Abstract
Amyloid aggregation is linked to an increasing number of human disorders from nonneurological pathologies such as type-2 diabetes to neurodegenerative ones such as Alzheimer or Parkinson’s diseases. Thirty-six human proteins have shown the capacity to aggregate into pathological amyloid structures. To date, it is widely accepted that amyloid folding/aggregation is a universal process present in eukaryotic and prokaryotic cells. In the last decade, several studies have unequivocally demonstrated that bacterial inclusion bodies – insoluble protein aggregates usually formed during heterologous protein overexpression in bacteria – are mainly composed of overexpressed proteins in amyloid conformation. This fact shows that amyloid-prone proteins display a similar aggregation propensity in humans and bacteria, opening the possibility to use bacteria as simple models to study amyloid aggregation process and the potential effect of both anti-amyloid drugs and pro-aggregative compounds. Under these considerations, several in vitro and in cellulo methods, which exploit the amyloid properties of bacterial inclusion bodies, have been proposed in the last few years. Since these new methods are fast, simple, inexpensive, highly reproducible, and tunable, they have aroused great interest as preliminary screening tools in the search for anti-amyloid (beta-blocker) drugs for conformational diseases. The aim of this mini-review is to compile recently developed methods aimed at tracking amyloid aggregation in bacteria, discussing their advantages and limitations, and the future potential applications of inclusion bodies in anti-amyloid drug discovery.
Keywords: Inclusion bodies, amyloid, anti-amyloid drugs, conformational diseases, drug discovery, beta-blockers.
Graphical Abstract
[1]
Chiti, F.; Dobson, C.M. Protein misfolding, functional amyloid, and human disease. Annu. Rev. Biochem., 2006, 75, 333-366.
[3]
Carulla, N.; Caddy, G.L.; Hall, D.R.; Zurdo, J.; Gairi, M.; Feliz, M.; Giralt, E.; Robinson, C.V.; Dobson, C.M. Molecular recycling within amyloid fibrils. Nature, 2005, 436(7050), 554-558.
[4]
Ventura, S.; Villaverde, A. Protein quality in bacterial inclusion bodies. Trends Biotechnol., 2006, 24(4), 179-185.
[5]
Mitraki, A. Protein aggregation from inclusion bodies to amyloid and biomaterials. Adv. Protein Chem. Struct. Biol., 2010, 79, 89-125.
[6]
Carrio, M.; Gonzalez-Montalban, N.; Vera, A.; Villaverde, A.; Ventura, S. Amyloid-like properties of bacterial inclusion bodies. J. Mol. Biol., 2005, 347(5), 1025-1037.
[7]
Morell, M.; Bravo, R.; Espargaro, A.; Sisquella, X.; Aviles, F.X.; Fernandez-Busquets, X.; Ventura, S. Inclusion bodies: specificity in their aggregation process and amyloid-like structure. Biochim. Biophys. Acta, 2008, 1783(10), 1815-1825.
[8]
Wang, L.; Maji, S.K.; Sawaya, M.R.; Eisenberg, D.; Riek, R. Bacterial inclusion bodies contain amyloid-like structure. PLoS Biol., 2008, 6(8), e195.
[9]
de Groot, N.S.; Espargaro, A.; Morell, M.; Ventura, S. Studies on bacterial inclusion bodies. Future Microbiol., 2008, 3, 423-435.
[10]
de Groot, N.S.; Sabate, R.; Ventura, S. Amyloids in bacterial inclusion bodies. Trends Biochem. Sci., 2009, 34(8), 408-416.
[11]
Wasmer, C.; Benkemoun, L.; Sabate, R.; Steinmetz, M.O.; Coulary-Salin, B.; Wang, L.; Riek, R.; Saupe, S.J.; Meier, B.H. Solid-state NMR spectroscopy reveals that E. coli inclusion bodies of HET-s(218-289) are amyloids. Angew. Chem. Int. Ed. Engl., 2009, 48(26), 4858-4860.
[12]
Carrio, M.M.; Corchero, J.L.; Villaverde, A. Dynamics of in vivo protein aggregation: Building inclusion bodies in recombinant bacteria. FEMS Microbiol. Lett., 1998, 169(1), 9-15.
