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Article ; Online: Human serum triggers antibiotic tolerance in Staphylococcus aureus.

Ledger, Elizabeth V K / Mesnage, Stéphane / Edwards, Andrew M

2022 Volume 13, Issue 1, Page(s) 2041

Abstract: Staphylococcus aureus frequently causes infections that are challenging to treat, leading to high rates of persistent and relapsing infection. Here, to understand how the host environment influences treatment outcomes, we study the impact of human serum ... ...

Abstract	Staphylococcus aureus frequently causes infections that are challenging to treat, leading to high rates of persistent and relapsing infection. Here, to understand how the host environment influences treatment outcomes, we study the impact of human serum on staphylococcal antibiotic susceptibility. We show that serum triggers a high degree of tolerance to the lipopeptide antibiotic daptomycin and several other classes of antibiotic. Serum-induced daptomycin tolerance is due to two independent mechanisms. Firstly, the host defence peptide LL-37 induces tolerance by triggering the staphylococcal GraRS two-component system, leading to increased peptidoglycan accumulation. Secondly, GraRS-independent increases in membrane cardiolipin abundance are required for full tolerance. When both mechanisms are blocked, S. aureus incubated in serum is as susceptible to daptomycin as when grown in laboratory media. Our work demonstrates that host factors can significantly modulate antibiotic susceptibility via diverse mechanisms, and combination therapy may provide a way to mitigate this.
MeSH term(s)	Anti-Bacterial Agents/pharmacology ; Daptomycin/pharmacology ; Humans ; Microbial Sensitivity Tests ; Staphylococcal Infections/drug therapy ; Staphylococcus aureus
Chemical Substances	Anti-Bacterial Agents ; Daptomycin (NWQ5N31VKK)
Language	English
Publishing date	2022-04-19
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-022-29717-3
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Article ; Online: A moonlighting role for LysM peptidoglycan binding domains underpins Enterococcus faecalis daughter cell separation.

Salamaga, Bartłomiej / Turner, Robert D / Elsarmane, Fathe / Galley, Nicola F / Kulakauskas, Saulius / Mesnage, Stéphane

Communications biology

2023 Volume 6, Issue 1, Page(s) 428

Abstract: Control of cell size and morphology is of paramount importance for bacterial fitness. In the opportunistic pathogen Enterococcus faecalis, the formation of diplococci and short cell chains facilitates innate immune evasion and dissemination in the host. ... ...

Abstract	Control of cell size and morphology is of paramount importance for bacterial fitness. In the opportunistic pathogen Enterococcus faecalis, the formation of diplococci and short cell chains facilitates innate immune evasion and dissemination in the host. Minimisation of cell chain size relies on the activity of a peptidoglycan hydrolase called AtlA, dedicated to septum cleavage. To prevent autolysis, AtlA activity is tightly controlled, both temporally and spatially. Here, we show that the restricted localization of AtlA at the septum occurs via an unexpected mechanism. We demonstrate that the C-terminal LysM domain that allows the enzyme to bind peptidoglycan is essential to target this enzyme to the septum inside the cell before its translocation across the membrane. We identify a membrane-bound cytoplasmic protein partner (called AdmA) involved in the recruitment of AtlA via its LysM domains. This work reveals a moonlighting role for LysM domains, and a mechanism evolved to restrict the subcellular localization of a potentially lethal autolysin to its site of action.
MeSH term(s)	Enterococcus faecalis/metabolism ; Peptidoglycan/metabolism ; Bacterial Proteins/metabolism ; Cell Wall/metabolism ; N-Acetylmuramoyl-L-alanine Amidase/genetics ; N-Acetylmuramoyl-L-alanine Amidase/metabolism ; Cell Separation
Chemical Substances	Peptidoglycan ; Bacterial Proteins ; N-Acetylmuramoyl-L-alanine Amidase (EC 3.5.1.28)
Language	English
Publishing date	2023-04-18
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2399-3642
ISSN (online)	2399-3642
DOI	10.1038/s42003-023-04808-z
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Article ; Online: 1

Davis, Jessica L / Hounslow, Andrea M / Baxter, Nicola J / Mesnage, Stéphane / Williamson, Mike P

Biomolecular NMR assignments

2022 Volume 16, Issue 2, Page(s) 247–251

Abstract: Enterococcus faecalis is a major causative agent of hospital acquired infections. The ability of E. faecalis to evade the host immune system is essential during pathogenesis, which has been shown to be dependent on the complete separation of daughter ... ...

