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Cox I, Xu ZY, Grzywacz R, Ong WJ, Rasco BC, Kitamura N, Hoskins D, Neupane S, Ruland TJ, Allmond JM, King TT, Lubna RS, Rykaczewski KP, Schatz H, Sherrill BM, Tarasov OB, Ayangeakaa AD, Berg HC, Bleuel DL, Cerizza G, Christie J, Chester A, Davis J, Dembski C, Doetsch AA, Duarte JG, Estrade A, Fijałkowska A, Gray TJ, Good EC, Haak K, Hanai S, Harke JT, Harris C, Hermansen K, Hoff DEM, Jain R, Karny M, Kolos K, Laminack A, Liddick SN, Longfellow B, Lyons S, Madurga M, Mogannam MJ, Nowicki A, Ogunbeku TH, Owens-Fryar G, Rajabali MM, Richard AL, Ronning EK, Rose GE, Siegl K, Singh M, Spyrou A, Sweet A, Tsantiri A, Walters WB, Yokoyama R. Proton Shell Gaps in N=28 Nuclei from the First Complete Spectroscopy Study with FRIB Decay Station Initiator. Phys Rev Lett 2024; 132:152503. [PMID: 38682970 DOI: 10.1103/physrevlett.132.152503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/12/2023] [Accepted: 03/08/2024] [Indexed: 05/01/2024]
Abstract
The first complete measurement of the β-decay strength distribution of _{17}^{45}Cl_{28} was performed at the Facility for Rare Isotope Beams (FRIB) with the FRIB Decay Station Initiator during the second FRIB experiment. The measurement involved the detection of neutrons and γ rays in two focal planes of the FRIB Decay Station Initiator in a single experiment for the first time. This enabled an analytical consistency in extracting the β-decay strength distribution over the large range of excitation energies, including neutron unbound states. We observe a rapid increase in the β-decay strength distribution above the neutron separation energy in _{18}^{45}Ar_{27}. This was interpreted to be caused by the transitioning of neutrons into protons excited across the Z=20 shell gap. The SDPF-MU interaction with reduced shell gap best reproduced the data. The measurement demonstrates a new approach that is sensitive to the proton shell gap in neutron rich nuclei according to SDPF-MU calculations.
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Affiliation(s)
- I Cox
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Z Y Xu
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - R Grzywacz
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996, USA
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - W-J Ong
- Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - B C Rasco
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - N Kitamura
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - D Hoskins
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - S Neupane
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996, USA
- Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - T J Ruland
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- Department of Physics and Astronomy, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - J M Allmond
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - T T King
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - R S Lubna
- Facility for Rare Isotope Beams, Michigan State University, East Lansing, Michigan 48824, USA
| | - K P Rykaczewski
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - H Schatz
- Facility for Rare Isotope Beams, Michigan State University, East Lansing, Michigan 48824, USA
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824, USA
| | - B M Sherrill
- Facility for Rare Isotope Beams, Michigan State University, East Lansing, Michigan 48824, USA
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824, USA
| | - O B Tarasov
- Facility for Rare Isotope Beams, Michigan State University, East Lansing, Michigan 48824, USA
| | - A D Ayangeakaa
- Department of Physics and Astronomy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
- Triangle Universities Nuclear Laboratory, Duke University, Durham, North Carolina 27708, USA
| | - H C Berg
- Facility for Rare Isotope Beams, Michigan State University, East Lansing, Michigan 48824, USA
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824, USA
| | - D L Bleuel
- Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - G Cerizza
- Facility for Rare Isotope Beams, Michigan State University, East Lansing, Michigan 48824, USA
| | - J Christie
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - A Chester
- Facility for Rare Isotope Beams, Michigan State University, East Lansing, Michigan 48824, USA
| | - J Davis
- Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - C Dembski
- Facility for Rare Isotope Beams, Michigan State University, East Lansing, Michigan 48824, USA
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824, USA
| | - A A Doetsch
- Facility for Rare Isotope Beams, Michigan State University, East Lansing, Michigan 48824, USA
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824, USA
| | - J G Duarte
- Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - A Estrade
- Department of Physics, Central Michigan University, Mount Pleasant, Michigan 48859, USA
| | - A Fijałkowska
- Faculty of Physics, University of Warsaw, PL 02-093 Warsaw, Poland
| | - T J Gray
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - E C Good
- Facility for Rare Isotope Beams, Michigan State University, East Lansing, Michigan 48824, USA
| | - K Haak
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824, USA
| | - S Hanai
- Center for Nuclear Study, University of Tokyo, Wako, Saitama 351-0198, Japan
| | - J T Harke
- Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - C Harris
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824, USA
| | - K Hermansen
- Facility for Rare Isotope Beams, Michigan State University, East Lansing, Michigan 48824, USA
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824, USA
| | - D E M Hoff
- Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - R Jain
- Facility for Rare Isotope Beams, Michigan State University, East Lansing, Michigan 48824, USA
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824, USA
| | - M Karny
- Faculty of Physics, University of Warsaw, PL 02-093 Warsaw, Poland
| | - K Kolos
- Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - A Laminack
- Physics Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - S N Liddick
- Facility for Rare Isotope Beams, Michigan State University, East Lansing, Michigan 48824, USA
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
| | - B Longfellow
- Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - S Lyons
- Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - M Madurga
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - M J Mogannam