[13]
Bowden, G.A.; Paredes, A.M.; Georgiou, G. Structure and morphology of protein inclusion bodies in Escherichia coli. Biotechnology (N. Y.), 1991, 9(8), 725-730.
[14]
Arie, J.P.; Miot, M.; Sassoon, N.; Betton, J.M. Formation of active inclusion bodies in the periplasm of Escherichia coli. Mol. Microbiol., 2006, 62(2), 427-437.
[15]
Garcia-Fruitos, E.; Gonzalez-Montalban, N.; Morell, M.; Vera, A.; Ferraz, R.M.; Aris, A.; Ventura, S.; Villaverde, A. Aggregation as bacterial inclusion bodies does not imply inactivation of enzymes and fluorescent proteins. Microb. Cell Fact., 2005, 4, 27.
[16]
Carrio, M.M.; Villaverde, A. Role of molecular chaperones in inclusion body formation. FEBS Lett., 2003, 537(1-3), 215-221.
[17]
Carrio, M.M.; Villaverde, A. Construction and deconstruction of bacterial inclusion bodies. J. Biotechnol., 2002, 96(1), 3-12.
[18]
Clark, E.D. Protein refolding for industrial processes. Curr. Opin. Biotechnol., 2001, 12(2), 202-207.
[19]
Schrodel, A.; de Marco, A. Characterization of the aggregates formed during recombinant protein expression in bacteria. BMC Biochem., 2005, 6, 10.
[20]
Garcia-Fruitos, E.; Aris, A.; Villaverde, A. Localization of functional polypeptides in bacterial inclusion bodies. Appl. Environ. Microbiol., 2007, 73(1), 289-294.
[21]
Rinas, U.; Hoffmann, F.; Betiku, E.; Estape, D.; Marten, S. Inclusion body anatomy and functioning of chaperone-mediated in vivo inclusion body disassembly during high-level recombinant protein production in Escherichia coli. J. Biotechnol., 2007, 127(2), 244-257.
[22]
Ehgartner, D.; Sagmeister, P.; Langemann, T.; Meitz, A.; Lubitz, W.; Herwig, C. A novel method to recover inclusion body protein from recombinant E. coli fed-batch processes based on phage PhiX174-derived lysis protein E. Appl. Microbiol. Biotechnol., 2017, 101(14), 5603-5614.
[23]
Wasmer, C.; Soragni, A.; Sabate, R.; Lange, A.; Riek, R.; Meier, B.H. Infectious and noninfectious amyloids of the HET-s(218-289) prion have different NMR spectra. Angew. Chem. Int. Ed. Engl., 2008, 47(31), 5839-5841.
[24]
Villar-Pique, A.; Espargaro, A.; Ventura, S.; Sabate, R. Screening for amyloid aggregation: in-silico, in-vitro and in-vivo detection. Curr. Protein Pept. Sci., 2014, 15(5), 477-489.
[25]
Carrio, M.M.; Corchero, J.L.; Villaverde, A. Proteolytic digestion of bacterial inclusion body proteins during dynamic transition between soluble and insoluble forms. Biochim. Biophys. Acta, 1999, 1434(1), 170-176.
[26]
de Groot, N.S.; Aviles, F.X.; Vendrell, J.; Ventura, S. Mutagenesis of the central hydrophobic cluster in Abeta42 Alzheimer’s peptide. Side-chain properties correlate with aggregation propensities. FEBS J., 2006, 273(3), 658-668.
[27]
de Groot, N.S.; Ventura, S. Effect of temperature on protein quality in bacterial inclusion bodies. FEBS Lett., 2006, 580(27), 6471-6476.
[28]
de Groot, N.S.; Ventura, S. Protein activity in bacterial inclusion bodies correlates with predicted aggregation rates. J. Biotechnol., 2006, 125(1), 110-113.
[29]
Beharry, C.; Alaniz, M.E.; Alonso Adel, C. Expression of Alzheimer-like pathological human tau induces a behavioral motor and olfactory learning deficit in Drosophila melanogaster. J. Alzheimers Dis., 2013, 37(3), 539-550.
[30]
Costa, R.; Speretta, E.; Crowther, D.C.; Cardoso, I. Testing the therapeutic potential of doxycycline in a Drosophila melanogaster model of Alzheimer disease. J. Biol. Chem., 2011, 286(48), 41647-41655.
