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Article ; Online: Functional amyloids signal their arrival.

Badtke, Matthew P / Hammer, Neal D / Chapman, Matthew R

2009 Volume 2, Issue 80, Page(s) pe43

Abstract: Amyloids have traditionally been associated with misfolded protein aggregates and debilitating neurodegenerative diseases. However, a growing number of functional amyloids have now been described that demonstrate that amyloid formation can be an integral ...

Abstract	Amyloids have traditionally been associated with misfolded protein aggregates and debilitating neurodegenerative diseases. However, a growing number of functional amyloids have now been described that demonstrate that amyloid formation can be an integral part of normal cellular physiology. Functional amyloid production is highly regulated, and the resulting fibers serve a variety of roles for the cells that produce them. A new role for amyloid as storage reservoirs for peptide hormones within mammalian secretory granules has been discovered. More than 30 different peptide hormones have been found to form amyloids in vitro, and both rats and mice have been shown to store hormone amyloid deposits in secretory granules. Thus, the emerging evidence adds to the diverse roles of amyloid and raises intriguing questions for both the peptide hormone and the functional amyloid fields.
MeSH term(s)	Amyloid/metabolism ; Animals ; Humans ; Mice ; Peptide Hormones/metabolism ; Protein Folding ; Rats ; Secretory Vesicles/metabolism
Chemical Substances	Amyloid ; Peptide Hormones
Language	English
Publishing date	2009-07-21
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	2417226-1
ISSN	1937-9145 ; 1945-0877
ISSN (online)	1937-9145
ISSN	1945-0877
DOI	10.1126/scisignal.280pe43
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Article ; Online: Diversity, biogenesis and function of microbial amyloids.

Blanco, Luz P / Evans, Margery L / Smith, Daniel R / Badtke, Matthew P / Chapman, Matthew R

Trends in microbiology

2011 Volume 20, Issue 2, Page(s) 66–73

Abstract: Amyloid is a distinct β-sheet-rich fold that many proteins can acquire. Frequently associated with neurodegenerative diseases in humans, including Alzheimer's, Parkinson's and Huntington's diseases, amyloids are traditionally considered the product of ... ...

Abstract	Amyloid is a distinct β-sheet-rich fold that many proteins can acquire. Frequently associated with neurodegenerative diseases in humans, including Alzheimer's, Parkinson's and Huntington's diseases, amyloids are traditionally considered the product of protein misfolding. However, the amyloid fold is now recognized as a ubiquitous part of normal cellular biology. Functional amyloids have been identified in nearly all facets of cellular life, with microbial functional amyloids leading the way. Unlike disease-associated amyloids, functional amyloids are assembled by dedicated, directed pathways and ultimately perform a physiological function that benefits the organism. The evolved amyloid assembly and disassembly pathways of microbes have provided novel insights into how cells have harnessed the amyloid assembly process for productive means. An understanding of functional amyloid biogenesis promises to provide a fresh perspective on the molecular events that underlie disease-associated amyloidogenesis. Here, we review functional microbial amyloids with an emphasis on curli fibers and their role in promoting biofilm formation and other community behaviors.
MeSH term(s)	Adhesins, Bacterial/chemistry ; Adhesins, Bacterial/metabolism ; Amyloid/chemistry ; Amyloid/metabolism ; Bacteria/chemistry ; Bacteria/metabolism ; Biodiversity ; Biofilms/growth & development ; Escherichia coli Proteins/chemistry ; Escherichia coli Proteins/metabolism ; Protein Folding ; Protein Multimerization ; Protein Structure, Secondary ; Protein Structure, Tertiary
Chemical Substances	Adhesins, Bacterial ; Amyloid ; CsgB protein, E coli ; Escherichia coli Proteins ; csgA protein, E coli
Language	English
Publishing date	2011-12-23
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	1158963-2
ISSN	1878-4380 ; 0966-842X
ISSN (online)	1878-4380
ISSN	0966-842X
DOI	10.1016/j.tim.2011.11.005
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Zs.A 3738: Show issues

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Article ; Online: Combining genetic and biochemical approaches to identify functional molecular contact points.

Badtke, Matthew P / Cao, Feng / Tavis, John E

Biological procedures online

2006 Volume 8, Page(s) 77–86

Abstract: Protein-protein interactions are required for many viral and cellular functions and are potential targets for novel therapies. Here we detail a series of genetic and biochemical techniques used in combination to find an essential molecular contact point ... ...

