1
|
York A, Lloyd AJ, Del Genio CI, Shearer J, Hinxman KJ, Fritz K, Fulop V, Dowson CG, Khalid S, Roper DI. Structure-based modeling and dynamics of MurM, a Streptococcus pneumoniae penicillin resistance determinant present at the cytoplasmic membrane. Structure 2021; 29:731-742.e6. [PMID: 33740396 PMCID: PMC8280954 DOI: 10.1016/j.str.2021.03.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 01/13/2021] [Accepted: 03/01/2021] [Indexed: 11/28/2022]
Abstract
Branched Lipid II, required for the formation of indirectly crosslinked peptidoglycan, is generated by MurM, a protein essential for high-level penicillin resistance in the human pathogen Streptococcus pneumoniae. We have solved the X-ray crystal structure of Staphylococcus aureus FemX, an isofunctional homolog, and have used this as a template to generate a MurM homology model. Using this model, we perform molecular docking and molecular dynamics to examine the interaction of MurM with the phospholipid bilayer and the membrane-embedded Lipid II substrate. Our model suggests that MurM is associated with the major membrane phospholipid cardiolipin, and experimental evidence confirms that the activity of MurM is enhanced by this phospholipid and inhibited by its direct precursor phosphatidylglycerol. The spatial association of pneumococcal membrane phospholipids and their impact on MurM activity may therefore be critical to the final architecture of peptidoglycan and the expression of clinically relevant penicillin resistance in this pathogen.
Collapse
Affiliation(s)
- Anna York
- School of Life Science, University of Warwick, Coventry, West Midlands CV4 7AL, UK
| | - Adrian J Lloyd
- School of Life Science, University of Warwick, Coventry, West Midlands CV4 7AL, UK
| | - Charo I Del Genio
- Centre for Fluid and Complex Systems, School of Computing, Electronics and Mathematics, University of Coventry, West Midlands CV1 5FB, UK
| | - Jonathan Shearer
- School of Chemistry, University of Southampton, Southampton, Hampshire SO17 1BJ, UK
| | - Karen J Hinxman
- School of Life Science, University of Warwick, Coventry, West Midlands CV4 7AL, UK
| | - Konstantin Fritz
- School of Life Science, University of Warwick, Coventry, West Midlands CV4 7AL, UK
| | - Vilmos Fulop
- School of Life Science, University of Warwick, Coventry, West Midlands CV4 7AL, UK
| | - Christopher G Dowson
- School of Life Science, University of Warwick, Coventry, West Midlands CV4 7AL, UK
| | - Syma Khalid
- School of Chemistry, University of Southampton, Southampton, Hampshire SO17 1BJ, UK.
| | - David I Roper
- School of Life Science, University of Warwick, Coventry, West Midlands CV4 7AL, UK; Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA.
| |
Collapse
|
2
|
Fonvielle M, Bouhss A, Hoareau C, Patin D, Mengin-Lecreulx D, Iannazzo L, Sakkas N, El Sagheer A, Brown T, Ethève-Quelquejeu M, Arthur M. Synthesis of Lipid-Carbohydrate-Peptidyl-RNA Conjugates to Explore the Limits Imposed by the Substrate Specificity of Cell Wall Enzymes on the Acquisition of Drug Resistance. Chemistry 2018; 24:14911-14915. [PMID: 30020544 DOI: 10.1002/chem.201802360] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 07/16/2018] [Indexed: 01/10/2023]
Abstract
Conjugation of RNA with multiple partners to obtain mimics of complex biomolecules is limited by the identification of orthogonal reactions. Here, lipid-carbohydrate-peptidyl-RNA conjugates were obtained by post-functionalization reactions, solid-phase synthesis, and enzymatic steps, to generate molecules mimicking the substrates of FmhB, an essential peptidoglycan synthesis enzyme of Staphylococcus aureus. Mimics of Gly-tRNAGly and lipid intermediate II (undecaprenyl-diphospho-disaccharide-pentapeptide) were combined in a single "bi-substrate" inhibitor (IC50 =56 nm). The synthetic route was exploited to generate substrates and inhibitors containing d-lactate residue (d-Lac) instead of d-Ala at the C-terminus of the pentapeptide stem, a modification responsible for vancomycin resistance in the enterococci. The substitution impaired recognition of peptidoglycan precursors by FmhB. The associated fitness cost may account for limited dissemination of vancomycin resistance genes in S. aureus.
