1
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Schäper S, Brito AD, Saraiva BM, Squyres GR, Holmes MJ, Garner EC, Hensel Z, Henriques R, Pinho MG. Cell constriction requires processive septal peptidoglycan synthase movement independent of FtsZ treadmilling in Staphylococcus aureus. Nat Microbiol 2024; 9:1049-1063. [PMID: 38480900 PMCID: PMC10994846 DOI: 10.1038/s41564-024-01629-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 02/01/2024] [Indexed: 04/06/2024]
Abstract
Bacterial cell division requires recruitment of peptidoglycan (PG) synthases to the division site by the tubulin homologue, FtsZ. Septal PG synthases promote septum growth. FtsZ treadmilling is proposed to drive the processive movement of septal PG synthases and septal constriction in some bacteria; however, the precise mechanisms spatio-temporally regulating PG synthase movement and activity and FtsZ treadmilling are poorly understood. Here using single-molecule imaging of division proteins in the Gram-positive pathogen Staphylococcus aureus, we showed that the septal PG synthase complex FtsW/PBP1 and its putative activator protein, DivIB, move with similar velocity around the division site. Impairing FtsZ treadmilling did not affect FtsW or DivIB velocities or septum constriction rates. Contrarily, PG synthesis inhibition decelerated or stopped directional movement of FtsW and DivIB, and septum constriction. Our findings suggest that a single population of processively moving FtsW/PBP1 associated with DivIB drives cell constriction independently of FtsZ treadmilling in S. aureus.
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Affiliation(s)
- Simon Schäper
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal.
| | - António D Brito
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Bruno M Saraiva
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Georgia R Squyres
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Matthew J Holmes
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Ethan C Garner
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Zach Hensel
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal
| | - Ricardo Henriques
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- MRC-Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Mariana G Pinho
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal.
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2
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Radler P, Loose M. A dynamic duo: Understanding the roles of FtsZ and FtsA for Escherichia coli cell division through in vitro approaches. Eur J Cell Biol 2024; 103:151380. [PMID: 38218128 DOI: 10.1016/j.ejcb.2023.151380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 12/22/2023] [Accepted: 12/24/2023] [Indexed: 01/15/2024] Open
Abstract
Bacteria divide by binary fission. The protein machine responsible for this process is the divisome, a transient assembly of more than 30 proteins in and on the surface of the cytoplasmic membrane. Together, they constrict the cell envelope and remodel the peptidoglycan layer to eventually split the cell into two. For Escherichia coli, most molecular players involved in this process have probably been identified, but obtaining the quantitative information needed for a mechanistic understanding can often not be achieved from experiments in vivo alone. Since the discovery of the Z-ring more than 30 years ago, in vitro reconstitution experiments have been crucial to shed light on molecular processes normally hidden in the complex environment of the living cell. In this review, we summarize how rebuilding the divisome from purified components - or at least parts of it - have been instrumental to obtain the detailed mechanistic understanding of the bacterial cell division machinery that we have today.
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Affiliation(s)
- Philipp Radler
- Institute for Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria; University of Vienna, Djerassiplatz 1, 1030 Wien, Austria.
| | - Martin Loose
- Institute for Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria.
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3
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Nishikawa S, Sato G, Takada S, Kohyama S, Honda G, Yanagisawa M, Hori Y, Doi N, Yoshinaga N, Fujiwara K. Multimolecular Competition Effect as a Modulator of Protein Localization and Biochemical Networks in Cell-Size Space. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308030. [PMID: 38054641 PMCID: PMC10853730 DOI: 10.1002/advs.202308030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/22/2023] [Indexed: 12/07/2023]
Abstract
Cells are small, closed spaces filled with various types of macromolecules. Although it is shown that the characteristics of biochemical reactions in vitro are quite different from those in living cells, the role of the co-existence of various macromolecules in cell-size space remains still elusive. Here, using a constructive approach, it is demonstrated that the co-existence of various macromolecules themselves has the ability to tune protein localization for spatiotemporal regulation and a biochemical reaction system in a cell-size space. Both experimental and theoretical analyses reveal that enhancement of interfacial effects by a large surface-area-to-volume ratio facilitates membrane localization of molecules in the cell-size space, and the interfacial effects are alleviated by competitive binding to lipid membranes among multiple proteins even if their membrane affinities are weak. These results indicate that competition for membrane binding among various macromolecules in the cell-size space plays a role in regulating the spatiotemporal molecular organization and biochemical reaction networks. These findings shed light on the importance of surrounding molecules for biochemical reactions using purified elements in small spaces.
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Affiliation(s)
- Saki Nishikawa
- Department of Biosciences and InformaticsFaculty of Science and TechnologyKeio University3‐14‐1 Hiyoshi, Kohoku‐kuYokohamaKanagawa223‐8522Japan
| | - Gaku Sato
- Department of Biosciences and InformaticsFaculty of Science and TechnologyKeio University3‐14‐1 Hiyoshi, Kohoku‐kuYokohamaKanagawa223‐8522Japan
| | - Sakura Takada
- Department of Biosciences and InformaticsFaculty of Science and TechnologyKeio University3‐14‐1 Hiyoshi, Kohoku‐kuYokohamaKanagawa223‐8522Japan
| | - Shunshi Kohyama
- Department of Biosciences and InformaticsFaculty of Science and TechnologyKeio University3‐14‐1 Hiyoshi, Kohoku‐kuYokohamaKanagawa223‐8522Japan
- Present address:
Department for Cellular and Molecular BiophysicsMax Planck Institute for BiochemistryAm Klopferspitz 18D‐82152MartinsriedGermany
| | - Gen Honda
- Komaba Institute for ScienceGraduate School of Arts and SciencesThe University of TokyoKomaba 3‐8‐1MeguroTokyo153‐8902Japan
| | - Miho Yanagisawa
- Komaba Institute for ScienceGraduate School of Arts and SciencesThe University of TokyoKomaba 3‐8‐1MeguroTokyo153‐8902Japan
- Graduate School of ScienceThe University of TokyoHongo 7‐3‐1BunkyoTokyo113‐0033Japan
- Center for Complex Systems BiologyUniversal Biology InstituteThe University of TokyoKomaba 3‐8‐1MeguroTokyo153‐8902Japan
| | - Yutaka Hori
- Department of Applied Physics and Physico‐informaticsFaculty of Science and TechnologyKeio University3‐14‐1 Hiyoshi, Kohoku‐kuYokohamaKanagawa223‐8522Japan
| | - Nobuhide Doi
- Department of Biosciences and InformaticsFaculty of Science and TechnologyKeio University3‐14‐1 Hiyoshi, Kohoku‐kuYokohamaKanagawa223‐8522Japan
| | - Natsuhiko Yoshinaga
- WPI Advanced Institute for Materials Research (WPI‐AIMR)Tohoku UniversityKatahira 2‐1‐1, Aoba‐KuSendai980‐8577Japan
- MathAM‐OILAISTSendai980‐8577Japan
| | - Kei Fujiwara
- Department of Biosciences and InformaticsFaculty of Science and TechnologyKeio University3‐14‐1 Hiyoshi, Kohoku‐kuYokohamaKanagawa223‐8522Japan
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4
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Morrison JJ, Camberg JL. Building the Bacterial Divisome at the Septum. Subcell Biochem 2024; 104:49-71. [PMID: 38963483 DOI: 10.1007/978-3-031-58843-3_4] [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] [Indexed: 07/05/2024]
Abstract
Across living organisms, division is necessary for cell survival and passing heritable information to the next generation. For this reason, cell division is highly conserved among eukaryotes and prokaryotes. Among the most highly conserved cell division proteins in eukaryotes are tubulin and actin. Tubulin polymerizes to form microtubules, which assemble into cytoskeletal structures in eukaryotes, such as the mitotic spindle that pulls chromatids apart during mitosis. Actin polymerizes to form a morphological framework for the eukaryotic cell, or cytoskeleton, that undergoes reorganization during mitosis. In prokaryotes, two of the most highly conserved cell division proteins are the tubulin homolog FtsZ and the actin homolog FtsA. In this chapter, the functions of the essential bacterial cell division proteins FtsZ and FtsA and their roles in assembly of the divisome at the septum, the site of cell division, will be discussed. In most bacteria, including Escherichia coli, the tubulin homolog FtsZ polymerizes at midcell, and this step is crucial for recruitment of many other proteins to the division site. For this reason, both FtsZ abundance and polymerization are tightly regulated by a variety of proteins. The actin-like FtsA protein polymerizes and tethers FtsZ polymers to the cytoplasmic membrane. Additionally, FtsA interacts with later stage cell division proteins, which are essential for division and for building the new cell wall at the septum. Recent studies have investigated how actin-like polymerization of FtsA on the lipid membrane may impact division, and we will discuss this and other ways that division in bacteria is regulated through FtsZ and FtsA.
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Affiliation(s)
- Josiah J Morrison
- Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, RI, USA
| | - Jodi L Camberg
- Department of Cell and Molecular Biology, The University of Rhode Island, Kingston, RI, USA.
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5
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Carrasco V, Berríos-Pastén C, Canales N, Órdenes A, Wilson CAM, Monasterio O. Bioinformatics, thermodynamics, and mechanical resistance of the FtsZ-ZipA complex of Escherichia coli supports a highly dynamic protein interaction in the divisome. Biochim Biophys Acta Gen Subj 2023; 1867:130471. [PMID: 37806464 DOI: 10.1016/j.bbagen.2023.130471] [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: 04/25/2023] [Revised: 09/05/2023] [Accepted: 09/28/2023] [Indexed: 10/10/2023]
Abstract
In most microorganisms, cell division is guided by the divisome, a multiprotein complex that assembles at the equator of the cell and is responsible for the synthesis of new cell wall material. FtsZ, the first protein to assemble into this complex forms protofilaments in the cytosol which are anchored to the inner side of the cytosolic membrane by the proteins ZipA and FtsA. FtsZ protofilaments generate a force that deforms the cytosolic membrane and may contribute to the constriction force that leads to the septation of the cell. It has not been studied yet how the membrane protein anchors respond to this force generated by FtsZ. Here we studied the effect of force in the FtsZ-ZipA interaction. We used SMD and obtained the distance to the transition state of key interacting amino acids and SASA of FtsZ and ZipA through the dissociation. The SMD mechanism was corroborated by ITC, and the thermodynamic parameters ΔG0, ΔH0 and ΔS0 were obtained. Finally, we used force spectroscopy by optical tweezers to determine the lifetime of the interaction and rupture probability and their dependence on force at single molecule level. We also obtained the transition state distance, and free energy of the interaction. With the gathering of structural, thermodynamic, kinetic and force parameters we conclude that interaction between FtsZ and ZipA proteins is consistence with the highly dynamic treadmilling process and at least seven ZipA molecules are required to bind to a FtsZ protofilaments to transduce a significant force.
