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Screening of plant-based natural compounds as an inhibitor of FtsZ from Salmonella Typhi using the computational, biochemical and in vitro cell-based studies. Int J Biol Macromol 2022; 219:428-437. [PMID: 35932806 DOI: 10.1016/j.ijbiomac.2022.07.241] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 07/27/2022] [Accepted: 07/30/2022] [Indexed: 11/22/2022]
Abstract
Salmonella Typhi is emerging as a drug-resistant pathogen, particularly in developing countries. Hence, the progressive development of new antibiotics against novel drug targets is essential to prevent the spread of infections and mortality. The cell division protein FtsZ is an ideal drug target as the cell wall synthesis in bacteria is driven by the dynamic treadmilling nature of the FtsZ. The polymerization of the FtsZ provides the essential mechanical constricting force and flexibility to modulate the cell wall synthesis. Any alteration in FtsZ polymerization leads to the bactericidal or bacteriostatic effect. In this study, we have evaluated the secondary metabolites of natural compounds berberine chloride, cinnamaldehyde, scopoletin, quercetin and eugenol as potential inhibitors of FtsZ from Salmonella Typhi (stFtsZ) using computational, biochemical, and in vivo cell-based assays. Out of these five compounds, berberine chloride and cinnamaldehyde exhibited the best binding affinity of Kd = 7 μM and 10 μM, respectively and inhibit stFtsZ GTPase activity and polymerization by 70 %. The compound berberine chloride showed the best MIC of 500 μg/mL and 175 μg/mL against gram-negative and gram-positive bacterial strains. The findings support that these natural compounds can be used as a backbone structure to develop a broad spectrum of antibacterial agents.
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2
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Wang J, Bulgheresi S, den Blaauwen T. The Longitudinal Dividing Bacterium Candidatus Thiosymbion Oneisti Has a Natural Temperature-Sensitive FtsZ Protein with Low GTPase Activity. Int J Mol Sci 2022; 23:3016. [PMID: 35328438 PMCID: PMC8953583 DOI: 10.3390/ijms23063016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/28/2022] [Accepted: 03/09/2022] [Indexed: 02/01/2023] Open
Abstract
FtsZ, the bacterial tubulin-homolog, plays a central role in cell division and polymerizes into a ring-like structure at midcell to coordinate other cell division proteins. The rod-shaped gamma-proteobacterium Candidatus Thiosymbion oneisti has a medial discontinuous ellipsoidal "Z-ring." Ca. T. oneisti FtsZ shows temperature-sensitive characteristics when it is expressed in Escherichia coli, where it localizes at midcell. The overexpression of Ca. T. oneisti FtsZ interferes with cell division and results in filamentous cells. In addition, it forms ring- and barrel-like structures independently of E. coli FtsZ, which suggests that the difference in shape and size of the Ca. T. oneisti FtsZ ring is likely the result of its interaction with Z-ring organizing proteins. Similar to some temperature-sensitive alleles of E. coli FtsZ, Ca. T. oneisti FtsZ has a weak GTPase and does not polymerize in vitro. The temperature sensitivity of Ca. Thiosymbion oneisti FtsZ is likely an adaptation to the preferred temperature of less than 30 °C of its host, the nematode Laxus oneistus.
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Affiliation(s)
- Jinglan Wang
- Bacterial Cell Biology and Physiology, Swammerdam Institute for Life Science, University of Amsterdam, 1098 XH Amsterdam, The Netherlands;
| | - Silvia Bulgheresi
- Environmental Cell Biology, Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria;
| | - Tanneke den Blaauwen
- Bacterial Cell Biology and Physiology, Swammerdam Institute for Life Science, University of Amsterdam, 1098 XH Amsterdam, The Netherlands;
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3
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Chen Y, Li Y, Yuan C, Liu S, Xin F, Deng X, Wang X. Streptococcus mutans cell division protein FtsZ has higher GTPase and polymerization activities in acidic environment. Mol Oral Microbiol 2022; 37:97-108. [PMID: 35218317 DOI: 10.1111/omi.12364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 01/18/2022] [Accepted: 02/23/2022] [Indexed: 11/29/2022]
Abstract
The acid tolerance of Streptococcus mutans plays an important role in its cariogenic process. S. mutans initiates a powerful transcriptional and physiological adaptation mechanism, eventually shielding the cellular machinery from acid damage and contributing to bacterial survival under acidic stress conditions. Although S. mutans contains complex regulatory systems, existing studies have shown that S. mutans, unlike Escherichia coli, cannot maintain a neutral intracellular environment. As the pH of the extracellular environment decreases, the intracellular pH decreases in parallel. There is insufficient knowledge regarding the acid resistance of the intracellular proteins of S. mutans, particularly when it comes to the key cytoskeletal division protein FtsZ. In this study, the data showed that S. mutans had similar cell division progress in acidic and neutral environments. The splitting position was in the middle of cells, and the cytoplasm were divided evenly in the acidic environment. Additionally, the treadmilling velocity of S. mutans FtsZ in the middle of cells was not affected by the acidic environment. S. mutans FtsZ had higher GTPase activity in pH 6.0 buffer than in the neutral environment. Furthermore, the polymerization of S. mutans FtsZ in the acidic environment was more robust than that in the neutral environment. After two particular amino acids of S. mutans FtsZ amino acids were mutated (E88K, L269K), the polymerization of S. mutans FtsZ in the acidic environment was significantly reduced. Overall, S. mutans FtsZ exhibited higher functional activity in pH 6.0 buffer in vitro. The acid resistance of S. mutans FtsZ is affected by its particular amino acids. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Yuxing Chen
- Department of Cariology and Endodontology & National Clinical Research Center for Oral Disease, School and Hospital of Stomatology, Peking University, Beijing, PR China
| | - Yongliang Li
- Department of Geriatric Dentistry, School and Hospital of Stomatology, Peking University, Beijing, PR China
| | - Chongyang Yuan
- Department of Cariology and Endodontology & National Clinical Research Center for Oral Disease, School and Hospital of Stomatology, Peking University, Beijing, PR China
| | - Shujun Liu
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Fengjiao Xin
- Laboratory of Biomanufacturing and Food Engineering, Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Xuliang Deng
- Department of Geriatric Dentistry, School and Hospital of Stomatology, Peking University, Beijing, PR China
| | - Xiaoyan Wang
- Department of Cariology and Endodontology & National Clinical Research Center for Oral Disease, School and Hospital of Stomatology, Peking University, Beijing, PR China
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4
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When the metabolism meets the cell cycle in bacteria. Curr Opin Microbiol 2021; 60:104-113. [PMID: 33677348 DOI: 10.1016/j.mib.2021.02.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 12/20/2022]
Abstract
Nutrients availability is the sinews of the war for single microbial cells, driving growth and cell cycle progression. Therefore, coordinating cellular processes with nutrients availability is crucial, not only to survive upon famine or fluctuating conditions but also to rapidly thrive and colonize plentiful environments. While metabolism is traditionally seen as a set of chemical reactions taking place in cells to extract energy and produce building blocks from available nutrients, numerous connections between metabolic pathways and cell cycle phases have been documented. The few regulatory systems described at the molecular levels show that regulation is mediated either by a second messenger molecule or by a metabolite and/or a metabolic enzyme. In the latter case, a secondary moonlighting regulatory function evolved independently of the primary catalytic function of the enzyme. In this review, we summarize our current understanding of the complex cross-talks between metabolism and cell cycle in bacteria.
