The VanNieuwenhze Group

FDAAS

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We developed a series of fluorescent probes, named fluorescent D-amino acids (FDAAs), for bacterial peptidoglycan labeling. These probes incorporate to peptidoglycan through the activity of cell wall synthases, indicating the formation and remodeling of peptidoglycan in situ.

Figure 1 legends: FDAAs labeling in Bacillus subtilis (Gram-positive) and Escherichia coli (Gram-negative). Hsu et, al. 10.1039/C7SC01800B

Figure 2 legends: Successive FDAA labeling in polar growing bacteria, Streptomyces venezuelae. This labeling method is also known as virtual time-lapse labeling. Hsu et, al. 10.1039/C7SC01800B

Figure 3 legends: Structures and spectra of FDAAs developed in the VanNieuwenhze Lab.

Figure 4 legends: Photochemical and physical properties of FDAAs. Hsu et, al. 10.1039/C7SC01800B

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FDAA application and reference

First Author	Research Title	Journal/Year
Developing D-amino acid-based probes for PG study
E. Kuru	In situ probing of newly synthesized peptidoglycan in live bacteria with fluorescent D-amino acids	ACIEE 2012
M. Siegrist	D-amino acid chemical reporters reveal peptidoglycan dynamics of an intracellular pathogen	ACS Chem. Biol. 2012
M. Lebar	Reconstitution of peptidoglycan cross-linking leads to improved fluorescent probes of cell wall synthesis	JACS 2014
E. Kuru	Synthesis of fluorescent D-amino acids and their use for probing peptidoglycan synthesis and bacterial growth in situ	Nat. Protoc. 2014
J. Fura	D-amino acid probes for penicillin binding protein-based bacterial surface labeling	ASBMB 2015
S. Pidgeon	Metabolic profiling of bacteria by unnatural c-terminated D-amino acids	ACIEE 2015
S. Pidgeon	Metabolic remodeling of bacterial surfaces via tetrazine ligations	Chem. Commun. 2015
Y. Hsu	Full color palette of fluorescent D‐amino acids for in situ labeling of bacterial cell walls	Chem. Sci. 2017
Identifying the formation and/or structures of PG
M. Pilhofer	Discovery of chlamydial peptidoglycan reveals bacteria with murein sacculi but without Ftsz	Nat. Commun. 2013
G. Billings	De novo morphogenesis in L-forms via geometric control of cell growth	Mol. Microbiol. 2014
G. Liechti	A new metabolic cell-wall labelling method reveals peptidoglycan in Chlamydia trachomatis	Nature 2014
M. van Teeseling	Anammox planctomycetes have a peptidoglycan cell wall	Nat. Commun. 2015
G. Liechti	Pathogenic chlamydia lack a classical sacculus but synthesize a narrow, mid-cell peptidoglycan ring, regulated by mreb, for cell division	PLoS Pathog. 2016
Studying bacterial morphogenesis and PG growth pattern
E. Tocheva	Peptidoglycan transformations during Bacillus subtilis sporulation	Mol. Microbiol. 2013
A. Berezuk	Site-directed fluorescence labeling reveals a revised n-terminal membrane topology and functional periplasmic residues in the escherichia coli cell division protein Ftsk	J Biol. Chem. 2014
C. Kerr	Salinity-dependent impacts of Proq, Prc, and Spr deficiencies on Escherichia coli cell structure	J Bacteriol. 2014
A. Möll	Cell separation in Vibrio cholerae is mediated by a single amidase whose action is modulated by two nonredundant activators	J Bacteriol. 2014
T. Ursell	Rod-like bacterial shape is maintained by feedback between cell curvature and cytoskeletal localization	PNAS 2014
J. Monteiro	Cell shape dynamics during the staphylococcal cell cycle	Nat. Commun. 2015
H. Samal	Molecular modeling, simulation and virtual screening of murd ligase protein from Salmonella typhimurium LT2	J Pharmacol. Toxicol. Methods 2015
M. Williams	Short-stalked Prosthecomicrobium hirschii cells have a Caulobacter-like cell cycle	J Bacteriol. 2016
A. Bisson-Filho	Treadmilling by Ftsz filaments drives peptidoglycan synthesis and bacterial cell division	Science 2017