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Affiliation(s)
- Valentina Carrasco
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras, 3425 Ñuñoa, Región Metropolitana, Chile; Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Dr. Carlos Lorca Tobar 964, Independencia, Región Metropolitana, Santiago, Chile..
| | - Camilo Berríos-Pastén
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras, 3425 Ñuñoa, Región Metropolitana, Chile.
| | - Nicolás Canales
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras, 3425 Ñuñoa, Región Metropolitana, Chile.
| | - Alexis Órdenes
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras, 3425 Ñuñoa, Región Metropolitana, Chile
| | - Christian A M Wilson
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Dr. Carlos Lorca Tobar 964, Independencia, Región Metropolitana, Santiago, Chile..
| | - Octavio Monasterio
- Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Las Palmeras, 3425 Ñuñoa, Región Metropolitana, Chile.
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6
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Reverte-López M, Gavrilovic S, Merino-Salomón A, Eto H, Yagüe Relimpio A, Rivas G, Schwille P. Protein-Based Patterning to Spatially Functionalize Biomimetic Membranes. SMALL METHODS 2023; 7:e2300173. [PMID: 37350500 DOI: 10.1002/smtd.202300173] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/08/2023] [Indexed: 06/24/2023]
Abstract
The bottom-up reconstitution of proteins for their modular engineering into synthetic cellular systems can reveal hidden protein functions in vitro. This is particularly evident for the bacterial Min proteins, a paradigm for self-organizing reaction-diffusion systems that displays an unexpected functionality of potential interest for bioengineering: the directional active transport of any diffusible cargo molecule on membranes. Here, the MinDE protein system is reported as a versatile surface patterning tool for the rational design of synthetically assembled 3D systems. Employing two-photon lithography, microswimmer-like structures coated with tailored lipid bilayers are fabricated and demonstrate that Min proteins can uniformly pattern bioactive molecules on their surface. Moreover, it is shown that the MinDE system can form stationary patterns inside lipid vesicles, which allow the targeting and distinctive clustering of higher-order protein structures on their inner leaflet. Given their facile use and robust function, Min proteins thus constitute a valuable molecular toolkit for spatially patterned functionalization of artificial biosystems like cell mimics and microcarriers.
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Affiliation(s)
- María Reverte-López
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Svetozar Gavrilovic
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Adrián Merino-Salomón
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Hiromune Eto
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), Utrecht, 3584 CT, The Netherlands
| | - Ana Yagüe Relimpio
- Department of Cellular Biophysics, Max Planck for Medical Research, 69120, Heidelberg, Germany
| | - Germán Rivas
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, 28040, Spain
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
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7
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Chen L, Li X, Wang Y, Guo Z, Wang G, Zhang Y. The performance of plant essential oils against lactic acid bacteria and adverse microorganisms in silage production. FRONTIERS IN PLANT SCIENCE 2023; 14:1285722. [PMID: 38023889 PMCID: PMC10667483 DOI: 10.3389/fpls.2023.1285722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 10/25/2023] [Indexed: 12/01/2023]
Abstract
Plant essential oils have played an important role in the field of antibiotic alternatives because of their efficient bacteriostatic and fungistatic activity. As plant essential oils are widely used, their activity to improve the quality of plant silage has also been explored. This review expounds on the active ingredients of essential oils, their bacteriostatic and fungistatic activity, and mechanisms, as well as discusses the application of plant essential oils in plant silage fermentation, to provide a reference for the development and application of plant essential oils as silage additives in plant silage fermentation feed.
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Affiliation(s)
- Lijuan Chen
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Xi Li
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Yili Wang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Zelin Guo
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Guoming Wang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Yunhua Zhang
- College of Resources and Environment, Anhui Agricultural University, Hefei, China
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8
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Naha A, Haeusser DP, Margolin W. Anchors: A way for FtsZ filaments to stay membrane bound. Mol Microbiol 2023; 120:525-538. [PMID: 37503768 PMCID: PMC10593102 DOI: 10.1111/mmi.15067] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/10/2023] [Accepted: 04/12/2023] [Indexed: 07/29/2023]
Abstract
Most bacteria use the tubulin homolog FtsZ to organize their cell division. FtsZ polymers initially assemble into mobile complexes that circle around a ring-like structure at the cell midpoint, followed by the recruitment of other proteins that will constrict the cytoplasmic membrane and synthesize septal peptidoglycan to divide the cell. Despite the need for FtsZ polymers to associate with the membrane, FtsZ lacks intrinsic membrane binding ability. Consequently, FtsZ polymers have evolved to interact with the membrane through adaptor proteins that both bind FtsZ and the membrane. Here, we discuss recent progress in understanding the functions of these FtsZ membrane tethers. Some, such as FtsA and SepF, are widely conserved and assemble into varied oligomeric structures bound to the membrane through an amphipathic helix. Other less-conserved proteins, such as EzrA and ZipA, have transmembrane domains, make extended structures, and seem to bind to FtsZ through two separate interactions. This review emphasizes that most FtsZs use multiple membrane tethers with overlapping functions, which not only attach FtsZ polymers to the membrane but also organize them in specific higher-order structures that can optimize cell division activity. We discuss gaps in our knowledge of these concepts and how future studies can address them.
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Affiliation(s)
- Arindam Naha
- Department of Microbiology and Molecular Genetics, UTHealth-Houston, Houston, TX 77030, USA
| | - Daniel P. Haeusser
- Department of Microbiology and Molecular Genetics, UTHealth-Houston, Houston, TX 77030, USA
- Department of Biology, Canisius College, Buffalo, NY 14208, USA
| | - William Margolin
- Department of Microbiology and Molecular Genetics, UTHealth-Houston, Houston, TX 77030, USA
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9
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Sato T, Matsuda S, Aoki W. Optimizing conditions to construct artificial cells using commercial in vitro transcription-translation system (PUREfrex2.0). J Biosci Bioeng 2023; 136:334-339. [PMID: 37517904 DOI: 10.1016/j.jbiosc.2023.07.004] [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: 05/08/2023] [Revised: 07/03/2023] [Accepted: 07/12/2023] [Indexed: 08/01/2023]
Abstract
Artificial cells containing in vitro transcription and translation (IVTT) systems inside liposomes are important for the reconstruction and analysis of various biological systems. To improve the accessibility of artificial cell research, it is important that artificial cells can be constructed using only commercially available components. Here, we optimized the construction of artificial cells containing PUREfrex2.0, a commercially available IVTT with high transcriptional and translational activity. Specifically, the composition of the inner and outer s olutions of the liposomes and the concentrations of lipids, glucose/sucrose, potassium glutamate, and magnesium acetate were systematically optimized, and finally we found a protocol for the stable construction of artificial cells containing PUREfre×2.0. These findings are expected to be important in expanding the artificial cell research community.
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Affiliation(s)
- Toshiko Sato
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan.
| | | | - Wataru Aoki
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan.
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10
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Nanninga N. Molecular Cytology of 'Little Animals': Personal Recollections of Escherichia coli (and Bacillus subtilis). Life (Basel) 2023; 13:1782. [PMID: 37629639 PMCID: PMC10455606 DOI: 10.3390/life13081782] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/09/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
This article relates personal recollections and starts with the origin of electron microscopy in the sixties of the previous century at the University of Amsterdam. Novel fixation and embedding techniques marked the discovery of the internal bacterial structures not visible by light microscopy. A special status became reserved for the freeze-fracture technique. By freeze-fracturing chemically fixed cells, it proved possible to examine the morphological effects of fixation. From there on, the focus switched from bacterial structure as such to their cell cycle. This invoked bacterial physiology and steady-state growth combined with electron microscopy. Electron-microscopic autoradiography with pulses of [3H] Dap revealed that segregation of replicating DNA cannot proceed according to a model of zonal growth (with envelope-attached DNA). This stimulated us to further investigate the sacculus, the peptidoglycan macromolecule. In particular, we focused on the involvement of penicillin-binding proteins such as PBP2 and PBP3, and their role in division. Adding aztreonam (an inhibitor of PBP3) blocked ongoing divisions but not the initiation of new ones. A PBP3-independent peptidoglycan synthesis (PIPS) appeared to precede a PBP3-dependent step. The possible chemical nature of PIPS is discussed.
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Affiliation(s)
- Nanne Nanninga
- Molecular Cytology, Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, 1098 XH Amsterdam, The Netherlands
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11
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Bartelds MW, García-Blay Ó, Verhagen PGA, Wubbolts EJ, van Sluijs B, Heus HA, de Greef TFA, Huck WTS, Hansen MMK. Noise Minimization in Cell-Free Gene Expression. ACS Synth Biol 2023; 12:2217-2225. [PMID: 37478000 PMCID: PMC10443034 DOI: 10.1021/acssynbio.3c00174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Indexed: 07/23/2023]
Abstract
Biochemical reactions that involve small numbers of molecules are accompanied by a degree of inherent randomness that results in noisy reaction outcomes. In synthetic biology, the ability to minimize noise particularly during the reconstitution of future synthetic protocells is an outstanding challenge to secure robust and reproducible behavior. Here we show that by encapsulation of a bacterial cell-free gene expression system in water-in-oil droplets, in vitro-synthesized MazF reduces cell-free gene expression noise >2-fold. With stochastic simulations we identify that this noise minimization acts through both increased degradation and the autoregulatory feedback of MazF. Specifically, we find that the expression of MazF enhances the degradation rate of mRNA up to 18-fold in a sequence-dependent manner. This sequence specificity of MazF would allow targeted noise control, making it ideal to integrate into synthetic gene networks. Therefore, including MazF production in synthetic biology can significantly minimize gene expression noise, impacting future design principles of more complex cell-free gene circuits.
