1
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Taguchi A, Nakashima R, Nishino K. Structural Basis of Nucleotide Selectivity in Pyruvate Kinase. J Mol Biol 2024; 436:168708. [PMID: 39009072 DOI: 10.1016/j.jmb.2024.168708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 07/09/2024] [Accepted: 07/10/2024] [Indexed: 07/17/2024]
Abstract
Nucleoside triphosphates are indispensable in numerous biological processes, with enzymes involved in their biogenesis playing pivotal roles in cell proliferation. Pyruvate kinase (PYK), commonly regarded as the terminal glycolytic enzyme that generates ATP in tandem with pyruvate, is also capable of synthesizing a wide range of nucleoside triphosphates from their diphosphate precursors. Despite their substrate promiscuity, some PYKs show preference towards specific nucleotides, suggesting an underlying mechanism for differentiating nucleotide bases. However, the thorough characterization of this mechanism has been hindered by the paucity of nucleotide-bound PYK structures. Here, we present crystal structures of Streptococcus pneumoniae PYK in complex with four different nucleotides. These structures facilitate direct comparison of the protein-nucleotide interactions and offer structural insights into its pronounced selectivity for GTP synthesis. Notably, this selectivity is dependent on a sequence motif in the nucleotide recognition site that is widely present among prokaryotic PYKs, particularly in Firmicutes species. We show that pneumococcal cell growth is significantly impaired when expressing a PYK variant with compromised GTP and UTP synthesis activity, underscoring the importance of PYK in maintaining nucleotide homeostasis. Our findings collectively advance our understanding of PYK biochemistry and prokaryotic metabolism.
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Affiliation(s)
- Atsushi Taguchi
- SANKEN, Osaka University, Ibaraki, Osaka 567-0047, Japan; Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871, Japan.
| | | | - Kunihiko Nishino
- SANKEN, Osaka University, Ibaraki, Osaka 567-0047, Japan; Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871, Japan; Center for Infectious Disease Education and Research, Osaka University, Suita, Osaka 565-0871, Japan.
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2
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Basak P, Dastidar DG, Ghosh D, Chakraborty T, Sau S, Chakrabarti G. Staphylococcus aureus major cell division protein FtsZ assembly is inhibited by silibinin, a natural flavonolignan that also blocked bacterial growth and biofilm formation. Int J Biol Macromol 2024; 279:135252. [PMID: 39222779 DOI: 10.1016/j.ijbiomac.2024.135252] [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: 05/22/2024] [Revised: 08/29/2024] [Accepted: 08/30/2024] [Indexed: 09/04/2024]
Abstract
The bacterial cell division protein FtsZ has been considered a potential therapeutic target due to its rapid treadmilling that induces cellular wall construction in bacteria. The current study discovered a novel antimicrobial compound, silibinin, a natural flavonolignan and its impact on the recombinant S. aureus FtsZ (SaFtsZ). Silibinin inhibited S. aureus Newman growth in a dose-dependent manner. The IC50 and MIC values for silibinin were 75 μM and 200 μM, respectively. It had no cytotoxicity against HEK293 cells in vitro. Silibinin also enlarged the bacterial cell morphology by ∼40 folds and showed antibiofilm property. It perturbed the S. aureus membrane potential both at IC50 conc. and at MIC conc. Further, it inhibited both the polymerization and GTPase activity of SaFtsZ. It did not inhibit tubulin assembly, a eukaryotic FtsZ homolog. A fluorescence quenching study yielded the Kd value for SaFtsZ-Silibinin interaction and binding stoichiometry 0.857 ± 0.188 μM and 1:1, respectively. Both in silico study and competition assay indicated that silibinin binds at the GTP binding site on SaFtsZ. The Ki value for the silibinin-mediated inhibition of SaFtsZ was 8.8 μM. Therefore, these findings have comprehensively shown the antimicrobial behavior of silibinin on S. aureus Newman cells targeting SaFtsZ.
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Affiliation(s)
- Prithvi Basak
- Department of Biotechnology, Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, WB 700 019, India
| | - Debabrata Ghosh Dastidar
- Guru Nanak Institute of Pharmaceutical Science & Technology, 157/F Nilgunj Road, Panihati, Kolkata 700114, West Bengal, India
| | - Dipanjan Ghosh
- Department of Biotechnology, Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, WB 700 019, India
| | - Tushar Chakraborty
- Department of Biological Sciences, Bose Institute, Kolkata 700091, West Bengal, India
| | - Subrata Sau
- Department of Biological Sciences, Bose Institute, Kolkata 700091, West Bengal, India
| | - Gopal Chakrabarti
- Department of Biotechnology, Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, WB 700 019, India.
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3
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Cui XH, Wei YC, Li XG, Qi XQ, Wu LF, Zhang WJ. N-terminus GTPase domain of the cytoskeleton protein FtsZ plays a critical role in its adaptation to high hydrostatic pressure. Front Microbiol 2024; 15:1441398. [PMID: 39220037 PMCID: PMC11362102 DOI: 10.3389/fmicb.2024.1441398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Accepted: 07/30/2024] [Indexed: 09/04/2024] Open
Abstract
Studies in model microorganisms showed that cell division is highly vulnerable to high hydrostatic pressure (HHP). Disassembly of FtsZ filaments induced by HHP results in the failure of cell division and formation of filamentous cells in E. coli. The specific characteristics of FtsZ that allow for functional cell division in the deep-sea environments, especially in obligate piezophiles that grow exclusively under HHP condition, remain enigmatic. In this study, by using a self-developed HHP in-situ fixation apparatus, we investigated the effect of HHP on FtsZ by examining the subcellular localization of GFP-tagged FtsZ in vivo and the stability of FtsZ filament in vitro. We compared the pressure tolerance of FtsZ proteins from pressure-sensitive strain Shewanella oneidensis MR-1 (FtsZSo) and obligately piezophilic strain Shewanella benthica DB21MT-2 (FtsZSb). Our findings showed that, unlike FtsZSo, HHP hardly affected the Z-ring formation of FtsZSb, and filaments composed of FtsZSb were more stable after incubation under 50 MPa. By constructing chimeric and single amino acid mutated FtsZ proteins, we identified five residues in the N-terminal GTPase domain of FtsZSb whose mutation would impair the Z-ring formation under HHP conditions. Overall, these results demonstrate that FtsZ from the obligately piezophilic strain exhibits superior pressure tolerance than its homologue from shallow water species, both in vivo and in vitro. Differences in pressure tolerance of FtsZ are largely attributed to the N-terminal GTPase domain. This represents the first in-depth study of the adaptation of microbial cytoskeleton protein FtsZ to high hydrostatic pressure, which may provide insights into understanding the complex bioprocess of cell division under extreme environments.
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Affiliation(s)
- Xue-Hua Cui
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yu-Chen Wei
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Xue-Gong Li
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- Institution of Deep-Sea Life Sciences, IDSSE-BGI, Sanya, China
| | - Xiao-Qing Qi
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- Institution of Deep-Sea Life Sciences, IDSSE-BGI, Sanya, China
| | - Long-Fei Wu
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- Institution of Deep-Sea Life Sciences, IDSSE-BGI, Sanya, China
- Aix Marseille University, CNRS, LCB, Marseille, France
| | - Wei-Jia Zhang
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- Institution of Deep-Sea Life Sciences, IDSSE-BGI, Sanya, China
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4
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Chakraborty J, Poddar S, Dutta S, Bahulekar V, Harne S, Srinivasan R, Gayathri P. Dynamics of interdomain rotation facilitates FtsZ filament assembly. J Biol Chem 2024; 300:107336. [PMID: 38718863 PMCID: PMC11157280 DOI: 10.1016/j.jbc.2024.107336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/31/2024] Open
Abstract
FtsZ, the tubulin homolog essential for bacterial cell division, assembles as the Z-ring at the division site, and directs peptidoglycan synthesis by treadmilling. It is unclear how FtsZ achieves kinetic polarity that drives treadmilling. To obtain insights into fundamental features of FtsZ assembly dynamics independent of peptidoglycan synthesis, we carried out structural and biochemical characterization of FtsZ from the cell wall-less bacteria, Spiroplasma melliferum (SmFtsZ). Interestingly the structures of SmFtsZ, bound to GDP and GMPPNP respectively, were captured as domain swapped dimers. SmFtsZ was found to be a slower GTPase with a higher critical concentration (CC) compared to Escherichia coli FtsZ (EcFtsZ). In FtsZs, a conformational switch from R-state (close) to T-state (open) favors polymerization. We identified that Phe224, located at the interdomain cleft of SmFtsZ, is crucial for R- to T-state transition. SmFtsZF224M exhibited higher GTPase activity and lower CC, whereas the corresponding EcFtsZM225F resulted in cell division defects in E. coli. Our results demonstrate that relative rotation of the domains is a rate-limiting step of polymerization. Our structural analysis suggests that the rotation is plausibly triggered upon addition of a GTP-bound monomer to the filament through interaction of the preformed N-terminal domain (NTD). Hence, addition of monomers to the NTD-exposed end of filament is slower in comparison to the C-terminal domain (CTD) end, thus explaining kinetic polarity. In summary, the study highlights the importance of interdomain interactions and conformational changes in regulating FtsZ assembly dynamics.
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Affiliation(s)
- Joyeeta Chakraborty
- Biology Division, Indian Institute of Science Education and Research, Pune, India
| | - Sakshi Poddar
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, India; Homi Bhabha National Institutes (HBNI), Training School Complex, Mumbai, India
| | - Soumyajit Dutta
- Biology Division, Indian Institute of Science Education and Research, Pune, India
| | - Vaishnavi Bahulekar
- Biology Division, Indian Institute of Science Education and Research, Pune, India
| | - Shrikant Harne
- Biology Division, Indian Institute of Science Education and Research, Pune, India
| | - Ramanujam Srinivasan
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, India; Homi Bhabha National Institutes (HBNI), Training School Complex, Mumbai, India
| | - Pananghat Gayathri
- Biology Division, Indian Institute of Science Education and Research, Pune, India.
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5
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Radler P, Loose M. A dynamic duo: Understanding the roles of FtsZ and FtsA for Escherichia coli cell division through in vitro approaches. Eur J Cell Biol 2024; 103:151380. [PMID: 38218128 DOI: 10.1016/j.ejcb.2023.151380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 12/22/2023] [Accepted: 12/24/2023] [Indexed: 01/15/2024] Open
Abstract
Bacteria divide by binary fission. The protein machine responsible for this process is the divisome, a transient assembly of more than 30 proteins in and on the surface of the cytoplasmic membrane. Together, they constrict the cell envelope and remodel the peptidoglycan layer to eventually split the cell into two. For Escherichia coli, most molecular players involved in this process have probably been identified, but obtaining the quantitative information needed for a mechanistic understanding can often not be achieved from experiments in vivo alone. Since the discovery of the Z-ring more than 30 years ago, in vitro reconstitution experiments have been crucial to shed light on molecular processes normally hidden in the complex environment of the living cell. In this review, we summarize how rebuilding the divisome from purified components - or at least parts of it - have been instrumental to obtain the detailed mechanistic understanding of the bacterial cell division machinery that we have today.
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Affiliation(s)
- Philipp Radler
- Institute for Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria; University of Vienna, Djerassiplatz 1, 1030 Wien, Austria.
| | - Martin Loose
- Institute for Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria.
