1
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Royzenblat SK, Freddolino L. Spatio-temporal organization of the E. coli chromosome from base to cellular length scales. EcoSal Plus 2024:eesp00012022. [PMID: 38864557 DOI: 10.1128/ecosalplus.esp-0001-2022] [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: 05/19/2023] [Accepted: 04/17/2024] [Indexed: 06/13/2024]
Abstract
Escherichia coli has been a vital model organism for studying chromosomal structure, thanks, in part, to its small and circular genome (4.6 million base pairs) and well-characterized biochemical pathways. Over the last several decades, we have made considerable progress in understanding the intricacies of the structure and subsequent function of the E. coli nucleoid. At the smallest scale, DNA, with no physical constraints, takes on a shape reminiscent of a randomly twisted cable, forming mostly random coils but partly affected by its stiffness. This ball-of-spaghetti-like shape forms a structure several times too large to fit into the cell. Once the physiological constraints of the cell are added, the DNA takes on overtwisted (negatively supercoiled) structures, which are shaped by an intricate interplay of many proteins carrying out essential biological processes. At shorter length scales (up to about 1 kb), nucleoid-associated proteins organize and condense the chromosome by inducing loops, bends, and forming bridges. Zooming out further and including cellular processes, topological domains are formed, which are flanked by supercoiling barriers. At the megabase-scale both large, highly self-interacting regions (macrodomains) and strong contacts between distant but co-regulated genes have been observed. At the largest scale, the nucleoid forms a helical ellipsoid. In this review, we will explore the history and recent advances that pave the way for a better understanding of E. coli chromosome organization and structure, discussing the cellular processes that drive changes in DNA shape, and what contributes to compaction and formation of dynamic structures, and in turn how bacterial chromatin affects key processes such as transcription and replication.
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Affiliation(s)
- Sonya K Royzenblat
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Lydia Freddolino
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Computational Medicine & Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA
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2
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Monterroso B, Margolin W, Boersma AJ, Rivas G, Poolman B, Zorrilla S. Macromolecular Crowding, Phase Separation, and Homeostasis in the Orchestration of Bacterial Cellular Functions. Chem Rev 2024; 124:1899-1949. [PMID: 38331392 PMCID: PMC10906006 DOI: 10.1021/acs.chemrev.3c00622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 12/01/2023] [Accepted: 01/10/2024] [Indexed: 02/10/2024]
Abstract
Macromolecular crowding affects the activity of proteins and functional macromolecular complexes in all cells, including bacteria. Crowding, together with physicochemical parameters such as pH, ionic strength, and the energy status, influences the structure of the cytoplasm and thereby indirectly macromolecular function. Notably, crowding also promotes the formation of biomolecular condensates by phase separation, initially identified in eukaryotic cells but more recently discovered to play key functions in bacteria. Bacterial cells require a variety of mechanisms to maintain physicochemical homeostasis, in particular in environments with fluctuating conditions, and the formation of biomolecular condensates is emerging as one such mechanism. In this work, we connect physicochemical homeostasis and macromolecular crowding with the formation and function of biomolecular condensates in the bacterial cell and compare the supramolecular structures found in bacteria with those of eukaryotic cells. We focus on the effects of crowding and phase separation on the control of bacterial chromosome replication, segregation, and cell division, and we discuss the contribution of biomolecular condensates to bacterial cell fitness and adaptation to environmental stress.
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Affiliation(s)
- Begoña Monterroso
- Department
of Structural and Chemical Biology, 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, UTHealth-Houston, Houston, Texas 77030, United States
| | - Arnold J. Boersma
- Cellular
Protein Chemistry, Bijvoet Centre for Biomolecular Research, Faculty
of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Germán Rivas
- Department
of Structural and Chemical Biology, Centro de Investigaciones Biológicas
Margarita Salas, Consejo Superior de Investigaciones
Científicas (CSIC), 28040 Madrid, Spain
| | - Bert Poolman
- Department
of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Silvia Zorrilla
- Department
of Structural and Chemical Biology, Centro de Investigaciones Biológicas
Margarita Salas, Consejo Superior de Investigaciones
Científicas (CSIC), 28040 Madrid, Spain
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3
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Suigo L, Monterroso B, Sobrinos-Sanguino M, Alfonso C, Straniero V, Rivas G, Zorrilla S, Valoti E, Margolin W. Benzodioxane-benzamides as promising inhibitors of Escherichia coli FtsZ. Int J Biol Macromol 2023; 253:126398. [PMID: 37634788 DOI: 10.1016/j.ijbiomac.2023.126398] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/02/2023] [Accepted: 08/16/2023] [Indexed: 08/29/2023]
Abstract
The conserved process of cell division in bacteria has been a long-standing target for antimicrobials, although there are few examples of potent broad-spectrum compounds that inhibit this process. Most currently available compounds acting on division are directed towards the FtsZ protein, a self-assembling GTPase that is a central element of the division machinery in most bacteria. Benzodioxane-benzamides are promising candidates, but poorly explored in Gram-negatives. We have tested a number of these compounds on E. coli FtsZ and found that many of them significantly stabilized the polymers against disassembly and reduced the GTPase activity. Reconstitution in crowded cell-like conditions showed that FtsZ bundles were also susceptible to these compounds, including some compounds that were inactive on protofilaments in dilute conditions. They efficiently killed E. coli cells defective in the AcrAB efflux pump. The activity of the compounds on cell growth and division generally showed a good correlation with their effect in vitro, and our experiments are consistent with FtsZ being the target in vivo. Our results uncover the detrimental effects of benzodioxane-benzamides on permeable E. coli cells via its central division protein, implying that lead compounds may be found within this class for the development of antibiotics against Gram-negative bacteria.
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Affiliation(s)
- Lorenzo Suigo
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Luigi Mangiagalli, 25, 20133 Milano, Italy
| | - Begoña Monterroso
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain
| | - Marta Sobrinos-Sanguino
- 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
| | - Valentina Straniero
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Luigi Mangiagalli, 25, 20133 Milano, Italy
| | - Germán Rivas
- 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.
| | - Ermanno Valoti
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Luigi Mangiagalli, 25, 20133 Milano, Italy.
| | - William Margolin
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas, Houston 77030, TX, USA.
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4
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Wang N, Sun H, Zhao K, Shi R, Wang S, Zhou Y, Zhai M, Huang C, Chen Y. The C-terminal domain of MinC, a cell division regulation protein, is sufficient to form a copolymer with MinD. FEBS J 2023; 290:4921-4932. [PMID: 37329190 DOI: 10.1111/febs.16890] [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: 01/10/2023] [Revised: 05/19/2023] [Accepted: 06/15/2023] [Indexed: 06/18/2023]
Abstract
Assembly of cell division protein FtsZ into the Z-ring at the division site is a key step in bacterial cell division. The Min proteins can restrict the Z-ring to the middle of the cell. MinC is the main protein that obstructs Z-ring formation by inhibiting FtsZ assembly. Its N-terminal domain (MinCN ) regulates the localization of the Z-ring by inhibiting FtsZ polymerization, while its C-terminal domain (MinCC ) binds to MinD as well as to FtsZ. Previous studies have shown that MinC and MinD form copolymers in vitro. This copolymer may greatly enhance the binding of MinC to FtsZ, and/or prevent FtsZ filaments from diffusing to the ends of the cell. Here, we investigated the assembly properties of MinCC -MinD of Pseudomonas aeruginosa. We found that MinCC is sufficient to form the copolymers. Although MinCC -MinD assembles into larger bundles, most likely because MinCC is spatially more readily bound to MinD, its copolymerization has similar dynamic properties: the concentration of MinD dominates their copolymerization. The critical concentration of MinD is around 3 μm and when MinD concentration is high enough, a low concentration MinCC could still be copolymerized. We also found that MinCC -MinD can still rapidly bind to FtsZ protofilaments, providing direct evidence that MinCC also interacts directly with FtsZ. However, although the presence of minCC can slightly improve the division defect of minC-knockout strains and shorten the cell length from an average of 12.2 ± 6.7 to 6.6 ± 3.6 μm, it is still insufficient for the normal growth and division of bacteria.
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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, China
| | - Haiyu Sun
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Kairui Zhao
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, Northwest University, Xi'an, China
| | - Runqing Shi
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Shenping Wang
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Yao Zhou
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Meiting Zhai
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, Northwest University, Xi'an, China
| | - Chenghao Huang
- 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
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, Northwest University, Xi'an, China
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5
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Monterroso B, Robles-Ramos MÁ, Sobrinos-Sanguino M, Luque-Ortega JR, Alfonso C, Margolin W, Rivas G, Zorrilla S. Bacterial division ring stabilizing ZapA versus destabilizing SlmA modulate FtsZ switching between biomolecular condensates and polymers. Open Biol 2023; 13:220324. [PMID: 36854378 PMCID: PMC9974302 DOI: 10.1098/rsob.220324] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023] Open
Abstract
Cytokinesis is a fundamental process for bacterial survival and proliferation, involving the formation of a ring by filaments of the GTPase FtsZ, spatio-temporally regulated through the coordinated action of several factors. The mechanisms of this regulation remain largely unsolved, but the inhibition of FtsZ polymerization by the nucleoid occlusion factor SlmA and filament stabilization by the widely conserved cross-linking protein ZapA are known to play key roles. It was recently described that FtsZ, SlmA and its target DNA sequences (SlmA-binding sequence (SBS)) form phase-separated biomolecular condensates, a type of structure associated with cellular compartmentalization and resistance to stress. Using biochemical reconstitution and orthogonal biophysical approaches, we show that FtsZ-SlmA-SBS condensates captured ZapA in crowding conditions and when encapsulated inside cell-like microfluidics microdroplets. We found that, through non-competitive binding, the nucleotide-dependent FtsZ condensate/polymer interconversion was regulated by the ZapA/SlmA ratio. This suggests a highly concentration-responsive tuning of the interconversion that favours FtsZ polymer stabilization by ZapA under conditions mimicking intracellular crowding. These results highlight the importance of biomolecular condensates as concentration hubs for bacterial division factors, which can provide clues to their role in cell function and bacterial survival of stress conditions, such as those generated by antibiotic treatment.
