The Rapoport lab studies how proteins move across membranes and how membranes are shaped.

We are interested in the molecular mechanisms by which proteins are transported across the endoplasmic reticulum (ER) membrane. Proteins are transported through a protein-conducting channel, formed from a conserved trimeric membrane protein complex, called the Sec61p complex in eukaryotes, and the SecY complex in prokaryotes. The channel is a passive pore that needs to associate with partners that provide a driving force for translocation. We have solved the Xray structure of the resting channel formed from the SecY complex from an archaebacterium and, more recently, the structure of bacterial channels that are “preactivated” by the ATPase SecA. These structures have led to a number of predictions that we are currently testing.

A major direction in the lab is to understand the mechanism of co-translational translocation, in which the ribosome is the major partner. Our present work concentrates on the structure of ribosome- nascent chain-channel complexes. We try to obtain structural information using electron cryo-microscopy (collaboration with the group of Christopher Akey at Boston University), using complexes of non-translating ribosomes and channel. Our current goal is to obtain high-resolution electron microscopy structures of ribosome-channel complexes that contain a translocating polypeptide chain.

Another goal is to understand the mechanism of posttranslational translocation in bacteria, in which the ATPase SecA is the major channel partner. We have obtained crystal structures of a complex containing the channel and SecA, which has led to proposals on the mechanism of translocation. We are currently testing these ideas with biochemical experiments.

We are also interested in the process by which misfolded proteins are transported from the ER back into the cytosol for degradation by the proteasome (a process called ERAD). Depending on the localization of the misfolded domain of an ER protein, there are three different ERAD pathways, each employing a distinct ubiquitin-ligase complex. The pathways converge at the point of the p97/Cdc48p ATPase complex, which recognizes ubiquitinated substrates and moves them into the cytosol. Our current efforts are directed towards further elucidation of the molecular mechanism of the ERAD pathways using reconstituted systems with purified components. We are particularly interested in identifying the protein-conducting channel.

A third major project in the lab concerns the mechanism by which the endoplasmic reticulum adopts its characteristic shape. We have used an in vitro assay in Xenopus egg extracts to identify reticulon 4A as a component involved in tubule formation. The reticulons and DP-1/Yop1p shape the tubular ER in all eukaryotic cells. We try to understand the precise mechanism by which these proteins induce tubules. We have identified a class of membrane-bound GTPases that mediate the fusion of ER tubules. We now try to elucidate the mechanism of fusion. Finally, we are interested how tubular junctions and sheets of the ER are generated, and how sheets are stacked on top of each other.

Other project:
Mechanisms by which proteins are transported into peroxisomes.

Selected Publications:

Baldridge, R.D. and Rapoport, T.A. (2016), Cell 166, 1-14.  Autoubiquitination of the Hrd1 ligase triggers protein retrotranslocation in ERAD.  PMCID: PMC4946995
 
Li, L., Park, E., Ling., J., Ingram, J., Ploegh, H., and Rapoport, T.A. (2016) Nature 531(7594), 395-9.  Crystal structure of a substrate-engaged SecY protein-translocation channel. PMCID: PMC4855518
 
Terasaki, M., Shemesh, T., Kasthuri, N., Klemm, R.W., Schalek, R., Hayworth, K.J., Hand, A.R., Huber, G., Lichtman, J.W., Rapoport, T.A., and Kozlov, M.M. (2013) Cell 154(2), 285-296.
Stacked endoplasmic  reticulum sheets are connected by heliocoidal membrane motifs. PMCID: PMC3767119.
 
Voeltz, G.K., Prinz, W.A., Shibata, Y., Rist, J.M., and Rapoport, T.A. (2006) Cell 124, 573-86.  A class of membrane proteins shaping the tubular endoplasmic reticulum.
 
van den Berg, L., Clemons, W., Collinson, I., Modis, Y., Hartmann, E., Harrison, S.C., and Rapoport, T.A. (2004) Nature 427, 36-44.  X-ray structure of a protein-conducting channel.