1
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Halogenation of tyrosine perturbs large-scale protein self-organization. Nat Commun 2022; 13:4843. [PMID: 35977922 PMCID: PMC9385671 DOI: 10.1038/s41467-022-32535-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 08/04/2022] [Indexed: 11/08/2022] Open
Abstract
Protein halogenation is a common non-enzymatic post-translational modification contributing to aging, oxidative stress-related diseases and cancer. Here, we report a genetically encodable halogenation of tyrosine residues in a reconstituted prokaryotic filamentous cell-division protein (FtsZ) as a platform to elucidate the implications of halogenation that can be extrapolated to living systems of much higher complexity. We show how single halogenations can fine-tune protein structures and dynamics of FtsZ with subtle perturbations collectively amplified by the process of FtsZ self-organization. Based on experiments and theories, we have gained valuable insights into the mechanism of halogen influence. The bending of FtsZ structures occurs by affecting surface charges and internal domain distances and is reflected in the decline of GTPase activities by reducing GTP binding energy during polymerization. Our results point to a better understanding of the physiological and pathological effects of protein halogenation and may contribute to the development of potential diagnostic tools.
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2
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Vélez M. How Does the Spatial Confinement of FtsZ to a Membrane Surface Affect Its Polymerization Properties and Function? Front Microbiol 2022; 13:757711. [PMID: 35592002 PMCID: PMC9111741 DOI: 10.3389/fmicb.2022.757711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 01/27/2022] [Indexed: 11/15/2022] Open
Abstract
FtsZ is the cytoskeletal protein that organizes the formation of the septal ring and orchestrates bacterial cell division. Its association to the membrane is essential for its function. In this mini-review I will address the question of how this association can interfere with the structure and dynamic properties of the filaments and argue that its dynamics could also remodel the underlying lipid membrane through its activity. Thus, lipid rearrangement might need to be considered when trying to understand FtsZ’s function. This new element could help understand how FtsZ assembly coordinates positioning and recruitment of the proteins forming the septal ring inside the cell with the activity of the machinery involved in peptidoglycan synthesis located in the periplasmic space.
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Affiliation(s)
- Marisela Vélez
- Instituto de Catálisis y Petroleoquímica, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
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3
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Lv D, Li J, Ye S. The Assembly Switch Mechanism of FtsZ Filament Revealed by All-Atom Molecular Dynamics Simulations and Coarse-Grained Models. Front Microbiol 2021; 12:639883. [PMID: 33859629 PMCID: PMC8042166 DOI: 10.3389/fmicb.2021.639883] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 03/05/2021] [Indexed: 01/14/2023] Open
Abstract
Bacterial cytoskeletal protein FtsZ binds and hydrolyzes GTP, and assembles into dynamic filaments that are essential for cell division. Here, we used a multi-scale computational strategy that combined all-atom molecular dynamics (MD) simulations and coarse-grained models to reveal the conformational dynamics of assembled FtsZ. We found that the top end of a filament is highly dynamic and can undergo T-to-R transitions in both GTP- and GDP-bound states. We observed several subcategories of nucleation related dimer species, which leading to a feasible nucleation pathway. In addition, we observed that FtsZ filament exhibits noticeable amounts of twisting, indicating a substantial helicity of the FtsZ filament. These results agree with the previously models and experimental data. Anisotropy network model (ANM) analysis revealed a polymerization enhanced assembly cooperativity, and indicated that the cooperative motions in FtsZ are encoded in the structure. Taken together, our study provides a molecular-level understanding of the diversity of the structural states of FtsZ and the relationships among polymerization, hydrolysis, and cooperative assembly, which should shed new light on the molecular basis of FtsZ’s cooperativity.
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Affiliation(s)
- Dashuai Lv
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Jingyuan Li
- Zhejiang Province Key Laboratory of Quantum Technology and Device, Department of Physics, Institute of Quantitative Biology, Hangzhou, China
| | - Sheng Ye
- Life Sciences Institute, Zhejiang University, Hangzhou, China.,Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin, China
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4
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Battaje RR, Bhondwe P, Dhaked HPS, Panda D. Evidence of conformational switch in Streptococcus pneumoniae FtsZ during polymerization. Protein Sci 2020; 30:523-530. [PMID: 33341988 DOI: 10.1002/pro.4015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/18/2020] [Accepted: 12/18/2020] [Indexed: 12/11/2022]
Abstract
FtsZ, the master coordinator of bacterial cell division, assembles into filaments in the presence of nucleotide. FtsZ from Streptococcus pneumoniae bears two tryptophan residues (W294 and W378) in its amino acid sequence. The tryptophan fluorescence of FtsZ increases during the assembly of FtsZ. We hypothesized that this increase in the fluorescence intensity was due to the change in the environment of one or both tryptophan residues. To examine this, we constructed two mutants (W294F and W378F) of FtsZ by individually replacing tryptophan with phenylalanine. The mutants displayed similar secondary structures, GTPase activity, and polymerization ability as the wild type FtsZ. During the polymerization, only one tryptophan (W294) showed an increase in its fluorescence intensity. Using time-correlated single-photon counting, the fluorescence lifetime of W294 was found to be significantly higher than W378, indicating that W294 was more buried in the structure than W378. The lifetime of W294 further increased during polymer formation, while that of W378 remained unchanged. Fluorescence quenching experiment suggested that the solvent exposure of W294 reduced during the polymerization of FtsZ. W294 is located near the T-7 loop of the protein, a region important for the monomer-monomer interaction during the formation of a protofilament. The results indicated that the region around W294 of S. pneumoniae FtsZ undergoes a conformational switch during polymerization as seen for FtsZ from other bacteria.
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Affiliation(s)
- Rachana Rao Battaje
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Prajakta Bhondwe
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | | | - Dulal Panda
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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5
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Han H, Wang Z, Li T, Teng D, Mao R, Hao Y, Yang N, Wang X, Wang J. Recent progress of bacterial FtsZ inhibitors with a focus on peptides. FEBS J 2020; 288:1091-1106. [PMID: 32681661 DOI: 10.1111/febs.15489] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 06/27/2020] [Accepted: 07/08/2020] [Indexed: 12/23/2022]
Abstract
In recent years, the rise of antibiotic resistance has become a primary health problem. With the emergence of bacterial resistance, the need to explore and develop novel antibacterial drugs has become increasingly urgent. Filamentous temperature-sensitive mutant Z (FtsZ), a crucial cell division protein of bacteria, has become a vital antibacterial target. FtsZ is a filamentous GTPase; it is highly conserved in bacteria and shares less than 20% sequence identity with the eukaryotic cytoskeleton protein tubulin, indicating that FtsZ-targeting antibacterial agents may have a low cytotoxicity toward eukaryotes. FtsZ can form a dynamic Z-ring in the center of the cell resulting in cell division. Furthermore, disturbance in the assembly of FtsZ may affect cellular dynamics and bacterial cell survival, making it a fascinating target for drug development. This review focuses on the recent discovery of FtsZ inhibitors, including peptides, natural products, and other synthetic small molecules, as well as their mechanism of action, which could facilitate the discovery of novel FtsZ-targeting clinical drugs in the future.
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Affiliation(s)
- Huihui Han
- Gene Engineering Laboratory, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Zhenlong Wang
- Gene Engineering Laboratory, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Ting Li
- Gene Engineering Laboratory, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Da Teng
- Gene Engineering Laboratory, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Ruoyu Mao
- Gene Engineering Laboratory, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Ya Hao
- Gene Engineering Laboratory, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Na Yang
- Gene Engineering Laboratory, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Xiumin Wang
- Gene Engineering Laboratory, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Jianhua Wang
- Gene Engineering Laboratory, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing, China
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6
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Surface Orientation and Binding Strength Modulate Shape of FtsZ on Lipid Surfaces. Int J Mol Sci 2019; 20:ijms20102545. [PMID: 31137602 PMCID: PMC6566678 DOI: 10.3390/ijms20102545] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/15/2019] [Accepted: 05/23/2019] [Indexed: 01/16/2023] Open
Abstract
We have used a simple model system to test the prediction that surface attachment strength of filaments presenting a torsion would affect their shape and properties. FtsZ from E. coli containing one cysteine in position 2 was covalently attached to a lipid bilayer containing maleimide lipids either in their head group (to simulate tight attachment) or at the end of a polyethylene glycol molecule attached to the head group (to simulate loose binding). We found that filaments tightly attached grew straight, growing from both ends, until they formed a two-dimensional lattice. Further monomer additions to their sides generated a dense layer of oriented filaments that fully covered the lipid membrane. After this point the surface became unstable and the bilayer detached from the surface. Filaments with a loose binding were initially curved and later evolved into straight thicker bundles that destabilized the membrane after reaching a certain surface density. Previously described theoretical models of FtsZ filament assembly on surfaces that include lateral interactions, spontaneous curvature, torsion, anchoring to the membrane, relative geometry of the surface and the filament ‘living-polymer’ condition in the presence of guanosine triphosphate (GTP) can offer some clues about the driving forces inducing these filament rearrangements.
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7
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Mateos-Gil P, Tarazona P, Vélez M. Bacterial cell division: modeling FtsZ assembly and force generation from single filament experimental data. FEMS Microbiol Rev 2019; 43:73-87. [PMID: 30376053 DOI: 10.1093/femsre/fuy039] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 10/26/2018] [Indexed: 12/24/2022] Open
Abstract
The bacterial cytoskeletal protein FtsZ binds and hydrolyzes GTP, self-aggregates into dynamic filaments and guides the assembly of the septal ring on the inner side of the membrane at midcell. This ring constricts the cell during division and is present in most bacteria. Despite exhaustive studies undertaken in the last 25 years after its discovery, we do not yet know the mechanism by which this GTP-dependent self-aggregating protein exerts force on the underlying membrane. This paper reviews recent experiments and theoretical models proposed to explain FtsZ filament dynamic assembly and force generation. It highlights how recent observations of single filaments on reconstituted model systems and computational modeling are contributing to develop new multiscale models that stress the importance of previously overlooked elements as monomer internal flexibility, filament twist and flexible anchoring to the cell membrane. These elements contribute to understand the rich behavior of these GTP consuming dynamic filaments on surfaces. The aim of this review is 2-fold: (1) to summarize recent multiscale models and their implications to understand the molecular mechanism of FtsZ assembly and force generation and (2) to update theoreticians with recent experimental results.
