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Wollweber F, Xu J, Ponce-Toledo RI, Marxer F, Rodrigues-Oliveira T, Pössnecker A, Luo ZH, Malit JJL, Kokhanovska A, Wieczorek M, Schleper C, Pilhofer M. Microtubules in Asgard archaea. Cell 2025; 188:2451-2464.e26. [PMID: 40120574 DOI: 10.1016/j.cell.2025.02.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2024] [Revised: 01/27/2025] [Accepted: 02/25/2025] [Indexed: 03/25/2025]
Abstract
Microtubules are a hallmark of eukaryotes. Archaeal and bacterial homologs of tubulins typically form homopolymers and non-tubular superstructures. The origin of heterodimeric tubulins assembling into microtubules remains unclear. Here, we report the discovery of microtubule-forming tubulins in Asgard archaea, the closest known relatives of eukaryotes. These Asgard tubulins (AtubA/B) are closely related to eukaryotic α/β-tubulins and the enigmatic bacterial tubulins BtubA/B. Proteomics of Candidatus Lokiarchaeum ossiferum showed that AtubA/B were highly expressed. Cryoelectron microscopy structures demonstrate that AtubA/B form eukaryote-like heterodimers, which assembled into 5-protofilament bona fide microtubules in vitro. The additional paralog AtubB2 lacks a nucleotide-binding site and competitively displaced AtubB. These AtubA/B2 heterodimers polymerized into 7-protofilament non-canonical microtubules. In a sub-population of Ca. Lokiarchaeum ossiferum cells, cryo-tomography revealed tubular structures, while expansion microscopy identified AtubA/B cytoskeletal assemblies. Our findings suggest a pre-eukaryotic origin of microtubules and provide a framework for understanding the fundamental principles of microtubule assembly.
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Affiliation(s)
- Florian Wollweber
- Department of Biology, Institute of Molecular Biology & Biophysics, Eidgenössische Technische Hochschule Zürich, Otto-Stern-Weg 5, 8093 Zürich, Switzerland
| | - Jingwei Xu
- Department of Biology, Institute of Molecular Biology & Biophysics, Eidgenössische Technische Hochschule Zürich, Otto-Stern-Weg 5, 8093 Zürich, Switzerland
| | - Rafael I Ponce-Toledo
- Department of Functional and Evolutionary Ecology, Archaea Biology and Ecogenomics Unit, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Florina Marxer
- Department of Biology, Institute of Molecular Biology & Biophysics, Eidgenössische Technische Hochschule Zürich, Otto-Stern-Weg 5, 8093 Zürich, Switzerland
| | - Thiago Rodrigues-Oliveira
- Department of Functional and Evolutionary Ecology, Archaea Biology and Ecogenomics Unit, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Anja Pössnecker
- Department of Biology, Institute of Molecular Biology & Biophysics, Eidgenössische Technische Hochschule Zürich, Otto-Stern-Weg 5, 8093 Zürich, Switzerland
| | - Zhen-Hao Luo
- Department of Functional and Evolutionary Ecology, Archaea Biology and Ecogenomics Unit, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Jessie James Limlingan Malit
- Department of Biology, Institute of Molecular Biology & Biophysics, Eidgenössische Technische Hochschule Zürich, Otto-Stern-Weg 5, 8093 Zürich, Switzerland
| | - Anastasiia Kokhanovska
- Department of Biology, Institute of Molecular Biology & Biophysics, Eidgenössische Technische Hochschule Zürich, Otto-Stern-Weg 5, 8093 Zürich, Switzerland
| | - Michal Wieczorek
- Department of Biology, Institute of Molecular Biology & Biophysics, Eidgenössische Technische Hochschule Zürich, Otto-Stern-Weg 5, 8093 Zürich, Switzerland
| | - Christa Schleper
- Department of Functional and Evolutionary Ecology, Archaea Biology and Ecogenomics Unit, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Martin Pilhofer
- Department of Biology, Institute of Molecular Biology & Biophysics, Eidgenössische Technische Hochschule Zürich, Otto-Stern-Weg 5, 8093 Zürich, Switzerland.
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2
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Rani R, Marinho Righetto G, Schäfer AB, Wenzel M. The Diverse Activities and Mechanisms of the Acylphloroglucinol Antibiotic Rhodomyrtone: Antibacterial Activity and Beyond. Antibiotics (Basel) 2024; 13:936. [PMID: 39452203 PMCID: PMC11504083 DOI: 10.3390/antibiotics13100936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2024] [Revised: 09/17/2024] [Accepted: 09/25/2024] [Indexed: 10/26/2024] Open
Abstract
Background/Objectives: The rose myrtle Rhodomyrtus tomentosa is a medicinal plant used in traditional Asian medicine. The active compound in R. tomentosa leaf extracts is rhodomyrtone, a chiral acylphloroglucinol. Rhodomyrtone exhibits an impressive breadth of activities, including antibacterial, antiviral, antiplasmodial, immunomodulatory, and anticancer properties. Its antibacterial properties have been extensively studied. Methods: We performed a comprehensive literature review on rhodomyrtone and summarized the current knowledge about this promising acylphloroglucinol antibiotic and its diverse functions in this review. Results: Rhodomyrtone shows nano to micromolar activities against a broad range of Gram-positive pathogens, including multidrug-resistant clinical isolates, and possesses a unique mechanism of action. It increases membrane fluidity and creates hyperfluid domains that attract membrane proteins prior to forming large membrane vesicles, effectively acting as a membrane protein trap. This mechanism affects a multitude of cellular processes, including cell division and cell wall synthesis. Additionally, rhodomyrtone reduces the expression of inflammatory cytokines, such as TNF-α, IL-17A, IL1β, and IL8. Generally showing low toxicity against mammalian cells, rhodomyrtone does inhibit the proliferation of cancer cell lines, such as epidermal carcinoma cells. The primary mechanism behind this activity appears to be the downregulation of adhesion kinases and growth factors. Furthermore, rhodomyrtone has shown antioxidant activity and displays cognitive effects, such as decreasing depressive symptoms in mice. Conclusions: Rhodomyrtone shows great promise as therapeutic agent, mostly for antibacterial but also for diverse other applications. Yet, bottlenecks such as resistance development and a better understanding of mammalian cell toxictiy demand careful assessment.
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Affiliation(s)
- Rupa Rani
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, 412 96 Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), 413 45 Gothenburg, Sweden
| | - Gabriela Marinho Righetto
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, 412 96 Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), 413 45 Gothenburg, Sweden
| | - Ann-Britt Schäfer
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, 412 96 Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), 413 45 Gothenburg, Sweden
| | - Michaela Wenzel
- Division of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, 412 96 Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), 413 45 Gothenburg, Sweden
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3
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Unnikrishnan M, Wang Y, Gruebele M, Murphy CJ. Nanoparticle-assisted tubulin assembly is environment dependent. Proc Natl Acad Sci U S A 2024; 121:e2403034121. [PMID: 38954547 PMCID: PMC11252952 DOI: 10.1073/pnas.2403034121] [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: 02/12/2024] [Accepted: 05/30/2024] [Indexed: 07/04/2024] Open
Abstract
Nanomaterials acquire a biomolecular corona upon introduction to biological media, leading to biological transformations such as changes in protein function, unmasking of epitopes, and protein fibrilization. Ex vivo studies to investigate the effect of nanoparticles on protein-protein interactions are typically performed in buffer and are rarely measured quantitatively in live cells. Here, we measure the differential effect of silica nanoparticles on protein association in vitro vs. in mammalian cells. BtubA and BtubB are a pair of bacterial tubulin proteins identified in Prosthecobacter strains that self-assemble like eukaryotic tubulin, first into dimers and then into microtubules in vitro or in vivo. Förster resonance energy transfer labeling of each of the Btub monomers with a donor (mEGFP) and acceptor (mRuby3) fluorescent protein provides a quantitative tool to measure their binding interactions in the presence of unfunctionalized silica nanoparticles in buffer and in cells using fluorescence spectroscopy and microscopy. We show that silica nanoparticles enhance BtubAB dimerization in buffer due to protein corona formation. However, these nanoparticles have little effect on bacterial tubulin self-assembly in the complex mammalian cellular environment. Thus, the effect of nanomaterials on protein-protein interactions may not be readily translated from the test tube to the cell in the absence of particle surface functionalization that can enable targeted protein-nanoparticle interactions to withstand competitive binding in the nanoparticle corona from other biomolecules.
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Affiliation(s)
- Mahima Unnikrishnan
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL61801
| | - Yuhan Wang
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL61801
| | - Martin Gruebele
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL61801
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL61801
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, IL61801
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL61801
| | - Catherine J. Murphy
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL61801
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL61801
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4
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Golyshev SA, Lyupina YV, Kravchuk OI, Mikhailov KV, Gornostaev NG, Burakov AV. Transient Interphase Microtubules Appear in Differentiating Sponge Cells. Cells 2024; 13:736. [PMID: 38727272 PMCID: PMC11082956 DOI: 10.3390/cells13090736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 04/09/2024] [Accepted: 04/22/2024] [Indexed: 05/13/2024] Open
Abstract
Microtubules are an indispensable component of all eukaryotic cells due to their role in mitotic spindle formation, yet their organization and number can vary greatly in the interphase. The last common ancestor of all eukaryotes already had microtubules and microtubule motor proteins moving along them. Sponges are traditionally regarded as the oldest animal phylum. Their body does not have a clear differentiation into tissues, but it contains several distinguishable cell types. The choanocytes stand out among them and are responsible for creating a flow of water with their flagella and increasing the filtering and feeding efficiency of the sponge. Choanocyte flagella contain microtubules, but thus far, observing a developed system of cytoplasmic microtubules in non-flagellated interphase sponge cells has been mostly unsuccessful. In this work, we combine transcriptomic analysis, immunofluorescence, and electron microscopy with time-lapse recording to demonstrate that microtubules appear in the cytoplasm of sponge cells only when transdifferentiation processes are activated. We conclude that dynamic cytoplasmic microtubules in the cells of sponges are not a persistent but rather a transient structure, associated with cellular plasticity.
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Affiliation(s)
- Sergei A. Golyshev
- A.N. Belozersky Institute of Physical and Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia; (S.A.G.); (K.V.M.)
| | - Yulia V. Lyupina
- N.K. Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow 119334, Russia; (Y.V.L.); (O.I.K.); (N.G.G.)
| | - Oksana I. Kravchuk
- N.K. Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow 119334, Russia; (Y.V.L.); (O.I.K.); (N.G.G.)
| | - Kirill V. Mikhailov
- A.N. Belozersky Institute of Physical and Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia; (S.A.G.); (K.V.M.)
- Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127051, Russia
| | - Nicolay G. Gornostaev
- N.K. Koltzov Institute of Developmental Biology, Russian Academy of Sciences, Moscow 119334, Russia; (Y.V.L.); (O.I.K.); (N.G.G.)
| | - Anton V. Burakov
- A.N. Belozersky Institute of Physical and Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia; (S.A.G.); (K.V.M.)
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5
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Wang Y, Unnikrishnan M, Ramsey B, El Andlosy D, Keeley AT, Murphy CJ, Gruebele M. In-Cell Association of a Bioorthogonal Tubulin. Biomacromolecules 2024; 25:1282-1290. [PMID: 38251876 DOI: 10.1021/acs.biomac.3c01253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
Studies of proteins from one organism in another organism's cells have shown that such exogenous proteins stick more, pointing toward coevolution of the cytoplasm and protein surface to minimize stickiness. Here we flip this question around by asking whether exogenous proteins can assemble efficiently into their target complexes in a non-native cytoplasm. We use as our model system the assembly of BtubA and BtubB from Prosthecobacter hosted in human U-2 OS cells. BtubA and B evolved from eukaryotic tubulins after horizontal gene transfer, but they have low surface sequence identity with the homologous human tubulins and do not respond to tubulin drugs such as nocodazole. In U-2 OS cells, BtubA and B assemble efficiently into dimers compared to in vitro, and the wild-type BtubA and B proteins subsequently are able to form microtubules as well. We find that generic crowding effects (Ficoll 70 in vitro) contribute significantly to efficient dimer assembly when compared to sticking interactions (U-2 OS cell lysate in vitro), consistent with the notion that a generic mechanism such as crowding can be effective at driving assembly of exogenous proteins, even when protein-cytoplasm quinary structure and sticking have been modified in a non-native cytoplasm. A simple Monte Carlo model of in vitro and in-cell interactions, treating BtubA and B as sticky dipoles in a matrix of sticky or nonsticky crowders, rationalizes all the experimental trends with two adjustable parameters and reveals nucleation as the likely mechanism for the time-scale separation between dimer- and tubule formation in-cell and in vitro.