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Affiliation(s)
- Mart W. Bartelds
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Óscar García-Blay
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Pieter G. A. Verhagen
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Elise J. Wubbolts
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Bob van Sluijs
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Hans A. Heus
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Tom F. A. de Greef
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
- Computational
Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology,
P.O. Box 513, 5600 MB Eindhoven, The Netherlands
- Center
for Living Technologies, Eindhoven-Wageningen-Utrecht
Alliance, 5600 MB Eindhoven, The Netherlands
| | - Wilhelm T. S. Huck
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Maike M. K. Hansen
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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12
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Noba K, Yoshimoto S, Tanaka Y, Yokoyama T, Matsuura T, Hori K. Simple Method for the Creation of a Bacteria-Sized Unilamellar Liposome with Different Proteins Localized to the Respective Sides of the Membrane. ACS Synth Biol 2023; 12:1437-1446. [PMID: 37155350 DOI: 10.1021/acssynbio.2c00564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Artificial cells are membrane vesicles mimicking cellular functions. To date, giant unilamellar vesicles made from a single lipid membrane with a diameter of 10 μm or more have been used to create artificial cells. However, the creation of artificial cells that mimic the membrane structure and size of bacteria has been limited due to technical restrictions of conventional liposome preparation methods. Here, we created bacteria-sized large unilamellar vesicles (LUVs) with proteins localized asymmetrically to the lipid bilayer. Liposomes containing benzylguanine-modified phospholipids were prepared by combining the conventional water-in-oil emulsion method and the extruder method, and green fluorescent protein fused with SNAP-tag was localized to the inner leaflet of the lipid bilayer. Biotinylated lipid molecules were then inserted externally, and the outer leaflet was modified with streptavidin. The resulting liposomes had a size distribution in the range of 500-2000 nm with a peak at 841 nm (the coefficient of variation was 10.3%), which was similar to that of spherical bacterial cells. Fluorescence microscopy, quantitative evaluation using flow cytometry, and western blotting proved the intended localization of different proteins on the lipid membrane. Cryogenic electron microscopy and quantitative evaluation by α-hemolysin insertion revealed that most of the created liposomes were unilamellar. Our simple method for the preparation of bacteria-sized LUVs with asymmetrically localized proteins will contribute to the creation of artificial bacterial cells for investigating functions and the significance of their surface structure and size.
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Affiliation(s)
- Kosaku Noba
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan
| | - Shogo Yoshimoto
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan
| | - Yoshikazu Tanaka
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-Ku, Sendai 980-8577, Japan
| | - Takeshi Yokoyama
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-Ku, Sendai 980-8577, Japan
| | - Tomoaki Matsuura
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama 2-12-1-i7E-307, Meguro-Ku, Tokyo 152-8550, Japan
| | - Katsutoshi Hori
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan
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13
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Godino E, Danelon C. Gene-Directed FtsZ Ring Assembly Generates Constricted Liposomes with Stable Membrane Necks. Adv Biol (Weinh) 2023; 7:e2200172. [PMID: 36593513 DOI: 10.1002/adbi.202200172] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 11/15/2022] [Indexed: 01/04/2023]
Abstract
Mimicking bacterial cell division in well-defined cell-free systems has the potential to elucidate the minimal set of proteins required for cytoskeletal formation, membrane constriction, and final abscission. Membrane-anchored FtsZ polymers are often regarded as a sufficient system to realize this chain of events. By using purified FtsZ and its membrane-binding protein FtsA or the gain-of-function mutant FtsA* expressed in PURE (Protein synthesis Using Reconstituted Elements) from a DNA template, it is shown in this study that cytoskeletal structures are formed, and yield constricted liposomes exhibiting various morphologies. However, the resulting buds remain attached to the parental liposome by a narrow membrane neck. No division events can be monitored even after long-time tracking by fluorescence microscopy, nor when the osmolarity of the external solution is increased. The results provide evidence that reconstituted FtsA-FtsZ proto-rings coating the membrane necks are too stable to enable abscission. The prospect of combining a DNA-encoded FtsZ system with assisting mechanisms to achieve synthetic cell division is discussed.
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Affiliation(s)
- Elisa Godino
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, 2629HZ, The Netherlands
| | - Christophe Danelon
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, 2629HZ, The Netherlands
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14
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Gonzales DT, Suraritdechachai S, Tang TYD. Compartmentalized Cell-Free Expression Systems for Building Synthetic Cells. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2023; 186:77-101. [PMID: 37306700 DOI: 10.1007/10_2023_221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
One of the grand challenges in bottom-up synthetic biology is the design and construction of synthetic cellular systems. One strategy toward this goal is the systematic reconstitution of biological processes using purified or non-living molecular components to recreate specific cellular functions such as metabolism, intercellular communication, signal transduction, and growth and division. Cell-free expression systems (CFES) are in vitro reconstitutions of the transcription and translation machinery found in cells and are a key technology for bottom-up synthetic biology. The open and simplified reaction environment of CFES has helped researchers discover fundamental concepts in the molecular biology of the cell. In recent decades, there has been a drive to encapsulate CFES reactions into cell-like compartments with the aim of building synthetic cells and multicellular systems. In this chapter, we discuss recent progress in compartmentalizing CFES to build simple and minimal models of biological processes that can help provide a better understanding of the process of self-assembly in molecularly complex systems.
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Affiliation(s)
- David T Gonzales
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
| | | | - T -Y Dora Tang
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
- Center for Systems Biology Dresden, Dresden, Germany.
- Physics of Life, Cluster of Excellence, TU Dresden, Dresden, Germany.
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15
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Pelletier JF, Glass JI, Strychalski EA. Cellular mechanics during division of a genomically minimal cell. Trends Cell Biol 2022; 32:900-907. [PMID: 35907702 DOI: 10.1016/j.tcb.2022.06.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 06/17/2022] [Accepted: 06/20/2022] [Indexed: 01/21/2023]
Abstract
Genomically minimal cells, such as JCVI-syn3.0 and JCVI-syn3A, offer an empowering framework to study relationships between genotype and phenotype. With a polygenic basis, the fundamental physiological process of cell division depends on multiple genes of known and unknown function in JCVI-syn3A. A physical description of cellular mechanics can further understanding of the contributions of genes to cell division in this genomically minimal context. We review current knowledge on genes in JCVI-syn3A contributing to two physical parameters relevant to cell division, namely, the surface-area-to-volume ratio and membrane curvature. This physical view of JCVI-syn3A may inform the attribution of gene functions and conserved processes in bacterial physiology, as well as whole-cell models and the engineering of synthetic cells.
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Affiliation(s)
- James F Pelletier
- Centro Nacional de Biotecnología, 28049 Madrid, Spain; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - John I Glass
- J. Craig Venter Institute, La Jolla, CA 92037, USA
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16
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Herianto S, Chien PJ, Ho JAA, Tu HL. Liposome-based artificial cells: From gene expression to reconstitution of cellular functions and phenotypes. BIOMATERIALS ADVANCES 2022; 142:213156. [PMID: 36302330 DOI: 10.1016/j.bioadv.2022.213156] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
Bottom-up approaches in creating artificial cells that can mimic natural cells have significant implications for both basic research and translational application. Among various artificial cell models, liposome is one of the most sophisticated systems. By encapsulating proteins and associated biomolecules, they can functionally reconstitute foundational features of biological cells, such as the ability to divide, communicate, and undergo shape deformation. Yet constructing liposome artificial cells from the genetic level, which is central to generate self-sustained systems remains highly challenging. Indeed, many studies have successfully established the expression of gene-coded proteins inside liposomes. Further, recent endeavors to build a direct integration of gene-expressed proteins for reconstituting molecular functions and phenotypes in liposomes have also significantly increased. Thus, this review presents the development of liposome-based artificial cells to demonstrate the process of gene-expressed proteins and their reconstitution to perform desired molecular and cell-like functions. The molecular and cellular phenotypes discussed here include the self-production of membrane phospholipids, division, shape deformation, self-DNA/RNA replication, fusion, and intercellular communication. Together, this review gives a comprehensive overview of gene-expressing liposomes that can stimulate further research of this technology and achieve artificial cells with superior properties in the future.
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Affiliation(s)
- Samuel Herianto
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan; Chemical Biology and Molecular Biophysics, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan; Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Po-Jen Chien
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Ja-An Annie Ho
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan; BioAnalytical Chemistry and Nanobiomedicine Laboratory, Department of Biochemical Science and Technology, National Taiwan University, Taipei 10617, Taiwan
| | - Hsiung-Lin Tu
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan; Chemical Biology and Molecular Biophysics, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan.
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17
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In vitro assembly, positioning and contraction of a division ring in minimal cells. Nat Commun 2022; 13:6098. [PMID: 36243816 PMCID: PMC9569390 DOI: 10.1038/s41467-022-33679-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 09/27/2022] [Indexed: 02/07/2023] Open
Abstract
Constructing a minimal machinery for autonomous self-division of synthetic cells is a major goal of bottom-up synthetic biology. One paradigm has been the E. coli divisome, with the MinCDE protein system guiding assembly and positioning of a presumably contractile ring based on FtsZ and its membrane adaptor FtsA. Here, we demonstrate the full in vitro reconstitution of this machinery consisting of five proteins within lipid vesicles, allowing to observe the following sequence of events in real time: 1) Assembly of an isotropic filamentous FtsZ network, 2) its condensation into a ring-like structure, along with pole-to-pole mode selection of Min oscillations resulting in equatorial positioning, and 3) onset of ring constriction, deforming the vesicles from spherical shape. Besides demonstrating these essential features, we highlight the importance of decisive experimental factors, such as macromolecular crowding. Our results provide an exceptional showcase of the emergence of cell division in a minimal system, and may represent a step towards developing a synthetic cell.
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18
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Hirschi S, Ward TR, Meier WP, Müller DJ, Fotiadis D. Synthetic Biology: Bottom-Up Assembly of Molecular Systems. Chem Rev 2022; 122:16294-16328. [PMID: 36179355 DOI: 10.1021/acs.chemrev.2c00339] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The bottom-up assembly of biological and chemical components opens exciting opportunities to engineer artificial vesicular systems for applications with previously unmet requirements. The modular combination of scaffolds and functional building blocks enables the engineering of complex systems with biomimetic or new-to-nature functionalities. Inspired by the compartmentalized organization of cells and organelles, lipid or polymer vesicles are widely used as model membrane systems to investigate the translocation of solutes and the transduction of signals by membrane proteins. The bottom-up assembly and functionalization of such artificial compartments enables full control over their composition and can thus provide specifically optimized environments for synthetic biological processes. This review aims to inspire future endeavors by providing a diverse toolbox of molecular modules, engineering methodologies, and different approaches to assemble artificial vesicular systems. Important technical and practical aspects are addressed and selected applications are presented, highlighting particular achievements and limitations of the bottom-up approach. Complementing the cutting-edge technological achievements, fundamental aspects are also discussed to cater to the inherently diverse background of the target audience, which results from the interdisciplinary nature of synthetic biology. The engineering of proteins as functional modules and the use of lipids and block copolymers as scaffold modules for the assembly of functionalized vesicular systems are explored in detail. Particular emphasis is placed on ensuring the controlled assembly of these components into increasingly complex vesicular systems. Finally, all descriptions are presented in the greater context of engineering valuable synthetic biological systems for applications in biocatalysis, biosensing, bioremediation, or targeted drug delivery.
