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Comparison of crude lysate pellets from isogenic strains of yeast with different prion composition: Identification of prion-associated proteins

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Abstract

A new approach involving the comparative analysis of proteins of crude cell lysate pellets from isogenic strains of Saccharomyces cerevisiae distinguished by their prion composition permitted us to identify a large group of prion-associated proteins in yeast cells. 35 proteins whose aggregation state depends on prion content have been identified by 2D-electrophoresis followed by the MALDI analysis of a recipient [psi ] strain and of [PSI +] cytoductant. Approximately half of these proteins belong to functional groups of chaperones and enzymes involved in glucose metabolism. Other proteins are involved in translation, stress response and protein degradation. The data obtained are compared with the results of other groups who used different approaches to detect proteins involved in prion aggregates.

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References

  • Baci, L., Bertini, I., Boca, M., Girotto, S., Martinelli, M., Valentine, J.S., and Vieru, M., SOD1 and Amyotrophic Lateral Sclerosis: Mutations and Oligomerization. PLoS ONE, 2008, vol. 3, pp. e1677.

    Article  Google Scholar 

  • Bagriantsev, S.N., Gracheva, E.O., Richmond, J.E., and Liebman, S.W., Variant-Specific [PSI+] Infection Is Transmitted by Sup35 Polymers within [PSI +] Aggregates with Heterogeneous Protein Composition. Mol. Biol. Cell., 2008, vol. 19, pp. 2433–2443.

    Article  CAS  PubMed  Google Scholar 

  • Buchan, J.R., Muhlrad, D., and Parker, R., P. Bodies Promote Stress Granule Assembly in Saccharomyces cerevisiae. J. Cell. Biol., 2008, vol. 183, pp. 441–455.

    Article  CAS  PubMed  Google Scholar 

  • Cashikar, A.G., Duennwald, M., and Lindquist, S.L., A Chaperone Pathway in Protein Disaggregation: HSP26 Alters the Nature of Protein Aggregates to Facilitate Reactivation by HSP104. J. Biol. Chem., 2005, vol. 280, pp. 23869–23875.

    Article  CAS  PubMed  Google Scholar 

  • Chernoff, Y.O., Cellular Control of Prion Formation and Propagation in Yeast, in Prions and Prion Diseases: Current Perspectives, Wymondham: Horizon Bioscience, 2004, pp. 257–303.

    Google Scholar 

  • Chernoff, Y.O., Identity Determinants of Infectious Proteins. Proc. Natl. Acad. Sci. USA, 2008, vol. 105, pp. 13191–13192.

    Article  CAS  PubMed  Google Scholar 

  • Chernoff, Y.O., Lindquist, S.L., Ono, B., Inge-Vechtomov, S.G., and Liebman, S.W., Role of the Chaperone Protein hsp104 in Propagation of the Yeast Prion-Like Factor [PSI +]. Science, 1995, vol. 268, pp. 880–884.

    Article  CAS  PubMed  Google Scholar 

  • Chernoff, Y.O., Newnam, G.P., Kumar, J., Allen, K., and Zink, A.D., Evidence of a Protein Mutator in Yeast: Role of the Hsp70-Related Chaperone Ssb in Formation, Stability, and Toxicity of the [PSI] Prion. Mol. Cell. Biol., 1999, vol. 19, pp. 8103–8112.

    CAS  PubMed  Google Scholar 

  • Chernoff, Y.O., Uptain, S.M., and Lindquist, S.L., Analysis of Prion Factors in Yeast. Meth. Enzymol., 2002, vol. 351, pp. 499–537.

    Article  CAS  PubMed  Google Scholar 

  • Chernova, T.A., Allen, K.D., Wesoloski, L.M., Shanks, J.R., Chernoff, Y.O., and Wilkinson, K.D., Pleiotropic Effects of Ubp6 Loss on Drug Sensitivities and Yeast Prion Are Due to Depletion of the Free Ubiquitin Pool. J. Biol. Chem., 2003, vol. 278, pp. 52102–52115.

    Article  CAS  PubMed  Google Scholar 

  • Cox, B.S., Byrne, L., and Tuite, M.F., Prion Stability, in Protein-Based Inheritance, Austin, Texas: Landes Bioscience, 2007, pp. 56–72.

    Google Scholar 

  • Derkatch, I.L. and Liebman, S.W., Prion-Prion Interactions, in Protein-Based Inheritance, Austin, Texas: Landes Bioscience, 2007, pp. 39–55.

    Google Scholar 

  • Du, Z., Park, K.-W., Yu, H., Fan, Q., and Li, L., Newly Identified Prion Linked to the Chromatin-Remodeling Factor Swi1 in Saccharomyces cerevisiae, Nature Genetics, 2008, vol. 40, pp. 460–465.