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5
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Cabral AD, Rafiei N, de Araujo ED, Radu TB, Toutah K, Nino D, Murcar-Evans BI, Milstein JN, Kraskouskaya D, Gunning PT. Sensitive Detection of Broad-Spectrum Bacteria with Small-Molecule Fluorescent Excimer Chemosensors. ACS Sens 2020; 5:2753-2762. [PMID: 32803944 DOI: 10.1021/acssensors.9b02490] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Antibiotic resistance is a major problem for world health, triggered by the unnecessary usage of broad-spectrum antibiotics on purportedly infected patients. Current clinical standards require lengthy protocols for the detection of bacterial species in sterile physiological fluids. In this work, a class of small-molecule fluorescent chemosensors termed ProxyPhos was shown to be capable of rapid, sensitive, and facile detection of broad-spectrum bacteria. The sensors act via a turn-on fluorescent excimer mechanism, where close-proximity binding of multiple sensor units amplifies a red shift emission signal. ProxyPhos sensors were able to detect down to 10 CFUs of model strains by flow cytometry assays and showed selectivity over mammalian cells in a bacterial coculture through fluorescence microscopy. The studies reveal that the zinc(II)-chelates cyclen and cyclam are novel and effective binding units for the detection of both Gram-negative and Gram-positive bacterial strains. Mode of action studies revealed that the chemosensors detect Gram-negative and Gram-positive strains with two distinct mechanisms. Preliminary studies applying ProxyPhos sensors to sterile physiological fluids (cerebrospinal fluid) in flow cytometry assays were successful. The results suggest that ProxyPhos sensors can be developed as a rapid, inexpensive, and robust tool for the "yes-no" detection of broad-spectrum bacteria in sterile fluids.
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Affiliation(s)
- Aaron D. Cabral
- Department of Chemical & Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road North, Mississauga, Ontario L5L 1C6, Canada
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Nafiseh Rafiei
- Department of Chemical & Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road North, Mississauga, Ontario L5L 1C6, Canada
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario M5S 3G9, Canada
| | - Elvin D. de Araujo
- Department of Chemical & Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road North, Mississauga, Ontario L5L 1C6, Canada
| | - Tudor B. Radu
- Department of Chemical & Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road North, Mississauga, Ontario L5L 1C6, Canada
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Krimo Toutah
- Department of Chemical & Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road North, Mississauga, Ontario L5L 1C6, Canada
| | - Daniel Nino
- Department of Chemical & Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road North, Mississauga, Ontario L5L 1C6, Canada
- Department of Physics, University of Toronto, 60 St. George Street, Toronto, Ontario M5S 1A7, Canada
| | - Bronte I. Murcar-Evans
- Department of Chemical & Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road North, Mississauga, Ontario L5L 1C6, Canada
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Joshua N. Milstein
- Department of Chemical & Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road North, Mississauga, Ontario L5L 1C6, Canada
- Department of Physics, University of Toronto, 60 St. George Street, Toronto, Ontario M5S 1A7, Canada
| | - Dziyana Kraskouskaya
- Department of Chemical & Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road North, Mississauga, Ontario L5L 1C6, Canada
| | - Patrick T. Gunning
- Department of Chemical & Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road North, Mississauga, Ontario L5L 1C6, Canada
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
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6
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Meyer J, Del Vecchio G, Seitz V, Massaly N, Stein C. Modulation of μ-opioid receptor activation by acidic pH is dependent on ligand structure and an ionizable amino acid residue. Br J Pharmacol 2019; 176:4510-4520. [PMID: 31355457 PMCID: PMC6932940 DOI: 10.1111/bph.14810] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 07/12/2019] [Accepted: 07/14/2019] [Indexed: 12/22/2022] Open
Abstract
Background and Purpose Adverse side effects of conventional opioids can be avoided if ligands selectively activate peripheral opioid receptors in injured tissue. Injury and inflammation are typically accompanied by acidification. In this study, we examined influences of low pH and mutation of the ionizable amino acid residue H2976.52 on μ‐opioid receptor binding and signalling induced by the μ‐opioid receptor ligands fentanyl, DAMGO, and naloxone. Experimental Approach HEK 293 cells stably transfected with μ‐opioid receptors were used to study opioid ligand binding, [35S]‐GTPγS binding, and cAMP reduction at physiological and acidic pH. We used μ‐opioid receptors mutated at H2976.52 to A (MOR‐H2976.52A) to delineate ligand‐specific interactions with H2976.52. Key Results Low pH and the mutant receptor MOR‐H2976.52A impaired naloxone binding and antagonism of cAMP reduction. In addition, DAMGO binding and G‐protein activation were decreased under these conditions. Fentanyl‐induced signalling was not influenced by pH and largely independent of H2976.52. Conclusions and Implications Our investigations indicate that low pH selectively impairs μ‐opioid receptor signalling modulated by ligands capable of forming hydrogen bonds with H2976.52. We propose that protonation of H2976.52 at acidic pH reduces binding and subsequent signalling of such ligands. Novel agonists targeting opioid receptors in injured tissue might benefit from lack of hydrogen bond formation with H2976.52.
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Affiliation(s)
- Johanna Meyer
- Department of Experimental Anesthesiology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Germany
| | - Giovanna Del Vecchio
- Department of Experimental Anesthesiology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Germany
| | - Viola Seitz
- Department of Experimental Anesthesiology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Germany
| | - Nicolas Massaly
- Department of Experimental Anesthesiology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Germany
| | - Christoph Stein
- Department of Experimental Anesthesiology, Campus Benjamin Franklin, Charité-Universitätsmedizin Berlin, Germany
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Roseboom W, Nazir MG, Meiresonne NY, Mohammadi T, Verheul J, Buncherd H, Bonvin AMJJ, de Koning LJ, de Koster CG, de Jong L, den Blaauwen T. Mapping the Contact Sites of the Escherichia coli Division-Initiating Proteins FtsZ and ZapA by BAMG Cross-Linking and Site-Directed Mutagenesis. Int J Mol Sci 2018; 19:ijms19102928. [PMID: 30261644 PMCID: PMC6213154 DOI: 10.3390/ijms19102928] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 09/13/2018] [Accepted: 09/19/2018] [Indexed: 12/21/2022] Open
Abstract
Cell division in bacteria is initiated by the polymerization of FtsZ at midcell in a ring-like structure called the Z-ring. ZapA and other proteins assist Z-ring formation and ZapA binds ZapB, which senses the presence of the nucleoids. The FtsZ–ZapA binding interface was analyzed by chemical cross-linking mass spectrometry (CXMS) under in vitro FtsZ-polymerizing conditions in the presence of GTP. Amino acids residue K42 from ZapA was cross-linked to amino acid residues K51 and K66 from FtsZ, close to the interphase between FtsZ molecules in protofilaments. Five different cross-links confirmed the tetrameric structure of ZapA. A number of FtsZ cross-links suggests that its C-terminal domain of 55 residues, thought to be largely disordered, has a limited freedom to move in space. Site-directed mutagenesis of ZapA reveals an interaction site in the globular head of the protein close to K42. Using the information on the cross-links and the mutants that lost the ability to interact with FtsZ, a model of the FtsZ protofilament–ZapA tetramer complex was obtained by information-driven docking with the HADDOCK2.2 webserver.