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6
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Kumar H, Manoharan A, Anbarasu A, Ramaiah S. Computational study of the piperidine and FtsZ interaction in Salmonella Typhi: implications for disrupting cell division machinery. J Biomol Struct Dyn 2024:1-14. [PMID: 38321931 DOI: 10.1080/07391102.2024.2314272] [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: 10/08/2022] [Accepted: 01/29/2024] [Indexed: 02/08/2024]
Abstract
FtsZ, a bacterial cell division protein, is essential for assembling the contractile Z-ring crucial in bacterial cytokinesis. Consequently, inhibiting FtsZ could impede proto-filaments, disrupting FtsZ and other associated proteins vital for cell division machinery. Conduct an in-silico drug interaction study to identify novel drug candidates that inhibit the FtsZ protein, aiming to prevent Multi-Drug Resistant (MDR) Salmonella Typhi. Data mining was performed based on piperidine compounds, which were subsequently screened for safe pharmacokinetic profiles. Compounds that met favorable drug-likeness criteria underwent virtual screening against the FtsZ drug target. Two compounds were chosen for molecular docking and molecular dynamic simulation to verify the binding affinity and stability between the target protein and the potential compounds. The 400 isoforms of piperidine analogues were curated, among them potent compound ZINC000000005416 found to possess high binding affinity (-8.49 kcal/mol) and low dissociation constant (0.597 µM). The highest binding affinity shown by ZINC000000005416 was validated by hydrogen bonds, hydrophobic interaction, and salt bridges with the functional domain of the cell division regulatory protein. Docking profiles, when correlated with molecular dynamic simulation (MDS) depicted stable trajectories and compatible conformational changes in the FtsZ-ZINC000000005416 complex. The stable simulated trajectories were validated through free-energy calculations using the Molecular Mechanics-Poisson Boltzmann Surface Area (MM/PBSA) module. Low energy conformations, although the simulation trajectory confirmed the stable ZINC000000005416-FtsZ interaction, which encouraged experimental validations. This study encourages further exploration of the compound ZINC000000005416 as a drug candidate inhibiting FtsZ protein against MDR Salmonella Typhi.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hithesh Kumar
- Department of Bio-Sciences, School of Biosciences and Technology (SBST), Vellore Institute of Technology, Vellore, India
- Medical and Biological Computing Laboratory, Department of Biotechnology, School of Biosciences and Technology (SBST), Vellore Institute of Technology, Vellore, India
| | - Anand Manoharan
- Department of Paediatrics, The CHILDS Trust Medical Research Foundation, Kanchi Kamakoti CHILDS Trust Hospital, Chennai, India
| | - Anand Anbarasu
- Medical and Biological Computing Laboratory, Department of Biotechnology, School of Biosciences and Technology (SBST), Vellore Institute of Technology, Vellore, India
| | - Sudha Ramaiah
- Department of Bio-Sciences, School of Biosciences and Technology (SBST), Vellore Institute of Technology, Vellore, India
- Medical and Biological Computing Laboratory, Department of Biotechnology, School of Biosciences and Technology (SBST), Vellore Institute of Technology, Vellore, India
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7
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Ramm B, Schumacher D, Harms A, Heermann T, Klos P, Müller F, Schwille P, Søgaard-Andersen L. Biomolecular condensate drives polymerization and bundling of the bacterial tubulin FtsZ to regulate cell division. Nat Commun 2023; 14:3825. [PMID: 37380708 DOI: 10.1038/s41467-023-39513-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 06/07/2023] [Indexed: 06/30/2023] Open
Abstract
Cell division is spatiotemporally precisely regulated, but the underlying mechanisms are incompletely understood. In the social bacterium Myxococcus xanthus, the PomX/PomY/PomZ proteins form a single megadalton-sized complex that directly positions and stimulates cytokinetic ring formation by the tubulin homolog FtsZ. Here, we study the structure and mechanism of this complex in vitro and in vivo. We demonstrate that PomY forms liquid-like biomolecular condensates by phase separation, while PomX self-assembles into filaments generating a single large cellular structure. The PomX structure enriches PomY, thereby guaranteeing the formation of precisely one PomY condensate per cell through surface-assisted condensation. In vitro, PomY condensates selectively enrich FtsZ and nucleate GTP-dependent FtsZ polymerization and bundle FtsZ filaments, suggesting a cell division site positioning mechanism in which the single PomY condensate enriches FtsZ to guide FtsZ-ring formation and division. This mechanism shares features with microtubule nucleation by biomolecular condensates in eukaryotes, supporting this mechanism's ancient origin.
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Affiliation(s)
- Beatrice Ramm
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
- Department of Physics, Princeton University, Princeton, NJ, 08544, USA.
| | - Dominik Schumacher
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043, Marburg, Germany.
| | - Andrea Harms
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043, Marburg, Germany
| | - Tamara Heermann
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Philipp Klos
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043, Marburg, Germany
| | - Franziska Müller
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043, Marburg, Germany
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
| | - Lotte Søgaard-Andersen
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043, Marburg, Germany.
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Myszka K, Tomaś N, Juzwa W, Wolko Ł. Chlorogenic Acid Inhibits Rahnella aquatilis KM25 Growth and Proteolytic Activity in Fish-Based Products. Microorganisms 2023; 11:1367. [PMID: 37374869 DOI: 10.3390/microorganisms11061367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 05/04/2023] [Accepted: 05/20/2023] [Indexed: 06/29/2023] Open
Abstract
This work verified the antiproliferative and antiproteolytic activities of chlorogenic acid against Rahnella aquatilis KM25, a spoilage organism of raw salmon stored at 4 °C. Chlorogenic acid limited the growth of R. aqatilis KM25 in vitro at a concentration of 2.0 mg/mL. The dead (46%), viable (25%), and injured (20%) cell subpopulations were identified by flow cytometry following treatment of R. aquatilis KM25 with the examined agent. The exposure of R. aquatilis KM25 to chlorogenic acid altered its morphology. Changes in cell dimensions, mostly in length parameters from 0.778 µm to 1.09 µm, were found. The length of untreated cells ranged from 0.958 µm to 1.53 µm. The RT-qPCR experiments revealed changes in the expression of genes responsible for the proliferation and proteolytic activity of cells. Chlorogenic acid caused a significant reduction in the mRNA levels of the ftsZ, ftsA, ftsN, tolB, and M4 genes (-2.5, -1.5, -2.0, -1.5, and -1.5, respectively). In situ experiments confirmed the potential of chlorogenic acid to limit bacterial growth. A similar effect was noted in samples treated with benzoic acid, where the growth inhibition of R. aquatilis KM25 was 85-95%. Reduction of microbial R. aquatilis KM25 proliferation significantly limited total volatile base nitrogen (TVB-N) and trimethylamine (TMA-N) formation during storage, extending the shelf life of model products. The TVB-N and TMA-N parameters did not exceed the upper levels of the maximum permissible limit of acceptability. In this work, the TVB-N and TMA-N parameters were 10-25 mg/100 g and 2.5-20.5 mg/100 g, respectively; for samples with benzoic acid-supplemented marinades, the parameters TVB-N and TMA-N were 7.5-25.0 mg/100 g and 2.0-20.0 mg/100 g, respectively. Based on the results of this work, it can be concluded that chlorogenic acid can increase the safety, shelf life, and quality of fishery products.
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Affiliation(s)
- Kamila Myszka
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, Wojska Polskiego 48, 60-627 Poznan, Poland
| | - Natalia Tomaś
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, Wojska Polskiego 48, 60-627 Poznan, Poland
| | - Wojciech Juzwa
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, Wojska Polskiego 48, 60-627 Poznan, Poland
| | - Łukasz Wolko
- Department of Biochemistry and Biotechnology, Poznan University of Life Sciences, Dojazd 11, 60-632 Poznan, Poland
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Porter KJ, Cao L, Osteryoung KW. Dynamics of the Synechococcus elongatus cytoskeletal GTPase FtsZ yields mechanistic and evolutionary insight into cyanobacterial and chloroplast FtsZs. J Biol Chem 2023; 299:102917. [PMID: 36657643 PMCID: PMC9975276 DOI: 10.1016/j.jbc.2023.102917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/09/2023] [Accepted: 01/10/2023] [Indexed: 01/17/2023] Open
Abstract
The division of cyanobacteria and their chloroplast descendants is orchestrated by filamenting temperature-sensitive Z (FtsZ), a cytoskeletal GTPase that polymerizes into protofilaments that form a "Z ring" at the division site. The Z ring has both a scaffolding function for division-complex assembly and a GTPase-dependent contractile function that drives cell or organelle constriction. A single FtsZ performs these functions in bacteria, whereas in chloroplasts, they are performed by two copolymerizing FtsZs, called AtFtsZ2 and AtFtsZ1 in Arabidopsis thaliana, which promote protofilament stability and dynamics, respectively. To probe the differences between cyanobacterial and chloroplast FtsZs, we used light scattering to characterize the in vitro protofilament dynamics of FtsZ from the cyanobacterium Synechococcus elongatus PCC 7942 (SeFtsZ) and investigate how coassembly of AtFtsZ2 or AtFtsZ1 with SeFtsZ influences overall dynamics. SeFtsZ protofilaments assembled rapidly and began disassembling before GTP depletion, whereas AtFtsZ2 protofilaments were far more stable, persisting beyond GTP depletion. Coassembled SeFtsZ-AtFtsZ2 protofilaments began disassembling before GTP depletion, similar to SeFtsZ. In contrast, AtFtsZ1 did not alter disassembly onset when coassembled with SeFtsZ, but fluorescence recovery after photobleaching analysis showed it increased the turnover of SeFtsZ subunits from SeFtsZ-AtFtsZ1 protofilaments, mirroring its effect upon coassembly with AtFtsZ2. Comparisons of our findings with previous work revealed consistent differences between cyanobacterial and chloroplast FtsZ dynamics and suggest that the scaffolding and dynamics-promoting functions were partially separated during evolution of two chloroplast FtsZs from their cyanobacterial predecessor. They also suggest that chloroplasts may have evolved a mechanism distinct from that in cyanobacteria for promoting FtsZ protofilament dynamics.
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Affiliation(s)
- Katie J Porter
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, USA
| | - Lingyan Cao
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, USA
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Du RL, Chow HY, Chen YW, Chan PH, Daniel RA, Wong KY. Gossypol acetate: A natural polyphenol derivative with antimicrobial activities against the essential cell division protein FtsZ. Front Microbiol 2023; 13:1080308. [PMID: 36713210 PMCID: PMC9878342 DOI: 10.3389/fmicb.2022.1080308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/28/2022] [Indexed: 01/14/2023] Open
Abstract
Antimicrobial resistance has attracted worldwide attention and remains an urgent issue to resolve. Discovery of novel compounds is regarded as one way to circumvent the development of resistance and increase the available treatment options. Gossypol is a natural polyphenolic aldehyde, and it has attracted increasing attention as a possible antibacterial drug. In this paper, we studied the antimicrobial properties (minimum inhibitory concentrations) of gossypol acetate against both Gram-positive and Gram-negative bacteria strains and dig up targets of gossypol acetate using in vitro assays, including studying its effects on functions (GTPase activity and polymerization) of Filamenting temperature sensitive mutant Z (FtsZ) and its interactions with FtsZ using isothermal titration calorimetry (ITC), and in vivo assays, including visualization of cell morphologies and proteins localizations using a microscope. Lastly, Bacterial membrane permeability changes were studied, and the cytotoxicity of gossypol acetate was determined. We also estimated the interactions of gossypol acetate with the promising target. We found that gossypol acetate can inhibit the growth of Gram-positive bacteria such as the model organism Bacillus subtilis and the pathogen Staphylococcus aureus [both methicillin-sensitive (MSSA) and methicillin-resistant (MRSA)]. In addition, gossypol acetate can also inhibit the growth of Gram-negative bacteria when the outer membrane is permeabilized by Polymyxin B nonapeptide (PMBN). Using a cell biological approach, we show that gossypol acetate affects cell division in bacteria by interfering with the assembly of the cell division FtsZ ring. Biochemical analysis shows that the GTPase activity of FtsZ was inhibited and polymerization of FtsZ was enhanced in vitro, consistent with the block to cell division in the bacteria tested. The binding mode of gossypol acetate in FtsZ was modeled using molecular docking and provides an understanding of the compound mode of action. The results point to gossypol (S2303) as a promising antimicrobial compound that inhibits cell division by affecting FtsZ polymerization and has potential to be developed into an effective antimicrobial drug by chemical modification to minimize its cytotoxic effects in eukaryotic cells that were identified in this work.