    Article  CAS  Google Scholar 

  • Elam, J.S., Taylor, A.B., Strange, R., Antonyuk, S., Doucette, P.A., Rodriguez, J.A., Hasnain, S.S., Hayward, L.J., Valentine, J.S., Yeates, T.O., and Hart, P.J., Amyloid-Like Filaments and Water-Filled Nanotubes Formed by SOD1 Mutant Proteins Linked to Familial ALS. Nat. Struct. Biol., 2003, vol. 10, pp. 461–467.

    Article  CAS  PubMed  Google Scholar 

  • Erjavec, N., Larsson, L., Grantham, J., and Nystrom, T., Accelerated Aging and Failure to Segregate Damaged Proteins in Sir2 Mutants Can Be Suppressed by Overproducing the Protein Aggregation-Remodeling Factor Hsp104p. Genes Dev., 2007, vol. 21, pp. 2410–2421.

    Article  CAS  PubMed  Google Scholar 

  • Glabe, C.G., Statistical Classification of Toxic Amyloid Oligomers. J. Biol. Chem., 2008, vol. 283, pp. 29639–29643.

    Article  CAS  PubMed  Google Scholar 

  • Griffith, J.S., Self-Replication and Scrapie. Nature, 1967, vol. 215, pp. 1943–1044.

    Google Scholar 

  • Harrison, L.B., Yu, Z., Stajich, J.E., Dietrich, F.S., and Harrison, P.M., Evolution of Budding Yeast Prion-Determinant Sequences across Diverse Fungi. J. Mol. Biol., 2007, vol. 368, pp. 273–282.

    Article  CAS  PubMed  Google Scholar 

  • Herczenik, E. and Gebbink, M.F.B.G., Molecular and Cellular Aspects of Protein Misfolding and Disease. FASEB J., 2008, vol. 22, pp. 2115–2133.

    Article  CAS  PubMed  Google Scholar 

  • Jones, G.W. and Masison, D.C.. Saccharomyces cerevisiae Hsp70 Mutations Affect [PSI+] Prion Propagation and Cell Growth Differently and Implicate Hsp40 and Tetratri-copeptide Repeat Cochaperones in Impairment of [PSI +]. Genetics, 2003, vol. 163, pp. 495–506.

    CAS  PubMed  Google Scholar 

  • Jung, G., Jones, G., Wegrzyn, R.D., and Masison, D.C., A Role for Cytosolic Hsp70 in Yeast [PSI+] Prion Propagation and [PSI+] as a Cellular Stress. Genetics, 2000, vol. 156, pp. 559–570.

    CAS  PubMed  Google Scholar 

  • Kryndushkin, D.S., Alexandrov, I.M., Ter-Avanesyan, M.D., and Kushnirov, V.V., Yeast [PSI+] Protein Aggregates Are Formed by Small Sup35 Polymers Fragmented by Hsp104. J. Biol. Chem., 2003, vol. 278, pp. 49636–49643.

    Article  CAS  PubMed  Google Scholar 

  • Kushnirov, V.V., Alexandrov, I.M., Mitkevich, O.V., Shkundina, I.S., and Ter-Avanesyan, M.D., Purification and Analysis of Prion and Amyloid Aggregates. Methods, 2006, vol. 39, pp. 50–55.

    Article  CAS  PubMed  Google Scholar 

  • Kushnirov, V.V., Vishnevskaya, A.B., Alexandrov, A.M., and Ter-Avanesyan, M.D., Prion and Nonprion Amyloids: A Comparison Inspired by the Yeast Sup35 Protein, in Protein-Based Inheritance, Austin, Texas: Landes Bioscience, 2007, pp. 73–82.

    Google Scholar 

  • Laemmli, U.K., Cleavage of Structural Proteins during the Assembly of the Head of Bacteriophage T4. Nature, 1970, vol. 227, pp. 680–685.

    Article  CAS  PubMed  Google Scholar 

  • Lian, H.Y., Jiang, Y., Zhang, H., Jones, G.W., and Perrett, S., The Yeast Prion Protein Ure2: Structure, Functions, and Folding. Biochim. Biophys. Acta, 2006, vol. 1764, pp. 535–545.

    CAS  PubMed  Google Scholar 

  • Lian, H.Y., Zhang, H., Zhang, Z.-R., Loovers, H.M., Jones, G.W., Rowling, P.J.E., Itzhaki, L.S., Zhou, J.-M., and Perrett, S., Hsp40 Interacts Directly with the Native State of the Yeast Prion Protein Ure2 and Inhibits Formation of Amyloid-Like Fibrils. J. Biol. Chem., 2007, vol. 282, pp. 11931–11940.

