1887

Chapter 13 : What Genomics Has Taught Us about Bacterial Cell Wall Biosynthesis

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Ebook: Choose a downloadable PDF or ePub file. Chapter is a downloadable PDF file. File must be downloaded within 48 hours of purchase

Buy this Chapter
Digital (?) $15.00

Preview this chapter:
Zoom in
Zoomout

What Genomics Has Taught Us about Bacterial Cell Wall Biosynthesis, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555815530/9781555814519_Chap13-1.gif /docserver/preview/fulltext/10.1128/9781555815530/9781555814519_Chap13-2.gif

Abstract:

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 , 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.

Citation: Dover L. 2007. What Genomics Has Taught Us about Bacterial Cell Wall Biosynthesis, p 327-360. In Pallen M, Nelson K, Preston G (ed), Bacterial Pathogenomics. ASM Press, Washington, DC. doi: 10.1128/9781555815530.ch13

Key Concept Ranking

Cell Wall Biosynthesis
0.5049915
Bacterial Cell Wall
0.45103645
High-Performance Liquid Chromatography
0.4336052
Bacterial Cell Shapes
0.424739
Integral Membrane Proteins
0.41450593
0.5049915
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

Image of FIGURE 1
FIGURE 1

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 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 Gly 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.

Citation: Dover L. 2007. What Genomics Has Taught Us about Bacterial Cell Wall Biosynthesis, p 327-360. In Pallen M, Nelson K, Preston G (ed), Bacterial Pathogenomics. ASM Press, Washington, DC. doi: 10.1128/9781555815530.ch13
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 2
FIGURE 2

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 , where three sporulation-specific genes are included. Similarly, a sporulation-specific PBP gene I’ SpoVD ( ) is indicated above the PBP-encoding column. The discontinuity in the 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, ;W, ;L, ;I, ;I , ;E, ;Y, ;D, ; Fw, ;G, ;C, ;B, , Dd, ;Q, ;A, ; Fz, .

Citation: Dover L. 2007. What Genomics Has Taught Us about Bacterial Cell Wall Biosynthesis, p 327-360. In Pallen M, Nelson K, Preston G (ed), Bacterial Pathogenomics. ASM Press, Washington, DC. doi: 10.1128/9781555815530.ch13
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of FIGURE 3
FIGURE 3

Architecture and genetic organization of cell wall. (A) Adaptation of current model of cell wall ( ), which favors the scaffold model of PG organization. The 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 [ ]) 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 . Probable orthologues are linked by gray bars. The central lines crossing these bars are numbered with respect to gene product function. In , a homologous continuum encompassing orthologues of through to 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 also occurs in , although some 480 kb distant.

Citation: Dover L. 2007. What Genomics Has Taught Us about Bacterial Cell Wall Biosynthesis, p 327-360. In Pallen M, Nelson K, Preston G (ed), Bacterial Pathogenomics. ASM Press, Washington, DC. doi: 10.1128/9781555815530.ch13
Permissions and Reprints Request Permissions
Download as Powerpoint

