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Darbyshire A, Mothersole R, Wolthers KR. Biosynthesis of meso-lanthionine in Fusobacterium nucleatum. Arch Biochem Biophys 2023:109666. [PMID: 37329940 DOI: 10.1016/j.abb.2023.109666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 06/01/2023] [Accepted: 06/09/2023] [Indexed: 06/19/2023]
Abstract
The opportunistic oral pathogen, Fusobacterium nucleatum contains meso-lanthionine as the diaminodicarboxylic acid in the pentapeptide crosslink of the peptidoglycan layer. The diastereomer, l,l-lanthionine is formed by lanthionine synthase, a PLP-dependent enzyme that catalyzes the β-replacement of l-cysteine with a second equivalent of l-cysteine. In this study, we explored possible enzymatic mechanisms for the formation of meso-lanthionine. Our inhibition studies with lanthionine synthase, described herein, revealed that meso-diaminopimelate, a bioisostere of meso-lanthionine, is a more potent inhibitor of lanthionine synthase compared to the diastereomer, l,l-diaminopimelate. These results suggested that lanthionine synthase could also form meso-lanthionine by the β-replacement of l-cysteine with d-cysteine. Through steady-state and pre-steady state kinetic analysis, we confirm that d-cysteine reacts with the ⍺-aminoacylate intermediate with a kon that was 2-3-fold faster and Kd value that was 2-3fold lower compared to l-cysteine. However, given that intracellular levels of d-cysteine levels are assumed to be significantly lower than that of l-cysteine, we also determined if the gene product, FN1732, with low sequence identity to diaminopimelate epimerase could convert l,l-lanthionine to meso-lanthionine. Using diaminopimelate dehydrogenase in a coupled spectrophotometric assay, we show that FN1732 can convert l,l-lanthionine to meso-lanthionine with a kcat of 0.07 ± 0.001 s-1 and a KM of 1.9 ± 0.1 mM. In summary, our results provide two possible enzymatic mechanisms for the biosynthesis of meso-lanthionine in F. nucleatum.
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Affiliation(s)
- Amanda Darbyshire
- Department of Chemistry, University of British Columbia, Okanagan Campus, Kelowna, B.C, V1V 1V7, Canada
| | - Robert Mothersole
- Department of Chemistry, University of British Columbia, Okanagan Campus, Kelowna, B.C, V1V 1V7, Canada
| | - Kirsten R Wolthers
- Department of Chemistry, University of British Columbia, Okanagan Campus, 3247 University Way, Kelowna, Canada.
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2
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Vacariu CM, Tanner ME. Recent Advances in the Synthesis and Biological Applications of Peptidoglycan Fragments. Chemistry 2022; 28:e202200788. [PMID: 35560956 DOI: 10.1002/chem.202200788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Indexed: 11/09/2022]
Abstract
The biosynthesis, breakdown, and modification of peptidoglycan (PG) play vital roles in both bacterial viability and in the response of human physiology to bacterial infection. Studies on PG biochemistry are hampered by the fact that PG is an inhomogeneous insoluble macromolecule. Chemical synthesis is therefore an important means to obtain PG fragments that may serve as enzyme substrates and elicitors of the human immune response. This review outlines the recent advances in the synthesis and biochemical studies of PG fragments, PG biosynthetic intermediates (such as Park's nucleotides and PG lipids), and PG breakdown products (such as muramyl dipeptides and anhydro-muramic acid-containing fragments). A rich variety of synthetic approaches has been applied to preparing such compounds since carbohydrate, peptide, and phospholipid chemical methodologies must all be applied.
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Affiliation(s)
- Condurache M Vacariu
- Department of Chemistry, University of British Columbia, V6T 1Z1, Vancouver, British Columbia, Canada
| | - Martin E Tanner
- Department of Chemistry, University of British Columbia, V6T 1Z1, Vancouver, British Columbia, Canada
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3
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Apostolos AJ, Ocius KL, Koyasseril-Yehiya TM, Santamaria C, Silva JRA, Lameira J, Alves CN, Siegrist MS, Pires MM. Metabolic Processing of Selenium-Based Bioisosteres of meso-Diaminopimelic Acid in Live Bacteria. Biochemistry 2022; 61:1404-1414. [PMID: 35687722 DOI: 10.1021/acs.biochem.2c00120] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A primary component of all known bacterial cell walls is the peptidoglycan (PG) layer, which is composed of repeating units of sugars connected to short and unusual peptides. The various steps within PG biosynthesis are targets of potent antibiotics as proper assembly of the PG is essential for cellular growth and survival. Synthetic mimics of PG have proven to be indispensable tools to study the bacterial cell structure, growth, and remodeling. Yet, a common component of PG, meso-diaminopimelic acid (m-DAP) at the third position of the stem peptide, remains challenging to access synthetically and is not commercially available. Here, we describe the synthesis and metabolic processing of a selenium-based bioisostere of m-DAP (selenolanthionine) and show that it is installed within the PG of live bacteria by the native cell wall crosslinking machinery in mycobacterial species. This PG probe has an orthogonal release mechanism that could be important for downstream proteomics studies. Finally, we describe a bead-based assay that is compatible with high-throughput screening of cell wall enzymes. We envision that this probe will supplement the current methods available for investigating PG crosslinking in m-DAP-containing organisms.