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Affiliation(s)
- Yuhan Wang
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Mahima Unnikrishnan
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Brooke Ramsey
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Driss El Andlosy
- Computer Science and Technologies Department, Parkland Community College, Champaign, Illinois 61821, United States
| | - Alex T Keeley
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Catherine J Murphy
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Martin Gruebele
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
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6
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Fekry M, Dave KK, Badgujar D, Hamnevik E, Aurelius O, Dobritzsch D, Danielson UH. The Crystal Structure of Tyrosinase from Verrucomicrobium spinosum Reveals It to Be an Atypical Bacterial Tyrosinase. Biomolecules 2023; 13:1360. [PMID: 37759761 PMCID: PMC10526336 DOI: 10.3390/biom13091360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 09/01/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
Tyrosinases belong to the type-III copper enzyme family, which is involved in melanin production in a wide range of organisms. Despite similar overall characteristics and functions, their structures, activities, substrate specificities and regulation vary. The tyrosinase from the bacterium Verrucomicrobium spinosum (vsTyr) is produced as a pre-pro-enzyme in which a C-terminal extension serves as an inactivation domain. It does not require a caddie protein for copper ion incorporation, which makes it similar to eukaryotic tyrosinases. To gain an understanding of the catalytic machinery and regulation of vsTyr activity, we determined the structure of the catalytically active "core domain" of vsTyr by X-ray crystallography. The analysis showed that vsTyr is an atypical bacterial tyrosinase not only because it is independent of a caddie protein but also because it shows the highest structural (and sequence) similarity to plant-derived members of the type-III copper enzyme family and is more closely related to fungal tyrosinases regarding active site features. By modelling the structure of the pre-pro-enzyme using AlphaFold, we observed that Phe453, located in the C-terminal extension, is appropriately positioned to function as a "gatekeeper" residue. Our findings raise questions concerning the evolutionary origin of vsTyr.
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Affiliation(s)
- Mostafa Fekry
- Department of Chemistry—BMC, Uppsala University, SE 751 23 Uppsala, Sweden; (M.F.); (K.K.D.); (D.B.); (E.H.); (D.D.)
- Biophysics Department, Faculty of Science, Cairo University, Giza 12613, Egypt
| | - Khyati K. Dave
- Department of Chemistry—BMC, Uppsala University, SE 751 23 Uppsala, Sweden; (M.F.); (K.K.D.); (D.B.); (E.H.); (D.D.)
| | - Dilip Badgujar
- Department of Chemistry—BMC, Uppsala University, SE 751 23 Uppsala, Sweden; (M.F.); (K.K.D.); (D.B.); (E.H.); (D.D.)
| | - Emil Hamnevik
- Department of Chemistry—BMC, Uppsala University, SE 751 23 Uppsala, Sweden; (M.F.); (K.K.D.); (D.B.); (E.H.); (D.D.)
| | | | - Doreen Dobritzsch
- Department of Chemistry—BMC, Uppsala University, SE 751 23 Uppsala, Sweden; (M.F.); (K.K.D.); (D.B.); (E.H.); (D.D.)
| | - U. Helena Danielson
- Department of Chemistry—BMC, Uppsala University, SE 751 23 Uppsala, Sweden; (M.F.); (K.K.D.); (D.B.); (E.H.); (D.D.)
- Science for Life Laboratory, Drug Discovery & Development Platform, Uppsala University, SE 751 23 Uppsala, Sweden
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Godino E, Restrepo Sierra AM, Danelon C. Imaging Flow Cytometry for High-Throughput Phenotyping of Synthetic Cells. ACS Synth Biol 2023. [PMID: 37155828 PMCID: PMC10367129 DOI: 10.1021/acssynbio.3c00074] [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
The reconstitution of basic cellular functions in micrometer-sized liposomes has led to a surge of interest in the construction of synthetic cells. Microscopy and flow cytometry are powerful tools for characterizing biological processes in liposomes with fluorescence readouts. However, applying each method separately leads to a compromise between information-rich imaging by microscopy and statistical population analysis by flow cytometry. To address this shortcoming, we here introduce imaging flow cytometry (IFC) for high-throughput, microscopy-based screening of gene-expressing liposomes in laminar flow. We developed a comprehensive pipeline and analysis toolset based on a commercial IFC instrument and software. About 60 thousands of liposome events were collected per run starting from one microliter of the stock liposome solution. Robust population statistics from individual liposome images was performed based on fluorescence and morphological parameters. This allowed us to quantify complex phenotypes covering a wide range of liposomal states that are relevant for building a synthetic cell. The general applicability, current workflow limitations, and future prospects of IFC in synthetic cell research are finally discussed.
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Affiliation(s)
- Elisa Godino
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629HZ Delft, The Netherlands
| | - Ana Maria Restrepo Sierra
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629HZ Delft, The Netherlands
| | - Christophe Danelon
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629HZ Delft, The Netherlands
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France
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Discovery of a Novel Inner Membrane-Associated Bacterial Structure Related to the Flagellar Type III Secretion System. J Bacteriol 2022; 204:e0014422. [PMID: 35862756 PMCID: PMC9380563 DOI: 10.1128/jb.00144-22] [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] [Indexed: 11/24/2022] Open
Abstract
The bacterial flagellar type III secretion system (fT3SS) is a suite of membrane-embedded and cytoplasmic proteins responsible for building the flagellar motility machinery. Homologous nonflagellar (NF-T3SS) proteins form the injectisome machinery that bacteria use to deliver effector proteins into eukaryotic cells, and other family members were recently reported to be involved in the formation of membrane nanotubes. Here, we describe a novel, evolutionarily widespread, hat-shaped structure embedded in the inner membranes of bacteria, of yet-unidentified function, that is present in species containing fT3SS. Mutant analysis suggests a relationship between this novel structure and the fT3SS, but not the NF-T3SS. While the function of this novel structure remains unknown, we hypothesize that either some of the fT3SS proteins assemble within the hat-like structure, perhaps including the fT3SS core complex, or that fT3SS components regulate other proteins that form part of this novel structure. IMPORTANCE The type III secretion system (T3SS) is a fascinating suite of proteins involved in building diverse macromolecular systems, including the bacterial flagellar motility machine, the injectisome machinery that bacteria use to inject effector proteins into host cells, and probably membrane nanotubes which connect bacterial cells. Here, we accidentally discovered a novel inner membrane-associated complex related to the flagellar T3SS. Examining our lab database, which is comprised of more than 40,000 cryo-tomograms of dozens of species, we discovered that this novel structure is both ubiquitous and ancient, being present in highly divergent classes of bacteria. Discovering a novel, widespread structure related to what are among the best-studied molecular machines in bacteria will open new venues for research aiming at understanding the function and evolution of T3SS proteins.
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Osorio C, Sfera A, Anton JJ, Thomas KG, Andronescu CV, Li E, Yahia RW, Avalos AG, Kozlakidis Z. Virus-Induced Membrane Fusion in Neurodegenerative Disorders. Front Cell Infect Microbiol 2022; 12:845580. [PMID: 35531328 PMCID: PMC9070112 DOI: 10.3389/fcimb.2022.845580] [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: 01/04/2022] [Accepted: 03/01/2022] [Indexed: 12/15/2022] Open
Abstract
A growing body of epidemiological and research data has associated neurotropic viruses with accelerated brain aging and increased risk of neurodegenerative disorders. Many viruses replicate optimally in senescent cells, as they offer a hospitable microenvironment with persistently elevated cytosolic calcium, abundant intracellular iron, and low interferon type I. As cell-cell fusion is a major driver of cellular senescence, many viruses have developed the ability to promote this phenotype by forming syncytia. Cell-cell fusion is associated with immunosuppression mediated by phosphatidylserine externalization that enable viruses to evade host defenses. In hosts, virus-induced immune dysfunction and premature cellular senescence may predispose to neurodegenerative disorders. This concept is supported by novel studies that found postinfectious cognitive dysfunction in several viral illnesses, including human immunodeficiency virus-1, herpes simplex virus-1, and SARS-CoV-2. Virus-induced pathological syncytia may provide a unified framework for conceptualizing neuronal cell cycle reentry, aneuploidy, somatic mosaicism, viral spreading of pathological Tau and elimination of viable synapses and neurons by neurotoxic astrocytes and microglia. In this narrative review, we take a closer look at cell-cell fusion and vesicular merger in the pathogenesis of neurodegenerative disorders. We present a "decentralized" information processing model that conceptualizes neurodegeneration as a systemic illness, triggered by cytoskeletal pathology. We also discuss strategies for reversing cell-cell fusion, including, TMEM16F inhibitors, calcium channel blockers, senolytics, and tubulin stabilizing agents. Finally, going beyond neurodegeneration, we examine the potential benefit of harnessing fusion as a therapeutic strategy in regenerative medicine.
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Affiliation(s)
- Carolina Osorio
- Department of Psychiatry, Loma Linda University, Loma Linda, CA, United States
| | - Adonis Sfera
- Department of Psychiatry, Loma Linda University, Loma Linda, CA, United States
- Department of Psychiatry, Patton State Hospital, San Bernardino, CA, United States
| | - Jonathan J. Anton
- Department of Psychiatry, Patton State Hospital, San Bernardino, CA, United States
| | - Karina G. Thomas
- Department of Psychiatry, Patton State Hospital, San Bernardino, CA, United States
| | - Christina V. Andronescu
- Medical Anthropology – Department of Anthropology, Stanford University, Stanford, CA, United States
| | - Erica Li
- School of Medicine, University of California, Riverside, Riverside, CA, United States
| | - Rayan W. Yahia
- School of Medicine, University of California, Riverside, Riverside, CA, United States
| | - Andrea García Avalos
- Universidad Nacional Autónoma de México (UNAM), Facultad de Medicina Campus, Ciudad de Mexico, Mexico
| | - Zisis Kozlakidis
- International Agency for Research on Cancer (IARC), Lyon, France
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10
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Ishay Y, Potruch A, Schwartz A, Berg M, Jamil K, Agus S, Ilan Y. A digital health platform for assisting the diagnosis and monitoring of COVID-19 progression: An adjuvant approach for augmenting the antiviral response and mitigating the immune-mediated target organ damage. Biomed Pharmacother 2021; 143:112228. [PMID: 34649354 PMCID: PMC8455249 DOI: 10.1016/j.biopha.2021.112228] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 09/17/2021] [Accepted: 09/18/2021] [Indexed: 01/08/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), which is a respiratory illness associated with high mortality, has been classified as a pandemic. The major obstacles for the clinicians to contain the disease are limited information availability, difficulty in disease diagnosis, predicting disease prognosis, and lack of disease monitoring tools. Additionally, the lack of valid therapies has further contributed to the difficulties in containing the pandemic. Recent studies have reported that the dysregulation of the immune system leads to an ineffective antiviral response and promotes pathological immune response, which manifests as ARDS, myocarditis, and hepatitis. In this study, a novel platform has been described for disseminating information to physicians for the diagnosis and monitoring of patients with COVID-19. An adjuvant approach using compounds that can potentiate antiviral immune response and mitigate COVID-19-induced immune-mediated target organ damage has been presented. A prolonged beneficial effect is achieved by implementing algorithm-based individualized variability measures in the treatment regimen.
