Dynamic interplay between a TonB-dependent heme transporter and a TonB protein in a membrane environment
ABSTRACT The envelope of Gram-negative bacteria is composed of two membranes separated by the periplasmic space. This organization imposes geometrical and distance constraints that are key for the mechanism of action of multicomponent systems spanning the envelope. However, consideration of all thre...
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American Society for Microbiology
2024-12-01
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| Series: | mBio |
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| Online Access: | https://journals.asm.org/doi/10.1128/mbio.01781-24 |
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| author | Kamolrat Somboon Oliver Melling Maylis Lejeune Glaucia M. S. Pinheiro Annick Paquelin Benjamin Bardiaux Michael Nilges Phillippe Delepelaire Syma Khalid Nadia Izadi-Pruneyre |
| author_facet | Kamolrat Somboon Oliver Melling Maylis Lejeune Glaucia M. S. Pinheiro Annick Paquelin Benjamin Bardiaux Michael Nilges Phillippe Delepelaire Syma Khalid Nadia Izadi-Pruneyre |
| author_sort | Kamolrat Somboon |
| collection | DOAJ |
| description | ABSTRACT The envelope of Gram-negative bacteria is composed of two membranes separated by the periplasmic space. This organization imposes geometrical and distance constraints that are key for the mechanism of action of multicomponent systems spanning the envelope. However, consideration of all three compartments by experimental approaches is still elusive. Here, we have used the state-of-the-art molecular dynamics simulation in an Escherichia coli envelope model to obtain a dynamic view of molecular interactions between the outer membrane heme transporter HasR and the inner membrane TonB-like protein HasB. Their interaction allows the transfer of the inner membrane proton-motive force derived energy to the transporter for heme internalization. The simulations that incorporate both membranes show the key role of periplasmic domains of both proteins and their dynamics in complex formation and stability. They revealed a previously unidentified network of HasR-HasB protein-protein interactions in the periplasm. Experimental validation (mutations, in vivo phenotypic and biophysical assays) provides support for the simulation-predicted interactions. Based on structural and sequence conservation, the network of interaction revealed in this study is expected to occur in other nutrient import systems.IMPORTANCEGram-negative bacteria import scarce nutrients such as metals and vitamins by an energized mechanism involving a multicomponent protein system that spans the cell envelope. It consists of an outer membrane TonB-dependent transporter (TBDT) and a TonB complex in the inner membrane that provides the proton motive force energy for the nutrient entry. Despite the intense research efforts focused on this system (a) from structural and fundamental microbiology perspectives and (b) for the interest in the development of new antibacterial strategies, the molecular mechanism of the system is not at all well understood. The lack of understanding comes from incomplete structural data and the experimental difficulties of studying an inherently flexible multicomponent complex that resides within the heterogeneous environment of the double membrane bacterial cell envelope. To address these challenges and obtain a comprehensive view of the molecular interactions at atomic level, here, we have used the combined power of advanced molecular simulations and complementary microbiology and biochemical experiments. Our results represent a significant step forward in understanding the structural and molecular bases of this vital mechanism. |
| format | Article |
| id | doaj-art-be8f5c7b6a3f4f2eaebf700a79f137bd |
| institution | OA Journals |
| issn | 2150-7511 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | American Society for Microbiology |
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| series | mBio |
