Protein Folding in the Cytosol

<p>Prefoldin structure<br> Siegert et al., 2000, Cell 103, 621-632</p> Zoom Image

Prefoldin structure
Siegert et al., 2000, Cell 103, 621-632

Gupta, A.J., Haldar, S., Miličić, G., Hartl, F.U. and Hayer-Hartl, M. (2014). Active cage mechanism of chaperonin-assisted protein folding demonstrated at single-molecule level. J Mol Biol. 426, 2739-2754.

  In vitro studies over the last decade have outlined the basic mechanisms of two major chaperone systems that participate in protein folding in the cytosol, the Hsp70s and the chaperonins. Relatively little is known, however, about the actual role of these components in protein folding in vivo. Major questions being addressed in the laboratory concern the quantitative contribution of the various chaperone systems to overall protein folding and the mechanisms by which they select their substrates. As a long-term goal we wish to understand chaperone usage at a proteome-wide level for the three branches of life.

Two major types of chaperones act in de novo folding in the cytosol: Nascent chain-binding chaperones, such as trigger factor, the Hsp70s and prefoldin, stabilize nascent chains on ribosomes in a folding-competent, non-aggregated state. Folding is either achieved upon controlled chain release from this first set of chaperones or upon chain transfer to chaperones that act down-stream, such as the chaperonins. These are large, cylindrical complexes that provide a central compartment for a single protein chain to fold unimpaired by aggregation. These two classes of chaperone have been highly conserved in evolution and can cooperate in a topologically and timely ordered manner. However, the mechanism of

this cooperation is only poorly understood.

We are employing a range of methods from biophysics to cell biology to understand the mechanisms of these chaperone systems. Translation and folding experiments are performed in bacterial and eukaryotoc in vitro translation systems, as well as in Escherichia coli, certain mesophile archaea, S. cerivisiae and mammalian cells in culture. Ultimately, we try to define a complex process in intact cells and then to reconstitute it in vitro at the level of purified components. Advanced proteomics methods are used to understand the function of the cellular chaperone machinery at a systems level. These efforts are funded by
“Interaction Proteome” and "Prospects", two multi-centered, integrated projects of the EU.



Hartl, F.U. and Hayer-Hartl, M. (2002). Molecular chaperones in the cytosol: From nascent chain to folded protein. Science 295 , 1852-1858.

Young, J. C., Barral, J. M., and Hartl, F. U. (2003). More than folding: Localized functions of cytosolic chaperones. Trends Bioche. Sci. 28, 541-547.

Young, J.C., Agashe, V.R., Siegers, K., and Hartl, F.U. (2004). Pathways of chaperone-mediated protein folding in the cytosol. Nat Rev Mol Cell Biol. 5, 781-790.

Chang, H.-C., Tang, Y.-C., Hayer-Hartl, M., and Hartl, F. U. (2007). SnapShot: Molecular Chaperones, Part I. Cell 128, 212.e1-412.e2.

Tang, Y.-C.,Chang, H.-C., Hayer-Hartl, M., and Hartl, F. U. (2007). SnapShot: Molecular Chaperones, Part II. Cell 128, 412-412.e.1.

Kim, Y.E., Hipp, M., Bracher, A., Hayer-Hartl, M., and Hartl, F.U. (2013). Molecular chaperone functions in protein folding and proteostasis. Annual Rev Biochem 82, 323-355.

Research papers

Young, J.C., Hoogenraad , N.J. , and Hartl, F.U. (2003). Molecular chaperones Hsp90 and Hsp70 deliver preproteins to the mitochondrial import receptor Tom70. Cell 112 , 41-50.

Agashe, V.R., Guha, S., Chang, H.-C., Genevaux, P., Hayer-Hartl, M., Stemp, M., Georgopoulos, C., Hartl, F.U., and Barral, J.M. (2004). Function of trigger factor and DnaK in multi-domain protein folding: Increase in yield at the expense of folding speed. Cell 117 , 199-209.

Kerner, M.J., Naylor, D.J., Ishihama, Y., Maier, T., Chang, H.-C., Stines, A.P., Georgopoulos, C., Frishman, D., Hayer-Hartl, M., Mann, M. and Hartl, F.U. (2005). Proteome-wide analysis of chaperonin-dependent protein folding in Escherichia coli. Cell 122, 209-220.