Abstract	Enterococcus faecalis is a major causative agent of hospital acquired infections. The ability of E. faecalis to evade the host immune system is essential during pathogenesis, which has been shown to be dependent on the complete separation of daughter cells by peptidoglycan hydrolases. AtlE is a peptidoglycan hydrolase which is predicted to bind to the cell wall of E. faecalis, via six C-terminal repeat sequences. Here, we report the near complete assignment of one of these six repeats, as well as the predicted backbone structure and dynamics. This data will provide a platform for future NMR studies to explore the ligand recognition motif of AtlE and help to uncover its potential role in E. faecalis virulence.
MeSH term(s)	Bacterial Proteins/metabolism ; Cell Wall/chemistry ; Cell Wall/metabolism ; Enterococcus faecalis/chemistry ; Enterococcus faecalis/metabolism ; Ligands ; N-Acetylmuramoyl-L-alanine Amidase/analysis ; N-Acetylmuramoyl-L-alanine Amidase/metabolism ; Nuclear Magnetic Resonance, Biomolecular ; Peptidoglycan/analysis ; Peptidoglycan/chemistry ; Peptidoglycan/metabolism
Chemical Substances	Bacterial Proteins ; Ligands ; Peptidoglycan ; N-Acetylmuramoyl-L-alanine Amidase (EC 3.5.1.28)
Language	English
Publishing date	2022-06-04
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2388861-1
ISSN	1874-270X ; 1874-2718
ISSN (online)	1874-270X
ISSN	1874-2718
DOI	10.1007/s12104-022-10087-2
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Article ; Online: Structural Characterization of EnpA D,L-Endopeptidase from

Małecki, Piotr Henryk / Mitkowski, Paweł / Jagielska, Elżbieta / Trochimiak, Karolina / Mesnage, Stéphane / Sabała, Izabela

International journal of molecular sciences

2021 Volume 22, Issue 13

Abstract: The best-characterized members of the M23 family are glycyl-glycine hydrolases, such as lysostaphin (Lss) ... ...

Abstract	The best-characterized members of the M23 family are glycyl-glycine hydrolases, such as lysostaphin (Lss) from
MeSH term(s)	Amino Acid Sequence ; Bacterial Proteins/metabolism ; Catalytic Domain ; Endopeptidases/metabolism ; Enterococcus faecalis/genetics ; Enterococcus faecalis/metabolism ; N-Acetylmuramoyl-L-alanine Amidase/metabolism ; Peptide Hydrolases/metabolism ; Peptidoglycan/metabolism ; Prophages/genetics ; Prophages/metabolism ; Protein Binding ; Staphylococcus/metabolism ; Staphylococcus aureus/metabolism ; Substrate Specificity
Chemical Substances	Bacterial Proteins ; Peptidoglycan ; Endopeptidases (EC 3.4.-) ; Peptide Hydrolases (EC 3.4.-) ; N-Acetylmuramoyl-L-alanine Amidase (EC 3.5.1.28)
Language	English
Publishing date	2021-07-01
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms22137136
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Article ; Online: Unusual 1-3 peptidoglycan cross-links in Acetobacteraceae are made by L,D-transpeptidases with a catalytic domain distantly related to YkuD domains.

Alamán-Zárate, Marcel G / Rady, Brooks J / Evans, Caroline A / Pian, Brooke / Greetham, Darren / Marecos-Ortiz, Sabrina / Dickman, Mark J / Lidbury, Ian D E A / Lovering, Andrew L / Barstow, Buz M / Mesnage, Stéphane

The Journal of biological chemistry

2023 Volume 300, Issue 1, Page(s) 105494

Abstract: Peptidoglycan is an essential component of the bacterial cell envelope that contains glycan chains substituted by short peptide stems. Peptide stems are polymerized by D,D-transpeptidases, which make bonds between the amino acid in position four of a ... ...

