scholarly journals Amyloid proteins of plants and microorganisms: biological functions and participation in the formation of supra-organismal systems

2020 ◽  
Author(s):  
A. A. Nizhnikov
Keyword(s):  
Symbiotic Bacteria ◽  
Biological Functions ◽  
Amyloid Proteins ◽  
Protein Storage ◽  
Plant Seeds ◽  
Protein Fibrils ◽  
Functional Amyloids

Here we will review the latest advances in the study of functional amyloids of plants and symbiotic bacteria demonstrating the involvement of these protein fibrils in protein storage in plant seeds and formation of supra-organismal interactions.

scholarly journals Protein Co-Aggregation Related to Amyloids: Methods of Investigation, Diversity, and Classification

2018 ◽  
Vol 19 (8) ◽  
pp. 2292 ◽  
Author(s):  
Stanislav Bondarev ◽  
Kirill Antonets ◽  
Andrey Kajava ◽  
Anton Nizhnikov ◽  
Galina Zhouravleva
Keyword(s):  
Binding Site ◽  
Molecular Mechanisms ◽  
Amyloid Fibrils ◽  
Specific Binding ◽  
Protein S ◽  
Functional Protein ◽  
Functional Roles ◽  
Protein Fibrils ◽  
Protein Functions ◽  
Functional Amyloids

Amyloids are unbranched protein fibrils with a characteristic spatial structure. Although the amyloids were first described as protein deposits that are associated with the diseases, today it is becoming clear that these protein fibrils play multiple biological roles that are essential for different organisms, from archaea and bacteria to humans. The appearance of amyloid, first of all, causes changes in the intracellular quantity of the corresponding soluble protein(s), and at the same time the aggregate can include other proteins due to different molecular mechanisms. The co-aggregation may have different consequences even though usually this process leads to the depletion of a functional protein that may be associated with different diseases. The protein co-aggregation that is related to functional amyloids may mediate important biological processes and change of protein functions. In this review, we survey the known examples of the amyloid-related co-aggregation of proteins, discuss their pathogenic and functional roles, and analyze methods of their studies from bacteria and yeast to mammals. Such analysis allow for us to propose the following co-aggregation classes: (i) titration: deposition of soluble proteins on the amyloids formed by their functional partners, with such interactions mediated by a specific binding site; (ii) sequestration: interaction of amyloids with certain proteins lacking a specific binding site; (iii) axial co-aggregation of different proteins within the same amyloid fibril; and, (iv) lateral co-aggregation of amyloid fibrils, each formed by different proteins.

Fat - carbohydrate - protein: Storage in plant seeds

2013 ◽  
Vol 25 (4) ◽  
pp. 79-81 ◽  
Author(s):  
Ulrich Lüttge
Keyword(s):  
Protein Storage ◽  
Plant Seeds

scholarly journals Functional Amyloids Are the Rule Rather Than the Exception in Cellular Biology

2020 ◽  
Vol 8 (12) ◽  
pp. 1951
Author(s):  
Anthony Balistreri ◽  
Emily Goetzler ◽  
Matthew Chapman
Keyword(s):  
Functional Role ◽  
Cellular Systems ◽  
Regulatory Mechanisms ◽  
Cellular Biology ◽  
Biological Functions ◽  
Cellular Processes ◽  
Domains Of Life ◽  
Functional Amyloids ◽  
Definition Of ◽  
And Storage

Amyloids are a class of protein aggregates that have been historically characterized by their relationship with human disease. Indeed, amyloids can be the result of misfolded proteins that self-associate to form insoluble, extracellular plaques in diseased tissue. For the first 150 years of their study, the pathogen-first definition of amyloids was sufficient. However, new observations of amyloids foster an appreciation for non-pathological roles for amyloids in cellular systems. There is now evidence from all domains of life that amyloids can be non-pathogenic and functional, and that their formation can be the result of purposeful and controlled cellular processes. So-called functional amyloids fulfill an assortment of biological functions including acting as structural scaffolds, regulatory mechanisms, and storage mechanisms. The conceptual convergence of amyloids serving a functional role has been repeatedly confirmed by discoveries of additional functional amyloids. With dozens already known, and with the vigorous rate of discovery, the biology of amyloids is robustly represented by non-pathogenic amyloids.

scholarly journals A gut bacterial amyloid promotes α-synuclein aggregation and motor impairment in mice

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Timothy R Sampson ◽  
Collin Challis ◽  
Neha Jain ◽  
Anastasiya Moiseyenko ◽  
Mark S Ladinsky ◽  
...  
Keyword(s):  
Oral Treatment ◽  
Motor Impairment ◽  
Amyloid Formation ◽  
Amyloid Proteins ◽  
Motor Impairments ◽  
Behavioral Abnormalities ◽  
Biochemical Assays ◽  
Genetic And Environmental Factors ◽  
Functional Amyloids ◽  
The Brain