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Affiliation(s)
- Winfried Roseboom
- Mass Spectrometry of Biomacromolecules, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.
| | - Madhvi G Nazir
- Bacterial Cell Biology and Physiology, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.
| | - Nils Y Meiresonne
- Bacterial Cell Biology and Physiology, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.
| | - Tamimount Mohammadi
- Bacterial Cell Biology and Physiology, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.
| | - Jolanda Verheul
- Bacterial Cell Biology and Physiology, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.
| | - Hansuk Buncherd
- Mass Spectrometry of Biomacromolecules, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.
- Faculty of Medical Technology, Prince of Songkla University, Songkhla 90110, Thailand.
| | - Alexandre M J J Bonvin
- Computational Structural Biology, Faculty of Science-Chemistry, University of Utrecht, Padualaan 83584CH Utrecht, The Netherlands.
| | - Leo J de Koning
- Mass Spectrometry of Biomacromolecules, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.
| | - Chris G de Koster
- Mass Spectrometry of Biomacromolecules, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.
| | - Luitzen de Jong
- Mass Spectrometry of Biomacromolecules, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.
| | - Tanneke den Blaauwen
- Bacterial Cell Biology and Physiology, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands.
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8
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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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Abstract
In comparison with bacteria and eukaryotes, the large and diverse group of microorganisms known as archaea possess a great diversity of cytoskeletal proteins, including members of the tubulin superfamily. Many species contain FtsZ, CetZ and even possible tubulins; however, some major taxonomic groups do not contain any member of the tubulin superfamily. Studies using the model archaeon, Halferax volcanii have recently been instrumental in defining the fundamental roles of FtsZ and CetZ in archaeal cell division and cell shape regulation. Structural studies of archaeal tubulin superfamily proteins provide a definitive contribution to the cytoskeletal field, showing which protein-types must have developed prior to the divergence of archaea and eukaryotes. Several regions of the globular core domain - the "signature" motifs - combine in the 3D structure of the common molecular fold to form the GTP-binding site. They are the most conserved sequence elements and provide the primary basis for identification of new superfamily members through homology searches. The currently well-characterised proteins also all share a common mechanism of GTP-dependent polymerisation, in which GTP molecules are sandwiched between successive subunits that are arranged in a head-to-tail manner. However, some poorly-characterised archaeal protein families retain only some of the signature motifs and are unlikely to be capable of dynamic polymerisation, since the promotion of depolymerisation by hydrolysis to GDP depends on contributions from both subunits that sandwich the nucleotide in the polymer.
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Affiliation(s)
- Christopher H S Aylett
- Department of Biology, Institute for Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
| | - Iain G Duggin
- The iThree Institute, University of Technology Sydney, Sydney, NSW, 2007, Australia.
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10
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Arjes HA, Lai B, Emelue E, Steinbach A, Levin PA. Mutations in the bacterial cell division protein FtsZ highlight the role of GTP binding and longitudinal subunit interactions in assembly and function. BMC Microbiol 2015; 15:209. [PMID: 26463348 PMCID: PMC4603965 DOI: 10.1186/s12866-015-0544-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 10/02/2015] [Indexed: 11/28/2022] Open
Abstract
Background Assembly of the tubulin-like GTPase, FtsZ, at the future division site initiates the process of bacterial cytokinesis. The FtsZ ring serves as a platform for assembly of the division machinery and constricts at the leading edge of the invaginating septum during cytokinesis. In vitro, FtsZ assembles in a GTP-dependent manner, forming straight filaments that curve upon GTP hydrolysis. FtsZ binds but cannot hydrolyze GTP as a monomer. Instead, the active site for GTP hydrolysis is formed at the monomer-monomer interface upon dimerization. While the dynamics of GTP hydrolysis and assembly have been extensively studied in vitro, significantly less is known about the role of GTP binding and hydrolysis in vivo. ftsZ84, a GTPase defective allele of Escherichia coli ftsZ, provides a striking example of the disconnect between in vivo and in vitro FtsZ assembly. Results Although ftsZ84 mutants are defective for FtsZ ring formation and division under nonpermissive conditions, they are near wild type for ring formation and division under permissive conditions. In vitro, however, purified FtsZ84 is defective in GTP binding, hydrolysis and assembly under standard reaction conditions. To clarify the nature of the FtsZ84 assembly defect, we isolated and characterized three intragenic suppressors of ftsZ84. All three suppressor mutations increased the apparent affinity of FtsZ84 for GTP, consistent with improved subunit-subunit interactions along the longitudinal interface. Although kinetic analysis indicates that the suppressor mutations increase the affinity of FtsZ84 for GTP, all three exhibit reduced rates of GTP hydrolysis and fail to support assembly in vitro. Conclusion Together, our data suggest that FtsZ, and potentially other enzymes whose assembly is similarly regulated, can compensate for defects in catalysis through increases in substrate binding and subunit-subunit interactions. In addition, these results highlight the dichotomy between commonly used in vitro assembly conditions and FtsZ ring formation in the complex intracellular milieu. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0544-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Heidi A Arjes
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130, USA. .,Present address: Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.
| | - Bradley Lai
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130, USA.
| | - Ezinwanne Emelue
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130, USA.
| | - Adriana Steinbach
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130, USA.
| | - Petra Anne Levin
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130, USA.
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11
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Ortiz C, Natale P, Cueto L, Vicente M. The keepers of the ring: regulators of FtsZ assembly. FEMS Microbiol Rev 2015; 40:57-67. [PMID: 26377318 DOI: 10.1093/femsre/fuv040] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/21/2015] [Indexed: 11/13/2022] Open
Abstract
FtsZ, a GTPase distributed in the cytoplasm of most bacteria, is the major component of the machinery responsible for division (the divisome) in Escherichia coli. It interacts with additional proteins that contribute to its function forming a ring at the midcell that is essential to constrict the membrane. FtsZ is indirectly anchored to the membrane and it is prevented from polymerizing at locations where septation is undesired. Several properties of FtsZ are mediated by other proteins that function as keepers of the ring. ZipA and FtsA serve to anchor the ring, and together with a set of Zap proteins, they stabilize it. The MinCDE and SlmA proteins prevent the polymerization of FtsZ at sites other than the midcell. Finally, ClpP degrades FtsZ, an action prevented by ZipA. Many of the FtsZ keepers interact with FtsZ through a central hub located at its carboxy terminal end.
