Functional Bacterial Amyloids: Understanding Fibrillation, Regulating Biofilm Fibril Formation and Organizing Surface Assemblies

Abstract

Functional amyloid is produced by many organisms but is particularly well understood in bacteria, where proteins such as CsgA (E. coli) and FapC (Pseudomonas) are assembled as functional bacterial amyloid (FuBA) on the cell surface in a carefully optimized process. Besides a host of helper proteins, FuBA formation is aided by multiple imperfect repeats which stabilize amyloid and streamline the aggregation mechanism to a fast-track assembly dominated by primary nucleation. These repeats, which are found in variable numbers in Pseudomonas, are most likely the structural core of the fibrils, though we still lack experimental data to determine whether the repeats give rise to β-helix structures via stacked β-hairpins (highly likely for CsgA) or more complicated arrangements (possibly the case for FapC). The response of FuBA fibrillation to denaturants suggests that nucleation and elongation involve equal amounts of folding, but protein chaperones preferentially target nucleation for effective inhibition. Smart peptides can be designed based on these imperfect repeats and modified with various flanking sequences to divert aggregation to less stable structures, leading to a reduction in biofilm formation. Small molecules such as EGCG can also divert FuBA to less organized structures, such as partially-folded oligomeric species, with the same detrimental effect on biofilm. Finally, the strong tendency of FuBA to self-assemble can lead to the formation of very regular two-dimensional amyloid films on structured surfaces such as graphite, which strongly implies future use in biosensors or other nanobiomaterials. In summary, the properties of functional amyloid are a much-needed corrective to the unfortunate association of amyloid with neurodegenerative disease and a testimony to nature’s ability to get the best out of a protein fold.

RopB protein of Rhizobium leguminosarum bv. viciae adopts amyloid state during symbiotic interactions with pea (Pisum sativum L.)

“…To date, there have been identified about 30 bacterial amyloidogenic proteins ( Kosolapova et al., 2020 ). Amyloids of bacteria perform various physiological functions including biofilm matrix formation, adhesion, and toxins activity regulation ( Romero and Kolter, 2014 ; Cámara-Almirón et al., 2018 ; Sønderby et al., 2022 ). Many of those functions are associated with the interactions of bacteria with other organisms ( van Gerven et al., 2018 ).…”

The Pga59 cell wall protein is an amyloid forming protein involved in adhesion and biofilm establishment in the pathogenic yeast Candida albicans

“…For instance, the curli system in E. coli consists of amyloid fibres using the proteins CsgA and CsgB as substrates. These fibres extended in the extracellular matrix of the bacteria are involved in biofilm formation and surface colonisation 29 . Another example is the S. cerevisiae pyruvate kinase, Cdc19, which forms amyloid fibres aggregating into stress granules under different types of stress.…”

Search and Identification of Amyloid Proteins

“…At the same time, the so-called functional amyloids are characterized. This group includes proteins that are normally stored or function in the form of amyloid fibrils [ 2 , 3 ]. The search for and identification of proteins that form amyloid fibrils in various living objects is a rather difficult task.…”