Abstract	Peptidoglycan is an essential component of the bacterial cell envelope that contains glycan chains substituted by short peptide stems. Peptide stems are polymerized by D,D-transpeptidases, which make bonds between the amino acid in position four of a donor stem and the third residue of an acceptor stem (4-3 cross-links). Some bacterial peptidoglycans also contain 3-3 cross-links that are formed by another class of enzymes called L,D-transpeptidases which contain a YkuD catalytic domain. In this work, we investigate the formation of unusual bacterial 1-3 peptidoglycan cross-links. We describe a version of the PGFinder software that can identify 1-3 cross-links and report the high-resolution peptidoglycan structure of Gluconobacter oxydans (a model organism within the Acetobacteraceae family). We reveal that G. oxydans peptidoglycan contains peptide stems made of a single alanine as well as several dipeptide stems with unusual amino acids at their C-terminus. Using a bioinformatics approach, we identified a G. oxydans mutant from a transposon library with a drastic reduction in 1-3 cross-links. Through complementation experiments in G. oxydans and recombinant protein production in a heterologous host, we identify an L,D-transpeptidase enzyme with a domain distantly related to the YkuD domain responsible for these non-canonical reactions. This work revisits the enzymatic capabilities of L,D-transpeptidases, a versatile family of enzymes that play a key role in bacterial peptidoglycan remodelling.
MeSH term(s)	Amino Acids/genetics ; Bacterial Proteins/chemistry ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Catalytic Domain/genetics ; Peptidoglycan/chemistry ; Peptidoglycan/genetics ; Peptidoglycan/metabolism ; Peptidyl Transferases/chemistry ; Peptidyl Transferases/genetics ; Peptidyl Transferases/metabolism ; Software ; Gluconobacter oxydans/enzymology ; Gluconobacter oxydans/genetics ; Computational Biology ; Genetic Complementation Test ; Models, Molecular ; Protein Structure, Tertiary
Chemical Substances	Amino Acids ; Bacterial Proteins ; Peptidoglycan ; Peptidyl Transferases (EC 2.3.2.12)
Language	English
Publishing date	2023-11-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1016/j.jbc.2023.105494
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Article ; Online: Molecular imaging of glycan chains couples cell-wall polysaccharide architecture to bacterial cell morphology.

Turner, Robert D / Mesnage, Stéphane / Hobbs, Jamie K / Foster, Simon J

Nature communications

2018 Volume 9, Issue 1, Page(s) 1263

Abstract: Biopolymer composite cell walls maintain cell shape and resist forces in plants, fungi and bacteria. Peptidoglycan, a crucial antibiotic target and immunomodulator, performs this role in bacteria. The textbook structural model of peptidoglycan is a ... ...

Abstract	Biopolymer composite cell walls maintain cell shape and resist forces in plants, fungi and bacteria. Peptidoglycan, a crucial antibiotic target and immunomodulator, performs this role in bacteria. The textbook structural model of peptidoglycan is a highly ordered, crystalline material. Here we use atomic force microscopy (AFM) to image individual glycan chains in peptidoglycan from Escherichia coli in unprecedented detail. We quantify and map the extent to which chains are oriented in a similar direction (orientational order), showing it is much less ordered than previously depicted. Combining AFM with size exclusion chromatography, we reveal glycan chains up to 200 nm long. We show that altered cell shape is associated with substantial changes in peptidoglycan biophysical properties. Glycans from E. coli in its normal rod shape are long and circumferentially oriented, but when a spheroid shape is induced (chemically or genetically) glycans become short and disordered.
MeSH term(s)	Anti-Bacterial Agents/chemistry ; Bacillus subtilis/chemistry ; Cell Wall/chemistry ; Escherichia coli/chemistry ; Microscopy, Atomic Force ; Microscopy, Phase-Contrast ; Models, Molecular ; Molecular Imaging ; Peptidoglycan/chemistry ; Polymers/chemistry ; Polysaccharides/chemistry
Chemical Substances	Anti-Bacterial Agents ; Peptidoglycan ; Polymers ; Polysaccharides
Language	English
Publishing date	2018-03-28
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-018-03551-y
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Article ; Online: Towards an automated analysis of bacterial peptidoglycan structure.

Bern, Marshall / Beniston, Richard / Mesnage, Stéphane

Analytical and bioanalytical chemistry

2016 Volume 409, Issue 2, Page(s) 551–560

Abstract: Peptidoglycan (PG) is an essential component of the bacterial cell envelope. This macromolecule consists of glycan chains alternating N-acetylglucosamine and N-acetylmuramic acid, cross-linked by short peptides containing nonstandard amino acids. ... ...