Vabulas, R.M. and Hartl, F.U. (2005). Protein biogenesis upon acute nutrient restriction relies on proteasomal degradation of pre-existing proteins. Science 310, 1960-1963.

Tang, Y.-C., Chang, H.-C., Roeben, A., Wischnewski, D., Wischnewski, N., Kerner, M. J., Hartl, F. U., and Hayer-Hartl, M. (2006). Structural features of the GroEL-GroES nano-cage required for rapid folding of encapsulated protein. Cell 125, 903-914.

Dragovic, Z., Broadley, S.A., Shomura, Y., Bracher, A. and Hartl, F.U. (2006). Molecular chaperones of the Hsp110 family act as nucleotide exchange factors of Hsp70s. EMBO J. 25, 2519-2528.

Kaiser, C., Chang, H.-C., Agashe, V.R., Lakshmipathy, S.K., Etchells, S.A., Hartl, F.U. and Barral, J.M. (2006). Real-time observation of Trigger factor function on translating ribosomes. Nature 444, 455-460.

Lakshmipathy, S.K., Tomic, S., Kaiser, C.M., Chang, H.-C., Genevaux, P., Georgopoulos, C., Barral, J.M., Johnson, A.E., Hartl, F.U., and Etchells, S. (2007). Identification of nascent chain interaction sites on Trigger factor. J Biol Chem. 282, 12186-12193.

Ishihama, Y., Schmidt, T., Rappsilver, J., Mann, M. Hartl, F. U., Kerner, M. J., and Frishman, D. (2008). Protein abundance profiling of the Escherichia coli cytosol. BMC Genomics 9, 102.

Sharma, S., Chakraborty, K., Müller, B.K., Astola, N., Tang, Y.-C., Lamb, D.C., Hayer-Hartl, M. and Hartl, F.U. (2008). Monitoring protein conformation along the pathway of chaperonin-assisted protein folding. Cell 133, 142-153.

Tang, Y.-C., Chang, H.-C., Chakraborty, K., Hartl, F.U. and Hayer-Hartl, M. (2008). Essential role of the chaperonin compartment in vivo. EMBO J. 27, 1458-1468.

Polier, S., Dragovic, Z., Hartl, F.U. and Bracher, A. (2008). Structural basis for cooperative protein folding by Hsp70 and Hsp110 molecular chaperones. Cell 133, 1068-1079.

Brandt, F., Elcock, A.H., Etchells, S.A., Ortiz, J.O., Hartl, F.U.* and Baumeister, W.* (2009). The native 3D topology of bacterial polysomes. Cell 136, 261-271.

Hartl, F.U. and Hayer-Hartl, M. (2009). Converging concepts of protein folding in vitro and in vivo. Nat Struct Mol Biol. 16, 574-581.

Hirtreiter, A.M., Calloni, G., Forner, F., Scheibe, B., Puype, M., Vandekerckhove, J., Mann, M., Hartl, F.U.* and Hayer-Hartl, M.* (2009). Differential substrate specificity of group I and group II chaperonins in the archaeon Methanosarcina mazei. Mol Microbiol. 74, 1152-1168.

Chakraborty, K., Chatila, M., Sinha, J., Shi, Q., Poschner, B.C., Sikor, M., Jiang, G., Lamb, D.C., Hartl, F.U.*, and Hayer-Hartl, M.* (2010). Chaperonin-catalyzed rescue of entropically trapped states in protein folding. Cell 142, 112-122.

Tartaglia, G.G., Dobson, C.M., Hartl, F.U. and Vendruscolo, M. (2010). Physico-Chemical Determinants of chaperone requirements. J Mol Biol 400, 579-588.

Polier, S., Hartl, F.U., and Bracher, A. (2010). Interaction of the Hsp110 molecular chaperones from S. cerevisiae with substrate protein. J Mol Biol 401, 696-707.

Ortiz, J.O., Brandt, F., Matias, V.R.F., Sennels, L., Rappsilber, J., Scheres, S.H.W., Eibauer, M., Hartl, F.U., and Baumeister, W. (2010). Structure of hibernating ribosomes studied by cryoelectron tomography in vitro and in situ. J Cell Biol 190, 613-621.

Lakshmipathy, S.K., Gupta, R., Pinkert, S., Etchells, S.A. and Hartl, F.U. (2010). Versatility of Trigger factor interactions with ribosome-nascent chain complexes. J Biol Chem 285, 27911-27923.