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Affiliation(s)
- Ruo-Lan Du
- Department of Applied Biology and Chemical Technology and the State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Ho-Yin Chow
- Department of Applied Biology and Chemical Technology and the State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Yu Wei Chen
- Department of Applied Biology and Chemical Technology and the State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Pak-Ho Chan
- Department of Applied Biology and Chemical Technology and the State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Richard A. Daniel
- Centre for Bacterial Cell Biology, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom,Richard A. Daniel,
| | - Kwok-Yin Wong
- Department of Applied Biology and Chemical Technology and the State Key Laboratory of Chemical Biology and Drug Discovery, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China,*Correspondence: Kwok-Yin Wong,
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11
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Brown HJ, Duggin IG. Diversity and Potential Multifunctionality of Archaeal CetZ Tubulin-like Cytoskeletal Proteins. Biomolecules 2023; 13:biom13010134. [PMID: 36671519 PMCID: PMC9856176 DOI: 10.3390/biom13010134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/04/2023] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
Tubulin superfamily (TSF) proteins are widespread, and are known for their multifaceted roles as cytoskeletal proteins underpinning many basic cellular functions, including morphogenesis, division, and motility. In eukaryotes, tubulin assembles into microtubules, a major component of the dynamic cytoskeletal network of fibres, whereas the bacterial homolog FtsZ assembles the division ring at midcell. The functions of the lesser-known archaeal TSF proteins are beginning to be identified and show surprising diversity, including homologs of tubulin and FtsZ as well as a third archaea-specific family, CetZ, implicated in the regulation of cell shape and possibly other unknown functions. In this study, we define sequence and structural characteristics of the CetZ family and CetZ1 and CetZ2 subfamilies, identify CetZ groups and diversity amongst archaea, and identify potential functional relationships through analysis of the genomic neighbourhoods of cetZ genes. We identified at least three subfamilies of orthologous CetZ proteins in the archaeal class Halobacteria, including CetZ1 and CetZ2 as well as a novel uncharacterized subfamily. CetZ1 and CetZ2 were correlated to one another as well as to cell shape and motility phenotypes across diverse Halobacteria. Among other known CetZ clusters in orders Archaeoglobales, Methanomicrobiales, Methanosarcinales, and Thermococcales, an additional uncharacterized group from Archaeoglobales and Methanomicrobiales is affiliated strongly with Halobacteria CetZs, suggesting that they originated via horizontal transfer. Subgroups of Halobacteria CetZ2 and Thermococcales CetZ genes were found adjacent to different type IV pili regulons, suggesting potential utilization of CetZs by type IV systems. More broadly conserved cetZ gene neighbourhoods include nucleotide and cofactor biosynthesis (e.g., F420) and predicted cell surface sugar epimerase genes. These findings imply that CetZ subfamilies are involved in multiple functions linked to the cell surface, biosynthesis, and motility.
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12
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McCoy KM, Fritzsching KJ, McDermott AE. GTP-Bound Escherichia coli FtsZ Filaments Are Composed of Tense Monomers: a Dynamic Nuclear Polarization-Nuclear Magnetic Resonance Study Using Interface Detection. mBio 2022; 13:e0235822. [PMID: 36214571 PMCID: PMC9765660 DOI: 10.1128/mbio.02358-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 09/08/2022] [Indexed: 11/20/2022] Open
Abstract
FtsZ filaments are the major structural component of the bacterial Z ring and are drivers of bacterial division. Crystal structures for FtsZ from some Gram-positive bacteria in the presence of GTP analogs suggest the possibility of a high-energy, "tense" conformation. It remains important to elucidate whether this tense form is the dominant form in filaments. Using dynamic nuclear polarization (DNP) solid-state nuclear magnetic resonance (NMR) and differential isotopic labeling, we directly detected residues located at the intermonomer interface of GTP-bound wild-type (WT) Escherichia coli FtsZ filaments. We combined chemical shift prediction, homology modeling, and heteronuclear dipolar recoupling techniques to characterize the E. coli FtsZ filament interface and demonstrated that the monomers in active filaments assume a tense conformation. IMPORTANCE Bacterial replication is dependent on the cytoskeletal protein FtsZ, which forms filaments that scaffold and recruit other essential division proteins. While the FtsZ monomer is well studied across organisms, many questions remain about how the filaments form and function. Recently, a second monomer form was identified in Staphylococcus aureus that has far-reaching implications for FtsZ structure and function. However, to date, this form has not been directly observed outside S. aureus. In this study, we used solid-state NMR and dynamic nuclear polarization (DNP) to directly study the filaments of E. coli FtsZ to demonstrate that E. coli FtsZ filaments are primarily composed of this second, "tense" form of the monomer. This work is the first time GTP-bound, wild-type FtsZ filaments have been studied directly at atomic resolution and is an important step forward for the study of FtsZ filaments.
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Affiliation(s)
- Kelsey M. McCoy
- Department of Chemistry, Columbia University, New York, New York, USA
| | | | - Ann E. McDermott
- Department of Chemistry, Columbia University, New York, New York, USA
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13
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Donau C, Boekhoven J. The chemistry of chemically fueled droplets. TRENDS IN CHEMISTRY 2022. [DOI: 10.1016/j.trechm.2022.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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14
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Abstract
Atlastin (ATL) GTPases undergo trans dimerization and a power strokelike crossover conformational rearrangement to drive endoplasmic reticulum membrane fusion. Fusion depends on GTP, but the role of nucleotide hydrolysis has remained controversial. For instance, nonhydrolyzable GTP analogs block fusion altogether, suggesting a requirement for GTP hydrolysis in ATL dimerization and crossover, but this leaves unanswered the question of how the ATL dimer is disassembled after fusion. We recently used the truncated cytoplasmic domain of wild-type Drosophila ATL (DATL) and a novel hydrolysis-deficient D127N variant in single turnover assays to reveal that dimerization and crossover consistently precede GTP hydrolysis, with hydrolysis coinciding more closely with dimer disassembly. Moreover, while nonhydrolyzable analogs can bind the DATL G domain, they fail to fully recapitulate the GTP-bound state. This predicted that nucleotide hydrolysis would be dispensable for fusion. Here we report that the D127N variant of full-length DATL drives both outer and inner leaflet membrane fusion with little to no detectable hydrolysis of GTP. However, the trans dimer fails to disassemble and subsequent rounds of fusion fail to occur. Our findings confirm that ATL mediated fusion is driven in the GTP-bound state, with nucleotide hydrolysis serving to reset the fusion machinery for recycling.
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Affiliation(s)
- Daniel Crosby
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213
| | - Tina H. Lee
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213,*Address correspondence to: Tina H. Lee ()
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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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Synthesis, characterization, DFT studies, and molecular modeling of 2-(-(2-hydroxy-5-methoxyphenyl)-methylidene)-amino) nicotinic acid against some selected bacterial receptors. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2022. [DOI: 10.1007/s13738-022-02550-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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17
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The division protein FtsZ interacts with the small heat shock protein IbpA in Acholeplasma laidlawii. Biochim Biophys Acta Gen Subj 2022; 1866:130220. [DOI: 10.1016/j.bbagen.2022.130220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 07/26/2022] [Accepted: 07/31/2022] [Indexed: 11/16/2022]
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18
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RefZ and Noc Act Synthetically to Prevent Aberrant Divisions during Bacillus subtilis Sporulation. J Bacteriol 2022; 204:e0002322. [PMID: 35506695 DOI: 10.1128/jb.00023-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
During sporulation, Bacillus subtilis undergoes an atypical cell division that requires overriding mechanisms that protect chromosomes from damage and ensure inheritance by daughter cells. Instead of assembling between segregated chromosomes at midcell, the FtsZ-ring coalesces polarly, directing division over one chromosome. The DNA-binding protein RefZ facilitates the timely assembly of polar Z-rings and partially defines the region of chromosome initially captured in the forespore. RefZ binds to motifs (RBMs) located proximal to the origin of replication (oriC). Although refZ and the RBMs are conserved across the Bacillus genus, a refZ deletion mutant sporulates with wild-type efficiency, so the functional significance of RefZ during sporulation remains unclear. To further investigate RefZ function, we performed a candidate-based screen for synthetic sporulation defects by combining ΔrefZ with deletions of genes previously implicated in FtsZ regulation and/or chromosome capture. Combining ΔrefZ with deletions of ezrA, sepF, parA, or minD did not detectably affect sporulation. In contrast, a ΔrefZ Δnoc mutant exhibited a sporulation defect, revealing a genetic interaction between RefZ and Noc. Using reporters of sporulation progression, we determined the ΔrefZ Δnoc mutant exhibited sporulation delays after Spo0A activation but prior to late sporulation, with a subset of cells failing to divide polarly or activate the first forespore-specific sigma factor, SigF. The ΔrefZ Δnoc mutant also exhibited extensive dysregulation of cell division, producing cells with extra, misplaced, or otherwise aberrant septa. Our results reveal a previously unknown epistatic relationship that suggests refZ and noc contribute synthetically to regulating cell division and supporting spore development. IMPORTANCE The DNA-binding protein RefZ and its binding sites (RBMs) are conserved in sequence and location on the chromosome across the Bacillus genus and contribute to the timing of polar FtsZ-ring assembly during sporulation. Only a small number of noncoding and nonregulatory DNA motifs are known to be conserved in chromosomal position in bacteria, suggesting there is strong selective pressure for their maintenance; however, a refZ deletion mutant sporulates efficiently, providing no clues as to their functional significance. Here, we find that in the absence of the nucleoid occlusion factor Noc, deletion of refZ results in a sporulation defect characterized by developmental delays and aberrant divisions.
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Gurnani M, Chauhan A, Ranjan A, Tuli HS, Alkhanani MF, Haque S, Dhama K, Lal R, Jindal T. Filamentous Thermosensitive Mutant Z: An Appealing Target for Emerging Pathogens and a Trek on Its Natural Inhibitors. BIOLOGY 2022; 11:624. [PMID: 35625352 PMCID: PMC9138142 DOI: 10.3390/biology11050624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/18/2022] [Accepted: 04/01/2022] [Indexed: 12/14/2022]
Abstract
Antibiotic resistance is a major emerging issue in the health care sector, as highlighted by the WHO. Filamentous Thermosensitive mutant Z (Fts-Z) is gaining significant attention in the scientific community as a potential anti-bacterial target for fighting antibiotic resistance among several pathogenic bacteria. The Fts-Z plays a key role in bacterial cell division by allowing Z ring formation. Several in vitro and in silico experiments have demonstrated that inhibition of Fts-Z can lead to filamentous growth of the cells, and finally, cell death occurs. Many natural compounds that have successfully inhibited Fts-Z are also studied. This review article intended to highlight the structural-functional aspect of Fts-Z that leads to Z-ring formation and its contribution to the biochemistry and physiology of cells. The current trend of natural inhibitors of Fts-Z protein is also covered.