Abstract	Protein-protein interactions are required for many viral and cellular functions and are potential targets for novel therapies. Here we detail a series of genetic and biochemical techniques used in combination to find an essential molecular contact point on the duck hepatitis B virus polymerase. These techniques include differential immunoprecipitation, mutagenesis and peptide competition. The strength of these techniques is their ability to identify contact points on intact proteins or protein complexes employing functional assays. This approach can be used to aid identification of putative binding sites on proteins and protein complexes which are resistant to characterization by other methods.
Keywords	covid19
Language	English
Publishing date	2006-08-10
Publishing country	England
Document type	Journal Article
ZDB-ID	2027823-8
ISSN	1480-9222 ; 1480-9222
ISSN (online)	1480-9222
ISSN	1480-9222
DOI	10.1251/bpo121
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Article ; Online: CsgE is a curli secretion specificity factor that prevents amyloid fibre aggregation.

Nenninger, Ashley A / Robinson, Lloyd S / Hammer, Neal D / Epstein, Elisabeth Ashman / Badtke, Matthew P / Hultgren, Scott J / Chapman, Matthew R

Molecular microbiology

2011 Volume 81, Issue 2, Page(s) 486–499

Abstract: Curli are extracellular amyloid fibres produced by Escherichia coli that are critical for biofilm formation and adhesion to biotic and abiotic surfaces. CsgA and CsgB are the major and minor curli subunits, respectively, while CsgE, CsgF and CsgG direct ... ...

Abstract	Curli are extracellular amyloid fibres produced by Escherichia coli that are critical for biofilm formation and adhesion to biotic and abiotic surfaces. CsgA and CsgB are the major and minor curli subunits, respectively, while CsgE, CsgF and CsgG direct the extracellular localization and assembly of curli subunits into fibres. The secretion and stability of CsgA and CsgB are dependent on the outer membrane lipoprotein CsgG. Here, we identified functional interactions between CsgG and CsgE during curli secretion. We discovered that CsgG overexpression restored curli production to a csgE strain under curli-inducing conditions. In antibiotic sensitivity and protein secretion assays, CsgG expression alone allowed translocation of erythromycin and small periplasmic proteins across the outer membrane. Coexpression of CsgE with CsgG blocked non-specific protein and antibiotic passage across the outer membrane. However, CsgE did not block secretion of proteins containing a 22-amino-acid putative outer membrane secretion signal of CsgA (A22). Finally, using purified proteins, we found that CsgE prohibited the self-assembly of CsgA into amyloid fibres. Collectively, these data indicate that CsgE provides substrate specificity to the curli secretion pore CsgG, and acts directly on the secretion substrate CsgA to prevent premature subunit assembly.
MeSH term(s)	Bacterial Proteins/metabolism ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Escherichia coli Proteins/genetics ; Escherichia coli Proteins/metabolism ; Lipoproteins/genetics ; Lipoproteins/metabolism ; Membrane Transport Proteins/genetics ; Membrane Transport Proteins/metabolism ; Protein Binding ; Protein Denaturation ; Protein Interaction Mapping ; Protein Multimerization
Chemical Substances	Bacterial Proteins ; CsgB protein, E coli ; CsgE protein, E coli ; CsgG protein, E coli ; Escherichia coli Proteins ; Lipoproteins ; Membrane Transport Proteins ; csgA protein, E coli ; Crl protein, Bacteria (148349-72-8)
Language	English
Publishing date	2011-06-07
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	619315-8
ISSN	1365-2958 ; 0950-382X
ISSN (online)	1365-2958
ISSN	0950-382X
DOI	10.1111/j.1365-2958.2011.07706.x
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Article ; Online: An interdomain RNA binding site on the hepadnaviral polymerase that is essential for reverse transcription.

Badtke, Matthew P / Khan, Irfan / Cao, Feng / Hu, Jianming / Tavis, John E

Virology

2009 Volume 390, Issue 1, Page(s) 130–138

Abstract: The T3 motif on the duck hepatitis B virus reverse transcriptase (P) is proposed to be ... we found that T3 is needed for P to bind the viral RNA, the first step in DNA synthesis. A second motif, RT ... because mutating T3 and RT-1 had similar effects on RNA binding, exposure of antibody epitopes on P, and DNA ...