- Facility for Rare Isotope Beams, Michigan State University, East Lansing, Michigan 48824, USA
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
| | - A Nowicki
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - T H Ogunbeku
- Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - G Owens-Fryar
- Facility for Rare Isotope Beams, Michigan State University, East Lansing, Michigan 48824, USA
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824, USA
| | - M M Rajabali
- Physics Department, Tennessee Technological University, Cookeville, Tennessee 38505, USA
| | - A L Richard
- Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - E K Ronning
- Facility for Rare Isotope Beams, Michigan State University, East Lansing, Michigan 48824, USA
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
| | - G E Rose
- University of California, Berkeley, Berkeley, California 94704, USA
| | - K Siegl
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - M Singh
- Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee 37996, USA
- Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - A Spyrou
- Facility for Rare Isotope Beams, Michigan State University, East Lansing, Michigan 48824, USA
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824, USA
| | - A Sweet
- Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - A Tsantiri
- Facility for Rare Isotope Beams, Michigan State University, East Lansing, Michigan 48824, USA
- Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824, USA
| | - W B Walters
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA
| | - R Yokoyama
- Center for Nuclear Study, University of Tokyo, Wako, Saitama 351-0198, Japan
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2
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Hosu BG, Hill W, Samuel AD, Berg HC. Synchronized strobed phase contrast and fluorescence microscopy: the interlaced standard reimagined. Opt Express 2023; 31:5167-5180. [PMID: 36823805 PMCID: PMC10018787 DOI: 10.1364/oe.474045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 12/29/2022] [Accepted: 01/06/2023] [Indexed: 06/18/2023]
Abstract
We propose a simple, cost-effective method for synchronized phase contrast and fluorescence video acquisition in live samples. Counter-phased pulses of phase contrast illumination and fluorescence excitation light are synchronized with the exposure of the two fields of an interlaced camera sensor. This results in a video sequence in which each frame contains both exposure modes, each in half of its pixels. The method allows real-time acquisition and display of synchronized and spatially aligned phase contrast and fluorescence image sequences that can be separated by de-interlacing in two independent videos. The method can be implemented on any fluorescence microscope with a camera port without needing to modify the optical path.
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Affiliation(s)
- Basarab G. Hosu
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
- Rowland Institute at Harvard, Harvard University, Cambridge, MA 02142, USA
- Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Winfield Hill
- Rowland Institute at Harvard, Harvard University, Cambridge, MA 02142, USA
| | - Aravinthan D. Samuel
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Howard C. Berg
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
- Rowland Institute at Harvard, Harvard University, Cambridge, MA 02142, USA
- Department of Physics, Harvard University, Cambridge, MA 02138, USA
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3
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Markova M, von Neumann-Cosel P, Larsen AC, Bassauer S, Görgen A, Guttormsen M, Bello Garrote FL, Berg HC, Bjørøen MM, Dahl-Jacobsen T, Eriksen TK, Gjestvang D, Isaak J, Mbabane M, Paulsen W, Pedersen LG, Pettersen NIJ, Richter A, Sahin E, Scholz P, Siem S, Tveten GM, Valsdottir VM, Wiedeking M, Zeiser F. Comprehensive Test of the Brink-Axel Hypothesis in the Energy Region of the Pygmy Dipole Resonance. Phys Rev Lett 2021; 127:182501. [PMID: 34767384 DOI: 10.1103/physrevlett.127.182501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 04/15/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
The validity of the Brink-Axel hypothesis, which is especially important for numerous astrophysical calculations, is addressed for ^{116,120,124}Sn below the neutron separation energy by means of three independent experimental methods. The γ-ray strength functions (GSFs) extracted from primary γ-decay spectra following charged-particle reactions with the Oslo method and with the shape method demonstrate excellent agreement with those deduced from forward-angle inelastic proton scattering at relativistic beam energies. In addition, the GSFs are shown to be independent of excitation energies and spins of the initial and final states. The results provide a critical test of the generalized Brink-Axel hypothesis in heavy nuclei, demonstrating its applicability in the energy region of the pygmy dipole resonance.
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Affiliation(s)
- M Markova
- Department of Physics, University of Oslo, N-0316 Oslo, Norway
| | - P von Neumann-Cosel
- Institut für Kernphysik, Technische Universität Darmstadt, D-64289 Darmstadt, Germany
| | - A C Larsen
- Department of Physics, University of Oslo, N-0316 Oslo, Norway
| | - S Bassauer
- Institut für Kernphysik, Technische Universität Darmstadt, D-64289 Darmstadt, Germany
| | - A Görgen
- Department of Physics, University of Oslo, N-0316 Oslo, Norway
| | - M Guttormsen
- Department of Physics, University of Oslo, N-0316 Oslo, Norway
| | | | - H C Berg
- Department of Physics, University of Oslo, N-0316 Oslo, Norway
| | - M M Bjørøen
- Department of Physics, University of Oslo, N-0316 Oslo, Norway
| | - T Dahl-Jacobsen
- Department of Physics, University of Oslo, N-0316 Oslo, Norway
| | - T K Eriksen
- Department of Physics, University of Oslo, N-0316 Oslo, Norway
| | - D Gjestvang
- Department of Physics, University of Oslo, N-0316 Oslo, Norway
| | - J Isaak
- Institut für Kernphysik, Technische Universität Darmstadt, D-64289 Darmstadt, Germany
| | - M Mbabane
- Department of Physics, University of Oslo, N-0316 Oslo, Norway
| | - W Paulsen
- Department of Physics, University of Oslo, N-0316 Oslo, Norway
| | - L G Pedersen
- Department of Physics, University of Oslo, N-0316 Oslo, Norway
| | - N I J Pettersen
- Department of Physics, University of Oslo, N-0316 Oslo, Norway
| | - A Richter