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Affiliation(s)
- Begoña Monterroso
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain
| | - Miguel Ángel Robles-Ramos
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain
| | - Marta Sobrinos-Sanguino
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain
- Molecular Interactions Facility, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain
| | - Juan Román Luque-Ortega
- Molecular Interactions Facility, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain
| | - Carlos Alfonso
- Department of Structural and Chemical Biology, 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, UTHealth-Houston, Houston, TX 77030, USA
| | - Germán Rivas
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain
| | - Silvia Zorrilla
- Department of Structural and Chemical Biology, Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain
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6
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Models versus pathogens: how conserved is the FtsZ in bacteria? Biosci Rep 2023; 43:232502. [PMID: 36695643 PMCID: PMC9939409 DOI: 10.1042/bsr20221664] [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: 11/08/2022] [Revised: 01/10/2023] [Accepted: 01/25/2023] [Indexed: 01/26/2023] Open
Abstract
Combating anti-microbial resistance by developing alternative strategies is the need of the hour. Cell division, particularly FtsZ, is being extensively studied for its potential as an alternative target for anti-bacterial therapy. Bacillus subtilis and Escherichia coli are the two well-studied models for research on FtsZ, the leader protein of the cell division machinery. As representatives of gram-positive and gram-negative bacteria, respectively, these organisms have provided an extensive outlook into the process of cell division in rod-shaped bacteria. However, research on other shapes of bacteria, like cocci and ovococci, lags behind that of model rods. Even though most regions of FtsZ show sequence and structural conservation throughout bacteria, the differences in FtsZ functioning and interacting partners establish several different modes of division in different bacteria. In this review, we compare the features of FtsZ and cell division in the model rods B. subtilis and E. coli and the four pathogens: Staphylococcus aureus, Streptococcus pneumoniae, Mycobacterium tuberculosis, and Pseudomonas aeruginosa. Reviewing several recent articles on these pathogenic bacteria, we have highlighted the functioning of FtsZ, the unique roles of FtsZ-associated proteins, and the cell division processes in them. Further, we provide a detailed look at the anti-FtsZ compounds discovered and their target bacteria, emphasizing the need for elucidation of the anti-FtsZ mechanism of action in different bacteria. Current challenges and opportunities in the ongoing journey of identifying potent anti-FtsZ drugs have also been described.
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7
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Mishra D, Srinivasan R. Catching a Walker in the Act-DNA Partitioning by ParA Family of Proteins. Front Microbiol 2022; 13:856547. [PMID: 35694299 PMCID: PMC9178275 DOI: 10.3389/fmicb.2022.856547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 04/28/2022] [Indexed: 12/01/2022] Open
Abstract
Partitioning the replicated genetic material is a crucial process in the cell cycle program of any life form. In bacteria, many plasmids utilize cytoskeletal proteins that include ParM and TubZ, the ancestors of the eukaryotic actin and tubulin, respectively, to segregate the plasmids into the daughter cells. Another distinct class of cytoskeletal proteins, known as the Walker A type Cytoskeletal ATPases (WACA), is unique to Bacteria and Archaea. ParA, a WACA family protein, is involved in DNA partitioning and is more widespread. A centromere-like sequence parS, in the DNA is bound by ParB, an adaptor protein with CTPase activity to form the segregation complex. The ParA ATPase, interacts with the segregation complex and partitions the DNA into the daughter cells. Furthermore, the Walker A motif-containing ParA superfamily of proteins is associated with a diverse set of functions ranging from DNA segregation to cell division, cell polarity, chemotaxis cluster assembly, cellulose biosynthesis and carboxysome maintenance. Unifying principles underlying the varied range of cellular roles in which the ParA superfamily of proteins function are outlined. Here, we provide an overview of the recent findings on the structure and function of the ParB adaptor protein and review the current models and mechanisms by which the ParA family of proteins function in the partitioning of the replicated DNA into the newly born daughter cells.
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Affiliation(s)
- Dipika Mishra
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, India
- Homi Bhabha National Institutes, Mumbai, India
| | - Ramanujam Srinivasan
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, India
- Homi Bhabha National Institutes, Mumbai, India
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8
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Wang N, Zhang T, Du S, Zhou Y, Chen Y. How Do MinC-D Copolymers Act on Z-Ring Localization Regulation? A New Model of Bacillus subtilis Min System. Front Microbiol 2022; 13:841171. [PMID: 35495694 PMCID: PMC9051478 DOI: 10.3389/fmicb.2022.841171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
Abstract
Division site selection in rod-shaped bacteria is strictly regulated spatially by the Min system. Although many sophisticated studies, including in vitro recombination, have tried to explain these regulations, the precise mechanisms are still unclear. A previous model suggested that the concentration gradient of MinC, an FtsZ inhibitor, regulates the position of the Z-ring in the cell. In Escherichia coli, the oscillation of MinCDE proteins leads to a gradient of Min proteins with the average concentration being lowest in the middle and highest near the poles. In contrast to the Min system of E. coli, the Min system of Bacillus subtilis lacks MinE and exhibits a stable concentration distribution, which is regulated by the binding of DivIVA to the negative curvature membrane. The Min proteins first accumulate at the poles of the cell and relocalize near the division site when the membrane invagination begins. It is inconsistent with the previous model of high concentrations of MinC inhibiting Z-ring formation. Our preliminary data here using electron microscopy and light scattering technology reported that B. subtilis MinC (BsMinC) and MinD (BsMinD) also assembled into large straight copolymers in the presence of ATP, similar to the Min proteins of E. coli. Their assembly is fast and dominated by MinD concentration. When BsMinD is 5 μM, a clear light scattering signal can be observed even at 0.3 μM BsMinC. Here, we propose a new model based on the MinC-D copolymers. In our hypothesis, it is not the concentration gradient of MinC, but the MinC-D copolymer assembled in the region of high concentration MinD that plays a key role in the regulation of Z-ring positioning. In B. subtilis, the regions with high MinD concentration are initially at both ends of the cell and then appear at midcell when cell division began. MinC-D copolymer will polymerize and form a complex with MinJ and DivIVA. These complexes capture FtsZ protofilaments to prevent their diffusion away from the midcell and narrow the Z-ring in the middle of the cell.
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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, China
| | - Tingting Zhang
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, Northwest University, Xi’an, China
| | - Shuheng Du
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, China
| | - Yao Zhou
- 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
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, Northwest University, Xi’an, China
- *Correspondence: Yaodong Chen,
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9
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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: 18] [Impact Index Per Article: 6.0] [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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10
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Zhang Y, Zhang X, Cui H, Ma X, Hu G, Wei J, He Y, Hu Y. Residue 49 of AtMinD1 Plays a Key Role in the Guidance of Chloroplast Division by Regulating the ARC6-AtMinD1 Interaction. FRONTIERS IN PLANT SCIENCE 2021; 12:752790. [PMID: 34880885 PMCID: PMC8646090 DOI: 10.3389/fpls.2021.752790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 10/11/2021] [Indexed: 06/13/2023]
Abstract
Chloroplasts evolved from a free-living cyanobacterium through endosymbiosis. Similar to bacterial cell division, chloroplasts replicate by binary fission, which is controlled by the Minicell (Min) system through confining FtsZ ring formation at the mid-chloroplast division site. MinD, one of the most important members of the Min system, regulates the placement of the division site in plants and works cooperatively with MinE, ARC3, and MCD1. The loss of MinD function results in the asymmetric division of chloroplasts. In this study, we isolated one large dumbbell-shaped and asymmetric division chloroplast Arabidopsis mutant Chloroplast Division Mutant 75 (cdm75) that contains a missense mutation, changing the arginine at residue 49 to a histidine (R49H), and this mutant point is located in the N-terminal Conserved Terrestrial Sequence (NCTS) motif of AtMinD1, which is only typically found in terrestrial plants. This study provides sufficient evidence to prove that residues 1-49 of AtMinD1 are transferred into the chloroplast, and that the R49H mutation does not affect the function of the AtMinD1 chloroplast transit peptide. Subsequently, we showed that the point mutation of R49H could remove the punctate structure caused by residues 1-62 of the AtMinD1 sequence in the chloroplast, suggesting that the arginine in residue 49 (Arg49) is essential for localizing the punctate structure of AtMinD11 - 62 on the chloroplast envelope. Unexpectedly, we found that AtMinD1 could interact directly with ARC6, and that the R49H mutation could prevent not only the previously observed interaction between AtMinD1 and MCD1 but also the interaction between AtMinD1 and ARC6. Thus, we believe that these results show that the AtMinD1 NCTS motif is required for their protein interaction. Collectively, our results show that AtMinD1 can guide the placement of the division site to the mid chloroplast through its direct interaction with ARC6 and reveal the important role of AtMinD1 in regulating the AtMinD1-ARC6 interaction.