    Article  CAS  PubMed  Google Scholar 

  • Nemecek, J., Nakayashiki, T., and Wickner, R.B., A Prion of Yeast Metacaspase Homolog (Mca1p) Detected by a Genetic Screen. Proc. Natl. Acad. Sci. USA, 2009, vol. 106, pp. 1892–1896.

    Article  CAS  PubMed  Google Scholar 

  • Nevzglyadova, O.V., Artemov, A.V., Mittenberg, A.G., Mikhailova, E.V., Kuznetsova, I.M., Turoverov, K.K., and Soidla, T.R., Effect of the Red Pigment on Protein Amyloidization in Yeast. Tsitologiia, 2010a, vol. 51 (in press).

  • Nevzglyadova, O.V., Artemov, A.V., Mittenberg, A.G., Mikhailova, E.V., Kuznetsova, I.M., Turoverov, K.K., and Soidla, T.R., Yeast Protein Aggregates, Containing Chaperones and Glucose Metabolism Enzymes, in Molecular Chaperones: Roles, Structures and Mechanisms, Hauppauge, New York: Nova Publ., 2010b.

    Google Scholar 

  • Nevzglyadova, O.V., Artyomov, A.V., Mikhailova, E.V., and Soidla, T.R., The Impact of Manipulations with Cytoplasmically Inherited Factors on Nuclear Transmission and Degradation in Yeast Heterokaryons. Curr. Genet., 2004, vol. 45, pp. 273–282.

    Article  CAS  PubMed  Google Scholar 

  • Nevzglyadova, O.V., Kuznetsova, I.M., Artemov, A.V., Mikhailova, E.V., Turoverov, K.K., and Soidla, T.R., Estimating of Changes in the Amyloid and Prion Content of Yeast Cells. Tsitologiia, 2008, vol. 50 (1), pp. 40–48.

    Google Scholar 

  • Patel, B.K., Gavin-Smyth J., and Liebman, S.W., The Yeast Global Transcriptional Co-repressor Protein Cyc8 Can Propagate as a Prion. Nature Cell. Biol., 2009, vol 11, pp. 344–349.

    Article  CAS  PubMed  Google Scholar 

  • Prion Biology and Diseases, Prusiner, S.B., Ed., 2nd ed., Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, 2004.

    Google Scholar 

  • Protein-Based Inheritance, Chernoff, Y.O., Ed., Landes Bioscience: Austin, Texas, 2007.

    Google Scholar 

  • Rikhvanov, E.G., Romanova, N.V., and Chernoff, Y.O., Chaperone Effects on Prion and Nonprion Aggregates, in Protein-Based Inheritance, Austin, Texas: Landes Bioscience, 2007, pp. 83–92.

    Google Scholar 

  • Roberts, B.T. and Wickner, R.B., A Class of Prions That Propagate via Covalent Auto-activation. Genes Dev., 2003, vol. 17, pp. 2083–2087.

    Article  CAS  PubMed  Google Scholar 

  • Satpute-Krishnan, P. and Serio, T.R., Prion Protein Remodeling Confers an Immediate Phenotype Switch. Nature, 2005, vol. 437, pp. 262–265.

    Article  CAS  PubMed  Google Scholar 

  • Severin, S.E. and Solov’ev, G.A.. Praktikum po biokhimii (A Practical Course in Biochemistry), Moscow: Mosk. Gos. Univ., 1989.

    Google Scholar 

  • Sharma, D., Stanley, R.F., and Masison, D.C., Curing of Yeast [URE3] Prion by the Hsp40 Cochaperone Ydj1p Is Mediated by Hsp70. Genetics, 2009, vol. 181, pp. 129–137.

    Article  CAS  PubMed  Google Scholar 

  • Sherman, F., Fink, G.R., and Hicks, J.B.. Laboratory Course Manual for Methods in Yeast Genetics, Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press, 1986.

    Google Scholar 

  • Sitia, R. and Molteni, S.N., Stress, Protein (Mis)folding, and Signaling: The Redox Connection. Sci. STKE, 2004, vol. 239, p. e27.

    Google Scholar 

  • Takahashi, A., Hara, H., Kurahashi, H., and Nakamura, Y., A Systematic Evaluation of the Function of the Protein-Remodeling Factor Hsp104 in [PSI+] Prion Propagation in S. cerevisiae by Comprehensive Chromosomal Mutations. Prion, 2007, vol. 1, pp. 69–77.

    PubMed  Google Scholar 

  • Taneja, V., Maddelein, M.L., Talarek, N., Saupe, S.J., and Liebman, S.W., A Non-Q/N-Rich Prion Domain of a Foreign Prion, [Het-s], Can Propagate as a Prion in Yeast. Mol. Cell., 2007, vol. 27, pp. 67–77.

