Kentaro Noi, Aya Kitamura, Hidenori Hirai, Kunihiro Hongo, Toshihiko Sakurai, Tomohiro Mizobata, Yasushi Kawata^*

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Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science.
Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, Japan.
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Abstract: The Group II chaperonin from Thermoplasma acidophilum was added to the in vitro amyloid fibrillation reaction of yeast Sup35NM protein to assess its effects. By measuring the formation of Sup35NM fibrils in real time using the fluorescent dye Thioflavin T, we found that the addition of T. acidophilum-cpn α16, α1, and β1 proteins suppressed fibril formation. Addition of a 0.1 molar-equivalent T. acidophilum-cpn α16 relative to Sup35NM prolonged the initial lag-time of fibril formation and decreased the rate of fibril extension. Addition of 1 or 3 molar-equivalents of T. acidophilum-cpn monomers also produced a similar effect. Delayed addition of these chaperonins after the initial lag phase did not suppress fibril formation. Interestingly, these effects were also observed upon adding only the apical domain segments of α and β-subunits, and we also found that deletion of the helical protrusion in the apical domain of these segments led to an abolishment of the suppression effects. A synthetic peptide whose sequence corresponded to the helical protrusion also displayed a suppression effect, which indicated that archaeal group II chaperonin binds to Sup35NM through the helical protrusion of the apical domain. These findings suggest that group II chaperonin might be actively involved in suppressing amyloid fibril formation, in addition to acting as a protein folding assistant.

Keywords: Group II Chaperonin Monomer;Thermoplasma Acidophilum; Structure and Function; Suppression of Amyloid Fibril; Sup35NM Amyloid

Cite this paper: Noi, K. , Kitamura, A. , Hirai, H. , Hongo, K. , Sakurai, T. , Mizobata, T. and Kawata, Y. (2012) Suppression of Sup35 amyloid fibril formation by group II chaperonin from Thermoplasma acidophilum. American Journal of Molecular Biology, 2, 265-275. doi: 10.4236/ajmb.2012.23028.

References

[1]   Glover, J. R. and Lindquist, S. (1998) Hsp104, Hsp70, and Hsp40: a novel chaperone system that rescues previously aggregated proteins. Cell, 94, 73-82. http://dx.doi.org/10.1016/S0092-8674(00)81223-4

[2]   Chai, Y., Koppenhafer, S.L., Bonini, N.M. and Paulson, H.L. (1999) Analysis of the role of heat shock protein (Hsp) molecular chaperones in polyglutamine disease. Journal of Neuroscience, 19, 10338-10347.

[3]   Muchowski, P. J., Schaffar, G., Sittler, A., Wanker, E. E., Hayer-Hartl, M. K. and Hartl, F. U. (2000) Hsp70 and hsp40 chaperones can inhibit self-assembly of polyglutamine proteins into amyloid-like fibrils. Proceedings of the National Academy of Sciences USA, 97, 7841-7846. doi:10.1073/pnas.140202897

[4]   Stockel, J. and Hartl, F. U. (2001) Chaperonin-mediated de novo generation of prion protein aggregates. Journal of Molecular Biology, 313, 861-872. doi:10.1006/jmbi.2001.5085

[5]   Tam, S., Spiess, C., Auyeung, W., Joachimiak, L., Chen, B., Poirier, M.A. and Frydman, J. (2009) The chaperonin TRiC blocks a huntingtin sequence element that promotes the conformational switch to aggregation. Nature Structural and Molecular Biology, 16, 1279-1285. doi:10.1038/nsmb.1700

[6]   Behrends, C., Langer, C. A., Boteva, R., Bottcher, U. M., Stemp, M. J., Schaffar, G., Rao, B. V., Giese, A., Kretz-schmar, H., Siegers, K. and Hartl, F.U. (2006) Chaperonin TRiC promotes the assembly of polyQ expansion proteins into nontoxic oligomers. Molecular Cell, 23, 887-897. doi:10.1016/j.molcel.2006.08.017

[7]   Frydman, J., Nimmesgern, E., Erdjument-Bromage, H., Wall, J.S., Tempst, P. and Hartl, F.U. (1992) Function in protein folding of TRiC, a cytosolic ring complex containing TCP-1 and structurally related subunits. EMBO Journal, 11, 4767-4778.