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11
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DiBiasio EC, Dickinson RA, Trebino CE, Ferreira CN, Morrison JJ, Camberg JL. The Stress-Active Cell Division Protein ZapE Alters FtsZ Filament Architecture to Facilitate Division in Escherichia coli. Front Microbiol 2021; 12:733085. [PMID: 34646253 PMCID: PMC8503651 DOI: 10.3389/fmicb.2021.733085] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/25/2021] [Indexed: 11/13/2022] Open
Abstract
During pathogenic infections, bacterial cells experience environmental stress conditions, including low oxygen and thermal stress. Bacterial cells proliferate during infection and divide by a mechanism characterized by the assembly of a large cytoskeletal structure at the division site called the Z-ring. The major protein constituting the Z-ring is FtsZ, a tubulin homolog and GTPase that utilizes the nucleotide to assemble into dynamic polymers. In Escherichia coli, many cell division proteins interact with FtsZ and modulate Z-ring assembly, while others direct cell wall insertion and peptidoglycan remodeling. Here, we show that ZapE, an ATPase that accumulates during late constriction, directly interacts with FtsZ and phospholipids in vitro. In the presence of adenosine triphosphate (ATP), ZapE induces bundling of GTP-induced FtsZ polymers; however, ZapE also binds FtsZ in the absence of GTP. The ZapE mutant protein ZapE(K84A), which is defective for ATP hydrolysis, also interacts with FtsZ and induces FtsZ filament bundling. In vivo, cultures of zapE deletion cells contain a low percentage of filamentous cells, suggesting that they have a modest division defect; however, they are able to grow when exposed to stress, such as high temperature and limited oxygen. When combined with the chromosomal deletion of minC, which encodes an FtsZ disassembly factor, ΔzapE ΔminC cells experience growth delays that slow proliferation at high temperature and prevent recovery. This synthetic slow growth phenotype after exposure to stress suggests that ZapE may function to ensure proliferation during and after stress, and this is exacerbated when cells are also deleted for minC. Expression of either ZapE or ZapE(K84A) complements the aberrant growth phenotypes in vivo suggesting that the division-associated role of ZapE does not require ZapE ATP hydrolysis. These results support that ZapE is a stress-regulated cell division protein that interacts directly with FtsZ and phospholipids, promoting growth and division after exposure to environmental stress.
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Affiliation(s)
- Eric C DiBiasio
- Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, RI, United States
| | - Rebecca A Dickinson
- Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, RI, United States
| | - Catherine E Trebino
- Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, RI, United States
| | - Colby N Ferreira
- Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, RI, United States
| | - Josiah J Morrison
- Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, RI, United States
| | - Jodi L Camberg
- Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, RI, United States
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12
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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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13
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Labana P, Dornan MH, Lafrenière M, Czarny TL, Brown ED, Pezacki JP, Boddy CN. Armeniaspirols inhibit the AAA+ proteases ClpXP and ClpYQ leading to cell division arrest in Gram-positive bacteria. Cell Chem Biol 2021; 28:1703-1715.e11. [PMID: 34293284 DOI: 10.1016/j.chembiol.2021.07.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 04/22/2021] [Accepted: 06/29/2021] [Indexed: 01/16/2023]
Abstract
Multi-drug-resistant bacteria present an urgent threat to modern medicine, creating a desperate need for antibiotics with new modes of action. As natural products remain an unsurpassed source for clinically viable antibiotic compounds, we investigate the mechanism of action of armeniaspirol. The armeniaspirols are a structurally unique class of Gram-positive antibiotic discovered from Streptomyces armeniacus for which resistance cannot be readily obtained. We show that armeniaspirol inhibits the ATP-dependent proteases ClpXP and ClpYQ in vitro and in the model Gram-positive Bacillus subtilis. This inhibition dysregulates the divisome and elongasome supported by an upregulation of key proteins FtsZ, DivIVA, and MreB inducing cell division arrest. The inhibition of ClpXP and ClpYQ to dysregulate cell division represents a unique antibiotic mechanism of action and armeniaspirol is the only known natural product inhibitor of the coveted anti-virulence target ClpP. Thus, armeniaspirol possesses a promising lead scaffold for antibiotic development with unique pharmacology.
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Affiliation(s)
- Puneet Labana
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Mark H Dornan
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Matthew Lafrenière
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Tomasz L Czarny
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Eric D Brown
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - John P Pezacki
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Christopher N Boddy
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada.
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14
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Grant NA, Abdel Magid A, Franklin J, Dufour Y, Lenski RE. Changes in Cell Size and Shape during 50,000 Generations of Experimental Evolution with Escherichia coli. J Bacteriol 2021; 203:e00469-20. [PMID: 33649147 PMCID: PMC8088598 DOI: 10.1128/jb.00469-20] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 02/18/2021] [Indexed: 02/07/2023] Open
Abstract
Bacteria adopt a wide variety of sizes and shapes, with many species exhibiting stereotypical morphologies. How morphology changes, and over what timescales, is less clear. Previous work examining cell morphology in an experiment with Escherichia coli showed that populations evolved larger cells and, in some cases, cells that were less rod-like. That experiment has now run for over two more decades. Meanwhile, genome sequence data are available for these populations, and new computational methods enable high-throughput microscopic analyses. In this study, we measured stationary-phase cell volumes for the ancestor and 12 populations at 2,000, 10,000, and 50,000 generations, including measurements during exponential growth at the last time point. We measured the distribution of cell volumes for each sample using a Coulter counter and microscopy, the latter of which also provided data on cell shape. Our data confirm the trend toward larger cells while also revealing substantial variation in size and shape across replicate populations. Most populations first evolved wider cells but later reverted to the ancestral length-to-width ratio. All but one population evolved mutations in rod shape maintenance genes. We also observed many ghost-like cells in the only population that evolved the novel ability to grow on citrate, supporting the hypothesis that this lineage struggles with maintaining balanced growth. Lastly, we show that cell size and fitness remain correlated across 50,000 generations. Our results suggest that larger cells are beneficial in the experimental environment, while the reversion toward ancestral length-to-width ratios suggests partial compensation for the less favorable surface area-to-volume ratios of the evolved cells.IMPORTANCE Bacteria exhibit great morphological diversity, yet we have only a limited understanding of how their cell sizes and shapes evolve and of how these features affect organismal fitness. This knowledge gap reflects, in part, the paucity of the fossil record for bacteria. In this study, we revived and analyzed samples extending over 50,000 generations from 12 populations of experimentally evolving Escherichia coli to investigate the relation between cell size, shape, and fitness. Using this "frozen fossil record," we show that all 12 populations evolved larger cells concomitant with increased fitness, with substantial heterogeneity in cell size and shape across the replicate lines. Our work demonstrates that cell morphology can readily evolve and diversify, even among populations living in identical environments.
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Affiliation(s)
- Nkrumah A Grant
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan, USA
- Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, Michigan, USA
| | - Ali Abdel Magid
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan, USA
| | - Joshua Franklin
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan, USA
| | - Yann Dufour
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan, USA
| | - Richard E Lenski
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
- BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan, USA
- Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, Michigan, USA
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15
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Abstract
The molecular mechanisms that help to place the division septum in bacteria is of fundamental importance to ensure cell proliferation and maintenance of cell shape and size. The Min protein system, found in many rod-shaped bacteria, is thought to play a major role in division site selection. Division site selection is a vital process to ensure generation of viable offspring. In many rod-shaped bacteria, a dynamic protein system, termed the Min system, acts as a central regulator of division site placement. The Min system is best studied in Escherichia coli, where it shows a remarkable oscillation from pole to pole with a time-averaged density minimum at midcell. Several components of the Min system are conserved in the Gram-positive model organism Bacillus subtilis. However, in B. subtilis, it is commonly believed that the system forms a stationary bipolar gradient from the cell poles to midcell. Here, we show that the Min system of B. subtilis localizes dynamically to active sites of division, often organized in clusters. We provide physical modeling using measured diffusion constants that describe the observed enrichment of the Min system at the septum. Mathematical modeling suggests that the observed localization pattern of Min proteins corresponds to a dynamic equilibrium state. Our data provide evidence for the importance of ongoing septation for the Min dynamics, consistent with a major role of the Min system in controlling active division sites but not cell pole areas.
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16
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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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17
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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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18
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Characterization of DicB Inhibitory Activity in Cell Division Under Stress Conditions. Chem Res Chin Univ 2020. [DOI: 10.1007/s40242-020-0248-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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19
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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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20
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Regulation of filamentation by bacteria and its impact on the productivity of compounds in biotechnological processes. Appl Microbiol Biotechnol 2020; 104:4631-4642. [DOI: 10.1007/s00253-020-10590-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 03/18/2020] [Accepted: 03/25/2020] [Indexed: 12/29/2022]
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21
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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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22
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Ramm B, Heermann T, Schwille P. The E. coli MinCDE system in the regulation of protein patterns and gradients. Cell Mol Life Sci 2019; 76:4245-4273. [PMID: 31317204 PMCID: PMC6803595 DOI: 10.1007/s00018-019-03218-x] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/27/2019] [Accepted: 07/02/2019] [Indexed: 12/22/2022]
Abstract
Molecular self-organziation, also regarded as pattern formation, is crucial for the correct distribution of cellular content. The processes leading to spatiotemporal patterns often involve a multitude of molecules interacting in complex networks, so that only very few cellular pattern-forming systems can be regarded as well understood. Due to its compositional simplicity, the Escherichia coli MinCDE system has, thus, become a paradigm for protein pattern formation. This biological reaction diffusion system spatiotemporally positions the division machinery in E. coli and is closely related to ParA-type ATPases involved in most aspects of spatiotemporal organization in bacteria. The ATPase MinD and the ATPase-activating protein MinE self-organize on the membrane as a reaction matrix. In vivo, these two proteins typically oscillate from pole-to-pole, while in vitro they can form a variety of distinct patterns. MinC is a passenger protein supposedly operating as a downstream cue of the system, coupling it to the division machinery. The MinCDE system has helped to extract not only the principles underlying intracellular patterns, but also how they are shaped by cellular boundaries. Moreover, it serves as a model to investigate how patterns can confer information through specific and non-specific interactions with other molecules. Here, we review how the three Min proteins self-organize to form patterns, their response to geometric boundaries, and how these patterns can in turn induce patterns of other molecules, focusing primarily on experimental approaches and developments.