Abstract	The T3 motif on the duck hepatitis B virus reverse transcriptase (P) is proposed to be a binding site essential for viral replication, but its ligand and roles in DNA synthesis are unknown. Here, we found that T3 is needed for P to bind the viral RNA, the first step in DNA synthesis. A second motif, RT-1, was predicted to assist T3. T3 and RT-1 appear to form a composite RNA binding site because mutating T3 and RT-1 had similar effects on RNA binding, exposure of antibody epitopes on P, and DNA synthesis. The T3 and RT-1 motifs bound RNA non-specifically, yet they were essential for specific interactions between P and the viral RNA. This implies that specificity for the viral RNA is provided by a post-binding step. The T3:RT-1 motifs are conserved with the human hepatitis B virus and may be an attractive target for novel antiviral drug development.
MeSH term(s)	Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Binding Sites/genetics ; Hepadnaviridae/genetics ; Hepadnaviridae/metabolism ; Hepatitis B Virus, Duck/genetics ; Hepatitis B Virus, Duck/metabolism ; Hepatitis B virus/genetics ; Hepatitis B virus/metabolism ; Humans ; Models, Biological ; Models, Molecular ; Molecular Chaperones/metabolism ; Molecular Sequence Data ; RNA, Viral/metabolism ; RNA-Directed DNA Polymerase/chemistry ; RNA-Directed DNA Polymerase/genetics ; RNA-Directed DNA Polymerase/metabolism ; Reverse Transcription ; Sequence Homology, Amino Acid
Chemical Substances	Molecular Chaperones ; RNA, Viral ; RNA-Directed DNA Polymerase (EC 2.7.7.49)
Language	English
Publishing date	2009-05-24
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	200425-2
ISSN	1096-0341 ; 0042-6822
ISSN (online)	1096-0341
ISSN	0042-6822
DOI	10.1016/j.virol.2009.04.023
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Article ; Online: The C-terminal repeating units of CsgB direct bacterial functional amyloid nucleation.

Hammer, Neal D / McGuffie, Bryan A / Zhou, Yizhou / Badtke, Matthew P / Reinke, Ashley A / Brännström, Kristoffer / Gestwicki, Jason E / Olofsson, Anders / Almqvist, Fredrik / Chapman, Matthew R

Journal of molecular biology

2012 Volume 422, Issue 3, Page(s) 376–389

Abstract: Curli are functional amyloids produced by enteric bacteria. The major curli fiber subunit, CsgA, self-assembles into an amyloid fiber in vitro. The minor curli subunit protein, CsgB, is required for CsgA polymerization on the cell surface. Both CsgA and ... ...

Abstract	Curli are functional amyloids produced by enteric bacteria. The major curli fiber subunit, CsgA, self-assembles into an amyloid fiber in vitro. The minor curli subunit protein, CsgB, is required for CsgA polymerization on the cell surface. Both CsgA and CsgB are composed of five predicted β-strand-loop-β-strand-loop repeating units that feature conserved glutamine and asparagine residues. Because of this structural homology, we proposed that CsgB might form an amyloid template that initiates CsgA polymerization on the cell surface. To test this model, we purified wild-type CsgB and found that it self-assembled into amyloid fibers in vitro. Preformed CsgB fibers seeded CsgA polymerization as did soluble CsgB added to the surface of cells secreting soluble CsgA. To define the molecular basis of CsgB nucleation, we generated a series of mutants that removed each of the five repeating units. Each of these CsgB deletion mutants was capable of self-assembly in vitro. In vivo, membrane-localized mutants lacking the first, second, or third repeating units were able to convert CsgA into fibers. However, mutants missing either the fourth or fifth repeating units were unable to complement a csgB mutant. These mutant proteins were not localized to the outer membrane but were instead secreted into the extracellular milieu. Synthetic CsgB peptides corresponding to repeating units 1, 2, and 4 self-assembled into ordered amyloid polymers, while peptides corresponding to repeating units 3 and 5 did not, suggesting that there are redundant amyloidogenic domains in CsgB. Our results suggest a model where the rapid conversion of CsgB from unstructured protein to a β-sheet-rich amyloid template anchored to the cell surface is mediated by the C-terminal repeating units.
MeSH term(s)	Amino Acid Sequence ; Amyloid/chemistry ; Amyloid/genetics ; Amyloid/metabolism ; Bacterial Proteins/chemistry ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Cell Membrane/genetics ; Cell Membrane/metabolism ; Escherichia coli/genetics ; Escherichia coli/metabolism ; Escherichia coli Proteins/chemistry ; Escherichia coli Proteins/genetics ; Escherichia coli Proteins/metabolism ; Molecular Sequence Data ; Mutation ; Peptides/chemistry ; Peptides/genetics ; Peptides/metabolism ; Protein Multimerization ; Protein Structure, Secondary ; Protein Subunits ; Sequence Deletion ; Terminal Repeat Sequences
Chemical Substances	Amyloid ; Bacterial Proteins ; CsgB protein, E coli ; Escherichia coli Proteins ; Peptides ; Protein Subunits ; csgA protein, E coli ; Crl protein, Bacteria (148349-72-8)
Language	English
Publishing date	2012-06-07
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2012.05.043
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Zs.A 867: Show issues

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Article: Identification of an essential molecular contact point on the duck hepatitis B virus reverse transcriptase.

