Synthesis of fluorescent D-amino acids and their use for probing peptidoglycan synthesis and bacterial growth in situ

Nature Protocols

Volumn 10, Issue 1, 2015, Pages 33-52

  Kuru, Erkin ^a   Tekkam, Srinivas ^a   Hall, Edward ^a   Brun, Yves V ^a   Van Nieuwenhze, Michael S ^a  

^a INDIANA UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; ANTIBIOTIC AGENT; DEXTRO ALANINE; DEXTRO LYSINE; FLUORESCENT DYE; FUNCTIONAL GROUP; PEPTIDOGLYCAN; THIOL GROUP; VANCOMYCIN;

AGROBACTERIUM TUMEFACIENS; ARTICLE; BACTERIAL CELL WALL; BACTERIAL GROWTH; BURKHOLDERIA; BURKHOLDERIA PHYTOFIRMANS; CAULOBACTER VIBRIOIDES; CLINICAL PROTOCOL; CONTROLLED STUDY; COVALENT BOND; DRUG STRUCTURE; ESCHERICHIA COLI; FLUORESCENCE MICROSCOPY; GRAM POSITIVE BACTERIUM; NONHUMAN; PRIORITY JOURNAL; SPATIOTEMPORAL ANALYSIS; STREPTOCOCCUS PNEUMONIAE; STREPTOMYCES VENEZUELAE; SYNECHOCYSTIS; SYNTHESIS; VERRUCOMICROBIUM SPINOSUM; BACTERIUM; BIOSYNTHESIS; CHEMICAL STRUCTURE; CHEMISTRY; GENETIC PROCEDURES; GROWTH, DEVELOPMENT AND AGING; METABOLISM; PROCEDURES;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

AMINO ACIDS; BACTERIA; FLUORESCENT DYES; MICROSCOPY, FLUORESCENCE; MOLECULAR PROBE TECHNIQUES; MOLECULAR STRUCTURE; PEPTIDOGLYCAN;

EID: 84925969842     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2014.197     Document Type: Article

References (44)