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Affiliation(s)
- Manisha Gurnani
- Amity Institute of Environmental Science, Amity University, Noida 201301, India;
| | - Abhishek Chauhan
- Amity Institute of Environmental Toxicology, Safety and Management, Amity University, Noida 201303, India;
| | - Anuj Ranjan
- Academy of Biology and Biotechnology, Southern Federal University, 344006 Rostov-on-Don, Russia
| | - Hardeep Singh Tuli
- Department of Biotechnology, Maharishi Markandeshwar (Deemed to be University), Ambala 133207, India;
| | - Mustfa F. Alkhanani
- Emergency Service Department, College of Applied Sciences, AlMaarefa University, Riyadh 11597, Saudi Arabia;
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan 45142, Saudi Arabia;
- Faculty of Medicine, Görükle Campus, Bursa Uludağ University, Nilüfer, Bursa 16059, Turkey
| | - Kuldeep Dhama
- Division of Pathology, ICAR—Indian Veterinary Research Institute, Bareilly 243122, India;
| | - Rup Lal
- Department of Zoology, University of Delhi, Delhi 110021, India;
| | - Tanu Jindal
- Amity Institute of Environmental Toxicology, Safety and Management, Amity University, Noida 201303, India;
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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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21
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Ithurbide S, Gribaldo S, Albers SV, Pende N. Spotlight on FtsZ-based cell division in Archaea. Trends Microbiol 2022; 30:665-678. [PMID: 35246355 DOI: 10.1016/j.tim.2022.01.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 12/22/2021] [Accepted: 01/10/2022] [Indexed: 12/15/2022]
Abstract
Compared with the extensive knowledge on cell division in model eukaryotes and bacteria, little is known about how archaea divide. Interestingly, both endosomal sorting complex required for transport (ESCRT)-based and FtsZ-based cell division systems are found in members of the Archaea. In the past couple of years, several studies have started to shed light on FtsZ-based cell division processes in members of the Euryarchaeota. In this review we highlight recent findings in this emerging field of research. We present current knowledge of the cell division machinery of halophiles which relies on two FtsZ proteins, and we compare it with that of methanobacteria, which relies on only one FtsZ. Finally, we discuss how these differences relate to the distinct cell envelopes of these two archaeal model systems.
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Affiliation(s)
- Solenne Ithurbide
- Molecular Biology of Archaea, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Simonetta Gribaldo
- Evolutionary Biology of the Microbial Cell Unit, CNRS UMR2001, Department of Microbiology, Institut Pasteur, Paris, France.
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany.
| | - Nika Pende
- Evolutionary Biology of the Microbial Cell Unit, CNRS UMR2001, Department of Microbiology, Institut Pasteur, Paris, France
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Levin PA, Janakiraman A. Localization, Assembly, and Activation of the Escherichia coli Cell Division Machinery. EcoSal Plus 2021; 9:eESP00222021. [PMID: 34910577 PMCID: PMC8919703 DOI: 10.1128/ecosalplus.esp-0022-2021] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 11/14/2021] [Indexed: 01/01/2023]
Abstract
Decades of research, much of it in Escherichia coli, have yielded a wealth of insight into bacterial cell division. Here, we provide an overview of the E. coli division machinery with an emphasis on recent findings. We begin with a short historical perspective into the discovery of FtsZ, the tubulin homolog that is essential for division in bacteria and archaea. We then discuss assembly of the divisome, an FtsZ-dependent multiprotein platform, at the midcell septal site. Not simply a scaffold, the dynamic properties of polymeric FtsZ ensure the efficient and uniform synthesis of septal peptidoglycan. Next, we describe the remodeling of the cell wall, invagination of the cell envelope, and disassembly of the division apparatus culminating in scission of the mother cell into two daughter cells. We conclude this review by highlighting some of the open questions in the cell division field, emphasizing that much remains to be discovered, even in an organism as extensively studied as E. coli.
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Affiliation(s)
- Petra Anne Levin
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
- Center for Science & Engineering of Living Systems (CSELS), McKelvey School of Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Anuradha Janakiraman
- Department of Biology, The City College of New York, New York, New York, USA
- Programs in Biology and Biochemistry, The Graduate Center of the City University of New York, New York, New York, USA
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23
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Mahanty S, Rathinasamy K. The natural anthraquinone dye purpurin exerts antibacterial activity by perturbing the FtsZ assembly. Bioorg Med Chem 2021; 50:116463. [PMID: 34700238 DOI: 10.1016/j.bmc.2021.116463] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 10/03/2021] [Accepted: 10/05/2021] [Indexed: 11/29/2022]
Abstract
There is an increasing demand to discover novel antibacterial drugs to counter the ever-evolving genetic machinery of bacteria. The cell division protein FtsZ plays a vital role in bacterial cytokinesis and has been recognized as an effective antibacterial drug target. In this study, we have shown that the madder dye purpurin inhibited bacterial cytokinesis through perturbation of FtsZ assembly. Purpurin inhibited the growth of bacterial cells in a concentration-dependent manner and induced bacterial cell filamentation. Microscopy studies showed that it inhibited the localization of the Z ring at the midcell, and FtsZ was dispersed throughout the cells. Further, purpurin bound firmly to FtsZ with a dissociation constant of 11 µM and inhibited its assembly in vitro. It reduced the GTP hydrolysis by binding closer to the nucleotide-binding site of FtsZ. Purpurin inhibited the proliferation of mammalian cancer cells at higher concentrations without disturbing the polymerization of tubulin. The results collectively suggest that the natural anthraquinone purpurin can potently inhibit the growth of bacteria and serve as a lead molecule for the development of antibacterial agents.
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Affiliation(s)
- Susobhan Mahanty
- School of Biotechnology, National Institute of Technology Calicut, Calicut, Kerala, India
| | - Krishnan Rathinasamy
- School of Biotechnology, National Institute of Technology Calicut, Calicut, Kerala, India.
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The Division Defect of a Bacillus subtilis minD noc Double Mutant Can Be Suppressed by Spx-Dependent and Spx-Independent Mechanisms. J Bacteriol 2021; 203:e0024921. [PMID: 34181483 DOI: 10.1128/jb.00249-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
During growth, bacteria increase in size and divide. Division is initiated by the formation of the Z-ring, a ring-like cytoskeletal structure formed by treadmilling protofilaments of the tubulin homolog FtsZ. FtsZ localization is thought to be controlled by the Min and Noc systems, and here we explore why cell division fails at high temperature when the Min and Noc systems are simultaneously mutated. Microfluidic analysis of a minD noc double mutant indicated that FtsZ formed proto-Z-rings at periodic interchromosome locations but that the rings failed to mature and become functional. Extragenic suppressor analysis indicated that a variety of mutations restored high temperature growth to the minD noc double mutant, and while many were likely pleiotropic, others implicated the proteolysis of the transcription factor Spx. Further analysis indicated that a Spx-dependent pathway activated the expression of ZapA, a protein that primarily compensates for the absence of Noc. In addition, an Spx-independent pathway reduced the length of the cytokinetic period, perhaps by increasing divisome activity. Finally, we provide evidence of an as-yet-unidentified protein that is activated by Spx and governs the frequency of polar division and minicell formation. IMPORTANCE Bacteria must properly position the location of the cell division machinery in order to grow, divide, and ensure each daughter cell receives one copy of the chromosome. In Bacillus subtilis, cell division site selection depends on the Min and Noc systems, and while neither is individually essential, cells fail to grow at high temperature when both are mutated. Here, we show that cell division fails in the absence of Min and Noc, due not to a defect in FtsZ localization but rather to a failure in the maturation of the cell division machinery. Suppressor mutations that restored growth were selected, and while some activated the expression of ZapA via the Spx stress response pathway, others appeared to directly enhance divisome activity.
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25
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The archaeal protein SepF is essential for cell division in Haloferax volcanii. Nat Commun 2021; 12:3469. [PMID: 34103513 PMCID: PMC8187382 DOI: 10.1038/s41467-021-23686-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 05/07/2021] [Indexed: 02/05/2023] Open
Abstract
In most bacteria, cell division depends on the tubulin homolog FtsZ and other proteins, such as SepF, that form a complex termed the divisome. Cell division also depends on FtsZ in many archaea, but other components of the divisome are unknown. Here, we demonstrate that a SepF homolog plays important roles in cell division in Haloferax volcanii, a halophilic archaeon that is known to have two FtsZ homologs with slightly different functions (FtsZ1 and FtsZ2). SepF co-localizes with both FtsZ1 and FtsZ2 at midcell. Attempts to generate a sepF deletion mutant were unsuccessful, suggesting an essential role. Indeed, SepF depletion leads to severe cell division defects and formation of large cells. Overexpression of FtsZ1-GFP or FtsZ2-GFP in SepF-depleted cells results in formation of filamentous cells with a high number of FtsZ1 rings, while the number of FtsZ2 rings is not affected. Pull-down assays support that SepF interacts with FtsZ2 but not with FtsZ1, although SepF appears delocalized in the absence of FtsZ1. Archaeal SepF homologs lack a glycine residue known to be important for polymerization and function in bacteria, and purified H. volcanii SepF forms dimers, suggesting that polymerization might not be important for the function of archaeal SepF.
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26
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Porter KJ, Cao L, Chen Y, TerBush AD, Chen C, Erickson HP, Osteryoung KW. The Arabidopsis thaliana chloroplast division protein FtsZ1 counterbalances FtsZ2 filament stability in vitro. J Biol Chem 2021; 296:100627. [PMID: 33812992 PMCID: PMC8142252 DOI: 10.1016/j.jbc.2021.100627] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 03/30/2021] [Accepted: 03/31/2021] [Indexed: 11/18/2022] Open
Abstract
Bacterial cell and chloroplast division are driven by a contractile “Z ring” composed of the tubulin-like cytoskeletal GTPase FtsZ. Unlike bacterial Z rings, which consist of a single FtsZ, the chloroplast Z ring in plants is composed of two FtsZ proteins, FtsZ1 and FtsZ2. Both are required for chloroplast division in vivo, but their biochemical relationship is poorly understood. We used GTPase assays, light scattering, transmission electron microscopy, and sedimentation assays to investigate the assembly behavior of purified Arabidopsis thaliana (At) FtsZ1 and AtFtsZ2 both individually and together. Both proteins exhibited GTPase activity. AtFtsZ2 assembled relatively quickly, forming protofilament bundles that were exceptionally stable, as indicated by their sustained assembly and slow disassembly. AtFtsZ1 did not form detectable protofilaments on its own. When mixed with AtFtsZ2, AtFtsZ1 reduced the extent and rate of AtFtsZ2 assembly, consistent with its previously demonstrated ability to promote protofilament subunit turnover in living cells. Mixing the two FtsZ proteins did not increase the overall GTPase activity, indicating that the effect of AtFtsZ1 on AtFtsZ2 assembly was not due to a stimulation of GTPase activity. However, the GTPase activity of AtFtsZ1 was required to reduce AtFtsZ2 assembly. Truncated forms of AtFtsZ1 and AtFtsZ2 consisting of only their conserved core regions largely recapitulated the behaviors of the full-length proteins. Our in vitro findings provide evidence that FtsZ1 counterbalances the stability of FtsZ2 filaments in the regulation of chloroplast Z-ring dynamics and suggest that restraining FtsZ2 self-assembly is a critical function of FtsZ1 in chloroplasts.