- Institut für Kernphysik, Technische Universität Darmstadt, D-64289 Darmstadt, Germany
| | - E Sahin
- Department of Physics, University of Oslo, N-0316 Oslo, Norway
| | - P Scholz
- Institut für Kernphysik, Universität zu Köln, D-50937 Köln, Germany
- Department of Physics, University of Notre Dame, Notre Dame, Indiana 46556-5670, USA
| | - S Siem
- Department of Physics, University of Oslo, N-0316 Oslo, Norway
| | - G M Tveten
- Department of Physics, University of Oslo, N-0316 Oslo, Norway
| | - V M Valsdottir
- Department of Physics, University of Oslo, N-0316 Oslo, Norway
| | - M Wiedeking
- Department of Subatomic Physics, iThemba LABS, Somerset West 7129, South Africa
- School of Physics, University of the Witwatersrand, Johannesburg 2050, South Africa
| | - F Zeiser
- Department of Physics, University of Oslo, N-0316 Oslo, Norway
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4
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Hu H, Santiveri M, Wadhwa N, Berg HC, Erhardt M, Taylor NMI. Structural basis of torque generation in the bi-directional bacterial flagellar motor. Trends Biochem Sci 2021; 47:160-172. [PMID: 34294545 DOI: 10.1016/j.tibs.2021.06.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 06/16/2021] [Accepted: 06/18/2021] [Indexed: 12/11/2022]
Abstract
The flagellar stator unit is an oligomeric complex of two membrane proteins (MotA5B2) that powers bi-directional rotation of the bacterial flagellum. Harnessing the ion motive force across the cytoplasmic membrane, the stator unit operates as a miniature rotary motor itself to provide torque for rotation of the flagellum. Recent cryo-electron microscopic (cryo-EM) structures of the stator unit provided novel insights into its assembly, function, and subunit stoichiometry, revealing the ion flux pathway and the torque generation mechanism. Furthermore, in situ cryo-electron tomography (cryo-ET) studies revealed unprecedented details of the interactions between stator unit and rotor. In this review, we summarize recent advances in our understanding of the structure and function of the flagellar stator unit, torque generation, and directional switching of the motor.
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Affiliation(s)
- Haidai Hu
- Structural Biology of Molecular Machines Group, Protein Structure & Function Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Mònica Santiveri
- Structural Biology of Molecular Machines Group, Protein Structure & Function Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Navish Wadhwa
- Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA; Rowland Institute at Harvard, Harvard University, 100 Edwin H. Land Blvd, Cambridge, MA 02142, USA
| | - Howard C Berg
- Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA; Rowland Institute at Harvard, Harvard University, 100 Edwin H. Land Blvd, Cambridge, MA 02142, USA
| | - Marc Erhardt
- Institut für Biologie/Bakterienphysiologie, Humboldt-Universität zu Berlin, Philippstr. 13, 10115 Berlin, Germany
| | - Nicholas M I Taylor
- Structural Biology of Molecular Machines Group, Protein Structure & Function Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark.
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Abstract
Motility is important for the survival and dispersal of many bacteria, and it often plays a role during infections. Regulation of bacterial motility by chemical stimuli is well studied, but recent work has added a new dimension to the problem of motility control. The bidirectional flagellar motor of the bacterium Escherichia coli recruits or releases torque-generating units (stator units) in response to changes in load. Here, we show that this mechanosensitive remodeling of the flagellar motor is independent of direction of rotation. Remodeling rate constants in clockwise rotating motors and in counterclockwise rotating motors, measured previously, fall on the same curve if plotted against torque. Increased torque decreases the off rate of stator units from the motor, thereby increasing the number of active stator units at steady state. A simple mathematical model based on observed dynamics provides quantitative insight into the underlying molecular interactions. The torque-dependent remodeling mechanism represents a robust strategy to quickly regulate output (torque) in response to changes in demand (load).
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Affiliation(s)
- Navish Wadhwa
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138;
- Rowland Institute at Harvard, Harvard University, Cambridge, MA 02142
| | - Yuhai Tu
- T. J. Watson Research Center, IBM, Yorktown Heights, NY 10598
| | - Howard C Berg
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138
- Rowland Institute at Harvard, Harvard University, Cambridge, MA 02142
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Wadhwa N, Tu Y, Berg HC. Mechanobiology of Stator Remodeling in the Bacterial Flagellar Motor. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Santiveri M, Roa-Eguiara A, Kühne C, Wadhwa N, Hu H, Berg HC, Erhardt M, Taylor NM. Structure and Function of Stator Units of the Bacterial Flagellar Motor. Cell 2020; 183:244-257.e16. [DOI: 10.1016/j.cell.2020.08.016] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 07/09/2020] [Accepted: 08/11/2020] [Indexed: 12/17/2022]
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Shrivastava A, Berg HC. A molecular rack and pinion actuates a cell-surface adhesin and enables bacterial gliding motility. Sci Adv 2020; 6:eaay6616. [PMID: 32181348 PMCID: PMC7056307 DOI: 10.1126/sciadv.aay6616] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 12/10/2019] [Indexed: 06/10/2023]
Abstract
The gliding bacterium Flavobacterium johnsoniae is known to have an adhesin, SprB, that moves along the cell surface on a spiral track. Following viscous shear, cells can be tethered by the addition of an anti-SprB antibody, causing spinning at 3 Hz. Labeling the type 9 secretion system (T9SS) with a YFP fusion of GldL showed a yellow fluorescent spot near the rotation axis, indicating that the motor driving the motion is associated with the T9SS. The distance between the rotation axis and the track (90 nm) was determined after adding a Cy3 label for SprB. A rotary motor spinning a pinion of radius 90 nm at 3 Hz would cause a spot on its periphery to move at 1.5 μm/s, the gliding speed. We suggest the pinion drives a flexible tread that carries SprB along a track fixed to the cell surface. Cells glide when this adhesin adheres to the solid substratum.