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Affiliation(s)
- Yuval Ishay
- Department of Medicine, Hebrew University-Hadassah Medical Center, Jerusalem, Israel.
| | - Assaf Potruch
- Department of Medicine, Hebrew University-Hadassah Medical Center, Jerusalem, Israel.
| | - Asaf Schwartz
- Department of Medicine, Hebrew University-Hadassah Medical Center, Jerusalem, Israel.
| | - Marc Berg
- Altus Care powered by Oberon Sciences, Denmark, Israel; Department of Pediatrics, Lucile Packard Children's Hospital, Stanford, USA.
| | - Khurram Jamil
- Altus Care powered by Oberon Sciences, Denmark, Israel.
| | - Samuel Agus
- Altus Care powered by Oberon Sciences, Denmark, Israel.
| | - Yaron Ilan
- Department of Medicine, Hebrew University-Hadassah Medical Center, Jerusalem, Israel.
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11
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Kattan J, Doerr A, Dogterom M, Danelon C. Shaping Liposomes by Cell-Free Expressed Bacterial Microtubules. ACS Synth Biol 2021; 10:2447-2455. [PMID: 34585918 PMCID: PMC8524656 DOI: 10.1021/acssynbio.1c00278] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Genetic control over
a cytoskeletal network inside lipid vesicles
offers a potential route to controlled shape changes and DNA segregation
in synthetic cell biology. Bacterial microtubules (bMTs) are protein
filaments found in bacteria of the genus Prosthecobacter. They are formed by the tubulins BtubA and BtubB, which polymerize
in the presence of GTP. Here, we show that the tubulins BtubA/B can
be functionally expressed from DNA templates in a reconstituted transcription-translation
system, thus providing a cytosol-like environment to study their biochemical
and biophysical properties. We found that bMTs spontaneously interact
with lipid membranes and display treadmilling. When compartmentalized
inside liposomes, de novo synthesized BtubA/B tubulins
self-organize into cytoskeletal structures of different morphologies.
Moreover, bMTs can exert a pushing force on the membrane and deform
liposomes, a phenomenon that can be reversed by a light-activated
disassembly of the filaments. Our work establishes bMTs as a new building
block in synthetic biology. In the context of creating a synthetic
cell, bMTs could help shape the lipid compartment, establish polarity
or directional transport, and assist the division machinery.
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Affiliation(s)
- Johannes Kattan
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Anne Doerr
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Marileen Dogterom
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Christophe Danelon
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
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12
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Abstract
Cryo-electron tomography has stepped fully into the spotlight. Enthusiasm is high. Fortunately for us, this is an exciting time to be a cryotomographer, but there is still a way to go before declaring victory. Despite its potential, cryo-electron tomography possesses many inherent challenges. How do we image through thick cell samples, and possibly even tissue? How do we identify a protein of interest amidst the noisy, crowded environment of the cytoplasm? How do we target specific moments of a dynamic cellular process for tomographic imaging? In this review, we cover the history of cryo-electron tomography and how it came to be, roughly speaking, as well as the many approaches that have been developed to overcome its intrinsic limitations.
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Affiliation(s)
- Ryan K. Hylton
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA
| | - Matthew T. Swulius
- Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA
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13
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Devos DP. Reconciling Asgardarchaeota Phylogenetic Proximity to Eukaryotes and Planctomycetes Cellular Features in the Evolution of Life. Mol Biol Evol 2021; 38:3531-3542. [PMID: 34229349 PMCID: PMC8382908 DOI: 10.1093/molbev/msab186] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The relationship between the three domains of life—Archaea, Bacteria, and Eukarya—is one of Biology’s greatest mysteries. Current favored models imply two ancestral domains, Bacteria and Archaea, with eukaryotes originating within Archaea. This type of models has been supported by the recent description of the Asgardarchaeota, the closest prokaryotic relatives of eukaryotes. However, there are many problems associated with any scenarios implying that eukaryotes originated from within the Archaea, including genome mosaicism, phylogenies, the cellular organization of the Archaea, and their ancestral character. By contrast, all models of eukaryogenesis fail to consider two relevant discoveries: the detection of membrane coat proteins, and of phagocytosis-related processes in Planctomycetes, which are among the bacteria with the most developed endomembrane system. Consideration of these often overlooked features and others found in Planctomycetes and related bacteria suggest an evolutionary model based on a single ancestral domain. In this model, the proximity of Asgard and eukaryotes is not rejected but instead, Asgard are considered as diverging away from a common ancestor instead of on the way toward the eukaryotic ancestor. This model based on a single ancestral domain solves most of the ambiguities associated with the ones based on two ancestral domains. The single-domain model is better suited to explain the origin and evolution of all three domains of life, blurring the distinctions between them. Support for this model as well as the opportunities that it presents not only for reinterpreting previous results, but also for planning future experiments, are explored.
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Affiliation(s)
- Damien P Devos
- Centro Andaluz de Biología del Desarrollo (CABD) - CSIC, Junta de Andalucía, Universidad Pablo de Olavide, Carretera de Utrera Km 1, Seville, 41013, Spain
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14
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Jangampalli Adi P, Reddy PH. Phosphorylated tau targeted small-molecule PROTACs for the treatment of Alzheimer's disease and tauopathies. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166162. [PMID: 33940164 DOI: 10.1016/j.bbadis.2021.166162] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/24/2021] [Accepted: 04/26/2021] [Indexed: 10/21/2022]
Abstract
Tau is a microtubule-stabilizing protein that plays an important role in the formation of axonal microtubules in neurons. Phosphorylated tau (p-Tau) has received great attention in the field of Alzheimer's disease (AD) as a potential therapeutic target due to its involvement with synaptic damage and neuronal dysfunction. Mounting evidence suggests that amyloid beta (Aβ)-targeted clinical trials continuously failed; therefore, it is important to consider alternative therapeutic strategies such as p-tau-PROTACs targeted small molecules for AD and other tauopathies. The present article describes the characteristics of tau biology, structure, and function in both healthy and pathological states in AD. It also explains data from studies that have identified the involvement of p-tau in neuronal damage and synaptic and cognitive functions in AD. Current article also covers several aspects, including small molecule inhibitors, and the development of p-tau-PROTACs targeted drug molecules to treat patients with AD and other tauopathies.
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Affiliation(s)
| | - P Hemachandra Reddy
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Department of Pharmacology and Neuroscience, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Department of Neurology, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Department of Public Health, Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Department of Speech, Language, and Hearing Sciences, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA.
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15
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Ji G, Li Q, Shen Y, Gan J, Xu L, Wang Y, Luo H, Yang Y, Dong E, Zhang G, Liu B, Yue X, Zhang W, Yang H. Eradication of large established tumors by drug-loaded bacterial particles via a neutrophil-mediated mechanism. J Control Release 2021; 334:52-63. [PMID: 33878368 DOI: 10.1016/j.jconrel.2021.04.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 03/13/2021] [Accepted: 04/15/2021] [Indexed: 02/08/2023]
Abstract
The treatment of large established tumors remains a significant challenge and is generally hampered by poor drug penetration and intrinsic drug resistance of tumor cells in the central tumor region. In the present study, we developed bacterial particles (BactPs) to deliver chemotherapeutics into the tumor mass by hijacking neutrophils as natural cell-based carriers. BactPs loaded with doxorubicin, 5-fluorosuracil, or paclitaxel induced significantly greater tumor regression than unconjugated drugs. This effect was mediated by the ability of BactPs to incorporate chemotherapeutics and serve as vascular disrupting agents that trigger innate host responses and recruit phagocytic neutrophils. Vascular disruption resulted in extensive cell death in the central areas of the tumor mass. Recruited neutrophils acted as natural cellular carriers to deliver engulfed BactPs, which ensured drug delivery into the tumor mass and cytotoxic effects in areas that are normally inaccessible to traditional chemotherapy. Thus, BactPs eradicate large established tumors by functioning as vascular disrupters and natural drug carriers for neutrophil-mediated chemotherapy.
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Affiliation(s)
- Gaili Ji
- State Key Laboratory of Biotherapy and Cancer center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Qiqi Li
- State Key Laboratory of Biotherapy and Cancer center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Yuge Shen
- State Key Laboratory of Biotherapy and Cancer center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Jia Gan
- State Key Laboratory of Biotherapy and Cancer center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Lin Xu
- State Key Laboratory of Biotherapy and Cancer center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Yuxi Wang
- Department of Respiratory and Critical Care Medicine, West China Medical School/West China Hospital, Sichuan University, Chengdu, China
| | - Hui Luo
- State Key Laboratory of Biotherapy and Cancer center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Yun Yang
- State Key Laboratory of Biotherapy and Cancer center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - E Dong
- State Key Laboratory of Biotherapy and Cancer center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Guimin Zhang
- State Key Laboratory of Biotherapy and Cancer center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Binrui Liu
- State Key Laboratory of Biotherapy and Cancer center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Xiaozhu Yue
- State Key Laboratory of Biotherapy and Cancer center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Wei Zhang
- Molecular Medicine Research Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China.
| | - Hanshuo Yang
- State Key Laboratory of Biotherapy and Cancer center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China; Experimental and Research Animal Institute, Sichuan University, Chengdu 610041, China.
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16
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Chumová J, Kourová H, Trögelová L, Daniel G, Binarová P. γ-Tubulin Complexes and Fibrillar Arrays: Two Conserved High Molecular Forms with Many Cellular Functions. Cells 2021; 10:cells10040776. [PMID: 33915825 PMCID: PMC8066788 DOI: 10.3390/cells10040776] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 03/29/2021] [Accepted: 03/30/2021] [Indexed: 11/29/2022] Open
Abstract
Higher plants represent a large group of eukaryotes where centrosomes are absent. The functions of γ-tubulin small complexes (γ-TuSCs) and γ-tubulin ring complexes (γ-TuRCs) in metazoans and fungi in microtubule nucleation are well established and the majority of components found in the complexes are present in plants. However, plant microtubules are also nucleated in a γ-tubulin-dependent but γ-TuRC-independent manner. There is growing evidence that γ-tubulin is a microtubule nucleator without being complexed in γ-TuRC. Fibrillar arrays of γ-tubulin were demonstrated in plant and animal cells and the ability of γ-tubulin to assemble into linear oligomers/polymers was confirmed in vitro for both native and recombinant γ-tubulin. The functions of γ-tubulin as a template for microtubule nucleation or in promoting spontaneous nucleation is outlined. Higher plants represent an excellent model for studies on the role of γ-tubulin in nucleation due to their acentrosomal nature and high abundancy and conservation of γ-tubulin including its intrinsic ability to assemble filaments. The defining scaffolding or sequestration functions of plant γ-tubulin in microtubule organization or in nuclear processes will help our understanding of its cellular roles in eukaryotes.
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Affiliation(s)
- Jana Chumová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská1083, 142 20 Prague, Czech Republic; (J.C.); (H.K.); (L.T.)
| | - Hana Kourová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská1083, 142 20 Prague, Czech Republic; (J.C.); (H.K.); (L.T.)
| | - Lucie Trögelová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská1083, 142 20 Prague, Czech Republic; (J.C.); (H.K.); (L.T.)
| | - Geoffrey Daniel
- Department of Biomaterials and Technology/Wood Science, Swedish University of Agricultural Sciences, 750-07 Uppsala, Sweden;
| | - Pavla Binarová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská1083, 142 20 Prague, Czech Republic; (J.C.); (H.K.); (L.T.)