Gupta, R., Lakshmipathy, S.K., Chang, H.C., Etchells, S.A. and Hartl, F.U. (2010). Trigger factor lacking the PPIase domain can enhance the folding of eukaryotic multi-domain proteins in E. coli. FEBS Lett 584, 3620-3624.  

Brandt, F., Carlson. L.-A., Hartl, F.U., Baumeister, W., and Grünewald, K. (2010). The three-dimensional organization of polyribosomes in intact human cells. Mol Cell 39, 560-569.

Vabulas, R.M., Raychaudhuri, S., Hayer-Hartl, M., and Hartl, F.U. (2010). Protein Folding in the cytoplasm and the heat shock response. CSH Perspectives, Dec 1;2(12):a004390.

Hartl, F.U., Bracher, A., and Hayer-Hartl, M. (2011). Molecular chaperones in protein folding and proteostasis. Nature 475, 324-332.

Sharma, K., Vabulas, M., Macek, B., Pinkert, S., Cox, J., Mann, M., and Hartl, F.U. (2012). Quantitative proteomics reveals that Hsp90 inhibition preferentially targets kinases and the DNA damage response. Mol Cell Proteomics, Mar;11(3):M111.014654. Epub 2011 Dec 13.

Lamond, A.I., Uhlen, M, Horning, S., Makarov, A., Robinson, C.V., Serrano, L., Hartl, F.U., Baumeister, W., Werenskiold, A.K., Andersen, J.S., Vorm, O., Linial, M., Aebersold, R., and Mann, M. (2012). Advancing cell biology through proteomics in space and time (PROSPECTS). Mol Cell Proteomics, Mar;11(3):O112.017731. Epub 2012 Feb 6.

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). DnaK functions as a central hub in the E. coli chaperone network. Cell Reports 1, 251-264.

Leitner, A., Joachimiak, L.A., Bracher, A., Mönkemeyer, L., Walzthoeni, T., Chen, B., Pechmann, S., Holmes, S., Cong, Y., Ma, B., Ludtke, S., Chiu, W., Hartl, F.U., Aebersold, R., and Frydman, J. (2012). The molecular architecture of the eukaryotic chaperonin TRiC/CCT.  Structure 20, 814-825. 

Tsai, Y.C., Mueller-Cajar, O., Saschenbrecker, S, Hartl, F.U.*, and Hayer-Hartl, M.* (2012). Chaperonin co-factors, Cpn10 and Cpn20, of green algae and plants function as hetero-oligomeric ring complexes. J Biol Chem 287, 20471-20481.

Herzog, F., Kahraman, A., Böhringer, D., Mak, R., Bracher, A., Walzthoeni, T., Leitner, A., Beck, M., Hartl, F.U., Ban, N., Malmstöm, L., and Aebersold, R. (2012). Structural probing of a protein phosphatase 2A network by chemical cross-linking and mass spectrometry. Science 337, 1348-1352.

Rüßmann, F., Stemp, M.J., Mönkemeyer, L., Etchells, S.A., Bracher, and Hartl F.U. (2012). Folding of large multidomain proteins by partial encapsulation in the chaperonin TRiC/CCT. Proc Natl Acad Sci U S A 109, 21208-21215.

Li, Z., Hartl, F.U.,* and Bracher, A.* (2013). Structure and function of Hip, an attenuator of the Hsp70 chaperone cycle. Nature Struct Mol Biol. 20, 929-935.

Gupta, A.J., Haldar, S., Miličić, G., Hartl, F.U. and Hayer-Hartl, M. (2014). Active cage mechanism of chaperonin-assisted protein folding demonstrated at single-molecule level. J Mol Biol. 426, 2739-2754.

Georgescauld, F., Popova, K., Gupta, A.J., Bracher, A., Engen, J.R. , Hayer-Hart, M., and Hartl, F.U. (2014). GroEL/ES chaperonin modulates the mechanism and accelerates the rate of TIM-barrel domain folding. Cell 157, 922-934.

Durão, P., Aigner, H., Nagy, P., Muller-Cajar, O., Hartl, F.U. and Hayer-Hartl, M. (2014). Opposing effects of folding and assembly ahaperones on evolvability of RuBisCO. Nature Chem Biol., in press.

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