References

/content/book/10.1128/9781555815530.ch13
1. Alderwick, L. J.,, E. Radmacher,, M. Seidel,, R. Gande,, P. G. Hitchen,, H. R. Morris,, A. Dell,, H. Sahm,, L. Eggeling, and, G. S. Besra. 2005. Deletion of Cg-emb in Corynebacterianeae leads to a novel truncated cell wall arabinogalactan, whereas inactivation of Cg-ubiA results in an arabinan-deficient mutant with a cell wall galactan core. J. Biol. Chem. 280:3236232371.
2. Amano, K.,, H. Hayashi,, Y. Araki, and, E. Ito. 1977. The action of lysozyme on peptidoglycan with N-unsubstituted glucosamine residues. Isolation of glycan fragments and their susceptibility to lysozyme. Eur. J. Biochem. 76:299307.
3. Anderson, J. S.,, M. Matsuhashi,, M. A. Haskin, and, J. L. Strominger. 1965. Lipid-phosphoacetyl-muramyl-pentapeptide and lipid-phosphodisaccha-ride-pentapeptide: presumed membrane transport intermediates in cell wall synthesis. Proc. Natl. Acad. Sci. USA 53:881889.
4. Anderson, M. S.,, S. S. Eveland,, H. R. Onishi, and, D. L. Pompliano. 1996. Kinetic mechanism of the Escherichia coli UDPMurNAc-tripeptide D-alanyl-D-alanine-adding enzyme: use of a glutathione S-transferase fusion. Biochemistry 35:1626416269.
5. Araki, Y.,, S. Fukuoka,, S. Oba, and, E. Ito. 1971. Enzymatic deacetylation of N-acetylglu-cosamine residues in peptidoglycan from Bacillus cereus cell walls. Biochem. Biophys. Res. Commun. 45:751758.
6. Arbeloa, A.,, J. E. Hugonnet,, A. C. Sentilhes,, N. Josseaume,, L. Dubost,, C. Monsempes,, D. Blanot,, J. P. Brouard, and, M. Arthur. 2004. Synthesis of mosaic peptidoglycan cross-bridges by hybrid peptidoglycan assembly pathways in gram-positive bacteria. J. Biol. Chem. 279:4154641556.
7. Arbeloa, A.,, H. Segal,, J. E. Hugonnet,, N. Josseaume,, L. Dubost,, J. P. Brouard,, L. Gut-mann,, D. Mengin-Lecreulx, and, M. Arthur. 2004. Role of class A penicillin-binding proteins in PBP5-mediated beta-lactam resistance in Enterococcus faecalis. J. Bacteriol. 186:12211228.
8. Arthur, M., and, P. Courvalin. 1993. Genetics and mechanisms of glycopeptide resistance in enterococci. Antimicrob. Agents Chemother. 37:15631571.
9. Atrih, A.,, G. Bacher,, G. Allmaier,, M. P. Williamson, and, S. J. Foster. 1999. Analysis of peptidoglycan structure from vegetative cells of Bacillus subtilis 168 and role of PBP 5 in peptidoglycan maturation. J. Bacteriol. 181:39563966.
10. Azuma, I.,, D. W. Thomas,, A. Adam,, J. M. Ghuysen,, R. Bonaly,, J. F. Petit, and, E. Lederer. 1970. Occurrence of N-glycolylmuramic acid in bacterial cell walls. A preliminary survey. Biochim. Biophys. Acta 208:444451.
11. Barbour, A. G.,, K. Amano,, T. Hackstadt,, L. Perry, and, H. D. Caldwell. 1982. Chlamydia trachomatis has penicillin-binding proteins but not detectable muramic acid. J. Bacteriol. 151:420428.
12. Barnickel, G.,, D. Naumann,, H. Bradaczek,, H. Labischinski, and, P. Glesbrecht. 1983. Computer aided molecular modeling of the three-dimensional structure of bacterial peptidoglycan, p. 61–66. In R. Hakenbeck,, J.-V. Holtje, and, H. Labischinski (ed.), The Target of Penicillin. Walter de Gruyter & Co., Berlin, Germany.
13. Basu, J.,, R. Chattopadhyay,, M. Kundu, and, P. Chakrabarti. 1992. Purification and partial characterization of a penicillin-binding protein from Mycobacterium smegmatis. J. Bacteriol. 174:48294832.
14. Basu, J.,, S. Mahapatra,, M. Kundu,, S. Mukhopadhyay,, M. Nguyen-Disteche,, P. Dubois,, B. Joris,, J. Van Beeumen,, S. T. Cole,, P. Chakrabarti, and, J. M. Ghuysen. 1996. Identification and overexpression in Escherichia coli of a Mycobacterium leprae gene, pon1, encoding a high-molecular-mass class A penicillin-binding protein, PBP1. J. Bacteriol. 178:17071711.
15. Bavoil, P. M.,, R. Hsia, and, D. M. Ojcius. 2000. Closing in on Chlamydia and its intracellular bag of tricks. Microbiology 146:27232731.
16. Belanger, A. E.,, G. S. Besra,, M. E. Ford,, K. Mikusova,, J. T. Belisle,, P. J. Brennan, and, J. M. Inamine. 1996. The embAB genes of Mycobacterium avium encode an arabinosyl transferase involved in cell wall arabinan biosynthesis that is the target for the antimycobacterial drug ethambutol. Proc. Natl. Acad. Sci. USA 93:1191911924.
17. Belanger, A. E., and, J. M. Inamine. 2000. Genetics of cell wall biosnthesis. In G. F. Hatfull and, W. R. Jacobs, Jr. (ed.), Molecular Genetics of Mycobacteria. ASM Press, Washington, DC.
18. Belland, R. J.,, G. Zhong,, D. D. Crane,, D. Hogan,, D. Sturdevant,, J. Sharma,, W. L. Beatty, and, H. D. Caldwell. 2003. Genomic transcriptional profiling of the developmental cycle of Chlamydia trachomatis. Proc. Natl. Acad. Sci. USA 100:84788483.
19. Benson, T. E.,, C. T. Walsh, and, J. M. Hogle. 1996. The structure of the substrate-free form of MurB, an essential enzyme for the synthesis of bacterial cell walls. Structure 4:4754.
20. Bera, A.,, S. Herbert,, A. Jakob,, W. Vollmer, and, F. Gotz. 2005. Why are pathogenic staphylococci so lysozyme resistant? The peptidoglycan O-acetyltransferase OatA is the major determinant for lysozyme resistance of Staphylococcus aureus. Mol. Microbiol. 55:778787.
21. Berger-Bachi, B. 1983. Insertional inactivation of staphylococcal methicillin resistance by Tn551. J. Bacteriol. 154:479487.
22. Berger-Bachi, B.,, L. Barberis-Maino,, A. Strassle, and, F. H. Kayser. 1989. FemA, a host-mediated factor essential for methicillin resistance in Staphylococcus aureus: molecular cloning and characterization. Mol. Gen. Genet. 219:263269.
23. Bertoldi, M.,, B. Cellini,, A. Paiardini,, M. Di Salvo, and, C. Borri Voltattorni. 2003. Treponema denticola cystalysin exhibits significant ala-nine racemase activity accompanied by transami-nation: mechanistic implications. Biochem. J. 371:473483.
24. Besra, G. S., and, P. J. Brennan. 1997. The mycobacterial cell wall: biosynthesis of arabinogalactan and lipoarabinomannan. Biochem. Soc. Trans. 25:845850.
25. Besra, G. S.,, K. H. Khoo,, M. R. McNeil,, A. Dell,, H. R. Morris, and, P. J. Brennan. 1995. A new interpretation of the structure of the my-colyl-arabinogalactan complex of Mycobacterium tuberculosis as revealed through characterization of oligoglycosylalditol fragments by fast-atom bombardment mass spectrometry and 1H nuclear magnetic resonance spectroscopy. Biochemistry 34:42574266.
26. Beukes, M., and, J.W. Hastings. 2001. Self-protection against cell wall hydrolysis in Streptococcus milleri NMSCC 061 and analysis of the millericin B operon. Appl. Environ. Microbiol. 67:38883896.
27. Bhakta, S., and, J. Basu. 2002. Overexpression, purification and biochemical characterization of a class A high-molecular-mass penicillin-binding protein (PBP), PBP1* and its soluble derivative from Mycobacterium tuberculosis. Biochem. J. 361:635639.
28. Bi, E. F., and, J. Lutkenhaus. 1991. FtsZ ring structure associated with division in Escherichia coli. Nature 354:161164.
29. Blake, C. C.,, D. F. Koenig,, G. A. Mair,, A. C. North,, D. C. Phillips, and, V. R. Sarma. 1965. Structure of hen egg-white lysozyme. A three-dimensional Fourier synthesis at 2 Angstrom resolution. Nature 206:757761.