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Affiliation(s)
- Stephan Hirschi
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
| | - Thomas R Ward
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
| | - Wolfgang P Meier
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
| | - Daniel J Müller
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
| | - Dimitrios Fotiadis
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
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19
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Wagner AM, Eto H, Joseph A, Kohyama S, Haraszti T, Zamora RA, Vorobii M, Giannotti MI, Schwille P, Rodriguez-Emmenegger C. Dendrimersome Synthetic Cells Harbor Cell Division Machinery of Bacteria. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2202364. [PMID: 35579491 DOI: 10.1002/adma.202202364] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/11/2022] [Indexed: 06/15/2023]
Abstract
The integration of active cell machinery with synthetic building blocks is the bridge toward developing synthetic cells with biological functions and beyond. Self-replication is one of the most important tasks of living systems, and various complex machineries exist to execute it. In Escherichia coli, a contractile division ring is positioned to mid-cell by concentration oscillations of self-organizing proteins (MinCDE), where it severs membrane and cell wall. So far, the reconstitution of any cell division machinery has exclusively been tied to liposomes. Here, the reconstitution of a rudimentary bacterial divisome in fully synthetic bicomponent dendrimersomes is shown. By tuning the membrane composition, the interaction of biological machinery with synthetic membranes can be tailored to reproduce its dynamic behavior. This constitutes an important breakthrough in the assembly of synthetic cells with biological elements, as tuning of membrane-divisome interactions is the key to engineering emergent biological behavior from the bottom-up.
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Affiliation(s)
- Anna M Wagner
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52074, Aachen, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074, Aachen, Germany
| | - Hiromune Eto
- Max Planck Institute of Biochemistry, Department of Cellular and Molecular Biophysics, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Anton Joseph
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52074, Aachen, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074, Aachen, Germany
| | - Shunshi Kohyama
- Max Planck Institute of Biochemistry, Department of Cellular and Molecular Biophysics, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Tamás Haraszti
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52074, Aachen, Germany
| | - Ricardo A Zamora
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Carrer de Baldiri Reixac 10-12, Barcelona, 08028, Spain
- Network Biomedical Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, 28029, Spain
| | - Mariia Vorobii
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52074, Aachen, Germany
| | - Marina I Giannotti
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Carrer de Baldiri Reixac 10-12, Barcelona, 08028, Spain
- Network Biomedical Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, 28029, Spain
- University of Barcelona, Department of Materials Science and Physical Chemistry, Martí i Franquès 10, Barcelona, 08028, Spain
| | - Petra Schwille
- Max Planck Institute of Biochemistry, Department of Cellular and Molecular Biophysics, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Cesar Rodriguez-Emmenegger
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52074, Aachen, Germany
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Carrer de Baldiri Reixac 10-12, Barcelona, 08028, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, Barcelona, 08010, Spain
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20
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Sołtys K, Tarczewska A, Bystranowska D, Sozańska N. Getting Closer to Decrypting the Phase Transitions of Bacterial Biomolecules. Biomolecules 2022; 12:907. [PMID: 35883463 PMCID: PMC9312465 DOI: 10.3390/biom12070907] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/24/2022] [Accepted: 06/26/2022] [Indexed: 12/31/2022] Open
Abstract
Liquid-liquid phase separation (LLPS) of biomolecules has emerged as a new paradigm in cell biology, and the process is one proposed mechanism for the formation of membraneless organelles (MLOs). Bacterial cells have only recently drawn strong interest in terms of studies on both liquid-to-liquid and liquid-to-solid phase transitions. It seems that these processes drive the formation of prokaryotic cellular condensates that resemble eukaryotic MLOs. In this review, we present an overview of the key microbial biomolecules that undergo LLPS, as well as the formation and organization of biomacromolecular condensates within the intracellular space. We also discuss the current challenges in investigating bacterial biomacromolecular condensates. Additionally, we highlight a summary of recent knowledge about the participation of bacterial biomolecules in a phase transition and provide some new in silico analyses that can be helpful for further investigations.
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Affiliation(s)
- Katarzyna Sołtys
- Department of Biochemistry, Molecular Biology and Biotechnology, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wroclaw, Poland; (A.T.); (D.B.); (N.S.)
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21
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Corbin Goodman LC, Erickson HP. FtsZ at mid-cell is essential in Escherichia coli until the late stage of constriction. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35679326 DOI: 10.1099/mic.0.001194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
There has been recent debate as to the source of constriction force during cell division. FtsZ can generate a constriction force on tubular membranes in vitro, suggesting it may generate the constriction force in vivo. However, another study showed that mutants of FtsZ did not affect the rate of constriction, whereas mutants of the PG assembly did, suggesting that PG assembly may push the constriction from the outside. Supporting this model, two groups found that cells that have initiated constriction can complete septation while the Z ring is poisoned with the FtsZ targeting antibiotic PC190723. PC19 arrests treadmilling but leaves FtsZ in place. We sought to determine if a fully assembled Z ring is necessary during constriction. To do this, we used a temperature-sensitive FtsZ mutant, FtsZ84. FtsZ84 supports cell division at 30 °C, but it disassembles from the Z ring within 1 min upon a temperature jump to 42 °C. Following the temperature jump we found that cells in early constriction stop constricting. Cells that had progressed to the later stage of division finished constriction without a Z ring. These results show that in Escherichia coli, an assembled Z ring is essential for constriction except in the final stage, contradicting the simplest interpretation of previous studies using PC19.
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Affiliation(s)
| | - Harold P Erickson
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA.,Department of Cell Biology, Duke University, Durham, North Carolina, USA
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22
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Vélez M. How Does the Spatial Confinement of FtsZ to a Membrane Surface Affect Its Polymerization Properties and Function? Front Microbiol 2022; 13:757711. [PMID: 35592002 PMCID: PMC9111741 DOI: 10.3389/fmicb.2022.757711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 01/27/2022] [Indexed: 11/15/2022] Open
Abstract
FtsZ is the cytoskeletal protein that organizes the formation of the septal ring and orchestrates bacterial cell division. Its association to the membrane is essential for its function. In this mini-review I will address the question of how this association can interfere with the structure and dynamic properties of the filaments and argue that its dynamics could also remodel the underlying lipid membrane through its activity. Thus, lipid rearrangement might need to be considered when trying to understand FtsZ’s function. This new element could help understand how FtsZ assembly coordinates positioning and recruitment of the proteins forming the septal ring inside the cell with the activity of the machinery involved in peptidoglycan synthesis located in the periplasmic space.
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Affiliation(s)
- Marisela Vélez
- Instituto de Catálisis y Petroleoquímica, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
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23
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Shin J, Cole BD, Shan T, Jang Y. Heterogeneous Synthetic Vesicles toward Artificial Cells: Engineering Structure and Composition of Membranes for Multimodal Functionalities. Biomacromolecules 2022; 23:1505-1518. [PMID: 35266692 DOI: 10.1021/acs.biomac.1c01504] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The desire to develop artificial cells to imitate living cells in synthetic vesicle platforms has continuously increased over the past few decades. In particular, heterogeneous synthetic vesicles made from two or more building blocks have attracted attention for artificial cell applications based on their multifunctional modules with asymmetric structures. In addition to the traditional liposomes or polymersomes, polypeptides and proteins have recently been highlighted as potential building blocks to construct artificial cells owing to their specific biological functionalities. Incorporating one or more functionally folded, globular protein into synthetic vesicles enables more cell-like functions mediated by proteins. This Review highlights the recent research about synthetic vesicles toward artificial cell models, from traditional synthetic vesicles to protein-assembled vesicles with asymmetric structures. We aim to provide fundamental and practical insights into applying knowledge on molecular self-assembly to the bottom-up construction of artificial cell platforms with heterogeneous building blocks.
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Affiliation(s)
- Jooyong Shin
- Department of Chemical Engineering, University of Florida, Gainesville, Florida 32611, United States
| | - Blair D Cole
- Department of Chemical Engineering, University of Florida, Gainesville, Florida 32611, United States
| | - Ting Shan
- Department of Biomedical Engineering, University of Florida, Gainesville, Florida 32611, United States
| | - Yeongseon Jang
- Department of Chemical Engineering, University of Florida, Gainesville, Florida 32611, United States
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24
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Liu X, An J, Wang L, Sun Q, An C, Wu B, Hong C, Wang X, Dong S, Guo J, Feng Y, Gao H. A novel amphiphilic motif at the C-terminus of FtsZ1 facilitates chloroplast division. THE PLANT CELL 2022; 34:419-432. [PMID: 34755875 PMCID: PMC8773991 DOI: 10.1093/plcell/koab272] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 10/29/2021] [Indexed: 06/11/2023]
Abstract
In bacteria and chloroplasts, the GTPase filamentous temperature-sensitive Z (FtsZ) is essential for division and polymerizes to form rings that mark the division site. Plants contain two FtsZ subfamilies (FtsZ1 and FtsZ2) with different assembly dynamics. FtsZ1 lacks the C-terminal domain of a typical FtsZ protein. Here, we show that the conserved short motif FtsZ1Carboxyl-terminus (Z1C) (consisting of the amino acids RRLFF) with weak membrane-binding activity is present at the C-terminus of FtsZ1 in angiosperms. For a polymer-forming protein such as FtsZ, this activity is strong enough for membrane tethering. Arabidopsis thaliana plants with mutated Z1C motifs contained heterogeneously sized chloroplasts and parallel FtsZ rings or long FtsZ filaments, suggesting that the Z1C motif plays an important role in regulating FtsZ ring dynamics. Our findings uncover a type of amphiphilic beta-strand motif with weak membrane-binding activity and point to the importance of this motif for the dynamic regulation of protein complex formation.