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Affiliation(s)
- Alexis J Apostolos
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Karl L Ocius
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | | | - Carolina Santamaria
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts 01003-9298, United States.,Department of Microbiology, University of Massachusetts, Amherst, Massachusetts 01003-9298, United States
| | - José Rogério A Silva
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Pará 66075-110, Brazil
| | - Jerônimo Lameira
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Pará 66075-110, Brazil
| | - Cláudio N Alves
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Pará 66075-110, Brazil
| | - M Sloan Siegrist
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, Massachusetts 01003-9298, United States.,Department of Microbiology, University of Massachusetts, Amherst, Massachusetts 01003-9298, United States
| | - Marcos M Pires
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
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4
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Lin CSH, Chan ACK, Vermeulen J, Brockerman J, Soni AS, Tanner ME, Gaynor EC, McIntosh LP, Simorre JP, Murphy MEP. Peptidoglycan binding by a pocket on the accessory NTF2-domain of Pgp2 directs helical cell shape of Campylobacter jejuni. J Biol Chem 2021; 296:100528. [PMID: 33711341 PMCID: PMC8038945 DOI: 10.1016/j.jbc.2021.100528] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 03/01/2021] [Accepted: 03/08/2021] [Indexed: 01/25/2023] Open
Abstract
The helical morphology of Campylobacter jejuni, a bacterium involved in host gut colonization and pathogenesis in humans, is determined by the structure of the peptidoglycan (PG) layer. This structure is dictated by trimming of peptide stems by the LD-carboxypeptidase Pgp2 within the periplasm. The interaction interface between Pgp2 and PG to select sites for peptide trimming is unknown. We determined a 1.6 Å resolution crystal structure of Pgp2, which contains a conserved LD-carboxypeptidase domain and a previously uncharacterized domain with an NTF2-like fold (NTF2). We identified a pocket in the NTF2 domain formed by conserved residues and located ∼40 Å from the LD-carboxypeptidase active site. Expression of pgp2 in trans with substitutions of charged (Lys257, Lys307, Glu324) and hydrophobic residues (Phe242 and Tyr233) within the pocket did not restore helical morphology to a pgp2 deletion strain. Muropeptide analysis indicated a decrease of murotripeptides in the deletion strain expressing these mutants, suggesting reduced Pgp2 catalytic activity. Pgp2 but not the K307A mutant was pulled down by C. jejuni Δpgp2 PG sacculi, supporting a role for the pocket in PG binding. NMR spectroscopy was used to define the interaction interfaces of Pgp2 with several PG fragments, which bound to the active site within the LD-carboxypeptidase domain and the pocket of the NTF2 domain. We propose a model for Pgp2 binding to PG strands involving both the LD-carboxypeptidase domain and the accessory NTF2 domain to induce a helical cell shape.
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Affiliation(s)
- Chang Sheng-Huei Lin
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Anson C K Chan
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jenny Vermeulen
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jacob Brockerman
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Arvind S Soni
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Martin E Tanner
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Erin C Gaynor
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lawrence P McIntosh
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada; Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Michael E P Murphy
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada.
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Apostolos AJ, Nelson JM, Silva JRA, Lameira J, Achimovich AM, Gahlmann A, Alves CN, Pires MM. Facile Synthesis and Metabolic Incorporation of m-DAP Bioisosteres Into Cell Walls of Live Bacteria. ACS Chem Biol 2020; 15:2966-2975. [PMID: 33078931 DOI: 10.1021/acschembio.0c00618] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Bacterial cell walls contain peptidoglycan (PG), a scaffold that provides proper rigidity to resist lysis from internal osmotic pressure and a barrier to protect cells against external stressors. It consists of repeating sugar units with a linkage to a stem peptide that becomes cross-linked by cell wall transpeptidases (TP). While synthetic PG fragments containing l-lysine in the third position on the stem peptide are easier to access, those with meso-diaminopimelic acid (m-DAP) pose a severe synthetic challenge. Herein, we describe a solid phase synthetic scheme based on widely available building blocks to assemble meso-cystine (m-CYT), which mimics key structural features of m-DAP. To demonstrate proper mimicry of m-DAP, cell wall probes were synthesized with m-CYT in place of m-DAP and evaluated for their metabolic processing in live bacterial cells. We found that m-CYT-based cell wall probes were properly processed by TPs in various bacterial species that endogenously contain m-DAP in their PG. Additionally, we have used hybrid quantum mechanical/molecular mechanical (QM/MM) and molecular dynamics (MD) simulations to explore the influence of m-DAP analogs on the PG cross-linking. The results showed that the cross-linking mechanism of transpeptidases occurred through a concerted process. We anticipate that this strategy, which is based on the use of inexpensive and commercially available building blocks, can be widely adopted to provide greater accessibility of PG mimics for m-DAP containing organisms.