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Affiliation(s)
- Pablo Mateos-Gil
- Institute of Molecular Biology and Biotechnology, FO.R.T.H, Vassilika Vouton, 70013 Heraklion, Greece
| | - Pedro Tarazona
- Condensed Matter Physics Center (IFIMAC) and Instituto de Ciencia de Materiales Nicolás Cabrera, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Marisela Vélez
- Instituto de Catálisis y Petroleoquímica CSIC, c/ Marie Curie 2, Cantoblanco, 28049 Madrid, Spain
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8
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Hakeem S, Singh I, Sharma P, Uppal A, Khajuria Y, Verma V, Uversky VN, Chandra R. Molecular dynamics analysis of the effects of GTP, GDP and benzimidazole derivative on structural dynamics of a cell division protein FtsZ from Mycobacterium tuberculosis. J Biomol Struct Dyn 2019; 37:4361-4373. [PMID: 30466358 DOI: 10.1080/07391102.2018.1548979] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The prevailing multi-drug resistance in Mycobacterium tuberculosis continues to remain one of the main challenges to combat tuberculosis. Hence, it becomes imperative to focus on novel drug targets. Filamenting temperature-sensitive mutant Z (FtsZ) is an essential cell division protein, a eukaryotic tubulin homologue and a promising drug target. During cytokinesis, FtsZ polymerises in the presence of GTP to form Z-ring and recruits other proteins at this site that eventually lead to the formation of daughter cells. Benzimidazoles were experimentally shown to inhibit Mtb-FtsZ, with one of the benzimidazole derivatives, M1, being reported to have the minimum inhibitory concentration (MIC) value of 3.13 µg/mL. In the present study, mechanism of destabilisation of FtsZ in the presence of M1 was computationally investigated in the presence of its substrate GTP/GDP employing molecular dynamics (MD) simulation analysis, principal component analysis (PCA), molecular mechanics combined with the generalised Born and surface area continuum salvation (MM-GBSA) and density functional theory (DFT). From the analyses, it is proposed that binding of M1 in the inter-domain cleft induces structural changes in the GTP-binding region that affect GTP binding, thus switching the preference of this protein towards depolymerised state and eventually inhibiting the cell division. Hence, this study provides mechanistic insights into the design of novel benzimidazole inhibitors against Mtb-FtsZ. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Supriya Hakeem
- School of Biotechnology, Shri Mata Vaishno Devi University (SMVDU) , Katra , India.,Bioinformatics Infrastructure Facility, School of Biotechnology, Shri Mata Vaishno Devi University (SMVDU) , Katra , India
| | - Inderpal Singh
- School of Biotechnology, Shri Mata Vaishno Devi University (SMVDU) , Katra , India.,Bioinformatics Infrastructure Facility, School of Biotechnology, Shri Mata Vaishno Devi University (SMVDU) , Katra , India
| | - Preeti Sharma
- School of Biotechnology, Shri Mata Vaishno Devi University (SMVDU) , Katra , India
| | - Anshul Uppal
- School of Physics, Shri Mata Vaishno Devi University (SMVDU) , Katra , India
| | - Yugal Khajuria
- School of Physics, Shri Mata Vaishno Devi University (SMVDU) , Katra , India
| | - Vijeshwar Verma
- School of Biotechnology, Shri Mata Vaishno Devi University (SMVDU) , Katra , India.,Bioinformatics Infrastructure Facility, School of Biotechnology, Shri Mata Vaishno Devi University (SMVDU) , Katra , India
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida , Tampa , FL , USA.,Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences , Pushchino , Russia
| | - Ratna Chandra
- School of Biotechnology, Shri Mata Vaishno Devi University (SMVDU) , Katra , India
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9
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Kusuma KD, Griffith R, Harry EJ, Bottomley AL, Ung AT. In silico Analysis of FtsZ Crystal Structures Towards a New Target for Antibiotics. Aust J Chem 2019. [DOI: 10.1071/ch18347] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The bacterial cell division protein FtsZ is conserved in most bacteria and essential for viability. There have been concerted efforts in developing inhibitors that target FtsZ as potential antibiotics. Key to this is an in-depth understanding of FtsZ structure at the molecular level across diverse bacterial species to ensure inhibitors have high affinity for the FtsZ target in a variety of clinically relevant pathogens. In this study, we show that FtsZ structures differ in three ways: (1) the H7 helix curvature; (2) the dimensions of the interdomain cleft; and (3) the opening/closing mechanism of the interdomain cleft, whereas no differences were observed in the dimensions of the nucleotide-binding pocket and T7 loop. Molecular dynamics simulation may suggest that there are two possible mechanisms for the process of opening and closing of the interdomain cleft on FtsZ structures. This discovery highlights significant differences between FtsZ structures at the molecular level and this knowledge is vital in assisting the design of potent FtsZ inhibitors.
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10
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Concha-Marambio L, Maldonado P, Lagos R, Monasterio O, Montecinos-Franjola F. Thermal adaptation of mesophilic and thermophilic FtsZ assembly by modulation of the critical concentration. PLoS One 2017; 12:e0185707. [PMID: 28982174 PMCID: PMC5628889 DOI: 10.1371/journal.pone.0185707] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Accepted: 09/18/2017] [Indexed: 01/16/2023] Open
Abstract
Cytokinesis is the last stage in the cell cycle. In prokaryotes, the protein FtsZ guides cell constriction by assembling into a contractile ring-shaped structure termed the Z-ring. Constriction of the Z-ring is driven by the GTPase activity of FtsZ that overcomes the energetic barrier between two protein conformations having different propensities to assemble into polymers. FtsZ is found in psychrophilic, mesophilic and thermophilic organisms thereby functioning at temperatures ranging from subzero to >100°C. To gain insight into the functional adaptations enabling assembly of FtsZ in distinct environmental conditions, we analyzed the energetics of FtsZ function from mesophilic Escherichia coli in comparison with FtsZ from thermophilic Methanocaldococcus jannaschii. Presumably, the assembly may be similarly modulated by temperature for both FtsZ orthologs. The temperature dependence of the first-order rates of nucleotide hydrolysis and of polymer disassembly, indicated an entropy-driven destabilization of the FtsZ-GTP intermediate. This destabilization was true for both mesophilic and thermophilic FtsZ, reflecting a conserved mechanism of disassembly. From the temperature dependence of the critical concentrations for polymerization, we detected a change of opposite sign in the heat capacity, that was partially explained by the specific changes in the solvent-accessible surface area between the free and polymerized states of FtsZ. At the physiological temperature, the assembly of both FtsZ orthologs was found to be driven by a small positive entropy. In contrast, the assembly occurred with a negative enthalpy for mesophilic FtsZ and with a positive enthalpy for thermophilic FtsZ. Notably, the assembly of both FtsZ orthologs is characterized by a critical concentration of similar value (1–2 μM) at the environmental temperatures of their host organisms. These findings suggest a simple but robust mechanism of adaptation of FtsZ, previously shown for eukaryotic tubulin, by adjustment of the critical concentration for polymerization.
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Affiliation(s)
- Luis Concha-Marambio
- Laboratorio de Biologia Estructural y Molecular/Departamento de Biologia/Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Paula Maldonado
- Laboratorio de Biologia Estructural y Molecular/Departamento de Biologia/Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Rosalba Lagos
- Laboratorio de Biologia Estructural y Molecular/Departamento de Biologia/Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Octavio Monasterio
- Laboratorio de Biologia Estructural y Molecular/Departamento de Biologia/Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- * E-mail: (OM); (FMF)
| | - Felipe Montecinos-Franjola
- Laboratorio de Biologia Estructural y Molecular/Departamento de Biologia/Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- * E-mail: (OM); (FMF)
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11
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Márquez IF, Mateos-Gil P, Shin JY, Lagos R, Monasterio O, Vélez M. Mutations on FtsZ lateral helix H3 that disrupt cell viability hamper reorganization of polymers on lipid surfaces. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017. [PMID: 28642045 DOI: 10.1016/j.bbamem.2017.06.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
FtsZ filaments localize at the middle of the bacterial cell and participate in the formation of a contractile ring responsible for cell division. Previous studies demonstrated that the highly conserved negative charge of glutamate 83 and the positive charge of arginine 85 located in the lateral helix H3 bend of Escherichia coli FtsZ are required for in vivo cell division. In order to understand how these lateral mutations impair the formation of a contractile ring,we extend previous in vitro characterization of these mutants in solution to study their behavior on lipid modified surfaces. We study their interaction with ZipAand look at their reorganization on the surface. We found that the dynamic bundling capacity of the mutant proteins is deficient, and this impairment increases the more the composition and spatial arrangement of the reconstituted system resembles the situation inside the cell: mutant proteins completely fail to reorganize to form higher order aggregates when bound to an E.coli lipid surface through oriented ZipA.We conclude that these surface lateral point mutations affect the dynamic reorganization of FtsZ filaments into bundles on the cell membrane, suggesting that this event is relevant for generating force and completing bacterial division.
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Affiliation(s)
- Ileana F Márquez
- Instituto de Catálisis y Petroleoquímica, c/Marie Curie 2, Cantoblanco, Madrid 28049, Spain
| | - Pablo Mateos-Gil
- Instituto de Catálisis y Petroleoquímica, c/Marie Curie 2, Cantoblanco, Madrid 28049, Spain
| | - Jae Yen Shin
- Departamento de Biología, Facultad de Ciencias, Casilla 653, Santiago 1, Chile
| | - Rosalba Lagos
- Departamento de Biología, Facultad de Ciencias, Casilla 653, Santiago 1, Chile
| | - Octavio Monasterio
- Departamento de Biología, Facultad de Ciencias, Casilla 653, Santiago 1, Chile
| | - Marisela Vélez
- Instituto de Catálisis y Petroleoquímica, c/Marie Curie 2, Cantoblanco, Madrid 28049, Spain.