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Affiliation(s)
- Cristina Ortiz
- Centro Nacional de Biotecnología - Consejo Superior de Investigaciones Científicas (CNB-CSIC), C/ Darwin 3, Madrid 28049, Spain
| | - Paolo Natale
- Centro Nacional de Biotecnología - Consejo Superior de Investigaciones Científicas (CNB-CSIC), C/ Darwin 3, Madrid 28049, Spain
| | - Laura Cueto
- Centro Nacional de Biotecnología - Consejo Superior de Investigaciones Científicas (CNB-CSIC), C/ Darwin 3, Madrid 28049, Spain
| | - Miguel Vicente
- Centro Nacional de Biotecnología - Consejo Superior de Investigaciones Científicas (CNB-CSIC), C/ Darwin 3, Madrid 28049, Spain
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12
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Salvarelli E, Krupka M, Rivas G, Mingorance J, Gómez-Puertas P, Alfonso C, Rico AI. The Cell Division Protein FtsZ from Streptococcus pneumoniae Exhibits a GTPase Activity Delay. J Biol Chem 2015; 290:25081-9. [PMID: 26330552 DOI: 10.1074/jbc.m115.650077] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Indexed: 11/06/2022] Open
Abstract
The cell division protein FtsZ assembles in vitro by a mechanism of cooperative association dependent on GTP, monovalent cations, and Mg(2+). We have analyzed the GTPase activity and assembly dynamics of Streptococcus pneumoniae FtsZ (SpnFtsZ). SpnFtsZ assembled in an apparently cooperative process, with a higher critical concentration than values reported for other FtsZ proteins. It sedimented in the presence of GTP as a high molecular mass polymer with a well defined size and tended to form double-stranded filaments in electron microscope preparations. GTPase activity depended on K(+) and Mg(2+) and was inhibited by Na(+). GTP hydrolysis exhibited a delay that included a lag phase followed by a GTP hydrolysis activation step, until reaction reached the GTPase rate. The lag phase was not found in polymer assembly, suggesting a transition from an initial non-GTP-hydrolyzing polymer that switches to a GTP-hydrolyzing polymer, supporting models that explain FtsZ polymer cooperativity.
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Affiliation(s)
- Estefanía Salvarelli
- From the Servicio de Microbiología, Hospital Universitario La Paz, IdiPAZ, 28046 Madrid, Spain, Biomol-Informatics S.L., Universidad Autónoma, 28049 Madrid, Spain,
| | | | - Germán Rivas
- the Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain
| | - Jesus Mingorance
- From the Servicio de Microbiología, Hospital Universitario La Paz, IdiPAZ, 28046 Madrid, Spain
| | - Paulino Gómez-Puertas
- Biomol-Informatics S.L., Universidad Autónoma, 28049 Madrid, Spain, the Molecular Modelling Group, Centro de Biología Molecular "Severo Ochoa," Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain, and
| | - Carlos Alfonso
- the Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain
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13
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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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14
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Cabré EJ, Monterroso B, Alfonso C, Sánchez-Gorostiaga A, Reija B, Jiménez M, Vicente M, Zorrilla S, Rivas G. The Nucleoid Occlusion SlmA Protein Accelerates the Disassembly of the FtsZ Protein Polymers without Affecting Their GTPase Activity. PLoS One 2015; 10:e0126434. [PMID: 25950808 PMCID: PMC4423959 DOI: 10.1371/journal.pone.0126434] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 04/02/2015] [Indexed: 11/20/2022] Open
Abstract
Division site selection is achieved in bacteria by different mechanisms, one of them being nucleoid occlusion, which prevents Z-ring assembly nearby the chromosome. Nucleoid occlusion in E. coli is mediated by SlmA, a sequence specific DNA binding protein that antagonizes FtsZ assembly. Here we show that, when bound to its specific target DNA sequences (SBS), SlmA reduces the lifetime of the FtsZ protofilaments in solution and of the FtsZ bundles when located inside permeable giant vesicles. This effect appears to be essentially uncoupled from the GTPase activity of the FtsZ protofilaments, which is insensitive to the presence of SlmA·SBS. The interaction of SlmA·SBS with either FtsZ protofilaments containing GTP or FtsZ oligomers containing GDP results in the disassembly of FtsZ polymers. We propose that SlmA·SBS complexes control the polymerization state of FtsZ by accelerating the disassembly of the FtsZ polymers leading to their fragmentation into shorter species that are still able to hydrolyze GTP at the same rate. SlmA defines therefore a new class of inhibitors of the FtsZ ring different from the SOS response regulator SulA and from the moonlighting enzyme OpgH, inhibitors of the GTPase activity. SlmA also shows differences compared with MinC, the inhibitor of the division site selection Min system, which shortens FtsZ protofilaments by interacting with the GDP form of FtsZ.
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Affiliation(s)
- Elisa J. Cabré
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Begoña Monterroso
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Carlos Alfonso
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Alicia Sánchez-Gorostiaga
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Belén Reija
- Instituto de Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Mercedes Jiménez
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Miguel Vicente
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Silvia Zorrilla
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Instituto de Química-Física Rocasolano, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- * E-mail: (GR); (SZ)
| | - Germán Rivas
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- * E-mail: (GR); (SZ)
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15
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Bacterial cell division proteins as antibiotic targets. Bioorg Chem 2014; 55:27-38. [PMID: 24755375 DOI: 10.1016/j.bioorg.2014.03.007] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 03/20/2014] [Accepted: 03/24/2014] [Indexed: 11/21/2022]
Abstract
Proteins involved in bacterial cell division often do not have a counterpart in eukaryotic cells and they are essential for the survival of the bacteria. The genetic accessibility of many bacterial species in combination with the Green Fluorescence Protein revolution to study localization of proteins and the availability of crystal structures has increased our knowledge on bacterial cell division considerably in this century. Consequently, bacterial cell division proteins are more and more recognized as potential new antibiotic targets. An international effort to find small molecules that inhibit the cell division initiating protein FtsZ has yielded many compounds of which some are promising as leads for preclinical use. The essential transglycosylase activity of peptidoglycan synthases has recently become accessible to inhibitor screening. Enzymatic assays for and structural information on essential integral membrane proteins such as MraY and FtsW involved in lipid II (the peptidoglycan building block precursor) biosynthesis have put these proteins on the list of potential new targets. This review summarises and discusses the results and approaches to the development of lead compounds that inhibit bacterial cell division.