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Affiliation(s)
- Xiaomin Liu
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
| | - Jinjie An
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Lulu Wang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Qingqing Sun
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Chuanjing An
- Department of Chemical Biology, State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Bibo Wu
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Conghao Hong
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Xiaoya Wang
- Department of Chemical Biology, State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Suwei Dong
- Department of Chemical Biology, State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Junhua Guo
- College of Life Science and Technology, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yue Feng
- College of Life Science and Technology, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
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25
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Levin PA, Janakiraman A. Localization, Assembly, and Activation of the Escherichia coli Cell Division Machinery. EcoSal Plus 2021; 9:eESP00222021. [PMID: 34910577 PMCID: PMC8919703 DOI: 10.1128/ecosalplus.esp-0022-2021] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 11/14/2021] [Indexed: 01/01/2023]
Abstract
Decades of research, much of it in Escherichia coli, have yielded a wealth of insight into bacterial cell division. Here, we provide an overview of the E. coli division machinery with an emphasis on recent findings. We begin with a short historical perspective into the discovery of FtsZ, the tubulin homolog that is essential for division in bacteria and archaea. We then discuss assembly of the divisome, an FtsZ-dependent multiprotein platform, at the midcell septal site. Not simply a scaffold, the dynamic properties of polymeric FtsZ ensure the efficient and uniform synthesis of septal peptidoglycan. Next, we describe the remodeling of the cell wall, invagination of the cell envelope, and disassembly of the division apparatus culminating in scission of the mother cell into two daughter cells. We conclude this review by highlighting some of the open questions in the cell division field, emphasizing that much remains to be discovered, even in an organism as extensively studied as E. coli.
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Affiliation(s)
- Petra Anne Levin
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
- Center for Science & Engineering of Living Systems (CSELS), McKelvey School of Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Anuradha Janakiraman
- Department of Biology, The City College of New York, New York, New York, USA
- Programs in Biology and Biochemistry, The Graduate Center of the City University of New York, New York, New York, USA
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26
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Uyeda A, Reyes SG, Kanamori T, Matsuura T. Identification of conditions for efficient cell-sized liposome preparation using commercially available reconstituted in vitro transcription-translation system. J Biosci Bioeng 2021; 133:181-186. [PMID: 34789414 DOI: 10.1016/j.jbiosc.2021.10.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/14/2021] [Accepted: 10/24/2021] [Indexed: 12/29/2022]
Abstract
Attempts to create complex molecular systems that mimic parts of cellular systems using a bottom-up approach have become important in the field of biology. Among various molecular systems, in vitro protein synthesis inside lipid vesicles (liposomes), which we refer to as the artificial cell, has become an attractive system because it possesses two fundamental features of living cells: central dogma, and compartmentalization. Here, we investigated the effect of altering the amount or concentration of four constituents of the artificial cell consisting of a commercially available reconstituted in vitro transcription-translation (IVTT) system. As this IVTT system is available worldwide, the results will be useful to the scientific community when shared, unlike those from a lab-made IVTT system. We succeeded in revealing the effect and trend of altering each parameter and identified a suitable condition for preparing liposomes that are unilamellar and can synthesize proteins equally as well as the original IVTT system. Because the commercially available reconstituted IVTT system is an important standardization tool and the constituents can be adjusted as desired, our results will be useful for the bottom-up creation of more complex molecular systems.
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Affiliation(s)
- Atsuko Uyeda
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Sabrina Galiñanes Reyes
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-i7E Ookayama, Meguro-Ku, Tokyo 152-8550, Japan.
| | - Takashi Kanamori
- GeneFrontier Corporation, SHARP Kashiwa Building, 4F, 273-1 Kashiwa, Kashiwa-shi, Chiba 277-0005, Japan.
| | - Tomoaki Matsuura
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-i7E Ookayama, Meguro-Ku, Tokyo 152-8550, Japan.
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27
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Zhao Y, Zhang H, Wang H, Ye M, Jin X. Role of formin INF2 in human diseases. Mol Biol Rep 2021; 49:735-746. [PMID: 34698992 DOI: 10.1007/s11033-021-06869-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 10/21/2021] [Indexed: 01/08/2023]
Abstract
Formin proteins catalyze actin nucleation and microfilament polymerization. Inverted formin 2 (INF2) is an atypical diaphanous-related formin characterized by polymerization and depolymerization of actin. Accumulating evidence showed that INF2 is associated with kidney disease focal segmental glomerulosclerosis and cancers, such as colorectal and thyroid cancer where it functions as a tumor suppressor, glioblastoma, breast, prostate, and gastric cancer, via its oncogenic function. However, studies on the underlying molecular mechanisms of the different roles of INF2 in diverse cancers are limited. This review comprehensively describes the structure, biochemical features, and primary pathogenic mutations of INF2.
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Affiliation(s)
- Yiting Zhao
- Department of Hepato-Biliary-Pancreatic Surgery, The Affiliated Ningbo Medical Center of LiHuiLi Hospital of Medical School of Ningbo University, Ningbo, 315048, China.,The Affiliated Hospital of Medical School, Ningbo University, Ningbo, 315020, China
| | - Hui Zhang
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, 315211, China.,The Affiliated Hospital of Medical School, Ningbo University, Ningbo, 315020, China
| | - Haibiao Wang
- Department of Hepato-Biliary-Pancreatic Surgery, The Affiliated Ningbo Medical Center of LiHuiLi Hospital of Medical School of Ningbo University, Ningbo, 315048, China. .,Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, 315211, China.
| | - Meng Ye
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, 315211, China. .,The Affiliated Hospital of Medical School, Ningbo University, Ningbo, 315020, China.
| | - Xiaofeng Jin
- Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, 315211, China. .,The Affiliated Hospital of Medical School, Ningbo University, Ningbo, 315020, China.
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28
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Schwille P, Frohn BP. Hidden protein functions and what they may teach us. Trends Cell Biol 2021; 32:102-109. [PMID: 34654605 DOI: 10.1016/j.tcb.2021.09.006] [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] [Received: 06/25/2021] [Revised: 09/07/2021] [Accepted: 09/22/2021] [Indexed: 11/15/2022]
Abstract
Bottom-up synthetic biology is a new research field with the goal of constructing living systems from a minimal number of functional components. The key challenges are, first, to identify a necessary canon of functions for a system to be considered alive, and second, to reconstitute these respective modules in vitro. When using proteins as obvious candidates, it appears that not only some of their described physiological functions fail to unfold outside the cellular context, but that completely new and unexpected functions are being observed. We put these insights in the context of other recent findings on protein functionality and discuss their potential role in the emergence and evolution of life.
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Affiliation(s)
- Petra Schwille
- Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany.
| | - Béla P Frohn
- Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
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29
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Dreher Y, Jahnke K, Schröter M, Göpfrich K. Light-Triggered Cargo Loading and Division of DNA-Containing Giant Unilamellar Lipid Vesicles. NANO LETTERS 2021; 21:5952-5957. [PMID: 34251204 PMCID: PMC8323123 DOI: 10.1021/acs.nanolett.1c00822] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 07/02/2021] [Indexed: 05/24/2023]
Abstract
A minimal synthetic cell should contain a substrate for information storage and have the capability to divide. Notable efforts were made to assemble functional synthetic cells from the bottom up, however often lacking the capability to reproduce. Here, we develop a mechanism to fully control reversible cargo loading and division of DNA-containing giant unilamellar vesicles (GUVs) with light. We make use of the photosensitizer Chlorin e6 (Ce6) which self-assembles into lipid bilayers and leads to local lipid peroxidation upon illumination. On the time scale of minutes, illumination induces the formation of transient pores, which we exploit for cargo encapsulation or controlled release. In combination with osmosis, complete division of two daughter GUVs can be triggered within seconds of illumination due to a spontaneous curvature increase. We ultimately demonstrate the division of a selected DNA-containing GUV with full spatiotemporal control-proving the relevance of the division mechanism for bottom-up synthetic biology.
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Affiliation(s)
- Yannik Dreher
- Max
Planck Institute for Medical Research, Biophysical Engineering Group, Jahnstraße 29, 69120 Heidelberg, Germany
- Department
of Physics and Astronomy, Heidelberg University, 69120 Heidelberg, Germany
| | - Kevin Jahnke
- Max
Planck Institute for Medical Research, Biophysical Engineering Group, Jahnstraße 29, 69120 Heidelberg, Germany
- Department
of Physics and Astronomy, Heidelberg University, 69120 Heidelberg, Germany
| | - Martin Schröter
- Max
Planck Institute for Medical Research, Department
of Cellular Biophysics, Jahnstraße 29, 69120 Heidelberg, Germany
| | - Kerstin Göpfrich
- Max
Planck Institute for Medical Research, Biophysical Engineering Group, Jahnstraße 29, 69120 Heidelberg, Germany
- Department
of Physics and Astronomy, Heidelberg University, 69120 Heidelberg, Germany
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30
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Ramirez-Diaz DA, Merino-Salomón A, Meyer F, Heymann M, Rivas G, Bramkamp M, Schwille P. FtsZ induces membrane deformations via torsional stress upon GTP hydrolysis. Nat Commun 2021; 12:3310. [PMID: 34083531 PMCID: PMC8175707 DOI: 10.1038/s41467-021-23387-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 04/27/2021] [Indexed: 01/28/2023] Open
Abstract
FtsZ is a key component in bacterial cell division, being the primary protein of the presumably contractile Z ring. In vivo and in vitro, it shows two distinctive features that could so far, however, not be mechanistically linked: self-organization into directionally treadmilling vortices on solid supported membranes, and shape deformation of flexible liposomes. In cells, circumferential treadmilling of FtsZ was shown to recruit septum-building enzymes, but an active force production remains elusive. To gain mechanistic understanding of FtsZ dependent membrane deformations and constriction, we design an in vitro assay based on soft lipid tubes pulled from FtsZ decorated giant lipid vesicles (GUVs) by optical tweezers. FtsZ filaments actively transform these tubes into spring-like structures, where GTPase activity promotes spring compression. Operating the optical tweezers in lateral vibration mode and assigning spring constants to FtsZ coated tubes, the directional forces that FtsZ-YFP-mts rings exert upon GTP hydrolysis can be estimated to be in the pN range. They are sufficient to induce membrane budding with constricting necks on both, giant vesicles and E.coli cells devoid of their cell walls. We hypothesize that these forces result from torsional stress in a GTPase activity dependent manner.