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12
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Wagstaff JM, Tsim M, Oliva MA, García-Sanchez A, Kureisaite-Ciziene D, Andreu JM, Löwe J. A Polymerization-Associated Structural Switch in FtsZ That Enables Treadmilling of Model Filaments. mBio 2017; 8:e00254-17. [PMID: 28465423 PMCID: PMC5414002 DOI: 10.1128/mbio.00254-17] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 04/13/2017] [Indexed: 02/07/2023] Open
Abstract
Bacterial cell division in many organisms involves a constricting cytokinetic ring that is orchestrated by the tubulin-like protein FtsZ. FtsZ forms dynamic filaments close to the membrane at the site of division that have recently been shown to treadmill around the division ring, guiding septal wall synthesis. Here, using X-ray crystallography of Staphylococcus aureus FtsZ (SaFtsZ), we reveal how an FtsZ can adopt two functionally distinct conformations, open and closed. The open form is found in SaFtsZ filaments formed in crystals and also in soluble filaments of Escherichia coli FtsZ as deduced by electron cryomicroscopy. The closed form is found within several crystal forms of two nonpolymerizing SaFtsZ mutants and corresponds to many previous FtsZ structures from other organisms. We argue that FtsZ's conformational switch is polymerization-associated, driven by the formation of the longitudinal intersubunit interfaces along the filament. We show that such a switch provides explanations for both how treadmilling may occur within a single-stranded filament and why filament assembly is cooperative.IMPORTANCE The FtsZ protein is a key molecule during bacterial cell division. FtsZ forms filaments that organize cell membrane constriction, as well as remodeling of the cell wall, to divide cells. FtsZ functions through nucleotide-driven filament dynamics that are poorly understood at the molecular level. In particular, mechanisms for cooperative assembly (nonlinear dependency on concentration) and treadmilling (preferential growth at one filament end and loss at the other) have remained elusive. Here, we show that most likely all FtsZ proteins have two distinct conformations, a "closed" form in monomeric FtsZ and an "open" form in filaments. The conformational switch that occurs upon polymerization explains cooperativity and, in concert with polymerization-dependent nucleotide hydrolysis, efficient treadmilling of FtsZ polymers.
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Affiliation(s)
| | - Matthew Tsim
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - María A Oliva
- Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
| | | | | | | | - Jan Löwe
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
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13
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Fujita J, Harada R, Maeda Y, Saito Y, Mizohata E, Inoue T, Shigeta Y, Matsumura H. Identification of the key interactions in structural transition pathway of FtsZ from Staphylococcus aureus. J Struct Biol 2017; 198:65-73. [PMID: 28456664 DOI: 10.1016/j.jsb.2017.04.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 04/18/2017] [Accepted: 04/25/2017] [Indexed: 10/19/2022]
Abstract
The tubulin-homolog protein FtsZ is essential for bacterial cell division. FtsZ polymerizes to form protofilaments that assemble into a contractile ring-shaped structure in the presence of GTP. Recent studies showed that FtsZ treadmilling coupled with the GTPase activity drives cell wall synthesis and bacterial cell division. The treadmilling caused by assembly and disassembly of FtsZ links to a conformational change of the monomer from a tense (T) to a relaxed (R) state, but considerable controversy still remains concerning the mechanism. In this study, we report crystal structures of FtsZ from Staphylococcus aureus corresponding to the T and R state conformations in the same crystal, indicating the structural equilibrium of the two state. The two structures identified a key residue Arg29, whose importance was also confirmed by our modified MD simulations. Crystal structures of the R29A mutant showed T and R state-like conformations with slight but important structural changes compared to those of wild-type. Collectively, these data provide new insights for understanding how intramolecular interactions are related to the structural transition of FtsZ.
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Affiliation(s)
- Junso Fujita
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Ryuhei Harada
- Graduate School of Pure and Applied Sciences/Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan.
| | - Yoko Maeda
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yuki Saito
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Eiichi Mizohata
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tsuyoshi Inoue
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yasuteru Shigeta
- Graduate School of Pure and Applied Sciences/Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
| | - Hiroyoshi Matsumura
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577, Japan.
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14
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Artola M, Ruíz-Avila LB, Ramírez-Aportela E, Martínez RF, Araujo-Bazán L, Vázquez-Villa H, Martín-Fontecha M, Oliva MA, Martín-Galiano AJ, Chacón P, López-Rodríguez ML, Andreu JM, Huecas S. The structural assembly switch of cell division protein FtsZ probed with fluorescent allosteric inhibitors. Chem Sci 2017; 8:1525-1534. [PMID: 28616148 PMCID: PMC5460597 DOI: 10.1039/c6sc03792e] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 10/19/2016] [Indexed: 11/21/2022] Open
Abstract
FtsZ is a widely conserved tubulin-like GTPase that directs bacterial cell division and a new target for antibiotic discovery. This protein assembly machine cooperatively polymerizes forming single-stranded filaments, by means of self-switching between inactive and actively associating monomer conformations. The structural switch mechanism was proposed to involve a movement of the C-terminal and N-terminal FtsZ domains, opening a cleft between them, allosterically coupled to the formation of a tight association interface between consecutive subunits along the filament. The effective antibacterial benzamide PC190723 binds into the open interdomain cleft and stabilizes FtsZ filaments, thus impairing correct formation of the FtsZ ring for cell division. We have designed fluorescent analogs of PC190723 to probe the FtsZ structural assembly switch. Among them, nitrobenzoxadiazole probes specifically bind to assembled FtsZ rather than to monomers. Probes with several spacer lengths between the fluorophore and benzamide moieties suggest a binding site extension along the interdomain cleft. These probes label FtsZ rings of live Bacillus subtilis and Staphylococcus aureus, without apparently modifying normal cell morphology and growth, but at high concentrations they induce impaired bacterial division phenotypes typical of benzamide antibacterials. During the FtsZ assembly-disassembly process, the fluorescence anisotropy of the probes changes upon binding and dissociating from FtsZ, thus reporting open and closed FtsZ interdomain clefts. Our results demonstrate the structural mechanism of the FtsZ assembly switch, and suggest that the probes bind into the open clefts in cellular FtsZ polymers preferably to unassembled FtsZ in the bacterial cytosol.
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Affiliation(s)
- Marta Artola
- Dept. Química Orgánica I , Facultad de Ciencias Químicas , UCM , 28040 Madrid , Spain
| | - Laura B Ruíz-Avila
- Centro de Investigaciones Biológicas , CSIC , Ramiro de Maeztu 9 , 28040 Madrid , Spain . ;
| | - Erney Ramírez-Aportela
- Centro de Investigaciones Biológicas , CSIC , Ramiro de Maeztu 9 , 28040 Madrid , Spain . ;
- Instituto de Química-Física Rocasolano , CSIC , Serrano 119 , 20006 Madrid , Spain
| | - R Fernando Martínez
- Dept. Química Orgánica I , Facultad de Ciencias Químicas , UCM , 28040 Madrid , Spain
| | - Lidia Araujo-Bazán
- Centro de Investigaciones Biológicas , CSIC , Ramiro de Maeztu 9 , 28040 Madrid , Spain . ;
| | - Henar Vázquez-Villa
- Dept. Química Orgánica I , Facultad de Ciencias Químicas , UCM , 28040 Madrid , Spain
| | - Mar Martín-Fontecha
- Dept. Química Orgánica I , Facultad de Ciencias Químicas , UCM , 28040 Madrid , Spain
| | - María A Oliva
- Centro de Investigaciones Biológicas , CSIC , Ramiro de Maeztu 9 , 28040 Madrid , Spain . ;
| | | | - Pablo Chacón
- Instituto de Química-Física Rocasolano , CSIC , Serrano 119 , 20006 Madrid , Spain
| | | | - José M Andreu
- Centro de Investigaciones Biológicas , CSIC , Ramiro de Maeztu 9 , 28040 Madrid , Spain . ;
| | - Sonia Huecas
- Centro de Investigaciones Biológicas , CSIC , Ramiro de Maeztu 9 , 28040 Madrid , Spain . ;
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15
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Mathew B, Hobrath JV, Ross L, Connelly MC, Lofton H, Rajagopalan M, Guy RK, Reynolds RC. Screening and Development of New Inhibitors of FtsZ from M. Tuberculosis. PLoS One 2016; 11:e0164100. [PMID: 27768711 PMCID: PMC5074515 DOI: 10.1371/journal.pone.0164100] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 09/20/2016] [Indexed: 12/14/2022] Open
Abstract
A variety of commercial analogs and a newer series of Sulindac derivatives were screened for inhibition of M. tuberculosis (Mtb) in vitro and specifically as inhibitors of the essential mycobacterial tubulin homolog, FtsZ. Due to the ease of preparing diverse analogs and a favorable in vivo pharmacokinetic and toxicity profile of a representative analog, the Sulindac scaffold may be useful for further development against Mtb with respect to in vitro bacterial growth inhibition and selective activity for Mtb FtsZ versus mammalian tubulin. Further discovery efforts will require separating reported mammalian cell activity from both antibacterial activity and inhibition of Mtb FtsZ. Modeling studies suggest that these analogs bind in a specific region of the Mtb FtsZ polymer that differs from human tubulin and, in combination with a pharmacophore model presented herein, future hybrid analogs of the reported active molecules that more efficiently bind in this pocket may improve antibacterial activity while improving other drug characteristics.