[31]
Luo, Y. Alzheimer’s disease, the nematode Caenorhabditis elegans, and ginkgo biloba leaf extract. Life Sci., 2006, 78(18), 2066-2072.
[32]
Prussing, K.; Voigt, A.; Schulz, J.B. Drosophila melanogaster as a model organism for Alzheimer’s disease. Mol. Neurodegener., 2013, 8, 35.
[33]
Pujols, J.; Pena-Diaz, S.; Lazaro, D.F.; Peccati, F.; Pinheiro, F.; Gonzalez, D.; Carija, A.; Navarro, S.; Conde-Gimenez, M.; Garcia, J.; Guardiola, S.; Giralt, E.; Salvatella, X.; Sancho, J.; Sodupe, M.; Outeiro, T.F.; Dalfo, E.; Ventura, S. Small molecule inhibits alpha-synuclein aggregation, disrupts amyloid fibrils, and prevents degeneration of dopaminergic neurons. Proc. Natl. Acad. Sci. USA, 2018, 115(41), 10481-10486.
[34]
Wu, B.K.; Yuan, R.Y.; Lien, H.W.; Hung, C.C.; Hwang, P.P.; Chen, R.P.; Chang, C.C.; Liao, Y.F.; Huang, C.J. Multiple signaling factors and drugs alleviate neuronal death induced by expression of human and zebrafish tau proteins in vivo. J. Biomed. Sci., 2016, 23, 25.
[35]
Newman, M.; Ebrahimie, E.; Lardelli, M. Using the zebrafish model for Alzheimer’s disease research. Front. Genet., 2014, 5, 189.
[36]
Garcia-Fruitos, E.; Sabate, R.; de Groot, N.S.; Villaverde, A.; Ventura, S. Biological role of bacterial inclusion bodies: A model for amyloid aggregation. FEBS J., 2011, 278(14), 2419-2427.
[37]
Hou, X.Q.; Yan, R.; Yang, C.; Zhang, L.; Su, R.Y.; Liu, S.J.; Zhang, S.J.; He, W.Q.; Fang, S.H.; Cheng, S.Y.; Su, Z.R.; Chen, Y.B.; Wang, Q. A novel assay for high-throughput screening of anti-Alzheimer’s disease drugs to determine their efficacy by real-time monitoring of changes in PC12 cell proliferation. Int. J. Mol. Med., 2014, 33(3), 543-549.
[38]
Ahn, M.; Kalume, F.; Pitstick, R.; Oehler, A.; Carlson, G.; DeArmond, S.J. Brain aggregates: An effective in vitro cell culture system modeling neurodegenerative diseases. J. Neuropathol. Exp. Neurol., 2016, 75(3), 256-262.
[39]
Villar-Pique, A.; Espargaro, A.; Ventura, S.; Sabate, R. In vivo amyloid aggregation kinetics tracked by time-lapse confocal microscopy in real-time. Biotechnol. J., 2016, 11(1), 172-177.
[40]
Cornejo, A.; Aguilar Sandoval, F.; Caballero, L.; Machuca, L.; Munoz, P.; Caballero, J.; Perry, G.; Ardiles, A.; Areche, C.; Melo, F. Rosmarinic acid prevents fibrillization and diminishes vibrational modes associated to beta sheet in tau protein linked to Alzheimer’s disease. J. Enzyme Inhib. Med. Chem., 2017, 32(1), 945-953.
[41]
Cornejo, A.; Jimenez, J.M.; Caballero, L.; Melo, F.; Maccioni, R.B. Fulvic acid inhibits aggregation and promotes disassembly of tau fibrils associated with Alzheimer’s disease. J. Alzheimers Dis., 2011, 27(1), 143-153.
[42]
Chua, S.W.; Cornejo, A.; van Eersel, J.; Stevens, C.H.; Vaca, I.; Cueto, M.; Kassiou, M.; Gladbach, A.; Macmillan, A.; Lewis, L.; Whan, R.; Ittner, L.M. The polyphenol altenusin inhibits in vitro fibrillization of tau and reduces induced tau pathology in primary neurons. ACS Chem. Neurosci., 2017, 8(4), 743-751.