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16
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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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17
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Sydor AM, Lebrette H, Ariyakumaran R, Cavazza C, Zamble DB. Relationship between Ni(II) and Zn(II) coordination and nucleotide binding by the Helicobacter pylori [NiFe]-hydrogenase and urease maturation factor HypB. J Biol Chem 2014; 289:3828-41. [PMID: 24338018 PMCID: PMC3924253 DOI: 10.1074/jbc.m113.502781] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 12/01/2013] [Indexed: 12/23/2022] Open
Abstract
The pathogen Helicobacter pylori requires two nickel-containing enzymes, urease and [NiFe]-hydrogenase, for efficient colonization of the human gastric mucosa. These enzymes possess complex metallocenters that are assembled by teams of proteins in multistep pathways. One essential accessory protein is the GTPase HypB, which is required for Ni(II) delivery to [NiFe]-hydrogenase and participates in urease maturation. Ni(II) or Zn(II) binding to a site embedded in the GTPase domain of HypB modulates the enzymatic activity, suggesting a mechanism of regulation. In this study, biochemical and structural analyses of H. pylori HypB (HpHypB) revealed an intricate link between nucleotide and metal binding. HpHypB nickel coordination, stoichiometry, and affinity were modulated by GTP and GDP, an effect not observed for zinc, and biochemical evidence suggests that His-107 coordination to nickel toggles on and off in a nucleotide-dependent manner. These results are consistent with the crystal structure of HpHypB loaded with Ni(II), GDP, and Pi, which reveals a nickel site distinct from that of zinc-loaded Methanocaldococcus jannaschii HypB as well as subtle changes to the protein structure. Furthermore, Cys-142, a metal ligand from the Switch II GTPase motif, was identified as a key component of the signal transduction between metal binding and the enzymatic activity. Finally, potassium accelerated the enzymatic activity of HpHypB but had no effect on the other biochemical properties of the protein. Altogether, this molecular level information about HpHypB provides insight into its cellular function and illuminates a possible mechanism of metal ion discrimination.
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Affiliation(s)
- Andrew M. Sydor
- From the Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada and
| | - Hugo Lebrette
- University Grenoble Alpes, Institut de Biologie Structurale (IBS), CEA, DSV, IBS and CNRS, IBS, F-38000 Grenoble, France
| | - Rishikesh Ariyakumaran
- From the Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada and
| | - Christine Cavazza
- University Grenoble Alpes, Institut de Biologie Structurale (IBS), CEA, DSV, IBS and CNRS, IBS, F-38000 Grenoble, France
| | - Deborah B. Zamble
- From the Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada and
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18
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Król E, Scheffers DJ. FtsZ polymerization assays: simple protocols and considerations. J Vis Exp 2013:e50844. [PMID: 24300445 PMCID: PMC3991336 DOI: 10.3791/50844] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
During bacterial cell division, the essential protein FtsZ assembles in the middle of the cell to form the so-called Z-ring. FtsZ polymerizes into long filaments in the presence of GTP in vitro, and polymerization is regulated by several accessory proteins. FtsZ polymerization has been extensively studied in vitro using basic methods including light scattering, sedimentation, GTP hydrolysis assays and electron microscopy. Buffer conditions influence both the polymerization properties of FtsZ, and the ability of FtsZ to interact with regulatory proteins. Here, we describe protocols for FtsZ polymerization studies and validate conditions and controls using Escherichia coli and Bacillus subtilis FtsZ as model proteins. A low speed sedimentation assay is introduced that allows the study of the interaction of FtsZ with proteins that bundle or tubulate FtsZ polymers. An improved GTPase assay protocol is described that allows testing of GTP hydrolysis over time using various conditions in a 96-well plate setup, with standardized incubation times that abolish variation in color development in the phosphate detection reaction. The preparation of samples for light scattering studies and electron microscopy is described. Several buffers are used to establish suitable buffer pH and salt concentration for FtsZ polymerization studies. A high concentration of KCl is the best for most of the experiments. Our methods provide a starting point for the in vitro characterization of FtsZ, not only from E. coli and B. subtilis but from any other bacterium. As such, the methods can be used for studies of the interaction of FtsZ with regulatory proteins or the testing of antibacterial drugs which may affect FtsZ polymerization.
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Affiliation(s)
- Ewa Król
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen
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19
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Natale P, Pazos M, Vicente M. TheEscherichia colidivisome: born to divide. Environ Microbiol 2013; 15:3169-82. [DOI: 10.1111/1462-2920.12227] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 07/18/2013] [Accepted: 07/23/2013] [Indexed: 11/27/2022]
Affiliation(s)
- Paolo Natale
- Centro Nacional de Biotecnología (CNB-CSIC); C/Darwin n° 3 E-28049 Madrid Spain
| | - Manuel Pazos
- Centro Nacional de Biotecnología (CNB-CSIC); C/Darwin n° 3 E-28049 Madrid Spain
| | - Miguel Vicente
- Centro Nacional de Biotecnología (CNB-CSIC); C/Darwin n° 3 E-28049 Madrid Spain
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20
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Ahijado-Guzmán R, Alfonso C, Reija B, Salvarelli E, Mingorance J, Zorrilla S, Monterroso B, Rivas G. Control by potassium of the size distribution of Escherichia coli FtsZ polymers is independent of GTPase activity. J Biol Chem 2013; 288:27358-27365. [PMID: 23940054 DOI: 10.1074/jbc.m113.482943] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The influence of potassium content (at neutral pH and millimolar Mg(2+)) on the size distribution of FtsZ polymers formed in the presence of constantly replenished GTP under steady-state conditions was studied by a combination of biophysical methods. The size of the GTP-FtsZ polymers decreased with lower potassium concentration, in contrast with the increase in the mass of the GDP-FtsZ oligomers, whereas no effect was observed on FtsZ GTPase activity and critical concentration of polymerization. Remarkably, the concerted formation of a narrow size distribution of GTP-FtsZ polymers previously observed at high salt concentration was maintained in all KCl concentrations tested. Polymers induced with guanosine 5'-(α,β-methylene)triphosphate, a slowly hydrolyzable analog of GTP, became larger and polydisperse as the potassium concentration was decreased. Our results suggest that the potassium dependence of the GTP-FtsZ polymer size may be related to changes in the subunit turnover rate that are independent of the GTP hydrolysis rate. The formation of a narrow size distribution of FtsZ polymers under very different solution conditions indicates that it is an inherent feature of FtsZ, not observed in other filament-forming proteins, with potential implications in the structural organization of the functional Z-ring.
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Affiliation(s)
- Rubén Ahijado-Guzmán
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid
| | - Carlos Alfonso
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid
| | - Belén Reija
- Instituto de Química-Física Rocasolano, CSIC, 28006 Madrid
| | - Estefanía Salvarelli
- Servicio de Microbiología, Hospital Universitario La Paz, IdiPAZ, 28046 Madrid; Biomol Informatics SL, Cantoblanco, 28049 Madrid, Spain
| | - Jesús Mingorance
- Servicio de Microbiología, Hospital Universitario La Paz, IdiPAZ, 28046 Madrid
| | | | - Begoña Monterroso
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid.
| | - Germán Rivas
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid.