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Affiliation(s)
- Abhishek Shrivastava
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
- The Biodesign Institute, Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, 85281, USA
| | - Howard C. Berg
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
- Rowland Institute at Harvard, Cambridge, MA 02142, USA
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Hosu BG, Berg HC. CW and CCW Conformations of the E. coli Flagellar Motor C-Ring Evaluated by Fluorescence Anisotropy. Biophys J 2019; 114:641-649. [PMID: 29414710 DOI: 10.1016/j.bpj.2017.12.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 11/30/2017] [Accepted: 12/01/2017] [Indexed: 11/17/2022] Open
Abstract
The molecular cascade that controls switching of the direction of rotation of Escherichia coli flagellar motors is well known, but the conformational changes that allow the rotor to switch are still unclear. The signaling molecule CheY, when phosphorylated, binds to the C-ring at the base of the rotor, raising the probability that the motor spins clockwise. When the concentration of CheY-P is so low that the motor rotates exclusively counterclockwise (CCW), the C-ring recruits more monomers of FliM and tetramers of FliN, the proteins to which CheY-P binds, thus increasing the motor's sensitivity to CheY-P and allowing it to switch once again. Motors that rotate exclusively CCW have more FliM and FliN subunits in their C-rings than motors that rotate exclusively clockwise. How are the new subunits accommodated? Does the diameter of the C-ring increase, or do FliM and FliN get packed in a different pattern, keeping the overall diameter of the C-ring constant? Here, by measuring fluorescence anisotropy of yellow fluorescent protein-labeled motors, we show that the CCW C-rings accommodate more FliM monomers without changing the spacing between them, and more FliN monomers at the same time as increasing their effective spacing and/or changing their orientation within the tetrameric structure.
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Affiliation(s)
- Basarab G Hosu
- Rowland Institute at Harvard, Harvard University, Cambridge, Massachusetts; Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts
| | - Howard C Berg
- Rowland Institute at Harvard, Harvard University, Cambridge, Massachusetts; Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts.
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10
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Shrivastava A, Berg HC. A Molecular Rack and Pinion Actuates a Cell-Surface Adhesin and Enables Bacterial Gliding Motility. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.2060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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11
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Affiliation(s)
- Kelly T Hughes
- Department of Biology, University of Utah, Salt Lake City, UT, USA.
| | - Howard C Berg
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.
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Shrivastava A, Roland T, Berg HC. The Screw-Like Movement of a Gliding Bacterium Is Powered by Spiral Motion of Cell-Surface Adhesins. Biophys J 2017; 111:1008-13. [PMID: 27602728 DOI: 10.1016/j.bpj.2016.07.043] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 07/10/2016] [Accepted: 07/26/2016] [Indexed: 11/24/2022] Open
Abstract
Flavobacterium johnsoniae, a rod-shaped bacterium, glides over surfaces at speeds of ∼2 μm/s. The propulsion of a cell-surface adhesin, SprB, is known to enable gliding. We used cephalexin to generate elongated cells with irregular shapes and followed their displacement in three dimensions. These cells rolled about their long axes as they moved forward, following a right-handed trajectory. We coated gold nanoparticles with an SprB antibody and tracked them in three dimensions in an evanescent field where the nanoparticles appeared brighter when they were closer to the glass. The nanoparticles followed a right-handed spiral trajectory on the surface of the cell. Thus, if SprB were to adhere to the glass rather than to a nanoparticle, the cell would move forward along a right-handed trajectory, as observed, but in a direction opposite to that of the nanoparticle.
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Affiliation(s)
- Abhishek Shrivastava
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts.
| | - Thibault Roland
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts
| | - Howard C Berg
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts.
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13
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Ko W, Lim S, Lee W, Kim Y, Berg HC, Peskin CS. Modeling polymorphic transformation of rotating bacterial flagella in a viscous fluid. Phys Rev E 2017; 95:063106. [PMID: 28709256 PMCID: PMC5656015 DOI: 10.1103/physreve.95.063106] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Indexed: 11/07/2022]
Abstract
The helical flagella that are attached to the cell body of bacteria such as Escherichia coli and Salmonella typhimurium allow the cell to swim in a fluid environment. These flagella are capable of polymorphic transformation in that they take on various helical shapes that differ in helical pitch, radius, and chirality. We present a mathematical model of a single flagellum described by Kirchhoff rod theory that is immersed in a fluid governed by Stokes equations. We perform numerical simulations to demonstrate two mechanisms by which polymorphic transformation can occur, as observed in experiments. First, we consider a flagellar filament attached to a rotary motor in which transformations are triggered by a reversal of the direction of motor rotation [L. Turner et al., J. Bacteriol. 182, 2793 (2000)10.1128/JB.182.10.2793-2801.2000]. We then consider a filament that is fixed on one end and immersed in an external fluid flow [H. Hotani, J. Mol. Biol. 156, 791 (1982)10.1016/0022-2836(82)90142-5]. The detailed dynamics of the helical flagellum interacting with a viscous fluid is discussed and comparisons with experimental and theoretical results are provided.
