Interactions in bacterial biofilm development: a structural perspective

Abstract

A community-based life style is the normal mode of growth and survival for many bacterial species. These cellular accretions or biofilms are initiated upon recognition of solid phases by cell surface exposed adhesive moieties. Further cell-cell interactions, cell signalling and bacterial replication leads to the establishment of dense populations encapsulated in a mainly self-produced extracellular matrix; this comprises a complex mixture of macromolecules. These fascinating architectures protect the inhabitants from radiation damage, dehydration, pH fluctuations and antimicrobial compounds. As such they can cause bacterial persistence in disease and problems in industrial applications. In this review we discuss the current understandings of these initial biofilm-forming processes based on structural data. We also briefly describe latter biofilm maturation and dispersal events, which although lack high-resolution insights, are the present focus for many structural biologists working in this field. Finally we give an overview of modern techniques aimed at preventing and disrupting problem biofilms.

Fig. (1)

Schematic representation of the biofilm life cycle. (1) Free swimming bacteria (2) adhere to a surface using cell surface displayed adhesin molecules. (3) Bacteria begin to divide and the expression of further macromolecules allows them to stick together in small microcolonies. (4) As these colonies grow they begin to secrete a complex mixture of carbohydrates, protein and lipids that encapsulates the bacteria. This biofilm matrix (fuzzy outline) provides protection and stability for the maturing biofilm. (5) When the biofilm reaches maturity, a number of factors will have developed a heterogeneous arrangement of cells and molecules within the biofilm, and given rise to solvent filled cavities and channels. This can lead to dispersal of cells from the cellular mass. (6) Upon signal from the environment (waste build up or demand for nutrients, for example), molecules are released that cause cell lysis and matrix dissemination. Many planktonic cells are now released and can find a new habitat.

Fig. (2)

Adhesive mechanisms of MSCRAMMs. (A) Schematic of S. aureus ClfA and FnBPA adapted from [46]. The N-terminal signal sequence (S) is followed by the A-region, B-region and at the C-terminus is the cell wall anchoring region containing the cell wall sorting region (W) containing the LPXTG motif (star), membrane-spanning hydrophobic domain (M) and the cytoplasmic positively charged C-terminal tail (C). The fibrinogen binding A-region of both ClfA and FnBPA contain three domains (N1-N3). The B-region of ClfA (R-region) is composed of mainly serine and aspartate residues whilst in FnBPA this is made up of 11 fibronectin binding domains (FnBDs: numbered 1-11). (B) Crystal structure of S. aureus ClfA with and without a fibrinogen peptide bound. (C) Model of the FnBR-1 region (residues 508-546) of FnBPA in complex with fibronectin (²F1³F1⁴F1⁵F1). The A-region is shown as a schematic and the FnBR-2-11 region is shown as dashed line (not to scale).

Fig. (3)

Adhesive mechanisms of SRRPs. (A) Schematic representation of a mature SRRP. The N-terminal unique adhesive region is projected away from the cell wall via the extensive SRR region. There is also a minor SRR at the N-terminal pole. The C-terminus is attached to the cell wall peptidoglycan (yellow spheres) through an LPxTG anchor sequence. (B) Conformations of the ‘open’ and ‘closed’ states of S. parasanguinis Fap1-NR. SAXS electron densities are shown as envelopes, coloured red (pH 5) or Blue (pH 8), and the structures have been docked into the maps. Acidic residues at the inter-subdomain boundary are highlighted as yellow spheres. (C) Crystal structure of the carbohydrate bound S. gordonii GspB_BR.

Fig. (4)

Hap-Hap mediated biofilm formation. (A) Crystal structure of the H. influenza Hap passenger domain (Haps) with the C-terminal pore shown as a schematic. (B) Crystallographic relationship between Hap_s molecules in the crystal. The interface of a dimer of Hap_s in trans (coloured orange and green) shows that a run of Asp/Asn residues (the Asp/Asn ladder) from one subunit packs against a complimentary but alternative surface of the other molecule (shown as electrostatic surfaces : dark regions). (C) The remaining Asp/Asn ladder from the latter molecule of the dimer is still accessible and with the burying of hydrophobicity, translations of these dimers can lead to great multimers forming. The modelled SLPI bound to each serine protease domain is coloured blue.

Fig. (5)

ECP-ECP mediated biofilm formation. (A) Model of the E. coli common pilus displayed on the cell surface with the usher pore (EcpC), the major pilus (EcpA) and the polymerized tip adhesin (EcpD) annotated. (B) Schematic representation of donor strand exchange between EcpA domains. One EcpA subunit (green) donates its N-terminal extension (NTE) to the adjacent EcpA subunit (purple) where it lines the hydrophobic groove. (C) Atomic model of ECP fibres. A single fibre from crystals of EcpA is shown as a surface (left) and as a cartoon with adjacent subunits coloured green and purple. The direction of polymerization in the fibre is shown with black arrows. Four subunits have been expanded to highlight the zig-zagging and helicity of EcpA along the fibre length. (D) Representation of ECP-ECP mediated antiparallel interactions. Cells 1-3 are shown with two ECP fibres intertwined by a half helical turn. One of these regions has been boxed and expanded, showing the atomic model which describes this event. Two antiparallel entwined ECP are shown from the side and top.

Fig. (6)

Fap1-Fap1 mediated biofilm formation. (A) Representation of Fap1-NR_α mediated Fap1-Fap1 interactions. Cells 1-5 are displayed with Fap1 filaments on their surfaces. A number of these fibres are interacting via their tips, and this has been expanded to show the surfaces of Fap1-NR orientated based on the Fap1-NR_α crystal structure. The Fap1-NR_α region has been further expanded to show the packing of five molecules from these crystals. The numbers represent the unique molecules of the asymmetric unit. (B) Fap1-NR_α crystals are formed from 3 types of dimer (A-C). Each dimer interface is drawn as an electrostatic surface and the specific contact areas are circled.