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Affiliation(s)
- Beatrice Ramm
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Tamara Heermann
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Petra Schwille
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
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23
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Ye Y, Ruiz-Martinez A, Wang P, Tartakovsky DM. Quantification of Predictive Uncertainty in Models of FtsZ ring assembly in Escherichia coli. J Theor Biol 2019; 484:110006. [PMID: 31539529 DOI: 10.1016/j.jtbi.2019.110006] [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: 06/24/2019] [Revised: 09/06/2019] [Accepted: 09/12/2019] [Indexed: 11/24/2022]
Abstract
Quantitative predictions of FtsZ protein polymerization are essential for understanding the self-regulating mechanisms in biochemical systems. Due to structural complexity and parametric uncertainty, existing kinetic models remain incomplete and their predictions error-prone. To address such challenges, we perform probabilistic uncertainty quantification and global sensitivity analysis of the concentrations of various protein species predicted with a recent FtsZ protein polymerization model. Our results yield a ranked list of modeling shortcomings that can be improved in order to develop more accurate predictions and more realistic representations of key mechanisms of such biochemical systems and their response to changes in internal or external conditions. Our conclusions and improvement recommendations can be extended to other kinetics models.
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Affiliation(s)
- Yanan Ye
- School of Mathematics and System Sciences, Beihang University, Beijing, China
| | - Alvaro Ruiz-Martinez
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Peng Wang
- School of Mathematics and System Sciences, Beihang University, Beijing, China; Beijing Advanced Innovation Center for Big Data and Brain Computing, Beihang University, Beijing.
| | - Daniel M Tartakovsky
- Department of Energy Resources Engineering, Stanford University, Stanford, CA 94305, USA.
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24
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Szewczak‐Harris A, Wagstaff J, Löwe J. Cryo-EM structure of the MinCD copolymeric filament from Pseudomonas aeruginosa at 3.1 Å resolution. FEBS Lett 2019; 593:1915-1926. [PMID: 31166018 PMCID: PMC6771821 DOI: 10.1002/1873-3468.13471] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 06/02/2019] [Accepted: 06/03/2019] [Indexed: 11/07/2022]
Abstract
Positioning of the division site in many bacterial species relies on the MinCDE system, which prevents the cytokinetic Z-ring from assembling anywhere but the mid-cell, through an oscillatory diffusion-reaction mechanism. MinD dimers bind to membranes and, via their partner MinC, inhibit the polymerization of cell division protein FtsZ into the Z-ring. MinC and MinD form polymeric assemblies in solution and on cell membranes. Here, we report the high-resolution cryo-EM structure of the copolymeric filaments of Pseudomonas aeruginosa MinCD. The filaments consist of three protofilaments made of alternating MinC and MinD dimers. The MinCD protofilaments are almost completely straight and assemble as single protofilaments on lipid membranes, which we also visualized by cryo-EM.
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Affiliation(s)
- Andrzej Szewczak‐Harris
- MRC Laboratory of Molecular BiologyCambridgeUK
- Present address:
Department of BiochemistryUniversity of CambridgeUK
| | | | - Jan Löwe
- MRC Laboratory of Molecular BiologyCambridgeUK
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25
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Hürtgen D, Härtel T, Murray SM, Sourjik V, Schwille P. Functional Modules of Minimal Cell Division for Synthetic Biology. ACTA ACUST UNITED AC 2019; 3:e1800315. [PMID: 32648714 DOI: 10.1002/adbi.201800315] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 03/11/2019] [Indexed: 12/22/2022]
Abstract
Cellular reproduction is one of the fundamental hallmarks of life. Therefore, the development of a minimal division machinery capable of proper genome condensation and organization, mid-cell positioning and segregation in space and time, and the final septation process constitute a fundamental challenge for synthetic biology. It is therefore important to be able to engineer such modules for the production of artificial minimal cells. A bottom-up assembly of molecular machines from bulk biochemicals complemented by in vivo experiments as well as computational modelling helps to approach such key cellular processes. Here, minimal functional modules involved in genome segregation and the division machinery and their spatial organization and positioning are reviewed, setting into perspective the design of a minimal cell. Furthermore, the milestones of recent in vitro reconstitution experiments in the context of cell division are discussed and their role in shedding light on fundamental cellular mechanisms that constitute spatiotemporal order is described. Lastly, current challenges in the field of bottom-up synthetic biology as well as possible future developments toward the development of minimal biomimetic systems are discussed.
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Affiliation(s)
- Daniel Hürtgen
- Max Planck Institute for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology (Synmikro), Karl-von-Frisch Straße 16, 35043, Marburg, Germany
| | - Tobias Härtel
- Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Seán M Murray
- Max Planck Institute for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology (Synmikro), Karl-von-Frisch Straße 16, 35043, Marburg, Germany
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology (Synmikro), Karl-von-Frisch Straße 16, 35043, Marburg, Germany
| | - Petra Schwille
- Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
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26
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Vendel KJA, Tschirpke S, Shamsi F, Dogterom M, Laan L. Minimal in vitro systems shed light on cell polarity. J Cell Sci 2019; 132:132/4/jcs217554. [PMID: 30700498 DOI: 10.1242/jcs.217554] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Cell polarity - the morphological and functional differentiation of cellular compartments in a directional manner - is required for processes such as orientation of cell division, directed cellular growth and motility. How the interplay of components within the complexity of a cell leads to cell polarity is still heavily debated. In this Review, we focus on one specific aspect of cell polarity: the non-uniform accumulation of proteins on the cell membrane. In cells, this is achieved through reaction-diffusion and/or cytoskeleton-based mechanisms. In reaction-diffusion systems, components are transformed into each other by chemical reactions and are moving through space by diffusion. In cytoskeleton-based processes, cellular components (i.e. proteins) are actively transported by microtubules (MTs) and actin filaments to specific locations in the cell. We examine how minimal systems - in vitro reconstitutions of a particular cellular function with a minimal number of components - are designed, how they contribute to our understanding of cell polarity (i.e. protein accumulation), and how they complement in vivo investigations. We start by discussing the Min protein system from Escherichia coli, which represents a reaction-diffusion system with a well-established minimal system. This is followed by a discussion of MT-based directed transport for cell polarity markers as an example of a cytoskeleton-based mechanism. To conclude, we discuss, as an example, the interplay of reaction-diffusion and cytoskeleton-based mechanisms during polarity establishment in budding yeast.
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Affiliation(s)
- Kim J A Vendel
- Bionanoscience Department, Kavli Institute of Nanoscience, Delft University of Technology, Delft 2600 GA, The Netherlands
| | - Sophie Tschirpke
- Bionanoscience Department, Kavli Institute of Nanoscience, Delft University of Technology, Delft 2600 GA, The Netherlands
| | - Fayezeh Shamsi
- Bionanoscience Department, Kavli Institute of Nanoscience, Delft University of Technology, Delft 2600 GA, The Netherlands
| | - Marileen Dogterom
- Bionanoscience Department, Kavli Institute of Nanoscience, Delft University of Technology, Delft 2600 GA, The Netherlands
| | - Liedewij Laan
- Bionanoscience Department, Kavli Institute of Nanoscience, Delft University of Technology, Delft 2600 GA, The Netherlands
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27
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MinC N- and C-Domain Interactions Modulate FtsZ Assembly, Division Site Selection, and MinD-Dependent Oscillation in Escherichia coli. J Bacteriol 2019; 201:JB.00374-18. [PMID: 30455283 DOI: 10.1128/jb.00374-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 11/15/2018] [Indexed: 11/20/2022] Open
Abstract
The Min system in Escherichia coli, consisting of MinC, MinD, and MinE proteins, regulates division site selection by preventing assembly of the FtsZ-ring (Z-ring) and exhibits polar oscillation in vivo MinC antagonizes FtsZ polymerization, and in vivo, the cellular location of MinC is controlled by a direct association with MinD at the membrane. To further understand the interactions of MinC with FtsZ and MinD, we performed a mutagenesis screen to identify substitutions in minC that are associated with defects in cell division. We identified amino acids in both the N- and C-domains of MinC that are important for direct interactions with FtsZ and MinD in vitro, as well as mutations that modify the observed in vivo oscillation of green fluorescent protein (GFP)-MinC. Our results indicate that there are two distinct surface-exposed sites on MinC that are important for direct interactions with FtsZ, one at a cleft on the surface of the N-domain and a second on the C-domain that is adjacent to the MinD interaction site. Mutation of either of these sites leads to slower oscillation of GFP-MinC in vivo, although the MinC mutant proteins are still capable of a direct interaction with MinD in phospholipid recruitment assays. Furthermore, we demonstrate that interactions between FtsZ and both sites of MinC identified here are important for assembly of FtsZ-MinC-MinD complexes and that the conserved C-terminal end of FtsZ is not required for MinC-MinD complex formation with GTP-dependent FtsZ polymers.IMPORTANCE Bacterial cell division proceeds through the coordinated assembly of the FtsZ-ring, or Z-ring, at the site of division. Assembly of the Z-ring requires polymerization of FtsZ, which is regulated by several proteins in the cell. In Escherichia coli, the Min system, which contains MinC, MinD, and MinE proteins, exhibits polar oscillation and inhibits the assembly of FtsZ at nonseptal locations. Here, we identify regions on the surface of MinC that are important for contacting FtsZ and destabilizing FtsZ polymers.