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Affiliation(s)
- William Ko
- Department of Mathematical Sciences, University of Cincinnati, 4199 French Hall West, Cincinnati, Ohio 45221, USA
| | - Sookkyung Lim
- Department of Mathematical Sciences, University of Cincinnati, 4199 French Hall West, Cincinnati, Ohio 45221, USA
| | - Wanho Lee
- National Institute for Mathematical Sciences, KT Daeduk 2 Research Center, 70, Yuseong-daero 1689-gil, Yuseong-gu, Daejeon 305-811, Republic of Korea
| | - Yongsam Kim
- Department of Mathematics, Chung-Ang University, Dongjakgu, Heukseokdong, Seoul 156-756, Republic of Korea
| | - Howard C Berg
- Rowland Institute at Harvard, 100 Edwin H. Land Boulevard, Cambridge, Massachusetts 02142, USA
| | - Charles S Peskin
- Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, New York 10012, USA
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14
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Abstract
A short review is given of recent work showing that the flagellar rotary motor of the bacterium Escherichia coli remodels to match its operating point (the fraction of time that it spins clockwise) to the requirements of the chemotaxis signaling network, and to provide the torque necessary to operate at different viscous loads.
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Affiliation(s)
- Howard C Berg
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, 02138.,Department of Physics, Harvard University, Cambridge, Massachusetts, 02138.,Rowland Institute at Harvard, Cambridge, Massachusetts, 02142
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15
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Lele PP, Roland T, Shrivastava A, Chen Y, Berg HC. The flagellar motor of Caulobacter crescentus generates more torque when a cell swims backward. Nat Phys 2016; 12:175-178. [PMID: 27499800 PMCID: PMC4973516 DOI: 10.1038/nphys3528] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 09/22/2015] [Indexed: 06/06/2023]
Abstract
Caulobacter crescentus, a monotrichous bacterium, swims by rotating a single right-handed helical filament. CW motor rotation thrusts the cell forward 1, a mode of motility known as the pusher mode; CCW motor rotation pulls the cell backward, a mode of motility referred to as the puller mode 2. The situation is opposite in E. coli, a peritrichous bacterium, where CCW rotation of multiple left-handed filaments drives the cell forward. The flagellar motor in E. coli generates more torque in the CCW direction than the CW direction in swimming cells 3,4. However, monotrichous bacteria including C. crescentus swim forward and backward at similar speeds, prompting the assumption that motor torques in the two modes are the same 5,6. Here, we present evidence that motors in C. crescentus develop higher torques in the puller mode than in the pusher mode, and suggest that the anisotropy in torque-generation is similar in two species, despite the differences in filament handedness and motor bias (probability of CW rotation).
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Affiliation(s)
- Pushkar P. Lele
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station TX 77843-3122
- Department of Molecular and Cellular Biology, Harvard University, Cambridge MA 02138
| | - Thibault Roland
- Department of Molecular and Cellular Biology, Harvard University, Cambridge MA 02138
| | - Abhishek Shrivastava
- Department of Molecular and Cellular Biology, Harvard University, Cambridge MA 02138
| | | | - Howard C. Berg
- Department of Molecular and Cellular Biology, Harvard University, Cambridge MA 02138
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16
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Abstract
Stimulation of Escherichia coli by exponential ramps of chemoattractants generates step changes in the concentration of the response regulator, CheY-P. Because flagellar motors are ultrasensitive, this should change the fraction of time that motors spin clockwise, the CWbias. However, early work failed to show changes in CWbias when ramps were shallow. This was explained by a model for motor remodeling that predicted plateaus in plots of CWbias versus [CheY-P]. We looked for these plateaus by examining distributions of CWbias in populations of cells with different mean [CheY-P]. We did not find such plateaus. Hence, we repeated the work on shallow ramps and found that motors did indeed respond. These responses were quantitatively described by combining motor remodeling with ultrasensitivity in a model that exhibited high sensitivities over a wide dynamic range.
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Affiliation(s)
- Pushkar P. Lele
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843–3122, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Abhishek Shrivastava
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Thibault Roland
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Howard C. Berg
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
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17
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Ping L, Wu Y, Hosu BG, Tang JX, Berg HC. Osmotic pressure in a bacterial swarm. Biophys J 2015; 107:871-8. [PMID: 25140422 DOI: 10.1016/j.bpj.2014.05.052] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 05/16/2014] [Accepted: 05/20/2014] [Indexed: 10/24/2022] Open
Abstract
Using Escherichia coli as a model organism, we studied how water is recruited by a bacterial swarm. A previous analysis of trajectories of small air bubbles revealed a stream of fluid flowing in a clockwise direction ahead of the swarm. A companion study suggested that water moves out of the agar into the swarm in a narrow region centered ∼ 30 μm from the leading edge of the swarm and then back into the agar (at a smaller rate) in a region centered ∼ 120 μm back from the leading edge. Presumably, these flows are driven by changes in osmolarity. Here, we utilized green/red fluorescent liposomes as reporters of osmolarity to verify this hypothesis. The stream of fluid that flows in front of the swarm contains osmolytes. Two distinct regions are observed inside the swarm near its leading edge: an outer high-osmolarity band (∼ 30 mOsm higher than the agar baseline) and an inner low-osmolarity band (isotonic or slightly hypotonic to the agar baseline). This profile supports the fluid-flow model derived from the drift of air bubbles and provides new (to our knowledge) insights into water maintenance in bacterial swarms. High osmotic pressure at the leading edge of the swarm extracts water from the underlying agar and promotes motility. The osmolyte is of high molecular weight and probably is lipopolysaccharide.
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Affiliation(s)
- Liyan Ping
- Rowland Institute at Harvard, Cambridge, Massachusetts
| | - Yilin Wu
- Department of Physics, Chinese University of Hong Kong, Hong Kong, P. R. China
| | - Basarab G Hosu
- Rowland Institute at Harvard, Cambridge, Massachusetts; Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts
| | - Jay X Tang
- Rowland Institute at Harvard, Cambridge, Massachusetts; Physics Department, Brown University, Providence, Rhode Island
| | - Howard C Berg
- Rowland Institute at Harvard, Cambridge, Massachusetts; Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts.