Cao, Feng / Badtke, Matthew P / Metzger, Lisa M / Yao, Ermei / Adeyemo, Babatunde / Gong, Yunhao / Tavis, John E

Journal of virology

2005 Volume 79, Issue 16, Page(s) 10164–10170

Abstract: The hepadnaviral polymerase (P) functions in a complex with viral nucleic acids and cellular ... chaperones. To begin to identify contacts between P and its partners, we assessed the exposure ... of the epitopes of six monoclonal antibodies (MAbs) to the terminal protein domain of the duck hepatitis B virus P ...

Abstract	The hepadnaviral polymerase (P) functions in a complex with viral nucleic acids and cellular chaperones. To begin to identify contacts between P and its partners, we assessed the exposure of the epitopes of six monoclonal antibodies (MAbs) to the terminal protein domain of the duck hepatitis B virus P protein in a partially denaturing buffer (RIPA) and a physiological buffer (IPP150). All MAbs immunoprecipitated in vitro translated P well in RIPA, but three immunoprecipitated P poorly in IPP150. Therefore, the epitopes for these MAbs were obscured in the native conformation of P but were exposed when P was in RIPA. Epitopes for MAbs that immunoprecipitated P poorly in IPP150 were between amino acids (aa) 138 and 202. Mutation of a highly conserved motif within this region (T3; aa 176 to 183) improved the immunoprecipitation of P by these MAbs and simultaneously inhibited DNA priming by P. Peptides containing the T3 motif inhibited DNA priming in a dose-dependent manner, whereas eight irrelevant peptides did not. T3 function appears to be conserved among the hepadnaviruses because mutating T3 ablated DNA synthesis in both duck hepatitis B virus and hepatitis B virus. These results indicate that (i) the conserved T3 motif is a molecular contact point whose ligand can be competed by soluble T3 peptides, (ii) the occupancy of T3 obscures the epitopes for three MAbs, and (iii) proper occupancy of T3 by its ligand is essential for DNA priming. Therefore, small-molecule ligands that compete for binding to T3 with its natural ligand could form a novel class of antiviral drugs.
MeSH term(s)	Amino Acid Sequence ; Antibodies, Monoclonal/immunology ; Binding Sites ; DNA/biosynthesis ; Epitopes ; Hepatitis B Virus, Duck/enzymology ; Molecular Sequence Data ; RNA-Directed DNA Polymerase/chemistry ; RNA-Directed DNA Polymerase/metabolism
Chemical Substances	Antibodies, Monoclonal ; Epitopes ; DNA (9007-49-2) ; RNA-Directed DNA Polymerase (EC 2.7.7.49)
Language	English
Publishing date	2005-08
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	80174-4
ISSN	1098-5514 ; 0022-538X
ISSN (online)	1098-5514
ISSN	0022-538X
DOI	10.1128/JVI.79.16.10164-10170.2005
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Article: The C-Terminal Repeating Units of CsgB Direct Bacterial Functional Amyloid Nucleation

Hammer, Neal D / McGuffie, Bryan A / Zhou, Yizhou / Badtke, Matthew P / Reinke, Ashley A / Brännström, Kristoffer / Gestwicki, Jason E / Olofsson, Anders / Almqvist, Fredrik / Chapman, Matthew R

Journal of molecular biology. 2012 Sept. 21, v. 422, no. 3

2012

Abstract	Curli are functional amyloids produced by enteric bacteria. The major curli fiber subunit, CsgA, self-assembles into an amyloid fiber in vitro. The minor curli subunit protein, CsgB, is required for CsgA polymerization on the cell surface. Both CsgA and CsgB are composed of five predicted β‐strand–loop–β‐strand–loop repeating units that feature conserved glutamine and asparagine residues. Because of this structural homology, we proposed that CsgB might form an amyloid template that initiates CsgA polymerization on the cell surface. To test this model, we purified wild-type CsgB and found that it self-assembled into amyloid fibers in vitro. Preformed CsgB fibers seeded CsgA polymerization as did soluble CsgB added to the surface of cells secreting soluble CsgA. To define the molecular basis of CsgB nucleation, we generated a series of mutants that removed each of the five repeating units. Each of these CsgB deletion mutants was capable of self-assembly in vitro. In vivo, membrane-localized mutants lacking the first, second, or third repeating units were able to convert CsgA into fibers. However, mutants missing either the fourth or fifth repeating units were unable to complement a csgB mutant. These mutant proteins were not localized to the outer membrane but were instead secreted into the extracellular milieu. Synthetic CsgB peptides corresponding to repeating units 1, 2, and 4 self‐assembled into ordered amyloid polymers, while peptides corresponding to repeating units 3 and 5 did not, suggesting that there are redundant amyloidogenic domains in CsgB. Our results suggest a model where the rapid conversion of CsgB from unstructured protein to a β-sheet-rich amyloid template anchored to the cell surface is mediated by the C-terminal repeating units.
Keywords	amyloid ; asparagine ; glutamine ; intestinal microorganisms ; models ; mutants ; peptides ; polymerization ; polymers ; protein subunits
Language	English
Dates of publication	2012-0921
Size	p. 376-389.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2012.05.043
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Article: Diversity, biogenesis and function of microbial amyloids