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Affiliation(s)
- Katie J Porter
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, USA
| | - Lingyan Cao
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, USA
| | - Yaodong Chen
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Allan D TerBush
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, USA
| | - Cheng Chen
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, USA
| | - Harold P Erickson
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina, USA
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Robles-Ramos MÁ, Zorrilla S, Alfonso C, Margolin W, Rivas G, Monterroso B. Assembly of bacterial cell division protein FtsZ into dynamic biomolecular condensates. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2021; 1868:118986. [PMID: 33581219 PMCID: PMC8529516 DOI: 10.1016/j.bbamcr.2021.118986] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 01/29/2021] [Accepted: 01/30/2021] [Indexed: 11/30/2022]
Abstract
Biomolecular condensation through phase separation may be a novel mechanism to regulate bacterial processes, including cell division. Previous work revealed that FtsZ, a protein essential for cytokinesis in most bacteria, forms biomolecular condensates with SlmA, a protein that protects the chromosome from damage inflicted by the division machinery in Escherichia coli. The absence of condensates composed solely of FtsZ under the conditions used in that study suggested this mechanism was restricted to nucleoid occlusion by SlmA or to bacteria containing this protein. Here we report that FtsZ alone, under physiologically relevant conditions, can demix into condensates in bulk and when encapsulated in synthetic cell-like systems generated by microfluidics. Condensate assembly depends on FtsZ being in the GDP-bound state and on conditions mimicking the crowded environment of the cytoplasm that promote its oligomerization. Condensates are dynamic and reversibly convert into filaments upon GTP addition. Notably, FtsZ lacking its C-terminal disordered region, a structural element likely to favor biomolecular condensation, also forms condensates, albeit less efficiently. The inherent tendency of FtsZ to form condensates susceptible to modulation by physiological factors, including binding partners, suggests that such mechanisms may play a more general role in bacterial division than initially envisioned.
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Affiliation(s)
- Miguel Ángel Robles-Ramos
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain
| | - Silvia Zorrilla
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain.
| | - Carlos Alfonso
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain
| | - William Margolin
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas, Houston, TX 77030, USA
| | - Germán Rivas
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain.
| | - Begoña Monterroso
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain.
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Zorrilla S, Monterroso B, Robles-Ramos MÁ, Margolin W, Rivas G. FtsZ Interactions and Biomolecular Condensates as Potential Targets for New Antibiotics. Antibiotics (Basel) 2021; 10:antibiotics10030254. [PMID: 33806332 PMCID: PMC7999717 DOI: 10.3390/antibiotics10030254] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 12/18/2022] Open
Abstract
FtsZ is an essential and central protein for cell division in most bacteria. Because of its ability to organize into dynamic polymers at the cell membrane and recruit other protein partners to form a “divisome”, FtsZ is a leading target in the quest for new antibacterial compounds. Strategies to potentially arrest the essential and tightly regulated cell division process include perturbing FtsZ’s ability to interact with itself and other divisome proteins. Here, we discuss the available methodologies to screen for and characterize those interactions. In addition to assays that measure protein-ligand interactions in solution, we also discuss the use of minimal membrane systems and cell-like compartments to better approximate the native bacterial cell environment and hence provide a more accurate assessment of a candidate compound’s potential in vivo effect. We particularly focus on ways to measure and inhibit under-explored interactions between FtsZ and partner proteins. Finally, we discuss recent evidence that FtsZ forms biomolecular condensates in vitro, and the potential implications of these assemblies in bacterial resistance to antibiotic treatment.
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Affiliation(s)
- Silvia Zorrilla
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain; (M.-Á.R.-R.); (G.R.)
- Correspondence: (S.Z.); (B.M.); Tel.: +34-91-837-3112 (S.Z. & B.M.)
| | - Begoña Monterroso
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain; (M.-Á.R.-R.); (G.R.)
- Correspondence: (S.Z.); (B.M.); Tel.: +34-91-837-3112 (S.Z. & B.M.)
| | - Miguel-Ángel Robles-Ramos
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain; (M.-Á.R.-R.); (G.R.)
| | - William Margolin
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas, Houston, TX 77030, USA;
| | - Germán Rivas
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain; (M.-Á.R.-R.); (G.R.)
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Silber N, Mayer C, Matos de Opitz CL, Sass P. Progression of the late-stage divisome is unaffected by the depletion of the cytoplasmic FtsZ pool. Commun Biol 2021; 4:270. [PMID: 33649500 PMCID: PMC7921118 DOI: 10.1038/s42003-021-01789-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 02/01/2021] [Indexed: 11/14/2022] Open
Abstract
Cell division is a central and essential process in most bacteria, and also due to its complexity and highly coordinated nature, it has emerged as a promising new antibiotic target pathway in recent years. We have previously shown that ADEP antibiotics preferably induce the degradation of the major cell division protein FtsZ, thereby primarily leading to a depletion of the cytoplasmic FtsZ pool that is needed for treadmilling FtsZ rings. To further investigate the physiological consequences of ADEP treatment, we here studied the effect of ADEP on the different stages of the FtsZ ring in rod-shaped bacteria. Our data reveal the disintegration of early FtsZ rings during ADEP treatment in Bacillus subtilis, indicating an essential role of the cytoplasmic FtsZ pool and thus FtsZ ring dynamics during initiation and maturation of the divisome. However, progressed FtsZ rings finalized cytokinesis once the septal peptidoglycan synthase PBP2b, a late-stage cell division protein, colocalized at the division site, thus implying that the concentration of the cytoplasmic FtsZ pool and FtsZ ring dynamics are less critical during the late stages of divisome assembly and progression.
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Affiliation(s)
- Nadine Silber
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle, Tübingen, Germany
- Cluster of Excellence - Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
| | - Christian Mayer
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle, Tübingen, Germany
- Cluster of Excellence - Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
| | - Cruz L Matos de Opitz
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle, Tübingen, Germany
- Cluster of Excellence - Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
| | - Peter Sass
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle, Tübingen, Germany.
- Cluster of Excellence - Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany.
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Fujita J, Sugiyama S, Terakado H, Miyazaki M, Ozawa M, Ueda N, Kuroda N, Tanaka SI, Yoshizawa T, Uchihashi T, Matsumura H. Dynamic Assembly/Disassembly of Staphylococcus aureus FtsZ Visualized by High-Speed Atomic Force Microscopy. Int J Mol Sci 2021; 22:ijms22041697. [PMID: 33567659 PMCID: PMC7914567 DOI: 10.3390/ijms22041697] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 02/04/2021] [Indexed: 12/24/2022] Open
Abstract
FtsZ is a key protein in bacterial cell division and is assembled into filamentous architectures. FtsZ filaments are thought to regulate bacterial cell division and have been investigated using many types of imaging techniques such as atomic force microscopy (AFM), but the time scale of the method was too long to trace the filament formation process. Development of high-speed AFM enables us to achieve sub-second time resolution and visualize the formation and dissociation process of FtsZ filaments. The analysis of the growth and dissociation rates of the C-terminal truncated FtsZ (FtsZt) filaments indicate the net growth and dissociation of FtsZt filaments in the growth and dissociation conditions, respectively. We also analyzed the curvatures of the full-length FtsZ (FtsZf) and FtsZt filaments, and the comparative analysis indicated the straight-shape preference of the FtsZt filaments than those of FtsZf. These findings provide insights into the fundamental dynamic behavior of FtsZ protofilaments and bacterial cell division.
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Affiliation(s)
- Junso Fujita
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan;
| | - Shogo Sugiyama
- Department of Physics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan;
| | - Haruna Terakado
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577, Japan; (H.T.); (M.M.); (M.O.); (N.U.); (N.K.); (S.-i.T.); (T.Y.)
| | - Maho Miyazaki
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577, Japan; (H.T.); (M.M.); (M.O.); (N.U.); (N.K.); (S.-i.T.); (T.Y.)
| | - Mayuki Ozawa
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577, Japan; (H.T.); (M.M.); (M.O.); (N.U.); (N.K.); (S.-i.T.); (T.Y.)
| | - Nanami Ueda
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577, Japan; (H.T.); (M.M.); (M.O.); (N.U.); (N.K.); (S.-i.T.); (T.Y.)
| | - Natsuko Kuroda
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577, Japan; (H.T.); (M.M.); (M.O.); (N.U.); (N.K.); (S.-i.T.); (T.Y.)
| | - Shun-ichi Tanaka
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577, Japan; (H.T.); (M.M.); (M.O.); (N.U.); (N.K.); (S.-i.T.); (T.Y.)
- Department of Biomolecular Chemistry, Kyoto Prefectural University, Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan
| | - Takuya Yoshizawa
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577, Japan; (H.T.); (M.M.); (M.O.); (N.U.); (N.K.); (S.-i.T.); (T.Y.)
| | - Takayuki Uchihashi
- Department of Physics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan;
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan
- Correspondence: (T.U.); (H.M.); Tel.: +81-52-789-2885 (T.U.); +81-77-561-4809 (H.M.)
| | - Hiroyoshi Matsumura
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga 525-8577, Japan; (H.T.); (M.M.); (M.O.); (N.U.); (N.K.); (S.-i.T.); (T.Y.)
- Correspondence: (T.U.); (H.M.); Tel.: +81-52-789-2885 (T.U.); +81-77-561-4809 (H.M.)
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Simulations of Proposed Mechanisms of FtsZ-Driven Cell Constriction. J Bacteriol 2021; 203:JB.00576-20. [PMID: 33199285 PMCID: PMC7811198 DOI: 10.1128/jb.00576-20] [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: 10/16/2020] [Accepted: 10/26/2020] [Indexed: 01/24/2023] Open
Abstract
FtsZ is thought to generate constrictive force to divide the cell, possibly via one of two predominant models in the field. In one, FtsZ filaments overlap to form complete rings which constrict as filaments slide past each other to maximize lateral contact. To divide, bacteria must constrict their membranes against significant force from turgor pressure. A tubulin homolog, FtsZ, is thought to drive constriction, but how FtsZ filaments might generate constrictive force in the absence of motor proteins is not well understood. There are two predominant models in the field. In one, FtsZ filaments overlap to form complete rings around the circumference of the cell, and attractive forces cause filaments to slide past each other to maximize lateral contact. In the other, filaments exert force on the membrane by a GTP-hydrolysis-induced switch in conformation from straight to bent. Here, we developed software, ZCONSTRICT, for quantitative three-dimensional (3D) simulations of Gram-negative bacterial cell division to test these two models and identify critical conditions required for them to work. We find that the avidity of any kind of lateral interactions quickly halts the sliding of filaments, so a mechanism such as depolymerization or treadmilling is required to sustain constriction by filament sliding. For filament bending, we find that a mechanism such as the presence of a rigid linker is required to constrain bending to within the division plane and maintain the distance observed in vivo between the filaments and the membrane. Of these two models, only the filament bending model is consistent with our lab’s recent observation of constriction associated with a single, short FtsZ filament. IMPORTANCE FtsZ is thought to generate constrictive force to divide the cell, possibly via one of two predominant models in the field. In one, FtsZ filaments overlap to form complete rings which constrict as filaments slide past each other to maximize lateral contact. In the other, filaments exert force on the membrane by switching conformation from straight to bent. Here, we developed software, ZCONSTRICT, for three-dimensional (3D) simulations to test these two models. We find that a mechanism such as depolymerization or treadmilling are required to sustain constriction by filament sliding. For filament bending, we find that a mechanism that constrains bending to within the division plane is required to maintain the distance observed in vivo between the filaments and the membrane.
