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Molecular chaperones and protein quality control: an introduction to the JBC Reviews thematic series

  • Johannes Buchner
    Correspondence
    To whom correspondence should be addressed: Technische Universität München Chemie, TU Munchen, Lichenbergr. 4, 85747 Garching, 85758 Germany. Tel.:49-89-49-89-28913340;
    Affiliations
    Department of Chemistry, Technical University of Munich, 85747 Garching, Germany
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Open AccessPublished:January 09, 2019DOI:https://doi.org/10.1074/jbc.REV118.006739
      Protein folding is a spontaneous process. However, under physiological conditions, proteins are inherently unstable, and the protein concentrations in living cells favor unspecific interactions between partially folded proteins. Thus, the cellular proteome requires the assistance of helper factors, the molecular chaperones, for quality control and the maintenance of protein homeostasis. This series of reviews delves into how these molecular machines work in the eukaryotic cell, how they convey resilience to life, how these functions have allowed expansion of the protein universe, and how we can target them for therapeutic purposes. Together, they present the progress made in recent years in our understanding of one of the most fundamental aspects of life.

      Introduction

      The life of proteins in cells is a difficult one. Proteins are structurally dynamic by nature. This allows them to perform their manifold functions. However, as a consequence, they are always on the verge of unfolding under physiological conditions. The cell is a crowded place with high protein concentrations and where proteins bump into each other constantly. Combined with the fragile nature of proteins, this could have detrimental consequences: proteins that lose part of their structure will readily entangle with other proteins and form unspecific aggregates. Thus, even under optimal conditions, it is hard to imagine how cells maintain a healthy and dynamic proteome. Life has to sustain the ever-changing environmental conditions, many of which negatively affect protein stability and function. The formation of amyloid structures, which serve as the basis for numerous devastating diseases, is an extreme example of the negative consequences of an uncontrolled aggregation process.
      To make life resilient, factors are needed that buffer the negative side of protein flexibility and even expand the accessible conformational space for proteins. This requires, in essence, a molecular quality control system surveying individual protein molecules in a promiscuous manner.
      Molecular chaperones are nature's solution to these challenges. They assist other proteins in acquiring and maintaining their structures, support cellular processes, and even link the activity of proteins to the stress status of the cell. By definition, they are not part of the final structure but form complexes with unfolded or partially folded non-native proteins. Often the energy of ATP is used for supporting conformational transitions in the chaperone proteins, which regulate their interaction with substrate proteins. This series of reviews walks through the surprisingly different ways in which chaperones function, taking us on a fascinating tour of cellular quality control.
      Protein folding starts at the ribosome. The kinetics of translation elongation plays an important role in determining the folding of the emerging polypeptide and has implications for diseases. Stein and Frydman (
      • Stein K.C.
      • Frydman J.
      The stop-and-go traffic regulating protein biogenesis: how translation kinetics control proteostasis.
      ) provide an update of our understanding of translation kinetics, describing the basis of local differences in translations speed, the consequences on protein fate, and the resulting regulatory principles as well as effects on downstream processes.
      As the nascent polypeptide chain leaves the ribosomal exit site, it further encounters a hub of molecular chaperones and modifying enzymes that act on the emerging protein. This population of chaperones, along with those that function elsewhere in the cell, is incredibly diverse, as Nature invented the concept of molecular chaperones several times independently. Accordingly, the different classes of chaperones discussed here are only functionally related; their sequences and structures are unique. We explore the function of different chaperone classes in several reviews in this series.
      One of the most versatile molecular chaperones is heat shock protein 70 (Hsp70). This protein is used in different contexts in the eukaryotic cell, ranging from de novo folding at the ribosome and protein translocation across membranes to the cooperation with other chaperone systems. Given its important function under physiological and stress conditions, Hsp70s are tightly regulated allosteric ATP-driven machines. The review by Mayer and Gierasch (
      • Mayer M.P.
      • Gierasch L.M.
      Recent advances in the structural and mechanistic aspects of Hsp70 molecular chaperones.
      ) discusses recent advances in understanding the conformational cross-talk between the two domains of Hsp70 involved in nucleotide and protein binding, respectively, and the two classes of co-chaperones that affect substrate interaction and the ATPase cycle.
      The theme of Hsp70 mechanism and co-chaperone regulation is expanded by the review by Hendershot and co-workers (
      • Pobre K.F.R.
      • Poet G.J.
      • Hendershot L.M.
      The endoplasmic reticulum (ER) chaperone BiP is a master regulator of ER functions: getting by with a little help from ERdj friends.
      ), which discusses specific aspects of the Hsp70 ER
      The abbreviations used are:
      ER
