Molecular Cell & Developmental Biology
225 Sinsheimer Laboratories
Phone: 831.459.4986
Fax: 831.459.3139
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Research in the Rexach lab focuses on two fundamental aspects of nucleocytoplasmic transport:

I. The mechanics of karyopherin movement across the nuclear pore complex

II. The architecture of the protein diffusion barrier in the nuclear pore complex

We are addressing these topics using a combination of cell biological, biochemical, biophysical, structural, genetic, molecular modeling and proteomics techniques in the model eukaryote S. cerevisiae.

Background: Structure and Function of the Nuclear Pore Complex

The nuclear pore complex (NPC) is a supramolecular protein structure in the nuclear envelope that creates a forty-nanometer channel connecting the cytoplasm and nucleoplasm of eukaryotic cells.  Its main function is to regulate the vital flow of proteins and RNA between these two major compartments.  Small particles diffuse freely across the NPC, but the flow of most large proteins and RNA is restricted and requires specific transit signals.  The signals are recognized by mobile receptors termed karyopherins (also called importins, exportins and transportins), which interact with proteins of the NPC (nucleoporins; Nups) to shuttle cargo across the NPC.  The process requires thermal energy to operate the NPC machinery, and chemical energy to impart directionality to the transport process via the Ran GTPase.

I. Mechanics of karyopherin-mediated transport across the nuclear pore complex

Many karyopherins and their cargo have been identified but a mechanistic description of how they are mobilized within the NPC is lacking. Each NPC contains more than 200 potential docking sites for karyopherins (provided by nucleoporins that contain FG repeats), so movement of karyopherin-cargo complexes across the NPC is envisioned to be a stochastic process that operates via repeated association-dissociation reactions of karyopherins with FG nucleoporins. Currently, we are charting the path of transport used by karyopherins within the NPC through the identification of nucleoporins that physically contact them in situ within the NPC transport conduit. We are also addressing the kinetics of karyopherin transport across the NPC by characterizing the dynamics of association and dissociation between karyopherins, cargos and nucleoporins, and by identifying factors (KaRFs) that function to accelerate the dissociation rate of the most stable, long-lived intermediate complexes in the transport processes.

II. Architecture of the protein diffusion barrier in the nuclear pore complex

Although the mechanics of karyopherin-mediated transport across the NPC are still poorly understood, it is clear that interactions between karyopherins and FG Nups are central to the translocation process.  Thus, knowledge of the structural characteristics of FG nucleoporins may explain how karyopherin-cargo complexes of different shapes and sizes can translocate across the NPC while its permeability barrier remains intact. To that end we are characterizing the structure of individual FG nucleoporins using biophysical, structural and molecular modeling techniques. We find that FG repeat regions of Nups are largely devoid of secondary structure and are mostly random coils 200-700 amino acids in length. Thus, the ~200 FG Nups present in each NPC could in principle form a flexible and highly amorphous meshwork of filaments at its center, which captures and ‘engulfs’ karyopherin-cargo complexes of different shapes and sizes as they move across the NPC. Indeed, we recently discovered that a discrete subset of FG nups self-assemble in vitro and in vivo into a meshwork of filaments held together by weak hydrophobic interactions between FG repeats. We are currently focusing our attention to elucidating the architecture and dynamics of this meshwork.

Selected Publications:

Denning, D. and Rexach, M. (2007) “Rapid evolution exposes the boundaries of domain structure and function in natively unfolded nucleoporins: Mol. Cell Prot. In press

Rexach, M. (2006) "A sorting importin on Sec61". Nat Struct Mol Biol. 13:476-478

Mason, D., Shulga, N., Undavai, S., Ferrando-May, E., Rexach, M., and Goldfarb, D. (2005) "Increased nuclear envelope permeability and Pep4p-dependent degradation of nucleoporins during hydrogen peroxide-induced cell death. FEMS Yeast Res. 5:1237-1251.

Denning, D., Patel, S., Uversky, V., Fink, A., Rexach, M  (2003) “Disorder in the nuclear pore complex: The FG repeat regions of nucleoporins are natively unfolded” PNAS 100: 2450-2455

Gilchrist, D., and Rexach, M. (2003) “Molecular basis for the rapid dissociation of nuclear localization signals from karyopherin a in the nucleoplasm” J. Biol. Chem. 278; 51937-51949

Pyhtila, B., and Rexach, M. (2003) “A gradient of affinity for the karyopherin Kap95p along the yeast nuclear pore complex” J. Biol Chem. 278; 42699-42709

Gilchrist, D., Mykytka, B., and Rexach, M. (2002) "Accelerating the rate of disassembly of karyopherin-cargo complexes." J. Biol. Chem. 277: 18161-18172.

Denning, D., Uversky, V., Patel, S., Fink, A., Rexach, M. (2002) "The S. cerevisiae nucleoporin Nup2p is a natively-unfolded protein." J. Biol. Chem. 277: 33447-33455.

Allen, N., Patel, S., Huang, L., Chalkley, R., Lutzmann, M., Hurt, E., Burlingame, A., Rexach, M. (2002) "Deciphering networks of protein interactions at the nuclear pore complex." Mol. Cell. Prot. 1.12; 930-946

Denning, D., Mykytka, B., Allen, N., Huang, L., Burlingame, A., and Rexach, M. (2001). "The nucleoporin Nup60p functions as a Gsp1p-GTP sensitive tether for Nup2 at the nuclear pore complex." J. Cell Biol. 154; 937-950.

Allen, N., Huang, L., Burlingame, A., and Rexach, M. (2001) "Proteomic analysis of nucleoporin-interacting proteins." J. Biol. Chem. 276: 29268-29274.