Mechanism of Amyloidogenesis of a Bacterial AAA+ Chaperone

Chan, Sze Wah Samuel; Yau, Jason; Ing, Christopher; Liu, Kaiyin; Farber, Patrick; Won, Amy; Bhandari, Vaibhav; Kara-Yacoubian, Nareg; Seraphim, Thiago Vargas; Chakrabarti, Nilmadhab; Kay, Lewis E.; Yip, Christopher M.; Pomès, Régis; Sharpe, Simon; Houry, Walid

doi:10.1016/j.str.2016.05.002

Cited by 14 publications

(12 citation statements)

References 55 publications

(57 reference statements)

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“…The concept of a protective loop shielding aggregation prone regions has also been proposed for other self-assembling proteins5455 and as a method of ‘negative design’ to prevent aggregation56. This mechanism of the loop moving out of the way to allow dimerisation resembles models previously proposed for several other amyloidogenic proteins suggesting that despite variations in sequence and initial structure, these proteins may share a common pathway for amyloid nucleation and subsequent protofibril and fibril formation.…”

Section: Discussionmentioning

confidence: 82%

Probing Medin Monomer Structure and its Amyloid Nucleation Using 13C-Direct Detection NMR in Combination with Structural Bioinformatics

Davies

Rigden

Phelan

et al. 2017

Sci Rep

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Aortic medial amyloid is the most prevalent amyloid found to date, but remarkably little is known about it. It is characterised by aberrant deposition of a 5.4 kDa protein called medin within the medial layer of large arteries. Here we employ a combined approach of ab initio protein modelling and 13C-direct detection NMR to generate a model for soluble monomeric medin comprising a stable core of three β-strands and shorter more labile strands at the termini. Molecular dynamics simulations suggested that detachment of the short, C-terminal β-strand from the soluble fold exposes key amyloidogenic regions as a potential site of nucleation enabling dimerisation and subsequent fibril formation. This mechanism resembles models proposed for several other amyloidogenic proteins suggesting that despite variations in sequence and protomer structure these proteins may share a common pathway for amyloid nucleation and subsequent protofibril and fibril formation.

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Section: Discussionmentioning

confidence: 82%

Probing Medin Monomer Structure and its Amyloid Nucleation Using 13C-Direct Detection NMR in Combination with Structural Bioinformatics

Davies

Rigden

Phelan

et al. 2017

Sci Rep

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“…Chan et al . analyzed the secondary structure of the amyloidogenic LARA domain of bacterial regulatory adenosine triphosphatase variant A (RavA) ( 22 ). Yamaguchi et al .…”

Section: Resultsmentioning

confidence: 99%

BeStSel: a web server for accurate protein secondary structure prediction and fold recognition from the circular dichroism spectra

Micsonai

Wien

Bulyáki

et al. 2018

Nucleic Acids Research

858

786

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Circular dichroism (CD) spectroscopy is a widely used method to study the protein secondary structure. However, for decades, the general opinion was that the correct estimation of β-sheet content is challenging because of the large spectral and structural diversity of β-sheets. Recently, we showed that the orientation and twisting of β-sheets account for the observed spectral diversity, and developed a new method to estimate accurately the secondary structure (PNAS, 112, E3095). BeStSel web server provides the Beta Structure Selection method to analyze the CD spectra recorded by conventional or synchrotron radiation CD equipment. Both normalized and measured data can be uploaded to the server either as a single spectrum or series of spectra. The originality of BeStSel is that it carries out a detailed secondary structure analysis providing information on eight secondary structure components including parallel-β structure and antiparallel β-sheets with three different groups of twist. Based on these, it predicts the protein fold down to the topology/homology level of the CATH protein fold classification. The server also provides a module to analyze the structures deposited in the PDB for BeStSel secondary structure contents in relation to Dictionary of Secondary Structure of Proteins data. The BeStSel server is freely accessible at http://bestsel.elte.hu.

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“…However, amyloidogenesis has not been extensively studied in microbes. The research in this area has accelerated in recent times with discovery of several cytosolic bacterial proteins such as E. coli RavA ( Chan et al, 2016 ), E. coli GroES ( Higurashi et al, 2005 ), E. coli RepA ( Giraldo, 2007 ; Fernández et al, 2016 ), Microcin E492 ( Aguilera et al, 2016 ), Clostridium botulinum Rho ( Pallares et al, 2015 ; Yuan and Hochschild, 2017 ) and M. tuberculosis CarD ( Kaur et al, 2018 ) added to the list of family of proteins with amyloidogenic properties. Our study provides the first report of the formation of amyloid-like fibrils by a soluble cytoplasmic transcription factor, HelD, in B. subtilis which also functions as a helicase.…”

Section: Discussionmentioning

confidence: 99%

Bacillus subtilis HelD, an RNA Polymerase Interacting Helicase, Forms Amyloid-Like Fibrils

2018

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HelD, an RNA polymerase binding protein from Bacillus subtilis, stimulates transcription and helps in timely adaptation of cells under diverse environmental conditions. At present, no structural information is available for HelD. In the current study, we performed size exclusion chromatography coupled to small angle X-ray scattering (SEC-SAXS) which suggests that HelD is predominantly monomeric and globular in solution. Using combination of size exclusion chromatography and analytical ultracentrifugation, we also show that HelD has a tendency to form higher order oligomers in solution. CD experiments suggest that HelD has both α-helical (∼35%) and β sheet (∼26%) secondary structural elements. Thermal melting experiments suggest that even at 90°C, there is only about 30% loss in secondary structural contents with Tm of 44°C. However, with the increase in temperature, there was a gain in the β-sheet content and significant irreversible loss of α-helical content. Using a combination of X-ray fiber diffraction analysis, and dye based assays including Thioflavin-T based fluorescence and Congo red binding assays, we discovered that HelD forms amyloid-like fibrils at physiologically relevant conditions in vitro. Using confocal imaging, we further show that HelD forms amyloid inclusions in Escherichia coli. Bioinformatics-based sequence analysis performed using three independent web-based servers suggests that HelD has more than 20 hot-spots spread across the sequence that may aid the formation of amyloid-like fibrils. This discovery adds one more member to the growing list of amyloid or amyloid-like fibril forming cytosolic proteins in bacteria. Future studies aimed at resolving the function of amyloid-like fibrils or amyloid inclusions may help better understand their role, if any, in the bacterial physiology.

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Mechanism of Amyloidogenesis of a Bacterial AAA+ Chaperone

Cited by 14 publications

References 55 publications

Probing Medin Monomer Structure and its Amyloid Nucleation Using 13C-Direct Detection NMR in Combination with Structural Bioinformatics

Probing Medin Monomer Structure and its Amyloid Nucleation Using 13C-Direct Detection NMR in Combination with Structural Bioinformatics

BeStSel: a web server for accurate protein secondary structure prediction and fold recognition from the circular dichroism spectra

Bacillus subtilis HelD, an RNA Polymerase Interacting Helicase, Forms Amyloid-Like Fibrils

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