      endoplasmic reticulum
      ERdj
      ER-localized DnaJ protein
      sHsp
      small Hsp.
      homologue BiP and its regulation by co-chaperones from the J-protein family (ERdjs). BiP is the major folding factor in the ER and therefore is of crucial importance for folding and protein secretion from the eukaryotic cell. The authors present a comprehensive picture of the contribution of ERdjs to substrate binding and their contribution to the allosteric mechanism of BiP.
      A basic aspect of Hsp70 function that was only discovered recently is the direct cooperation of Hsp70 with the Hsp90 chaperone. The review by Genest et al. (
      • Genest O.
      • Wickner S.
      • Doyle S.M.
      Hsp90 and Hsp70 chaperones: collaborators in protein remodeling.
      ) describes the structural basis for this interaction, which was initially shown for Escherichia coli and later on for Saccharomyces cerevisiae. Their data suggest that this interaction is a conserved mechanism for handing over substrate proteins from Hsp70 to Hsp90 despite the differences in the complexities of their chaperone machineries.
      Hsp70 not only cooperates with Hsp90, but also with small Hsps (sHsps). These proteins are set apart from other chaperones by their highly dynamic quaternary structures, leading to ensembles of different-sized oligomers with smaller oligomers being the more active chaperones. As they function in an ATP-independent manner, mechanisms for regulating their activities are needed. Recent progress in understanding their regulation together with their emerging and at first glance counter-intuitive role in the formation of specific aggregates in the cell is discussed in the review by Haselbeck et al. (
      • Haselbeck M.
      • Weinkauf S.
      • Buchner J.
      Small heat shock proteins: simplicity meets complexity.
      ).
      In addition to the general chaperones, which serve hundreds of different substrate proteins, there are also molecular chaperones that are more specialized. One of the most prominent is Hsp47, an ER-resident protein. It has been shown to be required for stabilizing pro-collagen in its triple-helix form. The review by Ito and Nagata (
      • Ito S.
      • Nagata K.
      Roles of the endoplasmic reticulum–resident, collagen-specific molecular chaperone Hsp47 in vertebrate cells and human disease.
      ) explores the function of Hsp47 in collagen folding and discusses recently identified additional client proteins for this specialized chaperone.
      Early in the research of molecular chaperones, it became clear that these proteins work together in networks as mentioned above. To fully appreciate the importance of this cooperation, systems approaches and global interaction analyses are needed. Rizzolo and Houry (
      • Rizzolo K.
      • Houry W.A.
      Multiple functionalities of molecular chaperones revealed through systematic mapping of their interaction networks.
      ) summarize the insight gained from different high-throughput approaches and explain why further efforts are required for a comprehensive understanding of the functional interplay of molecular chaperones.
      Given their importance as hubs for protein folding control, molecular chaperones have also become attractive as drug targets. It has been shown that Hsp70 and Hsp90 can be targeted specifically, as well as sHsps such as α-crystallin found in the eye lens. The review from the Gestwicki and Shao (
      • Gestwicki J.E.
      • Shao H.
      Inhibitors and chemical probes for molecular chaperone networks.
      ) describes the basic concepts of targeting chaperones, the progress achieved thus far, the challenges in targeting these promiscuous proteins, and the prospects for future research.
      Targeting chaperones also requires improved knowledge of where they are relevant in disease states. A review by Chiosis and co-workers (
      • Wang T.
      • Rodina A.
      • Dunphy M.P.
      • Corben A.
      • Modi S.
      • Guzman M.L.
      • Gewirth D.T.
      • Chiosis G.
      Chaperome heterogeneity and its implications for cancer study and treatment.
      ) presents a novel concept toward this end, termed the “epichaperone network.” Here, the focus is on physical complexes of chaperone proteins found in different tumor cells. These complexes are important for tumor cell survival and can thus be targeted by chemical compounds. The authors point to the further characterization of these complexes and identification of small molecules specifically affecting the activities of tumor-specific chaperone complexes as critical next steps.
      The final contribution of the review series (
      • Xie L.
      • Jakob U.
      Inorganic polyphosphate, a multifunctional polyanionic protein scaffold.
      ) challenges the molecular chaperone concept as outlined at the beginning of this overview. Do molecular chaperones have to be proteins? Xie and Jakob's answer is “no.” The authors summarize recent findings that cells also use polyphosphate, long chains of phosphates linked together via anhydride bounds, to keep proteins soluble and refoldable–thus fulfilling the basic requirements for a molecular chaperone.
      Despite the wealth of information presented in this series, it was not possible to cover all aspects and all molecular chaperones. Furthermore, even concerning the components of the system, there may be a slew of additional chaperone proteins or co-factors not identified yet. The question of what makes a protein a chaperone substrate is also not completely answered yet. We have, however, reached a certain level of understanding as summarized in the exciting reviews of this series, which allows us now to explore the still large and unknown territories of the fascinating world of molecular chaperones.

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