- Correspondence: ; Tel.: +420-241-062-130
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17
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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: 1.2] [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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18
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Jung W, Li J, Chaudhuri O, Kim T. Nonlinear Elastic and Inelastic Properties of Cells. J Biomech Eng 2020; 142:100806. [PMID: 32253428 PMCID: PMC7477719 DOI: 10.1115/1.4046863] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 03/27/2020] [Indexed: 12/15/2022]
Abstract
Mechanical forces play an important role in various physiological processes, such as morphogenesis, cytokinesis, and migration. Thus, in order to illuminate mechanisms underlying these physiological processes, it is crucial to understand how cells deform and respond to external mechanical stimuli. During recent decades, the mechanical properties of cells have been studied extensively using diverse measurement techniques. A number of experimental studies have shown that cells are far from linear elastic materials. Cells exhibit a wide variety of nonlinear elastic and inelastic properties. Such complicated properties of cells are known to emerge from unique mechanical characteristics of cellular components. In this review, we introduce major cellular components that largely govern cell mechanical properties and provide brief explanations of several experimental techniques used for rheological measurements of cell mechanics. Then, we discuss the representative nonlinear elastic and inelastic properties of cells. Finally, continuum and discrete computational models of cell mechanics, which model both nonlinear elastic and inelastic properties of cells, will be described.
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Affiliation(s)
- Wonyeong Jung
- Weldon School of Biomedical Engineering, Purdue University, 206 S. Martin Jischke Drive, West Lafayette, IN 47907
| | - Jing Li
- Weldon School of Biomedical Engineering, Purdue University, 206 S. Martin Jischke Drive, West Lafayette, IN 47907
| | - Ovijit Chaudhuri
- Department of Mechanical Engineering, Stanford University, 440 Escondido Mall, Stanford, CA 94305
| | - Taeyoon Kim
- Weldon School of Biomedical Engineering, Purdue University, 206 S. Martin Jischke Drive, West Lafayette, IN 47907
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19
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Forkosh E, Kenig A, Ilan Y. Introducing variability in targeting the microtubules: Review of current mechanisms and future directions in colchicine therapy. Pharmacol Res Perspect 2020; 8:e00616. [PMID: 32608157 PMCID: PMC7327382 DOI: 10.1002/prp2.616] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 05/25/2020] [Indexed: 12/14/2022] Open
Abstract
Microtubules (MTs) are highly dynamic polymers that constitute the cellular cytoskeleton and play a role in multiple cellular functions. Variability characterizes biological systems and is considered a part of the normal function of cells and organs. Variability contributes to cell plasticity and is a mechanism for overcoming errors in cellular level assembly and function, and potentially the whole organ level. Dynamic instability is a feature of biological variability that characterizes the function of MTs. The dynamic behavior of MTs constitutes the basis for multiple biological processes that contribute to cellular plasticity and the timing of cell signaling. Colchicine is a MT-modifying drug that exerts anti-inflammatory and anti-cancer effects. This review discusses some of the functions of colchicine and presents a platform for introducing variability while targeting MTs in intestinal cells, the microbiome, the gut, and the systemic immune system. This platform can be used for implementing novel therapies, improving response to chronic MT-based therapies, overcoming drug resistance, exerting gut-based systemic immune responses, and generating patient-tailored dynamic therapeutic regimens.
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Affiliation(s)
- Esther Forkosh
- Department of MedicineHebrew University‐Hadassah Medical CentreJerusalemIsrael
| | - Ariel Kenig
- Department of MedicineHebrew University‐Hadassah Medical CentreJerusalemIsrael
| | - Yaron Ilan
- Department of MedicineHebrew University‐Hadassah Medical CentreJerusalemIsrael
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20
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Wagner FR, Watanabe R, Schampers R, Singh D, Persoon H, Schaffer M, Fruhstorfer P, Plitzko J, Villa E. Preparing samples from whole cells using focused-ion-beam milling for cryo-electron tomography. Nat Protoc 2020; 15:2041-2070. [PMID: 32405053 PMCID: PMC8053421 DOI: 10.1038/s41596-020-0320-x] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 03/06/2020] [Indexed: 12/31/2022]
Abstract
Recent advances have made cryogenic (cryo) electron microscopy a key technique to achieve near-atomic-resolution structures of biochemically isolated macromolecular complexes. Cryo-electron tomography (cryo-ET) can give unprecedented insight into these complexes in the context of their natural environment. However, the application of cryo-ET is limited to samples that are thinner than most cells, thereby considerably reducing its applicability. Cryo-focused-ion-beam (cryo-FIB) milling has been used to carve (micromachining) out 100-250-nm-thin regions (called lamella) in the intact frozen cells. This procedure opens a window into the cells for high-resolution cryo-ET and structure determination of biomolecules in their native environment. Further combination with fluorescence microscopy allows users to determine cells or regions of interest for the targeted fabrication of lamellae and cryo-ET imaging. Here, we describe how to prepare lamellae using a microscope equipped with both FIB and scanning electron microscopy modalities. Such microscopes (Aquilos Cryo-FIB/Scios/Helios or CrossBeam) are routinely referred to as dual-beam microscopes, and they are equipped with a cryo-stage for all operations in cryogenic conditions. The basic principle of the described methodologies is also applicable for other types of dual-beam microscopes equipped with a cryo-stage. We also briefly describe how to integrate fluorescence microscopy data for targeted milling and critical considerations for cryo-ET data acquisition of the lamellae. Users familiar with cryo-electron microscopy who get basic training in dual-beam microscopy can complete the protocol within 2-3 d, allowing for several pause points during the procedure.
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Affiliation(s)
- Felix R Wagner
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
- Department of Molecular Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
| | - Reika Watanabe
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | | | - Digvijay Singh
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Hans Persoon
- Thermo Fisher Scientific, Eindhoven, the Netherlands
| | - Miroslava Schaffer
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Peter Fruhstorfer
- Thermo Fisher Scientific, Eindhoven, the Netherlands
- Eppendorf AG, Hamburg, Germany
| | - Jürgen Plitzko
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Elizabeth Villa
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA.
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21
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Cavalier-Smith T, Chao EEY. Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria). PROTOPLASMA 2020. [PMID: 31900730 DOI: 10.1007/s00709-019-01442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Palaeontologically, eubacteria are > 3× older than neomura (eukaryotes, archaebacteria). Cell biology contrasts ancestral eubacterial murein peptidoglycan walls and derived neomuran N-linked glycoprotein coats/walls. Misinterpreting long stems connecting clade neomura to eubacteria on ribosomal sequence trees (plus misinterpreted protein paralogue trees) obscured this historical pattern. Universal multiprotein ribosomal protein (RP) trees, more accurate than rRNA trees, are taxonomically undersampled. To reduce contradictions with genically richer eukaryote trees and improve eubacterial phylogeny, we constructed site-heterogeneous and maximum-likelihood universal three-domain, two-domain, and single-domain trees for 143 eukaryotes (branching now congruent with 187-protein trees), 60 archaebacteria, and 151 taxonomically representative eubacteria, using 51 and 26 RPs. Site-heterogeneous trees greatly improve eubacterial phylogeny and higher classification, e.g. showing gracilicute monophyly, that many 'rDNA-phyla' belong in Proteobacteria, and reveal robust new phyla Synthermota and Aquithermota. Monoderm Posibacteria and Mollicutes (two separate wall losses) are both polyphyletic: multiple outer membrane losses in Endobacteria occurred separately from Actinobacteria; neither phylum is related to Chloroflexi, the most divergent prokaryotes, which originated photosynthesis (new model proposed). RP trees support an eozoan root for eukaryotes and are consistent with archaebacteria being their sisters and rooted between Filarchaeota (=Proteoarchaeota, including 'Asgardia') and Euryarchaeota sensu-lato (including ultrasimplified 'DPANN' whose long branches often distort trees). Two-domain trees group eukaryotes within Planctobacteria, and archaebacteria with Planctobacteria/Sphingobacteria. Integrated molecular/palaeontological evidence favours negibacterial ancestors for neomura and all life. Unique presence of key pre-neomuran characters favours Planctobacteria only as ancestral to neomura, which apparently arose by coevolutionary repercussions (explained here in detail, including RP replacement) of simultaneous outer membrane and murein loss. Planctobacterial C-1 methanotrophic enzymes are likely ancestral to archaebacterial methanogenesis and β-propeller-α-solenoid proteins to eukaryotic vesicle coats, nuclear-pore-complexes, and intraciliary transport. Planctobacterial chaperone-independent 4/5-protofilament microtubules and MamK actin-ancestors prepared for eukaryote intracellular motility, mitosis, cytokinesis, and phagocytosis. We refute numerous wrong ideas about the universal tree.
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Affiliation(s)
| | - Ema E-Yung Chao
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
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22
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Cavalier-Smith T, Chao EEY. Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria). PROTOPLASMA 2020; 257:621-753. [PMID: 31900730 PMCID: PMC7203096 DOI: 10.1007/s00709-019-01442-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 09/19/2019] [Indexed: 05/02/2023]
Abstract
Palaeontologically, eubacteria are > 3× older than neomura (eukaryotes, archaebacteria). Cell biology contrasts ancestral eubacterial murein peptidoglycan walls and derived neomuran N-linked glycoprotein coats/walls. Misinterpreting long stems connecting clade neomura to eubacteria on ribosomal sequence trees (plus misinterpreted protein paralogue trees) obscured this historical pattern. Universal multiprotein ribosomal protein (RP) trees, more accurate than rRNA trees, are taxonomically undersampled. To reduce contradictions with genically richer eukaryote trees and improve eubacterial phylogeny, we constructed site-heterogeneous and maximum-likelihood universal three-domain, two-domain, and single-domain trees for 143 eukaryotes (branching now congruent with 187-protein trees), 60 archaebacteria, and 151 taxonomically representative eubacteria, using 51 and 26 RPs. Site-heterogeneous trees greatly improve eubacterial phylogeny and higher classification, e.g. showing gracilicute monophyly, that many 'rDNA-phyla' belong in Proteobacteria, and reveal robust new phyla Synthermota and Aquithermota. Monoderm Posibacteria and Mollicutes (two separate wall losses) are both polyphyletic: multiple outer membrane losses in Endobacteria occurred separately from Actinobacteria; neither phylum is related to Chloroflexi, the most divergent prokaryotes, which originated photosynthesis (new model proposed). RP trees support an eozoan root for eukaryotes and are consistent with archaebacteria being their sisters and rooted between Filarchaeota (=Proteoarchaeota, including 'Asgardia') and Euryarchaeota sensu-lato (including ultrasimplified 'DPANN' whose long branches often distort trees). Two-domain trees group eukaryotes within Planctobacteria, and archaebacteria with Planctobacteria/Sphingobacteria. Integrated molecular/palaeontological evidence favours negibacterial ancestors for neomura and all life. Unique presence of key pre-neomuran characters favours Planctobacteria only as ancestral to neomura, which apparently arose by coevolutionary repercussions (explained here in detail, including RP replacement) of simultaneous outer membrane and murein loss. Planctobacterial C-1 methanotrophic enzymes are likely ancestral to archaebacterial methanogenesis and β-propeller-α-solenoid proteins to eukaryotic vesicle coats, nuclear-pore-complexes, and intraciliary transport. Planctobacterial chaperone-independent 4/5-protofilament microtubules and MamK actin-ancestors prepared for eukaryote intracellular motility, mitosis, cytokinesis, and phagocytosis. We refute numerous wrong ideas about the universal tree.
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Affiliation(s)
| | - Ema E-Yung Chao
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
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23
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Bonandi E, Foschi F, Marucci C, Dapiaggi F, Sironi M, Pieraccini S, Christodoulou MS, de Asís Balaguer F, Díaz JF, Zidar N, Passarella D. Synthesis of Thicolchicine-Based Conjugates: Investigation towards Bivalent Tubulin/Microtubules Binders. Chempluschem 2020; 84:98-102. [PMID: 31950734 DOI: 10.1002/cplu.201800497] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 11/29/2018] [Indexed: 12/28/2022]
Abstract
Four different hybrid compounds have been efficiently synthesized by conjugation of deacetylthiocolchicine with pironetin-inspired derivatives. The modest bioactivity and the apparent absence of interaction with α-tubulin is explained by a posteriori in silico investigation, which suggests a relevant distance between the thiocolchicine binding site and the proper pocket on the α-tubulin. The modest activity on resistant cells suggested that the lipophilic nature of the linker used renders the resulting compounds better substrates for p-Gp efflux pumps. The study better clarifies the design of bivalent compounds that target hetero tubulin/microtubules.