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18
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19
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Shrivastava A, Lele PP, Berg HC. A rotary motor drives Flavobacterium gliding. Curr Biol 2015; 25:338-341. [PMID: 25619763 DOI: 10.1016/j.cub.2014.11.045] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 11/10/2014] [Accepted: 11/17/2014] [Indexed: 12/23/2022]
Abstract
Cells of Flavobacterium johnsoniae, a rod-shaped bacterium devoid of pili or flagella, glide over glass at speeds of 2-4 μm/s [1]. Gliding is powered by a protonmotive force [2], but the machinery required for this motion is not known. Usually, cells move along straight paths, but sometimes they exhibit a reciprocal motion, attach near one pole and flip end over end, or rotate. This behavior is similar to that of a Cytophaga species described earlier [3]. Development of genetic tools for F. johnsoniae led to discovery of proteins involved in gliding [4]. These include the surface adhesin SprB that forms filaments about 160 nm long by 6 nm in diameter, which, when labeled with a fluorescent antibody [2] or a latex bead [5], are seen to move longitudinally down the length of a cell, occasionally shifting positions to the right or the left. Evidently, interaction of these filaments with a surface produces gliding. To learn more about the gliding motor, we sheared cells to reduce the number and size of SprB filaments and tethered cells to glass by adding anti-SprB antibody. Cells spun about fixed points, mostly counterclockwise, rotating at speeds of 1 Hz or more. The torques required to sustain such speeds were large, comparable to those generated by the flagellar rotary motor. However, we found that a gliding motor runs at constant speed rather than at constant torque. Now, there are three rotary motors powered by protonmotive force: the bacterial flagellar motor, the Fo ATP synthase, and the gliding motor.
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Affiliation(s)
- Abhishek Shrivastava
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Pushkar P Lele
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Howard C Berg
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
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20
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Branch RW, Sayegh MN, Shen C, Nathan VSJ, Berg HC. Adaptive remodelling by FliN in the bacterial rotary motor. J Mol Biol 2014; 426:3314-3324. [PMID: 25046382 DOI: 10.1016/j.jmb.2014.07.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Revised: 07/07/2014] [Accepted: 07/11/2014] [Indexed: 01/19/2023]
Abstract
Sensory adaptation in the Escherichia coli chemosensory pathway has been the subject of interest for decades, with investigation focusing on the receptors that process extracellular inputs. Recent studies demonstrate that the flagellar motors responsible for cell locomotion also play a role, adding or subtracting FliM subunits to maximise sensitivity to pathway signals. It is difficult to reconcile this FliM remodelling with the observation that partner FliN subunits are relatively static fixtures in the motor. By fusing a fluorescent protein internally to FliN, we show that there is in fact significant FliN remodelling. The kinetics and stoichiometry of FliN in steady state and in adapting motors are investigated and found to match the behaviour of FliM in all respects except for timescale where FliN rates are about 4 times slower. We notice that motor adaptation is slower in the presence of the fluorescent protein, indicating a possible source for the difference. The behaviour of FliM and FliN is consistent with a kinetic and stoichiometric model that contradicts the traditional view of a packed, rigid motor architecture.
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Affiliation(s)
- Richard W Branch
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Michael N Sayegh
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Chong Shen
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Vedavalli S J Nathan
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Howard C Berg
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
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21
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Abstract
The flagellar motor of Escherichia coli adapts to changes in the steady-state level of the chemotaxis response regulator, CheY-P, by adjusting the number of FliM molecules to which CheY-P binds. Previous measurements of motor ultrasensitivity have been made on cells containing different amounts of CheY-P and, thus, different amounts of FliM in flagellar motors. Here, we designed an experiment to measure the sensitivity of motors containing fixed amounts of FliM, finding Hill coefficients about twice as large as those observed before. This ultrasensitivity provides further insights into the motor switching mechanism and plays important roles in chemotaxis signal amplification and coordination of multiple motors. The Hill coefficients observed here appear to be the highest known for allosteric protein complexes, either biological or synthetic. Extreme motor ultrasensitivity broadens our understanding of mechanisms of allostery and serves as an inspiration for future design of synthetic protein switches.
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Affiliation(s)
- Junhua Yuan
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
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22
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Abstract
We analyze a model for motor-level adaptation in Escherichia coli based upon the premise that clockwise (CW) and counter-clockwise (CCW) states have different preferred numbers of FliM subunits. We show that this model provides a simple mechanism for the recently observed motor-level adaptation, and it also explains the long-lasting puzzle on the thresholds observed when tethered cells are used to monitor responses to temporal ramps. We note that the motor-level adaptation has the same negative-feedback network design as the upstream receptor-level adaptation, and the tandem architecture of one control circuit followed by the other mitigates the effects of cell-to-cell variation and broadens the range of stimuli over which cells optimally respond.
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Affiliation(s)
- Yuhai Tu
- IBM T. J. Watson Research Center, 1101 Kitchwan Rd., Yorktown Heights, NY 10598, USA.