Collapse
Affiliation(s)
- Matthieu Fonvielle
- INSERM UMRS 1138, Sorbonne Universités, UPMC Univ Paris 06;, 'Sorbonne Paris Cité, Université Paris Descartes, Université Paris Diderot, Centre de Recherche des Cordeliers, 75006, Paris, France
| | - Ahmed Bouhss
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.,Present address: Laboratoire Structure-Activité des Biomolécules, Normales et Pathologiques (SABNP), Univ Evry, INSERM U1204, Université Paris-Saclay, 91025, Evry, France
| | - Coralie Hoareau
- INSERM UMRS 1138, Sorbonne Universités, UPMC Univ Paris 06;, 'Sorbonne Paris Cité, Université Paris Descartes, Université Paris Diderot, Centre de Recherche des Cordeliers, 75006, Paris, France
| | - Delphine Patin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Dominique Mengin-Lecreulx
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Laura Iannazzo
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes, UMR 8601, Paris, F-75005, France.,CNRS UMR 8601, Paris, F-75006, France
| | - Nicolas Sakkas
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes, UMR 8601, Paris, F-75005, France.,CNRS UMR 8601, Paris, F-75006, France
| | - Affaf El Sagheer
- Chemistry Branch, Dept. of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University, Suez, 43721, Egypt.,Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Tom Brown
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Mélanie Ethève-Quelquejeu
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes, UMR 8601, Paris, F-75005, France.,CNRS UMR 8601, Paris, F-75006, France
| | - Michel Arthur
- INSERM UMRS 1138, Sorbonne Universités, UPMC Univ Paris 06;, 'Sorbonne Paris Cité, Université Paris Descartes, Université Paris Diderot, Centre de Recherche des Cordeliers, 75006, Paris, France
| |
Collapse
|
3
|
Fonvielle M, Sakkas N, Iannazzo L, Le Fournis C, Patin D, Mengin-Lecreulx D, El-Sagheer A, Braud E, Cardon S, Brown T, Arthur M, Etheve-Quelquejeu M. Electrophilic RNA for Peptidyl-RNA Synthesis and Site-Specific Cross-Linking with tRNA-Binding Enzymes. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201606843] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Matthieu Fonvielle
- Laboratoire de Recherche Moléculaire sur les Antibiotiques Centre de Recherche des Cordeliers, Equipe 12, UMR S 1138; INSERM; Université Pierre et Marie Curie-Paris 6, Université Paris Descartes; 15 rue de L'Ecole de Médecine Paris F-75006 France
| | - Nicolas Sakkas
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques; Université Paris Descartes, UMR 8601; Paris F-75006 France
- CNRS UMR 8601; Paris F-75006 France
| | - Laura Iannazzo
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques; Université Paris Descartes, UMR 8601; Paris F-75006 France
- CNRS UMR 8601; Paris F-75006 France
| | - Chloé Le Fournis
- Laboratoire de Recherche Moléculaire sur les Antibiotiques Centre de Recherche des Cordeliers, Equipe 12, UMR S 1138; INSERM; Université Pierre et Marie Curie-Paris 6, Université Paris Descartes; 15 rue de L'Ecole de Médecine Paris F-75006 France
| | - Delphine Patin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud; Université Paris-Saclay; 91198 Gif-sur-Yvette cedex France
| | - Dominique Mengin-Lecreulx
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud; Université Paris-Saclay; 91198 Gif-sur-Yvette cedex France
| | - Afaf El-Sagheer
- Department of Chemistry; University of Oxford, Chemistry Research Laboratory; 12 Mansfield Road Oxford OX1 3TA UK
- Chemistry Branch, Dept. of Science and Mathematics, Faculty of Petroleum and Mining Engineering; Suez Canal University; Suez 43721 Egypt
| | - Emmanuelle Braud
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques; Université Paris Descartes, UMR 8601; Paris F-75006 France
- CNRS UMR 8601; Paris F-75006 France
| | - Sébastien Cardon
- Laboratoire de Recherche Moléculaire sur les Antibiotiques Centre de Recherche des Cordeliers, Equipe 12, UMR S 1138; INSERM; Université Pierre et Marie Curie-Paris 6, Université Paris Descartes; 15 rue de L'Ecole de Médecine Paris F-75006 France
| | - Tom Brown
- Department of Chemistry; University of Oxford, Chemistry Research Laboratory; 12 Mansfield Road Oxford OX1 3TA UK
| | - Michel Arthur
- Laboratoire de Recherche Moléculaire sur les Antibiotiques Centre de Recherche des Cordeliers, Equipe 12, UMR S 1138; INSERM; Université Pierre et Marie Curie-Paris 6, Université Paris Descartes; 15 rue de L'Ecole de Médecine Paris F-75006 France
| | - Mélanie Etheve-Quelquejeu
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques; Université Paris Descartes, UMR 8601; Paris F-75006 France
- CNRS UMR 8601; Paris F-75006 France
| |
Collapse
|
4
|
Fonvielle M, Sakkas N, Iannazzo L, Le Fournis C, Patin D, Mengin-Lecreulx D, El-Sagheer A, Braud E, Cardon S, Brown T, Arthur M, Etheve-Quelquejeu M. Electrophilic RNA for Peptidyl-RNA Synthesis and Site-Specific Cross-Linking with tRNA-Binding Enzymes. Angew Chem Int Ed Engl 2016; 55:13553-13557. [PMID: 27667506 DOI: 10.1002/anie.201606843] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 09/03/2016] [Indexed: 12/12/2022]
Abstract
RNA functionalization is challenging due to the instability of RNA and the limited range of available enzymatic reactions. We developed a strategy based on solid phase synthesis and post-functionalization to introduce an electrophilic site at the 3' end of tRNA analogues. The squarate diester used as an electrophile enabled sequential amidation and provided asymmetric squaramides with high selectivity. The squaramate-RNAs specifically reacted with the lysine of UDP-MurNAc-pentapeptide, a peptidoglycan precursor used by the aminoacyl-transferase FemXWv for synthesis of the bacterial cell wall. The peptidyl-RNA obtained with squaramate-RNA and unprotected UDP-MurNAc-pentapeptide efficiently inhibited FemXWv . The squaramate unit also promoted specific cross-linking of RNA to the catalytic Lys of FemXWv but not to related transferases recognizing different aminoacyl-tRNAs. Thus, squaramate-RNAs provide specificity for cross-linking with defined groups in complex biomolecules due to its unique reactivity.
