Bacterial Amyloids

Abstract

Amyloids are supramolecular protein assemblies based on fibrillar arrangements of β‐sheets that were first found as linked to neurodegenerative and systemic human diseases. However, there is now overwhelming evidence on alternative roles of amyloids as functional assemblies and as epigenetic determinants of beneficial traits, both in Fungi and Metazoa. Bacteria also use amyloids as functional devices, mainly as extracellular scaffolds in biofilms, but there is increasing evidence for functional roles of amyloids in the bacterial cytosol, and these have enabled to engineer minimal models of a ‘generic’ amyloid disease. Amyloids are thus key players in the physiology of bacteria and versatile building blocks in synthetic biology.

Key Concepts

  • Besides determining human diseases and functional traits in yeast, amyloids also play functional roles in bacteria.
  • Secreted bacterial amyloidogenic proteins scaffold the extracellular matrix in biofilms, bacterial consortia key for biofouling and antibiotic resistance.
  • Intracellular amyloid assemblies control regulation of gene expression by small RNAs, transcription termination and plasmid DNA replication in bacteria.
  • The assembly of antimicrobial peptides as amyloids counteracts their toxicity, while functional amyloids can be turned into cytotoxic models of disease.
  • Bacterial amyloids, due to their modularity and high stability, are excellent blocks for the design of synthetic supramolecular assemblies.

Keywords: amyloid; prion; bacteria; biofilm; sRNA regulation; Hfq; plasmid replication control; microcin E492; RepA‐WH1

Figure 1. Steps involved in microcin E492 production, antibacterial activity and amyloid formation. (1) MccE492 peptide precursor is synthesised from its coding gene mceA and must be co‐expressed with the immunity protein encoded by mceB. Besides, the MceC adds sugar moieties to the enterochelin siderophore, produced by the enzymes encoded in the ent genes (2), giving salmochelin. (3) The MceJI proteins catalyse the attachment of salmochelin to MccE492 peptide, originating mature (active) MccE492 (MccE492*). A mixture of unmodified (nonactive) and modified forms is secreted to the extracellular space through the dedicated exporter formed by MceHG and the outer membrane protein TolG, where the N‐terminal leader peptide carried by the MccE492 precursor is cleaved. Both enterochelin production and MccE492 maturation are induced in response to low iron availability. In this situation, a high proportion of modified MccE492 is exported, which can enter the target cells through the catechol siderophore receptors, resulting in a high antibacterial activity. The production of a high amount of modified MccE492, disfavours its amyloid aggregation, preventing toxin inactivation. At high iron availability, low amounts of enterochelin and salmochelin are produced, generating a low amount of MccE492*. Unmodified MccE492 accumulation favours its aggregation into amyloid fibres that lack antibacterial activity.
Figure 2. A sketch with the three intracellular bacterial functional amyloids characterised so far. (a) RepA, inhibiting premature DNA replication firing by sterically bringing together the replication origins of plasmids (green). (b) CbRho as an hexamer finishes mRNA (pink) transcription, while as an amyloid oligomer allows transcription to proceed further, generating longer mRNA molecules. (c) Hfq, a hexamer that can also assemble amyloid oligomers, is a global regulator of sRNA (magenta) stability as well as of genome packing, while it can also assemble pores at the bacterial membrane. In all cases, amyloidogenic modules (domains) have been depicted in blue, whereas functional ones were coloured yellow (RepA C‐terminal DNA‐binding domain) or cyan (CbRho and Hfq RNA binding modules).
Figure 3. The cytotoxic prion‐like protein RepA‐WH1. (a) TEM section though an E. coli cell showing the amyloidogenic precursors of RepA‐WH1 assembled at the nucleoid (yellow sector), as revealed by an antibody specific of the amyloidogenic conformation (arrows: gold particles). (b) At the membrane, RepA‐WH1 assembles as pores (EM 2D‐projection, bottom). These pores can be reconstituted in lipid vesicles (red: RepA‐WH1‐mCherry; green: confined calcein label). (c) In mature intracellular aggregates (electron‐dense areas), RepA‐WH1 monomers would assemble head‐to‐tail (β1–β2) as helical tubules (3D‐EM, left) with a diameter section alike that of the pores (right).
Figure 4. The three‐dimensional structures of the amyloidogenic modules of curli‐like fibrils (modelled as 2NNT; a), PSMα3 (PDB 5I55; b), TasA (PDB 5OF1; c) and RepA‐WH1 (PDB 1HKQ; d). Distinct folds, either all‐β (a), all‐α (b) or α + β (c and d), can be used to build amyloid fibres (fibril axes depicted as dotted lines in a and b), but implying conformational transformations into β‐sheet rich fibres (c and d), or the assembly of unaltered α‐helical building blocks into cross‐α fibres (b) that match the overall shape of bona fide amyloids (a).
Figure 5. Techniques to characterise the structure of amyloid self‐assemblies. (a) The hallmark cross‐β amyloid assembly consists in inter‐strand and inter‐sheet distances of 4.7 Å and 8–10 Å, respectively. Molecular imaging of amyloid fibrils is enabled by (b) AFM and (c) cryo‐TEM. Secondary and super‐secondary structures are addressed by (d) FTIR and (e) SRCD. (f) Left: Experimental setting for small angle X‐ray scattering (SAXS). The electrons in the fibril sample scatter X‐rays, which are registered by a detector as the amyloid signature reflection arches. Right: SAXS curves. The cross‐β reflections are seen at ∼0.7 and ∼1.35 Å−1, corresponding to inter‐sheet and inter‐strand distances (see left and a). (b) Source: Figure courtesy Marisela Vélez; (c) Source: Figure courtesy Sylvain Trepout; (d) Source: Figure courtesy Frederic Geinguenaud; (f) Source: Figure courtesy Thomas Bizien.
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Further Reading

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Molina‐García L , Gasset‐Rosa F , Moreno‐del Álamo M , et al. (2016) Addressing intracellular amyloidosis in bacteria with RepA‐WH1, a prion‐like protein. Methods in Molecular Biology 1779: 289–312.

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Marcoleta, Andrés, Wien, Frank, Arluison, Véronique, Lagos, Rosalba, and Giraldo, Rafael(Mar 2019) Bacterial Amyloids. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0028401]