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Affiliation(s)
- Elisa Bonandi
- Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133, Milano, Italy
| | - Francesca Foschi
- Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133, Milano, Italy
| | - Cristina Marucci
- Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133, Milano, Italy
| | - Federico Dapiaggi
- Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133, Milano, Italy
| | - Maurizio Sironi
- Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133, Milano, Italy
| | - Stefano Pieraccini
- Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133, Milano, Italy
| | - Michael S Christodoulou
- Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133, Milano, Italy.,Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, via Golgi 19, 20133, Milano, Italy
| | - Francisco de Asís Balaguer
- Chemical and Physical Biology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Cientificas CIB-CSIC, Madrid, 28040, Spain
| | - J Fernando Díaz
- Chemical and Physical Biology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Cientificas CIB-CSIC, Madrid, 28040, Spain
| | - Nace Zidar
- Faculty of Pharmacy, University of Ljubljana, Askerceva cesta 7, 1000, Ljubljana, Slovenia
| | - Daniele Passarella
- Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133, Milano, Italy
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24
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Li T, Tang H, Zhu J, Zhang JH. The finer scale of consciousness: quantum theory. ANNALS OF TRANSLATIONAL MEDICINE 2019; 7:585. [PMID: 31807566 DOI: 10.21037/atm.2019.09.09] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Consciousness is a multidisciplinary problem that has puzzled all human beings since the origin of human life. Being defined in various pointcuts by philosophers, biologists, physicists, and neuroscientists, the definitive explanation of consciousness is still suspending. The nature of consciousness has taken great evolution by centering on the behavioral and neuronal correlates of perception and cognition, for example, the theory of Neural Correlates of Consciousness, the Global Workspace Theory, the Integrated Information Theory. While tremendous progress has been achieved, they are not enough if we are to understand even basic facts-how and where does the consciousness emerge. The Quantum mechanics, a thriving branch of physics, has an inseparable relationship with consciousness (e.g., observer effect) since Planck created this subject and its derived quantum consciousness theory can perfectly fill this gap. In this review, we briefly introduce some consciousness hypotheses derived from quantum mechanics and focus on the framework of orchestrated objective reduction (Orch-OR), including its principal points and practicality.
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Affiliation(s)
- Tianwen Li
- Department of Neurosurgery, Fudan University Huashan Hospital, National Key Laboratory of Medical Neurobiology, the Institutes of Brain Science and the Collaborative Innovation Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai 200040, China
| | - Hailiang Tang
- Department of Neurosurgery, Fudan University Huashan Hospital, National Key Laboratory of Medical Neurobiology, the Institutes of Brain Science and the Collaborative Innovation Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai 200040, China
| | - Jianhong Zhu
- Department of Neurosurgery, Fudan University Huashan Hospital, National Key Laboratory of Medical Neurobiology, the Institutes of Brain Science and the Collaborative Innovation Center for Brain Science, Shanghai Medical College, Fudan University, Shanghai 200040, China
| | - John H Zhang
- Center for Neuroscience Research, Loma Linda University School of Medicine, Loma Linda, CA, USA
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25
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Abstract
For automated acquisition of tilt series for electron tomography, software needs to handle complications such as movements of the sample in x/y and z, increased projected thickness at high tilt, specimen drift, etc. In addition, many applications require special functionality such as low dose acquisition, automated sequential (batch) tomography, or montage tomography. After reviewing how these difficulties can be addressed and a closer look at what advanced acquisition strategies are employed in biosciences, this chapter introduces acquisition software both developed in academia as well as by hardware vendors. It covers the hardware requirements and compatibility, the functional principle and workflow implemented, as well as what advanced functions are supported by the individual programs.
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Affiliation(s)
- Guenter P Resch
- Nexperion e.U.-Solutions for Electron Microscopy, Vienna, Austria.
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26
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Ilan-Ber T, Ilan Y. The role of microtubules in the immune system and as potential targets for gut-based immunotherapy. Mol Immunol 2019; 111:73-82. [DOI: 10.1016/j.molimm.2019.04.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/11/2019] [Accepted: 04/23/2019] [Indexed: 12/18/2022]
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27
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Campos AI, Zampieri M. Metabolomics-Driven Exploration of the Chemical Drug Space to Predict Combination Antimicrobial Therapies. Mol Cell 2019; 74:1291-1303.e6. [PMID: 31047795 PMCID: PMC6591011 DOI: 10.1016/j.molcel.2019.04.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 12/27/2018] [Accepted: 03/28/2019] [Indexed: 01/12/2023]
Abstract
Alternative to the conventional search for single-target, single-compound treatments, combination therapies can open entirely new opportunities to fight antibiotic resistance. However, combinatorial complexity prohibits experimental testing of drug combinations on a large scale, and methods to rationally design combination therapies are lagging behind. Here, we developed a combined experimental-computational approach to predict drug-drug interactions using high-throughput metabolomics. The approach was tested on 1,279 pharmacologically diverse drugs applied to the gram-negative bacterium Escherichia coli. Combining our metabolic profiling of drug response with previously generated metabolic and chemogenomic profiles of 3,807 single-gene deletion strains revealed an unexpectedly large space of inhibited gene functions and enabled rational design of drug combinations. This approach is applicable to other therapeutic areas and can unveil unprecedented insights into drug tolerance, side effects, and repurposing. The compendium of drug-associated metabolome profiles is available at https://zampierigroup.shinyapps.io/EcoPrestMet, providing a valuable resource for the microbiological and pharmacological communities.
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Affiliation(s)
- Adrian I Campos
- Institute of Molecular Systems Biology, ETH Zurich, Otto-Stern-Weg 3, 8093 Zurich, Switzerland
| | - Mattia Zampieri
- Institute of Molecular Systems Biology, ETH Zurich, Otto-Stern-Weg 3, 8093 Zurich, Switzerland.
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28
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Nguyen LT, Oikonomou CM, Ding HJ, Kaplan M, Yao Q, Chang YW, Beeby M, Jensen GJ. Simulations suggest a constrictive force is required for Gram-negative bacterial cell division. Nat Commun 2019; 10:1259. [PMID: 30890709 PMCID: PMC6425016 DOI: 10.1038/s41467-019-09264-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 02/28/2019] [Indexed: 11/16/2022] Open
Abstract
To divide, Gram-negative bacterial cells must remodel cell wall at the division site. It remains debated, however, whether this cell wall remodeling alone can drive membrane constriction, or if a constrictive force from the tubulin homolog FtsZ is required. Previously, we constructed software (REMODELER 1) to simulate cell wall remodeling during growth. Here, we expanded this software to explore cell wall division (REMODELER 2). We found that simply organizing cell wall synthesis complexes at the midcell is not sufficient to cause invagination, even with the implementation of a make-before-break mechanism, in which new hoops of cell wall are made inside the existing hoops before bonds are cleaved. Division can occur, however, when a constrictive force brings the midcell into a compressed state before new hoops of relaxed cell wall are incorporated between existing hoops. Adding a make-before-break mechanism drives division with a smaller constrictive force sufficient to bring the midcell into a relaxed, but not necessarily compressed, state.
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Affiliation(s)
- Lam T Nguyen
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA, 91125, USA
| | - Catherine M Oikonomou
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA, 91125, USA
| | - H Jane Ding
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA, 91125, USA
| | - Mohammed Kaplan
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA, 91125, USA
| | - Qing Yao
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA, 91125, USA
| | - Yi-Wei Chang
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA, 91125, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 422 Curie Boulevard, Philadelphia, PA, 19104, USA
| | - Morgan Beeby
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA, 91125, USA
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA, 91125, USA.
- Howard Hughes Medical Institute, 1200 E. California Boulevard, Pasadena, CA, 91125, USA.
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29
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Chumová J, Kourová H, Trögelová L, Halada P, Binarová P. Microtubular and Nuclear Functions of γ-Tubulin: Are They LINCed? Cells 2019; 8:cells8030259. [PMID: 30893853 PMCID: PMC6468392 DOI: 10.3390/cells8030259] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 03/07/2019] [Accepted: 03/14/2019] [Indexed: 01/02/2023] Open
Abstract
γ-Tubulin is a conserved member of the tubulin superfamily with a function in microtubule nucleation. Proteins of γ-tubulin complexes serve as nucleation templates as well as a majority of other proteins contributing to centrosomal and non-centrosomal nucleation, conserved across eukaryotes. There is a growing amount of evidence of γ-tubulin functions besides microtubule nucleation in transcription, DNA damage response, chromatin remodeling, and on its interactions with tumor suppressors. However, the molecular mechanisms are not well understood. Furthermore, interactions with lamin and SUN proteins of the LINC complex suggest the role of γ-tubulin in the coupling of nuclear organization with cytoskeletons. γ-Tubulin that belongs to the clade of eukaryotic tubulins shows characteristics of both prokaryotic and eukaryotic tubulins. Both human and plant γ-tubulins preserve the ability of prokaryotic tubulins to assemble filaments and higher-order fibrillar networks. γ-Tubulin filaments, with bundling and aggregating capacity, are suggested to perform complex scaffolding and sequestration functions. In this review, we discuss a plethora of γ-tubulin molecular interactions and cellular functions, as well as recent advances in understanding the molecular mechanisms behind them.
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Affiliation(s)
- Jana Chumová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic.
| | - Hana Kourová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic.
| | - Lucie Trögelová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic.
| | - Petr Halada
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic.
| | - Pavla Binarová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic.
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30
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Pradeepkiran JA, Reddy AP, Reddy PH. Pharmacophore-based models for therapeutic drugs against phosphorylated tau in Alzheimer's disease. Drug Discov Today 2018; 24:616-623. [PMID: 30453058 DOI: 10.1016/j.drudis.2018.11.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Revised: 09/22/2018] [Accepted: 11/07/2018] [Indexed: 10/27/2022]
Abstract
Phosphorylated tau (P-tau) has received much attention in the field of Alzheimer's disease (AD), as a potential therapeutic target owing to its involvement with synaptic damage and neuronal dysfunction. The continuous failure of amyloid β (Aβ)-targeted therapeutics highlights the urgency to consider alternative therapeutic strategies for AD. The present review describes the latest developments in tau biology and function. It also explains abnormal interactions between P-tau with Aβ and the mitochondrial fission protein Drp1, leading to excessive mitochondrial fragmentation and synaptic damage in AD neurons. This article also addresses 3D pharmacophore-based drug models designed to treat patients with AD and other tauopathies.
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Affiliation(s)
- Jangampalli Adi Pradeepkiran
- Garrison Institute on Aging, Texas Tech University Health Sciences Center, 3601 4th Street, MS 9424, Lubbock, TX 79430, USA
| | - Arubala P Reddy
- Pharmacology & Neuroscience Department, Texas Tech University Health Sciences Center, 3601 4th Street, MS 9424, Lubbock, TX 79430, USA
| | - P Hemachandra Reddy
- Garrison Institute on Aging, Texas Tech University Health Sciences Center, 3601 4th Street, MS 9424, Lubbock, TX 79430, USA; Cell Biology & Biochemistry Department, Texas Tech University Health Sciences Center, 3601 4th Street, MS 9424, Lubbock, TX 79430, USA; Pharmacology & Neuroscience Department, Texas Tech University Health Sciences Center, 3601 4th Street, MS 9424, Lubbock, TX 79430, USA; Neurology Department, Texas Tech University Health Sciences Center, 3601 4th Street, MS 9424, Lubbock, TX 79430, USA; Speech, Language and Hearing Sciences Departments, Texas Tech University Health Sciences Center, 3601 4th Street, MS 9424, Lubbock, TX 79430, USA; Garrison Institute on Aging, South West Campus, Texas Tech University Health Sciences Center, 6630 S. Quaker Suite E, MS 7495, Lubbock, TX 79413, USA.