[8]   Gao, Y., Thomas, J. O., Chow, R. L., Lee, G. H. and Cowan, N.J. (1992) A cytoplasmic chaperonin that catalyzes beta-actin folding. Cell, 69, 1043-1050. http://dx.doi.org/10.1016/0092-8674(92)90622-J

[9]   Yaffe, M. B., Farr, G. W., Miklos, D., Horwich, A. L., Sternlicht, M.L. and Sternlicht, H. (1992) TCP1 complex is a molecular chaperone in tubulin biogenesis. Nature, 358, 245-248. http://dx.doi.org/10.1038/358245a0

[10]   Marco, S., Carrascosa, J. L. and Valpuesta, J. M. (1994) Reversible interaction of beta-actin along the channel of the TCP-1 cytoplasmic chaperonin. Biophysical Journal, 67, 364-368. http://dx.doi.org/10.1016/S0006-3495(94)80489-8

[11]   Farr, G. W., Scharl, E. C., Schumacher, R. J., Sondek, S. and Horwich, A. L. (1997) Chaperonin-mediated folding in the eukaryotic cytosol proceeds through rounds of release of native and nonnative forms. Cell, 89, 927-937. http://dx.doi.org/10.1016/S0092-8674(00)80278-0

[12]   Ditzel, L., Lowe, J., Stock, D., Stetter, K. O., Huber, H., Huber, R. and Steinbacher, S. (1998) Crystal structure of the thermosome, the archaeal chaperonin and homolog of CCT. Cell, 93, 125-138. http://dx.doi.org/10.1016/S0092-8674(00)81152-6

[13]   Bukau, B. and Horwich, A. L. (1998) The Hsp70 and Hsp60 chaperone machines. Cell, 92, 351-366. http://dx.doi.org/10.1016/S0092-8674(00)80928-9

[14]   Gething, M. J. and Sambrook, J. (1992) Protein folding in the cell. Nature, 355, 33-45. http://dx.doi.org/10.1038/355033a0

[15]   Yifrach, O. and Horovitz, A. (2000) Coupling between protein folding and allostery in the GroE chaperonin system. Proceedings of the National Academy of Sciences USA, 97, 1521-1524. doi:10.1073/pnas.040449997

[16]   Ranson, N. A., Farr, G. W., Roseman, A. M., Gowen, B., Fenton, W. A., Horwich, A. L. and Saibil, H. R. (2001) ATP-bound states of GroEL captured by cryo-electron microscopy. Cell, 107, 869-879. http://dx.doi.org/10.1016/S0092-8674(01)00617-1

[17]   Hartl, F. U. and Hayer-Hartl, M. (2002) Molecular chaperones in the cytosol: from nascent chain to folded protein. Science, 295, 1852-1858. doi:10.1126/science.1068408

[18]   Taniguchi, M., Yoshimi, T., Hongo, K., Mizobata, T. and Kawata, Y. (2004) Stopped-flow fluorescence analysis of the conformational changes in the GroEL apical domain: relationships between movements in the apical domain and the quaternary structure of GroEL. Journal of Biological Chemistry, 279, 16368-16376. doi:10.1074/jbc.M311806200

[19]   Braig, K., Otwinowski, Z., Hegde, R., Boisvert, D. C., Joachimiak, A., Horwich, A. L. and Sigler, P.B. (1994) The crystal structure of the bacterial chaperonin GroEL at 2.8 A. Nature, 371, 578-586. http://dx.doi.org/10.1038/371578a0

[20]   Hunt, J. F., Weaver, A. J., Landry, S. J., Gierasch, L. and Deisenhofer, J. (1996) The crystal structure of the GroES co-chaperonin at 2.8 A resolution. Nature, 379, 37-45. http://dx.doi.org/10.1038/379037a0

[21]   Meyer, A. S., Gillespie, J. R., Walther, D., Millet, I. S., Doniach, S. and Frydman, J. (2003) Closing the folding chamber of the eukaryotic chaperonin requires the transition state of ATP hydrolysis. Cell, 113, 369-381. http://dx.doi.org/10.1016/S0092-8674(03)00307-6

