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Chapter 13 : What Genomics Has Taught Us about Bacterial Cell Wall Biosynthesis
Category: Genomics and Bioinformatics; Bacterial Pathogenesis
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This chapter focuses only on the major structural polysaccharide components of bacterial cell walls, so to present a coherent commentary on the impact of genomics on the understanding of cell wall biosynthesis. The chapter is organized to relate a commentary on the basic processes of cell wall biosynthesis derived from decades of chemical analyses and classical genetics studies in the pregenomic era. Recently, researchers have made tremendous progress in imaging of bacterial cell walls by cryoelectron microscopy and atomic force microscopy, which has provided new detailed insights into cell wall organization in both gram-positive and gram-negative bacteria. The construction of the murein sacculus is essentially a two-stage process. In the first, a disaccharide-peptide monomer unit is assembled by using UDP-linked and then polyprenyl phosphate-linked intermediates. Next, transglycosylases (TGs) catalyze the polymerization of the glycan chains and transpeptidases (TPs); the penicillin-binding proteins (PBPs) cross-link the peptide cross-bridges between glycan chains and thus incorporate nascent material into the existing PG sacculus framework. An architecturally similar but less complex cell wall core structure is conserved across the Corynebacterineae, which presented the possibility that comparative genomics might scout new routes toward the understanding of the construction of these fascinating structures. In this era of rapidly emerging multidrug resistance, the efforts to understand bacterial pathogens through study of their cell wall biosynthesis, in identification of novel targets, by defining modes of action of current drugs, and by investigating the development of resistance, must keep pace with the rapidly evolving adversaries.
Schematic representation of PG biosynthesis. MurA and MurB catalyze the conversion of the UDP-GlcNAc to UDP-MurNAc before MurC and MurD initiate stem peptide synthesis by adding individual amino acid residues. MurE adds the diamino acid that is crucial to stem peptide cross linking. Ddl forms the dialaninyl peptide that is ligated to the UDP-MurNac-tripeptide. The completed UDP-MurNAc-pentapeptide is transferred via MraY to a polyprenyl monophosphate carrier lipid in the cytoplasmic membrane, represented here by the large gray bar. The introduction of a GlcNAc residue from UDP-GlcNAc via a β-1→4 linkage that completes the basic lipid II PG monomer unit is catalyzed by MurG. At this point in species that do not contain inter-peptide bridges, this lipid II is then translocated to the periplasmic face of the membrane, represented here by the arrow within the membrane, to take part in PG polymerization and cross linking. Interpeptide synthesis for S. aureus is depicted in the following reactions; FemX adds a single glycine residue to the ε-amino group of the lysine residue of the stem peptide. FemA and FemB then add pairs of Gly residues to the growing interpeptide to complete the Gly5 unit before translocation to the periplasmic face of the membrane, where glycan chains are polymerized via transglycosylases (TGs) and nascent strands are incorporated into existing murein, represented here by a more lightly shaded strand, by the transpeptidase (TP) activity of the PBPs. Both of these reactions likely occur concomitantly.
Maintenance of DCW gene clusters. The DCW clusters of several of the bacteria discussed herein are schematically represented; coding sequences are not represented to scale in order to facilitate alignment. The triangles denote the positions of single gene insertions within the cluster, apart from in B. subtilis, where three sporulation-specific genes are included. Similarly, a sporulation-specific PBP gene I’ SpoVD ( 48 ) is indicated above the PBP-encoding ftsI column. The discontinuity in the C. trachomatis alignment represents the conserved clustering of these genes at another part of the chromosome. When orthologues are removed from their position in the cluster but are retained in the genome in a locus nearby, they are placed to one side. The key to the gene symbols placed above each cluster is as follows: Z, mraZ;W, mraW;L, ftsL;I, ftsI;I , spoVD;E, murE;Y, mraY;D, murD; Fw, ftsW;G, murG;C, murC;B, murB, Dd, ddlB;Q, ftsQ;A, ftsA; Fz, ftsZ.
Architecture and genetic organization of Mycobacterium tuberculosis cell wall. (A) Adaptation of current model of cell wall ( 157 ), which favors the scaffold model of PG organization. The M. tuberculosis wall possesses a high proportion of covalently attached mycolic acid residues (black), which form the inner leaflet of an outer cell wall permeability barrier. The membranous structure is completed by intercalating trehalose-based mycolate containing glycolipids along with a diverse repertoire of complex lipids. The membrane structure is tethered to the peptidoglycan (PG, dark gray) of the murein sacculus via arabinogalactan (AG, light gray). The arabinan domain of the mycolylarabinogalactan (mAGP) is branched and linked to the coiled (in some recent models [ 58 ]) galactan domains that intercalate with the coiled glycan domains of PG; these polysaccharide chains are linked by the Rha-GlcNAc-phosphate linker unit shown. (B) Hexarabinofuranosyl motives representing sites for mycoalte deposition in the cell wall. (C) Conserved genetic organization of cell wall biosynthesis in Corynebacterineae. Probable orthologues are linked by gray bars. The central lines crossing these bars are numbered with respect to gene product function. In C. diphtheriae, a homologous continuum encompassing orthologues of glf through to accD4 is disrupted by the insertion of four genes that appear to encode glycine-betaine production. A smaller cluster with similar genetic organization to the region Rv3789 to embC also occurs in C. diphtheriae, although some 480 kb distant.