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28
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Ultee E, Ramijan K, Dame RT, Briegel A, Claessen D. Stress-induced adaptive morphogenesis in bacteria. Adv Microb Physiol 2019; 74:97-141. [PMID: 31126537 DOI: 10.1016/bs.ampbs.2019.02.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Bacteria thrive in virtually all environments. Like all other living organisms, bacteria may encounter various types of stresses, to which cells need to adapt. In this chapter, we describe how cells cope with stressful conditions and how this may lead to dramatic morphological changes. These changes may not only allow harmless cells to withstand environmental insults but can also benefit pathogenic bacteria by enabling them to escape from the immune system and the activity of antibiotics. A better understanding of stress-induced morphogenesis will help us to develop new approaches to combat such harmful pathogens.
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Affiliation(s)
- Eveline Ultee
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands; Centre for Microbial Cell Biology, Leiden University, Leiden, the Netherlands
| | - Karina Ramijan
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands; Centre for Microbial Cell Biology, Leiden University, Leiden, the Netherlands
| | - Remus T Dame
- Centre for Microbial Cell Biology, Leiden University, Leiden, the Netherlands; Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CE Leiden, the Netherlands
| | - Ariane Briegel
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands; Centre for Microbial Cell Biology, Leiden University, Leiden, the Netherlands
| | - Dennis Claessen
- Molecular Biotechnology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands; Centre for Microbial Cell Biology, Leiden University, Leiden, the Netherlands
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29
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Dewachter L, Verstraeten N, Fauvart M, Michiels J. An integrative view of cell cycle control in Escherichia coli. FEMS Microbiol Rev 2018; 42:116-136. [PMID: 29365084 DOI: 10.1093/femsre/fuy005] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 01/19/2018] [Indexed: 11/14/2022] Open
Abstract
Bacterial proliferation depends on the cells' capability to proceed through consecutive rounds of the cell cycle. The cell cycle consists of a series of events during which cells grow, copy their genome, partition the duplicated DNA into different cell halves and, ultimately, divide to produce two newly formed daughter cells. Cell cycle control is of the utmost importance to maintain the correct order of events and safeguard the integrity of the cell and its genomic information. This review covers insights into the regulation of individual key cell cycle events in Escherichia coli. The control of initiation of DNA replication, chromosome segregation and cell division is discussed. Furthermore, we highlight connections between these processes. Although detailed mechanistic insight into these connections is largely still emerging, it is clear that the different processes of the bacterial cell cycle are coordinated to one another. This careful coordination of events ensures that every daughter cell ends up with one complete and intact copy of the genome, which is vital for bacterial survival.
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Affiliation(s)
- Liselot Dewachter
- Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, B-3001 Leuven, Belgium.,VIB Center for Microbiology, B-3001 Leuven, Belgium
| | - Natalie Verstraeten
- Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, B-3001 Leuven, Belgium.,VIB Center for Microbiology, B-3001 Leuven, Belgium
| | - Maarten Fauvart
- Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, B-3001 Leuven, Belgium.,VIB Center for Microbiology, B-3001 Leuven, Belgium.,Department of Life Sciences and Imaging, Smart Electronics Unit, imec, B-3001 Leuven, Belgium
| | - Jan Michiels
- Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, B-3001 Leuven, Belgium.,VIB Center for Microbiology, B-3001 Leuven, Belgium
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30
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The MinDE system is a generic spatial cue for membrane protein distribution in vitro. Nat Commun 2018; 9:3942. [PMID: 30258191 PMCID: PMC6158289 DOI: 10.1038/s41467-018-06310-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 08/10/2018] [Indexed: 01/01/2023] Open
Abstract
The E. coli MinCDE system has become a paradigmatic reaction-diffusion system in biology. The membrane-bound ATPase MinD and ATPase-activating protein MinE oscillate between the cell poles followed by MinC, thus positioning the main division protein FtsZ at midcell. Here we report that these energy-consuming MinDE oscillations may play a role beyond constraining MinC/FtsZ localization. Using an in vitro reconstitution assay, we show that MinDE self-organization can spatially regulate a variety of functionally completely unrelated membrane proteins into patterns and gradients. By concentration waves sweeping over the membrane, they induce a direct net transport of tightly membrane-attached molecules. That the MinDE system can spatiotemporally control a much larger set of proteins than previously known, may constitute a MinC-independent pathway to division site selection and chromosome segregation. Moreover, the here described phenomenon of active transport through a traveling diffusion barrier may point to a general mechanism of spatiotemporal regulation in cells.
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31
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MacCready JS, Vecchiarelli AG. In long bacterial cells, the Min system can act off-center. Mol Microbiol 2018; 109:268-272. [DOI: 10.1111/mmi.13995] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Joshua S. MacCready
- Molecular, Cellular, and Developmental Biology; University of Michigan College of Literature Science and the Arts; Biological Sciences Building Ann Arbor MI USA
| | - Anthony G. Vecchiarelli
- Molecular, Cellular, and Developmental Biology; University of Michigan College of Literature Science and the Arts; Biological Sciences Building Ann Arbor MI USA
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32
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Guan F, Yu J, Yu J, Liu Y, Li Y, Feng XH, Huang KC, Chang Z, Ye S. Lateral interactions between protofilaments of the bacterial tubulin homolog FtsZ are essential for cell division. eLife 2018; 7:35578. [PMID: 29889022 PMCID: PMC6050046 DOI: 10.7554/elife.35578] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 06/10/2018] [Indexed: 01/01/2023] Open
Abstract
The prokaryotic tubulin homolog FtsZ polymerizes into protofilaments, which further assemble into higher-order structures at future division sites to form the Z-ring, a dynamic structure essential for bacterial cell division. The precise nature of interactions between FtsZ protofilaments that organize the Z-ring and their physiological significance remain enigmatic. In this study, we solved two crystallographic structures of a pair of FtsZ protofilaments, and demonstrated that they assemble in an antiparallel manner through the formation of two different inter-protofilament lateral interfaces. Our in vivo photocrosslinking studies confirmed that such lateral interactions occur in living cells, and disruption of the lateral interactions rendered cells unable to divide. The inherently weak lateral interactions enable FtsZ protofilaments to self-organize into a dynamic Z-ring. These results have fundamental implications for our understanding of bacterial cell division and for developing antibiotics that target this key process.
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Affiliation(s)
- Fenghui Guan
- Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, China.,Life Sciences Institute, Zheijiang University, Hangzhou, China
| | - Jiayu Yu
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Jie Yu
- Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, China.,Life Sciences Institute, Zheijiang University, Hangzhou, China
| | - Yang Liu
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Ying Li
- Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, China
| | - Xin-Hua Feng
- Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, China.,Life Sciences Institute, Zheijiang University, Hangzhou, China
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, United States.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, United States.,Chan Zuckerberg Biohub, San Francisco, United States
| | - Zengyi Chang
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Sheng Ye
- Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou, China.,Life Sciences Institute, Zheijiang University, Hangzhou, China
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33
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Flores SA, Howell M, Daniel JJ, Piccolo R, Brown PJB. Absence of the Min System Does Not Cause Major Cell Division Defects in Agrobacterium tumefaciens. Front Microbiol 2018; 9:681. [PMID: 29686659 PMCID: PMC5900048 DOI: 10.3389/fmicb.2018.00681] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 03/22/2018] [Indexed: 12/19/2022] Open
Abstract
In A. tumefaciens, the essential FtsZ protein is located at the growth pole before shifting to the mid-cell right before division. Loss of FtsZ causes a halt in cell separation and lysis of cells. To understand how FtsZ polymerization is regulated to properly localize the FtsZ ring at the mid-cell, we have conducted a systematic characterization of the Min system in A. tumefaciens. Our findings indicate that the Min system is not required for cell survival. Yet, we find that the deletion of either minE or minCDE results in a broad cell size distribution, including an increase in the proportion of short and long cells. We observe that the site of constriction is misplaced in the minE or minCDE deletion strains allowing for short cells to arise from sites of constriction near the cell poles. Remarkably, the short cells are viable and contain DNA. In order to observe chromosome replication and segregation in these strains, YFP-ParB is used as a proxy to track the origin of replication as cells elongate and divide. In the absence of the Min proteins, duplication and segregation of the origin of replication is frequently delayed. Taken together, our data suggest that the Min system contributes to the proper regulation of FtsZ placement and subsequent cell division. Furthermore, the failure to precisely place FtsZ rings at mid-cell in the min mutants impacts other cell cycle features including chromosome segregation.