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Affiliation(s)
- Bini Mathew
- Drug Discovery Division, Southern Research Institute, 2000 Ninth Avenue South, Birmingham, Alabama, 35205, United States of America
| | - Judith Varady Hobrath
- Drug Discovery Unit, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, United Kingdom
| | - Larry Ross
- Drug Discovery Division, Southern Research Institute, 2000 Ninth Avenue South, Birmingham, Alabama, 35205, United States of America
| | - Michele C. Connelly
- Dept. Chemical Biology & Therapeutics, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, United States of America
| | - Hava Lofton
- The University of Texas Health Science Center at Tyler, Tyler, Texas, 75708, United States of America
| | - Malini Rajagopalan
- The University of Texas Health Science Center at Tyler, Tyler, Texas, 75708, United States of America
| | - R. Kiplin Guy
- Dept. Chemical Biology & Therapeutics, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, United States of America
| | - Robert C. Reynolds
- Department of Chemistry, The University of Alabama at Birmingham, Birmingham, Alabama, 35294, United States of America
- Division of Hematology and Oncology, The University of Alabama at Birmingham, Birmingham, Alabama, 35294, United States of America
- * E-mail:
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16
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Dhaked HPS, Bhattacharya A, Yadav S, Dantu SC, Kumar A, Panda D. Mutation of Arg191 in FtsZ Impairs Cytokinetic Abscission of Bacillus subtilis Cells. Biochemistry 2016; 55:5754-5763. [DOI: 10.1021/acs.biochem.6b00493] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hemendra Pal Singh Dhaked
- Department
of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Anusri Bhattacharya
- Department
of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Saroj Yadav
- IITB-Monash
Research Academy, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Sarath Chandra Dantu
- Department
of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Ashutosh Kumar
- Department
of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Dulal Panda
- Department
of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
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17
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González de Prado Salas P, Tarazona P. Collective effects of torsion in FtsZ filaments. Phys Rev E 2016; 93:042407. [PMID: 27176329 DOI: 10.1103/physreve.93.042407] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Indexed: 11/07/2022]
Abstract
Recent evidence points to the presence of torsion in FtsZ bonds. In addition, experiments with FtsZ mutants on surfaces resulted in new aggregates that cannot be explained by older models for FtsZ dynamics. We use an interaction model for FtsZ derived from molecular dynamics simulations and expand a fine-grained lattice model used to describe FtsZ aggregates on a surface. This new model includes different anchoring angles for the monomers and allows bond twist, two ingredients that oppose each other resulting in a more dynamic and interesting system. We study the role and importance of these conflicting elements and how the aggregates are characterized by the different interaction parameters.
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Affiliation(s)
| | - Pedro Tarazona
- Departamento de Física Teórica de la Materia Condensada, Condensed Matter Physics Institute (IFIMAC) and Instituto de Ciencia de Materiales Nicolás Cabrera, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
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18
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Adams DW, Wu LJ, Errington J. A benzamide-dependent ftsZ mutant reveals residues crucial for Z-ring assembly. Mol Microbiol 2015; 99:1028-42. [PMID: 26601800 PMCID: PMC4832351 DOI: 10.1111/mmi.13286] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/2015] [Indexed: 12/14/2022]
Abstract
In almost all bacteria, cell division is co-ordinated by the essential tubulin homologue FtsZ and represents an attractive but as yet unexploited target for new antibiotics. The benzamides, e.g. PC190723, are potent FtsZ inhibitors that have the potential to yield an important new class of antibiotic. However, the evolution of resistance poses a challenge to their development. Here we show that a collection of PC190723-resistant and -dependent strains of Staphylococcus aureus exhibit severe growth and morphological defects, questioning whether these ftsZ mutations would be clinically relevant. Importantly, we show that the most commonly isolated substitution remains sensitive to the simplest benzamide 3-MBA and likely works by occluding compound binding. Extending this analysis to Bacillus subtilis, we isolated a novel benzamide-dependent strain that divides using unusual helical division events. The ftsZ mutation responsible encodes the substitution of a highly conserved residue, which lies outside the benzamide-binding site and forms part of an interface between the N- and C-terminal domains that we show is necessary for normal FtsZ function. Together with an intragenic suppressor mutation that mimics benzamide binding, the results provide genetic evidence that benzamides restrict conformational changes in FtsZ and also highlights their utility as tools to probe bacterial division.
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Affiliation(s)
- David William Adams
- Centre for Bacterial Cell Biology, Baddiley-Clark Building, Medical School, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
| | - Ling Juan Wu
- Centre for Bacterial Cell Biology, Baddiley-Clark Building, Medical School, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
| | - Jeff Errington
- Centre for Bacterial Cell Biology, Baddiley-Clark Building, Medical School, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
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19
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Huecas S, Marcelo F, Perona A, Ruiz-Ávila LB, Morreale A, Cañada FJ, Jiménez-Barbero J, Andreu JM. Beyond a Fluorescent Probe: Inhibition of Cell Division Protein FtsZ by mant-GTP Elucidated by NMR and Biochemical Approaches. ACS Chem Biol 2015; 10:2382-92. [PMID: 26247422 DOI: 10.1021/acschembio.5b00444] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
FtsZ is the organizer of cell division in most bacteria and a target in the quest for new antibiotics. FtsZ is a tubulin-like GTPase, in which the active site is completed at the interface with the next subunit in an assembled FtsZ filament. Fluorescent mant-GTP has been extensively used for competitive binding studies of nucleotide analogs and synthetic GTP-replacing inhibitors possessing antibacterial activity. However, its mode of binding and whether the mant tag interferes with FtsZ assembly function were unknown. Mant-GTP exists in equilibrium as a mixture of C2'- and C3'-substituted isomers. We have unraveled the molecular recognition process of mant-GTP by FtsZ monomers. Both isomers bind in the anti glycosidic bond conformation: 2'-mant-GTP in two ribose puckering conformations and 3'-mant-GTP in the preferred C2' endo conformation. In each case, the mant tag strongly interacts with FtsZ at an extension of the GTP binding site, which is also supported by molecular dynamics simulations. Importantly, mant-GTP binding induces archaeal FtsZ polymerization into inactive curved filaments that cannot hydrolyze the nucleotide, rather than straight GTP-hydrolyzing assemblies, and also inhibits normal assembly of FtsZ from the Gram-negative bacterium Escherichia coli but is hydrolyzed by FtsZ from Gram-positive Bacillus subtilis. Thus, the specific interactions provided by the fluorescent mant tag indicate a new way to search for synthetic FtsZ inhibitors that selectively suppress the cell division of bacterial pathogens.
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Affiliation(s)
- Sonia Huecas
- Centro de Investigaciones
Biológicas, CIB-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Filipa Marcelo
- Centro de Investigaciones
Biológicas, CIB-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
- UCIBIO, REQUIMTE, Dept. de Química, Faculdade de Ciências
e Tecnologia, UNL, 2829-516 Caparica, Portugal
| | - Almudena Perona
- Unidad de Bioinformática,
Centro de Biología Molecular Severo Ochoa, CBMSO−CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Laura B. Ruiz-Ávila
- Centro de Investigaciones
Biológicas, CIB-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Antonio Morreale
- Unidad de Bioinformática,
Centro de Biología Molecular Severo Ochoa, CBMSO−CSIC, Cantoblanco, 28049 Madrid, Spain
| | - F. Javier Cañada
- Centro de Investigaciones
Biológicas, CIB-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Jesús Jiménez-Barbero
- Centro de Investigaciones
Biológicas, CIB-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - José M. Andreu
- Centro de Investigaciones
Biológicas, CIB-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
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20
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Ramírez-Aportela E, López-Blanco JR, Andreu JM, Chacón P. Understanding nucleotide-regulated FtsZ filament dynamics and the monomer assembly switch with large-scale atomistic simulations. Biophys J 2015; 107:2164-76. [PMID: 25418101 DOI: 10.1016/j.bpj.2014.09.033] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 09/23/2014] [Accepted: 09/30/2014] [Indexed: 01/08/2023] Open
Abstract
Bacterial cytoskeletal protein FtsZ assembles in a head-to-tail manner, forming dynamic filaments that are essential for cell division. Here, we study their dynamics using unbiased atomistic molecular simulations from representative filament crystal structures. In agreement with experimental data, we find different filament curvatures that are supported by a nucleotide-regulated hinge motion between consecutive FtsZ monomers. Whereas GTP-FtsZ filaments bend and twist in a preferred orientation, thereby burying the nucleotide, the differently curved GDP-FtsZ filaments exhibit a heterogeneous distribution of open and closed interfaces between monomers. We identify a coordinated Mg(2+) ion as the key structural element in closing the nucleotide site and stabilizing GTP filaments, whereas the loss of the contacts with loop T7 from the next monomer in GDP filaments leads to open interfaces that are more prone to depolymerization. We monitored the FtsZ monomer assembly switch, which involves opening/closing of the cleft between the C-terminal domain and the H7 helix, and observed the relaxation of isolated and filament minus-end monomers into the closed-cleft inactive conformation. This result validates the proposed switch between the low-affinity monomeric closed-cleft conformation and the active open-cleft FtsZ conformation within filaments. Finally, we observed how the antibiotic PC190723 suppresses the disassembly switch and allosterically induces closure of the intermonomer interfaces, thus stabilizing the filament. Our studies provide detailed structural and dynamic insights into modulation of both the intrinsic curvature of the FtsZ filaments and the molecular switch coupled to the high-affinity end-wise association of FtsZ monomers.
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Affiliation(s)
- Erney Ramírez-Aportela
- Department of Biological Physical Chemistry, Instituto de Química-Física Rocasolano, CSIC, Madrid, Spain; Department of Chemical and Physical Biology, Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
| | - José Ramón López-Blanco
- Department of Biological Physical Chemistry, Instituto de Química-Física Rocasolano, CSIC, Madrid, Spain
| | - José Manuel Andreu
- Department of Chemical and Physical Biology, Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
| | - Pablo Chacón
- Department of Biological Physical Chemistry, Instituto de Química-Física Rocasolano, CSIC, Madrid, Spain.