Amyloids are a class of protein with unique self-aggregation properties, and their aberrant accumulation can lead to cellular dysfunctions associated with neurodegenerative diseases. While genetic and environmental factors can influence amyloid formation, molecular triggers and/or facilitators are not well defined. Growing evidence suggests that non-identical amyloid proteins may accelerate reciprocal amyloid aggregation in a prion-like fashion. While humans encode ~30 amyloidogenic proteins, the gut microbiome also produces functional amyloids. For example, curli are cell surface amyloid proteins abundantly expressed by certain gut bacteria. In mice overexpressing the human amyloid α-synuclein (αSyn), we reveal that colonization with curli-producing Escherichia coli promotes αSyn pathology in the gut and the brain. Curli expression is required for E. coli to exacerbate αSyn-induced behavioral deficits, including intestinal and motor impairments. Purified curli subunits accelerate αSyn aggregation in biochemical assays, while oral treatment of mice with a gut-restricted amyloid inhibitor prevents curli-mediated acceleration of pathology and behavioral abnormalities. We propose that exposure to microbial amyloids in the gastrointestinal tract can accelerate αSyn aggregation and disease in the gut and the brain.

A Buried Glutamate in the Cross-β Core Renders β-endorphin Fibrils Reversible

Nanoscale ◽  
2021 ◽  
Author(s):  
Yuying Liu ◽  
Yu Zhang ◽  
Yunxiang Sun ◽  
Feng Ding
Keyword(s):  
Biological Functions ◽  
Naturally Occurring ◽  
Irreversible Aggregation ◽  
The Cross ◽  
Living Organisms ◽  
Functional Amyloids

Functional amyloids are abundant in living organisms from prokaryotes to eukaryotes playing diverse biological functions. In contrast to the irreversible aggregation of most known pathological amyloids, we postulate that naturally-occurring...

scholarly journals Quantitating denaturation by formic acid: Imperfect repeats are essential to the stability of the functional amyloid protein FapC

2020 ◽  
Author(s):  
Line Friis Bakmann Christensen ◽  
Jan Stanislaw Nowak ◽  
Thorbjørn Vincent Sønderby ◽  
Signe Andrea Frank ◽  
Daniel Erik Otzen
Keyword(s):  
Formic Acid ◽  
Mechanical Stability ◽  
Complete Removal ◽  
Amyloid Formation ◽  
Amyloid Protein ◽  
Biological Functions ◽  
Functional Amyloid ◽  
High Concentrations ◽  
Functional Amyloids ◽  
The Stability

ABSTRACTBacterial functional amyloids are evolutionarily optimized to aggregate to help them fulfil their biological functions, e.g. to provide mechanical stability to biofilm. Amyloid is formed in Pseudomonas sp. by the protein FapC which contains 3 imperfect repeats connected by long linkers. Stepwise removal of these repeats slows down aggregation and increases the propensity of amyloids to fragment during the fibrillation process, but how these mechanistic properties link to fibril stability is unclear. Here we address this question. The extreme robustness of functional amyloid makes them resistant to conventional chemical denaturants, but they dissolve in formic acid (FA) at high concentrations. To quantify this, we first measured the denaturing potency of FA using 3 small acid-resistant proteins (S6, lysozyme and ubiquitin). This revealed a linear relationship between [FA] and the free energy of unfolding with a slope of mFA, as well as a robust correlation between protein residue size and mFA. We then measured the solubilisation of fibrils formed from different FapC variants (with varying number of repeats) as a function of [FA]. The resulting mFA values revealed a decline in the number of residues driving amyloid formation when at least 2 repeats were deleted. The midpoint of denaturation declined monotonically with progressive removal of repeats and correlated with solubility in SDS. Complete removal of all repeats led to fibrils which were solubilized at FA concentrations 2-3 orders of magnitude lower than the repeat-containing variants, showing that at least one imperfect repeat is required for the stability of functional amyloid.

scholarly journals Amyloid Proteins in Plant-Associated Microbial Communities

2021 ◽  
pp. 1-11
Author(s):  
Daniel Gómez-Pérez ◽  
Vasvi Chaudhry ◽  
Ariane Kemen ◽  
Eric Kemen
Keyword(s):  
Microbial Communities ◽  
Hydrophobic Surface ◽  
Pathogenic Fungi ◽  
Plant Colonization ◽  
Bacterial Survival ◽  
Amyloid Proteins ◽  
Host Interactions ◽  
Protein Research ◽  
Functional Amyloids ◽  
Functional Mechanisms