1. Schneider, T., Sahl, H.-G. An oldie but a goodie-cell wall biosynthesis as an antibiotic target pathway. Int. J. Med. Microbiol. 300, 2010 (2010).
2. Gould, I.M. Coping with antibiotic resistance: the impending crisis. Int. J. Antimicrob. Agents 36, S1-S2 (2010).
3. Neu, H.C. The crisis in antibiotic resistance. Science 257, 1064-1073 (1992).
4. van Dam, V., Olrichs, N., Breukink, E. Specific labeling of peptidoglycan precursors as a tool for bacterial cell wall studies. Chem. Bio. Chem. 10, 617-624 (2009).
5. van der Donk, W.A. Lighting up the nascent cell wall. ACS Chem. Biol. 1, 425-428 (2006).
6. Kuru, E. et al. In situ probing of newly synthesized peptidoglycan in live bacteria with fluorescent d-amino acids. Angew. Chem. Int. Ed. 51, 12519-12523 (2012).
7. Pilhofer, M. et al. Discovery of chlamydial peptidoglycan reveals bacteria with murein sacculi but without FtsZ. Nat. Commun. 4, 2856 (2013).
8. Pinho, M.G., Kjos, M., Veening, J.-V. How to get (a)round: mechanisms controlling growth and division of coccoid bacteria. Nat. Rev. Microbiol. 11, 601-614 (2013).
9. Ranjit, D.K., Young, K.D. The Rcs stress response and accessory envelope proteins are required for de novo generation of cell shape in Escherichia coli. J. Bacteriol. 195, 2452-2462 (2013).
10. Tocheva, E.I. et al. Peptidoglycan transformations during Bacillus subtilis sporulation. Mol. Microbiol. 88, 673-686 (2013).
11. Daniel, R.A., Errington, J. Control of cell morphogenesis in bacteria: two distinct ways to make a rod-shaped cell. Cell 113, 767-776 (2003).
12. Tiyanont, K. et al. Imaging peptidoglycan biosynthesis in Bacillus subtilis with fluorescent antibiotics. Proc. Natl. Acad. Sci. USA 103, 11033-11038 (2006).
13. de Pedro, M.A., Quintela, J., Holtje, J., Schwarz, H. Murein segregation in Escherichia coli. J. Bacteriol. 179, 2823-2834 (1997).
14. Olrichs, N.K. et al. A novel in vivo cell-wall labeling approach sheds new light on peptidoglycan synthesis in Escherichia coli. Chembiochem 12, 1124-1133 (2011).
15. Sadamoto, R., Niikura, K., Monde, K., Nishimura, S.-I. Cell wall engineering of living bacteria through biosynthesis. Methods Enzymol. 362, 273-286 (2003).
16. Sadamoto, R. et al. Cell-wall engineering of living bacteria. J. Am. Chem. Soc. 124, 9018-9019 (2002).
17. Sadamoto, R. et al. Control of bacterial adhesion by cell-wall engineering. J. Am. Chem. Soc. 126, 3755-3761 (2004).
18. Liechti, G.W. et al. A new metabolic cell-wall labelling method reveals peptidoglycan in Chlamydia trachomatis. Nature 506, 507-510 (2013).
19. Schouten, J.A. et al. Fluorescent reagents for in vitro studies of lipid-linked steps of bacterial peptidoglycan biosynthesis: derivatives of UDPMurNAc-pentapeptide containing d-cysteine at position 4 or 5. Mol. BioSyst. 2, 484-491 (2006).
20. de Pedro, M.A., Young, K.D., Höltje, J.-V., Schwarz, H. Branching of Eschereichia coli cells arises from multiple sites of inert peptidoglycan. J. Bacteriol. 185, 1147-1152 (2003).
21. Brown, P.J.B. et al. Polar growth in the alphaproteobacterial order rhizobiales. Proc. Natl. Acad. Sci. USA 109, 1697-1701 (2012).
22. Cava, F., Lam, H., de Pedro, M.A., Waldor, M.K. Emerging knowledge of regulatory roles of d-amino acids in bacteria. Cell. Mol. Life Sci. 68, 817-831 (2011).
23. Lam, H. et al. d-Amino acids govern stationary phase cell wall remodeling in bacteria. Science 325, 1552-1555 (2009).
24. Lupoli, T.J. et al. Transpeptidase-mediated incorporation of d-amino acids into bacterial peptidoglycan. J. Am. Chem. Soc. 133, 10748-10751 (2011).
25. Cava, F., de Pedro, M.A., Lam, H., Davis, B.M., Waldor, M.K. Distinct pathways for modification of the bacterial cell wall by non-canonical d-amino acids. EMBO J. 30, 3442-3453 (2011).
26. Siegrist, M.S. et al. d-Amino acid chemical reporters reveal peptidoglycan dynamics of an intracellular pathogen. ACS Chem. Biol. 8, 500-505 (2013).
27. Zapun, A. et al. In vitro reconstitution of peptidoglycan assembly from the Gram-positive pathogen Streptococcus pneumoniae. ACS Chem. Biol. 8, 2688-2696 (2013).
28. Bugg, T.D.H., Walsh, C.T. lntracellular steps of bacterial cell wall peptidoglycan biosynthesis: enzymology, antibiotics, and antibiotic resistance. Nat. Prod. Rep. 9, 199-215 (1992).
29. Höltje, J.-V. Growth of the stress-bearing and shape-maintaining murein sacculus of Escherichia coli. Microbiol. Mol. Biol. Rev. 62, 181-203 (1998).
30. Magnet, S., Dubost, L., Marie, A., Arthur, M., Guttmann, L. Identification of the l, d-transpeptidases for peptidoglycan cross-linking in Escherichia coli. J. Bacteriol. 190, 4782-4785 (2008).
31. Vollmer, W., Blanot, D., de Pedro, M.A. Peptidoglycan structure and architecture. FEMS Microbiol. Rev. 32, 149-167 (2008).
32. Kolb, H.C., Finn, M.G., Sharpless, K.B. Click chemistry: diverse chemical function from a few good reactions. Angew. Chem. Int. Ed. 40, 2004-2021 (2001).
33. Prescher, J.A., Bertozzi, C.R. Chemistry in living systems. Nat. Chem. Biol. 1, 13-20 (2005).
34. Fura, J.M., Sabulski, M.J., Pires, M.M. Amino acid mediated recruitment of endogenous antibodies to bacterial surfaces. ACS Chem. Biol. 9, 1480-1489 (2014).
35. Kerr, C.H., Culham, D.E., Marom, D., Wood, J.M. Salinity-dependent impacts of ProQ, Prc, and Spr deficiencies on Escherichia coli cell structure. J. Bacteriol. 196, 1286-1296 (2014).
36. Ursell, T.S. et al. Rod-like bacterial shape is maintained by feedback between cell curvature and cytoskeletal localization. Proc. Natl. Acad. Sci. USA 111, E1025-E1034 (2014).
37. Jiang, C., Brown, P.J., Ducret, A., Brun, Y.V. Sequential evolution of bacterial morphology by co-option of a developmental regulator. Nature 506, 489-493 (2014).
38. Eun, Y.J. et al. Divin: a small molecule inhibitor of bacterial divisome assembly. J. Am. Chem. Soc. 135, 9768-9776 (2013).
39. Fenton, A.K., Gerdes, K. Direct interaction of FtsZ and MreB is required for septum synthesis and cell division in Escherichia coli. EMBO J. 32, 1953-1965 (2013).
40. Cava, F., Kuru, E., Brun, Y.V., de Pedro, M.A. Modes of cell wall growth differentiation in rod-shaped bacteria. Curr. Opin. Microbiol. 16, 731-737 (2013).
41. Lupoli, T.J. et al. Lipoprotein activators stimulate Escherichia coli penicillin-binding proteins by different mechanisms. J. Am. Chem. Soc. 136, 52-55 (2014).
42. Shieh, P., Siegrist, M.S., Cullen, A.J., Bertozzi, C.R. Imaging bacterial peptidoglycan with near-infrared fluorogenic azide probes. Proc. Natl. Acad. Sci. USA 111, 5456-5461 (2014).
43. Takacs, C.N. et al. Growth medium-dependent glycine incorporation into the peptidoglycan of Caulobacter crescentus. PLoS ONE 8, e57579 (2013).
44. Fleurie, A. et al. Interplay of the serine/threonine-kinase StkP and the paralogs DivIVA and GpsB in pneumococcal cell elongation and division. PLoS Genet. 10, e1004275 (2014).