E. Cserti	Dynamics of the peptidoglycan biosynthetic machinery in the stalked budding bacterium Hyphomonas neptunium	Mol. Microbiol. 2017
A. Dajkovic	Hydrolysis of peptidoglycan is modulated by amidation of meso-diaminopimelic acid and Mg2+ in Bacillus subtilis	Mol. Microbiol. 2017
H. Veiga	Staphylococcus aureus requires at least one Ftsk/spoiiie protein for correct chromosome segregation	Mol. Microbiol. 2017
X. Yang	GTpase activity–coupled treadmilling of the bacterial tubulin Ftsz organizes septal cell wall synthesis	Science 2017
Q. Yao	Short Ftsz filaments can drive asymmetric cell envelope constriction at the onset of bacterial cytokinesis	EMBO J. 2017
Determining PG synthesis activity and sites
Y. Eun	Divin: a small molecule inhibitor of bacterial divisome assembly	JACS 2013
T. Cameron	Peptidoglycan synthesis machinery in Agrobacterium tumefaciens during unipolar growth and cell division	MBio. 2014
A. Fleurie	Interplay of the serine/threonine-kinase Stkp and the paralogs DivIVA and Gpsb in Pneumococcal cell elongation and division	PLoS Genet. 2014
A. Fleurie	Mapz marks the division sites and positions Ftsz rings in Streptococcus pneumoniae	Nature 2014
C. Jiang	Sequential evolution of bacterial morphology by co-option of a developmental regulator	Nature 2014
H. Tsui	Pbp2x localizes separately from Pbp2b and other peptidoglycan synthesis proteins during later stages of cell division of Streptococcus pneumoniae D39	Mol. Microbiol. 2014
T. Dörr	Endopeptidase-mediated beta lactam tolerance	PLoS Pathog. 2015
B. Liu	Roles for both Ftsa and the FtsBLQ subcomplex in FtsN-stimulated cell constriction in Escherichia coli	Mol. Microbiol. 2015
A. Möll	A D, D-carboxypeptidase is required for Vibrio cholerae halotolerance	Environ. Microbiol. 2015
K. Sundararajan	The bacterial tubulin Ftsz requires its intrinsically disordered linker to direct robust cell wall construction	Nat. Commun. 2015
K. Schirner	Lipid-linked cell wall precursors regulate membrane association of bacterial actin MreB	Nat. Chem. Biol. 2015
A. Tavares	MreC and MreD proteins are not required for growth of Staphylococcus aureus	PLoS ONE 2015
A. Yakhnina	The cell wall amidase AmiB is essential for Pseudomonas aeruginosa cell division, drug resistance and viability	Mol. Microbiol. 2015
B. Jutras	Lyme disease and relapsing fever Borrelia elongate through zones of peptidoglycan synthesis that mark division sites of daughter cells	PNAS 2016
S. Manuse	Structure–function analysis of the extracellular domain of the Pneumococcal cell division site positioning protein MapZ	Nat. Commun. 2016
A. Mura	Roles of the essential protein FtsA in cell growth and division in Streptococcus pneumoniae	J. Bacteriol. 2016
A. Pereira	Ftsz-dependent elongation of a Coccoid bacterium	MBio 2016
D. Ranjit	Colanic acid intermediates prevent de novo shape recovery of Escherichia coli spheroplasts, calling into question biological roles previously attributed to colanic acid	J Bacteriol. 2016
P. Yagȕe	Subcompartmentalization by cross-membranes during early growth of Streptomyces hyphae	Nat. Commun. 2016
D. Angeles	Pentapeptide-rich peptidoglycan at the Bacillus subtilis cell-division site	Mol. Microbiol. 2017
H. Botella	Mycobacterium tuberculosis protease MarP activates a peptidoglycan hydrolase during acid stress	EMBO J. 2017
L. Hamouche	Bacillus subtilis swarmer cells lead the swarm, multiply, and generate a trail of quiescent descendants	MBio 2017
A. Sugimoto	Deciphering the mode of action of cell wall-inhibiting antibiotics using metabolic labeling of growing peptidoglycan in Streptococcus pyogenes	Sci. Rep. 2017

Table 1. Examples of FDAAs applications in recent studies. Sub-headings classify the use of FDAAs in the experiment designs of each study.