Abstract	Peptidoglycan (PG) is an essential component of the bacterial cell envelope. This macromolecule consists of glycan chains alternating N-acetylglucosamine and N-acetylmuramic acid, cross-linked by short peptides containing nonstandard amino acids. Structural analysis of PG usually involves enzymatic digestion of glycan strands and separation of disaccharide peptides by reversed-phase HPLC followed by collection of individual peaks for MALDI-TOF and/or tandem mass spectrometry. Here, we report a novel strategy using shotgun proteomics techniques for a systematic and unbiased structural analysis of PG using high-resolution mass spectrometry and automated analysis of HCD and ETD fragmentation spectra with the Byonic software. Using the PG of the nosocomial pathogen Clostridium difficile as a proof of concept, we show that this high-throughput approach allows the identification of all PG monomers and dimers previously described, leaving only disambiguation of 3-3 and 4-3 cross-linking as a manual step. Our analysis confirms previous findings that C. difficile peptidoglycans include mainly deacetylated N-acetylglucosamine residues and 3-3 cross-links. The analysis also revealed a number of low abundance muropeptides with peptide sequences not previously reported. Graphical Abstract The bacterial cell envelope includes plasma membrane, peptidoglycan, and surface layer. Peptidoglycan is unique to bacteria and the target of the most important antibiotics; here it is analyzed by mass spectrometry.
MeSH term(s)	Automation ; Bacterial Proteins/chemistry ; Chemistry Techniques, Analytical/methods ; Peptidoglycan/chemistry ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
Chemical Substances	Bacterial Proteins ; Peptidoglycan
Language	English
Publishing date	2016-08-13
Publishing country	Germany
Document type	Journal Article
ZDB-ID	201093-8
ISSN	1618-2650 ; 0016-1152 ; 0372-7920
ISSN (online)	1618-2650
ISSN	0016-1152 ; 0372-7920
DOI	10.1007/s00216-016-9857-5
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Article ; Online: Clostridioides difficile canonical L,D-transpeptidases catalyze a novel type of peptidoglycan cross-links and are not required for beta-lactam resistance.

Galley, Nicola F / Greetham, Darren / Alamán-Zárate, Marcel G / Williamson, Mike P / Evans, Caroline A / Spittal, William D / Buddle, Jessica E / Freeman, Jane / Davis, Georgina L / Dickman, Mark J / Wilcox, Mark H / Lovering, Andrew L / Fagan, Robert P / Mesnage, Stéphane

The Journal of biological chemistry

2023 Volume 300, Issue 1, Page(s) 105529

Abstract: Clostridioides difficile is the leading cause of antibiotic-associated diarrhea worldwide with significant morbidity and mortality. This organism is naturally resistant to several beta-lactam antibiotics that inhibit the polymerization of peptidoglycan, ... ...

Abstract	Clostridioides difficile is the leading cause of antibiotic-associated diarrhea worldwide with significant morbidity and mortality. This organism is naturally resistant to several beta-lactam antibiotics that inhibit the polymerization of peptidoglycan, an essential component of the bacteria cell envelope. Previous work has revealed that C. difficile peptidoglycan has an unusual composition. It mostly contains 3-3 cross-links, catalyzed by enzymes called L,D-transpeptidases (Ldts) that are poorly inhibited by beta-lactams. It was therefore hypothesized that peptidoglycan polymerization by these enzymes could underpin antibiotic resistance. Here, we investigated the catalytic activity of the three canonical Ldts encoded by C. difficile (Ldt
MeSH term(s)	Bacterial Proteins/chemistry ; beta-Lactam Resistance ; beta-Lactams/pharmacology ; Catalysis ; Clostridioides difficile/enzymology ; Clostridioides difficile/genetics ; Peptidoglycan/chemistry ; Peptidyl Transferases/chemistry ; Peptidyl Transferases/genetics
Chemical Substances	Bacterial Proteins ; beta-Lactams ; Peptidoglycan ; Peptidyl Transferases (EC 2.3.2.12)
Language	English
Publishing date	2023-12-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1016/j.jbc.2023.105529
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Article ; Online: Molecular basis for substrate recognition and septum cleavage by AtlA, the major N-acetylglucosaminidase of Enterococcus faecalis.

