Exploring Proteins Containing Amyloidogenic Regions in the Proteomes of Bacteria of the Order <i>Rhizobiales</i>

Antonets, Kirill S.; Kliver, Sergei; Nizhnikov, Anton A.

doi:10.1177/1176934318768781

Cited by 7 publications

(7 citation statements)

References 92 publications

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“…Detergent-resistant fractions of R. leguminosarus were also found to contain other virulence proteins, like NodT, which is probably involved in the secretion of nodulation factors [94]. This corresponds to the previously obtained bioinformatic data, which demonstrated that amyloidogenic regions in proteins of species belonging to the order Rhizobiale tend to co-occur with membrane or extracellular proteins, many of which are associated with virulence of these bacteria [95]. Overall, it becomes apparent that amyloids play an important role in the virulence of bacteria by promoting their interaction with a multicellular host.…”

Section: Discussionsupporting

confidence: 68%

Two Novel Amyloid Proteins, RopA and RopB, from the Root Nodule Bacterium Rhizobium leguminosarum

et al. 2019

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Amyloids represent protein fibrils with a highly ordered spatial structure, which not only cause dozens of incurable human and animal diseases but also play vital biological roles in Archaea, Bacteria, and Eukarya. Despite the fact that association of bacterial amyloids with microbial pathogenesis and infectious diseases is well known, there is a lack of information concerning the amyloids of symbiotic bacteria. In this study, using the previously developed proteomic method for screening and identification of amyloids (PSIA), we identified amyloidogenic proteins in the proteome of the root nodule bacterium Rhizobium leguminosarum. Among 54 proteins identified, we selected two proteins, RopA and RopB, which are predicted to have β-barrel structure and are likely to be involved in the control of plant-microbial symbiosis. We demonstrated that the full-length RopA and RopB form bona fide amyloid fibrils in vitro. In particular, these fibrils are β-sheet-rich, bind Thioflavin T (ThT), exhibit green birefringence upon staining with Congo Red (CR), and resist treatment with ionic detergents and proteases. The heterologously expressed RopA and RopB intracellularly aggregate in yeast and assemble into amyloid fibrils at the surface of Escherichia coli. The capsules of the R. leguminosarum cells bind CR, exhibit green birefringence, and contain fibrils of RopA and RopB in vivo.

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Section: Discussionsupporting

confidence: 68%

Two Novel Amyloid Proteins, RopA and RopB, from the Root Nodule Bacterium Rhizobium leguminosarum

et al. 2019

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“…Furthermore, the results of the LEfSe analysis in female and male 3xTg-AD mice at 3 and 5 months old in fecal samples, show bacteria with a statistically significant change in LDA scores such as Xanthomonadaceae , Oxalobacteraceae , Streptomycetaceae , Koribacteraceae , and Streptomycetaceae families, Gemella , Dehalobacterium , Clostridium , Allobaculum , Selenomonas , Veillonella , Lactococcus , Desulfovibrio , Bradyrhizobium , Campylobacter , Erythrobacter , Neisseria , Flexispira , Microbacterium , Collinsella , Atopobium , Pedobacter , and the S1 genera. These microorganisms have been associated with both pre-clinical models and patients who present AD mainly; however, other bacteria are related to aging, cognitive decline, cerebral damage, and inflammatory response in mice and humans ( Thomas et al, 2012 ; Wang et al, 2016 ; Bonfili et al, 2017 ; Harach et al, 2017 ; Morris et al, 2017 ; Vogt et al, 2017 ; Zhang et al, 2017 ; Aguayo et al, 2018 ; Alonso et al, 2018 ; Antonets et al, 2018 ; Bäuerl et al, 2018 ; Dong et al, 2018 ; Zhuang et al, 2018 ; Haran et al, 2019 ; Li et al, 2019 ; Zhan et al, 2019 ; Beydoun et al, 2020 ; Na et al, 2020 ; Westfall et al, 2020 ). These results suggest that bacteria families and genera are representative microorganisms of gut microbiota of disease that could be considered a useful tool for diagnostic as well as a progression biomarker of AD.…”

