Abstract
Many bacteria can assemble functional amyloid fibers on their cell surface. Most bacterial amyloids contribute to biofilm or other community behaviors where cells interact with a surface or with other cells. Bacterial amyloids, like all functional amyloids, share structural and biochemical properties with disease-associated eukaryotic amyloids. The general ability of amyloids to bind specific dyes, like Congo red and Thioflavin T, and their resistance to denaturation have provided useful tools for scoring and quantifying bacterial amyloid formation. Here, we present basic approaches to study bacterial amyloids by focusing on the well-studied curli amyloid fibers expressed by Enterobacteriaceae. These methods exploit the specific tinctorial and biophysical properties of amyloids. The methods described here are straightforward and can be easily applied by any modern molecular biology lab for the study of other bacterial amyloids.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Abbreviations
- CR:
-
Congo Red
- csg:
-
Curli specific genes
- FA:
-
Formic acid
- HFIP:
-
Hexafluoro-2-propanol
- RT:
-
Room temperature
References
Cooper GJ, Willis AC, Clark A et al (1987) Purification and characterization of a peptide from amyloid-rich pancreases of type 2 diabetic patients. Proc Natl Acad Sci U S A 84(23):8628–8632
Glenner GG, Wong CW (1984) Alzheimer’s disease: initial report of the purification and characterization of a novel cerebrovascular amyloid protein. Biochem Biophys Res Commun 120(3):885–890
Prusiner SB (1996) Molecular biology and pathogenesis of prion diseases. Trends Biochem Sci 21(12):482–487
Blanco LP, Evans ML, Smith DR et al (2012) Diversity, biogenesis and function of microbial amyloids. Trends Microbiol 20(2):66–73
Knowles TP, Mezzenga R (2016) Amyloid fibrils as building blocks for natural and artificial functional materials. Adv Mater 28(31):6546–6561
Pham CL, Kwan AH, Sunde M (2014) Functional amyloid: widespread in nature, diverse in purpose. Essays Biochem 56:207–219
Schwartz K, Boles BR (2013) Microbial amyloids—functions and interactions within the host. Curr Opin Microbiol 16(1):93–99
Watt B, van Niel G, Raposo G et al (2013) PMEL: a pigment cell-specific model for functional amyloid formation. Pigment Cell Melanoma Res 26(3):300–315
Adcox HE, Vasicek EM, Dwivedi V et al (2016) Salmonella extracellular matrix components influence biofilm formation and gallbladder colonization. Infect Immun 84(11):3243–3251
Austin JW, Sanders G, Kay WW et al (1998) Thin aggregative fimbriae enhance Salmonella enteritidis biofilm formation. FEMS Microbiol Lett 162(2):295–301
Gallo PM, Rapsinski GJ, Wilson RP et al (2015) Amyloid-DNA composites of bacterial biofilms stimulate autoimmunity. Immunity 42(6):1171–1184
Gophna U, Barlev M, Seijffers R et al (2001) Curli fibers mediate internalization of Escherichia coli by eukaryotic cells. Infect Immun 69(4):2659–2665
Gophna U, Oelschlaeger TA, Hacker J et al (2002) Role of fibronectin in curli-mediated internalization. FEMS Microbiol Lett 212(1):55–58
Johansson C, Nilsson T, Olsén A et al (2001) The influence of curli, a MHC-I-binding bacterial surface structure, on macrophage-T cell interactions. FEMS Immunol Med Microbiol 30(1):21–29
Larsen P, Nielsen JL, Dueholm MS et al (2007) Amyloid adhesins are abundant in natural biofilms. Environ Microbiol 9(12):3077–3090
Rapsinski GJ, Wynosky-Dolfi MA, Oppong GO et al (2015) Toll-like receptor 2 and NLRP3 cooperate to recognize a functional bacterial amyloid, curli. Infect Immun 83(2):693–701
Romero D, Aguilar C, Losick R et al (2010) Amyloid fibers provide structural integrity to Bacillus subtilis biofilms. Proc Natl Acad Sci U S A 107(5):2230–2234
Tursi SA, Lee EY, Medeiros NJ et al (2017) Bacterial amyloid curli acts as a carrier for DNA to elicit an autoimmune response via TLR2 and TLR9. PLoS Pathog 13(4):e1006315