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21
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Buske PJ, Mittal A, Pappu RV, Levin PA. An intrinsically disordered linker plays a critical role in bacterial cell division. Semin Cell Dev Biol 2014; 37:3-10. [PMID: 25305578 DOI: 10.1016/j.semcdb.2014.09.017] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 09/13/2014] [Indexed: 02/07/2023]
Abstract
In bacteria, animals, fungi, and many single celled eukaryotes, division is initiated by the formation of a ring of cytoskeletal protein at the nascent division site. In bacteria, the tubulin-like GTPase FtsZ serves as the foundation for the cytokinetic ring. A conserved feature of FtsZ is an intrinsically disordered peptide known as the C-terminal linker. Chimeric experiments suggest the linker acts as a flexible boom allowing FtsZ to associate with the membrane through a conserved C-terminal domain and also modulates interactions both between FtsZ subunits and between FtsZ and modulatory proteins in the cytoplasm.
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Affiliation(s)
- P J Buske
- Department of Cellular and Molecular Pharmacology and The Howard Hughes Medical Institute, University of California, San Francisco, CA, USA
| | - Anuradha Mittal
- Department of Biomedical Engineering & Center for Biological Systems Engineering, Saint Louis, MO 63130, USA
| | - Rohit V Pappu
- Department of Biomedical Engineering & Center for Biological Systems Engineering, Saint Louis, MO 63130, USA
| | - Petra Anne Levin
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA.
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22
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Montecinos-Franjola F, James NG, Concha-Marambio L, Brunet JE, Lagos R, Monasterio O, Jameson DM. Single tryptophan mutants of FtsZ: nucleotide binding/exchange and conformational transitions. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1193-200. [PMID: 24704635 DOI: 10.1016/j.bbapap.2014.03.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 03/24/2014] [Accepted: 03/26/2014] [Indexed: 11/27/2022]
Abstract
Cell division protein FtsZ cooperatively self-assembles into straight filaments when bound to GTP. A set of conformational changes that are linked to FtsZ GTPase activity are involved in the transition from straight to curved filaments that eventually disassemble. In this work, we characterized the fluorescence of single Trp mutants as a reporter of the predicted conformational changes between the GDP- and GTP-states of Escherichia coli FtsZ. Steady-state fluorescence characterization showed the Trp senses different environments and displays low solvent accessibility. Time-resolved fluorescence data indicated that the main conformational changes in FtsZ occur at the interaction surface between the N and C domains, but also minor rearrangements were detected in the bulk of the N domain. Surprisingly, despite its location near the bottom protofilament interface at the C domain, the Trp 275 fluorescence lifetime did not report changes between the GDP and GTP states. The equilibrium unfolding of FtsZ features an intermediate that is stabilized by the nucleotide bound in the N-domain as well as by quaternary protein-protein interactions. In this context, we characterized the unfolding of the Trp mutants using time-resolved fluorescence and phasor plot analysis. A novel picture of the structural transition from the native state in the absence of denaturant, to the solvent-exposed unfolded state is presented. Taken together our results show that conformational changes between the GDP and GTP states of FtsZ, such as those observed in FtsZ unfolding, are restricted to the interaction surface between the N and C domains.
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Affiliation(s)
- Felipe Montecinos-Franjola
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800024, Chile.
| | - Nicholas G James
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu 96813, HI, USA.
| | - Luis Concha-Marambio
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800024, Chile.
| | - Juan E Brunet
- Instituto de Química, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Valparaíso 2373223, Chile.
| | - Rosalba Lagos
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800024, Chile.
| | - Octavio Monasterio
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800024, Chile.
| | - David M Jameson
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu 96813, HI, USA.
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23
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González de Prado Salas P, Hörger I, Martín-García F, Mendieta J, Alonso Á, Encinar M, Gómez-Puertas P, Vélez M, Tarazona P. Torsion and curvature of FtsZ filaments. SOFT MATTER 2014; 10:1977-1986. [PMID: 24652404 DOI: 10.1039/c3sm52516c] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
FtsZ filaments participate in bacterial cell division, but it is still not clear how their dynamic polymerization and shape exert force on the underlying membrane. We present a theoretical description of individual filaments that incorporates information from molecular dynamic simulations. The structure of the crystallized Methanococcus jannaschii FtsZ dimer was used to model a FtsZ pentamer that showed a curvature and a twist. The estimated bending and torsion angles between monomers and their fluctuations were included in the theoretical description. The MD data also permitted positioning the curvature with respect to the protein coordinates and allowed us to explore the effect of the relative orientation of the preferred curvature with respect to the surface plane. We find that maximum tension is attained when filaments are firmly attached and oriented with their curvature perpendicular to the surface and that the twist serves as a valve to release or to tighten the tension exerted by the curved filaments on the membrane. The theoretical model also shows that the presence of torsion can explain the shape distribution of short filaments observed by Atomic Force Microscopy in previously published experiments. New experiments with FtsZ covalently attached to lipid membranes show that the filament on-plane curvature depends on lipid head charge, confirming the predicted monomer orientation effects. This new model underlines the fact that the combination of the three elements, filament curvature, twist and the strength and orientation of its surface attachment, can modulate the force exerted on the membrane during cell division.
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24
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Matsui T, Han X, Yu J, Yao M, Tanaka I. Structural change in FtsZ Induced by intermolecular interactions between bound GTP and the T7 loop. J Biol Chem 2013; 289:3501-9. [PMID: 24347164 DOI: 10.1074/jbc.m113.514901] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
FtsZ is a prokaryotic homolog of tubulin and is a key molecule in bacterial cell division. FtsZ with bound GTP polymerizes into tubulin-like protofilaments. Upon polymerization, the T7 loop of one subunit is inserted into the nucleotide-binding pocket of the second subunit, which results in GTP hydrolysis. Thus, the T7 loop is important for both polymerization and hydrolysis in the tubulin/FtsZ family. Although x-ray crystallography revealed both straight and curved conformations of tubulin, only a curved structure was known for FtsZ. Recently, however, FtsZ from Staphylococcus aureus has been shown to have a very different conformation from the canonical FtsZ structure. The present study was performed to investigate the structure of FtsZ from Staphylococcus aureus by mutagenesis experiments; the effects of amino acid changes in the T7 loop on the structure as well as on GTPase activity were studied. These analyses indicated that FtsZ changes its conformation suitable for polymerization and GTP hydrolysis by movement between N- and C-subdomains via intermolecular interactions between bound nucleotide and residues in the T7 loop.
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Affiliation(s)
- Takashi Matsui
- From the Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan and
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25
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Marcelo F, Huecas S, Ruiz-Ávila LB, Cañada FJ, Perona A, Poveda A, Martín-Santamaría S, Morreale A, Jiménez-Barbero J, Andreu JM. Interactions of bacterial cell division protein FtsZ with C8-substituted guanine nucleotide inhibitors. A combined NMR, biochemical and molecular modeling perspective. J Am Chem Soc 2013; 135:16418-28. [PMID: 24079270 DOI: 10.1021/ja405515r] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
FtsZ is the key protein of bacterial cell-division and target for new antibiotics. Selective inhibition of FtsZ polymerization without impairing the assembly of the eukaryotic homologue tubulin was demonstrated with C8-substituted guanine nucleotides. By combining NMR techniques with biochemical and molecular modeling procedures, we have investigated the molecular recognition of C8-substituted-nucleotides by FtsZ from Methanococcus jannaschii (Mj-FtsZ) and Bacillus subtilis (Bs-FtsZ). STD epitope mapping and trNOESY bioactive conformation analysis of each nucleotide were employed to deduce differences in their recognition mode by each FtsZ species. GMP binds in the same anti conformation as GTP, whereas 8-pyrrolidino-GMP binds in the syn conformation. However, the anti conformation of 8-morpholino-GMP is selected by Bs-FtsZ, while Mj-FtsZ binds both anti- and syn-geometries. The inhibitory potencies of the C8-modified-nucleotides on the assembly of Bs-FtsZ, but not of Mj-FtsZ, correlate with their binding affinities. Thus, MorphGTP behaves as a nonhydrolyzable analog whose binding induces formation of Mj-FtsZ curved filaments, resembling polymers formed by the inactive forms of this protein. NMR data, combined with molecular modeling protocols, permit explanation of the mechanism of FtsZ assembly impairment by C8-substituted GTP analogs. The presence of the C8-substituent induces electrostatic remodeling and small structural displacements at the association interface between FtsZ monomers to form filaments, leading to complete assembly inhibition or to formation of abnormal FtsZ polymers. The inhibition of bacterial Bs-FtsZ assembly may be simply explained by steric clashes of the C8-GTP-analogs with the incoming FtsZ monomer. This information may facilitate the design of antibacterial FtsZ inhibitors replacing GTP.
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Affiliation(s)
- Filipa Marcelo
- Centro de Investigaciones Biológicas, CIB-CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
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26
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Ruiz-Avila LB, Huecas S, Artola M, Vergoñós A, Ramírez-Aportela E, Cercenado E, Barasoain I, Vázquez-Villa H, Martín-Fontecha M, Chacón P, López-Rodrı́guez ML, Andreu JM. Synthetic inhibitors of bacterial cell division targeting the GTP-binding site of FtsZ. ACS Chem Biol 2013; 8:2072-83. [PMID: 23855511 DOI: 10.1021/cb400208z] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cell division protein FtsZ is the organizer of the cytokinetic Z-ring in most bacteria and a target for new antibiotics. FtsZ assembles with GTP into filaments that hydrolyze the nucleotide at the association interface between monomers and then disassemble. We have replaced FtsZ's GTP with non-nucleotide synthetic inhibitors of bacterial division. We searched for these small molecules among compounds from the literature, from virtual screening (VS), and from our in-house synthetic library (UCM), employing a fluorescence anisotropy primary assay. From these screens we have identified the polyhydroxy aromatic compound UCM05 and its simplified analogue UCM44 that specifically bind to Bacillus subtilis FtsZ monomers with micromolar affinities and perturb normal assembly, as examined with light scattering, polymer sedimentation, and negative stain electron microscopy. On the other hand, these ligands induce the cooperative assembly of nucleotide-devoid archaeal FtsZ into distinct well-ordered polymers, different from GTP-induced filaments. These FtsZ inhibitors impair localization of FtsZ into the Z-ring and inhibit bacterial cell division. The chlorinated analogue UCM53 inhibits the growth of clinical isolates of antibiotic-resistant Staphylococcus aureus and Enterococcus faecalis. We suggest that these interfacial inhibitors recapitulate binding and some assembly-inducing effects of GTP but impair the correct structural dynamics of FtsZ filaments and thus inhibit bacterial division, possibly by binding to a small fraction of the FtsZ molecules in a bacterial cell, which opens a new approach to FtsZ-based antibacterial drug discovery.
