Global analysis of chaperone effects using a reconstituted cell-free translation system Tatsuya Niwaa, Takashi Kanamorib,1, Takuya Uedab,2, and Hideki Taguchia,2 aDepartment of Biomolecular Engineering, Graduate School of Biosciences and Biotechnology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8501, Japan; and bDepartment of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba 277-8562, Japan Edited by George H. Lorimer, University of Maryland, College Park, MD, and approved April 19, 2012 (received for review January 25, 2012) Protein folding is often hampered by protein aggregation, which can three chaperone systems are known to act cooperatively: TF and be prevented by a variety of chaperones in the cell. A dataset that DnaK exhibit overlapping cotranslational roles in vivo (13–15). evaluates which chaperones are effective for aggregation-prone Overexpression of DnaK/DnaJ and GroEL/GroES in E. coli proteins would provide an invaluable resource not only for un- rpoH mutant cells, which are deficient in heat-shock proteins, derstanding the roles of chaperones, but also for broader applications prevents aggregation of newly translated proteins (16). GroEL is in protein science and engineering. Therefore, we comprehensively believed to be involved in folding after the polypeptides are re- evaluated the effects of the major Escherichia coli chaperones, trigger leased from the ribosome, although the possible cotranslational factor, DnaK/DnaJ/GrpE, and GroEL/GroES, on ∼800 aggregation- involvement of GroEL has also been reported (17–20). prone cytosolic E. coli proteins, using a reconstituted chaperone-free Over the past two decades many efforts have been focused on translation system. Statistical analyses revealed the robustness and elucidating the mechanism of each chaperone as a molecular the intriguing properties of chaperones. The DnaK and GroEL systems machine (4, 9). The next question to be addressed is which drastically increased the solubilities of hundreds of proteins with chaperone is effective for certain proteins. A dataset on the weak biases, whereas trigger factor had only a marginal effect on substrate biases for each chaperone would provide an invaluable solubility. The combined addition of the chaperones was effective for resource, not only for understanding the role of chaperones in a subset of proteins that were not rescued by any single chaperone protein folding but also for applications to protein science and system, supporting the synergistic effect of these chaperones. The engineering. However, the mechanisms by which chaperones resource, which is accessible via a public database, can be used to recognize their substrates are not fully understood. Although BIOCHEMISTRY investigate the properties of proteins of interest in terms of their global analyses of chaperone–protein interactions in cells have solubilities and chaperone effects. been conducted (4, 7, 8, 21–24), no systematic evaluation of chaperone effects under uniform conditions has been performed. chaperonin | Hsp60 | Hsp70 | aggregates | proteome In this context, a reconstituted cell-free translation system that only contains the essential factors for protein synthesis is ideal to ewly synthesized proteins emerging from the ribosome must evaluate the role of chaperones, because the cell-free system is Nfold into their native structures to acquire their functions (1). chaperone-free. Therefore, we chose an E. coli reconstituted cell- Although protein folding is a spontaneous process, in which the free system, the PURE system (25, 26). Using the PURE system, amino acid sequence dictates the native structure (2), nonproduc- we previously analyzed the aggregation propensities of all E. coli tive intermolecular interactions result in aggregate formation (1, 3, proteins under a chaperone-free condition (6). In addition, the 4). Because protein stability is marginal in general, proteins always PURE system has been used to investigate the role of GroE in the have the inherent risk of aggregation (3, 4). Perturbations of cel- folding of some newly synthesized proteins (19, 20, 27). We have lular proteostasis (4), such as cellular stresses or heterologous extended those previous studies to a comprehensive evaluation of recombinant protein expression, often cause protein aggregation in the major E. coli chaperones, TF, DnaK/DnaJ/GrpE (DnaKJE), the cell and the formation of inclusion bodies, which are one of the and GroEL/GroES (GroE), on ∼800 aggregation-prone, cytosolic bottlenecks in various types of biological research, from traditional E. coli proteins. The scheme of the global analysis is shown in Fig. molecular biology to modern synthetic biology (3, 4). 