Section: Discussionmentioning

confidence: 99%

Spatial Memory and Gut Microbiota Alterations Are Already Present in Early Adulthood in a Pre-clinical Transgenic Model of Alzheimer’s Disease

et al. 2021

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The irreversible and progressive neurodegenerative Alzheimer’s disease (AD) is characterized by cognitive decline, extracellular β-amyloid peptide accumulation, and tau neurofibrillary tangles in the cortex and hippocampus. The triple-transgenic (3xTg) mouse model of AD presents memory impairment in several behavioral paradigms and histopathological alterations from 6 to 16 months old. Additionally, it seems that dysbiotic gut microbiota is present in both mouse models and patients of AD at the cognitive symptomatic stage. The present study aimed to assess spatial learning, memory retention, and gut microbiota alterations in an early adult stage of the 3xTg-AD mice as well as to explore its sexual dimorphism. We evaluated motor activity, novel-object localization training, and retention test as well as collected fecal samples to characterize relative abundance, alpha- and beta-diversity, and linear discriminant analysis (LDA) effect size (LEfSe) analysis in gut microbiota in both female and male 3xTg-AD mice, and controls [non-transgenic mice (NoTg)], at 3 and 5 months old. We found spatial memory deficits in female and male 3xTg-AD but no alteration neither during training nor in motor activity. Importantly, already at 3 months old, we observed decreased relative abundances of Actinobacteria and TM7 in 3xTg-AD compared to NoTg mice, while the beta diversity of gut microbiota was different in female and male 3xTg-AD mice in comparison to NoTg. Our results suggest that gut microbiota modifications in 3xTg-AD mice anticipate and thus could be causally related to cognitive decline already at the early adult age of AD. We propose that microbiota alterations may be used as an early and non-invasive diagnostic biomarker of AD.

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“…Every year, more and more data are accumulated on the amyloidogenic properties of proteins with a β-barrel structure predicted as their native one. Moreover, while for some of them the ability to form amyloid fibrils is currently predicted by proteomic screenings [ 221 ] or in silico methods [ 222 , 223 ], for others, experimental confirmation of the formation of bona fide amyloids on their basis has already been obtained in vitro and, more rarely, in vivo. Functional amyloids formed by β-barrel proteins in vivo have recently been identified in eukaryotes (plants) [ 18 ] and prokaryotes (bacteria) [ 62 , 63 , 64 ], where they are involved in nutrient storage and, probably, supra-organismal interactions.…”

Section: The Transition Of β-Barrel Proteins To Amyloidsmentioning

confidence: 99%

β-Barrels and Amyloids: Structural Transitions, Biological Functions, and Pathogenesis

Sulatskaya

Kosolapova

Bobylev

et al. 2021

IJMS

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Insoluble protein aggregates with fibrillar morphology called amyloids and β-barrel proteins both share a β-sheet-rich structure. Correctly folded β-barrel proteins can not only function in monomeric (dimeric) form, but also tend to interact with one another—followed, in several cases, by formation of higher order oligomers or even aggregates. In recent years, findings proving that β-barrel proteins can adopt cross-β amyloid folds have emerged. Different β-barrel proteins were shown to form amyloid fibrils in vitro. The formation of functional amyloids in vivo by β-barrel proteins for which the amyloid state is native was also discovered. In particular, several prokaryotic and eukaryotic proteins with β-barrel domains were demonstrated to form amyloids in vivo, where they participate in interspecies interactions and nutrient storage, respectively. According to recent observations, despite the variety of primary structures of amyloid-forming proteins, most of them can adopt a conformational state with the β-barrel topology. This state can be intermediate on the pathway of fibrillogenesis (“on-pathway state”), or can be formed as a result of an alternative assembly of partially unfolded monomers (“off-pathway state”). The β-barrel oligomers formed by amyloid proteins possess toxicity, and are likely to be involved in the development of amyloidoses, thus representing promising targets for potential therapy of these incurable diseases. Considering rapidly growing discoveries of the amyloid-forming β-barrels, we may suggest that their real number and diversity of functions are significantly higher than identified to date, and represent only “the tip of the iceberg”. Here, we summarize the data on the amyloid-forming β-barrel proteins, their physicochemical properties, and their biological functions, and discuss probable means and consequences of the amyloidogenesis of these proteins, along with structural relationships between these two widespread types of β-folds.

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

Cited by 7 publications

References 92 publications

Two Novel Amyloid Proteins, RopA and RopB, from the Root Nodule Bacterium Rhizobium leguminosarum

Two Novel Amyloid Proteins, RopA and RopB, from the Root Nodule Bacterium Rhizobium leguminosarum

Spatial Memory and Gut Microbiota Alterations Are Already Present in Early Adulthood in a Pre-clinical Transgenic Model of Alzheimer’s Disease

β-Barrels and Amyloids: Structural Transitions, Biological Functions, and Pathogenesis

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