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31
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Kim KW. Prokaryotic cytoskeletons: in situ and ex situ structures and cellular locations. Antonie van Leeuwenhoek 2018; 112:145-157. [PMID: 30128891 DOI: 10.1007/s10482-018-1142-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 08/11/2018] [Indexed: 01/12/2023]
Abstract
Cytoskeletons have long been perceived to be present only in eukaryotes. However, this notion changed drastically in the 1990s, with observations of cytoskeleton-like structures in several prokaryotes. Homologs of the main components of eukaryotic cytoskeletons, such as microtubules, microfilaments, and intermediate filaments, have been identified in bacteria and archaea. Tubulin homologs include filamenting temperature-sensitive mutant Z (FtsZ), bacterial tubulin A/B (BtubA/B), and tubulin/FtsZ-like protein (TubZ), whereas actin homologs comprise murein region B (MreB) and crenactin. Unlike other proteins, crescentin (CreS) is a homolog of intermediate filaments. Recent findings elucidated their localization, structural organization, and helical properties in prokaryotes, thus revising traditional models. FtsZ is involved in cell division, forming a bundle of overlapping filaments that cover the entire division plane. Cryogenic transmission electron microscopy identified tubular structures of BtubA/B that were not previously identified using conventional ultrathin plastic sections. TubZ generates two joint filaments to form a quadruplex structure. After a long debate, MreB, a cell shape determinant, was shown to form filament stretches that move circumferentially around rod-shaped bacteria. Initially characterized as single-stranded, crenactin was eventually identified as right-handed double-stranded helical filaments. CreS, another cell shape determinant, forms filament bundles located inside the inner membrane of the concave side of cells. These observations suggest that the use of in situ or ex situ microscopy in combination with structural analysis techniques will enable the elucidation and further understanding of the current models of prokaryotic cytoskeletons.
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Affiliation(s)
- Ki Woo Kim
- School of Ecology and Environmental System, Kyungpook National University, Sangju, 37224, Korea. .,Tree Diagnostic Center, Kyungpook National University, Sangju, 37224, Korea.
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32
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Reddy JSK, Pereira C. Understanding the emergence of microbial consciousness: From a perspective of the Subject-Object Model (SOM). J Integr Neurosci 2018; 16:S27-S36. [PMID: 29254105 DOI: 10.3233/jin-170064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Microorganisms demonstrate conscious-like intelligent behaviour, and this form of consciousness may have emerged from a quantum mediated mechanism as observed in cytoskeletal structures like the microtubules present in nerve cells which apparently have the architecture to quantum compute. This paper hypothesises the emergence of proto-consciousness in primitive cytoskeletal systems found in the microbial kingdoms of archaea, bacteria and eukarya. To explain this, we make use of the Subject-Object Model (SOM) of consciousness which evaluates the rise of the degree of consciousness to conscious behaviour in these systems supporting the hypothesis of emergence and propagation of conscious behaviour during the pre-Cambrian part of Earth's evolutionary history. Consciousness as proto-consciousness or sentience computed via primitive cytoskeletal structures substantiates as a driver for the intelligence observed in the microbial world during this period ranging from single-cellular to collective intelligence as a means to adapt and survive. The growth in complexity of intelligence, cytoskeletal system and adaptive behaviours are key to evolution, and thus supports the progression of the Lamarckian theory of evolution driven by quantum mediated proto-consciousness to consciousness as described in the SOM of consciousness.
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33
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Dey S, Ching K, Das M. Active and passive transport of cargo in a corrugated channel: A lattice model study. J Chem Phys 2018; 148:134907. [PMID: 29626914 DOI: 10.1063/1.5022163] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Inside cells, cargos such as vesicles and organelles are transported by molecular motors to their correct locations via active motion on cytoskeletal tracks and passive, Brownian diffusion. During the transportation of cargos, motor-cargo complexes (MCCs) navigate the confining and crowded environment of the cytoskeletal network and other macromolecules. Motivated by this, we study a minimal two-state model of motor-driven cargo transport in confinement and predict transport properties that can be tested in experiments. We assume that the motion of the MCC is directly affected by the entropic barrier due to confinement if it is in the passive, unbound state but not in the active, bound state where it moves with a constant bound velocity. We construct a lattice model based on a Fokker Planck description of the two-state system, study it using a kinetic Monte Carlo method and compare our numerical results with analytical expressions for a mean field limit. We find that the effect of confinement strongly depends on the bound velocity and the binding kinetics of the MCC. Confinement effectively reduces the effective diffusivity and average velocity, except when it results in an enhanced average binding rate and thereby leads to a larger average velocity than when unconfined.
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Affiliation(s)
- Supravat Dey
- School of Physics and Astronomy, Rochester Institute of Technology, Rochester, New York 14623, USA
| | - Kevin Ching
- School of Physics and Astronomy, Rochester Institute of Technology, Rochester, New York 14623, USA
| | - Moumita Das
- School of Physics and Astronomy, Rochester Institute of Technology, Rochester, New York 14623, USA
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34
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Cyrklaff M, Frischknecht F, Kudryashev M. Functional insights into pathogen biology from 3D electron microscopy. FEMS Microbiol Rev 2018; 41:828-853. [PMID: 28962014 DOI: 10.1093/femsre/fux041] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 07/25/2017] [Indexed: 01/10/2023] Open
Abstract
In recent years, novel imaging approaches revolutionised our understanding of the cellular and molecular biology of microorganisms. These include advances in fluorescent probes, dynamic live cell imaging, superresolution light and electron microscopy. Currently, a major transition in the experimental approach shifts electron microscopy studies from a complementary technique to a method of choice for structural and functional analysis. Here we review functional insights into the molecular architecture of viruses, bacteria and parasites as well as interactions with their respective host cells gained from studies using cryogenic electron tomography and related methodologies.
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Affiliation(s)
- Marek Cyrklaff
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Friedrich Frischknecht
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Mikhail Kudryashev
- Max Planck Institute of Biophysics, Max-von-Laue Strasse 3, 60438 Frankfurt, Germany.,Buchmann Institute for Molecular Life Sciences, Goethe University of Frankfurt, Max-von-Laue Strasse 17, 60438 Frankfurt, Germany
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35
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Chaaban S, Brouhard GJ. A microtubule bestiary: structural diversity in tubulin polymers. Mol Biol Cell 2018; 28:2924-2931. [PMID: 29084910 PMCID: PMC5662251 DOI: 10.1091/mbc.e16-05-0271] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 08/30/2017] [Accepted: 09/06/2017] [Indexed: 11/11/2022] Open
Abstract
Microtubules are long, slender polymers of αβ-tubulin found in all eukaryotic cells. Tubulins associate longitudinally to form protofilaments, and adjacent protofilaments associate laterally to form the microtubule. In the textbook view, microtubules are 1) composed of 13 protofilaments, 2) arranged in a radial array by the centrosome, and 3) built into the 9+2 axoneme. Although these canonical structures predominate in eukaryotes, microtubules with divergent protofilament numbers and higher-order microtubule assemblies have been discovered throughout the last century. Here we survey these noncanonical structures, from the 4-protofilament microtubules of Prosthecobacter to the 40-protofilament accessory microtubules of mantidfly sperm. We review the variety of protofilament numbers observed in different species, in different cells within the same species, and in different stages within the same cell. We describe the determinants of protofilament number, namely nucleation factors, tubulin isoforms, and posttranslational modifications. Finally, we speculate on the functional significance of these diverse polymers. Equipped with novel tubulin-purification tools, the field is now prepared to tackle the long-standing question of the evolutionary basis of microtubule structure.
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Affiliation(s)
- Sami Chaaban
- Department of Biology, McGill University, Montreal, QC H3A 1B1, Canada
| | - Gary J Brouhard
- Department of Biology, McGill University, Montreal, QC H3A 1B1, Canada
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36
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Chumová J, Trögelová L, Kourová H, Volc J, Sulimenko V, Halada P, Kučera O, Benada O, Kuchařová A, Klebanovych A, Dráber P, Daniel G, Binarová P. γ-Tubulin has a conserved intrinsic property of self-polymerization into double stranded filaments and fibrillar networks. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2018; 1865:734-748. [PMID: 29499229 DOI: 10.1016/j.bbamcr.2018.02.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 02/22/2018] [Accepted: 02/23/2018] [Indexed: 12/22/2022]
Abstract
γ-Tubulin is essential for microtubule nucleation and also plays less understood roles in nuclear and cell-cycle-related functions. High abundancy of γ-tubulin in acentrosomal Arabidopsis cells facilitated purification and biochemical characterization of large molecular species of γ-tubulin. TEM, fluorescence, and atomic force microscopy of purified high molecular γ-tubulin forms revealed the presence of linear filaments with a double protofilament substructure, filament bundles and aggregates. Filament formation from highly purified γ-tubulin free of γ-tubulin complex proteins (GCPs) was demonstrated for both plant and human γ-tubulin. Moreover, γ-tubulin associated with porcine brain microtubules formed oligomers. Experimental evidence on the intrinsic ability of γ-tubulin to oligomerize/polymerize was supported by conservation of α- and β-tubulin interfaces for longitudinal and lateral interactions for γ-tubulins. STED (stimulated emission depletion) microscopy of Arabidopsis cells revealed fine, short γ-tubulin fibrillar structures enriched on mitotic microtubular arrays that accumulated at polar regions of acentrosomal spindles and the outer nuclear envelope before mitosis, and were also present in nuclei. Fine fibrillar structures of γ-tubulin representing assemblies of higher order were localized in cell-cycle-dependent manner at sites of dispersed γ-tubulin location in acentrosomal plant cells as well as at sites of local γ-tubulin enrichment after drug treatment. Our findings that γ-tubulin preserves the capability of prokaryotic tubulins to self-organize into filaments assembling by lateral interaction into bundles/clusters help understanding of the relationship between structure and multiple cellular functions of this protein species and suggest that besides microtubule nucleation and organization, γ-tubulin may also have scaffolding or sequestration functions.
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Affiliation(s)
- Jana Chumová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Lucie Trögelová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Hana Kourová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Jindřich Volc
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Vadym Sulimenko
- Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Petr Halada
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Ondřej Kučera
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Chaberská 57, 182 00 Prague 8, Czech Republic
| | - Oldřich Benada
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Anna Kuchařová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Anastasiya Klebanovych
- Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Pavel Dráber
- Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Geoffrey Daniel
- Department of Forest Biomaterials Technology, Swedish University of Agricultural Sciences, Box 7008, Uppsala SE-75007, Sweden
| | - Pavla Binarová
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague 4, Czech Republic.