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Affiliation(s)
- Laura B. Ruiz-Avila
- Centro
de Investigaciones Biológicas, CSIC, Madrid, ‡Dpto. Química Orgánica
I, Facultad de Ciencias Químicas, UCM, Madrid, §Instituto de Química-Física
Rocasolano, CSIC, Madrid, and ∥Servicio de Microbiología, Hospital
General Universitario Gregorio Marañón, Madrid, Spain
| | - Sonia Huecas
- Centro
de Investigaciones Biológicas, CSIC, Madrid, ‡Dpto. Química Orgánica
I, Facultad de Ciencias Químicas, UCM, Madrid, §Instituto de Química-Física
Rocasolano, CSIC, Madrid, and ∥Servicio de Microbiología, Hospital
General Universitario Gregorio Marañón, Madrid, Spain
| | - Marta Artola
- Centro
de Investigaciones Biológicas, CSIC, Madrid, ‡Dpto. Química Orgánica
I, Facultad de Ciencias Químicas, UCM, Madrid, §Instituto de Química-Física
Rocasolano, CSIC, Madrid, and ∥Servicio de Microbiología, Hospital
General Universitario Gregorio Marañón, Madrid, Spain
| | - Albert Vergoñós
- Centro
de Investigaciones Biológicas, CSIC, Madrid, ‡Dpto. Química Orgánica
I, Facultad de Ciencias Químicas, UCM, Madrid, §Instituto de Química-Física
Rocasolano, CSIC, Madrid, and ∥Servicio de Microbiología, Hospital
General Universitario Gregorio Marañón, Madrid, Spain
| | - Erney Ramírez-Aportela
- Centro
de Investigaciones Biológicas, CSIC, Madrid, ‡Dpto. Química Orgánica
I, Facultad de Ciencias Químicas, UCM, Madrid, §Instituto de Química-Física
Rocasolano, CSIC, Madrid, and ∥Servicio de Microbiología, Hospital
General Universitario Gregorio Marañón, Madrid, Spain
| | - Emilia Cercenado
- Centro
de Investigaciones Biológicas, CSIC, Madrid, ‡Dpto. Química Orgánica
I, Facultad de Ciencias Químicas, UCM, Madrid, §Instituto de Química-Física
Rocasolano, CSIC, Madrid, and ∥Servicio de Microbiología, Hospital
General Universitario Gregorio Marañón, Madrid, Spain
| | - Isabel Barasoain
- Centro
de Investigaciones Biológicas, CSIC, Madrid, ‡Dpto. Química Orgánica
I, Facultad de Ciencias Químicas, UCM, Madrid, §Instituto de Química-Física
Rocasolano, CSIC, Madrid, and ∥Servicio de Microbiología, Hospital
General Universitario Gregorio Marañón, Madrid, Spain
| | - Henar Vázquez-Villa
- Centro
de Investigaciones Biológicas, CSIC, Madrid, ‡Dpto. Química Orgánica
I, Facultad de Ciencias Químicas, UCM, Madrid, §Instituto de Química-Física
Rocasolano, CSIC, Madrid, and ∥Servicio de Microbiología, Hospital
General Universitario Gregorio Marañón, Madrid, Spain
| | - Mar Martín-Fontecha
- Centro
de Investigaciones Biológicas, CSIC, Madrid, ‡Dpto. Química Orgánica
I, Facultad de Ciencias Químicas, UCM, Madrid, §Instituto de Química-Física
Rocasolano, CSIC, Madrid, and ∥Servicio de Microbiología, Hospital
General Universitario Gregorio Marañón, Madrid, Spain
| | - Pablo Chacón
- Centro
de Investigaciones Biológicas, CSIC, Madrid, ‡Dpto. Química Orgánica
I, Facultad de Ciencias Químicas, UCM, Madrid, §Instituto de Química-Física
Rocasolano, CSIC, Madrid, and ∥Servicio de Microbiología, Hospital
General Universitario Gregorio Marañón, Madrid, Spain
| | - María L. López-Rodrı́guez
- Centro
de Investigaciones Biológicas, CSIC, Madrid, ‡Dpto. Química Orgánica
I, Facultad de Ciencias Químicas, UCM, Madrid, §Instituto de Química-Física
Rocasolano, CSIC, Madrid, and ∥Servicio de Microbiología, Hospital
General Universitario Gregorio Marañón, Madrid, Spain
| | - José M. Andreu
- Centro
de Investigaciones Biológicas, CSIC, Madrid, ‡Dpto. Química Orgánica
I, Facultad de Ciencias Químicas, UCM, Madrid, §Instituto de Química-Física
Rocasolano, CSIC, Madrid, and ∥Servicio de Microbiología, Hospital
General Universitario Gregorio Marañón, Madrid, Spain
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27
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Bhattacharya A, Jindal B, Singh P, Datta A, Panda D. Plumbagin inhibits cytokinesis inBacillus subtilisby inhibiting FtsZ assembly - a mechanistic study of its antibacterial activity. FEBS J 2013; 280:4585-99. [DOI: 10.1111/febs.12429] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 06/24/2013] [Accepted: 07/04/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Anusri Bhattacharya
- Department of Chemistry; Indian Institute of Technology Bombay; Mumbai India
- Department of Biosciences and Bioengineering; Indian Institute of Technology Bombay; Mumbai India
| | - Bhavya Jindal
- Department of Biosciences and Bioengineering; Indian Institute of Technology Bombay; Mumbai India
| | - Parminder Singh
- Department of Biosciences and Bioengineering; Indian Institute of Technology Bombay; Mumbai India
| | - Anindya Datta
- Department of Chemistry; Indian Institute of Technology Bombay; Mumbai India
| | - Dulal Panda
- Department of Biosciences and Bioengineering; Indian Institute of Technology Bombay; Mumbai India
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28
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Encinar M, Kralicek AV, Martos A, Krupka M, Cid S, Alonso A, Rico AI, Jiménez M, Vélez M. Polymorphism of FtsZ filaments on lipid surfaces: role of monomer orientation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:9436-9446. [PMID: 23837832 DOI: 10.1021/la401673z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
FtsZ is a bacterial cytoskeletal protein involved in cell division. It forms a ringlike structure that attaches to the membrane to complete bacterial division. It binds and hydrolyzes GTP, assembling into polymers in a GTP-dependent manner. To test how the orientation of the monomers affects the curvature of the filaments on a surface, we performed site-directed mutagenesis on the E. coli FtsZ protein to insert cysteine residues at lateral locations to orient FtsZ on planar lipid bilayers. The E93C and S255C mutants were overproduced, purified, and found to be functionally active in solution, as well as being capable of sustaining cell division in vivo in complementation assays. Atomic force microscopy was used to observe the shape of the filament fibers formed on the surface. The FtsZ mutants were covalently linked to the lipids and could be polymerized on the bilayer surface in the presence of GTP. Unexpectedly, both mutants assembled into straight structures. E93C formed a well-defined lattice with monomers interacting at 60° and 120° angles, whereas S255C formed a more open array of straight thicker filament aggregates. These results indicate that filament curvature and bending are not fixed and that they can be modulated by the orientation of the monomers with respect to the membrane surface. As filament curvature has been associated with the force generation mechanism, these results point to a possible role of filament membrane attachment in lateral association and curvature, elements currently identified as relevant for force generation.
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Affiliation(s)
- Mario Encinar
- Instituto de Catálisis y Petroleoquímica, CSIC, Marie Curie, 2, Cantoblanco, 28049 Madrid, Spain
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29
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Buske PJ, Levin PA. A flexible C-terminal linker is required for proper FtsZ assembly in vitro and cytokinetic ring formation in vivo. Mol Microbiol 2013; 89:249-63. [PMID: 23692518 DOI: 10.1111/mmi.12272] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2013] [Indexed: 02/01/2023]
Abstract
Assembly of the cytoskeletal protein FtsZ into a ring-like structure is required for bacterial cell division. Structurally, FtsZ consists of four domains: the globular N-terminal core, a flexible linker, 8-9 conserved residues implicated in interactions with modulatory proteins, and a highly variable set of 4-10 residues at its very C terminus. Largely ignored and distinguished by lack of primary sequence conservation, the linker is presumed to be intrinsically disordered. Here we employ genetics, biochemistry and cytology to dissect the role of the linker in FtsZ function. Data from chimeric FtsZs substituting the native linker with sequences from unrelated FtsZs as well as a helical sequence from human beta-catenin indicate that while variations in the primary sequence are well tolerated, an intrinsically disordered linker is essential for Bacillus subtilis FtsZ assembly. Linker lengths ranging from 25 to 100 residues supported FtsZ assembly, but replacing the B. subtilis FtsZ linker with a 249-residue linker from Agrobacterium tumefaciens FtsZ interfered with cell division. Overall, our results support a model in which the linker acts as a flexible tether allowing FtsZ to associate with the membrane through a conserved C-terminal domain while simultaneously interacting with itself and modulatory proteins in the cytoplasm.