Tükel C, Raffatellu M, Humphries AD et al (2005) CsgA is a pathogen-associated molecular pattern of Salmonella enterica serotype Typhimurium that is recognized by Toll-like receptor 2. Mol Microbiol 58(1):289–304
Tükel C, Nishimori JH, Wilson RP et al (2010) Toll-like receptors 1 and 2 cooperatively mediate immune responses to curli, a common amyloid from enterobacterial biofilms. Cell Microbiol 12(10):1495–1505
Vidal O, Longin R, Prigent-Combaret C et al (1998) Isolation of an Escherichia coli K-12 mutant strain able to form biofilms on inert surfaces: involvement of a new ompR allele that increases curli expression. J Bacteriol 180(9):2442–2449
Chapman MR, Robinson LS, Pinkner JS et al (2002) Role of Escherichia coli curli operons in directing amyloid fiber formation. Science 295(5556):851–855
Collinson SK, Doig PC, Doran JL et al (1993) Thin, aggregative fimbriae mediate binding of Salmonella enteritidis to fibronectin. J Bacteriol 175(1):12–18
Claessen D, Rink R, de Jong W et al (2003) A novel class of secreted hydrophobic proteins is involved in aerial hyphae formation in Streptomyces coelicolor by forming amyloid-like fibrils. Genes Dev 17(14):1714–1726
Elliot MA, Karoonuthaisiri N, Huang J et al (2003) The chaplins: a family of hydrophobic cell-surface proteins involved in aerial mycelium formation in Streptomyces coelicolor. Genes Dev 17(14):1727–1740
de Jong W, Wösten HA, Dijkhuizen L et al (2009) Attachment of Streptomyces coelicolor is mediated by amyloidal fimbriae that are anchored to the cell surface via cellulose. Mol Microbiol 73(6):1128–1140
Shewmaker F, McGlinchey RP, Thurber KR et al (2009) The functional curli amyloid is not based on in-register parallel beta-sheet structure. J Biol Chem 284(37):25065–25076
Wang X, Smith DR, Jones JW et al (2007) In vitro polymerization of a functional Escherichia coli amyloid protein. J Biol Chem 282(6):3713–3719
Collinson SK, Parker JM, Hodges RS et al (1999) Structural predictions of AgfA, the insoluble fimbrial subunit of Salmonella thin aggregative fimbriae. J Mol Biol 290(3):741–756
Collinson SK, Emödy L, Müller KH et al (1991) Purification and characterization of thin, aggregative fimbriae from Salmonella enteritidis. J Bacteriol 173(15):4773–4781
Dueholm MS, Albertsen M, Otzen D et al (2012) Curli functional amyloid systems are phylogenetically widespread and display large diversity in operon and protein structure. PLoS One 7(12):e51274
Olsén A, Jonsson A, Normark S (1989) Fibronectin binding mediated by a novel class of surface organelles on Escherichia coli. Nature 338(6217):652–655
Zogaj X, Bokranz W, Nimtz M et al (2003) Production of cellulose and curli fimbriae by members of the family Enterobacteriaceae isolated from the human gastrointestinal tract. Infect Immun 71(7):4151–4158
Cao B, Zhao Y, Kou Y et al (2014) Structure of the nonameric bacterial amyloid secretion channel. Proc Natl Acad Sci U S A 111(50):E5439–E5444
Goyal P, Krasteva PV, Van Gerven N et al (2014) Structural and mechanistic insights into the bacterial amyloid secretion channel CsgG. Nature 516(7530):250–253
Hammar M, Bian Z, Normark S (1996) Nucleator-dependent intercellular assembly of adhesive curli organelles in Escherichia coli. Proc Natl Acad Sci U S A 93(13):6562–6566
Loferer H, Hammar M, Normark S (1997) Availability of the fibre subunit CsgA and the nucleator protein CsgB during assembly of fibronectin-binding curli is limited by the intracellular concentration of the novel lipoprotein CsgG. Mol Microbiol 26(1):11–23
Nenninger AA, Robinson LS, Hultgren SJ (2009) Localized and efficient curli nucleation requires the chaperone-like amyloid assembly protein CsgF. Proc Natl Acad Sci U S A 106(3):900–905