Roig-Zamboni, Véronique / Barelier, Sarah / Dixon, Robert / Galley, Nicola F / Ghanem, Amani / Nguyen, Quoc Phong / Cahuzac, Héloize / Salamaga, Bartłomiej / Davis, Peter J / Bourne, Yves / Mesnage, Stéphane / Vincent, Florence

The Journal of biological chemistry

2022 Volume 298, Issue 5, Page(s) 101915

Abstract: The cleavage of septal peptidoglycan at the end of cell division facilitates the separation of the two daughter cells. The hydrolases involved in this process (called autolysins) are potentially lethal enzymes that can cause cell death; their activity, ... ...

Abstract	The cleavage of septal peptidoglycan at the end of cell division facilitates the separation of the two daughter cells. The hydrolases involved in this process (called autolysins) are potentially lethal enzymes that can cause cell death; their activity, therefore, must be tightly controlled during cell growth. In Enterococcus faecalis, the N-acetylglucosaminidase AtlA plays a predominant role in cell separation. atlA mutants form long cell chains and are significantly less virulent in the zebrafish model of infection. The attenuated virulence of atlA mutants is underpinned by a limited dissemination of bacterial chains in the host organism and a more efficient uptake by phagocytes that clear the infection. AtlA has structural homologs in other important pathogens, such as Listeria monocytogenes and Salmonella typhimurium, and therefore represents an attractive model to design new inhibitors of bacterial pathogenesis. Here, we provide a 1.45 Å crystal structure of the E. faecalis AtlA catalytic domain that reveals a closed conformation of a conserved β-hairpin and a complex network of hydrogen bonds that bring two catalytic residues to the ideal distance for an inverting mechanism. Based on the model of the AtlA-substrate complex, we identify key residues critical for substrate recognition and septum cleavage during bacterial growth. We propose that this work will provide useful information for the rational design of specific inhibitors targeting this enterococcal virulence factor and its orthologs in other pathogens.
MeSH term(s)	Acetylglucosaminidase/chemistry ; Animals ; Bacterial Proteins/metabolism ; Enterococcus faecalis/enzymology ; Enterococcus faecalis/metabolism ; Peptidoglycan/metabolism ; Zebrafish/metabolism
Chemical Substances	Bacterial Proteins ; Peptidoglycan ; Acetylglucosaminidase (EC 3.2.1.52)
Language	English
Publishing date	2022-04-07
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1016/j.jbc.2022.101915
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Article ; Online: Complete Structure of the Enterococcal Polysaccharide Antigen (EPA) of Vancomycin-Resistant Enterococcus faecalis V583 Reveals that EPA Decorations Are Teichoic Acids Covalently Linked to a Rhamnopolysaccharide Backbone.

Guerardel, Yann / Sadovskaya, Irina / Maes, Emmanuel / Furlan, Sylviane / Chapot-Chartier, Marie-Pierre / Mesnage, Stéphane / Rigottier-Gois, Lionel / Serror, Pascale

mBio

2020 Volume 11, Issue 2

Abstract: All enterococci produce a complex polysaccharide called ... ...

Abstract	All enterococci produce a complex polysaccharide called the
MeSH term(s)	Antigens, Bacterial/chemistry ; Antigens, Bacterial/metabolism ; Deoxy Sugars/chemistry ; Deoxy Sugars/metabolism ; Enterococcus faecalis/metabolism ; Humans ; Mannans/chemistry ; Mannans/metabolism ; Polysaccharides/chemistry ; Polysaccharides/metabolism ; Teichoic Acids/chemistry ; Teichoic Acids/metabolism ; Vancomycin-Resistant Enterococci/metabolism
Chemical Substances	Antigens, Bacterial ; Deoxy Sugars ; Mannans ; Polysaccharides ; Teichoic Acids ; rhamnan (111018-90-7)
Language	English
Publishing date	2020-04-28
Publishing country	United States
Document type	Journal Article
ZDB-ID	2557172-2
ISSN	2150-7511 ; 2161-2129
ISSN (online)	2150-7511
ISSN	2161-2129
DOI	10.1128/mBio.00277-20
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