30. Bouhss, A.,, N. Josseaume,, D. Allanic,, M. Crouvoisier,, L. Gutmann,, J. L. Mainardi,, D. Mengin-Lecreulx,, J. van Heijenoort, and, M. Arthur. 2001. Identification of the UDP-MurNAc-pentapeptide:L-alanine ligase for synthesis of branched peptidoglycan precursors in Enterococcus faecalis. J. Bacteriol. 183:51225127.
31. Bouhss, A.,, N. Josseaume,, A. Severin,, K. Tabei,, J. E. Hugonnet,, D. Shlaes,, D. Mengin-Lecreulx,, J. Van Heijenoort, and, M. Arthur. 2002. Synthesis of the L-alanyl-L-alanine cross-bridge of Enterococcus faecalis peptidoglycan. J. Biol. Chem. 277:4593545941.
32. Brandish, P. E.,, K. I. Kimura,, M. Inukai,, R. Southgate,, J. T. Lonsdale, and, T. D. Bugg. 1996. Modes of action of tunicamycin, liposidomycin B, and mureidomycin A: inhibition of phospho-N-acetylmuramyl-pentapeptide translocase from Escherichia coli. Antimicrob. Agents Chemother. 40:16401644.
33. Brown, E. D.,, J. L. Marquardt,, J. P. Lee,, C. T. Walsh, and, K. S. Anderson. 1994. Detection and characterization of a phospholactoyl-enzyme adduct in the reaction catalyzed by UDP-N-acetylglucosamine enolpyruvoyl transferase, MurZ. Biochemistry 33:1063810645.
34. Brown, W. J., and, D. D. Rockey. 2000. Identification of an antigen localized to an apparent septum within dividing chlamydiae. Infect. Immun. 68:708715.
35. Bugg, T. D., and, C. T. Walsh. 1992. Intracellular steps of bacterial cell wall peptidoglycan biosynthesis: enzymology, antibiotics, and antibiotic resistance. Nat. Prod. Rep. 9:199215.
36. Bupp, K., and, J. van Heijenoort. 1993. The final step of peptidoglycan subunit assembly in Escherichia coli occurs in the cytoplasm. J. Bacteriol. 175:18411843.
37. Burman, L. G., and, J. T. Park. 1983. Changes in the composition of Escherichia coli murein as it ages during exponential growth. J. Bacteriol. 155:447453.
38. Callebaut, I.,, G. Labesse,, P. Durand,, A. Poupon,, L. Canard,, J. Chomilier,, B. Henrissat, and, J. P. Mornon. 1997. Deciphering protein sequence information through hydrophobic cluster analysis (HCA): current status and perspectives. Cell. Mol. Life Sci. 53:621645.
39. Carlson, J. H.,, S. F. Porcella,, G. McClarty, and, H. D. Caldwell. 2005. Comparative genomic analysis of Chlamydia trachomatis oculo-tropic and genitotropic strains. Infect. Immun. 73:64076418.
40. Cerdeno-Tarraga, A. M.,, A. Efstratiou,, L. G. Dover,, M. T. Holden,, M. Pallen,, S. D. Bentley,, G. S. Besra,, C. Churcher,, K. D. James,, A. De Zoysa,, T. Chillingworth,, A. Cronin,, L. Dowd,, T. Feltwell,, N. Hamlin,, S. Holroyd,, K. Jagels,, S. Moule,, M. A. Quail,, E. Rabbinowitsch,, K. M. Rutherford,, N. R. Thomson,, L. Unwin,, S. Whitehead,, B. G. Barrell, and, J. Parkhill. 2003. The complete genome sequence and analysis of Corynebacterium diphtheriae NCTC13129. Nucleic Acids Res. 31:65166523.
41. Chopra, I.,, C. Storey,, T. J. Falla, and, J. H. Pearce. 1998. Antibiotics, peptidoglycan synthesis and genomics: the chlamydial anomaly revisited. Microbiology 144(Pt. 10):26732678.
42. Christensen, B. G.,, W. J. Leanza,, T. R. Beattie,, A. A. Patchett,, B. H. Arison,, R. E. Ormond,, F. A. Kuehl, Jr.,, G. Albers-Schonberg, and, O. Jardetzky. 1969. Phosphonomycin: structure and synthesis. Science 166:123125.
43. Clarke, A. J.,, H. Strating, and, N. T. Blackburn. 2000. Pathways for O-acetylation of bacterial cell wall polymers, p. 187–212. In R. J. Doyle (ed.), Glycomicrobiology. Plenum Publishing Co. Ltd., New York.
44. Cole, S. T.,, R. Brosch,, J. Parkhill,, T. Garnier,, C. Churcher,, D. Harris,, S. V. Gordon,, K. Eiglmeier,, S. Gas,, C. E. Barry III,, F. Tekaia,, K. Badcock,, D. Basham,, D. Brown,, T. Chilling-worth,, R. Connor,, R. Davies,, K. Devlin,, T. Feltwell,, S. Gentles,, N. Hamlin,, S. Holroyd,, T. Hornsby,, K. Jagels,, A. Krogh,, J. McLean,, S. Moule,, L. Murphy,, K. Oliver,, J. Osborne,, M. A. Quail,, M. A. Rajandream,, J. Rogers,, S. Rutter,, K. Seeger,, J. Skelton,, R. Squares,, S. Squares,, J. E. Sulston,, K. Taylor,, S. Whitehead, and, B. G. Barrell. 1998. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393:537544.
45. Coutinho, P. M., and, B. Henrissat. 1999. Carbohydrate-active enzymes: an integrated database approach, p. 3–12. In H. J. Gilbert,, G. Davies,, B. Henrissat, and, B. Svensson (ed.), Carbohydrate-active Enzymes: An Integrated Database Approach. Royal Society of Chemistry, Cambridge, United Kingdom.
46. Daffe, M.,, P. J. Brennan, and, M. McNeil. 1990. Predominant structural features of the cell wall arabinogalactan of Mycobacterium tuberculosis as revealed through characterization of oligoglycosyl alditol fragments by gas chromatography/mass spectrometry and by 1H and 13C NMR analyses. J. Biol. Chem. 265:67346743.
47. Dai, K., and, J. Lutkenhaus. 1991. ftsZ is an essential cell division gene in Escherichia coli. J. Bacteriol. 173:35003506.
48. Daniel, R. A.,, S. Drake,, C. E. Buchanan,, R. Scholle, and, J. Errington. 1994. The Bacillus subtilis spoVD gene encodes a mother-cell-specific penicillin-binding protein required for spore morphogenesis. J. Mol. Biol. 235:209220.
49. Daniel, R. A.,, A. M. Williams, and, J. Erring-ton. 1996. A complex four-gene operon containing essential cell division gene pbpB in Bacillus subtilis. J. Bacteriol. 178:23432350.
50. DeHart, H. P.,, H. E. Heath,, L. S. Heath,, P. A. LeBlanc, and, G. L. Sloan. 1995. The lysostaphin endopeptidase resistance gene (epr) specifies modification of peptidoglycan cross bridges in Staphylococcus simulans and Staphylococcus aureus. Appl. Environ. Microbiol. 61:14751479.
51. de Jonge, B. L.,, T. Sidow,, Y. S. Chang,, H. Labischinski,, B. Berger-Bachi,, D. A. Gage, and, A. Tomasz. 1993. Altered muropeptide composition in Staphylococcus aureus strains with an inactivated femA locus. J. Bacteriol. 175:27792782.
52. de Jonge, B. L., and, A. Tomasz. 1993. Abnormal peptidoglycan produced in a methicillin-resistant strain of Staphylococcus aureus grown in the presence of methicillin: functional role for penicillin-binding protein 2A in cell wall synthesis. Antimicrob. Agents Chemother. 37:342346.
53. Dessen, A.,, N. Mouz,, E. Gordon,, J. Hopkins, and, O. Dideberg. 2001. Crystal structure of PBP2x from a highly penicillin-resistant Streptococcus pneumoniae clinical isolate: a mosaic framework containing 83 mutations. J. Biol. Chem. 276:4510645112.
54. Dewar, S. J.,, K. J. Begg, and, W. D. Donachie. 1992. Inhibition of cell division initiation by an imbalance in the ratio of FtsA to FtsZ. J. Bacteriol. 174:63146316.
55. Dietrich, C. P.,, A. V. Colucci, and, J. L. Strom-inger. 1967. Biosynthesis of the peptidoglycan of bacterial cell walls. V. Separation of protein and lipid components of the particulate enzyme from Micrococcus lysodeikticus and purification of the endogenous lipid acceptors. J. Biol. Chem. 242:32183225.
56. Dmitriev, B.,, F. Toukach, and, S. Ehlers. 2005. Towards a comprehensive view of the bacterial cell wall. Trends Microbiol. 13:569574.
57. Dmitriev, B. A.,, S. Ehlers, and, E. T. Rietschel. 1999. Layered murein revisited: a fundamentally new concept of bacterial cell wall structure, biogenesis and function. Med. Microbiol. Immunol. (Berl.) 187:173181.