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Affiliation(s)
- Sue A Flores
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Matthew Howell
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Jeremy J Daniel
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Rebecca Piccolo
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
| | - Pamela J B Brown
- Division of Biological Sciences, University of Missouri, Columbia, MO, United States
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34
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Efficient models of polymerization applied to FtsZ ring assembly in Escherichia coli. Proc Natl Acad Sci U S A 2018; 115:4933-4938. [PMID: 29686085 DOI: 10.1073/pnas.1719391115] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
High protein concentrations complicate modeling of polymer assembly kinetics by introducing structural complexity and a large variety of protein forms. We present a modeling approach that achieves orders of magnitude speed-up by replacing distributions of lengths and widths with their average counterparts and by introducing a hierarchical classification of species and reactions into sets. We have used this model to study FtsZ ring assembly in Escherichia coli The model's prediction of key features of the ring formation, such as time to reach the steady state, total concentration of FtsZ species in the ring, total concentration of monomers, and average dimensions of filaments and bundles, are all in agreement with the experimentally observed values. Besides validating our model against the in vivo observations, this study fills some knowledge gaps by proposing a specific structure of the ring, describing the influence of the total concentration in short and long kinetics processes, determining some characteristic mechanisms in polymer assembly regulation, and providing insights about the role of ZapA proteins, critical components for both positioning and stability of the ring.
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35
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Huang H, Wang P, Bian L, Osawa M, Erickson HP, Chen Y. The cell division protein MinD from Pseudomonas aeruginosa dominates the assembly of the MinC-MinD copolymers. J Biol Chem 2018; 293:7786-7795. [PMID: 29610277 DOI: 10.1074/jbc.ra117.001513] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Revised: 03/30/2018] [Indexed: 01/22/2023] Open
Abstract
Cell division of rod-shaped bacteria requires the Z ring, a ring of FtsZ filaments associated with the inner-membrane wall. The MinCDE proteins help localize the Z ring to the center of the Escherichia coli cell. MinC, which inhibits Z-ring assembly, is a passenger on MinD. Previous studies have shown that MinC-MinD from E. coli and Aquifex aeolicus assemble in vitro into extended filaments with a 1:1 stoichiometry. However, a recent study has raised questions about the function of the MinC-MinD copolymer in vivo, because its assembly appears to require a high concentration of these two proteins and has a long lag time, and its blockade does not affect in vivo activities. Here, we found that MinC and MinD from Pseudomonas aeruginosa coassemble into filaments with a 1:1 stoichiometry. We also found that the minimal concentration of ∼4 μm required for assembly applies only to MinD because above 4 μm MinD, even very low MinC concentrations sustained coassembly. As previously reported, the MinC-MinD coassembly exhibited a long lag of ∼100 s when initiated by ATP. Premixing MinD with ATP eliminated this lag, suggesting that it may be due to slow MinD dimerization following ATP activation. We also discovered that MinC-MinD copolymers quickly bound FtsZ filaments and formed huge bundles. Our results resolve previous questions about the low concentration of MinC and the lag time, insights that may inform future investigations into the exact role of the MinC-MinD copolymer in vivo.
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Affiliation(s)
- Haiyan Huang
- From the Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China 710069 and
| | - Ping Wang
- the Departments of Anesthesiology and
| | - Li Bian
- From the Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China 710069 and
| | - Masaki Osawa
- Cell Biology, Duke University Medical Center, Durham, North Carolina 27710
| | - Harold P Erickson
- Cell Biology, Duke University Medical Center, Durham, North Carolina 27710
| | - Yaodong Chen
- From the Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China 710069 and
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36
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Puffal J, García-Heredia A, Rahlwes KC, Siegrist MS, Morita YS. Spatial control of cell envelope biosynthesis in mycobacteria. Pathog Dis 2018; 76:4953754. [DOI: 10.1093/femspd/fty027] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 03/25/2018] [Indexed: 11/12/2022] Open
Affiliation(s)
- Julia Puffal
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
| | - Alam García-Heredia
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
| | - Kathryn C Rahlwes
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
| | - M Sloan Siegrist
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
| | - Yasu S Morita
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA 01003, USA
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37
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Mizuuchi K, Vecchiarelli AG. Mechanistic insights of the Min oscillator via cell-free reconstitution and imaging. Phys Biol 2018; 15:031001. [PMID: 29188788 DOI: 10.1088/1478-3975/aa9e5e] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The MinD and MinE proteins of Escherichia coli self-organize into a standing-wave oscillator on the membrane to help align division at mid-cell. When unleashed from cellular confines, MinD and MinE form a spectrum of patterns on artificial bilayers-static amoebas, traveling waves, traveling mushrooms, and bursts with standing-wave dynamics. We recently focused our cell-free studies on bursts because their dynamics recapitulate many features of Min oscillation observed in vivo. The data unveiled a patterning mechanism largely governed by MinE regulation of MinD interaction with membrane. We proposed that the MinD to MinE ratio on the membrane acts as a toggle switch between MinE-stimulated recruitment and release of MinD from the membrane. In this review, we summarize cell-free data on the Min system and expand upon a molecular mechanism that provides a biochemical explanation as to how these two 'simple' proteins can form the remarkable spectrum of patterns.
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Affiliation(s)
- Kiyoshi Mizuuchi
- Laboratory of Molecular Biology, National Institute of Diabetes, and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, United States of America
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38
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Chumová J, Trögelová L, Kourová H, Volc J, Sulimenko V, Halada P, Kučera O, Benada O, Kuchařová A, Klebanovych A, Dráber P, Daniel G, Binarová P. γ-Tubulin has a conserved intrinsic property of self-polymerization into double stranded filaments and fibrillar networks. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2018; 1865:734-748. [PMID: 29499229 DOI: 10.1016/j.bbamcr.2018.02.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 02/22/2018] [Accepted: 02/23/2018] [Indexed: 12/22/2022]
Abstract
γ-Tubulin is essential for microtubule nucleation and also plays less understood roles in nuclear and cell-cycle-related functions. High abundancy of γ-tubulin in acentrosomal Arabidopsis cells facilitated purification and biochemical characterization of large molecular species of γ-tubulin. TEM, fluorescence, and atomic force microscopy of purified high molecular γ-tubulin forms revealed the presence of linear filaments with a double protofilament substructure, filament bundles and aggregates. Filament formation from highly purified γ-tubulin free of γ-tubulin complex proteins (GCPs) was demonstrated for both plant and human γ-tubulin. Moreover, γ-tubulin associated with porcine brain microtubules formed oligomers. Experimental evidence on the intrinsic ability of γ-tubulin to oligomerize/polymerize was supported by conservation of α- and β-tubulin interfaces for longitudinal and lateral interactions for γ-tubulins. STED (stimulated emission depletion) microscopy of Arabidopsis cells revealed fine, short γ-tubulin fibrillar structures enriched on mitotic microtubular arrays that accumulated at polar regions of acentrosomal spindles and the outer nuclear envelope before mitosis, and were also present in nuclei. Fine fibrillar structures of γ-tubulin representing assemblies of higher order were localized in cell-cycle-dependent manner at sites of dispersed γ-tubulin location in acentrosomal plant cells as well as at sites of local γ-tubulin enrichment after drug treatment. Our findings that γ-tubulin preserves the capability of prokaryotic tubulins to self-organize into filaments assembling by lateral interaction into bundles/clusters help understanding of the relationship between structure and multiple cellular functions of this protein species and suggest that besides microtubule nucleation and organization, γ-tubulin may also have scaffolding or sequestration functions.
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Affiliation(s)
- Jana Chumová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Lucie Trögelová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Hana Kourová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Jindřich Volc
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Vadym Sulimenko
- Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Petr Halada
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Ondřej Kučera
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Chaberská 57, 182 00 Prague 8, Czech Republic
| | - Oldřich Benada
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Anna Kuchařová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Anastasiya Klebanovych
- Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Pavel Dráber
- Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Geoffrey Daniel
- Department of Forest Biomaterials Technology, Swedish University of Agricultural Sciences, Box 7008, Uppsala SE-75007, Sweden
| | - Pavla Binarová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague 4, Czech Republic.
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39
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Park KT, Dajkovic A, Wissel M, Du S, Lutkenhaus J. MinC and FtsZ mutant analysis provides insight into MinC/MinD-mediated Z ring disassembly. J Biol Chem 2018; 293:5834-5846. [PMID: 29414773 DOI: 10.1074/jbc.m117.815894] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 01/31/2018] [Indexed: 11/06/2022] Open
Abstract
The Min system negatively regulates the position of the Z ring, which serves as a scaffold for the divisome that mediates bacterial cytokinesis. In Escherichia coli, this system consists of MinC, which antagonizes assembly of the tubulin homologue FtsZ. MinC is recruited to the membrane by MinD and induced by MinE to oscillate between the cell poles. MinC is a dimer with each monomer consisting of functionally distinct MinCN and MinCC domains, both of which contact FtsZ. According to one model, MinCC/MinD binding to the FtsZ tail positions MinCN at the junction of two GDP-containing subunits in the filament, leading to filament breakage. Others posit that MinC sequesters FtsZ-GDP monomers or that MinCN caps the minus end of FtsZ polymers and that MinCC interferes with lateral interactions between FtsZ filaments. Here, we isolated minC mutations that impair MinCN function and analyzed FtsZ mutants resistant to MinC/MinD. Surprisingly, we found mutations in both minC and ftsZ that differentiate inhibition by MinC from inhibition by MinC/MinD. Analysis of these mutations suggests that inhibition of the Z ring by MinC alone is due to sequestration, whereas inhibition by MinC/MinD is not. In conclusion, our genetic and biochemical data support the model that MinC/MinD fragments FtsZ filaments.
