M60-like metalloprotease domain of the Escherichia coli YghJ protein forms amyloid fibrils

Белоусов, М. В.; Bondarev, Stanislav A.; Kosolapova, Anastasiia O.; Antonets, Kirill S.; Sulatskaya, Anna I.; Sulatsky, Maksim I.; Zhouravleva, Galina A.; Kuznetsova, Irina М.; Turoverov, Konstantin К.; Nizhnikov, Anton A.

doi:10.1371/journal.pone.0191317

Cited by 12 publications

(17 citation statements)

References 58 publications

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“…Bioinformatic prediction is a powerful tool to reveal prominent candidates for further experimental verification of their amyloid properties. 27 – 29 In this study, we focused on predicting the potentially amyloidogenic proteins in the species of the order Rhizobiales , which belongs to the class Alphaproteobacteria. Rhizobiales represent a uniquely diverse group of bacteria, embracing not only species capable of nitrogen fixation in the symbiosis with the leguminous plants but also dangerous pathogens of animals and plants.…”

Section: Introductionmentioning

confidence: 99%

Exploring Proteins Containing Amyloidogenic Regions in the Proteomes of Bacteria of the Order Rhizobiales

Antonets

Kliver

Nizhnikov

2018

Evol Bioinform Online

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Amyloids are protein fibrils with a highly ordered spatial structure called cross-β. To date, amyloids were shown to be implicated in a wide range of biological processes, both pathogenic and functional. In bacteria, functional amyloids are involved in forming biofilms, storing toxins, overcoming the surface tension, and other functions. Rhizobiales represent an economically important group of Alphaproteobacteria, various species of which are not only capable of fixing nitrogen in the symbiosis with leguminous plants but also act as the causative agents of infectious diseases in animals and plants. Here, we implemented bioinformatic screening for potentially amyloidogenic proteins in the proteomes of more than 80 species belonging to the order Rhizobiales. Using SARP (Sequence Analysis based on the Ranking of Probabilities) and Waltz bioinformatic algorithms, we identified the biological processes, where potentially amyloidogenic proteins are overrepresented. We detected protein domains and regions associated with amyloidogenic sequences in the proteomes of various Rhizobiales species. We demonstrated that amyloidogenic regions tend to occur in the membrane or extracellular proteins, many of which are involved in pathogenesis-related processes, including adhesion, assembly of flagellum, and transport of siderophores and lipopolysaccharides, and contain domains typical of the virulence factors (hemolysin, RTX, YadA, LptD); some of them (rhizobiocins, LptD) are also related to symbiosis.

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Section: Introductionmentioning

confidence: 99%

Exploring Proteins Containing Amyloidogenic Regions in the Proteomes of Bacteria of the Order Rhizobiales

Antonets

Kliver

Nizhnikov

2018

Evol Bioinform Online

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“…Moreover, as C-DAG is a cell-based system, it can be regarded as a more physiological technique of testing protein's amyloidogenic properties comparing to in vitro experiments. In several studies, it was shown that the results obtained using C-DAG generally strongly resemble the results of the study of protein's fibrils formation in vitro [37,40,49,50] or in vivo genetic tests for prion inheritance [51].…”

Section: Discussionmentioning

confidence: 75%

Amyloid properties of the yeast cell wall protein Toh1 and its interaction with prion proteins Rnq1 and Sup35

Sergeeva

Sopova

Belashova

et al. 2018

Prion

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Amyloids are non-branching fibrils that are composed of stacked monomers stabilized by intermolecular β-sheets. Some amyloids are associated with incurable diseases, whereas others, functional amyloids, regulate different vital processes. The prevalence and significance of functional amyloids in wildlife are still poorly understood. In recent years, by applying new approach of large-scale proteome screening, a number of novel candidate amyloids were identified in the yeast Saccharomyces cerevisiae, many of which are localized in the yeast cell wall. In this work, we showed that one of these proteins, Toh1, possess amyloid properties. The Toh1-YFP hybrid protein forms detergent-resistant aggregates in the yeast cells while being expressed under its own P TOH1 or inducible P CUP1 promoter. Using bacterial system for generation of extracellular amyloid aggregates C-DAG, we demonstrated that the N-terminal Toh1 fragment, containing amyloidogenic regions predicted in silico, binds Congo Red dye, manifests 'apple-green' birefringence when examined between crossed polarizers, and forms amyloid-like fibrillar aggregates visualized by TEM. We have established that the Toh1(20-365)-YFP hybrid protein fluorescent aggregates are co-localized with a high frequency with Rnq1C-CFP and Sup35NM-CFP aggregates in the yeast cells containing [PIN + ] and [PSI + ] prions, and physical interaction of these aggregated proteins was confirmed by FRET. This is one of a few known cases of physical interaction of non-Q/N-rich amyloid-like protein and Q/N-rich amyloids, suggesting that interaction of different amyloid proteins may be determined not only by similarity of their primary structures but also by similarity of their secondary structures and of conformational folds.

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“…Three proteins included in our analysis -CarD, HelD, and RepA proteinsphysically interact with nucleic acids one way or another [195 200]. In addition, aggregation ability was shown for YghJ protease [201] and transglutaminase TGZ [202].…”

Section: Aggregation Prone Porins and Enzymesmentioning

confidence: 99%

Amyloid and Amyloid-Like Aggregates: Diversity and the Term Crisis

Matiiv

Trubitsina

Matveenko

et al. 2020

Biochemistry Moscow

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Active accumulation of the data on new amyloids continuing nowadays dissolves boundaries of the term “amyloid”. Currently, it is most often used to designate aggregates with cross-β structure. At the same time, amyloids also exhibit a number of other unusual properties, such as: detergent and protease resistance, interaction with specific dyes, and ability to induce transition of some proteins from a soluble form to an aggregated one. The same features have been also demonstrated for the aggregates lacking cross-β structure, which are commonly called “amyloid-like” and combined into one group, although they are very diverse. We have collected and systematized information on the properties of more than two hundred known amyloids and amyloid-like proteins with emphasis on conflicting examples. In particular, a number of proteins in membraneless organelles form aggregates with cross-β structure that are morphologically indistinguishable from the other amyloids, but they can be dissolved in the presence of detergents, which is not typical for amyloids. Such paradoxes signify the need to clarify the existing definition of the term amyloid. On the other hand, the demonstrated structural diversity of the amyloid-like aggregates shows the necessity of their classification.

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M60-like metalloprotease domain of the Escherichia coli YghJ protein forms amyloid fibrils

Cited by 12 publications

References 58 publications

Exploring Proteins Containing Amyloidogenic Regions in the Proteomes of Bacteria of the Order Rhizobiales

Exploring Proteins Containing Amyloidogenic Regions in the Proteomes of Bacteria of the Order Rhizobiales

Amyloid properties of the yeast cell wall protein Toh1 and its interaction with prion proteins Rnq1 and Sup35

Amyloid and Amyloid-Like Aggregates: Diversity and the Term Crisis

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