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Shaaban M, Issa MY, Ghani MA, Hamed A, Abdelwahab AB. New pyranosyl cembranoid diterpenes from Sarcophyton trocheliophorum. Nat Prod Res 2018; 33:24-33. [DOI: 10.1080/14786419.2018.1431631] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Mohamed Shaaban
- Institute of Organic and Biomolecular Chemistry, University of Göttingen, Göttingen, Germany
- Chemistry of Natural Compounds Department, Pharmaceutical Industries Research Division, National Research Centre, Dokki-Cairo, Egypt
| | - Marwa Y. Issa
- Faculty of Pharmacy, Pharmacognosy Department, Cairo University, Cairo, Egypt
| | | | - Abdelaaty Hamed
- Faculty of Science, Chemistry Department, Al-Azhar University, Nasr City-Cairo, Egypt
| | - Ahmed B. Abdelwahab
- Chemistry of Natural Compounds Department, Pharmaceutical Industries Research Division, National Research Centre, Dokki-Cairo, Egypt
- Lorraine University, SRSMC, Boulevard Arago, France
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38
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Wagstaff J, Löwe J. Prokaryotic cytoskeletons: protein filaments organizing small cells. Nat Rev Microbiol 2018; 16:187-201. [PMID: 29355854 DOI: 10.1038/nrmicro.2017.153] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Most, if not all, bacterial and archaeal cells contain at least one protein filament system. Although these filament systems in some cases form structures that are very similar to eukaryotic cytoskeletons, the term 'prokaryotic cytoskeletons' is used to refer to many different kinds of protein filaments. Cytoskeletons achieve their functions through polymerization of protein monomers and the resulting ability to access length scales larger than the size of the monomer. Prokaryotic cytoskeletons are involved in many fundamental aspects of prokaryotic cell biology and have important roles in cell shape determination, cell division and nonchromosomal DNA segregation. Some of the filament-forming proteins have been classified into a small number of conserved protein families, for example, the almost ubiquitous tubulin and actin superfamilies. To understand what makes filaments special and how the cytoskeletons they form enable cells to perform essential functions, the structure and function of cytoskeletal molecules and their filaments have been investigated in diverse bacteria and archaea. In this Review, we bring these data together to highlight the diverse ways that linear protein polymers can be used to organize other molecules and structures in bacteria and archaea.
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Affiliation(s)
- James Wagstaff
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Jan Löwe
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
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39
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Satir P. Chirality of the cytoskeleton in the origins of cellular asymmetry. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0408. [PMID: 27821520 DOI: 10.1098/rstb.2015.0408] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/15/2016] [Indexed: 02/06/2023] Open
Abstract
Self-assembly of two important components of the cytoskeleton of eukaryotic cells, actin microfilaments and microtubules (MTs) results in polar filaments of one chirality. As is true for bacterial flagella, in actin microfilaments, screw direction is important for assembly processes and motility. For MTs, polar orientation within the cell is paramount. The alignment of these elements in the cell cytoplasm gives rise to emergent properties, including the potential for cell differentiation and specialization. Complex MTs with a characteristic chirality are found in basal bodies and centrioles; this chirality is preserved in cilia. In motile cilia, it is reflected in the direction of the effective stroke. The positioning of the basal body or cilia on the cell surface depends on polarity proteins. In evolution, survival depends on global polarity information relayed to the cell in part by orientation of the MT and actin filament cytoskeletons and the chirality of the basal body to determine left and right coordinates within a defined anterior-posterior cell and tissue axis.This article is part of the themed issue 'Provocative questions in left-right asymmetry'.
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Affiliation(s)
- Peter Satir
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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40
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Rivas-Marín E, Devos DP. The Paradigms They Are a-Changin': past, present and future of PVC bacteria research. Antonie van Leeuwenhoek 2017; 111:785-799. [PMID: 29058138 PMCID: PMC5945725 DOI: 10.1007/s10482-017-0962-z] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 10/10/2017] [Indexed: 11/22/2022]
Abstract
These are exciting times for PVC researchers! The PVC superphylum is composed of the bacterial phyla Planctomycetes, Verrucomicrobia, Chlamydiae (those three founders giving it its name), Lentisphaerae and Kirimatiellaeota as well as some uncultured candidate phyla, such as the Candidatus Omnitrophica (previously known as OP3). Despite early debates, most of the disagreements that surround this group of bacteria have been recently resolved. In this article, we review the history of the study of PVC bacteria, with a particular focus on the misinterpretations that emerged early in the field and their resolution. We begin with a historical perspective that describes the relevant facts of PVC research from the early times when they were not yet termed PVC. Those were controversial times and we refer to them as the “discovery age” of the field. We continue by describing new discoveries due to novel techniques and data that combined with the reinterpretations of old ones have contributed to solve most of the discordances and we refer to these times as the “illumination age” of PVC research. We follow by arguing that we are just entering the “golden age” of PVC research and that the future of this growing community is looking bright. We finish by suggesting a few of the directions that PVC researches might take in the future.
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Affiliation(s)
- Elena Rivas-Marín
- Centro Andaluz de Biología del Desarrollo (CABD)-CSIC, University Pablo de Olavide, Carretera Utrera, km 1, 41013, Seville, Spain
| | - Damien P Devos
- Centro Andaluz de Biología del Desarrollo (CABD)-CSIC, University Pablo de Olavide, Carretera Utrera, km 1, 41013, Seville, Spain.
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41
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Bacterial Tubulins: A Eukaryotic-Like Microtubule Cytoskeleton. Trends Microbiol 2017; 25:782-784. [PMID: 28869086 DOI: 10.1016/j.tim.2017.08.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 08/15/2017] [Indexed: 11/22/2022]
Abstract
Ever since their discovery, bacterial tubulins, found in several Prosthecobacter species, have raised curiosity as they are closely related to eukaryotic tubulin. Deng and colleagues now present new evidence for the functional homology of the two cytoskeletal systems where in vitro reconstituted Btub-microtubules display eukaryote-like biochemical and dynamic properties.
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42
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Bacterial Tubulins A and B Exhibit Polarized Growth, Mixed-Polarity Bundling, and Destabilization by GTP Hydrolysis. J Bacteriol 2017; 199:JB.00211-17. [PMID: 28716960 DOI: 10.1128/jb.00211-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 07/06/2017] [Indexed: 11/20/2022] Open
Abstract
Bacteria of the genus Prosthecobacter express homologs of eukaryotic α- and β-tubulin, called BtubA and BtubB (BtubA/B), that have been observed to assemble into filaments in the presence of GTP. BtubA/B polymers are proposed to be composed in vitro by two to six protofilaments in contrast to that in vivo, where they have been reported to form 5-protofilament tubes named bacterial microtubules (bMTs). The btubAB genes likely entered the Prosthecobacter lineage via horizontal gene transfer and may be derived from an early ancestor of the modern eukaryotic microtubule (MT). Previous biochemical studies revealed that BtubA/B polymerization is reversible and that BtubA/B folding does not require chaperones. To better understand BtubA/B filament behavior and gain insight into the evolution of microtubule dynamics, we characterized in vitro BtubA/B assembly using a combination of polymerization kinetics assays and microscopy. Like eukaryotic microtubules, BtubA/B filaments exhibit polarized growth with different assembly rates at each end. GTP hydrolysis stimulated by BtubA/B polymerization drives a stochastic mechanism of filament disassembly that occurs via polymer breakage and/or fast continuous depolymerization. We also observed treadmilling (continuous addition and loss of subunits at opposite ends) of BtubA/B filament fragments. Unlike MTs, polymerization of BtubA/B requires KCl, which reduces the critical concentration for BtubA/B assembly and induces it to form stable mixed-orientation bundles in the absence of any additional BtubA/B-binding proteins. The complex dynamics that we observe in stabilized and unstabilized BtubA/B filaments may reflect common properties of an ancestral eukaryotic tubulin polymer.IMPORTANCE Microtubules are polymers within all eukaryotic cells that perform critical functions; they segregate chromosomes, organize intracellular transport, and support the flagella. These functions rely on the remarkable range of tunable dynamic behaviors of microtubules. Bacterial tubulin A and B (BtubA/B) are evolutionarily related proteins that form polymers. They are proposed to be evolved from the ancestral eukaryotic tubulin, a missing link in microtubule evolution. Using microscopy and biochemical approaches to characterize BtubA/B assembly in vitro, we observed that they exhibit complex and structurally polarized dynamic behavior like eukaryotic microtubules but differ in how they self-associate into bundles and how this bundling affects their stability. Our results demonstrate the diversity of mechanisms through which tubulin homologs promote filament dynamics and monomer turnover.
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Abstract
FtsZ, a homolog of tubulin, is found in almost all bacteria and archaea where it has a primary role in cytokinesis. Evidence for structural homology between FtsZ and tubulin came from their crystal structures and identification of the GTP box. Tubulin and FtsZ constitute a distinct family of GTPases and show striking similarities in many of their polymerization properties. The differences between them, more so, the complexities of microtubule dynamic behavior in comparison to that of FtsZ, indicate that the evolution to tubulin is attributable to the incorporation of the complex functionalities in higher organisms. FtsZ and microtubules function as polymers in cell division but their roles differ in the division process. The structural and partial functional homology has made the study of their dynamic properties more interesting. In this review, we focus on the application of the information derived from studies on FtsZ dynamics to study microtubule dynamics and vice versa. The structural and functional aspects that led to the establishment of the homology between the two proteins are explained to emphasize the network of FtsZ and microtubule studies and how they are connected.
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Affiliation(s)
- Rachana Rao Battaje
- Department of Biosciences and BioengineeringIndian Institute of Technology Bombay, Mumbai, India
| | - Dulal Panda
- Department of Biosciences and BioengineeringIndian Institute of Technology Bombay, Mumbai, India
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44
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Plattner H. Evolutionary Cell Biology of Proteins from Protists to Humans and Plants. J Eukaryot Microbiol 2017; 65:255-289. [PMID: 28719054 DOI: 10.1111/jeu.12449] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 07/04/2017] [Accepted: 07/07/2017] [Indexed: 01/10/2023]
Abstract
During evolution, the cell as a fine-tuned machine had to undergo permanent adjustments to match changes in its environment, while "closed for repair work" was not possible. Evolution from protists (protozoa and unicellular algae) to multicellular organisms may have occurred in basically two lineages, Unikonta and Bikonta, culminating in mammals and angiosperms (flowering plants), respectively. Unicellular models for unikont evolution are myxamoebae (Dictyostelium) and increasingly also choanoflagellates, whereas for bikonts, ciliates are preferred models. Information accumulating from combined molecular database search and experimental verification allows new insights into evolutionary diversification and maintenance of genes/proteins from protozoa on, eventually with orthologs in bacteria. However, proteins have rarely been followed up systematically for maintenance or change of function or intracellular localization, acquirement of new domains, partial deletion (e.g. of subunits), and refunctionalization, etc. These aspects are discussed in this review, envisaging "evolutionary cell biology." Protozoan heritage is found for most important cellular structures and functions up to humans and flowering plants. Examples discussed include refunctionalization of voltage-dependent Ca2+ channels in cilia and replacement by other types during evolution. Altogether components serving Ca2+ signaling are very flexible throughout evolution, calmodulin being a most conservative example, in contrast to calcineurin whose catalytic subunit is lost in plants, whereas both subunits are maintained up to mammals for complex functions (immune defense and learning). Domain structure of R-type SNAREs differs in mono- and bikonta, as do Ca2+ -dependent protein kinases. Unprecedented selective expansion of the subunit a which connects multimeric base piece and head parts (V0, V1) of H+ -ATPase/pump may well reflect the intriguing vesicle trafficking system in ciliates, specifically in Paramecium. One of the most flexible proteins is centrin when its intracellular localization and function throughout evolution is traced. There are many more examples documenting evolutionary flexibility of translation products depending on requirements and potential for implantation within the actual cellular context at different levels of evolution. From estimates of gene and protein numbers per organism, it appears that much of the basic inventory of protozoan precursors could be transmitted to highest eukaryotic levels, with some losses and also with important additional "inventions."
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Affiliation(s)
- Helmut Plattner
- Department of Biology, University of Konstanz, P. O. Box M625, Konstanz, 78457, Germany
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45
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Uncharacterized Bacterial Structures Revealed by Electron Cryotomography. J Bacteriol 2017; 199:JB.00100-17. [PMID: 28607161 DOI: 10.1128/jb.00100-17] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 05/27/2017] [Indexed: 01/06/2023] Open
Abstract
Electron cryotomography (ECT) can reveal the native structure and arrangement of macromolecular complexes inside intact cells. This technique has greatly advanced our understanding of the ultrastructure of bacterial cells. We now view bacteria as structurally complex assemblies of macromolecular machines rather than as undifferentiated bags of enzymes. To date, our group has applied ECT to nearly 90 different bacterial species, collecting more than 15,000 cryotomograms. In addition to known structures, we have observed, to our knowledge, several uncharacterized features in these tomograms. Some are completely novel structures; others expand the features or species range of known structure types. Here, we present a survey of these uncharacterized bacterial structures in the hopes of accelerating their identification and study, and furthering our understanding of the structural complexity of bacterial cells.IMPORTANCE Bacteria are more structurally complex than is commonly appreciated. Here we present a survey of previously uncharacterized structures that we observed in bacterial cells by electron cryotomography, structures that will initiate new lines of research investigating their identities and roles.