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Affiliation(s)
- P J Buske
- Department of Biology, Washington University in St Louis, St Louis, MO 63130, USA
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30
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Natarajan K, Senapati S. Probing the conformational flexibility of monomeric FtsZ in GTP-bound, GDP-bound, and nucleotide-free states. Biochemistry 2013; 52:3543-51. [PMID: 23617789 DOI: 10.1021/bi400170f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The mechanism of nucleotide-regulated assembly and disassembly of the prokaryotic cell division protein FtsZ is not yet clearly understood. In this work, we attempt to characterize the functional motions in monomeric FtsZ through molecular dynamics simulations and essential dynamics (ED) analyses and correlate those motions to FtsZ assembly and disassembly. Results suggest that the nucleotide binding subdomain of FtsZ can switch between multitudes of curved conformations in all nucleotide states, but it prefers to be in an assembly competent less curved conformation in the GTP-bound state. Further, the GDP to GTP exchange invokes a subtle conformational change in the nucleotide binding pocket that tends to align the top portion of core helix H7 along the longitudinal axis of the protein. ED analyses suggest that the longitudinal movements of H7 and the adjacent H6-H7 region modulate the motions of C-domain elements coherently. These longitudinal movements of functionally relevant H7, H6-H7, T3, T7, and H10 regions are likely to facilitate the assembly of GTP-FtsZ into straight filament. On the other hand, the observed radial or random movements of FtsZ residues in the GDP state might not allow the monomers to assemble as efficiently as GTP-bound monomers and could produce curved filaments. Our results correlate very well with recent mutagenesis data that inferred FtsZ conformational flexibility and the involvement of the H6-H7 region in assembly.
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Affiliation(s)
- Kathiresan Natarajan
- Department of Biotechnology, Indian Institute of Technology Madras , Chennai 600036, India
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31
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Wasserstrom S, Grantcharova N, Ubhayasekera W, Ausmees N, Sandblad L, Flärdh K. Non-sporulating ftsZ mutants in Streptomyces coelicolor reveal amino acid residues critical for FtsZ polymerization dynamics. Microbiology (Reading) 2013; 159:890-901. [DOI: 10.1099/mic.0.066480-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
| | - Nina Grantcharova
- Department of Cell and Molecular Biology, Uppsala University, 751 24 Uppsala, Sweden
| | - Wimal Ubhayasekera
- Department of Cell and Molecular Biology, Uppsala University, 751 24 Uppsala, Sweden
| | - Nora Ausmees
- Department of Cell and Molecular Biology, Uppsala University, 751 24 Uppsala, Sweden
- Department of Biology, Lund University, 223 62 Lund, Sweden
| | - Linda Sandblad
- Department of Molecular Biology, 901 87 Umeå University, Sweden
| | - Klas Flärdh
- Department of Cell and Molecular Biology, Uppsala University, 751 24 Uppsala, Sweden
- Department of Biology, Lund University, 223 62 Lund, Sweden
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32
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Montecinos-Franjola F, Ross JA, Sánchez SA, Brunet JE, Lagos R, Jameson DM, Monasterio O. Studies on the dissociation and urea-induced unfolding of FtsZ support the dimer nucleus polymerization mechanism. Biophys J 2012; 102:2176-85. [PMID: 22824282 DOI: 10.1016/j.bpj.2012.03.064] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Revised: 01/31/2012] [Accepted: 03/12/2012] [Indexed: 01/23/2023] Open
Abstract
FtsZ is a major protein in bacterial cytokinesis that polymerizes into single filaments. A dimer has been proposed to be the nucleating species in FtsZ polymerization. To investigate the influence of the self-assembly of FtsZ on its unfolding pathway, we characterized its oligomerization and unfolding thermodynamics. We studied the assembly using size-exclusion chromatography and fluorescence spectroscopy, and the unfolding using circular dichroism and two-photon fluorescence correlation spectroscopy. The chromatographic analysis demonstrated the presence of monomers, dimers, and tetramers with populations dependent on protein concentration. Dilution experiments using fluorescent conjugates revealed dimer-to-monomer and tetramer-to-dimer dissociation constants in the micromolar range. Measurements of fluorescence lifetimes and rotational correlation times of the conjugates supported the presence of tetramers at high protein concentrations and monomers at low protein concentrations. The unfolding study demonstrated that the three-state unfolding of FtsZ was due to the mainly dimeric state of the protein, and that the monomer unfolds through a two-state mechanism. The monomer-to-dimer equilibrium characterized here (K(d) = 9 μM) indicates a significant fraction (~10%) of stable dimers at the critical concentration for polymerization, supporting a role of the dimeric species in the first steps of FtsZ polymerization.
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Affiliation(s)
- Felipe Montecinos-Franjola
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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33
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Matsui T, Yamane J, Mogi N, Yamaguchi H, Takemoto H, Yao M, Tanaka I. Structural reorganization of the bacterial cell-division protein FtsZ from Staphylococcus aureus. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:1175-88. [PMID: 22948918 DOI: 10.1107/s0907444912022640] [Citation(s) in RCA: 126] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 05/18/2012] [Indexed: 11/10/2022]
Abstract
FtsZ is a key molecule in bacterial cell division. In the presence of GTP, it polymerizes into tubulin-like protofilaments by head-to-tail association. Protofilaments of FtsZ seem to adopt a straight or a curved conformation in relation to the bound nucleotide. However, although several bacterial and archaeal FtsZ structures have been determined, all of the structures reported previously are considered to have a curved conformation. In this study, structures of FtsZ from Staphylococcus aureus (SaFtsZ) were determined in apo, GDP-bound and inhibitor-complex forms and it was found that SaFtsZ undergoes marked conformational changes. The accumulated evidence suggests that the GDP-bound structure has the features of the straight form. The structural change between the curved and straight forms shows intriguing similarity to the eukaryotic cytoskeletal protein tubulin. Furthermore, the structure of the apo form showed an unexpectedly large conformational change in the core region. FtsZ has also been recognized as a novel target for antibacterial drugs. The structure of the complex with the inhibitor PC190723, which has potent and selective antistaphylococcal activity, indicated that the inhibitor binds at the cleft between the two subdomains.
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Affiliation(s)
- Takashi Matsui
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Hokkaido, Japan
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34
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Nucleotide-dependent conformations of FtsZ dimers and force generation observed through molecular dynamics simulations. Proc Natl Acad Sci U S A 2012; 109:9432-7. [PMID: 22647609 DOI: 10.1073/pnas.1120761109] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The bacterial cytoskeletal protein FtsZ is a GTPase that is thought to provide mechanical constriction force via an unidentified mechanism. Purified FtsZ polymerizes into filaments with varying structures in vitro: while GTP-bound FtsZ assembles into straight or gently curved filaments, GDP-bound FtsZ forms highly curved filaments, prompting the hypothesis that a difference in the inherent curvature of FtsZ filaments provides mechanical force. However, no nucleotide-dependent structural transition of FtsZ monomers has been observed to support this force generation model. Here, we present a series of all-atom molecular dynamics simulations probing the effects of nucleotide binding on the structure of an FtsZ dimer. We found that the FtsZ-dimer structure is dependent on nucleotide-binding state. While a GTP-bound FtsZ dimer retained a firm monomer-monomer contact, a GDP-bound FtsZ dimer lost some of the monomer-monomer association, leading to a "hinge-opening" event that resulted in a more bent dimer, while leaving each monomer structure largely unaffected. We constructed models of FtsZ filaments and found that a GDP-FtsZ filament is much more curved than a GTP-FtsZ filament, with the degree of curvature matching prior experimental data. FtsZ dynamics were used to estimate the amount of force an FtsZ filament could exert when hydrolysis occurs (20-30 pN per monomer). This magnitude of force is sufficient to direct inward cell-wall growth during division, and to produce the observed degree of membrane pinching in liposomes. Taken together, our data provide molecular-scale insight on the origin of FtsZ-based constriction force, and the mechanism underlying prokaryotic cell division.
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35
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Molecular dynamics simulation of GTPase activity in polymers of the cell division protein FtsZ. FEBS Lett 2012; 586:1236-9. [PMID: 22575662 DOI: 10.1016/j.febslet.2012.03.042] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Revised: 02/01/2012] [Accepted: 03/20/2012] [Indexed: 11/22/2022]
Abstract
FtsZ, the prokaryotic ortholog of tubulin, assembles into polymers in the bacterial division ring. The interfaces between monomers contain a GTP molecule, but the relationship between polymerization and GTPase activity is not unequivocally proven. A set of short FtsZ polymers were modelled and the formation of active GTPase structures was monitored using molecular dynamics. Only the interfaces nearest the polymer ends exhibited an adequate geometry for GTP hydrolysis. Simulated conversion of interfaces from close-to-end to internal position and vice versa resulted in their spontaneous rearrangement between active and inactive conformations. This predicted behavior of FtsZ polymer ends was supported by in vitro experiments.
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36
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Schaffner-Barbero C, Martín-Fontecha M, Chacón P, Andreu JM. Targeting the assembly of bacterial cell division protein FtsZ with small molecules. ACS Chem Biol 2012; 7:269-77. [PMID: 22047077 DOI: 10.1021/cb2003626] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
FtsZ is the key protein of bacterial cell division and an emergent target for new antibiotics. It is a filament-forming GTPase and a structural homologue of eukaryotic tubulin. A number of FtsZ-interacting compounds have been reported, some of which have powerful antibacterial activity. Here we review recent advances and new approaches in modulating FtsZ assembly with small molecules. This includes analyzing their chemical features, binding sites, mechanisms of action, the methods employed, and computational insights, aimed at a better understanding of their molecular recognition by FtsZ and at rational antibiotic design.