58. Dmitriev, B. A.,, S. Ehlers,, E. T. Rietschel, and, P. J. Brennan. 2000. Molecular mechanics of the mycobacterial cell wall: from horizontal layers to vertical scaffolds. Int. J. Med. Microbiol. 290:251258.
59. Dmitriev, B. A.,, F. V. Toukach,, O. Holst,, E.T. Rietschel, and, S. Ehlers. 2004. Tertiary structure of Staphylococcus aureus cell wall murein. J. Bacteriol. 186:71417148.
60. Dmitriev, B. A.,, F. V. Toukach,, K. J. Schaper,, O. Holst,, E.T. Rietschel, and, S. Ehlers. 2003. Tertiary structure of bacterial murein: the scaffold model. J. Bacteriol. 185:34583468.
61. Donachie, W. D. 1993. The cell cycle of Escherichia coli. Annu. Rev. Microbiol. 47:199230.
62. Doublet, P.,, J. van Heijenoort, and, D. Mengin-Lecreulx. 1992. Identification of the Escherichia coli murI gene, which is required for the biosynthesis of D-glutamic acid, a specific component of bacterial peptidoglycan. J. Bacteriol. 174:57725779.
63. Dougherty, T. J.,, J. A. Thanassi, and, M. J. Pucci. 1993. The Escherichia coli mutant requiring D-glutamic acid is the result of mutations in two distinct genetic loci. J. Bacteriol. 175:111116.
64. Dover, L. G.,, A. M. Cerdeno-Tarraga,, M. J. Pallen,, J. Parkhill, and, G. S. Besra. 2004. Comparative cell wall core biosynthesis in the mycolated pathogens, Mycobacterium tuberculosis and Corynebacterium diphtheriae. FEMS Microbiol. Rev. 28:225250.
65. Dye, C.,, S. Scheele,, P. Dolin,, V. Pathania, and, M. C. Raviglione. 1999. Consensus statement. Global burden of tuberculosis: estimated incidence, prevalence, and mortality by country. WHO Global Surveillance and Monitoring Project. JAMA 282:677686.
66. Eiglmeier, K.,, J. Parkhill,, N. Honore,, T. Garnier,, F. Tekaia,, A. Telenti,, P. Klatser,, K. D. James,, N. R. Thomson,, P. R. Wheeler,, C. Churcher,, D. Harris,, K. Mungall,, B. G. Barrell, and, S. T. Cole. 2001. The decaying genome of Mycobacterium leprae. Lepr. Rev. 72:387398.
67. Ellner, J. J.,, A. R. Hinman,, S. W. Dooley,, M. A. Fischl,, K. A. Sepkowitz,, M. J. Gold-berger,, T. M. Shinnick,, M. D. Iseman, and, W. R. Jacobs, Jr. 1993. Tuberculosis symposium: emerging problems and promise. J. Infect. Dis. 168:537551.
68. El Zoeiby, A.,, F. Sanschagrin, and, R. C. Levesque. 2003. Structure and function of the Mur enzymes: development of novel inhibitors. Mol. Microbiol. 47:112.
69. Enarson, D. A., and, J. F. Murray. 1996. Global epidemiology of tuberculosis, p. 3–11. In B. R. Bloom (ed.), Tuberculosis: Pathogenesis, Protection and Control. ASM Press, Washington, DC.
70. Escuyer, V. E.,, M. A. Lety,, J. B. Torrelles,, K. H. Khoo,, J. B. Tang,, C. D. Rithner,, C. Frehel,, M. R. McNeil,, P. J. Brennan, and, D. Chatterjee. 2001. The role of the embA and embB gene products in the biosynthesis of the terminal hexaarabinofuranosyl motif of Mycobacterium smegmatis arabinogalactan. J. Biol. Chem. 276:4885448862.
71. Everett, K. D., and, T. P. Hatch. 1995. Architecture of the cell envelope of Chlamydia psittaci 6BC. J. Bacteriol. 177:877882.
72. Filipe, S. R.,, E. Severina, and, A. Tomasz. 2000. Distribution of the mosaic structured murM genes among natural populations of Streptococcus pneumoniae. J. Bacteriol. 182:67986805.
73. Filipe, S. R.,, E. Severina, and, A. Tomasz. 2001. The role of murMN operon in penicillin resistance and antibiotic tolerance of Streptococcus pneumoniae. Microb. Drug Resist. 7:303316.
74. Filipe, S. R., and, A. Tomasz. 2000. Inhibition of the expression of penicillin resistance in Streptococcus pneumoniae by inactivation of cell wall muropeptide branching genes. Proc. Natl. Acad. Sci. USA 97:48914896.
75. Firmin, J. L.,, K. E. Wilson,, R. W. Carlson,, A. E. Davies, and, J. A. Downie. 1993. Resistance to nodulation of cv. Afghanistan peas is overcome by nodX, which mediates an O-acetylation of the Rhizobium leguminosarum lipo-oligosaccha-ride nodulation factor. Mol. Microbiol. 10:351360.
76. Fleischmann, R. D.,, M. D. Adams,, O. White,, R. A. Clayton,, E. F. Kirkness,, A. R. Kerlavage,, C. J. Bult,, J. F. Tomb,, B. A. Dougherty,, J. M. Merrick, et al. 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:496512.
77. Fleischmann, R. D.,, D. Alland,, J. A. Eisen,, L. Carpenter,, O. White,, J. Peterson,, R. DeBoy,, R. Dodson,, M. Gwinn,, D. Haft,, E. Hickey,, J. F. Kolonay,, W. C. Nelson,, L. A. Umayam,, M. Ermolaeva,, S. L. Salzberg,, A. Delcher,, T. Utterback,, J. Weidman,, H. Khouri,, J. Gill,, A. Mikula,, W. Bishai,, W. R. Jacobs, Jr.,, J. C. Venter, and, C. M. Fraser. 2002. Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains. J. Bacteriol. 184:54795490.
78. Fotheringham, I. G.,, S. A. Bledig, and, P. P. Taylor. 1998. Characterization of the genes encoding D-amino acid transaminase and glutamate racemase, two D-glutamate biosynthetic enzymes of Bacillus sphaericus ATCC 10208. J. Bacteriol. 180:43194323.
79. Franklin, M. J., and, D. E. Ohman. 1996. Identification of algI and algJ in the Pseudomonas aeruginosa alginate biosynthetic gene cluster which are required for alginate O acetylation. J. Bacteriol. 178:21862195.
80. Fuchs-Cleveland, E., and, C. Gilvarg. 1976. Oligomeric intermediate in peptidoglycan bio-synthesis in Bacillus megaterium. Proc. Natl. Acad. Sci. USA 73:42004204.
81. Gaboriaud, C.,, V. Bissery,, T. Benchetrit, and, J. P. Mornon. 1987. Hydrophobic cluster analysis: an efficient new way to compare and analyse amino acid sequences. FEBS Lett. 224:149155.
82. Gande, R.,, K. J. Gibson,, A. K. Brown,, K. Krumbach,, L. G. Dover,, H. Sahm,, S. Shioyama,, T. Oikawa,, G. S. Besra, and, L. Eggeling. 2004. Acyl-CoA carboxylases (accD2 and accD3), together with a unique polyketide synthase (Cg-pks), are key to mycolic acid biosyn-thesis in Corynebacterianeae such as Corynebacterium glutamicum and Mycobacterium tuberculosis. J. Biol. Chem. 279:4484744857.
83. Gao, L. Y.,, F. Laval,, E. H. Lawson,, R. K. Groger,, A. Woodruff,, J. H. Morisaki,, J. S. Cox,, M. Daffe, and, E. J. Brown. 2003. Requirement for kasB in Mycobacterium mycolic acid biosynthesis, cell wall impermeability and intra-cellular survival: implications for therapy. Mol. Microbiol. 49:15471563.
84. Garnier, T.,, K. Eiglmeier,, J. C. Camus,, N. Medina,, H. Mansoor,, M. Pryor,, S. Duthoy,, S. Grondin,, C. Lacroix,, C. Monsempe,, S. Simon,, B. Harris,, R. Atkin,, J. Doggett,, R. Mayes,, L. Keating,, P. R. Wheeler,, J. Parkhill,, B. G. Barrell,, S. T. Cole,, S. V. Gordon, and, R. G. Hewinson. 2003. The complete genome sequence of Mycobacterium bovis. Proc. Natl. Acad. Sci. USA 100:78777882.
85. Geremia, R. A.,, E. A. Petroni,, L. Ielpi, and, B. Henrissat. 1996. Towards a classification of glycosyltransferases based on amino acid sequence similarities: prokaryotic alpha-mannosyltransferases. Biochem. J. 318(Pt. 1):133138.
86. Ghuysen, J. M. 1991. Serine beta-lactamases and penicillin-binding proteins. Annu. Rev. Microbiol. 45:3767.
87. Ghuysen, J. M. 1968. Use of bacteriolytic enzymes in determination of wall structure and their role in cell metabolism. Bacteriol. Rev. 32:425464.
88. Ghuysen, J. M., and, C. Goffin. 1999. Lack of cell wall peptidoglycan versus penicillin sensitivity: new insights into the chlamydial anomaly. Antimicrob. Agents Chemother. 43:23392344.