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21
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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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22
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Jamous C, Basdevant N, Ha-Duong T. Influence of GTP/GDP and magnesium ion on the solvated structure of the protein FtsZ: a molecular dynamics study. J Biomol Struct Dyn 2013; 32:916-27. [PMID: 23782014 DOI: 10.1080/07391102.2013.799436] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
We present here a structural analysis of ten extensive all-atom molecular dynamics simulations of the monomeric protein FtsZ in various binding states. Since the polymerization and GTPase activities of FtsZ depend on the nature of a bound nucleotide as well as on the presence of a magnesium ion, we studied the structural differences between the average conformations of the following five systems: FtsZ-Apo, FtsZ-GTP, FtsZ-GDP, FtsZ-GTP-Mg, and FtsZ-GDP-Mg. The in silico solvated average structure of FtsZ-Apo significantly differs from the crystallographic structure 1W59 of FtsZ which was crystallized in a dimeric form without nucleotide and magnesium. The simulated Apo form of the protein also clearly differs from the FtsZ structures when it is bound to its ligand, the most important discrepancies being located in the loops surrounding the nucleotide binding pocket. The three average structures of FtsZ-GTP, FtsZ-GDP, and FtsZ-GTP-Mg are overall similar, except for the loop T7 located at the opposite side of the binding pocket and whose conformation in FtsZ-GDP notably differs from the one in FtsZ-GTP and FtsZ-GTP-Mg. The presence of a magnesium ion in the binding pocket has no impact on the FtsZ conformation when it is bound to GTP. In contrast, when the protein is bound to GDP, the divalent cation causes a translation of the nucleotide outwards the pocket, inducing a significant conformational change of the loop H6-H7 and the top of helix H7.
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Affiliation(s)
- Carla Jamous
- a LAMBE - UMR CNRS 8587, Université d'Evry-Val-d'Essonne, Rue du Père André Jarlan , 91025 , Evry Cedex , France
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23
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Rico AI, Krupka M, Vicente M. In the beginning, Escherichia coli assembled the proto-ring: an initial phase of division. J Biol Chem 2013; 288:20830-20836. [PMID: 23740256 DOI: 10.1074/jbc.r113.479519] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Cell division in Escherichia coli begins by assembling three proteins, FtsZ, FtsA, and ZipA, to form a proto-ring at midcell. These proteins nucleate an assembly of at least 35 components, the divisome. The structuring of FtsZ to form a ring and the processes that effect constriction have been explained by alternative but not mutually exclusive mechanisms. We discuss how FtsA and ZipA provide anchoring of the cytoplasmic FtsZ to the membrane and how a temporal sequence of alternative protein interactions may operate in the maturation and stability of the proto-ring. How the force needed for constriction is generated and how the proto-ring proteins relate to peptidoglycan synthesis remain as the main challenges for future research.
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Affiliation(s)
- Ana Isabel Rico
- From the Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain
| | - Marcin Krupka
- From the Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain
| | - Miguel Vicente
- From the Centro Nacional de Biotecnología (CNB), Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain.
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24
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López E, Madero L, López-Pascual J, Latterich M. Clinical proteomics and OMICS clues useful in translational medicine research. Proteome Sci 2012; 10:35. [PMID: 22642823 PMCID: PMC3536680 DOI: 10.1186/1477-5956-10-35] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Accepted: 05/04/2012] [Indexed: 12/21/2022] Open
Abstract
Since the advent of the new proteomics era more than a decade ago, large-scale studies of protein profiling have been used to identify distinctive molecular signatures in a wide array of biological systems, spanning areas of basic biological research, clinical diagnostics, and biomarker discovery directed toward therapeutic applications. Recent advances in protein separation and identification techniques have significantly improved proteomic approaches, leading to enhancement of the depth and breadth of proteome coverage. Proteomic signatures, specific for multiple diseases, including cancer and pre-invasive lesions, are emerging. This article combines, in a simple manner, relevant proteomic and OMICS clues used in the discovery and development of diagnostic and prognostic biomarkers that are applicable to all clinical fields, thus helping to improve applications of clinical proteomic strategies for translational medicine research.
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Affiliation(s)
- Elena López
- Centro de Investigación i + 12, Hospital 12 de Octubre, Av, De Córdoba s/n, 28040, Madrid, Spain.
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25
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Depolymerization dynamics of individual filaments of bacterial cytoskeletal protein FtsZ. Proc Natl Acad Sci U S A 2012; 109:8133-8. [PMID: 22566654 DOI: 10.1073/pnas.1204844109] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
We report observation and analysis of the depolymerization filaments of the bacterial cytoskeletal protein FtsZ (filament temperature-sensitive Z) formed on a mica surface. At low concentration, proteins adsorbed on the surface polymerize forming curved filaments that close into rings that remain stable for some time before opening irreversibly and fully depolymerizing. The distribution of ring lifetimes (T) as a function of length (N), shows that the rate of ring aperture correlates with filament length. If this ring lifetime is expressed as a bond survival time, (T(b) ≡ NT), this correlation is abolished, indicating that these rupture events occur randomly and independently at each monomer interface. After rings open irreversibly, depolymerization of the remaining filaments is fast, but can be slowed down and followed using a nonhydrolyzing GTP analogue. The histogram of depolymerization velocities of individual filaments has an asymmetric distribution that can be fit with a computer model that assumes two rupture rates, a slow one similar to the one observed for ring aperture, affecting monomers in the central part of the filaments, and a faster one affecting monomers closer to the open ends. From the quantitative analysis, we conclude that the depolymerization rate is affected both by nucleotide hydrolysis rate and by its exchange along the filament, that all monomer interfaces are equally competent for hydrolysis, although depolymerization is faster at the open ends than in central filament regions, and that all monomer-monomer interactions, regardless of the nucleotide present, can adopt a curved configuration.
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26
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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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Mateos-Gil P, Márquez I, López-Navajas P, Jiménez M, Vicente M, Mingorance J, Rivas G, Vélez M. FtsZ polymers bound to lipid bilayers through ZipA form dynamic two dimensional networks. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1818:806-13. [PMID: 22198391 DOI: 10.1016/j.bbamem.2011.12.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Revised: 12/08/2011] [Accepted: 12/09/2011] [Indexed: 10/14/2022]
Abstract
Bacteria divide by forming a contractile ring around their midcell region. FtsZ, a cytoskeletal soluble protein structurally related to tubulin, is the main component of this division machinery. It forms filaments that bundle at the inner side of the cytoplasmic membrane. These FtsZ bundles do not attach to bare lipid surfaces. In Escherichia coli they remain near the membrane surface by attaching to the membrane protein ZipA and FtsA. In order to study the structure and dynamics of the ZipA-FtsZ bundles formed on a lipid surface, we have oriented a soluble form of ZipA (sZipA), with its transmembrane domain substituted by a histidine tag, on supported lipid membranes. Atomic force microscopy has been used to visualize the polymers formed on top of this biomimetic surface. In the presence of GTP, when sZipA is present, FtsZ polymers restructure forming higher order structures. The lipid composition of the underlying membrane affects the aggregation kinetics and the shape of the structures formed. On the negatively charged E. coli lipid membranes, filaments condense from initially disperse material to form a network that is more dynamic and flexible than the one formed on phosphatidyl choline bilayers. These FtsZ-ZipA filament bundles are interconnected, retain their capacity to dynamically restructure, to fragment, to anneal and to condense laterally.
