Structural constraints and dynamics of bacterial cell wall architecture

Abstract

The peptidoglycan wall (PG) is a unique structure which confers physical strength and defined shape to bacteria. It consists of a net-like macromolecule of peptide interlinked glycan chains overlying the cell membrane. The structure and layout of the PG dictates that the wall has to be continuously modified as bacteria go through division, morphological differentiation, and adaptive responses. The PG is poorly known in structural terms. However, to understand morphogenesis a precise knowledge of glycan strand arrangement and of local effects of the different kinds of subunits is essential. The scarcity of data led to a conception of the PG as a regular, highly ordered structure which strongly influenced growth models. Here, we review the structure of the PG to define a more realistic conceptual framework. We discuss the consequences of the plasticity of murein architecture in morphogenesis and try to define a set of minimal structural constraints that must be fulfilled by any model to be compatible with present day information.

Keywords: HPLC; cell wall; chain length; cross-link; muropeptides; peptidoglycan; structure.

FIGURE 1

The basic PG subunit. (A) Explicit formula for N-acetyl-glucosaminyl-(β,1→4)-N-acetyl-muramyl-L-Alanyl-D-Glutaminyl(γ)-L-(meso)diaminopimelyl-D-alanyl-D-alanine (disaccharide–pentapeptide or M5). (B) Computer generated 3D representation of the same molecule after energy optimization. Red signals the glycan part, blue the stem peptide and green the terminal D-ala residue. Molecules were generated with Chemsketch (http://www.acdlabs.com/resources/freeware/chemsketch/), subjected to geometry and molecular mechanics optimization with Avogadro software (http://avogadro.cc/) using the MMFF94s field force, the steepest descent algorithm and a convergence of 10^-7. Muropeptides were modeled in the absence of solvent. The optimized molecular structure was visualized and prepared for publication with Molsoft ICM software (http://www.molsoft.com/).

FIGURE 2

Elimination of the terminal D-ala residue has strong influence on the 3D structure of PG subunits. PG monomeric subunits derived from the M5 by elimination of the terminal D-ala (M4) or the terminal D-ala-D-ala (M3) are compared in two orientations, transversal to (upper panel) and from above (lower panel) the surface of the sacculus. To facilitate comparison muropeptides were rotated until GlcNAc residues overlap. Red designates the glycan moiety and blue the stem peptide. Terminal D-ala residues are highlighted in yellow. The 3D structures were calculates as in Figure 1. Hydrogen atoms were removed in the image, but considered for the calculation of the molecular surface.

FIGURE 3

Structure of linear PG polymers. (A) Sugar backbone for a 12-mer linear PG polymer, with a helical pitch of three subunits/turn. The backbone is derived from the structure of (B) a PG strand made up of 12 M5 subunits. Red designates the glycan moiety and blue the stem peptides. The D-ala-D-ala dipeptides are highlighted in yellow, and the (meso)DAP free NH₂ groups in green. The 3D structures were calculated as in Figures 1 and 2.

FIGURE 4

Comparison of LD and DD cross-linked PG dimers. 3D representations of molecules from the LD cross-linked bis-disaccharide-tripeptide (D33), and the DD cross-linked disaccharide-tetrapeptide-disaccharide-tripeptide (D43) dimers were generated as described in Figures 1 and 2. Upper images correspond to a transversal view, and lower images to a view from above. Each pair was oriented according to the GlcNAc residues indicated by the black arrows. Red, green, and blue designate the disaccharide for the donor moiety, the disaccharide for the acceptor moiety and the stem peptide, respectively. Yellow highlights the position of the cross-link. Note the inverted orientation predicted for the donor and acceptor moieties.

FIGURE 5

The structure of cross-linked trimers and tetramers. (A) Simplified formula and 3D representation of a molecule of the DD cross-linked trimer tris-disaccharide tetrapeptide. For a better visualization of the relative orientation of the strands, the glycans were extended by the addition of two disaccharides, one at each side, to each of the cross-linked moieties. Red, yellow, and green designate each of the glycan strands, and blue the peptide moiety. (B) Simplified formula and 3D representation of a molecule of the DD cross-linked tetramer tetra-disaccharide tetrapeptide. Red designates the glycan moieties and blue the stem peptides. The 3D structure was calculated as in Figures 1 and 2.