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Lewicka E, Mitura M, Steczkiewicz K, Kieracinska J, Skrzynska K, Adamczyk M, Jagura-Burdzy G. Unique Properties of the Alpha-Helical DNA-Binding Protein KfrA Encoded by the IncU Incompatibility Group Plasmid RA3 and Its Host-Dependent Role in Plasmid Maintenance. Appl Environ Microbiol 2021; 87:e01771-20. [PMID: 33097508 PMCID: PMC7783346 DOI: 10.1128/aem.01771-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/18/2020] [Indexed: 01/15/2023] Open
Abstract
KfrA, encoded on the broad-host-range RA3 plasmid, is an alpha-helical DNA-binding protein that acts as a transcriptional autoregulator. The KfrARA3 operator site overlaps the kfrA promoter and is composed of five 9-bp direct repeats (DRs). Here, the biological properties of KfrA were studied using both in vivo and in vitro approaches. Localization of the DNA-binding helix-turn-helix motif (HTH) was mapped to the N29-R52 region by protein structure modeling and confirmed by alanine scanning. KfrA repressor ability depended on the number and orientation of DRs in the operator, as well as the ability of the protein to oligomerize. The long alpha-helical tail from residues 54 to 355 was shown to be involved in self-interactions, whereas the region from residue 54 to 177 was involved in heterodimerization with KfrC, another RA3-encoded alpha-helical protein. KfrA also interacted with the segrosome proteins IncC (ParA) and KorB (ParB), representatives of the class Ia active partition systems. Deletion of the kfr genes from the RA3 stability module decreased the plasmid retention in diverse hosts in a species-dependent manner. The specific interactions of KfrA with DNA are essential not only for the transcriptional regulatory function but also for the accessory role of KfrA in stable plasmid maintenance.IMPORTANCE Alpha-helical coiled-coil KfrA-type proteins are encoded by various broad-host-range low-copy-number conjugative plasmids. The DNA-binding protein KfrA encoded on the RA3 plasmid, a member of the IncU incompatibility group, oligomerizes, forms a complex with another plasmid-encoded, alpha-helical protein, KfrC, and interacts with the segrosome proteins IncC and KorB. The unique mode of KfrA dimer binding to the repetitive operator is required for a KfrA role in the stable maintenance of RA3 plasmid in distinct hosts.
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Affiliation(s)
- Ewa Lewicka
- Institute of Biochemistry and Biophysics, Department of Microbial Biochemistry, PAS, Warsaw, Poland
| | - Monika Mitura
- Institute of Biochemistry and Biophysics, Department of Microbial Biochemistry, PAS, Warsaw, Poland
| | - Kamil Steczkiewicz
- Institute of Biochemistry and Biophysics, Department of Bioinformatics, PAS, Warsaw, Poland
| | - Justyna Kieracinska
- Institute of Biochemistry and Biophysics, Department of Microbial Biochemistry, PAS, Warsaw, Poland
- Warsaw University of Technology, Faculty of Chemistry, Chair of Drug and Cosmetics Biotechnology, Warsaw, Poland
| | - Kamila Skrzynska
- Warsaw University of Technology, Faculty of Chemistry, Chair of Drug and Cosmetics Biotechnology, Warsaw, Poland
| | - Malgorzata Adamczyk
- Warsaw University of Technology, Faculty of Chemistry, Chair of Drug and Cosmetics Biotechnology, Warsaw, Poland
| | - Grazyna Jagura-Burdzy
- Institute of Biochemistry and Biophysics, Department of Microbial Biochemistry, PAS, Warsaw, Poland
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Springstein BL, Nürnberg DJ, Weiss GL, Pilhofer M, Stucken K. Structural Determinants and Their Role in Cyanobacterial Morphogenesis. Life (Basel) 2020; 10:E355. [PMID: 33348886 PMCID: PMC7766704 DOI: 10.3390/life10120355] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/04/2020] [Accepted: 12/09/2020] [Indexed: 12/16/2022] Open
Abstract
Cells have to erect and sustain an organized and dynamically adaptable structure for an efficient mode of operation that allows drastic morphological changes during cell growth and cell division. These manifold tasks are complied by the so-called cytoskeleton and its associated proteins. In bacteria, FtsZ and MreB, the bacterial homologs to tubulin and actin, respectively, as well as coiled-coil-rich proteins of intermediate filament (IF)-like function to fulfil these tasks. Despite generally being characterized as Gram-negative, cyanobacteria have a remarkably thick peptidoglycan layer and possess Gram-positive-specific cell division proteins such as SepF and DivIVA-like proteins, besides Gram-negative and cyanobacterial-specific cell division proteins like MinE, SepI, ZipN (Ftn2) and ZipS (Ftn6). The diversity of cellular morphologies and cell growth strategies in cyanobacteria could therefore be the result of additional unidentified structural determinants such as cytoskeletal proteins. In this article, we review the current advances in the understanding of the cyanobacterial cell shape, cell division and cell growth.
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Affiliation(s)
- Benjamin L. Springstein
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Dennis J. Nürnberg
- Department of Physics, Biophysics and Biochemistry of Photosynthetic Organisms, Freie Universität Berlin, 14195 Berlin, Germany;
| | - Gregor L. Weiss
- Department of Biology, Institute of Molecular Biology & Biophysics, ETH Zürich, 8092 Zürich, Switzerland; (G.L.W.); (M.P.)
| | - Martin Pilhofer
- Department of Biology, Institute of Molecular Biology & Biophysics, ETH Zürich, 8092 Zürich, Switzerland; (G.L.W.); (M.P.)
| | - Karina Stucken
- Department of Food Engineering, Universidad de La Serena, La Serena 1720010, Chile;
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Assembly properties of bacterial tubulin homolog FtsZ regulated by the positive regulator protein ZipA and ZapA from Pseudomonas aeruginosa. Sci Rep 2020; 10:21369. [PMID: 33288818 PMCID: PMC7721900 DOI: 10.1038/s41598-020-78431-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 11/25/2020] [Indexed: 12/21/2022] Open
Abstract
Bacterial tubulin homolog FtsZ self-assembles into dynamic protofilaments, which forms the scaffold for the contractile ring (Z-ring) to achieve bacterial cell division. Here, we study the biochemical properties of FtsZ from Pseudomonas aeruginosa (PaFtsZ) and the effects of its two positive regulator proteins, ZipA and ZapA. Similar to Escherichia coli FtsZ, PaFtsZ had a strong GTPase activity, ~ 7.8 GTP min-1 FtsZ-1 at pH 7.5, and assembled into mainly short single filaments in vitro. However, PaFtsZ protofilaments were mixtures of straight and “intermediate-curved” (100–300 nm diameter) in pH 7.5 solution and formed some bundles in pH 6.5 solution. The effects of ZipA on PaFtsZ assembly varied with pH. In pH 6.5 buffer ZipA induced PaFtsZ to form large bundles. In pH 7.5 buffer PaFtsZ-ZipA protofilaments were not bundled, but ZipA enhanced PaFtsZ assembly and promoted more curved filaments. Comparable to ZapA from other bacterial species, ZapA from P. aeruginosa induced PaFtsZ protofilaments to associate into long straight loose bundles and/or sheets at both pH 6.5 and pH 7.5, which had little effect on the GTPase activity of PaFtsZ. These results provide us further information that ZipA functions as an enhancer of FtsZ curved filaments, while ZapA works as a stabilizer of FtsZ straight filaments.
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Bandekar AC, Subedi S, Ioerger TR, Sassetti CM. Cell-Cycle-Associated Expression Patterns Predict Gene Function in Mycobacteria. Curr Biol 2020; 30:3961-3971.e6. [PMID: 32916109 PMCID: PMC7578119 DOI: 10.1016/j.cub.2020.07.070] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 05/26/2020] [Accepted: 07/22/2020] [Indexed: 12/20/2022]
Abstract
Although the major events in prokaryotic cell cycle progression are likely to be coordinated with transcriptional and metabolic changes, these processes remain poorly characterized. Unlike many rapidly growing bacteria, DNA replication and cell division are temporally resolved in mycobacteria, making these slow-growing organisms a potentially useful system to investigate the prokaryotic cell cycle. To determine whether cell-cycle-dependent gene regulation occurs in mycobacteria, we characterized the temporal changes in the transcriptome of synchronously replicating populations of Mycobacterium tuberculosis (Mtb). By enriching for genes that display a sinusoidal expression pattern, we discover 485 genes that oscillate with a period consistent with the cell cycle. During cytokinesis, the timing of gene induction could be used to predict the timing of gene function, as mRNA abundance was found to correlate with the order in which proteins were recruited to the developing septum. Similarly, the expression pattern of primary metabolic genes could be used to predict the relative importance of these pathways for different cell cycle processes. Pyrimidine synthetic genes peaked during DNA replication, and their depletion caused a filamentation phenotype that phenocopied defects in this process. In contrast, the inosine monophasphate dehydrogenase dedicated to guanosine synthesis, GuaB2, displayed the opposite expression pattern and its depletion perturbed septation. Together, these data imply obligate coordination between primary metabolism and cell division and identify periodically regulated genes that can be related to specific cell biological functions.
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Affiliation(s)
- Aditya C Bandekar
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA
| | - Sishir Subedi
- Department of Computer Science and Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Thomas R Ioerger
- Department of Computer Science and Engineering, Texas A&M University, College Station, TX 77843, USA.
| | - Christopher M Sassetti
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
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Ur Rahman M, Wang P, Wang N, Chen Y. A key bacterial cytoskeletal cell division protein FtsZ as a novel therapeutic antibacterial drug target. Bosn J Basic Med Sci 2020; 20:310-318. [PMID: 32020845 PMCID: PMC7416170 DOI: 10.17305/bjbms.2020.4597] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 01/25/2020] [Indexed: 12/18/2022] Open
Abstract
Nowadays, the emergence of multidrug-resistant bacterial strains initiates the urgent need for the elucidation of the new drug targets for the discovery of antimicrobial drugs. Filamenting temperature-sensitive mutant Z (FtsZ), a eukaryotic tubulin homolog, is a GTP-dependent prokaryotic cytoskeletal protein and is conserved among most bacterial strains. In vitro studies revealed that FtsZ self-assembles into dynamic protofilaments or bundles and forms a dynamic Z-ring at the center of the cell in vivo, leading to septation and consequent cell division. Speculations on the ability of FtsZ in the blockage of cell division make FtsZ a highly attractive target for developing novel antibiotics. Researchers have been working on synthetic molecules and natural products as inhibitors of FtsZ. Accumulating data suggest that FtsZ may provide the platform for the development of novel antibiotics. In this review, we summarize recent advances in the properties of FtsZ protein and bacterial cell division, as well as in the development of FtsZ inhibitors.
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Affiliation(s)
- Mujeeb Ur Rahman
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Ping Wang
- Department of Anesthesiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Na Wang
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Yaodong Chen
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
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Corbin LC, Erickson HP. A Unified Model for Treadmilling and Nucleation of Single-Stranded FtsZ Protofilaments. Biophys J 2020; 119:792-805. [PMID: 32763138 DOI: 10.1016/j.bpj.2020.05.041] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 05/19/2020] [Accepted: 05/27/2020] [Indexed: 10/25/2022] Open
Abstract
Bacterial cell division is tightly coupled to the dynamic behavior of FtsZ, a tubulin homolog. Recent experimental work in vitro and in vivo has attributed FtsZ's assembly dynamics to treadmilling, in which subunits add to the bottom and dissociate from the top of protofilaments. However, the molecular mechanisms producing treadmilling have yet to be characterized and quantified. We have developed a Monte Carlo model for FtsZ assembly that explains treadmilling, and also explains assembly nucleation by the same mechanisms. A key element of the model is a conformational change from R (relaxed), which is highly favored for monomers, to T (tense), which is favored for subunits in a protofilament. This model was created in MATLAB. Kinetic parameters were converted to probabilities of execution during a single, small time step. These were used to stochastically determine FtsZ dynamics. Our model is able to accurately describe the results of several in vitro and in vivo studies for a variety of FtsZ flavors. With standard conditions, the model FtsZ polymerized and produced protofilaments that treadmilled at 23 nm/s, hydrolyzed GTP at 3.6-3.7 GTP min-1 FtsZ-1, and had an average length of 30-40 subunits, all similar to experimental results. Adding a bottom capper resulted in shorter protofilaments and higher GTPase, similar to the effect of the known bottom capper protein MciZ. The model could match nucleation kinetics of several flavors of FtsZ using the same parameters as treadmilling and varying only the R to T transition of monomers.
