the external media, bypassing the outer membrane barrier: thus the slow entry of drugs through the outer membrane acts synergistically with the direct efflux process, to prevent the intracellular accumulation of noxious compounds. In addition, some of the pumps involved in this direct excretion process has an incredibly wide range of substrates: E. coli AcrB, which is constitutively expressed, can pump out most of the currently used antibiotics, disinfectants, detergents, dyes, and even solvents.  We are actively studying the molecular mechanisms of these fascinating transporters, as well as their physiological and genetic regulation.  The overexpression of pumps of this type can create multidrug resistance in one single event, and indeed contributes to the phenomenon of extensive multidrug resistance (and sometimes even pan-resistance) of gram-negative pathogens, creating infections for which doctors are left without a single effective antibiotic to use.

Selected Publications

The challenge of efflux-mediated antibiotic resistance in Gram-negative bacteria. [X.-Z. Li, P. Plesiat and H. Nikaido. (2015) Clin. Microbiol. Rev. 28, 337-418]

Properties of AdeABC and AdeIJK efflux systems of Acinetobacter baumannii compared with those of the AcrAB-TolC system of
Escherichia coli. [E. Sugawara and H. Nikaido. (2014) Antimicrob. Agents Chemother. 58, 7250-7257]

High salt concentrations increase permeability through OmpC channels of Escherichia coli. [S. Kojima and H. Nikaido. (2014) J. Biol. Chem. 289, 26464-26473]

Mycobacterial outer membrane is a lipid bilayer and the inner membrane is unusually rich in diacyl phosphatidylinositol dimannosides. [R. Bansal-Mutalik and H. Nikaido. (2014) Proc. Nat. Acad. Sci. U.S.A. 111, 4958-4963]

Some ligands enhance the efflux of other ligands by the Escherichia coli multidrug pump AcrB. [A. D. Kinana, A. V. Vargiu and H. Nikaido (2013) Biochemistry 52, 8342-8351]

Permeation rates of penicillins indicate that Escherichia coli porins function primarily as nonspecific channels. [S. Kojima and H. Nikaido (2013) Proc. Nat. Acad. Sci. U.S.A. 110, E2629-E2634]

Multidrug binding properties of the AcrB efflux characterized by molecular dynamic simulations. [A. V. Vargiu and H. Nikaido. (2012) Proc. Nat. Acad. Sci. USA 109, 20637-20642]

Quantitative lipid composition of cell envelopes of Corynebacterium glutamicum elucidated through reverse micelle extraction. [R. Bansal-Mutalik and H. Nikaido (2011) Proc. Nat. Acad. Sci. USA 108, 15360-15365.]

Mechanism of recognition of compounds of diverse structures by the multidrug efflux pump AcrB of Escherichia coli. [Y. Takatsuka, C. Chen, and H. Nikaido (2010) Proc. Nat. Acad. Sci. USA 107, 6559-6565.]

Covalently linked trimer of the AcrB multidrug efflux pump provides support for the functional rotating mechanism. [Y. Takatsuka and H. Nikaido. (2009) J. Bacteriol. 191, 1729-1737]

Kinetic behavior of the major multidrug efflux pump AcrB of Escherichia coli [K. Nagano and H. Nikaido. (2009) Proc. Nat. Acad. Sci. USA 106, 5854-5858]

Last Updated 2015-09-17