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Affiliation(s)
- Pablo Mateos-Gil
- Instituto de Ciencia de Materiales Nicolás Cabrera, Universidad Autónoma de Madrid, Madrid, Spain
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Salvarelli E, Krupka M, Rivas G, Vicente M, Mingorance J. Independence between GTPase active sites in the Escherichia coli cell division protein FtsZ. FEBS Lett 2011; 585:3880-3. [PMID: 22064072 DOI: 10.1016/j.febslet.2011.10.046] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Revised: 10/24/2011] [Accepted: 10/25/2011] [Indexed: 10/15/2022]
Abstract
We have analyzed the substrate kinetics of the GTPase activity of FtsZ and the effects of two different GTPase inhibitors, GDP and the slowly hydrolyzable GTP analogue GMPCPP. In the absence of inhibitors the GTPase activity follows simple Michaelis-Menten kinetics, and both GDP and GMPCPP inhibited the activity in a competitive manner. These results indicate that the GTPase active sites in FtsZ filaments are independent of each other, a feature relevant to elucidate the role of GTP hydrolysis in FtsZ function and cell division.
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29
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López E, Wesselink JJ, López I, Mendieta J, Gómez-Puertas P, Muñoz SR. Technical phosphoproteomic and bioinformatic tools useful in cancer research. J Clin Bioinforma 2011; 1:26. [PMID: 21967744 PMCID: PMC3195713 DOI: 10.1186/2043-9113-1-26] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Accepted: 10/03/2011] [Indexed: 12/22/2022] Open
Abstract
Reversible protein phosphorylation is one of the most important forms of cellular regulation. Thus, phosphoproteomic analysis of protein phosphorylation in cells is a powerful tool to evaluate cell functional status. The importance of protein kinase-regulated signal transduction pathways in human cancer has led to the development of drugs that inhibit protein kinases at the apex or intermediary levels of these pathways. Phosphoproteomic analysis of these signalling pathways will provide important insights for operation and connectivity of these pathways to facilitate identification of the best targets for cancer therapies. Enrichment of phosphorylated proteins or peptides from tissue or bodily fluid samples is required. The application of technologies such as phosphoenrichments, mass spectrometry (MS) coupled to bioinformatics tools is crucial for the identification and quantification of protein phosphorylation sites for advancing in such relevant clinical research. A combination of different phosphopeptide enrichments, quantitative techniques and bioinformatic tools is necessary to achieve good phospho-regulation data and good structural analysis of protein studies. The current and most useful proteomics and bioinformatics techniques will be explained with research examples. Our aim in this article is to be helpful for cancer research via detailing proteomics and bioinformatic tools.
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Affiliation(s)
- Elena López
- Centro de Investigación i+12 del Hospital Universitario 12 de Octubre, Avda de Córdoba s/n Madrid, 28041, Spain
| | - Jan-Jaap Wesselink
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM) Campus de Cantoblanco, c/Nicolás Cabrera, 1, 28049 Madrid, Spain.,Biomol-Informatics, S.L., Parque Científico de Madrid, Campus de Cantoblanco, c/Faraday 7, 28049 Madrid, Spain
| | - Isabel López
- Servicio de Hematología Hospital QUIRÓN, Madrid, Diego de Velázquez 1 28223, Pozuelo Madrid Spain
| | - Jesús Mendieta
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM) Campus de Cantoblanco, c/Nicolás Cabrera, 1, 28049 Madrid, Spain.,Biomol-Informatics, S.L., Parque Científico de Madrid, Campus de Cantoblanco, c/Faraday 7, 28049 Madrid, Spain
| | - Paulino Gómez-Puertas
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM) Campus de Cantoblanco, c/Nicolás Cabrera, 1, 28049 Madrid, Spain
| | - Sarbelio Rodríguez Muñoz
- Servicio de Digestivo, Hospital Universitario 12 Octubre, Avda de Córdoba s/n Madrid, 28041, Spain
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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: 33] [Impact Index Per Article: 2.5] [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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31
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Pacheco-Gómez R, Roper DI, Dafforn TR, Rodger A. The pH dependence of polymerization and bundling by the essential bacterial cytoskeletal protein FtsZ. PLoS One 2011; 6:e19369. [PMID: 21738567 PMCID: PMC3125165 DOI: 10.1371/journal.pone.0019369] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Accepted: 04/02/2011] [Indexed: 11/19/2022] Open
Abstract
There is a growing body of evidence that bacterial cell division is an intricate coordinated process of comparable complexity to that seen in eukaryotic cells. The dynamic assembly of Escherichia coli FtsZ in the presence of GTP is fundamental to its activity. FtsZ polymerization is a very attractive target for novel antibiotics given its fundamental and universal function. In this study our aim was to understand further the GTP-dependent FtsZ polymerization mechanism and our main focus is on the pH dependence of its behaviour. A key feature of this work is the use of linear dichroism (LD) to follow the polymerization of FtsZ monomers into polymeric structures. LD is the differential absorption of light polarized parallel and perpendicular to an orientation direction (in this case that provided by shear flow). It thus readily distinguishes between FtsZ polymers and monomers. It also distinguishes FtsZ polymers and less well-defined aggregates, which light scattering methodologies do not. The polymerization of FtsZ over a range of pHs was studied by right-angled light scattering to probe mass of FtsZ structures, LD to probe real-time formation of linear polymeric fibres, a specially developed phosphate release assay to relate guanosine triphosphate (GTP) hydrolysis to polymer formation, and electron microscopy (EM) imaging of reaction products as a function of time and pH. We have found that lowering the pH from neutral to 6.5 does not change the nature of the FtsZ polymers in solution—it simply facilitates the polymerization so the fibres present are longer and more abundant. Conversely, lowering the pH to 6.0 has much the same effect as introducing divalent cations or the FtsZ-associated protein YgfE (a putative ZapA orthologue in E. coli)—it stablizes associations of protofilaments.