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Affiliation(s)
- Claudia Schaffner-Barbero
- Tubulins and
FtsZ, Centro de
Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Mar Martín-Fontecha
- Medicinal Chemistry, Dept. Química
Orgánica I, Facultad de Ciencias Químicas, UCM, Avda. Complutense s/n, 28040 Madrid, Spain
| | - Pablo Chacón
- Structural Bioinformatics, Instituto
de Química Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
| | - José M. Andreu
- Tubulins and
FtsZ, Centro de
Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
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37
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Guardia CMA, Gauto DF, Di Lella S, Rabinovich GA, Martí MA, Estrin DA. An integrated computational analysis of the structure, dynamics, and ligand binding interactions of the human galectin network. J Chem Inf Model 2011; 51:1918-30. [PMID: 21702482 DOI: 10.1021/ci200180h] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Galectins, a family of evolutionarily conserved animal lectins, have been shown to modulate signaling processes leading to inflammation, apoptosis, immunoregulation, and angiogenesis through their ability to interact with poly-N-acetyllactosamine-enriched glycoconjugates. To date 16 human galectin carbohydrate recognition domains have been established by sequence analysis and found to be expressed in several tissues. Given the divergent functions of these lectins, it is of vital importance to understand common and differential features in order to search for specific inhibitors of individual members of the human galectin family. In this work we performed an integrated computational analysis of all individual members of the human galectin family. In the first place, we have built homology-based models for galectin-4 and -12 N-terminus, placental protein 13 (PP13) and PP13-like protein for which no experimental structural information is available. We have then performed classical molecular dynamics simulations of the whole 15 members family in free and ligand-bound states to analyze protein and protein-ligand interaction dynamics. Our results show that all galectins adopt the same fold, and the carbohydrate recognition domains are very similar with structural differences located in specific loops. These differences are reflected in the dynamics characteristics, where mobility differences translate into entropy values which significantly influence their ligand affinity. Thus, ligand selectivity appears to be modulated by subtle differences in the monosaccharide binding sites. Taken together, our results may contribute to the understanding, at a molecular level, of the structural and dynamical determinants that distinguish individual human galectins.
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Affiliation(s)
- Carlos M A Guardia
- Departamento de Química Inorgánica, Analítica y Química Física, INQUIMAE-CONICET, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón II, C1428EHA Ciudad de Buenos Aires, Argentina
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38
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Reija B, Monterroso B, Jiménez M, Vicente M, Rivas G, Zorrilla S. Development of a homogeneous fluorescence anisotropy assay to monitor and measure FtsZ assembly in solution. Anal Biochem 2011; 418:89-96. [PMID: 21802401 DOI: 10.1016/j.ab.2011.07.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Revised: 06/24/2011] [Accepted: 07/01/2011] [Indexed: 11/25/2022]
Abstract
We present here a fluorescence anisotropy method for the quantification of the polymerization of FtsZ, an essential protein for cytokinesis in prokaryotes whose GTP-dependent assembly initiates the formation of the divisome complex. Using Alexa 488 labeled wild-type FtsZ as a tracer, the assay allows determination of the critical concentration of FtsZ polymerization from the dependence of the measured steady-state fluorescence anisotropy on the concentration of FtsZ. The incorporation of the labeled protein into FtsZ polymers and the lack of spectral changes on assembly were independently confirmed by time-resolved fluorescence and fluorescence correlation spectroscopy. Critical concentration values determined by this new assay are compatible with those reported previously under the same conditions by other well-established methods. As a proof of principle, data on the sensitivity of the assay to changes in FtsZ assembly in response to Mg(2+) concentration or to the presence of high concentrations of Ficoll 70 as crowding agent are shown. The proposed method is sensitive, low sample consuming, rapid, and reliable, and it can be extended to other cooperatively polymerizing systems. In addition, it can help to discover new antimicrobials that may interfere with FtsZ polymerization because it can be easily adapted to systematic screening assays.
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Affiliation(s)
- Belén Reija
- Instituto de Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas, E-28006 Madrid, Spain
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39
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Chen Y, Erickson HP. Conformational changes of FtsZ reported by tryptophan mutants. Biochemistry 2011; 50:4675-84. [PMID: 21510681 DOI: 10.1021/bi200106d] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
E. coli FtsZ has no native tryptophan. We showed previously that the mutant FtsZ L68W gave a 2.5-fold increase in trp fluorescence when assembly was induced by GTP. L68 is probably buried in the protofilament interface upon assembly, causing the fluorescence increase. In the present study we introduced trp residues at several other locations and examined them for assembly-induced fluorescence changes. L189W, located on helix H7 and buried between the N- and C-terminal subdomains, showed a large fluorescence increase, comparable to L68W. This may reflect a shift or rotation of the two subdomains relative to each other. L160W showed a smaller increase in fluorescence, and Y222W a decrease in fluorescence, upon assembly. These two are located on the surface of the N and C subdomains, near the domain boundary. The changes in fluorescence may reflect movements of the domains or of nearby side chains. We prepared a double mutant Y222W/S151C and coupled ATTO-655 to the cys. The Cα of trp in the C-terminal subdomain was 10 Å away from that of the cys in the N-terminal subdomain, permitting the ATTO to make van der Waals contact with the trp. The ATTO fluorescence showed strong tryptophan-induced quenching. The quenching was reduced following assembly, consistent with a movement apart of the two subdomains. Movements of one to several angstroms are probably sufficient to account for the changes in trp fluorescence and trp-induced quenching of ATTO. Assembly in GDP plus DEAE dextran produces tubular polymers that are related to the highly curved, mini-ring conformation. No change in trp fluorescence was observed upon assembly of these tubes, suggesting that the mini-ring conformation is the same as that of a relaxed, monomeric FtsZ.
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Affiliation(s)
- Yaodong Chen
- Department of Cell Biology, Duke University Medical Center, Durham, NC 27710-3709, USA
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FtsZ in bacterial cytokinesis: cytoskeleton and force generator all in one. Microbiol Mol Biol Rev 2011; 74:504-28. [PMID: 21119015 DOI: 10.1128/mmbr.00021-10] [Citation(s) in RCA: 460] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
FtsZ, a bacterial homolog of tubulin, is well established as forming the cytoskeletal framework for the cytokinetic ring. Recent work has shown that purified FtsZ, in the absence of any other division proteins, can assemble Z rings when incorporated inside tubular liposomes. Moreover, these artificial Z rings can generate a constriction force, demonstrating that FtsZ is its own force generator. Here we review light microscope observations of how Z rings assemble in bacteria. Assembly begins with long-pitch helices that condense into the Z ring. Once formed, the Z ring can transition to short-pitch helices that are suggestive of its structure. FtsZ assembles in vitro into short protofilaments that are ∼30 subunits long. We present models for how these protofilaments might be further assembled into the Z ring. We discuss recent experiments on assembly dynamics of FtsZ in vitro, with particular attention to how two regulatory proteins, SulA and MinC, inhibit assembly. Recent efforts to develop antibacterial drugs that target FtsZ are reviewed. Finally, we discuss evidence of how FtsZ generates a constriction force: by protofilament bending into a curved conformation.
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Adams DW, Wu LJ, Czaplewski LG, Errington J. Multiple effects of benzamide antibiotics on FtsZ function. Mol Microbiol 2011; 80:68-84. [PMID: 21276094 DOI: 10.1111/j.1365-2958.2011.07559.x] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Cell division in almost all bacteria is orchestrated by the essential tubulin homologue FtsZ, which assembles into a ring-like structure and acts as a scaffold for the division machinery. Division was recently validated as an important target for antibiotics by the demonstration that low-molecular-weight inhibitors of FtsZ, called benzamides, can cure mice infected with Staphylococcus aureus. In treated cells of Bacillus subtilis we show that FtsZ assembles into foci throughout the cell, including abnormal locations at the cell poles and over the nucleoid. These foci are not inactive aggregates because they remain dynamic, turning over almost as rapidly as untreated polymers. Remarkably, although division is completely blocked, the foci efficiently recruit division proteins that normally co-assemble with FtsZ. However, they show no affinity for components of the Min or Nucleoid occlusion systems. In vitro, the benzamides strongly promote the polymerization of FtsZ, into hyperstable polymers, which are highly curved. Importantly, even at low concentrations, benzamides transform the structure of the Z ring, resulting in abnormal helical cell division events. We propose that benzamides act principally by promoting an FtsZ protomer conformation that is incompatible with a higher-order level of assembly needed to make a division ring.
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Affiliation(s)
- David W Adams
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK
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Schaffner-Barbero C, Gil-Redondo R, Ruiz-Avila LB, Huecas S, Läppchen T, den Blaauwen T, Diaz JF, Morreale A, Andreu JM. Insights into nucleotide recognition by cell division protein FtsZ from a mant-GTP competition assay and molecular dynamics. Biochemistry 2010; 49:10458-72. [PMID: 21058659 DOI: 10.1021/bi101577p] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Essential cell division protein FtsZ forms the bacterial cytokinetic ring and is a target for new antibiotics. FtsZ monomers bind GTP and assemble into filaments. Hydrolysis to GDP at the association interface between monomers leads to filament disassembly. We have developed a homogeneous competition assay, employing the fluorescence anisotropy change of mant-GTP upon binding to nucleotide-free FtsZ, which detects compounds binding to the nucleotide site in FtsZ monomers and measures their affinities within the millimolar to 10 nM range. We have employed this method to determine the apparent contributions of the guanine, ribose, and the α-, β-, and γ-phosphates to the free energy change of nucleotide binding. Similar relative contributions have also been estimated through molecular dynamics and binding free energy calculations, employing the crystal structures of FtsZ-nucleotide complexes. We find an energetically dominant contribution of the β-phosphate, comparable to the whole guanosine moiety. GTP and GDP bind with similar observed affinity to FtsZ monomers. Loss of the regulatory γ-phosphate results in a predicted accommodation of GDP which has not been observed in the crystal structures. The binding affinities of a series of C8-substituted GTP analogues, known to inhibit FtsZ but not eukaryotic tubulin assembly, correlate with their inhibitory capacity on FtsZ polymerization. Our methods permit testing of FtsZ inhibitors targeting its nucleotide site, as well as compounds from virtual screening of large synthetic libraries. Our results give insight into the FtsZ-nucleotide interactions, which could be useful in the rational design of new inhibitors, especially GTP phosphate mimetics.
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