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Affiliation(s)
- Diego A Ramirez-Diaz
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried, Germany
- Graduate School for Quantitative Biosciences (QBM), Ludwig-Maximillians-University, Munich, Germany
| | - Adrián Merino-Salomón
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried, Germany
- International Max Planck Research School for Molecular Life Sciences (IMPRS-LS), Munich, Germany
| | - Fabian Meyer
- Institute of General Microbiology, Christian-Albrechts-Unversity, Kiel, Germany
| | - Michael Heymann
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried, Germany
- Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Stuttgart, Germany
| | - Germán Rivas
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Cientificas (CSIC), Madrid, Spain
| | - Marc Bramkamp
- Institute of General Microbiology, Christian-Albrechts-Unversity, Kiel, Germany
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried, Germany.
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31
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Kretschmer S, Heermann T, Tassinari A, Glock P, Schwille P. Increasing MinD's Membrane Affinity Yields Standing Wave Oscillations and Functional Gradients on Flat Membranes. ACS Synth Biol 2021; 10:939-949. [PMID: 33881306 PMCID: PMC8155659 DOI: 10.1021/acssynbio.0c00604] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Indexed: 11/28/2022]
Abstract
The formation of large-scale patterns through molecular self-organization is a basic principle of life. Accordingly, the engineering of protein patterns and gradients is of prime relevance for synthetic biology. As a paradigm for such pattern formation, the bacterial MinDE protein system is based on self-organization of the ATPase MinD and ATPase-activating protein MinE on lipid membranes. Min patterns can be tightly regulated by tuning physical or biochemical parameters. Among the biochemically engineerable modules, MinD's membrane targeting sequence, despite being a key regulating element, has received little attention. Here we attempt to engineer patterns by modulating the membrane affinity of MinD. Unlike the traveling waves or stationary patterns commonly observed in vitro on flat supported membranes, standing-wave oscillations emerge upon elongating MinD's membrane targeting sequence via rationally guided mutagenesis. These patterns are capable of forming gradients and thereby spatially target co-reconstituted downstream proteins, highlighting their functional potential in designing new life-like systems.
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Affiliation(s)
- Simon Kretschmer
- Department
of Cellular and Molecular Biophysics, Max-Planck-Institute
of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
- Current
affiliation: Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California 94158, United States
| | - Tamara Heermann
- Department
of Cellular and Molecular Biophysics, Max-Planck-Institute
of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Andrea Tassinari
- Department
of Cellular and Molecular Biophysics, Max-Planck-Institute
of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Philipp Glock
- Department
of Cellular and Molecular Biophysics, Max-Planck-Institute
of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Petra Schwille
- Department
of Cellular and Molecular Biophysics, Max-Planck-Institute
of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
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32
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Erickson HP. How Teichoic Acids Could Support a Periplasm in Gram-Positive Bacteria, and Let Cell Division Cheat Turgor Pressure. Front Microbiol 2021; 12:664704. [PMID: 34040598 PMCID: PMC8141598 DOI: 10.3389/fmicb.2021.664704] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/06/2021] [Indexed: 12/17/2022] Open
Abstract
The cytoplasm of bacteria is maintained at a higher osmolality than the growth medium, which generates a turgor pressure. The cell membrane (CM) cannot support a large turgor, so there are two possibilities for transferring the pressure to the peptidoglycan cell wall (PGW): (1) the CM could be pressed directly against the PGW, or (2) the CM could be separated from the PGW by a periplasmic space that is isoosmotic with the cytoplasm. There is strong evidence for gram-negative bacteria that a periplasm exists and is isoosmotic with the cytoplasm. No comparable studies have been done for gram-positive bacteria. Here I suggest that a periplasmic space is probably essential in order for the periplasmic proteins to function, including especially the PBPs that remodel the peptidoglycan wall. I then present a semi-quantitative analysis of how teichoic acids could support a periplasm that is isoosmotic with the cytoplasm. The fixed anionic charge density of teichoic acids in the periplasm is ∼0.5 M, which would bring in ∼0.5 M Na+ neutralizing ions. This approximately balances the excess osmolality of the cytoplasm that would produce a turgor pressure of 19 atm. The 0.5 M fixed charge density is similar to that of proteoglycans in articular cartilage, suggesting a comparability ability to support pressure. An isoosmotic periplasm would be especially important for cell division, since it would allow CM constriction and PGW synthesis to avoid turgor pressure.
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Affiliation(s)
- Harold P Erickson
- Department of Cell Biology, Duke University Medical Center, Durham, NC, United States
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33
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Dreher Y, Jahnke K, Bobkova E, Spatz JP, Göpfrich K. Division and Regrowth of Phase‐Separated Giant Unilamellar Vesicles**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202014174] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Yannik Dreher
- Biophysical Engineering Group Max Planck Institute for Medical Research Jahnstraße 29 69120 Heidelberg Germany
- Department of Physics and Astronomy Heidelberg University 69120 Heidelberg Germany
| | - Kevin Jahnke
- Biophysical Engineering Group Max Planck Institute for Medical Research Jahnstraße 29 69120 Heidelberg Germany
- Department of Physics and Astronomy Heidelberg University 69120 Heidelberg Germany
| | - Elizaveta Bobkova
- Biophysical Engineering Group Max Planck Institute for Medical Research Jahnstraße 29 69120 Heidelberg Germany
- Department of Physics and Astronomy Heidelberg University 69120 Heidelberg Germany
| | - Joachim P. Spatz
- Department of Cellular Biophysics Max Planck Institute for Medical Research Jahnstraße 29 69120 Heidelberg Germany
- Institute for Molecular Systems Engineering (IMSE) Heidelberg University Im Neuenheimer Feld 225 69120 Heidelberg Germany
- Max Planck School Matter to Life Jahnstraße 29 69120 Heidelberg Germany
| | - Kerstin Göpfrich
- Biophysical Engineering Group Max Planck Institute for Medical Research Jahnstraße 29 69120 Heidelberg Germany
- Department of Physics and Astronomy Heidelberg University 69120 Heidelberg Germany
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34
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Cell division in the archaeon Haloferax volcanii relies on two FtsZ proteins with distinct functions in division ring assembly and constriction. Nat Microbiol 2021; 6:594-605. [PMID: 33903747 PMCID: PMC7611241 DOI: 10.1038/s41564-021-00894-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 03/22/2021] [Indexed: 02/02/2023]
Abstract
In bacteria, the tubulin homologue FtsZ assembles a cytokinetic ring, termed the Z ring, and plays a key role in the machinery that constricts to divide the cells. Many archaea encode two FtsZ proteins from distinct families, FtsZ1 and FtsZ2, with previously unclear functions. Here, we show that Haloferax volcanii cannot divide properly without either or both FtsZ proteins, but DNA replication continues and cells proliferate in alternative ways, such as blebbing and fragmentation, via remarkable envelope plasticity. FtsZ1 and FtsZ2 colocalize to form the dynamic division ring. However, FtsZ1 can assemble rings independent of FtsZ2, and stabilizes FtsZ2 in the ring, whereas FtsZ2 functions primarily in the constriction mechanism. FtsZ1 also influenced cell shape, suggesting it forms a hub-like platform at midcell for the assembly of shape-related systems too. Both FtsZ1 and FtsZ2 are widespread in archaea with a single S-layer envelope, but archaea with a pseudomurein wall and division septum only have FtsZ1. FtsZ1 is therefore likely to provide a fundamental recruitment role in diverse archaea, and FtsZ2 is required for constriction of a flexible S-layer envelope, where an internal constriction force might dominate the division mechanism, in contrast with the single-FtsZ bacteria and archaea that divide primarily by wall ingrowth.
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35
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Single-molecule imaging reveals that Z-ring condensation is essential for cell division in Bacillus subtilis. Nat Microbiol 2021; 6:553-562. [PMID: 33737746 PMCID: PMC8085161 DOI: 10.1038/s41564-021-00878-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 02/11/2021] [Indexed: 01/31/2023]
Abstract
Although many components of the cell division machinery in bacteria have been identified1,2, the mechanisms by which they work together to divide the cell remain poorly understood. Key among these components is the tubulin FtsZ, which forms a Z ring at the midcell. FtsZ recruits the other cell division proteins, collectively called the divisome, and the Z ring constricts as the cell divides. We applied live-cell single-molecule imaging to describe the dynamics of the divisome in detail, and to evaluate the individual roles of FtsZ-binding proteins (ZBPs), specifically FtsA and the ZBPs EzrA, SepF and ZapA, in cytokinesis. We show that the divisome comprises two subcomplexes that move differently: stationary ZBPs that transiently bind to treadmilling FtsZ filaments, and a moving complex that includes cell wall synthases. Our imaging analyses reveal that ZBPs bundle FtsZ filaments together and condense them into Z rings, and that this condensation is necessary for cytokinesis.
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36
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Song D, Zhang N, Zhang P, Zhang N, Chen W, Zhang L, Guo T, Gu X, Ma S. Design, synthesis and evaluation of novel 9-arylalkyl-10-methylacridinium derivatives as highly potent FtsZ-targeting antibacterial agents. Eur J Med Chem 2021; 221:113480. [PMID: 33964649 DOI: 10.1016/j.ejmech.2021.113480] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/13/2021] [Accepted: 04/15/2021] [Indexed: 01/28/2023]
Abstract
With the increasing incidence of antibiotic resistance, new antibacterial agents having novel mechanisms of action hence are in an urgent need to combat infectious diseases caused by multidrug-resistant (MDR) pathogens. Four novel series of substituted 9-arylalkyl-10-methylacridinium derivatives as FtsZ inhibitors were designed, synthesized and evaluated for their antibacterial activities against various Gram-positive and Gram-negative bacteria. The results demonstrated that they exhibited broad-spectrum activities with substantial efficacy against MRSA and VRE, which were superior or comparable to the berberine, sanguinarine, linezolid, ciprofloxacin and vancomycin. In particular, the most promising compound 15f showed rapid bactericidal properties, which avoid the emergence of drug resistance. However, 15f showed no inhibitory effect on Gram-negative bacteria but biofilm formation study gave possible answers. Further target identification and mechanistic studies revealed that 15f functioned as an effective FtsZ inhibitor to alter the dynamics of FtsZ self-polymerization, which resulted in termination of the cell division and caused cell death. Further cytotoxicity and animal studies demonstrated that 15f not only displayed efficacy in a murine model of bacteremia in vivo, but also no significant hemolysis to mammalian cells. Overall, this compound with novel skeleton could serve as an antibacterial lead of FtsZ inhibitor for further evaluation of drug-likeness.
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Affiliation(s)
- Di Song
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan, 250012, China
| | - Nan Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan, 250012, China
| | - Panpan Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan, 250012, China
| | - Na Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan, 250012, China
| | - Weijin Chen
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan, 250012, China
| | - Long Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan, 250012, China
| | - Ting Guo
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan, 250012, China
| | - Xiaotong Gu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan, 250012, China
| | - Shutao Ma
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan, 250012, China.