89. Glauner, B., and, U. Schwarz. 1983. The analysis of murein composition with high-pressure-liquid chromatography, p. 29–34. In R. Hakenbeck,, J.-V. Holtje, and, H. Labischinski (ed.), The Target of Penicillin. Walter de Gruyter & Co., Berlin, Germany.
90. Gmeiner, J.,, P. Essig, and, H. H. Martin. 1982. Characterization of minor fragments after digestion of Escherichia coli murein with endo-N, O-diacetylmuramidase from Chalaropsis, and determination of glycan chain length. FEBS Lett. 138:109112.
91. Goffin, C., and, J. M. Ghuysen. 2002. Biochemistry and comparative genomics of SxxK superfamily acyltransferases offer a clue to the mycobacterial paradox: presence of penicillin-susceptible target proteins versus lack of efficiency of penicillin as therapeutic agent. Micro-biol. Mol. Biol. Rev. 66:702738.
92. Goffin, C., and, J. M. Ghuysen. 1998. Multi-modular penicillin-binding proteins: an enigmatic family of orthologs and paralogs. Microbiol. Mol. Biol. Rev. 62:10791093.
93. Gunetileke, K. G., and, R. A. Anwar. 1966. Biosynthesis of uridine diphospho-N-acetyl muramic acid. J. Biol. Chem. 241:57405743.
94. Gunetileke, K. G., and, R. A. Anwar. 1968. Biosynthesis of uridine diphospho-N-acetylmuramic acid. II. Purification and properties of pyruvate-uridine diphospho-N-acetylglucosamine transferase and characterization of uridine diphospho-N-acetylenopyruvylglucosamine. J. Biol. Chem. 243:57705778.
95. Hakenbeck, R.,, N. Balmelle,, B. Weber,, C. Gardes,, W. Keck, and, A. de Saizieu. 2001. Mosaic genes and mosaic chromosomes: intra- and interspecies genomic variation of Streptococcus pneumoniae. Infect. Immun. 69:24772486.
96. Hakenbeck, R., and, J. Coyette. 1998. Resistant penicillin-binding proteins. Cell. Mol. Life Sci. 54:332340.
97. Hamase, K.,, R. Konno,, A. Morikawa, and, K. Zaitsu. 2005. Sensitive determination of D–amino acids in mammals and the effect of D–amino-acid oxidase activity on their amounts. Biol. Pharm. Bull. 28:15781584.
98. Harz, H.,, K. Burgdorf, and, J. V. Holtje. 1990. Isolation and separation of the glycan strands from murein of Escherichia coli by reversed-phase high-performance liquid chromatography. Anal. Biochem. 190:120128.
99. Hatch, T. 1998. Chlamydia: old ideas crushed, new mysteries bared. Science 282:638639.
100. Hatch, T. P. 1996. Disulfide cross-linked envelope proteins: the functional equivalent of peptidoglycan in chlamydiae? J. Bacteriol. 178:15.
101. Hayashi, H.,, K. Amano,, Y. Araki, and, E. Ito. 1973. Action of lysozyme on oligosaccharides from peptidoglycan N-unacetylated at glucosamine residues. Biochem. Biophys. Res. Commun. 50:641648.
102. Hayashi, H.,, Y. Araki, and, E. Ito. 1973. Occurrence of glucosamine residues with free amino groups in cell wall peptidoglycan from bacilli as a factor responsible for resistance to lysozyme. J. Bacteriol. 113:592598.
103. Heath, H. E.,, L. S. Heath,, J. D. Nitterauer,, K. E. Rose, and, G. L. Sloan. 1989. Plasmid-encoded lysostaphin endopeptidase resistance of Staphylococcus simulans biovar staphylolyticus. Biochem. Biophys. Res. Commun. 160:11061109.
104. Hendlin, D.,, B. M. Frost,, E. Thiele,, H. Kropp,, M. E. Valiant,, B. Pelak,, B. Weiss-berger,, C. Cornin, and, A. K. Miller. 1969. Phosphonomycin. 3. Evaluation in vitro. Antimicrob. Agents Chemother. 9:297302.
105. Hesek, D.,, M. Lee,, K. Morio, and, S. Mobashery. 2004. Synthesis of a fragment of bacterial cell wall. J. Org. Chem. 69:21372146.
106. Hesse, L.,, J. Bostock,, S. Dementin,, D. Blanot,, D. Mengin-Lecreulx, and, I. Chopra. 2003. Functional and biochemical analysis of Chlamydia trachomatis MurC, an enzyme displaying UDP-N-acetylmuramate:amino acid ligase activity. J. Bacteriol. 185:65076512.
107. Hiramatsu, K.,, L. Cui,, M. Kuroda, and, T. Ito. 2001. The emergence and evolution of methicillin-resistant Staphylococcus aureus. Trends Microbiol. 9:486493.
108. Holmes, R. K. 2000. Biology and molecular epidemiology of diphtheria toxin and the tox gene. J. Infect. Dis. 181(Suppl. 1):S156S167.
109. Holtje, J. V. 1996. A hypothetical holoenzyme involved in the replication of the murein sacculus of Escherichia coli. Microbiology 142(Pt. 8): 19111918.
110. How, S. J.,, D. Hobson, and, C.A. Hart. 1984. Studies in vitro of the nature and synthesis of the cell wall of Chlamydia trachomatis. Curr. Microbiol. 10:269274.
111. Huang, H.,, M. S. Scherman,, W. D’Haeze,, D. Vereecke,, M. Holsters,, D. C. Crick, and, M. R. McNeil. 2005. Identification and active expression of the Mycobacterium tuberculosis gene encoding 5-phospho-{alpha}-D-ribose-1-diphosphate: decaprenyl-phosphate 5-phospho-ribosyltransferase, the first enzyme committed to decaprenylphosphoryl-D-arabinose synthesis. J. Biol. Chem. 280:2453924543.
112. Hurlimann-Dalel, R. L.,, C. Ryffel,, F. H. Kayser, and, B. Berger-Bachi. 1992. Survey of the methicillin resistance–associated genes mecA, mecR1-mecI, and femA-femB in clinical isolates of methicillin-resistant Staphylococcus aureus. Antimicrob. Agents Chemother. 36:26172621.
113. Ikeda, M.,, M. Wachi,, H. K. Jung,, F. Ishino, and, M. Matsuhashi. 1991. The Escherichia coli mraY gene encoding UDP-N-acetylmuramoyl-pentapeptide: undecaprenyl-phosphate phospho-N-acetylmuramoyl-pentapeptide transferase. J. Bacteriol. 173:10211026.
114. Ito, E., and, J. L. Strominger. 1960. Enzymatic synthesis of the peptide in a uridine nucleotide from Staphylococcus aureus. J. Biol. Chem. 235:PC5PC6.
115. Itoh, T.,, K. Takemoto,, H. Mori, and, T. Gojobori. 1999. Evolutionary instability of operon structures disclosed by sequence comparisons of complete microbial genomes. Mol. Biol. Evol. 16:332346.
116. Ivanova, N.,, A. Sorokin,, I. Anderson,, N. Galleron,, B. Candelon,, V. Kapatral,, A. Bhattacharyya,, G. Reznik,, N. Mikhailova,, A. Lapidus,, L. Chu,, M. Mazur,, E. Goltsman,, N. Larsen,, M. D’Souza,, T. Walunas,, Y. Grechkin,, G. Pusch,, R. Haselkorn,, M. Fonstein,, S. D. Ehrlich,, R. Overbeek, and, N. Kyrpides. 2003. Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis. Nature 423:8791.
117. Janczura, E.,, M. Leyh-Bouille,, C. Cocito, and, J. M. Ghuysen. 1981. Primary structure of the wall peptidoglycan of leprosy-derived corynebacteria. J. Bacteriol. 145:775779.
118. Jones, D., and, D. V. Havlir. 2002. Nontuberculous mycobacteria in the HIV infected patient. Clin. Chest Med. 23:665674.
119. Joseleau-Petit, D.,, D. Thevenet, and, R. D’Ari. 1994. ppGpp concentration, growth without PBP2 activity, and growth-rate control in Escherichia coli. Mol. Microbiol. 13:911917.
120. Kalinowski, J.,, B. Bathe,, D. Bartels,, N. Bischoff,, M. Bott,, A. Burkovski,, N. Dusch,, L. Eggeling,, B. J. Eikmanns,, L. Gaigalat,, A. Goesmann,, M. Hartmann,, K. Huthmacher,, R. Kramer,, B. Linke,, A. C. McHardy,, F. Meyer,, B. Mockel,, W. Pfefferle,, A. Puhler,, D. A. Rey,, C. Ruckert,, O. Rupp,, H. Sahm,, V. F. Wendisch,, I. Wiegrabe, and, A. Tauch. 2003. The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins. J. Biotechnol. 104:525.