[43]
Villar-Pique, A.; Espargaro, A.; Sabate, R.; de Groot, N.S.; Ventura, S. Using bacterial inclusion bodies to screen for amyloid aggregation inhibitors. Microb. Cell Fact., 2012, 11, 55.
[44]
Carrio, M.M.; Cubarsi, R.; Villaverde, A. Fine architecture of bacterial inclusion bodies. FEBS Lett., 2000, 471(1), 7-11.
[45]
Espargaro, A.; Sabate, R.; Ventura, S. Kinetic and thermodynamic stability of bacterial intracellular aggregates. FEBS Lett., 2008, 582(25-26), 3669-3673.
[46]
Dasari, M.; Espargaro, A.; Sabate, R.; Lopez del Amo, J.M.; Fink, U.; Grelle, G.; Bieschke, J.; Ventura, S.; Reif, B. Bacterial inclusion bodies of Alzheimer’s disease beta-amyloid peptides can be employed to study native-like aggregation intermediate states. ChemBioChem, 2011, 12(3), 407-423.
[47]
de Groot, N.S.; Espargaro, A.; Morell, M.; Ventura, S. Studies on bacterial inclusion bodies. Future Microbiol., 2008, 3(4), 423-435.
[48]
Sabate, R.; Estelrich, J. Evidence of the existence of micelles in the fibrillogenesis of beta-amyloid peptide. J. Phys. Chem. B, 2005, 109(21), 11027-11032.
[49]
Sabate, R.; Baxa, U.; Benkemoun, L.; Sanchez de Groot, N.; Coulary-Salin, B.; Maddelein, M.L.; Malato, L.; Ventura, S.; Steven, A.C.; Saupe, S.J. Prion and non-prion amyloids of the HET-s prion forming domain. J. Mol. Biol., 2007, 370(4), 768-783.
[50]
Tanaka, M.; Chien, P.; Naber, N.; Cooke, R.; Weissman, J.S. Conformational variations in an infectious protein determine prion strain differences. Nature, 2004, 428(6980), 323-328.
[51]
Sabate, R.; Villar-Pique, A.; Espargaro, A.; Ventura, S. Temperature dependence of the aggregation kinetics of Sup35 and Ure2p yeast prions. Biomacromolecules, 2012, 13(2), 474-483.
[52]
Bocharova, O.V.; Breydo, L.; Parfenov, A.S.; Salnikov, V.V.; Baskakov, I.V. In vitro conversion of full-length mammalian prion protein produces amyloid form with physical properties of PrP(Sc). J. Mol. Biol., 2005, 346(2), 645-659.
[53]
Caballero, A.B.; Terol-Ordaz, L.; Espargaro, A.; Vazquez, G.; Nicolas, E.; Sabate, R.; Gamez, P. Histidine-rich oligopeptides to lessen copper-mediated amyloid-beta toxicity. Chemistry, 2016, 22(21), 7268-7280.
[54]
Jarrett, J.T.; Lansbury, P.T., Jr Seeding “one-dimensional crystallization” of amyloid: A pathogenic mechanism in Alzheimer’s disease and scrapie? Cell, 1993, 73(6), 1055-1058.
[55]
Sabate, R.; Gallardo, M.; Estelrich, J. An autocatalytic reaction as a model for the kinetics of the aggregation of beta-amyloid. Biopolymers, 2003, 71(2), 190-195.
[56]
Sumbria, R.K.; Hui, E.K.; Lu, J.Z.; Boado, R.J.; Pardridge, W.M. Disaggregation of amyloid plaque in brain of Alzheimer’s disease transgenic mice with daily subcutaneous administration of a tetravalent bispecific antibody that targets the transferrin receptor and the Abeta amyloid peptide. Mol. Pharm., 2013, 10(9), 3507-3513.
[57]
Solomon, B.; Koppel, R.; Frankel, D.; Hanan-Aharon, E. Disaggregation of Alzheimer beta-amyloid by site-directed mAb. Proc. Natl. Acad. Sci. USA, 1997, 94(8), 4109-4112.
[58]
Cruz, L.; Urbanc, B.; Buldyrev, S.V.; Christie, R.; Gomez-Isla, T.; Havlin, S.; McNamara, M.; Stanley, H.E.; Hyman, B.T. Aggregation and disaggregation of senile plaques in Alzheimer disease. Proc. Natl. Acad. Sci. USA, 1997, 94(14), 7612-7616.