Nenninger AA, Robinson LS, Hammer ND et al (2011) CsgE is a curli secretion specificity factor that prevents amyloid fibre aggregation. Mol Microbiol 81(2):486–499
Robinson LS, Ashman EM, Hultgren SJ et al (2006) Secretion of curli fibre subunits is mediated by the outer membrane-localized CsgG protein. Mol Microbiol 59(3):870–881
Evans ML, Chorell E, Taylor JD et al (2015) The bacterial curli system possesses a potent and selective inhibitor of amyloid formation. Mol Cell 57(3):445–455
Hammer ND, Schmidt JC, Chapman MR (2007) The curli nucleator protein, CsgB, contains an amyloidogenic domain that directs CsgA polymerization. Proc Natl Acad Sci U S A 104(30):12494–12499
Hammar M, Arnqvist A, Bian Z et al (1995) Expression of two csg operons is required for production of fibronectin- and congo red-binding curli polymers in Escherichia coli K-12. Mol Microbiol 18(4):661–670
Weiss-Muszkat M, Shakh D, Zhou Y et al (2010) Biofilm formation by and multicellular behavior of Escherichia coli O55:H7, an atypical enteropathogenic strain. Appl Environ Microbiol 76(5):1545–1554
Wang X, Chapman MR (2008) Sequence determinants of bacterial amyloid formation. J Mol Biol 380(3):570–580
Wang X, Hammer ND, Chapman MR (2008) The molecular basis of functional bacterial amyloid polymerization and nucleation. J Biol Chem 283(31):21530–21539
Wang X, Zhou Y, Ren JJ et al (2010) Gatekeeper residues in the major curlin subunit modulate bacterial amyloid fiber biogenesis. Proc Natl Acad Sci U S A 107(1):163–168
Cegelski L, Pinkner JS, Hammer ND et al (2009) Small-molecule inhibitors target Escherichia coli amyloid biogenesis and biofilm formation. Nat Chem Biol 5(12):913–919
Andersson EK, Bengtsson C, Evans ML et al (2013) Modulation of curli assembly and pellicle biofilm formation by chemical and protein chaperones. Chem Biol 20(10):1245–1254
Chorell E, Andersson E, Evans ML et al (2015) Bacterial chaperones CsgE and CsgC differentially modulate human α-synuclein amyloid formation via transient contacts. PLoS One 10:e0140194
Evans ML, Schmidt JC, Ilbert M et al (2011) E. coli chaperones DnaK, Hsp33 and Spy inhibit bacterial functional amyloid assembly. Prion 5(4):323–334
Bokranz W, Wang X, Tschäpe H et al (2005) Expression of cellulose and curli fimbriae by Escherichia coli isolated from the gastrointestinal tract. J Med Microbiol 54(Pt 12):1171–1182
Bian Z, Brauner A, Li Y et al (2000) Expression of and cytokine activation by Escherichia coli curli fibers in human sepsis. J Infect Dis 181(2):602–612
Kikuchi T, Mizunoe Y, Takade A et al (2005) Curli fibers are required for development of biofilm architecture in Escherichia coli K-12 and enhance bacterial adherence to human uroepithelial cells. Microbiol Immunol 49(9):875–884
White AP, Gibson DL, Collinson SK et al (2003) Extracellular polysaccharides associated with thin aggregative fimbriae of Salmonella enterica serovar enteritidis. J Bacteriol 185(18):5398–5407
Baba T, Ara T, Hasegawa M et al (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2:2006.0008
Acknowledgments
We thank members of the Chapman laboratory for helpful discussions and review of this manuscript, especially DRS and LB. This work was supported by the National Institutes of Health Grant R01 GM118651 to MRC.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2018 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Evans, M.L., Gichana, E., Zhou, Y., Chapman, M.R. (2018). Bacterial Amyloids. In: Sigurdsson, E., Calero, M., Gasset, M. (eds) Amyloid Proteins. Methods in Molecular Biology, vol 1779. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7816-8_17
Download citation
DOI: https://doi.org/10.1007/978-1-4939-7816-8_17
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-7815-1
Online ISBN: 978-1-4939-7816-8
eBook Packages: Springer Protocols