    Article  CAS  PubMed  Google Scholar 

  • Towbin, H., Staehelin, T., and Gordon, J., Electrophoretic Transfer of Proteins from Polyacrylamide Gels to Nitrocellulose Sheets: Procedure and Some Applications. Proc. Natl. Acad. Sci. USA, 1979, vol. 76, pp. 4350–4354.

    Article  CAS  PubMed  Google Scholar 

  • Tuite M.F. and Cox, B.S., The Genetic Control of the Formation and Propagation of the [PSI+] Prion in Yeast. Prion, 2007, vol. 1, pp. 101–109.

    PubMed  Google Scholar 

  • Uversky, V.N., Oldfield, C.J., and Dunker, A.K., Intrinsically Disordered Proteins in Human Diseases: Introducing the D2 Concept. Annu. Rev. Biophys., 2008, vol. 37, pp. 215–246.

    Article  CAS  PubMed  Google Scholar 

  • Uversky, V.N., Amyloidogenesis of Natively Unfolded Proteins. Curr. Alzheimer Res., 2008, vol. 5, pp. 260–287.

    Article  CAS  PubMed  Google Scholar 

  • Wang, Y., Meriin, A.B., Costello, C.E., and Sherman, M.Y., Characterization of Proteins Associated with Polyglutamine Aggregates: A Novel Approach towards Isolation of Aggregates from Protein Conformation Disorders. Prion, 2007, vol. 1, pp. 128–135.

    PubMed  Google Scholar 

  • Wang, Y., Meriin, A.B., Zaarur, N., Romanova, N.V., Chernoff, Y.O., Costello, C.E., and Sherman, M.Y., Abnormal Proteins Can Form Aggresome in Yeast: Aggresome-Targeting Signals and Components of the Machinery. FASEB J., 2008, vol. 23, pp. 451–463.

    Article  PubMed  Google Scholar 

  • Watt, N.T., Taylor, D.R., Gillott, A., Thomas, D.A., Sumudhu, W., Perera, S., and Hooper, N.G., Reactive Oxygen Species-Mediated β-Cleavage of the Prion Protein in the Cellular Response to Oxidative Stress. J. Biol. Chem., 2005, vol. 280, pp. 35914–35921.

    Article  CAS  PubMed  Google Scholar 

  • Wickner, R.B., [URE3] as an Altered URE2 Protein: Evidence for a Prion Analog in S. cerevisiae, Science, 1994, vol. 264, pp. 566–569.

    Article  CAS  PubMed  Google Scholar 

  • Wickner, R.B., Edskes, H.K., and Shewmaker, F., How to Find a Prion: [URE3], [PSI +] and [beta]. Methods, 2006, vol. 39, pp. 3–8.

    Article  CAS  PubMed  Google Scholar 

  • Wickner, R.B., Edskes, H.K., Shewmaker, F., Nakayashiki, T., Engel, A., McCann, L., and Kryndushkin, D., Yeast Prions: Evolution of the Prion Concept. Prion, 2007, vol. 1, pp. 94–100.

    PubMed  Google Scholar 

  • Wickner, R.B., Shewmaker, F., Kryndushkin, D., and Edskes, H.K., Protein Inheritance (Prions) Based on Parallel In-register β-Sheet Amyloid Structures. BioEssays, 2008, vol. 30, pp. 955–964.

    Article  CAS  PubMed  Google Scholar 

  • Zakharov, I.A. and Yarovoy, B., Cytoduction as a New Tool in Studying the Cytoplasmic Heredity in Yeast. Mol. Cell. Biochem., 1977, vol. 14, pp. 15–18.

    Article  CAS  PubMed  Google Scholar 

  • Zhou, R.Y., Li, X.L., Li, L.H., Li, X.Y., and Feng, F.J., Evolution and Differentiation of the Prion Protein Gene (PRNP) among Species. J. Heredity, 2008, vol. 99, pp. 647–652.

    Article  CAS  Google Scholar 

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Correspondence to O. V. Nevzglyadova.

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Original Russian Text © O.V. Nevzglyadova, A.V. Artemov, A.G. Mittenberg, E.I. Kostyleva, E.V. Mikhailova, K.V. Solovyov, I.M. Kuznetsova, K.K. Turoverov, T.R. Soidla, 2010, published in Tsitologiya, Vol. 52, No. 1, 2010, pp. 63–79.

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Nevzglyadova, O.V., Artemov, A.V., Mittenberg, A.G. et al. Comparison of crude lysate pellets from isogenic strains of yeast with different prion composition: Identification of prion-associated proteins. Cell Tiss. Biol. 4, 36–53 (2010). https://doi.org/10.1134/S1990519X10010049

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