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Affiliation(s)
- Kyung-Tae Park
- From the Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, Kansas 66160
| | - Alex Dajkovic
- From the Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, Kansas 66160
| | - Mark Wissel
- From the Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, Kansas 66160
| | - Shishen Du
- From the Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, Kansas 66160
| | - Joe Lutkenhaus
- From the Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, Kansas 66160
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40
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Valenčíková R, Krascsenitsová E, Labajová N, Makroczyová J, Barák I. Clostridial DivIVA and MinD interact in the absence of MinJ. Anaerobe 2018; 50:22-31. [PMID: 29408597 DOI: 10.1016/j.anaerobe.2018.01.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 01/04/2018] [Accepted: 01/29/2018] [Indexed: 11/25/2022]
Abstract
One of the key regulators ensuring proper Z-ring placement in rod-shaped bacteria is the Min system. It does so by creating a concentration gradient of the MinC septation inhibitor along the cell axis. In Escherichia coli, this gradient is established by a MinE-mediated pole-to-pole oscillation of the MinCDE complex. In Bacillus subtilis, the creation of an inhibitory gradient relies on the MinJ and DivIVA pair of topological determinants, which target MinCD to the newly formed cell poles. Introducing the E. coli oscillating Min system into B. subtilis leads to a sporulation defect, suggesting that oscillation is incompatible with sporulation. However, Clostridia, close endospore-forming relatives of Bacilli, do encode oscillating Min homologues in various combinations together with homologues from the less dynamic B. subtilis Min system. Here we address the questions of how these two systems could exist side-by-side and how they influence one another by studying the Clostridium beijerinckii and Clostridium difficile Min systems. The toolbox of genetic manipulations and fluorescent protein fusions in Clostridia is limited, therefore B. subtilis and E. coli were chosen as heterologous systems for studying these proteins. In B. subtilis, MinD and DivIVA interact through MinJ; here, however, we discovered that the MinD and DivIVA proteins of both C. difficile, and C. beijerinckii, interact directly, which is surprising in the latter case, since that organism also encodes a MinJ homologue. We confirm this interaction using both in vitro and in vivo methods. We also show that C. beijerinckii MinJ is probably not in direct contact with DivIVACb and, unlike B. subtilis MinJ, does not mediate the MinDCb and DivIVACb interaction. Our results suggest that the Clostridia Min system uses a new mechanism of function.
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Affiliation(s)
- Romana Valenčíková
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia
| | - Eva Krascsenitsová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia
| | - Naďa Labajová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia
| | - Jana Makroczyová
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia
| | - Imrich Barák
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia.
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41
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Muchová K, Chromiková Z, Valenčíková R, Barák I. Interaction of the Morphogenic Protein RodZ with the Bacillus subtilis Min System. Front Microbiol 2018; 8:2650. [PMID: 29403445 PMCID: PMC5778138 DOI: 10.3389/fmicb.2017.02650] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 12/19/2017] [Indexed: 12/01/2022] Open
Abstract
Vegetative cell division in Bacillus subtilis takes place precisely at the middle of the cell to ensure that two viable daughter cells are formed. The first event in cell division is the positioning of the FtsZ Z-ring at the correct site. This is controlled by the coordinated action of both negative and positive regulators. The existence of positive regulators has been inferred, but none have presently been identified in B. subtilis. Noc and the Min system belong to negative regulators; Noc prevents division from occurring over the chromosomes, and the Min system inhibits cell division at the poles. Here we report that the morphogenic protein, RodZ, an essential cell shape determinant, is also required for proper septum positioning during vegetative growth. In rodZ mutant cells, the vegetative septum is positioned off center, giving rise to small, round, DNA-containing cells. Searching for the molecular mechanism giving rise to this phenotype led us to discover that RodZ directly interacts with MinJ. We hypothesize that RodZ may aid the Min system in preventing non-medial vegetative division.
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Affiliation(s)
| | | | | | - Imrich Barák
- Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
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42
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Miyagi A, Ramm B, Schwille P, Scheuring S. High-Speed Atomic Force Microscopy Reveals the Inner Workings of the MinDE Protein Oscillator. NANO LETTERS 2018; 18:288-296. [PMID: 29210266 DOI: 10.1021/acs.nanolett.7b04128] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The MinDE protein system from E. coli has recently been identified as a minimal biological oscillator, based on two proteins only: The ATPase MinD and the ATPase activating protein MinE. In E. coli, the system works as the molecular ruler to place the divisome at midcell for cell division. Despite its compositional simplicity, the molecular mechanism leading to protein patterns and oscillations is still insufficiently understood. Here we used high-speed atomic force microscopy to analyze the mechanism of MinDE membrane association/dissociation dynamics on isolated membrane patches, down to the level of individual point oscillators. This nanoscale analysis shows that MinD association to and dissociation from the membrane are both highly cooperative but mechanistically different processes. We propose that they represent the two directions of a single allosteric switch leading to MinD filament formation and depolymerization. Association/dissociation are separated by rather long apparently silent periods. The membrane-associated period is characterized by MinD filament multivalent binding, avidity, while the dissociated period is defined by seeding of individual MinD. Analyzing association/dissociation kinetics with varying MinD and MinE concentrations and dependent on membrane patch size allowed us to disentangle the essential dynamic variables of the MinDE oscillation cycle.
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Affiliation(s)
- Atsushi Miyagi
- U1006 INSERM, Aix-Marseille Université, Parc Scientifique et Technologique de Luminy , 13009 Marseille, France
| | - Beatrice Ramm
- Max Planck Institute of Biochemistry , Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Petra Schwille
- Max Planck Institute of Biochemistry , Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Simon Scheuring
- U1006 INSERM, Aix-Marseille Université, Parc Scientifique et Technologique de Luminy , 13009 Marseille, France
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43
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Chloroplast division protein ARC3 acts on FtsZ2 by preventing filament bundling and enhancing GTPase activity. Biochem J 2018; 475:99-115. [PMID: 29138260 DOI: 10.1042/bcj20170697] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Revised: 11/09/2017] [Accepted: 11/10/2017] [Indexed: 01/28/2023]
Abstract
Chloroplasts evolved from cyanobacterial endosymbiotic ancestors and their division is a complex process initiated by the assembly of cytoskeletal FtsZ (Filamentous temperature sensitive Z) proteins into a ring structure at the division site (Z-ring). The cyanobacterial Z-ring positioning system (MinCDE proteins) is also conserved in chloroplasts, except that MinC was lost and replaced by the eukaryotic ARC3 (accumulation and replication of chloroplasts). Both MinC and ARC3 act as negative regulators of FtsZ assembly, but ARC3 bears little sequence similarity with MinC. Here, light scattering assays, co-sedimentation, GTPase assay and transmission electron microscopy in conjunction with single-particle analysis have been used to elucidate the structure of ARC3 and its effect on its main target in chloroplast division, FtsZ2. Analysis of FtsZ2 in vitro assembly reactions in the presence and absence of GMPCPP showed that ARC3 promotes FtsZ2 debundling and disassembly of existing filaments in a concentration-dependent manner and requires GTP hydrolysis. Three-dimensional reconstruction of ARC3 revealed an almost circular molecule in which the FtsZ-binding N-terminus and the C-terminal PARC6 (paralog of ARC6)-binding MORN (Membrane Occupation and Recognition Nexus) domain are in close proximity and suggest a model for PARC6-enabled binding of ARC3 to FtsZ2. The latter is corroborated by in vivo data.
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Yang S, Pei H, Zhang X, Wei Q, Zhu J, Zheng J, Jia Z. Characterization of DicB by partially masking its potent inhibitory activity of cell division. Open Biol 2017; 6:rsob.160082. [PMID: 27466443 PMCID: PMC4967827 DOI: 10.1098/rsob.160082] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Accepted: 07/01/2016] [Indexed: 11/12/2022] Open
Abstract
DicB, a protein encoded by the Kim (Qin) prophage in Escherichia coli, inhibits cell division through interaction with MinC. Thus far, characterization of DicB has been severely hampered owing to its potent activity which ceases cell division and leads to cell death. In this work, through fusing maltose-binding protein to the N-terminus of DicB (MBP–DicB), we successfully expressed and purified recombinant DicB that enabled in vitro analysis for the first time. More importantly, taking advantage of the reduced inhibitory activity of MBP–DicB, we were able to study its effects on cell growth and morphology. Inhibition of cell growth by MBP–DicB was systematically evaluated using various DicB constructs, and their corresponding effects on cell morphology were also investigated. Our results revealed that the N-terminal segment of DicB plays an essential functional role, in contrast to its C-terminal tail. The N-terminus of DicB is of critical importance as even the first amino acid (following the initial Met) could not be removed, although it could be mutated. This study provides the first glimpse of the molecular determinants underlying DicB's function.