Blanco, Luz P. / Evans, Margery L. / Smith, Daniel R. / Badtke, Matthew P. / Chapman, Matthew R.

Trends in microbiology

Volume v. 20,, Issue no. 2

Abstract	Amyloid is a distinct β-sheet-rich fold that many proteins can acquire. Frequently associated with neurodegenerative diseases in humans, including Alzheimer's, Parkinson's and Huntington's diseases, amyloids are traditionally considered the product of protein misfolding. However, the amyloid fold is now recognized as a ubiquitous part of normal cellular biology. Functional amyloids have been identified in nearly all facets of cellular life, with microbial functional amyloids leading the way. Unlike disease-associated amyloids, functional amyloids are assembled by dedicated, directed pathways and ultimately perform a physiological function that benefits the organism. The evolved amyloid assembly and disassembly pathways of microbes have provided novel insights into how cells have harnessed the amyloid assembly process for productive means. An understanding of functional amyloid biogenesis promises to provide a fresh perspective on the molecular events that underlie disease-associated amyloidogenesis. Here, we review functional microbial amyloids with an emphasis on curli fibers and their role in promoting biofilm formation and other community behaviors.
Keywords	protein folding ; cell biology ; biofilm ; neurodegenerative diseases ; Alzheimer disease ; biogenesis ; humans ; amyloid ; microorganisms
Language	English
Document type	Article
ISSN	0966-842X
Database	AGRIS - International Information System for the Agricultural Sciences and Technology

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Article: C-Terminal Repeating Units of CsgB Direct Bacterial Functional Amyloid Nucleation

Hammer, Neal D. / McGuffie, Bryan A. / Zhou, Yizhou / Badtke, Matthew P. / Reinke, Ashley A. / Brännström, Kristoffer / Gestwicki, Jason E. / Olofsson, Anders / Almqvist, Fredrik / Chapman, Matthew R.

Journal of molecular biology

Volume v. 422,, Issue no. 3

Abstract	Curli are functional amyloids produced by enteric bacteria. The major curli fiber subunit, CsgA, self-assembles into an amyloid fiber in vitro. The minor curli subunit protein, CsgB, is required for CsgA polymerization on the cell surface. Both CsgA and CsgB are composed of five predicted β‐strand–loop–β‐strand–loop repeating units that feature conserved glutamine and asparagine residues. Because of this structural homology, we proposed that CsgB might form an amyloid template that initiates CsgA polymerization on the cell surface. To test this model, we purified wild-type CsgB and found that it self-assembled into amyloid fibers in vitro. Preformed CsgB fibers seeded CsgA polymerization as did soluble CsgB added to the surface of cells secreting soluble CsgA. To define the molecular basis of CsgB nucleation, we generated a series of mutants that removed each of the five repeating units. Each of these CsgB deletion mutants was capable of self-assembly in vitro. In vivo, membrane-localized mutants lacking the first, second, or third repeating units were able to convert CsgA into fibers. However, mutants missing either the fourth or fifth repeating units were unable to complement a csgB mutant. These mutant proteins were not localized to the outer membrane but were instead secreted into the extracellular milieu. Synthetic CsgB peptides corresponding to repeating units 1, 2, and 4 self‐assembled into ordered amyloid polymers, while peptides corresponding to repeating units 3 and 5 did not, suggesting that there are redundant amyloidogenic domains in CsgB. Our results suggest a model where the rapid conversion of CsgB from unstructured protein to a β-sheet-rich amyloid template anchored to the cell surface is mediated by the C-terminal repeating units.
Keywords	models ; asparagine ; peptides ; intestinal microorganisms ; polymerization ; glutamine ; polymers ; amyloid ; protein subunits ; mutants
Language	English
Document type	Article
ISSN	0022-2836
Database	AGRIS - International Information System for the Agricultural Sciences and Technology

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