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Affiliation(s)
- Alexis J. Apostolos
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Julia M. Nelson
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - José Rogério A. Silva
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais Universidade Federal do Pará, Belém, Pará 66075-110, Brazil
| | - Jerônimo Lameira
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais Universidade Federal do Pará, Belém, Pará 66075-110, Brazil
| | - Alecia M. Achimovich
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine and Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Andreas Gahlmann
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine and Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Cláudio N. Alves
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais Universidade Federal do Pará, Belém, Pará 66075-110, Brazil
| | - Marcos M. Pires
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
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6
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Synthesis of Conformationally Constrained d-Glu- meso-DAP Analogs as Innate Immune Agonists. Molecules 2020; 25:molecules25225228. [PMID: 33182604 PMCID: PMC7698283 DOI: 10.3390/molecules25225228] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/02/2020] [Accepted: 11/04/2020] [Indexed: 11/30/2022] Open
Abstract
The dipeptide d-Glu-meso-DAP (iE-DAP) is the minimal structural fragment capable of activating the innate immune receptor nucleotide-binding oligomerization domain protein (NOD1). The meso-diaminopimelic acid (meso-DAP) moiety is known to be very stringent in terms of the allowed structural modifications which still retain the NOD1 activity. The aim of our study was to further explore the chemical space around the meso-DAP portion and provide a deeper understanding of the structural features required for NOD1 agonism. In order to achieve the rigidization of the terminal amine functionality of meso-DAP, isoxazoline and pyridine heterocycles were introduced into its side-chain. Further, we incorporated the obtained meso-DAP mimetics into the structure of iE-DAP. Collectively, nine innovative iE-DAP derivatives additionally equipped with lauroyl or didodecyl moieties at the α-amino group of d-Glu have been prepared and examined for their NOD1 activating capacity. Overall, the results obtained indicate that constraining the terminal amino group of meso-DAP abrogates the compounds’ ability to activate NOD1, since only compound 6b retained noteworthy NOD1 agonistic activity, and underpin the stringent nature of this amino acid with regard to the allowed structural modifications.
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7
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Salama NR. Cell morphology as a virulence determinant: lessons from Helicobacter pylori. Curr Opin Microbiol 2020; 54:11-17. [PMID: 32014717 PMCID: PMC7247928 DOI: 10.1016/j.mib.2019.12.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 12/30/2019] [Indexed: 02/06/2023]
Abstract
A genetic screen for colonization factors of the human stomach pathogen Helicobacter pylori took a surprising turn with the discovery that some colonization mutants had lost helical cell morphology. Further pursuit of direct morphology screens revealed a large H. pylori 'shapesome' complex consisting of peptidoglycan modification and precursor synthesis enzymes, a cytoskeletal element and putative scaffold or regulatory proteins that promote enhanced asymmetric cell wall growth. Functional characterization of H. pylori shape mutants indicates multiple roles for cell shape during colonization of mucosal surfaces. Conservation of both the molecular constituents of the H. pylori cell shape program and a newly appreciated enrichment of this morphotype at mucosal surface suggests that helical organisms may be particularly well poised to exploit host perturbations to become pathogens.
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Affiliation(s)
- Nina R Salama
- Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N, Seattle, WA 98109, United States.
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8
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Soni AS, Vacariu CM, Chen JY, Tanner ME. Synthesis of a meso-Oxa-Diaminopimelic Acid Containing Peptidoglycan Pentapeptide and Coupling to the GlcNAc- anhydro-MurNAc Disaccharide. Org Lett 2020; 22:2313-2317. [PMID: 32133861 DOI: 10.1021/acs.orglett.0c00505] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The syntheses of peptidoglycan (PG)-derived peptides containing meso-diaminopimelic acid (meso-Dap) are typically quite lengthy due to the need to prepare orthogonally protected meso-Dap. In this work, the preparation of the PG pentapeptide containing the isosteric analog meso-oxa-Dap is described. The synthesis relies on the ring opening of a peptide embedded aziridine via the attack of a serine residue. The pentapeptide was attached to a GlcNAc-anhydro-MurNAc disaccharide, to produce a putative substrate for the AmpG pore protein.
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Affiliation(s)
- Arvind S Soni
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Condarache M Vacariu
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Jeff Y Chen
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Martin E Tanner
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
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