[59]
Kim, H.Y.; Kim, H.V.; Jo, S.; Lee, C.J.; Choi, S.Y.; Kim, D.J.; Kim, Y. Corrigendum: EPPS rescues hippocampus-dependent cognitive deficits in APP/PS1 mice by disaggregation of amyloid-beta oligomers and plaques. Nat. Commun., 2016, 7, 10755.
[60]
Kim, H.Y.; Kim, H.V.; Jo, S.; Lee, C.J.; Choi, S.Y.; Kim, D.J.; Kim, Y. EPPS rescues hippocampus-dependent cognitive deficits in APP/PS1 mice by disaggregation of amyloid-beta oligomers and plaques. Nat. Commun., 2015, 6, 8997.
[61]
Barabasi, A.L.; Oltvai, Z.N. Network biology: Understanding the cell’s functional organization. Nat. Rev. Genet., 2004, 5(2), 101-113.
[62]
Viayna, E.; Sola, I.; Di Pietro, O.; Munoz-Torrero, D. Human disease and drug pharmacology, complex as real life. Curr. Med. Chem., 2013, 20(13), 1623-1634.
[63]
Lee, J.A.; Uhlik, M.T.; Moxham, C.M.; Tomandl, D.; Sall, D.J. Modern phenotypic drug discovery is a viable, neoclassic pharma strategy. J. Med. Chem., 2012, 55(10), 4527-4538.
[64]
Espargaro, A.; Sabate, R.; Ventura, S. Thioflavin-S staining coupled to flow cytometry. A screening tool to detect in vivo protein aggregation. Mol. Biosyst., 2012, 8(11), 2839-2844.
[65]
Pouplana, S.; Espargaro, A.; Galdeano, C.; Viayna, E.; Sola, I.; Ventura, S.; Munoz-Torrero, D.; Sabate, R. Thioflavin-S staining of bacterial inclusion bodies for the fast, simple, and inexpensive screening of amyloid aggregation inhibitors. Curr. Med. Chem., 2014, 21(9), 1152-1159.
[66]
Viayna, E.; Sabate, R.; Munoz-Torrero, D. Dual inhibitors of beta-amyloid aggregation and acetylcholinesterase as multi-target anti-Alzheimer drug candidates. Curr. Top. Med. Chem., 2013, 13(15), 1820-1842.
[67]
Perez-Areales, F.J.; Betari, N.; Viayna, A.; Pont, C.; Espargaro, A.; Bartolini, M.; De Simone, A.; Rinaldi Alvarenga, J.F.; Perez, B.; Sabate, R.; Lamuela-Raventos, R.M.; Andrisano, V.; Luque, F.J.; Munoz-Torrero, D. Design, synthesis and multitarget biological profiling of second-generation anti-Alzheimer rhein-huprine hybrids. Future Med. Chem., 2017, 9(10), 965-981.
[68]
Viayna, E.; Sola, I.; Bartolini, M.; De Simone, A.; Tapia-Rojas, C.; Serrano, F.G.; Sabate, R.; Juarez-Jimenez, J.; Perez, B.; Luque, F.J.; Andrisano, V.; Clos, M.V.; Inestrosa, N.C.; Munoz-Torrero, D. Synthesis and multitarget biological profiling of a novel family of rhein derivatives as disease-modifying anti-Alzheimer agents. J. Med. Chem., 2014, 57(6), 2549-2567.
[69]
Di Pietro, O.; Perez-Areales, F.J.; Juarez-Jimenez, J.; Espargaro, A.; Clos, M.V.; Perez, B.; Lavilla, R.; Sabate, R.; Luque, F.J.; Munoz-Torrero, D. Tetrahydrobenzo[h][1,6]naphthyridine-6-chlorotacrine hybrids as a new family of anti-Alzheimer agents targeting beta-amyloid, tau, and cholinesterase pathologies. Eur. J. Med. Chem., 2014, 84, 107-117.
[70]
Perez-Areales, F.J.; Di Pietro, O.; Espargaro, A.; Vallverdu-Queralt, A.; Galdeano, C.; Ragusa, I.M.; Viayna, E.; Guillou, C.; Clos, M.V.; Perez, B.; Sabate, R.; Lamuela-Raventos, R.M.; Luque, F.J.; Munoz-Torrero, D. Shogaol-huprine hybrids: dual antioxidant and anticholinesterase agents with beta-amyloid and tau anti-aggregating properties. Bioorg. Med. Chem., 2014, 22(19), 5298-5307.