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Affiliation(s)
- Lauren C Corbin
- Department of Biomedical Engineering, Duke University, Durham, North Carolina
| | - Harold P Erickson
- Department of Biomedical Engineering, Duke University, Durham, North Carolina; Department of Cell Biology, Duke University, Durham, North Carolina.
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Swain A, Anil Kumar AV. A stochastic model for dynamics of FtsZ filaments and the formation of Z -ring. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2020; 43:43. [PMID: 32617695 DOI: 10.1140/epje/i2020-11967-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 06/16/2020] [Indexed: 06/11/2023]
Abstract
Understanding the mechanisms responsible for the formation and growth of FtsZ polymers and their subsequent formation of the Z -ring is important for gaining insight into the cell division in prokaryotic cells. In this work, we present a minimal stochastic model that qualitatively reproduces in vitro observations of polymerization, formation of dynamic contractile ring that is stable for a long time and depolymerization shown by FtsZ polymer filaments. In this stochastic model, we explore different mechanisms for ring breaking and hydrolysis. In addition to hydrolysis, which is known to regulate the dynamics of other tubulin polymers like microtubules, we find that the presence of the ring allows for an additional mechanism for regulating the dynamics of FtsZ polymers. Ring breaking dynamics in the presence of hydrolysis naturally induce rescue and catastrophe events in this model irrespective of the mechanism of hydrolysis.
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Affiliation(s)
- Arabind Swain
- School of Physical Sciences, National Institute of Science Education and Research, 752050, Jatni, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, 400094, Mumbai, India
| | - A V Anil Kumar
- School of Physical Sciences, National Institute of Science Education and Research, 752050, Jatni, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, 400094, Mumbai, India
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Photochemically-Generated Silver Chloride Nanoparticles Stabilized by a Peptide Inhibitor of Cell Division and Its Antimicrobial Properties. J Inorg Organomet Polym Mater 2020. [DOI: 10.1007/s10904-019-01427-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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40
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Cell Division Protein FtsZ Is Unfolded for N-Terminal Degradation by Antibiotic-Activated ClpP. mBio 2020; 11:mBio.01006-20. [PMID: 32605984 PMCID: PMC7327170 DOI: 10.1128/mbio.01006-20] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Acyldepsipeptide (ADEP) antibiotics effectively kill multidrug-resistant Gram-positive pathogens, including vancomycin-resistant enterococcus, penicillin-resistant Streptococcus pneumoniae (PRSP), and methicillin-resistant Staphylococcus aureus (MRSA). The antibacterial activity of ADEP depends on a new mechanism of action, i.e., the deregulation of bacterial protease ClpP that leads to bacterial self-digestion. Our data allow new insights into the mode of ADEP action by providing a molecular explanation for the distinct bacterial phenotypes observed at low versus high ADEP concentrations. In addition, we show that ClpP alone, in the absence of any unfoldase or energy-consuming system, and only activated by the small molecule antibiotic ADEP, leads to the unfolding of the cell division protein FtsZ. Antibiotic acyldepsipeptides (ADEPs) deregulate ClpP, the proteolytic core of the bacterial Clp protease, thereby inhibiting its native functions and concomitantly activating it for uncontrolled proteolysis of nonnative substrates. Importantly, although ADEP-activated ClpP is assumed to target multiple polypeptide and protein substrates in the bacterial cell, not all proteins seem equally susceptible. In Bacillus subtilis, the cell division protein FtsZ emerged to be particularly sensitive to degradation by ADEP-activated ClpP at low inhibitory ADEP concentrations. In fact, FtsZ is the only bacterial protein that has been confirmed to be degraded in vitro as well as within bacterial cells so far. However, the molecular reason for this preferred degradation remained elusive. Here, we report the unexpected finding that ADEP-activated ClpP alone, in the absence of any Clp-ATPase, leads to an unfolding and subsequent degradation of the N-terminal domain of FtsZ, which can be prevented by the stabilization of the FtsZ fold via nucleotide binding. At elevated antibiotic concentrations, importantly, the C terminus of FtsZ is notably targeted for degradation in addition to the N terminus. Our results show that different target structures are more or less accessible to ClpP, depending on the ADEP level present. Moreover, our data assign a Clp-ATPase-independent protein unfolding capability to the ClpP core of the bacterial Clp protease and suggest that the protein fold of FtsZ may be more flexible than previously anticipated.
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Silber N, Matos de Opitz CL, Mayer C, Sass P. Cell division protein FtsZ: from structure and mechanism to antibiotic target. Future Microbiol 2020; 15:801-831. [DOI: 10.2217/fmb-2019-0348] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Antimicrobial resistance to virtually all clinically applied antibiotic classes severely limits the available options to treat bacterial infections. Hence, there is an urgent need to develop and evaluate new antibiotics and targets with resistance-breaking properties. Bacterial cell division has emerged as a new antibiotic target pathway to counteract multidrug-resistant pathogens. New approaches in antibiotic discovery and bacterial cell biology helped to identify compounds that either directly interact with the major cell division protein FtsZ, thereby perturbing the function and dynamics of the cell division machinery, or affect the structural integrity of FtsZ by inducing its degradation. The impressive antimicrobial activities and resistance-breaking properties of certain compounds validate the inhibition of bacterial cell division as a promising strategy for antibiotic intervention.
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Affiliation(s)
- Nadine Silber
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology & Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, Tübingen 72076, Germany
| | - Cruz L Matos de Opitz
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology & Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, Tübingen 72076, Germany
| | - Christian Mayer
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology & Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, Tübingen 72076, Germany
| | - Peter Sass
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology & Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, Tübingen 72076, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen 72076, Germany
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Naz F, Mashkoor M, Sharma P, Haque MA, Kapil A, Kumar M, Kaur P, Abdul Samath E. Drug repurposing approach to target FtsZ cell division protein from Salmonella Typhi. Int J Biol Macromol 2020; 159:1073-1083. [PMID: 32417543 DOI: 10.1016/j.ijbiomac.2020.05.063] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/04/2020] [Accepted: 05/09/2020] [Indexed: 10/24/2022]
Abstract
Drug repurposing is an efficient alternative approach to counter the increasing drug-resistant pathogens to treat infectious diseases. FtsZ is an essential bacterial cytokinesis protein involved in the formation of cell-division complex and targeting FtsZ using FDA approved drugs is a promising strategy to identify and develop a new antibacterial drug. Using in silico pharmacophore-based screening of drug bank, molecular docking and molecular dynamics simulations, we identified six drugs inhibiting the function of stFtsZ from Salmonella Typhi. The selected drugs target stFtsZ at the hydrophobic cleft formed between the C-terminal domain and helix α7 with binding energy better than -8 kcal/mol. Out of these six drugs, benzethonium chloride showed promising results at 8 μM concentration where it inhibits stFtsZ GTPase activity by 80% and prevents polymerization. Benzethonium chloride also possesses an excellent antibacterial activity against the bacterial culture of Salmonella Typhi (ATCC 19430), Staphylococcus aureus (ATCC 43300) and Escherichia coli (ATCC 25922) with the MIC values of 8 μg/mL, 1 μg/mL and 12 μg/mL, respectively. Based on our current study, the scaffold of benzethonium chloride can be used for the development of broad-spectrum antibacterial agents against drug-resistant pathogens.
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Affiliation(s)
- Farah Naz
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Muneera Mashkoor
- Department of Computer Science, Jamia Millia Islamia, New Delhi 110025, India
| | - Priyanka Sharma
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Md Anzarul Haque
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Arti Kapil
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Manoj Kumar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Punit Kaur
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
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Abstract
Bacterial cell division is initiated by the midcell assembly of polymers of the tubulin-like GTPase FtsZ. The FtsZ ring (Z-ring) is a discontinuous structure made of dynamic patches of FtsZ that undergo treadmilling motion. Roughly a dozen additional essential proteins are recruited to the division site by the dynamic Z-ring scaffold and subsequently activate cell wall synthesis to drive cell envelope constriction during division. In this Cell Science at a Glance article and the accompanying poster, we summarize our understanding of the assembly and activation of the bacterial cell division machinery. We introduce polymerization properties of FtsZ and discuss our current knowledge of divisome assembly and activation. We further highlight the intimate relationship between the structure and dynamics of FtsZ and the movement and activity of cell wall synthases at the division site, before concluding with a perspective on the most important open questions on bacterial cell division.
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Affiliation(s)
- Christopher R Mahone
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Erin D Goley
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Dissecting the Functional Contributions of the Intrinsically Disordered C-terminal Tail of Bacillus subtilis FtsZ. J Mol Biol 2020; 432:3205-3221. [PMID: 32198113 DOI: 10.1016/j.jmb.2020.03.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 02/13/2020] [Accepted: 03/07/2020] [Indexed: 01/12/2023]
Abstract
FtsZ is a bacterial GTPase that is central to the spatial and temporal control of cell division. It is a filament-forming enzyme that encompasses a well-folded core domain and a disordered C-terminal tail (CTT). The CTT is essential for ensuring proper assembly of the cytokinetic ring, and its deletion leads to mis-localization of FtsZ, aberrant assembly, and cell death. In this work, we dissect the contributions of modules within the disordered CTT to assembly and enzymatic activity of Bacillus subtilis FtsZ (Bs-FtsZ). The CTT features a hypervariable C-terminal linker (CTL) and a conserved C-terminal peptide (CTP). Our in vitro studies show that the CTL weakens the driving forces for forming single-stranded active polymers and suppresses lateral associations of these polymers, whereas the CTP promotes the formation of alternative assemblies. Accordingly, in full-length Bs-FtsZ, the CTL acts as a spacer that spatially separates the CTP sticker from the core, thus ensuring filament formation through core-driven polymerization and lateral associations through CTP-mediated interactions. We also find that the CTL weakens GTP binding while enhancing the catalytic rate, whereas the CTP has opposite effects. The joint contributions of the CTL and CTP make Bs-FtsZ, an enzyme that is only half as efficient as a truncated version that lacks the CTT. Overall, our data suggest that the CTT acts as an auto-regulator of Bs-FtsZ assembly and as an auto-inhibitor of enzymatic activity. Based on our results, we propose hypotheses regarding the hypervariability of CTLs and compare FtsZs to other bacterial proteins with tethered IDRs.