[22]   Nitsch, M., Klumpp, M., Lupas, A. and Baumeister, W. (1997) The thermosome: alternating alpha and beta-sub-units within the chaperonin of the archaeon Thermoplasma acidophilum. Journal of Molecular Biology, 267, 142-149. http://dx.doi.org/10.1006/jmbi.1996.0849

[23]   Ruepp, A., Graml, W., Santos-Martinez, M. L., Koretke, K. K., Volker, C., Mewes, H. W., Frishman, D., Stocker, S., Lupas, A. N. and Baumeister, W. (2000) The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum. Nature, 407, 508-513. doi:10.1038/35035069

[24]   Bosch, G., Baumeister, W. and Essen, L.O. (2000) Crystal structure of the beta-apical domain of the thermosome reveals structural plasticity in the protrusion region. Journal of Molecular Biology, 301, 19-25. doi:10.1006/jmbi.2000.3955

[25]   Heller, M., John, M., Coles, M., Bosch, G., Baumeister, W. and Kessler, H. (2004) NMR studies on the substrate-binding domains of the thermosome: structural plasticity in the protrusion region. Journal of Molecular Biology, 336, 717-729. doi:10.1016/j.jmb.2003.12.035

[26]   Gutsche, I., Mihalache, O., Hegerl, R., Typke, D. and Baumeister, W. (2000) ATPase cycle controls the conformation of an archaeal chaperonin as visualized by cryo-electron microscopy. FEBS Letters, 477, 278-282. http://dx.doi.org/10.1016/S0014-5793(00)01811-1

[27]   Hirai, H., Noi, K., Hongo, K., Mizobata, T. and Kawata, Y. (2008) Functional characterization of the recombinant group II chaperonin alpha from Thermoplasma acidophilum. Journal of Biochemistry, 143, 505-515. doi:10.1093/jb/mvm241

[28]   Noi, K., Hirai, H., Hongo, K., Mizobata, T. and Kawata, Y. (2009) A potentially versatile nucleotide hydrolysis activity of group II chaperonin monomers from Thermoplasma acidophilum. Biochemistry, 48, 9405-9415. doi:10.1021/bi900959c

[29]   Cavicchioli, R., Pilak, O., Harrop, S. J., Siddiqui, K. S., Chong, K., De Francisci, D., Burg, D., Williams, T. J. and Curmi, P. M. G. (2011) Chaperonins from an Antarctic archaeon are predominantly monomeric: crystal structure of an open state monomer. Environmental Microbiology, 13, 2232-2249. doi:10.1111/j.1462-2920.2011.02477.x

[30]   Stansfield, I., Jones, K.M., Kushnirov, V.V., Dagkesamanskaya, A.R., Poznyakovski, A.I., Paushkin, S.V., Nierras, C.R., Cox, B.S., Ter-Avanesyan, M.D. and Tuite, M.F. (1995) The products of the SUP45 (eRF1) and SUP35 genes interact to mediate translation termination in Saccharomyces cerevisiae. EMBO Journal, 14, 4365-4373.

[31]   Spiess, C., Miller, E. J., McClellan, A. J. and Frydman, J. (2006) Identification of the TRiC/CCT substrate binding sites uncovers the function of subunit diversity in eukaryotic chaperonins. Molecular Cell, 24, 25-37. doi:10.1016/j.molcel.2006.09.003

[32]   Yagi, H., Kusaka, E., Hongo, K., Mizobata, T. and Kawata, Y. (2005) Amyloid fibril formation of alpha-synu- clein is accelerated by preformed amyloid seeds of other proteins: implications for the mechanism of transmissible conformational diseases. Journal of Biological Chemistry, 280, 38609-38616. doi:10.1074/jbc.M508623200

[33]   Glover, J. R., Kowal, A. S., Schirmer, E. C., Patino, M. M., Liu, J. J. and Lindquist, S. (1997) Self-seeded fibers formed by Sup35, the protein determinant of [PSI+], a heritable prion-like factor of S. cerevisiae. Cell, 89, 811-819. http://dx.doi.org/10.1016/S0092-8674(00)80264-0