Collapse
Affiliation(s)
- Matthieu Fonvielle
- Laboratoire de Recherche Moléculaire sur les Antibiotiques Centre de Recherche des Cordeliers, Equipe 12, UMR S 1138; INSERM, Université Pierre et Marie Curie-Paris 6, Université Paris Descartes, 15 rue de L'Ecole de Médecine, Paris, F-75006, France
| | - Nicolas Sakkas
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes, UMR 8601, Paris, F-75006, France.,CNRS UMR 8601, Paris, F-75006, France
| | - Laura Iannazzo
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes, UMR 8601, Paris, F-75006, France.,CNRS UMR 8601, Paris, F-75006, France
| | - Chloé Le Fournis
- Laboratoire de Recherche Moléculaire sur les Antibiotiques Centre de Recherche des Cordeliers, Equipe 12, UMR S 1138; INSERM, Université Pierre et Marie Curie-Paris 6, Université Paris Descartes, 15 rue de L'Ecole de Médecine, Paris, F-75006, France
| | - Delphine Patin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Dominique Mengin-Lecreulx
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Afaf El-Sagheer
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK.,Chemistry Branch, Dept. of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez Canal University, Suez, 43721, Egypt
| | - Emmanuelle Braud
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes, UMR 8601, Paris, F-75006, France.,CNRS UMR 8601, Paris, F-75006, France
| | - Sébastien Cardon
- Laboratoire de Recherche Moléculaire sur les Antibiotiques Centre de Recherche des Cordeliers, Equipe 12, UMR S 1138; INSERM, Université Pierre et Marie Curie-Paris 6, Université Paris Descartes, 15 rue de L'Ecole de Médecine, Paris, F-75006, France
| | - Tom Brown
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Michel Arthur
- Laboratoire de Recherche Moléculaire sur les Antibiotiques Centre de Recherche des Cordeliers, Equipe 12, UMR S 1138; INSERM, Université Pierre et Marie Curie-Paris 6, Université Paris Descartes, 15 rue de L'Ecole de Médecine, Paris, F-75006, France.
| | - Mélanie Etheve-Quelquejeu
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, Université Paris Descartes, UMR 8601, Paris, F-75006, France. .,CNRS UMR 8601, Paris, F-75006, France.
| |
Collapse
|
5
|
Salah Ud-Din AIM, Tikhomirova A, Roujeinikova A. Structure and Functional Diversity of GCN5-Related N-Acetyltransferases (GNAT). Int J Mol Sci 2016; 17:E1018. [PMID: 27367672 PMCID: PMC4964394 DOI: 10.3390/ijms17071018] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 06/14/2016] [Accepted: 06/20/2016] [Indexed: 12/17/2022] Open
Abstract
General control non-repressible 5 (GCN5)-related N-acetyltransferases (GNAT) catalyze the transfer of an acyl moiety from acyl coenzyme A (acyl-CoA) to a diverse group of substrates and are widely distributed in all domains of life. This review of the currently available data acquired on GNAT enzymes by a combination of structural, mutagenesis and kinetic methods summarizes the key similarities and differences between several distinctly different families within the GNAT superfamily, with an emphasis on the mechanistic insights obtained from the analysis of the complexes with substrates or inhibitors. It discusses the structural basis for the common acetyltransferase mechanism, outlines the factors important for the substrate recognition, and describes the mechanism of action of inhibitors of these enzymes. It is anticipated that understanding of the structural basis behind the reaction and substrate specificity of the enzymes from this superfamily can be exploited in the development of novel therapeutics to treat human diseases and combat emerging multidrug-resistant microbial infections.
Collapse
Affiliation(s)
- Abu Iftiaf Md Salah Ud-Din
- Infection and Immunity Program, Monash Biomedicine Discovery Institute; Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia.
| | - Alexandra Tikhomirova
- Infection and Immunity Program, Monash Biomedicine Discovery Institute; Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia.
| | - Anna Roujeinikova
- Infection and Immunity Program, Monash Biomedicine Discovery Institute; Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia.
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.
| |
Collapse
|
6
|
Iannazzo L, Laisné G, Fonvielle M, Braud E, Herbeuval JP, Arthur M, Etheve-Quelquejeu M. Synthesis of 3′-Fluoro-tRNA Analogues for Exploring Non-ribosomal Peptide Synthesis in Bacteria. Chembiochem 2015; 16:477-86. [DOI: 10.1002/cbic.201402523] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Indexed: 11/08/2022]
|