Amyloids have proven to be a widespread phenomenon rather than an exception. Many proteins presenting the hallmarks of this characteristic beta sheet-rich folding have been described to date. Particularly common are functional amyloids that play an important role in the promotion of survival and pathogenicity in prokaryotes. Here, we describe important developments in amyloid protein research that relate to microbe-microbe and microbe-host interactions in the plant microbiome. Starting with biofilms, which are a broad strategy for bacterial persistence that is extremely important for plant colonization. Microbes rely on amyloid-based mechanisms to adhere and create a protective coating that shelters them from external stresses and promotes cooperation. Another strategy generally carried out by amyloids is the formation of hydrophobic surface layers. Known as hydrophobins, these proteins coat the aerial hyphae and spores of plant pathogenic fungi, as well as certain bacterial biofilms. They contribute to plant virulence through promoting dissemination and infectivity. Furthermore, antimicrobial activity is an interesting outcome of the amyloid structure that has potential application in medicine and agriculture. There are many known antimicrobial amyloids released by animals and plants; however, those produced by bacteria or fungi remain still largely unknown. Finally, we discuss amyloid proteins with a more indirect mode of action in their host interactions. These include virulence-promoting harpins, signaling transduction that functions through amyloid templating, and root nodule bacteria proteins that promote plant-microbe symbiosis. In summary, amyloids are an interesting paradigm for their many functional mechanisms linked to bacterial survival in plant-associated microbial communities.

scholarly journals Multifunctional Amyloids in the Biology of Gram-Positive Bacteria

2020 ◽  
Vol 8 (12) ◽  
pp. 2020
Author(s):  
Ana Álvarez-Mena ◽  
Jesús Cámara-Almirón ◽  
Antonio de Vicente ◽  
Diego Romero
Keyword(s):  
Biological Functions ◽  
Interspecies Interactions ◽  
Cellular Functions ◽  
Gram Positive ◽  
Multifunctional Proteins ◽  
Gram Positive Bacteria ◽  
The Matrix ◽  
Functional Amyloids

Since they were discovered, amyloids have proven to be versatile proteins able to participate in a variety of cellular functions across all kingdoms of life. This multitask trait seems to reside in their ability to coexist as monomers, aggregates or fibrillar entities, with morphological and biochemical peculiarities. It is precisely this common molecular behaviour that allows amyloids to cross react with one another, triggering heterologous aggregation. In bacteria, many of these functional amyloids are devoted to the assembly of biofilms by organizing the matrix scaffold that keeps cells together. However, consistent with their notion of multifunctional proteins, functional amyloids participate in other biological roles within the same organisms, and emerging unprecedented functions are being discovered. In this review, we focus on functional amyloids reported in gram-positive bacteria, which are diverse in their assembly mechanisms and remarkably specific in their biological functions that they perform. Finally, we consider cross-seeding between functional amyloids as an emerging theme in interspecies interactions that contributes to the diversification of bacterial biology.

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

2021 ◽  
Vol 22 (21) ◽  
pp. 11316
Author(s):  
Anna I. Sulatskaya ◽  
Anastasiia O. Kosolapova ◽  
Alexander G. Bobylev ◽  
Mikhail V. Belousov ◽  
Kirill S. Antonets ◽  
...  
Keyword(s):  
Amyloid Fibrils ◽  
Biological Functions ◽  
Interspecies Interactions ◽  
Structural Relationships ◽  
Fibrillar Morphology ◽  
Dimeric Form ◽  
Functional Amyloids ◽  
Partially Unfolded

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.

Membrane–cytoskeleton interactions in cholesterol-dependent domain formation

2015 ◽  
Vol 57 ◽  
pp. 177-187 ◽  
Author(s):  
Jennifer N. Byrum ◽  
William Rodgers
Keyword(s):  
Biological Properties ◽  
Membrane Rafts ◽  
Membrane Domains ◽  
Biological Functions ◽  
Membrane Cytoskeleton ◽  
Heterogeneous Structures ◽  
Integral Role ◽  
Model Cell ◽  
Actomyosin Cytoskeleton ◽  
Dependent Domain

Since the inception of the fluid mosaic model, cell membranes have come to be recognized as heterogeneous structures composed of discrete protein and lipid domains of various dimensions and biological functions. The structural and biological properties of membrane domains are represented by CDM (cholesterol-dependent membrane) domains, frequently referred to as membrane ‘rafts’. Biological functions attributed to CDMs include signal transduction. In T-cells, CDMs function in the regulation of the Src family kinase Lck (p56lck) by sequestering Lck from its activator CD45. Despite evidence of discrete CDM domains with specific functions, the mechanism by which they form and are maintained within a fluid and dynamic lipid bilayer is not completely understood. In the present chapter, we discuss recent advances showing that the actomyosin cytoskeleton has an integral role in the formation of CDM domains. Using Lck as a model, we also discuss recent findings regarding cytoskeleton-dependent CDM domain functions in protein regulation.

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