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46
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Nitti A, Pacini A, Pasini D. Chiral Nanotubes. NANOMATERIALS (BASEL, SWITZERLAND) 2017; 7:E167. [PMID: 28677640 PMCID: PMC5535233 DOI: 10.3390/nano7070167] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 06/22/2017] [Accepted: 06/28/2017] [Indexed: 01/01/2023]
Abstract
Organic nanotubes, as assembled nanospaces, in which to carry out host-guest chemistry, reversible binding of smaller species for transport, sensing, storage or chemical transformation purposes, are currently attracting substantial interest, both as biological ion channel mimics, or for addressing tailored material properties. Nature's materials and machinery are universally asymmetric, and, for chemical entities, controlled asymmetry comes from chirality. Together with carbon nanotubes, conformationally stable molecular building blocks and macrocycles have been used for the realization of organic nanotubes, by means of their assembly in the third dimension. In both cases, chiral properties have started to be fully exploited to date. In this paper, we review recent exciting developments in the synthesis and assembly of chiral nanotubes, and of their functional properties. This review will include examples of either molecule-based or macrocycle-based systems, and will try and rationalize the supramolecular interactions at play for the three-dimensional (3D) assembly of the nanoscale architectures.
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Affiliation(s)
- Andrea Nitti
- Department of Chemistry, University of Pavia, Viale Taramelli, 12-27100 Pavia, Italy.
| | - Aurora Pacini
- Department of Chemistry, University of Pavia, Viale Taramelli, 12-27100 Pavia, Italy.
- INSTM Research Unit, University of Pavia, Viale Taramelli, 12-27100 Pavia, Italy.
| | - Dario Pasini
- Department of Chemistry, University of Pavia, Viale Taramelli, 12-27100 Pavia, Italy.
- INSTM Research Unit, University of Pavia, Viale Taramelli, 12-27100 Pavia, Italy.
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47
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Four-stranded mini microtubules formed by Prosthecobacter BtubAB show dynamic instability. Proc Natl Acad Sci U S A 2017; 114:E5950-E5958. [PMID: 28673988 DOI: 10.1073/pnas.1705062114] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Microtubules, the dynamic, yet stiff hollow tubes built from αβ-tubulin protein heterodimers, are thought to be present only in eukaryotic cells. Here, we report a 3.6-Å helical reconstruction electron cryomicroscopy structure of four-stranded mini microtubules formed by bacterial tubulin-like Prosthecobacter dejongeii BtubAB proteins. Despite their much smaller diameter, mini microtubules share many key structural features with eukaryotic microtubules, such as an M-loop, alternating subunits, and a seam that breaks overall helical symmetry. Using in vitro total internal reflection fluorescence microscopy, we show that bacterial mini microtubules treadmill and display dynamic instability, another hallmark of eukaryotic microtubules. The third protein in the btub gene cluster, BtubC, previously known as "bacterial kinesin light chain," binds along protofilaments every 8 nm, inhibits BtubAB mini microtubule catastrophe, and increases rescue. Our work reveals that some bacteria contain regulated and dynamic cytomotive microtubule systems that were once thought to be only useful in much larger and sophisticated eukaryotic cells.
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48
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Popp D, Loh ND, Zorgati H, Ghoshdastider U, Liow LT, Ivanova MI, Larsson M, DePonte DP, Bean R, Beyerlein KR, Gati C, Oberthuer D, Arnlund D, Brändén G, Berntsen P, Cascio D, Chavas LMG, Chen JPJ, Ding K, Fleckenstein H, Gumprecht L, Harimoorthy R, Mossou E, Sawaya MR, Brewster AS, Hattne J, Sauter NK, Seibert M, Seuring C, Stellato F, Tilp T, Eisenberg DS, Messerschmidt M, Williams GJ, Koglin JE, Makowski L, Millane RP, Forsyth T, Boutet S, White TA, Barty A, Chapman H, Chen SL, Liang M, Neutze R, Robinson RC. Flow-aligned, single-shot fiber diffraction using a femtosecond X-ray free-electron laser. Cytoskeleton (Hoboken) 2017; 74:472-481. [PMID: 28574190 DOI: 10.1002/cm.21378] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 05/25/2017] [Accepted: 05/29/2017] [Indexed: 01/26/2023]
Abstract
A major goal for X-ray free-electron laser (XFEL) based science is to elucidate structures of biological molecules without the need for crystals. Filament systems may provide some of the first single macromolecular structures elucidated by XFEL radiation, since they contain one-dimensional translational symmetry and thereby occupy the diffraction intensity region between the extremes of crystals and single molecules. Here, we demonstrate flow alignment of as few as 100 filaments (Escherichia coli pili, F-actin, and amyloid fibrils), which when intersected by femtosecond X-ray pulses result in diffraction patterns similar to those obtained from classical fiber diffraction studies. We also determine that F-actin can be flow-aligned to a disorientation of approximately 5 degrees. Using this XFEL-based technique, we determine that gelsolin amyloids are comprised of stacked β-strands running perpendicular to the filament axis, and that a range of order from fibrillar to crystalline is discernable for individual α-synuclein amyloids.
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Affiliation(s)
- David Popp
- Institute of Molecular and Cell Biology, Biopolis, A*STAR (Agency for Science, Technology and Research), 138673, Singapore
| | - N Duane Loh
- Department of Physics, National University of Singapore, 117557, Singapore.,Centre for BioImaging Sciences, National University of Singapore, 117546, Singapore
| | - Habiba Zorgati
- Institute of Molecular and Cell Biology, Biopolis, A*STAR (Agency for Science, Technology and Research), 138673, Singapore.,Department of Biochemistry, National University of Singapore, 117597, Singapore
| | - Umesh Ghoshdastider
- Institute of Molecular and Cell Biology, Biopolis, A*STAR (Agency for Science, Technology and Research), 138673, Singapore
| | - Lu Ting Liow
- Department of Medicine, National University of Singapore, 119074, Singapore
| | - Magdalena I Ivanova
- Department of Neurology, University of Michigan, 109 Zina Pitcher Pl, Ann Arbor, Michigan, 48109
| | - Mårten Larsson
- Institute of Molecular and Cell Biology, Biopolis, A*STAR (Agency for Science, Technology and Research), 138673, Singapore
| | - Daniel P DePonte
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025
| | - Richard Bean
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg, 22607, Germany
| | - Kenneth R Beyerlein
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg, 22607, Germany
| | - Cornelius Gati
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg, 22607, Germany
| | - Dominik Oberthuer
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg, 22607, Germany.,Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, 22607, Germany
| | - David Arnlund
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Gisela Brändén
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Peter Berntsen
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Duilio Cascio
- Howard Hughes Medical Institute, University of California, Los Angeles, California, 90095
| | - Leonard M G Chavas
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg, 22607, Germany
| | - Joe P J Chen
- Department of Electrical and Computer Engineering, Computational Imaging Group, University of Canterbury, Christchurch, New Zealand
| | - Ke Ding
- Institute of Molecular and Cell Biology, Biopolis, A*STAR (Agency for Science, Technology and Research), 138673, Singapore
| | - Holger Fleckenstein
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg, 22607, Germany
| | - Lars Gumprecht
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg, 22607, Germany
| | - Rajiv Harimoorthy
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Estelle Mossou
- Institut Laue-Langevin, Grenoble, 38000, France.,EPSAM/ISTM, Keele University, Staffordshire, ST5 5BG, United Kingdom
| | - Michael R Sawaya
- Howard Hughes Medical Institute, University of California, Los Angeles, California, 90095
| | - Aaron S Brewster
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Johan Hattne
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Nicholas K Sauter
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Marvin Seibert
- Department of Cell and Molecular Biology, Molecular Biophysics, Uppsala University, Uppsala, 751 24, Sweden
| | - Carolin Seuring
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg, 22607, Germany
| | - Francesco Stellato
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg, 22607, Germany
| | - Thomas Tilp
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg, 22607, Germany
| | - David S Eisenberg
- Howard Hughes Medical Institute, University of California, Los Angeles, California, 90095
| | - Marc Messerschmidt
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025
| | - Garth J Williams
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025
| | - Jason E Koglin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025
| | - Lee Makowski
- Department of Bioengineering, Northeastern University, 360 Huntington Ave, Boston, Massachusetts, 02115
| | - Rick P Millane
- Department of Electrical and Computer Engineering, Computational Imaging Group, University of Canterbury, Christchurch, New Zealand
| | - Trevor Forsyth
- Institut Laue-Langevin, Grenoble, 38000, France.,EPSAM/ISTM, Keele University, Staffordshire, ST5 5BG, United Kingdom
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025
| | - Thomas A White
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg, 22607, Germany
| | - Anton Barty
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg, 22607, Germany
| | - Henry Chapman
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg, 22607, Germany.,Department of Physics, University of Hamburg, Luruper Chaussee 149, Hamburg, 22607, Germany
| | - Swaine L Chen
- Department of Medicine, National University of Singapore, 119074, Singapore.,Genome Institute of Singapore, Biopolis, A*STAR (Agency for Science, Technology and Research), 138672, Singapore
| | - Mengning Liang
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg, 22607, Germany
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Robert C Robinson
- Institute of Molecular and Cell Biology, Biopolis, A*STAR (Agency for Science, Technology and Research), 138673, Singapore.,Department of Biochemistry, National University of Singapore, 117597, Singapore.,Research Institute for Interdisciplinary Science, Okayama University, Okayama, 700-8530, Japan
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49
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Abstract
Electron cryotomography (ECT) provides three-dimensional views of macromolecular complexes inside cells in a native frozen-hydrated state. Over the last two decades, ECT has revealed the ultrastructure of cells in unprecedented detail. It has also allowed us to visualize the structures of macromolecular machines in their native context inside intact cells. In many cases, such machines cannot be purified intact for in vitro study. In other cases, the function of a structure is lost outside the cell, so that the mechanism can be understood only by observation in situ. In this review, we describe the technique and its history and provide examples of its power when applied to cell biology. We also discuss the integration of ECT with other techniques, including lower-resolution fluorescence imaging and higher-resolution atomic structure determination, to cover the full scale of cellular processes.
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Affiliation(s)
- Catherine M Oikonomou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125; ,
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125; , .,Howard Hughes Medical Institute, Pasadena, California 91125
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50
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Bacterial kinesin light chain (Bklc) links the Btub cytoskeleton to membranes. Sci Rep 2017; 7:45668. [PMID: 28358387 PMCID: PMC5372463 DOI: 10.1038/srep45668] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 03/01/2017] [Indexed: 11/23/2022] Open
Abstract
Bacterial kinesin light chain is a TPR domain-containing protein encoded by the bklc gene, which co-localizes with the bacterial tubulin (btub) genes in a conserved operon in Prosthecobacter. Btub heterodimers show high structural homology with eukaryotic tubulin and assemble into head-to-tail protofilaments. Intriguingly, Bklc is homologous to the light chain of the microtubule motor kinesin and could thus represent an additional eukaryotic-like cytoskeletal element in bacteria. Using biochemical characterization as well as cryo-electron tomography we show here that Bklc interacts specifically with Btub protofilaments, as well as lipid vesicles and could thus play a role in anchoring the Btub filaments to the membrane protrusions in Prosthecobacter where they specifically localize in vivo. This work sheds new light into possible ways in which the microtubule cytoskeleton may have evolved linking precursors of microtubules to the membrane via the kinesin moiety that in today’s eukaryotic cytoskeleton links vesicle-packaged cargo to microtubules.
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