1: the one-by-one synthesis of individual aggregation-prone pro- To counteract the inevitable tendency toward protein aggre- teins in the presence of each chaperone, the quantification of gation, cells have evolved a variety of chaperones (5). Chaperones solubility by a centrifugation-based assay, and the statistical prevent irreversible aggregate formation by binding nonnative analyses of the collected data. This is an “in vitro (reconstituted) proteins and then assisting with productive folding (3, 4). Indeed, ” Escherichia coli proteome approach, in which the properties of thousands of when more than 3,000 proteins were synthesized proteins, including proteins with extremely low abundance in cells, by reconstituted cell-free translation under chaperone-free con- are investigated individually after cell-free translation. This large ditions, a substantial fraction of the proteome, a quarter of the fi dataset is an invaluable resource for investigations of the prop- proteins quanti ed, was aggregation-prone (6), implying that erties of proteins of interest. In addition, the statistical analysis of chaperones are required to rescue the aggregation-prone proteins. the data revealed many intriguing properties of chaperones in The best-characterized chaperones are those in E. coli (4). In terms of substrate recognition. E. coli, three major chaperone systems are known to be involved in the folding of newly synthesized proteins in the cytoplasm (4). The first is trigger factor (TF), which directly associates with the Author contributions: T.N., T.U., and H.T. designed research; T.N. and T.K. performed ribosome and interacts with nascent chains cotranslationally (7). research; T.N., T.K., T.U., and H.T. contributed new reagents/analytic tools; T.N., T.U., The second is DnaK, a member of the Hsp70 family that is and H.T. analyzed data; and T.N., T.U., and H.T. wrote the paper. widely conserved in all kingdoms of life and is considered to act The authors declare no conflict of interest. on a broad spectrum of proteins in cooperation with the This article is a PNAS Direct Submission. cochaperones, DnaJ and GrpE (4, 8, 9). The third is GroEL, 1Present address: GeneFrontier Corporation, Kashiwa, Chiba 277-0882, Japan. – which belongs to a well-conserved chaperonin family (4, 10 12). 2To whom correspondence may be addressed. E-mail: [email protected] or taguchi@ In the presence of ATP, GroEL forms a large cylindrical com- bio.titech.ac.jp. plex with the cochaperonin GroES, which encapsulates substrate This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. proteins within its cavity to assist with folding (4, 10–12). These 1073/pnas.1201380109/-/DCSupplemental. www.pnas.org/cgi/doi/10.1073/pnas.1201380109 PNAS Early Edition | 1of6 Downloaded by guest on September 26, 2021 physiological concentration, based on previous assessments of chaperone activities under cell-free conditions (19, 28, 29). The in vitro activities of each chaperone were confirmed (Fig. S1 and Materials and Methods). The [35S]methionine-labeled proteins were electrophoresed on SDS gels and quantified (Fig. 2A). The aggregation propensity was examined by a centrifugation assay (6). Briefly, an aliquot of the translation mixture was centrifuged, and then the supernatant fractions were electrophoresed and quanti- fied (Fig. 1). The solubility was defined as the proportion of the protein in the supernatant fraction to that in the uncentrifuged total protein sample. Typical results are shown in Fig. 2A.Almost all of the proteins (788 of 792) were quantified for their solubilities under each condition. Experimental error (defined as a SD) in the assay has been previously estimated to be 10% (6, 27). Indeed, the analysis in the absence of chaperones was reproducible, because the SD of the solubilities between the current and previous data (6) was less than 10% on average (Fig. S2A), and the solubilities of more than 90% of the translated proteins in the absence of a chaperone (718 of 788) were less than 30% (Fig. S2B). Because all of the translated proteins belong to the aggregation- prone group, which might occlude the exit tunnel in the ribosome, one might ask whether chaperones could facilitate protein syn- thesis by preventing aggregation. However, the presence of the chaperones had little influence on the yields of translated proteins (Fig. S3), suggesting that the overall translation efficiencies were not accelerated by any of the chaperones. Overview of the Dataset. In total, more than 3,000 assays (788 pro- teins × 4 conditions = 3,152) were conducted (Dataset S1). The arranged data, combined with data obtained from our previous ag- gregation analysis, are freely accessible at our online database (eSol database: http://tp-esol.genes.nig.ac.jp). Overall, the