Chaperone interactions with ribosome-bound nascent chains: Role in protein folding

• Applicant: Professor Dr. Franz-Ulrich Hartl
• Subject Area: Biochemistry
• Term: from 2008 to 2014
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 50070218

• Final Report Year: 2014

Final Report Abstract

Proteins are the functionally most versatile macromolecules in our cells. They are synthesized as polymer chains of amino acids on ribosomes. But before a newly-synthesized protein can become biologically active, it must first fold into a well-defined three-dimensional structure. Protein folding is a complex process that is prone to errors. Aberrant protein folding may lead to the formation of faulty protein clumps (aggregates) between normally separate protein molecules, and these aggregates are the cause of numerous diseases, including Alzheimer’s and Parkinson’s disease. Thus, understanding how cells ensure the correct synthesis and folding of proteins is not only of fundamental biological interest but is also medically highly relevant. Over the last two decades scientists have realized that the folding process does not occur spontaneously, as had long been assumed, but instead requires assistance by specialized cellular machinery, so-called molecular chaperones. These chaperones, themselves proteins, interact with newly-synthesized protein chains as soon as they emerge from the ribosome and act to prevent their misfolding and aggregation. The detailed mechanisms underlying these activities are not yet well understood. In this project we have investigated the chaperone machinery involved in early protein folding steps on the ribosome and analyzed the supra-molecular organization of ribosomes into actively protein synthesizing poly- ribosome complexes. Our results show that new (nascent) protein chains can begin to fold as soon as a certain chain length has been reached that allows formation of compact or native-like structure. This process is accompanied and to some extent modulated by molecular chaperones. For example, the chaperone Trigger factor delays premature folding and thereby suppresses misfolding reactions that would be difficult to reverse at a later point in biogenesis. In collaboration with the group of Wolfgang Baumeister, using a specialized technique of electron microscopy (cryoelectron tomography), we made the surprising discovery that the ribosomes form highly organized assemblies (poly-ribosomes). Multiple ribosomes are densely-packed against each other, adopting a pseudo- helical topology, each ribosome synthesizing the same kind of protein chain. Importantly, this arrangement ensures that new protein chains are kept apart during synthesis and cannot clump together. Thus, the ribosome machinery itself contributes to minimizing protein aggregation. This first layer of optimization is then further supported by molecular chaperones that shield the nascent proteins. These findings provide new insights into the cellular mechanisms that supervise protein folding − arguably one of the most important processes in biology.

Publications

• (2009). The native 3D organization of bacterial polysomes. Cell 136, 261-271
  Brandt, F., Etchells, S.A., Ortiz, J.O., Elcock, A.H., Hartl, F.U., and Baumeister, W.
  
• (2010). Physico-Chemical Determinants of chaperone requirements. J Mol Biol 400, 579-588
  Tartaglia, G.G., Dobson, C.M., Hartl, F.U. and Vendruscolo, M.
  
• (2010). The threedimensional organization of polyribosomes in intact human cells. Mol Cell 39, 560-569
  Brandt, F., Carlson, L.-A., Hartl, F.U., Baumeister, W. and Grunewald, K.
  
• (2010). Trigger factor lacking the PPIase domain can enhance the folding of eukaryotic multi-domain proteins in E. coli. FEBS Lett 584, 3620-3624
  Gupta, R., Lakshmipathy, S.K., Chang, H.C., Etchells, S.A. and Hartl, F.U.
  
• (2010). Versatility of Trigger factor interactions with ribosome-nascent chain complexes. J Biol Chem 285, 27911-27923
  Lakshmipathy, S.K., Gupta, R., Pinkert, S., Etchells, S.A. and Hartl, F.U.
  
• (2011). Molecular chaperones in protein folding and proteostasis. Nature 475, 324-332
  Hartl, F.U., Bracher, A., and Hayer-Hartl, M.
  
• (2012). DnaK functions as a central hub in the E. coli chaperone network. Cell Reports 1, 251-264
  Calloni, G., Chen, T., Schermann, S.M., Chang, H.-C., Genevaux, P., Agostini, F., Tartaglia, G.G., Hayer-Hartl, M., and Hartl, F.U.
  
• (2012). Folding of large multidomain proteins by partial encapsulation in the chaperonin TRiC/CCT. Proc Natl Acad Sci USA 109, 21208-21215
  Rüßmann, F., Stemp, M.J., Mönkemeyer, L., Etchells, S.A., Bracher, and Hartl F.U.