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37
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Porter KJ, Cao L, Chen Y, TerBush AD, Chen C, Erickson HP, Osteryoung KW. The Arabidopsis thaliana chloroplast division protein FtsZ1 counterbalances FtsZ2 filament stability in vitro. J Biol Chem 2021; 296:100627. [PMID: 33812992 PMCID: PMC8142252 DOI: 10.1016/j.jbc.2021.100627] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 03/30/2021] [Accepted: 03/31/2021] [Indexed: 11/18/2022] Open
Abstract
Bacterial cell and chloroplast division are driven by a contractile “Z ring” composed of the tubulin-like cytoskeletal GTPase FtsZ. Unlike bacterial Z rings, which consist of a single FtsZ, the chloroplast Z ring in plants is composed of two FtsZ proteins, FtsZ1 and FtsZ2. Both are required for chloroplast division in vivo, but their biochemical relationship is poorly understood. We used GTPase assays, light scattering, transmission electron microscopy, and sedimentation assays to investigate the assembly behavior of purified Arabidopsis thaliana (At) FtsZ1 and AtFtsZ2 both individually and together. Both proteins exhibited GTPase activity. AtFtsZ2 assembled relatively quickly, forming protofilament bundles that were exceptionally stable, as indicated by their sustained assembly and slow disassembly. AtFtsZ1 did not form detectable protofilaments on its own. When mixed with AtFtsZ2, AtFtsZ1 reduced the extent and rate of AtFtsZ2 assembly, consistent with its previously demonstrated ability to promote protofilament subunit turnover in living cells. Mixing the two FtsZ proteins did not increase the overall GTPase activity, indicating that the effect of AtFtsZ1 on AtFtsZ2 assembly was not due to a stimulation of GTPase activity. However, the GTPase activity of AtFtsZ1 was required to reduce AtFtsZ2 assembly. Truncated forms of AtFtsZ1 and AtFtsZ2 consisting of only their conserved core regions largely recapitulated the behaviors of the full-length proteins. Our in vitro findings provide evidence that FtsZ1 counterbalances the stability of FtsZ2 filaments in the regulation of chloroplast Z-ring dynamics and suggest that restraining FtsZ2 self-assembly is a critical function of FtsZ1 in chloroplasts.
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Affiliation(s)
- Katie J Porter
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, USA
| | - Lingyan Cao
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, USA
| | - Yaodong Chen
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Allan D TerBush
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, USA
| | - Cheng Chen
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, USA
| | - Harold P Erickson
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina, USA
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38
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Dreher Y, Jahnke K, Bobkova E, Spatz JP, Göpfrich K. Division and Regrowth of Phase-Separated Giant Unilamellar Vesicles*. Angew Chem Int Ed Engl 2021; 60:10661-10669. [PMID: 33355974 PMCID: PMC8252472 DOI: 10.1002/anie.202014174] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 12/13/2020] [Indexed: 01/01/2023]
Abstract
Success in the bottom‐up assembly of synthetic cells will depend on strategies for the division of protocellular compartments. Here, we describe the controlled division of phase‐separated giant unilamellar lipid vesicles (GUVs). We derive an analytical model based on the vesicle geometry, which makes four quantitative predictions that we verify experimentally. We find that the osmolarity ratio required for division is 2
, independent of the GUV size, while asymmetric division happens at lower osmolarity ratios. Remarkably, we show that a suitable osmolarity change can be triggered by water evaporation, enzymatic decomposition of sucrose or light‐triggered uncaging of CMNB‐fluorescein. The latter provides full spatiotemporal control, such that a target GUV undergoes division whereas the surrounding GUVs remain unaffected. Finally, we grow phase‐separated vesicles from single‐phased vesicles by targeted fusion of the opposite lipid type with programmable DNA tags to enable subsequent division cycles.
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Affiliation(s)
- Yannik Dreher
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Jahnstraße 29, 69120, Heidelberg, Germany.,Department of Physics and Astronomy, Heidelberg University, 69120, Heidelberg, Germany
| | - Kevin Jahnke
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Jahnstraße 29, 69120, Heidelberg, Germany.,Department of Physics and Astronomy, Heidelberg University, 69120, Heidelberg, Germany
| | - Elizaveta Bobkova
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Jahnstraße 29, 69120, Heidelberg, Germany.,Department of Physics and Astronomy, Heidelberg University, 69120, Heidelberg, Germany
| | - Joachim P Spatz
- Department of Cellular Biophysics, Max Planck Institute for Medical Research, Jahnstraße 29, 69120, Heidelberg, Germany.,Institute for Molecular Systems Engineering (IMSE), Heidelberg University, Im Neuenheimer Feld 225, 69120, Heidelberg, Germany.,Max Planck School Matter to Life, Jahnstraße 29, 69120, Heidelberg, Germany
| | - Kerstin Göpfrich
- Biophysical Engineering Group, Max Planck Institute for Medical Research, Jahnstraße 29, 69120, Heidelberg, Germany.,Department of Physics and Astronomy, Heidelberg University, 69120, Heidelberg, Germany
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39
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Abstract
Giant unilamellar vesicles (GUVs) have gained great popularity as mimicries for cellular membranes. As their sizes are comfortably above the optical resolution limit, and their lipid composition is easily controlled, they are ideal for quantitative light microscopic investigation of dynamic processes in and on membranes. However, reconstitution of functional proteins into the lumen or the GUV membrane itself has proven technically challenging. In recent years, a selection of techniques has been introduced that tremendously improve GUV-assay development and enable the precise investigation of protein-membrane interactions under well-controlled conditions. Moreover, due to these methodological advances, GUVs are considered important candidates as protocells in bottom-up synthetic biology. In this review, we discuss the state of the art of the most important vesicle production and protein encapsulation methods and highlight some key protein systems whose functional reconstitution has advanced the field.
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Affiliation(s)
- Thomas Litschel
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried 82152, Germany; ,
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried 82152, Germany; ,
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40
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Sun H, Jia H, Ramirez‐Diaz DA, Budisa N, Schwille P. Fine-Tuning Protein Self-Organization by Orthogonal Chemo-Optogenetic Tools. Angew Chem Int Ed Engl 2021; 60:4501-4506. [PMID: 33155720 PMCID: PMC7986231 DOI: 10.1002/anie.202008691] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 11/04/2020] [Indexed: 12/18/2022]
Abstract
A universal gain-of-function approach for the spatiotemporal control of protein activity is highly desirable when reconstituting biological modules in vitro. Here we used orthogonal translation with a photocaged amino acid to map and elucidate molecular mechanisms in the self-organization of the prokaryotic filamentous cell-division protein (FtsZ) that is highly relevant for the assembly of the division ring in bacteria. We masked a tyrosine residue of FtsZ by site-specific incorporation of a photocaged tyrosine analogue. While the mutant still shows self-assembly into filaments, dynamic self-organization into ring patterns can no longer be observed. UV-mediated uncaging revealed that tyrosine 222 is essential for the regulation of the protein's GTPase activity, self-organization, and treadmilling dynamics. Thus, the light-mediated assembly of functional protein modules appears to be a promising minimal-regulation strategy for building up molecular complexity towards a minimal cell.
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Affiliation(s)
- Huan Sun
- Technical University of BerlinMüller-Breslau-Str. 1010623BerlinGermany
| | - Haiyang Jia
- Max Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | | | - Nediljko Budisa
- Technical University of BerlinMüller-Breslau-Str. 1010623BerlinGermany
- Present address: University of Manitoba44 DysartRdR3T 2N2WinnipegMBCanada
| | - Petra Schwille
- Max Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
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41
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FtsZ: The Force Awakens. J Indian Inst Sci 2021. [DOI: 10.1007/s41745-020-00215-z] [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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42
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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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43
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Sun H, Jia H, Ramirez‐Diaz DA, Budisa N, Schwille P. Fine‐Tuning Protein Self‐Organization by Orthogonal Chemo‐Optogenetic Tools. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202008691] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Huan Sun
- Technical University of Berlin Müller-Breslau-Str. 10 10623 Berlin Germany
| | - Haiyang Jia
- Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany
| | | | - Nediljko Budisa
- Technical University of Berlin Müller-Breslau-Str. 10 10623 Berlin Germany
- Present address: University of Manitoba 44 DysartRd R3T 2N2 Winnipeg MB Canada
| | - Petra Schwille
- Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany
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44
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Springstein BL, Nürnberg DJ, Weiss GL, Pilhofer M, Stucken K. Structural Determinants and Their Role in Cyanobacterial Morphogenesis. Life (Basel) 2020; 10:E355. [PMID: 33348886 PMCID: PMC7766704 DOI: 10.3390/life10120355] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/04/2020] [Accepted: 12/09/2020] [Indexed: 12/16/2022] Open
Abstract
Cells have to erect and sustain an organized and dynamically adaptable structure for an efficient mode of operation that allows drastic morphological changes during cell growth and cell division. These manifold tasks are complied by the so-called cytoskeleton and its associated proteins. In bacteria, FtsZ and MreB, the bacterial homologs to tubulin and actin, respectively, as well as coiled-coil-rich proteins of intermediate filament (IF)-like function to fulfil these tasks. Despite generally being characterized as Gram-negative, cyanobacteria have a remarkably thick peptidoglycan layer and possess Gram-positive-specific cell division proteins such as SepF and DivIVA-like proteins, besides Gram-negative and cyanobacterial-specific cell division proteins like MinE, SepI, ZipN (Ftn2) and ZipS (Ftn6). The diversity of cellular morphologies and cell growth strategies in cyanobacteria could therefore be the result of additional unidentified structural determinants such as cytoskeletal proteins. In this article, we review the current advances in the understanding of the cyanobacterial cell shape, cell division and cell growth.