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The Min System Disassembles FtsZ Foci and Inhibits Polar Peptidoglycan Remodeling in Bacillus subtilis. mBio 2020; 11:mBio.03197-19. [PMID: 32184253 PMCID: PMC7078482 DOI: 10.1128/mbio.03197-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
A microfluidic system coupled with fluorescence microscopy is a powerful approach for quantitative analysis of bacterial growth. Here, we measure parameters of growth and dynamic localization of the cell division initiation protein FtsZ in Bacillus subtilis Consistent with previous reports, we found that after division, FtsZ rings remain at the cell poles, and polar FtsZ ring disassembly coincides with rapid Z-ring accumulation at the midcell. In cells mutated for minD, however, the polar FtsZ rings persist indefinitely, suggesting that the primary function of the Min system is in Z-ring disassembly. The inability to recycle FtsZ monomers in the minD mutant results in the simultaneous maintenance of multiple Z-rings that are restricted by competition for newly synthesized FtsZ. Although the parameters of FtsZ dynamics change in the minD mutant, the overall cell division time remains the same, albeit with elongated cells necessary to accumulate a critical threshold amount of FtsZ for promoting medial division. Finally, the minD mutant characteristically produces minicells composed of polar peptidoglycan shown to be inert for remodeling in the wild type. Polar peptidoglycan, however, loses its inert character in the minD mutant, suggesting that the Min system not only is important for recycling FtsZ but also may have a secondary role in the spatiotemporal regulation of peptidoglycan remodeling.IMPORTANCE Many bacteria grow and divide by binary fission in which a mother cell divides into two identical daughter cells. To produce two equally sized daughters, the division machinery, guided by FtsZ, must dynamically localize to the midcell each cell cycle. Here, we quantitatively analyzed FtsZ dynamics during growth and found that the Min system of Bacillus subtilis is essential to disassemble FtsZ rings after division. Moreover, a failure to efficiently recycle FtsZ results in an increase in cell size. Finally, we show that the Min system has an additional role in inhibiting cell wall turnover and contributes to the "inert" property of cell walls at the poles.
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Huecas S, Canosa-Valls AJ, Araújo-Bazán L, Ruiz FM, Laurents DV, Fernández-Tornero C, Andreu JM. Nucleotide-induced folding of cell division protein FtsZ from Staphylococcus aureus. FEBS J 2020; 287:4048-4067. [PMID: 31997533 DOI: 10.1111/febs.15235] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 12/12/2019] [Accepted: 01/09/2020] [Indexed: 11/29/2022]
Abstract
The essential bacterial division protein FtsZ uses GTP binding and hydrolysis to assemble into dynamic filaments that treadmill around the Z-ring, guiding septal wall synthesis and cell division. FtsZ is a structural homolog of tubulin and a target for discovering new antibiotics. Here, using FtsZ from the pathogen S. aureus (SaFtsZ), we reveal that, prior to assembly, FtsZ monomers require nucleotide binding for folding; this is possibly relevant to other mesophilic FtsZs. Apo-SaFtsZ is essentially unfolded, as assessed by nuclear magnetic resonance and circular dichroism. Binding of GTP (≥ 1 mm) dramatically shifts the equilibrium toward the active folded protein. Supportingly, SaFtsZ refolded with GDP crystallizes in a native structure. Apo-SaFtsZ also folds with 3.4 m glycerol, enabling high-affinity GTP binding (KD 20 nm determined by isothermal titration calorimetry) similar to thermophilic stable FtsZ. Other stabilizing agents that enhance nucleotide binding include ethylene glycol, trimethylamine N-oxide, and several bacterial osmolytes. High salt stabilizes SaFtsZ without bound nucleotide in an inactive twisted conformation. We identified a cavity behind the SaFtsZ-GDP nucleotide-binding pocket that harbors different small compounds, which is available for extended nucleotide-replacing inhibitors. Furthermore, we devised a competition assay to detect any inhibitors that overlap the nucleotide site of SaFtsZ, or Escherichia coli FtsZ, employing osmolyte-stabilized apo-FtsZs and the specific fluorescence anisotropy change in mant-GTP upon dissociation from the protein. This robust assay provides a basis to screening for high-affinity GTP-replacing ligands, which combined with structural studies and phenotypic profiling should facilitate development of a next generation of FtsZ-targeting antibacterial inhibitors.
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Affiliation(s)
- Sonia Huecas
- Centro de Investigaciones Biológicas Margarita Salas CSIC, Madrid, Spain
| | | | - Lidia Araújo-Bazán
- Centro de Investigaciones Biológicas Margarita Salas CSIC, Madrid, Spain
| | - Federico M Ruiz
- Centro de Investigaciones Biológicas Margarita Salas CSIC, Madrid, Spain
| | | | | | - José M Andreu
- Centro de Investigaciones Biológicas Margarita Salas CSIC, Madrid, Spain
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Lee SC, Collins R, Lin YP, Jamshad M, Broughton C, Harris SA, Hanson BS, Tognoloni C, Parslow RA, Terry AE, Rodger A, Smith CJ, Edler KJ, Ford R, Roper DI, Dafforn TR. Nano-encapsulated Escherichia coli Divisome Anchor ZipA, and in Complex with FtsZ. Sci Rep 2019; 9:18712. [PMID: 31822696 PMCID: PMC6904479 DOI: 10.1038/s41598-019-54999-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 11/10/2019] [Indexed: 12/21/2022] Open
Abstract
The E. coli membrane protein ZipA, binds to the tubulin homologue FtsZ, in the early stage of cell division. We isolated ZipA in a Styrene Maleic Acid lipid particle (SMALP) preserving its position and integrity with native E. coli membrane lipids. Direct binding of ZipA to FtsZ is demonstrated, including FtsZ fibre bundles decorated with ZipA. Using Cryo-Electron Microscopy, small-angle X-ray and neutron scattering, we determine the encapsulated-ZipA structure in isolation, and in complex with FtsZ to a resolution of 1.6 nm. Three regions can be identified from the structure which correspond to, SMALP encapsulated membrane and ZipA transmembrane helix, a separate short compact tether, and ZipA globular head which binds FtsZ. The complex extends 12 nm from the membrane in a compact structure, supported by mesoscale modelling techniques, measuring the movement and stiffness of the regions within ZipA provides molecular scale analysis and visualisation of the early divisome.
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Affiliation(s)
- Sarah C Lee
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
| | - Richard Collins
- Faculty of Life Sciences, A4032 Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - Yu-Pin Lin
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Mohammed Jamshad
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Claire Broughton
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Sarah A Harris
- School of Physics and Astronomy and Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, UK
| | - Benjamin S Hanson
- School of Physics and Astronomy and Astbury Centre for Structural and Molecular Biology, University of Leeds, Leeds, UK
| | - Cecilia Tognoloni
- Department of Chemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Rosemary A Parslow
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Ann E Terry
- MAX IV Laboratory Lund University, P.O. Box 118, SE-221 00, Lund, Sweden
| | - Alison Rodger
- Department of Molecular Sciences, Macquarie University, Macquarie, NSW, 2109, Australia
| | - Corinne J Smith
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Karen J Edler
- Department of Chemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Robert Ford
- Faculty of Life Sciences, A4032 Michael Smith Building, Oxford Road, Manchester, M13 9PT, UK
| | - David I Roper
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Timothy R Dafforn
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
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FtsA-FtsZ interaction in Vibrio cholerae causes conformational change of FtsA resulting in inhibition of ATP hydrolysis and polymerization. Int J Biol Macromol 2019; 142:18-32. [PMID: 31790740 DOI: 10.1016/j.ijbiomac.2019.11.217] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 11/26/2019] [Accepted: 11/26/2019] [Indexed: 11/23/2022]
Abstract
Proper interaction between the divisome proteins FtsA and FtsZ is important for the bacterial cell division which is not well characterized till date. In this study, the objective was to understand the mechanism of FtsA-FtsZ interaction using full-length recombinant proteins. We cloned, over-expressed, purified and subsequently characterized FtsA of Vibrio cholerae (VcFtsA). We found that VcFtsA polymerization assembly was dependent on Ca2+ ions, which is unique among FtsA proteins reported until now. VcFtsA also showed ATPase activity and its assembly was ATP dependent. Binding parameters of the interaction between the two full-length proteins, VcFtsA, and VcFtsZ determined by fluorescence spectrophotometry yielded a Kd value of around 38 μM. The Kd value of the interaction was 3 μM when VcFtsA was in ATP bound state. We found that VcFtsZ after interacting with VcFtsA causes a change of secondary structure in the later one leading to loss of its ability to hydrolyze ATP, subsequently halting the VcFtsA polymerization. On the other hand, a double-mutant of VcFtsA (VcFtsA-D242E,R300E), that does not bind to VcFtsZ, polymerized in the presence of VcFtsZ. Though FtsA proteins among different organisms show 70-80% homology in their sequences, assembly of VcFtsA showed a difference in its regulatory processes.
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Wang N, Bian L, Ma X, Meng Y, Chen CS, Rahman MU, Zhang T, Li Z, Wang P, Chen Y. Assembly properties of the bacterial tubulin homolog FtsZ from the cyanobacterium Synechocystis sp. PCC 6803. J Biol Chem 2019; 294:16309-16319. [PMID: 31519752 DOI: 10.1074/jbc.ra119.009621] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 09/10/2019] [Indexed: 11/06/2022] Open
Abstract
The tubulin homolog FtsZ is the major cytoskeletal protein in the bacterial cell division machinery, conserved in almost all bacteria, archaea, and chloroplasts. Bacterial FtsZ assembles spontaneously into single protofilaments, sheets, and bundles in vitro, and it also accumulates at the site of division early during cell division, where it forms a dynamic protein complex, the contractile ring or Z-ring. The biochemical properties of FtsZ proteins from many bacteria have been studied, but comparable insights into FtsZs from cyanobacteria are limited. Here, using EM and light-scattering assays, we studied the biochemical and assembly properties of SyFtsZ, the FtsZ protein from the cyanobacterial strain Synechocystis sp. PCC 6803. SyFtsZ had a slow GTPase activity of ∼0.4 GTP/FtsZ molecule/min and assembled into thick, straight protofilament bundles and curved bundles, designated toroids. The assembly of SyFtsZ in the presence of GTP occurred in two stages. The first stage consisted of the assembly of single-stranded straight protofilaments and opened circles; in the second stage, the protofilaments associated into straight protofilament bundles and toroids. In addition to these assemblies, we also observed highly curved oligomers and minirings after GTP hydrolysis or in the presence of excess GDP. The three types of protofilaments of SyFtsZ observed here provide support for the hypothesis that a constriction force due to curved protofilaments bends the membrane. In summary, our findings indicate that, unlike other bacterial FtsZ, SyFtsZ assembles into thick protofilament bundles. This bundling is similar to that of chloroplast FtsZ, consistent with its origin in cyanobacteria.
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Affiliation(s)
- Na Wang
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Li Bian
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Xueqin Ma
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Yufeng Meng
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Cyndi S Chen
- Department of Anesthesiology, Duke University Medical Center, Durham, North Carolina 27710
| | - Mujeeb Ur Rahman
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Tingting Zhang
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Zhe Li
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Ping Wang
- Department of Anesthesiology, Duke University Medical Center, Durham, North Carolina 27710
| | - Yaodong Chen
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
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50
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Kusuma KD, Payne M, Ung AT, Bottomley AL, Harry EJ. FtsZ as an Antibacterial Target: Status and Guidelines for Progressing This Avenue. ACS Infect Dis 2019; 5:1279-1294. [PMID: 31268666 DOI: 10.1021/acsinfecdis.9b00055] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The disturbing increase in the number of bacterial pathogens that are resistant to multiple, or sometimes all, current antibiotics highlights the desperate need to pursue the discovery and development of novel classes of antibacterials. The wealth of knowledge available about the bacterial cell division machinery has aided target-driven approaches to identify new inhibitor compounds. The main division target being pursued is the highly conserved and essential protein FtsZ. Despite very active research on FtsZ inhibitors for several years, this protein is not yet targeted by any commercial antibiotic. Here, we discuss the suitability of FtsZ as an antibacterial target for drug development and review progress achieved in this area. We use hindsight to highlight the gaps that have slowed progress in FtsZ inhibitor development and to suggest guidelines for concluding that FtsZ is actually the target of these molecules, a key missing link in several studies. In moving forward, a multidisciplinary, communicative, and collaborative process, with sharing of research expertise, is critical if we are to succeed.
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