121. Kamiryo, T., and, M. Matsuhashi. 1969. Sequential addition of glycine from glycyl-tRNA to the lipid-linked precursors of cell wall peptidoglycan in Staphylococcus aureus. Biochem. Biophys. Res. Commun. 36:215222.
122. Kato, J.,, H. Suzuki, and, Y. Hirota. 1985. Dispensability of either penicillin-binding protein-1a or -1b involved in the essential process for cell elongation in Escherichia coli. Mol. Gen. Genet. 200:272277.
123. Kobayashi, N.,, H. Wu,, K. Kojima,, K. Taniguchi,, S. Urasawa,, N. Uehara,, Y. Omizu,, Y. Kishi,, A. Yagihashi, and, I. Kurokawa. 1994. Detection of mecA, femA, and femB genes in clinical strains of staphylococci using polymerase chain reaction. Epidemiol. Infect. 113:259266.
124. Koch, A. L. 1998. Orientation of the peptidoglycan chains in the sacculus of Escherichia coli. Res. Microbiol. 149:689701.
125. Konno, R.,, A. Niwa, and, Y. Yasumura. 1990. Intestinal bacterial origin of D-alanine in urine of mutant mice lacking D-amino-acid oxidase. Biochem. J. 268:263265.
126. Kopp, U.,, M. Roos,, J. Wecke, and, H. Labischinski. 1996. Staphylococcal peptidoglycan interpeptide bridge biosynthesis: a novel antistaphylococcal target? Microb. Drug Resist. 2:2941.
127. Koronakis, V.,, J. Eswaran, and, C. Hughes. 2004. Structure and function of TolC: the bacterial exit duct for proteins and drugs. Annu. Rev. Biochem. 73:467489.
128. Kremer, L.,, L. G. Dover,, C. Morehouse,, P. Hitchin,, M. Everett,, H. R. Morris,, A. Dell,, P. J. Brennan,, M. R. McNeil,, C. Flaherty,, K. Duncan, and, G. S. Besra. 2001. Galactan biosynthesis in Mycobacterium tuberculosis. Identification of a bifunctional UDP-galactofuranosyl-transferase. J. Biol. Chem. 276:2643026440.
129. Kuroda, M.,, T. Ohta,, I. Uchiyama,, T. Baba,, H. Yuzawa,, I. Kobayashi,, L. Cui,, A. Oguchi,, K. Aoki,, Y. Nagai,, J. Lian,, T. Ito,, M. Kanamori,, H. Matsumaru,, A. Maruyama,, H. Murakami,, A. Hosoyama,, Y. Mizutani-Ui,, N. K. Takahashi,, T. Sawano,, R. Inoue,, C. Kaito,, K. Sekimizu,, H. Hirakawa,, S. Kuhara,, S. Goto,, J. Yabuzaki,, M. Kanehisa,, A. Yamashita,, K. Oshima,, K. Furuya,, C. Yoshino,, T. Shiba,, M. Hattori,, N. Ogasawara,, H. Hayashi, and, K. Hiramatsu. 2001. Whole genome sequencing of meticillin-resistant Staphylococcus aureus. Lancet 357:12251240.
130. Lee, R. E.,, K. Mikusova,, P. J. Brennan, and, G. S. Besra. 1995. Synthesis of the mycobacterial arabinose donor beta-D-arabinofuranosyl-1-monophosphoryldecaprenol, development of a basic arabinosyltransferase assy, and identification of ethambutol as an arabinosyltransferase inhibitor. J. Am. Chem. Soc. 117:1182911832.
131. Lemesle-Varloot, L.,, B. Henrissat,, C. Gabo-riaud,, V. Bissery,, A. Morgat, and, J. P. Mornon. 1990. Hydrophobic cluster analysis: procedures to derive structural and functional information from 2-D-representation of protein sequences. Biochimie 72:555574.
132. Lepage, S.,, P. Dubois,, T. K. Ghosh,, B. Joris,, S. Mahapatra,, M. Kundu,, J. Basu,, P. Chakrabarti,, S. T. Cole,, M. Nguyen-Disteche, and, J. M. Ghuysen. 1997. Dual multimodular class A penicillin-binding proteins in Mycobacterium leprae. J. Bacteriol. 179:46274630.
133. Li, L.,, J. P. Bannantine,, Q. Zhang,, A. Amonsin,, B. J. May,, D. Alt,, N. Banerji,, S. Kanjilal, and, V. Kapur. 2005. The complete genome sequence of Mycobacterium avium sub-species paratuberculosis. Proc. Natl. Acad. Sci. USA 102:1234412349.
134. Ma, Y.,, J. A. Mills,, J. T. Belisle,, V. Vissa,, M. Howell,, K. Bowlin,, M. S. Scherman, and, M. McNeil. 1997. Determination of the pathway for rhamnose biosynthesis in mycobacteria: cloning, sequencing and expression of the Mycobacterium tuberculosis gene encoding alpha-D-glucose-1-phosphate thymidylyltransferase. Microbiology 143(Pt. 3):937945.
135. Ma, Y.,, F. Pan, and, M. McNeil. 2002. Formation of dTDP-rhamnose is essential for growth of mycobacteria. J. Bacteriol. 184:33923395.
136. Ma, Y.,, R. J. Stern,, M. S. Scherman,, V. D. Vissa,, W. Yan,, V. C. Jones,, F. Zhang,, S. G. Franzblau,, W. H. Lewis, and, M. R. McNeil. 2001. Drug targeting Mycobacterium tuberculosis cell wall synthesis: genetics of dTDP-rhamnose synthetic enzymes and development of a microtiter plate-based screen for inhibitors of conversion of dTDP-glucose to dTDP-rhamnose. Antimicrob. Agents Chemother. 45:14071416.
137. Mahapatra, S.,, S. Bhakta,, J. Ahamed, and, J. Basu. 2000. Characterization of derivatives of the high-molecular-mass penicillin-binding protein (PBP) 1 of Mycobacterium leprae. Biochem. J. 350(Pt. 1):7580.
138. Maidhof, H.,, B. Reinicke,, P. Blumel,, B. Berger-Bachi, and, H. Labischinski. 1991. femA, which encodes a factor essential for expression of methicillin resistance, affects glycine content of peptidoglycan in methicillin-resistant and methicillin-susceptible Staphylococcus aureus strains. J. Bacteriol. 173:35073513.
139. Matias, V. R.,, A. Al-Amoudi,, J. Dubochet, and, T. J. Beveridge. 2003. Cryo-transmission electron microscopy of frozen-hydrated sections of Escherichia coli and Pseudomonas aeruginosa. J. Bacteriol. 185:61126118.
140. Matias, V. R., and, T. J. Beveridge. 2005. Cryo-electron microscopy reveals native polymeric cell wall structure in Bacillus subtilis 168 and the existence of a periplasmic space. Mol. Microbiol. 56:240251.
141. Matias, V. R., and, T. J. Beveridge. 2006. Native cell wall organization shown by cryo-electron microscopy confirms the existence of a periplasmic space in Staphylococcus aureus. J. Bacteriol. 188:10111021.
142. Matsuhashi, M.,, C. P. Dietrich, and, J. L. Strominger. 1965. Incorporation of glycine into the cell wall glycopeptide in Staphylococcus aureus: role of sRNA and lipid intermediates. Proc. Natl. Acad. Sci. USA 54:587594.
143. Matsumoto, A., and, G. P. Manire. 1970. Electron microscopic observations on the effects of penicillin on the morphology of Chlamydia psittaci. J. Bacteriol. 101:278285.
144. Mattos-Guaraldi, A. L.,, L. O. Moreira,, P.V. Damasco, and, R. Hirata Junior. 2003. Diphtheria remains a threat to health in the developing world—an overview. Mem. Inst. Oswaldo Cruz 98:987993.
145. McCoy, A. J., and, A.T. Maurelli. 2006. Building the invisible wall: updating the chlamydial peptidoglycan anomaly. Trends Microbiol. 14:7077.
146. McCoy, A. J., and, A.T. Maurelli. 2005. Characterization of Chlamydia MurC-Ddl, a fusion protein exhibiting D-alanyl-D-alanine ligase activity involved in peptidoglycan synthesis and D-cycloserine sensitivity. Mol. Microbiol. 57:4152.
147. McCoy, A. J.,, R. C. Sandlin, and, A. T. Maurelli. 2003. In vitro and in vivo functional activity of Chlamydia MurA, a UDP-N-acetylglucosamine enolpyruvyl transferase involved in peptidoglycan synthesis and fos-fomycin resistance. J. Bacteriol. 185:12181228.
148. McNeil, M. 1999. Arabinogalactan in mycobacteria: structure, biosynthesis and genetics, p. 207– 223. In J. B. Goldberg (ed.), Genetics of Bacterial Polysaccharides. CRC Press, Washington, DC.
149. McNeil, M. R.,, K. G. Robuck,, M. Harter, and, P. J. Brennan. 1994. Enzymatic evidence for the presence of a critical terminal hexaarabinoside in the cell walls of Mycobacterium tuberculosis. Glycobiology 4:165173.