[71]
Sola, I.; Aso, E.; Frattini, D.; Lopez-Gonzalez, I.; Espargaro, A.; Sabate, R.; Di Pietro, O.; Luque, F.J.; Clos, M.V.; Ferrer, I.; Munoz-Torrero, D. Novel levetiracetam derivatives that are effective against the Alzheimer-like phenotype in mice: Synthesis, in vitro, ex vivo, and in vivo efficacy studies. J. Med. Chem., 2015, 58(15), 6018-6032.
[72]
Wang, S.N.; Li, Q.; Jing, M.H.; Alba, E.; Yang, X.H.; Sabate, R.; Han, Y.F.; Pi, R.B.; Lan, W.J.; Yang, X.B.; Chen, J.K. Natural xanthones from Garcinia mangostana with multifunctional activities for the therapy of Alzheimer’s disease. Neurochem. Res., 2016, 41(7), 1806-1817.
[73]
Espargaro, A.; Ginex, T.; Vadell, M.D.; Busquets, M.A.; Estelrich, J.; Munoz-Torrero, D.; Luque, F.J.; Sabate, R. Combined in vitro cell-based/in silico screening of naturally occurring flavonoids and phenolic compounds as potential anti-Alzheimer drugs. J. Nat. Prod., 2017, 80(2), 278-289.
[74]
Panek, D.; Wieckowska, A.; Jonczyk, J.; Godyn, J.; Bajda, M.; Wichur, T.; Pasieka, A.; Knez, D.; Pislar, A.; Korabecny, J.; Soukup, O.; Sepsova, V.; Sabate, R.; Kos, J.; Gobec, S.; Malawska, B. Design, synthesis, and biological evaluation of 1-benzylamino-2-hydroxyalkyl derivatives as new potential disease-modifying multifunctional anti-Alzheimer’s agents. ACS Chem. Neurosci., 2018, 9(5), 1074-1094.
[75]
Schramm, S.; Huang, G.; Gunesch, S.; Lang, F.; Roa, J.; Hogger, P.; Sabate, R.; Maher, P.; Decker, M. Regioselective synthesis of 7-O-esters of the flavonolignan silibinin and SARs lead to compounds with overadditive neuroprotective effects. Eur. J. Med. Chem., 2018, 146, 93-107.
[76]
Wehle, S.; Espargaró, A.; Sabaté, R.; Decker, M. Investigation into the stability and reactivity of the pentacyclic alkaloid dehydroevodiamine and the benz-analog thereof. Tetrahedron, 2016, 72(20), 2535-2543.
[77]
Navarro, S.; Ventura, S. Fluorescent dye ProteoStat to detect and discriminate intracellular amyloid-like aggregates in Escherichia coli. Biotechnol. J., 2014, 9(10), 1259-1266.
[78]
Navarro, S.; Carija, A.; Munoz-Torrero, D.; Ventura, S. A fast and specific method to screen for intracellular amyloid inhibitors using bacterial model systems. Eur. J. Med. Chem., 2016, 121, 785-792.
[79]
Gonzalez-Montalban, N.; Garcia-Fruitos, E.; Ventura, S.; Aris, A.; Villaverde, A. The chaperone DnaK controls the fractioning of functional protein between soluble and insoluble cell fractions in inclusion body-forming cells. Microb. Cell Fact., 2006, 5, 26.
[80]
Mogk, A.; Deuerling, E.; Vorderwulbecke, S.; Vierling, E.; Bukau, B. Small heat shock proteins, ClpB and the DnaK system form a functional triade in reversing protein aggregation. Mol. Microbiol., 2003, 50(2), 585-595.
[81]
Schlieker, C.; Tews, I.; Bukau, B.; Mogk, A. Solubilization of aggregated proteins by ClpB/DnaK relies on the continuous extraction of unfolded polypeptides. FEBS Lett., 2004, 578(3), 351-356.
Related Journals
Protein & Peptide Letters
Related Books
Frontiers in Protein and Peptide Sciences
Article Metrics
46
4
1
1