The role of filamentous matrix molecules in shaping the architecture and emergent properties of bacterial biofilms

Abstract

Numerous bacteria naturally occur within spatially organised, multicellular communities called biofilms. Moreover, most bacterial infections proceed with biofilm formation, posing major challenges to human health. Within biofilms, bacterial cells are embedded in a primarily self-produced extracellular matrix, which is a defining feature of all biofilms. The biofilm matrix is a complex, viscous mixture primarily composed of polymeric substances such as polysaccharides, filamentous protein fibres, and extracellular DNA. The structured arrangement of the matrix bestows bacteria with beneficial emergent properties that are not displayed by planktonic cells, conferring protection against physical and chemical stresses, including antibiotic treatment. However, a lack of multi-scale information at the molecular level has prevented a better understanding of this matrix and its properties. Here, we review recent progress on the molecular characterisation of filamentous biofilm matrix components and their three-dimensional spatial organisation within biofilms.

Keywords: bacteria; biofilms; extracellular matrix; microbiology; structural biology.

Figure 1.. Structural features of biofilm matrix fibres.

Monomeric and fibre forms are shown for each example: curli fibres composed of CsgA subunits (structural model from AlphaFold2 and cryo-EM [92], PDB ID 8C50), TasA (monomer PDB ID 5OF1 [97], fibre PDB ID 8AUR [24]), putative PSMα3 fibres as predicted from its crystal structure [20] (PDB ID 5I55), and the Csu pilus (monomer PDB ID 5D6H [30], fibre PDB ID 7ZL4 [31]).

Figure 2.. Multi-scale studies elucidate the interactions of cells with the extracellular matrix that give rise to the complex three-dimensional architecture found in biofilms.

First column (from left): General principles of cell-matrix interactions: Many of the fibrous components in biofilms either cross-link cells with matrix polysaccharides or DNA (upper) or form bundles in which cells are embedded (lower). A mixture of chemical and entropic effects may contribute to both mechanisms. Second column: Atomic models of biofilm fibres produced in recent years, including the V. cholerae RbmC adhesin AlphaFold prediction [169,170] annotated by domain function as described previously [64], an archaic CUP pilus from A. baumannii [29,31], Pf4 phage [46], and TasA fibres [24]. Third column: Localisation of RbmC expression in V. cholerae microcolonies as shown by fluorescence microscopy (from reference [62]; reprinted with permission from AAAS), CupE pilus extending from a P. aeruginosa cell visualised by electron cryotomography [33], and formation of bundles by Pf4 [46] and TasA [24]. Fourth column: RbmC expression in V. cholerae biofilms (from reference [62]); reprinted with permission from AAAS), fluorescent P. aeruginosa biofilms showcasing a distinct mushroom-shaped 3D architecture that depends on the expression of CupE pili (reprinted with permission from reference [32]), encapsulation of P. aeruginosa cells by Pf4 liquid crystalline droplets [46], and SEM imaging of B. subtilis biofilms with and without tasA [120].