150. McPherson, D. C., and, D. L. Popham. 2003. Peptidoglycan synthesis in the absence of class A penicillin-binding proteins in Bacillus subtilis. J. Bacteriol. 185:14231431.
151. Mengin-Lecreulx, D.,, L. Texier,, M. Rousseau, and, J. van Heijenoort. 1991. The murG gene of Escherichia coli codes for the UDP-N-acetylglucosamine: N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase involved in the membrane steps of peptidoglycan synthesis. J. Bacteriol. 173:46254636.
152. Meroueh, S. O.,, K. Z. Bencze,, D. Hesek,, M. Lee,, J. Fisher,, T. L. Stemmier, and, S. Mobashery. 2006. Three-dimensional structure of the bacterial cell wall peptidoglycan. Proc. Natl. Acad. Sci. USA 103:44044409.
153. Mikusova, K.,, H. Huang,, T. Yagi,, M. Holsters,, D. Vereecke,, W. D’Haeze,, M. S. Scherman,, P. J. Brennan,, M. R. McNeil, and, D. C. Crick. 2005. Decaprenylphosphoryl arabinofuranose, the donor of the D-arabinofuranosyl residues of mycobacterial arabinan, is formed via a two-step epimerization of decaprenylphosphoryl ribose. J. Bacteriol. 187:80208025.
154. Mikusova, K.,, M. Mikus,, G. S. Besra,, I. Hancock, and, P. J. Brennan. 1996. Biosyn-thesis of the linkage region of the mycobacterial cell wall. J. Biol. Chem. 271:78207828.
155. Mikusova, K.,, T. Yagi,, R. Stern,, M. R. McNeil,, G. S. Besra,, D. C. Crick, and, P. J. Brennan. 2000. Biosynthesis of the galactan component of the mycobacterial cell wall. J. Biol. Chem. 275:3389033897.
156. Mingorance, J.,, J. Tamames, and, M. Vicente. 2004. Genomic channeling in bacterial cell division. J. Mol. Recognit. 17:481487.
157. Minnikin, D. E.,, L. Kremer,, L. G. Dover, and, G. S. Besra. 2002. The methyl-branched fortifications of Mycobacterium tuberculosis. Chem. Biol. 9:545553.
158. Miyao, A.,, A. Yoshimura,, T. Sato,, T. Yamamoto,, G. Theeragool, and, Y. Kobayashi. 1992. Sequence of the Bacillus subtilis homolog of the Escherichia coli cell-division gene mur G. Gene 118:147148.
159. Mizyed, S.,, A. Oddone,, B. Byczynski,, D. W. Hughes, and, P. J. Berti. 2005. UDP-N-acetylmuramic acid (UDP-MurNAc) is a potent inhibitor of MurA (enolpyruvyl-UDP-GlcNAc synthase). Biochemistry 44:40114017.
160. Montigiani, S.,, F. Falugi,, M. Scarselli,, O. Finco,, R. Petracca,, G. Galli,, M. Mariani,, R. Manetti,, M. Agnusdei,, R. Cevenini,, M. Donati,, R. Nogarotto,, N. Norais,, I. Gara-guso,, S. Nuti,, G. Saletti,, D. Rosa,, G. Ratti, and, G. Grandi. 2002. Genomic approach for analysis of surface proteins in Chlamydia pneumoniae. Infect. Immun. 70:368379.
161. Morikawa, A.,, K. Hamase, and, K. Zaitsu. 2003. Determination of D-alanine in the rat central nervous system and periphery using column-switching high-performance liquid chromatography. Anal. Biochem. 312:6672.
162. Moulder, J. W. 1991. Interaction of chlamydiae and host cells in vitro. Microbiol. Rev. 55:143190.
163. Moulder, J. W. 1993. Why is Chlamydia sensitive to penicillin in the absence of peptidoglycan? Infect. Agents Dis. 2:8799.
164. Nachega, J. B., and, R. E. Chaisson. 2003. Tuberculosis drug resistance: a global threat. Clin. Infect. Dis. 36:S24S30.
165. Nakagawa, J.,, S. Tamaki,, S. Tomioka, and, M. Matsuhashi. 1984. Functional biosynthesis of cell wall peptidoglycan by polymorphic bi-functional polypeptides. Penicillin-binding protein 1Bs of Escherichia coli with activities of transglycosylase and transpeptidase. J. Biol. Chem. 259:1393713946.
166. Neuhaus, F. C. 1962. The enzymatic synthesis of D-alanyl-D-alanine. I. Purification and properties of D-alanyl-D-alanine synthetase. J. Biol. Chem. 237:778786.
167. Nicholson, T. L.,, L. Olinger,, K. Chong,, G. Schoolnik, and, R. S. Stephens. 2003. Global stage-specific gene regulation during the developmental cycle of Chlamydia trachomatis. J. Bacteriol. 185:31793189.
168. Nikaido, H., and, M. Vaara. 1987. Outer membrane, p. 3–6. In J. L. Ingraham,, K. B. Low,, B. Magasanik,, M. Schaechter,, H. E. Umbarger, and, F. C. Neidhardt (ed.), Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, vol. 1. ASM Press, Washington, DC.
169. Nikolaichik, Y. A., and, W. D. Donachie. 2000. Conservation of gene order amongst cell wall and cell division genes in Eubacteria, and ribosomal genes in Eubacteria and Eukaryotic organelles. Genetica 108:17.
170. Nishio, Y.,, Y. Nakamura,, Y. Kawarabayasi,, Y. Usuda,, E. Kimura,, S. Sugimoto,, K. Matsui,, A. Yamagishi,, H. Kikuchi,, K. Ikeo, and, T. Gojobori. 2003. Comparative complete genome sequence analysis of the amino acid replacements responsible for the thermostability of Corynebacterium efficiens. Genome Res. 13:15721579.
171. Nurminen, M.,, M. Leinonen,, P. Saikku, and, P. H. Makela. 1983. The genus-specific antigen of Chlamydia: resemblance to the lipopolysaccharide of enteric bacteria. Science 220:12791281.
172. Obermann, W., and, J.V. Holtje. 1994. Alterations of murein structure and of penicillin-binding proteins in minicells from Escherichia coli. Microbiology 140(Pt. 1):7987.
173. Pan, F.,, M. Jackson,, Y. Ma, and, M. McNeil. 2001. Cell wall core galactofuran synthesis is essential for growth of mycobacteria. J. Bacteriol. 183:39913998.
174. Park, J. T. 1952. Uridine-5′-pyrophosphate derivatives. I. Isolation from Staphylococcus aureus. J. Biol. Chem. 194:877884.
175. Park, J. T. 1952. Uridine-5′-pyrophosphate derivatives. II. A structure common to three derivatives. J. Biol. Chem. 194:885895.
176. Park, J. T. 1952. Uridine-5′-pyrophosphate derivatives. III. Amino acid–containing derivatives. J. Biol. Chem. 194:897904.
177. Park, J. T., and, M. J. Johnson. 1949. Accumulation of labile phosphate in Staphylococcus aureus grown in the presence of penicillin. Biochemical evidence for the formation of a covalent acyl-phosphate linkage between UDP-N-acetylmuramate and ATP. J. Biol. Chem. 179:585592.
178. Petit, J. F.,, A. Adam,, J. Wietzerbin-Falszpan,, E. Lederer, and, J. M. Ghuysen. 1969. Chemical structure of the cell wall of Mycobacterium smegmatis. I. Isolation and partial characterization of the peptidoglycan. Biochem. Biophys. Res. Commun. 35:478485.
179. Pinho, M. G.,, H. de Lencastre, and, A. Tomasz. 2001. An acquired and a native penicillin-binding protein cooperate in building the cell wall of drug-resistant staphylococci. Proc. Natl. Acad. Sci. USA 98:1088610891.
180. Pinho, M. G.,, S. R. Filipe,, H. de Lencastre, and, A. Tomasz. 2001. Complementation of the essential peptidoglycan transpeptidase function of penicillin-binding protein 2 (PBP2) by the drug resistance protein PBP2A in Staphylococcus aureus. J. Bacteriol. 183:65256531.
181. Plapp, R., and, J. L. Strominger. 1970. Biosynthesis of the peptidoglycan of bacterial cell walls. XVII. Biosynthesis of peptidoglycan and of interpeptide bridges in Lactobacillus viridescens. J. Biol. Chem. 245:36673674.
182. Popham, D. L., and, P. Setlow. 1996. Pheno-types of Bacillus subtilis mutants lacking multiple class A high-molecular-weight penicillin-binding proteins. J. Bacteriol. 178:20792085.
183. Portevin, D.,, C. de Sousa-D’Auria,, C. Houssin,, C. Grimaldi,, M. Chami,, M. Daffe, and, C. Guilhot. 2004. A polyketide synthase catalyzes the last condensation step of mycolic acid biosynthesis in mycobacteria and related organisms. Proc. Natl. Acad. Sci. USA 101:314319.