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Affiliation(s)
- Benjamin L. Springstein
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Dennis J. Nürnberg
- Department of Physics, Biophysics and Biochemistry of Photosynthetic Organisms, Freie Universität Berlin, 14195 Berlin, Germany;
| | - Gregor L. Weiss
- Department of Biology, Institute of Molecular Biology & Biophysics, ETH Zürich, 8092 Zürich, Switzerland; (G.L.W.); (M.P.)
| | - Martin Pilhofer
- Department of Biology, Institute of Molecular Biology & Biophysics, ETH Zürich, 8092 Zürich, Switzerland; (G.L.W.); (M.P.)
| | - Karina Stucken
- Department of Food Engineering, Universidad de La Serena, La Serena 1720010, Chile;
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45
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Assembly properties of bacterial tubulin homolog FtsZ regulated by the positive regulator protein ZipA and ZapA from Pseudomonas aeruginosa. Sci Rep 2020; 10:21369. [PMID: 33288818 PMCID: PMC7721900 DOI: 10.1038/s41598-020-78431-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 11/25/2020] [Indexed: 12/21/2022] Open
Abstract
Bacterial tubulin homolog FtsZ self-assembles into dynamic protofilaments, which forms the scaffold for the contractile ring (Z-ring) to achieve bacterial cell division. Here, we study the biochemical properties of FtsZ from Pseudomonas aeruginosa (PaFtsZ) and the effects of its two positive regulator proteins, ZipA and ZapA. Similar to Escherichia coli FtsZ, PaFtsZ had a strong GTPase activity, ~ 7.8 GTP min-1 FtsZ-1 at pH 7.5, and assembled into mainly short single filaments in vitro. However, PaFtsZ protofilaments were mixtures of straight and “intermediate-curved” (100–300 nm diameter) in pH 7.5 solution and formed some bundles in pH 6.5 solution. The effects of ZipA on PaFtsZ assembly varied with pH. In pH 6.5 buffer ZipA induced PaFtsZ to form large bundles. In pH 7.5 buffer PaFtsZ-ZipA protofilaments were not bundled, but ZipA enhanced PaFtsZ assembly and promoted more curved filaments. Comparable to ZapA from other bacterial species, ZapA from P. aeruginosa induced PaFtsZ protofilaments to associate into long straight loose bundles and/or sheets at both pH 6.5 and pH 7.5, which had little effect on the GTPase activity of PaFtsZ. These results provide us further information that ZipA functions as an enhancer of FtsZ curved filaments, while ZapA works as a stabilizer of FtsZ straight filaments.
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46
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Yamamoto S, Saito R, Nakamura S, Sogawa H, Karpov P, Shulga S, Blume Y, Kurita N. Proposal of Potent Inhibitors for a Bacterial Cell Division Protein FtsZ: Molecular Simulations Based on Molecular Docking and ab Initio Molecular Orbital Calculations. Antibiotics (Basel) 2020; 9:E846. [PMID: 33256135 PMCID: PMC7761175 DOI: 10.3390/antibiotics9120846] [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: 11/03/2020] [Revised: 11/24/2020] [Accepted: 11/25/2020] [Indexed: 11/21/2022] Open
Abstract
The inhibition of a bacterial cell division protein, filamentous temperature-sensitive Z (FtsZ), prevents the reproduction of Mycobacteria. To propose potent inhibitors of FtsZ, the binding properties of FtsZ with various derivatives of Zantrin ZZ3 were investigated at an electronic level, using molecular simulations. We here employed protein-ligand docking, classical molecular mechanics (MM) optimizations, and ab initio fragment molecular orbital (FMO) calculations. Based on the specific interactions between FtsZ and the derivatives, as determined by FMO calculations, we proposed novel ligands, which can strongly bind to FtsZ and inhibit its aggregations. The introduction of a hydroxyl group into ZZ3 was found to enhance its binding affinity to FtsZ.
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Affiliation(s)
- Shohei Yamamoto
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan; (S.Y.); (R.S.); (S.N.); (H.S.)
| | - Ryosuke Saito
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan; (S.Y.); (R.S.); (S.N.); (H.S.)
| | - Shunya Nakamura
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan; (S.Y.); (R.S.); (S.N.); (H.S.)
| | - Haruki Sogawa
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan; (S.Y.); (R.S.); (S.N.); (H.S.)
| | - Pavel Karpov
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, 2a, Osypovskogo str., Kyiv-123, 04123 Kyiv, Ukraine; (P.K.); (S.S.); (Y.B.)
| | - Sergey Shulga
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, 2a, Osypovskogo str., Kyiv-123, 04123 Kyiv, Ukraine; (P.K.); (S.S.); (Y.B.)
| | - Yaroslav Blume
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, 2a, Osypovskogo str., Kyiv-123, 04123 Kyiv, Ukraine; (P.K.); (S.S.); (Y.B.)
| | - Noriyuki Kurita
- Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan; (S.Y.); (R.S.); (S.N.); (H.S.)
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47
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Ganzinger KA, Merino‐Salomón A, García‐Soriano DA, Butterfield AN, Litschel T, Siedler F, Schwille P. FtsZ Reorganization Facilitates Deformation of Giant Vesicles in Microfluidic Traps**. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202001928] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Kristina A. Ganzinger
- Department of Cellular and Molecular Biophysics Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany
- Living Matter AMOLF P.O. Box 41883-1009 DB Amsterdam The Netherlands
| | - Adrián Merino‐Salomón
- Department of Cellular and Molecular Biophysics Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany
| | - Daniela A. García‐Soriano
- Department of Cellular and Molecular Biophysics Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany
| | - A. Nelson Butterfield
- Department of Cellular and Molecular Biophysics Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany
| | - Thomas Litschel
- Department of Cellular and Molecular Biophysics Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany
| | - Frank Siedler
- Department of Cellular and Molecular Biophysics Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany
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48
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Ganzinger KA, Merino‐Salomón A, García‐Soriano DA, Butterfield AN, Litschel T, Siedler F, Schwille P. FtsZ Reorganization Facilitates Deformation of Giant Vesicles in Microfluidic Traps*. Angew Chem Int Ed Engl 2020; 59:21372-21376. [PMID: 32735732 PMCID: PMC7756778 DOI: 10.1002/anie.202001928] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 07/27/2020] [Indexed: 12/23/2022]
Abstract
The geometry of reaction compartments can affect the local outcome of interface-restricted reactions. Giant unilamellar vesicles (GUVs) are commonly used to generate cell-sized, membrane-bound reaction compartments, which are, however, always spherical. Herein, we report the development of a microfluidic chip to trap and reversibly deform GUVs into cigar-like shapes. When trapping and elongating GUVs that contain the primary protein of the bacterial Z ring, FtsZ, we find that membrane-bound FtsZ filaments align preferentially with the short GUV axis. When GUVs are released from this confinement and membrane tension is relaxed, FtsZ reorganizes reversibly from filaments into dynamic rings that stabilize membrane protrusions; a process that allows reversible GUV deformation. We conclude that microfluidic traps are useful for manipulating both geometry and tension of GUVs, and for investigating how both affect the outcome of spatially-sensitive reactions inside them, such as that of protein self-organization.
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Affiliation(s)
- Kristina A. Ganzinger
- Department of Cellular and Molecular BiophysicsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
- Living MatterAMOLFP.O. Box 41883-1009 DBAmsterdamThe Netherlands
| | - Adrián Merino‐Salomón
- Department of Cellular and Molecular BiophysicsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Daniela A. García‐Soriano
- Department of Cellular and Molecular BiophysicsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - A. Nelson Butterfield
- Department of Cellular and Molecular BiophysicsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Thomas Litschel
- Department of Cellular and Molecular BiophysicsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Frank Siedler
- Department of Cellular and Molecular BiophysicsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Petra Schwille
- Department of Cellular and Molecular BiophysicsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
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49
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Gözen I, Dommersnes P. Biological lipid nanotubes and their potential role in evolution. THE EUROPEAN PHYSICAL JOURNAL. SPECIAL TOPICS 2020; 229:2843-2862. [PMID: 33224439 PMCID: PMC7666715 DOI: 10.1140/epjst/e2020-000130-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 08/03/2020] [Indexed: 06/11/2023]
Abstract
The membrane of cells and organelles are highly deformable fluid interfaces, and can take on a multitude of shapes. One distinctive and particularly interesting property of biological membranes is their ability to from long and uniform nanotubes. These nanoconduits are surprisingly omnipresent in all domains of life, from archaea, bacteria, to plants and mammals. Some of these tubes have been known for a century, while others were only recently discovered. Their designations are different in different branches of biology, e.g. they are called stromule in plants and tunneling nanotubes in mammals. The mechanical transformation of flat membranes to tubes involves typically a combination of membrane anchoring and external forces, leading to a pulling action that results in very rapid membrane nanotube formation - micrometer long tubes can form in a matter of seconds. Their radius is set by a mechanical balance of tension and bending forces. There also exists a large class of membrane nanotubes that form due to curvature inducing molecules. It seems plausible that nanotube formation and functionality in plants and animals may have been inherited from their bacterial ancestors during endosymbiotic evolution. Here we attempt to connect observations of nanotubes in different branches of biology, and outline their similarities and differences with the aim of providing a perspective on their joint functions and evolutionary origin.
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Affiliation(s)
- Irep Gözen
- Centre for Molecular Medicine Norway, Faculty of Medicine, University of Oslo, Oslo, 0318 Norway
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, 0315 Norway
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Göteborg, 412 96 Sweden
| | - Paul Dommersnes
- Department of Physics, Norwegian University of Science and Technology, Hoegskoleringen 5, 7491 Trondheim, Norway
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50
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Vibhute MA, Schaap MH, Maas RJM, Nelissen FHT, Spruijt E, Heus HA, Hansen MMK, Huck WTS. Transcription and Translation in Cytomimetic Protocells Perform Most Efficiently at Distinct Macromolecular Crowding Conditions. ACS Synth Biol 2020; 9:2797-2807. [PMID: 32976714 PMCID: PMC7573978 DOI: 10.1021/acssynbio.0c00330] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
![]()
The formation of
cytomimetic protocells that capture the physicochemical
aspects of living cells is an important goal in bottom-up synthetic
biology. Here, we recreated the crowded cytoplasm in liposome-based
protocells and studied the kinetics of cell-free gene expression in
these crowded containers. We found that diffusion of key components
is affected not only by macromolecular crowding but also by enzymatic
activity in the protocell. Surprisingly, size-dependent diffusion
in crowded conditions yielded two distinct maxima for protein synthesis,
reflecting the differential impact of crowding on transcription and
translation. Our experimental data show, for the first time, that
macromolecular crowding induces a switch from reaction to diffusion
control and that this switch depends on the sizes of the macromolecules
involved. These results highlight the need to control the physical
environment in the design of synthetic cells.
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Affiliation(s)
- Mahesh A. Vibhute
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Mark H. Schaap
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Roel J. M. Maas
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Frank H. T. Nelissen
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Evan Spruijt
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Hans A. Heus
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Maike M. K. Hansen
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Wilhelm T. S. Huck
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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