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Affiliation(s)
- Raúl Pacheco-Gómez
- Molecular Organization and Assembly in Cells Doctoral Training Centre, University of Warwick, Coventry, United Kingdom
| | - David I. Roper
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Timothy R. Dafforn
- Department of Biosciences, University of Birmingham, Edgebaston, Birmingham, United Kingdom
| | - Alison Rodger
- Molecular Organization and Assembly in Cells Doctoral Training Centre, University of Warwick, Coventry, United Kingdom
- Department of Chemistry, University of Warwick, Coventry, United Kingdom
- * E-mail:
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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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Mingorance J, Rivas G, Vélez M, Gómez-Puertas P, Vicente M. Strong FtsZ is with the force: mechanisms to constrict bacteria. Trends Microbiol 2010; 18:348-56. [PMID: 20598544 DOI: 10.1016/j.tim.2010.06.001] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2010] [Revised: 05/10/2010] [Accepted: 06/01/2010] [Indexed: 10/19/2022]
Abstract
FtsZ, the best-known prokaryotic division protein, assembles at midcell with other proteins forming a ring during septation. Widely conserved in bacteria, FtsZ represents the ancestor of tubulin. In the presence of GTP it forms polymers able to associate into multi-stranded flexible structures. FtsZ research is aimed at determining the role of the Z-ring in division, describing the polymerization and potential force-generating mechanisms and evaluating the roles of nucleotide exchange and hydrolysis. Systems to reconstruct the FtsZ ring in vitro have been described and some of its mechanical properties have been reproduced using in silico modeling. We discuss current research in FtsZ, some of the controversies, and finally propose further research needed to complete a model of FtsZ action that reconciles its in vitro properties with its role in division.
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Affiliation(s)
- Jesús Mingorance
- Unidad de Investigación y Servicio de Microbiología, Hospital Universitario La Paz (IdiPAZ), Paseo de La Castellana, 261, 28046 Madrid, Spain.
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Calculations of binding affinity between C8-substituted GTP analogs and the bacterial cell-division protein FtsZ. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2010; 39:1573-80. [PMID: 20559630 PMCID: PMC2975913 DOI: 10.1007/s00249-010-0614-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Revised: 05/21/2010] [Accepted: 05/26/2010] [Indexed: 11/20/2022]
Abstract
The FtsZ protein is a self-polymerizing GTPase that plays a central role in bacterial cell division. Several C8-substituted GTP analogs are known to inhibit the polymerization of FtsZ by competing for the same binding site as its endogenous activating ligand GTP. Free energy calculations of the relative binding affinities to FtsZ for a set of five C8-substituted GTP analogs were performed. The calculated values agree well with the available experimental data, and the main contribution to the free energy differences is determined to be the conformational restriction of the ligands. The dihedral angle distributions around the glycosidic bond of these compounds in water are known to vary considerably depending on the physicochemical properties of the substituent at C8. However, within the FtsZ protein, this substitution has a negligible influence on the dihedral angle distributions, which fall within the narrow range of −140° to −90° for all investigated compounds. The corresponding ensemble average of the coupling constants 3J(C4,H1′) is calculated to be 2.95 ± 0.1 Hz. The contribution of the conformational selection of the GTP analogs upon binding was quantified from the corresponding populations. The obtained restraining free energy values follow the same trend as the relative binding affinities to FtsZ, indicating their dominant contribution.
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Mohammadi T, Ploeger GEJ, Verheul J, Comvalius AD, Martos A, Alfonso C, van Marle J, Rivas G, den Blaauwen T. The GTPase activity of Escherichia coli FtsZ determines the magnitude of the FtsZ polymer bundling by ZapA in vitro. Biochemistry 2009; 48:11056-66. [PMID: 19842714 PMCID: PMC2778355 DOI: 10.1021/bi901461p] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
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FtsZ polymerizes in a ring-like structure at mid cell to initiate cell division in Escherichia coli. The ring is stabilized by a number of proteins among which the widely conserved ZapA protein. Using antibodies against ZapA, we found surprisingly that the cellular concentration of ZapA is approximately equal to that of FtsZ. This raised the question of how the cell can prevent their interaction and thereby the premature stabilization of FtsZ protofilaments in nondividing cells. Therefore, we studied the FtsZ−ZapA interaction at the physiological pH of 7.5 instead of pH 6.5 (the optimal pH for FtsZ polymerization), under conditions that stimulate protofilament formation (5 mM MgCl2) and under conditions that stimulate and stabilize protofilaments (10 mM MgCl2). Using pelleting, light scattering, and GTPase assays, it was found that stabilization and bundling of FtsZ polymers by ZapA was inversely correlated to the GTPase activity of FtsZ. As GTP hydrolysis is the rate-limiting factor for depolymerization of FtsZ, we propose that ZapA will only enhance the cooperativity of polymer association during the transition from helical filament to mid cell ring and will not stabilize the short single protofilaments in the cytoplasm. All thus far published in vitro data on the interaction between FtsZ and ZapA have been obtained with His-ZapA. We found that in our case the presence of a His tag fused to ZapA prevented the protein to complement a ΔzapA strain in vivo and that it affected the interaction between FtsZ and ZapA in vitro.
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Affiliation(s)
- Tamimount Mohammadi
- Swammerdam Institute for Life Sciences, Molecular Cytology, Science Park 904, 1098 XH Amsterdam, The Netherlands
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Goh S, Boberek JM, Nakashima N, Stach J, Good L. Concurrent growth rate and transcript analyses reveal essential gene stringency in Escherichia coli. PLoS One 2009; 4:e6061. [PMID: 19557168 PMCID: PMC2698124 DOI: 10.1371/journal.pone.0006061] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2008] [Accepted: 06/02/2009] [Indexed: 01/29/2023] Open
Abstract
Background Genes essential for bacterial growth are of particular scientific interest. Many putative essential genes have been identified or predicted in several species, however, little is known about gene expression requirement stringency, which may be an important aspect of bacterial physiology and likely a determining factor in drug target development. Methodology/Principal Findings Working from the premise that essential genes differ in absolute requirement for growth, we describe silencing of putative essential genes in E. coli to obtain a titration of declining growth rates and transcript levels by using antisense peptide nucleic acids (PNA) and expressed antisense RNA. The relationship between mRNA decline and growth rate decline reflects the degree of essentiality, or stringency, of an essential gene, which is here defined by the minimum transcript level for a 50% reduction in growth rate (MTL50). When applied to four growth essential genes, both RNA silencing methods resulted in MTL50 values that reveal acpP as the most stringently required of the four genes examined, with ftsZ the next most stringently required. The established antibacterial targets murA and fabI were less stringently required. Conclusions RNA silencing can reveal stringent requirements for gene expression with respect to growth. This method may be used to validate existing essential genes and to quantify drug target requirement.
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Affiliation(s)
- Shan Goh
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
- Department of Pathology and Infectious Diseases, Royal Veterinary College, University of London, London, United Kingdom
| | - Jaroslaw M. Boberek
- Department of Pathology and Infectious Diseases, Royal Veterinary College, University of London, London, United Kingdom
| | - Nobutaka Nakashima
- Research Institute of Genome-based biofactory, Toyohira-Ku, Sapporo, Japan
| | - Jem Stach
- School of Biology, University of Newcastle, Newcastle upon Tyne, United Kingdom
| | - Liam Good
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, Sweden
- Department of Pathology and Infectious Diseases, Royal Veterinary College, University of London, London, United Kingdom
- * E-mail:
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