184. Portevin, D.,, C. de Sousa-D’Auria,, H. Montrozier,, C. Houssin,, A. Stella,, M. A. Laneelle,, F. Bardou,, C. Guilhot, and, M. Daffe. 2005. The acyl-AMP ligase FadD32 and AccD4-containing acyl-CoA carboxylase are required for the synthesis of mycolic acids and essential for mycobacterial growth: identification of the carboxylation product and determination of the acyl-CoA carboxylase components. J. Biol. Chem. 280:88628874.
185. Psylinakis, E.,, I. G. Boneca,, K. Mavromatis,, A. Deli,, E. Hayhurst,, S. J. Foster,, K. M. Varum, and, V. Bouriotis. 2005. Peptidoglycan N-acetylglucosamine deacetylases from Bacillus cereus, highly conserved proteins in Bacillus anthracis. J. Biol. Chem. 280:3085630863.
186. Pucci, M. J.,, L. F. Discotto, and, T. J. Dougherty. 1992. Cloning and identification of the Escherichia coli murB DNA sequence, which encodes UDP-N-acetylenolpyruvoylglucosamine reductase. J. Bacteriol. 174:16901693.
187. Pucci, M. J.,, J. A. Thanassi,, L. F. Discotto,, R. E. Kessler, and, T. J. Dougherty. 1997. Identification and characterization of cell wall-cell division gene clusters in pathogenic gram-positive cocci. J. Bacteriol. 179:56325635.
188. Puech, V.,, M. Chami,, A. Lemassu,, M. A. Laneelle,, B. Schiffler,, P. Gounon,, N. Bayan,, R. Benz, and, M. Daffe. 2001. Structure of the cell envelope of corynebacteria: importance of the non-covalently bound lipids in the formation of the cell wall permeability barrier and fracture plane. Microbiology 147:13651382.
189. Ramaswamy, S. V.,, A. G. Amin,, S. Goksel,, C. E. Stager,, S. J. Dou,, H. El Sahly,, S. L. Moghazeh,, B. N. Kreiswirth, and, J. M. Musser. 2000. Molecular genetic analysis of nucleotide polymorphisms associated with ethambutol resistance in human isolates of Mycobacterium tuberculosis. Antimicrob. Agents Chemother. 44:326336.
190. Read, T. D.,, R. C. Brunham,, C. Shen,, S. R. Gill,, J. F. Heidelberg,, O. White,, E. K. Hickey,, J. Peterson,, T. Utterback,, K. Berry,, S. Bass,, K. Linher,, J. Weidman,, H. Khouri,, B. Craven,, C. Bowman,, R. Dodson,, M. Gwinn,, W. Nelson,, R. DeBoy,, J. Kolonay,, G. McClarty,, S. L. Salzberg,, J. Eisen, and, C. M. Fraser. 2000. Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39. Nucleic Acids Res. 28:13971406.
191. Read, T. D.,, G. S. Myers,, R. C. Brunham,, W. C. Nelson,, I. T. Paulsen,, J. Heidelberg,, E. Holtzapple,, H. Khouri,, N. B. Federova,, H. A. Carty,, L. A. Umayam,, D. H. Haft,, J. Peterson,, M. J. Beanan,, O. White,, S. L. Salzberg,, R. C. Hsia,, G. McClarty,, R. G. Rank,, P. M. Bavoil, and, C. M. Fraser. 2003. Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): examining the role of niche-specific genes in the evolution of the Chlamydiaceae. Nucleic Acids Res. 31:21342147.
192. Read, T. D.,, S. N. Peterson,, N. Tourasse,, L. W. Baillie,, I. T. Paulsen,, K. E. Nelson,, H. Tettelin,, D. E. Fouts,, J. A. Eisen,, S. R. Gill,, E. K. Holtzapple,, O. A. Okstad,, E. Helga-son,, J. Rilstone,, M. Wu,, J. F. Kolonay,, M. J. Beanan,, R. J. Dodson,, L. M. Brinkac,, M. Gwinn,, R. T. DeBoy,, R. Madpu,, S. C. Daugherty,, A. S. Durkin,, D. H. Haft,, W. C. Nelson,, J. D. Peterson,, M. Pop,, H. M. Khouri,, D. Radune,, J. L. Benton,, Y. Mahamoud,, L. Jiang,, I. R. Hance,, J. F. Weidman,, K. J. Berry,, R. D. Plaut,, A. M. Wolf,, K. L. Watkins,, W. C. Nierman,, A. Hazen,, R. Cline,, C. Redmond,, J. E. Thwaite,, O. White,, S. L. Salzberg,, B. Thomason,, A. M. Fried-lander,, T. M. Koehler,, P. C. Hanna,, A. B. Kolsto, and, C. M. Fraser. 2003. The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature 423:8186.
193. Reddy, P. S.,, A. Raghavan, and, D. Chatterji. 1995. Evidence for a ppGpp-binding site on Escherichia coli RNA polymerase: proximity relationship with the rifampicin-binding domain. Mol. Microbiol. 15:255265.
194. Rockey, D. D.,, J. Lenart, and, R. S. Stephens. 2000. Genome sequencing and our understanding of chlamydiae. Infect. Immun. 68:54735479.
195. Rohrer, S., and, B. Berger-Bachi. 2003. FemABX peptidyl transferases: a link between branched-chain cell wall peptide formation and beta-lactam resistance in gram-positive cocci. Antimicrob. Agents Chemother. 47:837846.
196. Rohrer, S.,, K. Ehlert,, M. Tschierske,, H. Labischinski, and, B. Berger-Bachi. 1999. The essential Staphylococcus aureus gene fmhB is involved in the first step of peptidoglycan pentaglycine interpeptide formation. Proc. Natl. Acad. Sci. USA 96:93519356.
197. Sasaki, S.,, F. Takeshita,, K. Okuda, and, N. Ishii. 2001. Mycobacterium leprae and leprosy: a compendium. Microbiol. Immunol. 45:729736.
198. Satta, G.,, R. Fontana, and, P. Canepari. 1994. The two-competing site (TCS) model for cell shape regulation in bacteria: the envelope as an integration point for the regulatory circuits of essential physiological events. Adv. Microb. Physiol. 36:181245.
199. Sauvage, E.,, F. Kerff,, E. Fonze,, R. Herman,, B. Schoot,, J. P. Marquette,, Y. Taburet,, D. Prevost,, J. Dumas,, G. Leonard,, P. Stefanic,, J. Coyette, and, P. Charlier. 2002. The 2.4-A crystal structure of the penicillin-resistant penicillin-binding protein PBP5fm from Enterococcus faecium in complex with benzylpenicillin. Cell. Mol. Life Sci. 59:12231232.
200. Saxena, I. M.,, R. M. Brown, Jr.,, M. Fevre,, R. A. Geremia, and, B. Henrissat. 1995. Multidomain architecture of beta-glycosyl transferases: implications for mechanism of action. J. Bacteriol. 177:14191424.
201. Scheffers, D. J., and, M. G. Pinho. 2005. Bacterial cell wall synthesis: new insights from localization studies. Microbiol. Mol. Biol. Rev. 69:585607.
202. Scherman, M.,, A. Weston,, K. Duncan,, A. Whittington,, R. Upton,, L. Deng,, R. Comber,, J. D. Friedrich, and, M. McNeil. 1995. Biosynthetic origin of mycobacterial cell wall arabinosyl residues. J. Bacteriol. 177:71257130.
203. Scherman, M. S.,, L. Kalbe-Bournonville,, D. Bush,, Y. Xin,, L. Deng, and, M. McNeil. 1996. Polyprenylphosphate-pentoses in mycobacteria are synthesized from 5- phosphori-bose pyrophosphate. J. Biol. Chem. 271:2965229658.
204. Schleifer, K. H., and, O. Kandler. 1972. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol. Rev. 36:407477.
205. Schneider, T.,, M. M. Senn,, B. Berger-Bachi,, A. Tossi,, H. G. Sahl, and, I. Wiede-mann. 2004. In vitro assembly of a complete, pentaglycine interpeptide bridge containing cell wall precursor (lipid II-Gly5) of Staphylococcus aureus. Mol. Microbiol. 53:675685.
206. Schonbrunn, E.,, S. Sack,, S. Eschenburg,, A. Perrakis,, F. Krekel,, N. Amrhein, and, E. Mandelkow. 1996. Crystal structure of UDP-N-acetylglucosamine enolpyruvyltransferase, the target of the antibiotic fosfomycin. Structure 4:10651075.
207. Selinger, D. W.,, R. M. Saxena,, K. J. Cheung,, G. M. Church, and, C. Rosenow. 2003. Global RNA half-life analysis in Escherichia coli reveals positional patterns of transcript degradation. Genome Res.. 13:216223.
208. Severin, A., and, A. Tomasz. 1996. Naturally occurring peptidoglycan variants of Streptococcus pneumoniae. J. Bacteriol. 178:168174.