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23
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Abstract
In the bacterial chemotaxis network, receptor clusters process input1–3, and flagellar motors generate output4. Receptor and motor complexes are coupled by the diffusible protein CheY-P. Receptor output (the steady-state concentration of CheY-P) varies from cell to cell5. However, the motor is ultrasensitive, with a narrow [CheY-P] operating range6. How might the match between receptor output and motor input be optimized? Here we show that the motor can shift its operating range by changing its composition. The number of FliM subunits in the C-ring increases in response to a decrement in the concentration of CheY-P, increasing motor sensitivity. This shift in sensitivity explains the slow partial adaptation observed in mutants that lack the receptor methyltransferase and methylesterase7–8 and why motors exhibit signal-dependent FliM turnover9. Adaptive remodelling is likely to be a common feature in the operation of many molecular machines.
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Affiliation(s)
- Junhua Yuan
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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24
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Shimizu TS, Tu Y, Berg HC. A modular gradient-sensing network for chemotaxis in Escherichia coli revealed by responses to time-varying stimuli. Mol Syst Biol 2010; 6:382. [PMID: 20571531 PMCID: PMC2913400 DOI: 10.1038/msb.2010.37] [Citation(s) in RCA: 157] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2009] [Accepted: 05/07/2010] [Indexed: 11/09/2022] Open
Abstract
Combining in vivo FRET with time-varying stimuli, such as steps, ramps, and sinusoids allowed deduction of the molecular mechanisms underlying cellular signal processing. The bacterial chemotaxis pathway can be described as a two-module feedback circuit, the transfer functions of which we have characterized quantitatively by experiment. Model-driven experimental design allowed the use of a single FRET pair for measurements of both transfer functions of the pathway. The adaptation module's transfer function revealed that feedback near steady state is weak, consistent with high sensitivity to shallow gradients, but also strong steady-state fluctuations in pathway output. The measured response to oscillatory stimuli defines the frequency band over which the chemotaxis system can compute time derivatives.
In searching for better environments, bacteria sample their surroundings by random motility, and make temporal comparisons of experienced sensory cues to bias their movement toward favorable directions (Berg and Brown, 1972). Thus, the problem of sensing spatial gradients is reduced to time-derivative computations, carried out by a signaling pathway that is well characterized at the molecular level in Escherichia coli. Here, we study the physiology of this signal processing system in vivo by fluorescence resonance energy transfer (FRET) experiments in which live cells are stimulated by time-varying chemoeffector signals. By measuring FRET between the active response regulator of the pathway CheY-P and its phosphatase CheZ, each labeled with GFP variants, we obtain a readout that is directly proportional to pathway activity (Sourjik et al, 2007). We analyze the measured response functions in terms of mechanistic models of signaling, and discuss functional consequences of the observed quantitative characteristics. Experiments are guided by a coarse-grained modular model (Tu et al, 2008) of the sensory network (Figure 1), in which we identify two important ‘transfer functions': one corresponding to the receptor–kinase complex, which responds to changes in input ligand concentration on a fast time scale, and another corresponding to the adaptation system, which provides negative feedback, opposing the effect of ligand on a slower time scale. For the receptor module, we calibrate an allosteric MWC-type model of the receptor–kinase complex by FRET measurements of the ‘open-loop' transfer function G([L],m) using step stimuli. This calibration provides a basis for using the same FRET readout (between CheY-P and CheZ) to further study properties of the adaptation module. It is well known that adaptation in E. coli's chemotaxis system uses integral feedback, which guarantees exact restoration of the baseline activity after transient responses to step stimuli (Barkai and Leibler, 1997; Yi et al, 2000). However, the output of time-derivative computations during smoothly varying stimuli depends not only on the presence of integral feedback, but also on what is being integrated. As this integrand can in general be any function of the output, we represent it by a black-box function F(a) in our model, and set out to determine its shape by experiments with time-varying stimuli. We first apply exponential ramp stimuli—waveforms in which the logarithm of the stimulus level varies linearly with time, at a fixed rate r. It was shown many years ago that during such a stimulus, the kinase output of the pathway changes to a new constant value, ac that is dependent on the applied ramp rate, r (Block et al, 1983). A plot of ac versus r (Figure 5A) can thus be considered as an output of time-derivative computations by the network, and could also be used to study the ‘gradient sensitivity' of bacteria traveling at constant speeds. To obtain the feedback transfer function, F(a), we apply a simple coordinate transformation, identified using our model, to the same ramp-response data (Figure 5B). This function reveals how the temporal rate of change of the feedback signal m depends on the current output signal a. The shape of this function is analyzed using a biochemical reaction scheme, from which in vivo kinetic parameters of the feedback enzymes, CheR and CheB, are extracted. The fitted Michaelis constants for these enzymatic reactions are small compared with the steady-state abundance of their substrates, thus indicating that these enzymes operate close to saturation in vivo. The slope of the function near steady state can be used to assess the strength of feedback, and to compute the relaxation time of the system, τm. Relaxation is found to be slow (i.e. large τm), consistent with large fluctuations about the steady-state activity caused by the near-saturation kinetics of the feedback enzymes (Emonet and Cluzel, 2008). Finally, exponential sine-wave stimuli are used to map out the system's frequency response (Figure 5C). The measured data points for both the amplitude and phase of the response are found to be in excellent agreement with model predictions based on parameters from the independently measured step and ramp responses. No curve fitting was required to obtain this agreement. Although the amplitude response as a function of frequency resembles a first-order high-pass filter with a well-defined cutoff frequency, νm, we point out that the chemotaxis pathway is actually a low-pass filter if the time derivative of the input is viewed as the input signal. In this latter perspective, νm defines an upper bound for the frequency band over which time-derivative computations can be carried out. The two types of measurements yield complementary information regarding time-derivative