[34]   Zahn, R., Buckle, A. M., Perrett, S., Johnson, C. M., Corrales, F. J., Golbik, R. and Fersht, A. R. (1996) Chaperone activity and structure of monomeric polypeptide binding domains of GroEL. Proceedings of the National Academy of Sciences USA, 93, 15024-15029. http://dx.doi.org/10.1073/pnas.93.26.15024

[35]   Klumpp, M., Baumeister, W. and Essen, L. O. (1997) Structure of the substrate binding domain of the thermosome, an archaeal group II chaperonin. Cell, 91, 263-270. http://dx.doi.org/10.1016/S0092-8674(00)80408-0

[36]   Jayasinghe, M., Tewmey, C. and Stan, G. (2010) Versatile substrate protein recognition mechanism of the eukaryotic chaperonin CCT. Proteins, 78, 1254-1265. doi:10.1002/prot.22644

[37]   Tipton, K. A., Verges, K. J. and Weissman, J. S. (2008) In vivo monitoring of the prion replication cycle reveals a critical role for Sis1 in delivering substrates to Hsp104. Molecular Cell, 32, 584-591. doi:10.1016/j.molcel.2008.11.003

[38]   Shorter, J. and Lindquist, S. (2008) Hsp104, Hsp70 and Hsp40 interplay regulates formation, growth and elimination of Sup35 prions. EMBO Journal, 27, 2712-2724. doi:10.1038/emboj.2008.194

[39]   Kubota, S., Kubota, H. and Nagata, K. (2006) Cytosolic chaperonin protects folding intermediates of Gbeta from aggregation by recognizing hydrophobic beta-strands. Proceedings of the National Academy of Sciences USA, 103, 8360-8365. doi:10.1073/pnas.0600195103

[40]   Krishnan, R. and Lindquist, S. L. (2005) Structural insights into a yeast prion illuminate nucleation and strain diversity. Nature, 435, 765-772. doi:10.1038/nature03679

[41]   Fenton, W. A., Kashi, Y., Furtak, K. and Horwich, A. L. (1994) Residues in chaperonin GroEL required for polypeptide binding and release. Nature, 371, 614-619. http://dx.doi.org/10.1038/371614a0

[42]   Xu, Z., Horwich, A. L. and Sigler, P.B. (1997) The crystal structure of the asymmetric GroEL-GroES-(ADP)7 chaperonin complex. Nature, 388, 741-750. http://dx.doi.org/10.1038/41944

[43]   Tanaka, N. and Fersht, A. R. (1999) Identification of substrate binding site of GroEL minichaperone in solution. Journal of Molecular Biology, 292, 173-180. http://dx.doi.org/10.1006/jmbi.1999.3041

[44]   Llorca, O., McCormack, E. A., Hynes, G., Grantham, J., Cordell, J., Carrascosa, J. L., Willison, K. R., Fernandez, J. J. and Valpuesta, J. M. (1999) Eukaryotic type II chaperonin CCT interacts with actin through specific subunits. Nature, 402, 693-696. http://dx.doi.org/10.1038/45294

[45]   Dekker, C., Stirling, P. C., McCormack, E. A., Filmore, H., Paul, A., Brost, R. L., Costanzo, M., Boone, C., Leroux, M. R. and Willison, K. R. (2008) The interaction network of the chaperonin CCT. EMBO Journal, 27, 1827-1839. doi:10.1038/emboj.2008.108

[46]   Yam, A. Y., Xia, Y., Lin, H. T., Burlingame, A., Gerstein, M. and Frydman, J. (2008) Defining the TRiC/CCT interactome links chaperonin function to stabilization of newly made proteins with complex topologies. Nature Structural and Molecular Biology, 15, 1255-1262. doi:10.1038/nsmb.1515

[47]   Koradi, R., Billeter, M. and Wuthrich, K. (1996) MOLMOL: a program for display and analysis of macromolecular structures. Journal of Molecular Graphics, 14, 51-55, 29-32.