| spelling | doaj-art-be8f5c7b6a3f4f2eaebf700a79f137bd2025-08-20T02:33:47ZengAmerican Society for MicrobiologymBio2150-75112024-12-01151210.1128/mbio.01781-24Dynamic interplay between a TonB-dependent heme transporter and a TonB protein in a membrane environmentKamolrat Somboon0Oliver Melling1Maylis Lejeune2Glaucia M. S. Pinheiro3Annick Paquelin4Benjamin Bardiaux5Michael Nilges6Phillippe Delepelaire7Syma Khalid8Nadia Izadi-Pruneyre9School of Chemistry, University of Southampton, Southampton, United KingdomSchool of Chemistry, University of Southampton, Southampton, United KingdomInstitut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Bioinformatics Unit, Paris, FranceInstitut Pasteur, Université Paris Cité, CNRS UMR3528, Bacterial Transmembrane Systems Unit, Paris, FranceInstitut de Biologie Physico-Chimique, UMR 7099, CNRS Université de Paris, Paris, FranceInstitut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Bioinformatics Unit, Paris, FranceInstitut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Bioinformatics Unit, Paris, FranceInstitut de Biologie Physico-Chimique, UMR 7099, CNRS Université de Paris, Paris, FranceSchool of Chemistry, University of Southampton, Southampton, United KingdomInstitut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Bioinformatics Unit, Paris, FranceABSTRACT The envelope of Gram-negative bacteria is composed of two membranes separated by the periplasmic space. This organization imposes geometrical and distance constraints that are key for the mechanism of action of multicomponent systems spanning the envelope. However, consideration of all three compartments by experimental approaches is still elusive. Here, we have used the state-of-the-art molecular dynamics simulation in an Escherichia coli envelope model to obtain a dynamic view of molecular interactions between the outer membrane heme transporter HasR and the inner membrane TonB-like protein HasB. Their interaction allows the transfer of the inner membrane proton-motive force derived energy to the transporter for heme internalization. The simulations that incorporate both membranes show the key role of periplasmic domains of both proteins and their dynamics in complex formation and stability. They revealed a previously unidentified network of HasR-HasB protein-protein interactions in the periplasm. Experimental validation (mutations, in vivo phenotypic and biophysical assays) provides support for the simulation-predicted interactions. Based on structural and sequence conservation, the network of interaction revealed in this study is expected to occur in other nutrient import systems.IMPORTANCEGram-negative bacteria import scarce nutrients such as metals and vitamins by an energized mechanism involving a multicomponent protein system that spans the cell envelope. It consists of an outer membrane TonB-dependent transporter (TBDT) and a TonB complex in the inner membrane that provides the proton motive force energy for the nutrient entry. Despite the intense research efforts focused on this system (a) from structural and fundamental microbiology perspectives and (b) for the interest in the development of new antibacterial strategies, the molecular mechanism of the system is not at all well understood. The lack of understanding comes from incomplete structural data and the experimental difficulties of studying an inherently flexible multicomponent complex that resides within the heterogeneous environment of the double membrane bacterial cell envelope. To address these challenges and obtain a comprehensive view of the molecular interactions at atomic level, here, we have used the combined power of advanced molecular simulations and complementary microbiology and biochemical experiments. Our results represent a significant step forward in understanding the structural and molecular bases of this vital mechanism.https://journals.asm.org/doi/10.1128/mbio.01781-24bacterial membraneenergy transductionton systemheme transport |
| spellingShingle | Kamolrat Somboon Oliver Melling Maylis Lejeune Glaucia M. S. Pinheiro Annick Paquelin Benjamin Bardiaux Michael Nilges Phillippe Delepelaire Syma Khalid Nadia Izadi-Pruneyre Dynamic interplay between a TonB-dependent heme transporter and a TonB protein in a membrane environment mBio bacterial membrane energy transduction ton system heme transport |
| title | Dynamic interplay between a TonB-dependent heme transporter and a TonB protein in a membrane environment |
| title_full | Dynamic interplay between a TonB-dependent heme transporter and a TonB protein in a membrane environment |
| title_fullStr | Dynamic interplay between a TonB-dependent heme transporter and a TonB protein in a membrane environment |
| title_full_unstemmed | Dynamic interplay between a TonB-dependent heme transporter and a TonB protein in a membrane environment |
| title_short | Dynamic interplay between a TonB-dependent heme transporter and a TonB protein in a membrane environment |
| title_sort | dynamic interplay between a tonb dependent heme transporter and a tonb protein in a membrane environment |
| topic | bacterial membrane energy transduction ton system heme transport |
| url | https://journals.asm.org/doi/10.1128/mbio.01781-24 |
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