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Affiliation(s)
- Shaoyuan Yang
- College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Hairun Pei
- College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Xiaoying Zhang
- College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Qiang Wei
- College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Jia Zhu
- College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Jimin Zheng
- College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China
| | - Zongchao Jia
- College of Chemistry, Beijing Normal University, Beijing 100875, People's Republic of China Department of Biomedical and Molecular Sciences, Queen's University, Ontario, Canada K7L 3N6
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45
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MinD directly interacting with FtsZ at the H10 helix suggests a model for robust activation of MinC to destabilize FtsZ polymers. Biochem J 2017; 474:3189-3205. [PMID: 28743721 DOI: 10.1042/bcj20170357] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 07/10/2017] [Accepted: 07/25/2017] [Indexed: 12/30/2022]
Abstract
Cell division in bacteria is a highly controlled and regulated process. FtsZ, a bacterial cytoskeletal protein, forms a ring-like structure known as the Z-ring and recruits more than a dozen other cell division proteins. The Min system oscillates between the poles and inhibits the Z-ring formation at the poles by perturbing FtsZ assembly. This leads to an increase in the FtsZ concentration at the mid-cell and helps in Z-ring positioning. MinC, the effector protein, interferes with Z-ring formation through two different mechanisms mediated by its two domains with the help of MinD. However, the mechanism by which MinD triggers MinC activity is not yet known. We showed that MinD directly interacts with FtsZ with an affinity stronger than the reported MinC-FtsZ interaction. We determined the MinD-binding site of FtsZ using computational, mutational and biochemical analyses. Our study showed that MinD binds to the H10 helix of FtsZ. Single-point mutations at the charged residues in the H10 helix resulted in a decrease in the FtsZ affinity towards MinD. Based on our findings, we propose a novel model for MinCD-FtsZ interaction, where MinD through its direct interaction with FtsZ would trigger MinC activity to inhibit FtsZ functions.
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Ruiz-Martinez A, Bartol TM, Sejnowski TJ, Tartakovsky DM. Efficient Multiscale Models of Polymer Assembly. Biophys J 2017; 111:185-96. [PMID: 27410746 DOI: 10.1016/j.bpj.2016.05.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 04/24/2016] [Accepted: 05/09/2016] [Indexed: 12/25/2022] Open
Abstract
Protein polymerization and bundling play a central role in cell physiology. Predictive modeling of these processes remains an open challenge, especially when the proteins involved become large and their concentrations high. We present an effective kinetics model of filament formation, bundling, and depolymerization after GTP hydrolysis, which involves a relatively small number of species and reactions, and remains robust over a wide range of concentrations and timescales. We apply this general model to study assembly of FtsZ protein, a basic element in the division process of prokaryotic cells such as Escherichia coli, Bacillus subtilis, or Caulobacter crescentus. This analysis demonstrates that our model outperforms its counterparts in terms of both accuracy and computational efficiency. Because our model comprises only 17 ordinary differential equations, its computational cost is orders-of-magnitude smaller than the current alternatives consisting of up to 1000 ordinary differential equations. It also provides, to our knowledge, a new insight into the characteristics and functioning of FtsZ proteins at high concentrations. The simplicity and versatility of our model render it a powerful computational tool, which can be used either as a standalone descriptor of other biopolymers' assembly or as a component in more complete kinetic models.
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Affiliation(s)
- Alvaro Ruiz-Martinez
- Department of Mechanical and Aerospace Engineering, University of California-San Diego, La Jolla, California
| | - Thomas M Bartol
- Computational Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, California
| | - Terrence J Sejnowski
- Computational Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, California; Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, California; The Division of Biological Studies Sciences, University of California-San Diego, La Jolla, California.
| | - Daniel M Tartakovsky
- Department of Mechanical and Aerospace Engineering, University of California-San Diego, La Jolla, California.
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Abstract
Bacillus subtilis is the best described member of the Gram positive bacteria. It is a typical rod shaped bacterium and grows by elongation in its long axis, before dividing at mid cell to generate two similar daughter cells. B. subtilis is a particularly interesting model for cell cycle studies because it also carries out a modified, asymmetrical division during endospore formation, which can be simply induced by starvation. Cell growth occurs strictly by elongation of the rod, which maintains a constant diameter at all growth rates. This process involves expansion of the cell wall, requiring intercalation of new peptidoglycan and teichoic acid material, as well as controlled hydrolysis of existing wall material. Actin-like MreB proteins are the key spatial regulators that orchestrate the plethora of enzymes needed for cell elongation, many of which are thought to assemble into functional complexes called elongasomes. Cell division requires a switch in the orientation of cell wall synthesis and is organised by a tubulin-like protein FtsZ. FtsZ forms a ring-like structure at the site of impending division, which is specified by a range of mainly negative regulators. There it recruits a set of dedicated division proteins to form a structure called the divisome, which brings about the process of division. During sporulation, both the positioning and fine structure of the division septum are altered, and again, several dedicated proteins that contribute specifically to this process have been identified. This chapter summarises our current understanding of elongation and division in B. subtilis, with particular emphasis on the cytoskeletal proteins MreB and FtsZ, and highlights where the major gaps in our understanding remain.
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48
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Schumacher MA, Huang KH, Zeng W, Janakiraman A. Structure of the Z Ring-associated Protein, ZapD, Bound to the C-terminal Domain of the Tubulin-like Protein, FtsZ, Suggests Mechanism of Z Ring Stabilization through FtsZ Cross-linking. J Biol Chem 2017; 292:3740-3750. [PMID: 28100778 DOI: 10.1074/jbc.m116.773192] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 01/17/2017] [Indexed: 11/06/2022] Open
Abstract
Cell division in most bacteria is mediated by the tubulin-like FtsZ protein, which polymerizes in a GTP-dependent manner to form the cytokinetic Z ring. A diverse repertoire of FtsZ-binding proteins affects FtsZ localization and polymerization to ensure correct Z ring formation. Many of these proteins bind the C-terminal domain (CTD) of FtsZ, which serves as a hub for FtsZ regulation. FtsZ ring-associated proteins, ZapA-D (Zaps), are important FtsZ regulatory proteins that stabilize FtsZ assembly and enhance Z ring formation by increasing lateral assembly of FtsZ protofilaments, which then form the Z ring. There are no structures of a Zap protein bound to FtsZ; therefore, how these proteins affect FtsZ polymerization has been unclear. Recent data showed ZapD binds specifically to the FtsZ CTD. Thus, to obtain insight into the ZapD-CTD interaction and how it may mediate FtsZ protofilament assembly, we determined the Escherichia coli ZapD-FtsZ CTD structure to 2.67 Å resolution. The structure shows that the CTD docks within a hydrophobic cleft in the ZapD helical domain and adopts an unusual structure composed of two turns of helix separated by a proline kink. FtsZ CTD residue Phe-377 inserts into the ZapD pocket, anchoring the CTD in place and permitting hydrophobic contacts between FtsZ residues Ile-374, Pro-375, and Leu-378 with ZapD residues Leu-74, Trp-77, Leu-91, and Leu-174. The structural findings were supported by mutagenesis coupled with biochemical and in vivo studies. The combined data suggest that ZapD acts as a molecular cross-linking reagent between FtsZ protofilaments to enhance FtsZ assembly.
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Affiliation(s)
- Maria A Schumacher
- From the Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710,
| | - Kuo-Hsiang Huang
- the Department of Biology, City College of City University of New York, New York, New York 10031, and.,the Graduate Center, City University of New York, New York, New York 10016
| | - Wenjie Zeng
- From the Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710
| | - Anuradha Janakiraman
- the Department of Biology, City College of City University of New York, New York, New York 10031, and .,the Graduate Center, City University of New York, New York, New York 10016
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49
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Loose M, Zieske K, Schwille P. Reconstitution of Protein Dynamics Involved in Bacterial Cell Division. Subcell Biochem 2017; 84:419-444. [PMID: 28500535 DOI: 10.1007/978-3-319-53047-5_15] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Even simple cells like bacteria have precisely regulated cellular anatomies, which allow them to grow, divide and to respond to internal or external cues with high fidelity. How spatial and temporal intracellular organization in prokaryotic cells is achieved and maintained on the basis of locally interacting proteins still remains largely a mystery. Bulk biochemical assays with purified components and in vivo experiments help us to approach key cellular processes from two opposite ends, in terms of minimal and maximal complexity. However, to understand how cellular phenomena emerge, that are more than the sum of their parts, we have to assemble cellular subsystems step by step from the bottom up. Here, we review recent in vitro reconstitution experiments with proteins of the bacterial cell division machinery and illustrate how they help to shed light on fundamental cellular mechanisms that constitute spatiotemporal order and regulate cell division.
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Affiliation(s)
- Martin Loose
- Institute for Science and Technology Austria (IST Austria), Klosterneuburg, Austria.
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50
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Abstract
FtsZ assembles in vitro into protofilaments (pfs) that are one subunit thick and ~50 subunits long. In vivo these pfs assemble further into the Z ring, which, along with accessory division proteins, constricts to divide the cell. We have reconstituted Z rings in liposomes in vitro, using pure FtsZ that was modified with a membrane targeting sequence to directly bind the membrane. This FtsZ-mts assembled Z rings and constricted the liposomes without any accessory proteins. We proposed that the force for constriction was generated by a conformational change from straight to curved pfs. Evidence supporting this mechanism came from switching the membrane tether to the opposite side of the pf. These switched-tether pfs assembled "inside-out" Z rings, and squeezed the liposomes from the outside, as expected for the bending model. We propose three steps for the full process of cytokinesis: (a) pf bending generates a constriction force on the inner membrane, but the rigid peptidoglycan wall initially prevents any invagination; (b) downstream proteins associate to the Z ring and remodel the peptidoglycan, permitting it to follow the constricting FtsZ to a diameter of ~250 nm; the final steps of closure of the septum and membrane fusion are achieved by excess membrane synthesis and membrane fluctuations.
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Affiliation(s)
- Harold P Erickson
- Department of Cell Biology, Duke University, Durham, NC, 27710, USA.
| | - Masaki Osawa
- Department of Cell Biology, Duke University, Durham, NC, 27710, USA
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