computations by E. coli. The ramp-responses characterize the asymptotically constant output when a temporal gradient is held fixed over extended periods. Interestingly, the ramp responses do not depend on receptor cooperativity, but only on properties of the adaptation system, and thus can be used to reveal the in vivo adaptation kinetics, even outside the linear regime of the kinase response. The frequency response is highly relevant in considering spatial searches in the real world, in which experienced gradients are not held fixed in time. The characteristic cutoff frequency νm is found by working within the linear regime of the kinase response, and depends on parameters from both modules (it increases with both cooperativity in the receptor module, and the strength of feedback in the adaptation module). Both ramp responses and sine-wave responses were measured at two different temperatures (22 and 32°C), and found to differ significantly. Both the slope of F(a) near steady state, from ramp experiments, and the characteristic cutoff frequency, from sine-wave experiments, were higher by a factor of ∼3 at 32°C. Fits of the enzymatic model to F(a) suggest that temperature affects the maximal velocity (Vmax) more strongly than the Michaelis constants (Km) for CheR and CheB. Successful application of inter-molecular FRET in live cells using GFP variants always requires some degree of serendipity. Genetic fusions to these bulky fluorophores can impair the function of the original proteins, and even when fusions are functional, efficient FRET still requires the fused fluorophores to come within the small (<10 nm) Förster radius on interactions between the labeled proteins. Thus, when a successful FRET pair is identified, it is desirable to make the most of it. We have shown here that combined with careful temporal control of input stimuli, and appropriately calibrated models, a single FRET pair can be used to study the structure of multiple transfer functions within a signaling network. The Escherichia coli chemotaxis-signaling pathway computes time derivatives of chemoeffector concentrations. This network features modules for signal reception/amplification and robust adaptation, with sensing of chemoeffector gradients determined by the way in which these modules are coupled in vivo. We characterized these modules and their coupling by using fluorescence resonance energy transfer to measure intracellular responses to time-varying stimuli. Receptor sensitivity was characterized by step stimuli, the gradient sensitivity by exponential ramp stimuli, and the frequency response by exponential sine-wave stimuli. Analysis of these data revealed the structure of the feedback transfer function linking the amplification and adaptation modules. Feedback near steady state was found to be weak, consistent with strong fluctuations and slow recovery from small perturbations. Gradient sensitivity and frequency response both depended strongly on temperature. We found that time derivatives can be computed by the chemotaxis system for input frequencies below 0.006 Hz at 22°C and below 0.018 Hz at 32°C. Our results show how dynamic input–output measurements, time honored in physiology, can serve as powerful tools in deciphering cell-signaling mechanisms.
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Affiliation(s)
- Thomas S Shimizu
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
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25
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Yuan J, Berg HC. Thermal and solvent-isotope effects on the flagellar rotary motor near zero load. Biophys J 2010; 98:2121-6. [PMID: 20483319 DOI: 10.1016/j.bpj.2010.01.061] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Revised: 01/15/2010] [Accepted: 01/22/2010] [Indexed: 11/28/2022] Open
Abstract
In Escherichia coli, the behavior of the flagellar rotary motor near zero load can be studied by scattering light from nanogold spheres attached to proximal hooks of cells lacking flagellar filaments. We used this method to monitor changes in speed when cells were subjected to changes in temperature or shifted from a medium made with H(2)O to one made with D(2)O. In H(2)O, the speed increased with temperature in a near-exponential manner, with an activation enthalpy of 52 +/- 4 kJ/mol (12.0 +/- 1.0 kcal/mol). In D(2)O, the speed increased in a similar manner, with an activation enthalpy of 50 +/- 4 kJ/mol. The speed in H(2)O was higher than that in D(2)O by a factor of 1.53 +/- 0.14. We performed comparison studies of variations in temperature and solvent isotope, using motors operating at high loads. The variations were small, consistent with previous observations. The implications of these results for proton translocation are discussed.
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Affiliation(s)
- Junhua Yuan
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
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26
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Berg HC, Purcell EM. A method for separating according to mass a mixture of macromolecules or small particles suspended in a fluid, I. Theory. Proc Natl Acad Sci U S A 2010; 58:862-9. [PMID: 16578671 PMCID: PMC335716 DOI: 10.1073/pnas.58.3.862] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- H C Berg
- LYMAN LABORATORY OF PHYSICS, HARVARD UNIVERSITY
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27
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Abstract
Flagellated bacteria, such as Escherichia coli, are able to swim up gradients of chemical attractants by modulating the direction of rotation of their flagellar motors, which spin alternately clockwise (CW) and counterclockwise (CCW). Chemotactic behavior has been studied under a variety of conditions, mostly at high loads (at large motor torques). Here, we examine motor switching at low loads. Nano-gold spheres of various sizes were attached to hooks (the flexible coupling at the base of the flagellar filament) of cells lacking flagellar filaments in media containing different concentrations of the viscous agent Ficoll. The speeds and directions of rotation of the spheres were measured. Contrary to the case at high loads, motor switching rates increased appreciably with load. Both the CW-->CCW and CCW-->CW switching rates increased linearly with motor torque. Evidently, the switch senses stator-rotor interactions as well as the CheY-P concentration.
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Affiliation(s)
- Junhua Yuan
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
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28
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Abstract
There are mutants of Salmonella enterica (with mutations in fliF and fliL) that shed flagella when they are swimming in a viscous medium or on the surface of soft agar. Filaments with hooks and the distal rod segment FlgG are recovered. We tried to extract flagellar filaments from such cells by pulling on them with an optical trap but failed, even when we used forces large enough to straighten the filaments. Thus, flagella are firmly anchored.
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29
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Elizabeth Hulme S, DiLuzio WR, Shevkoplyas SS, Turner L, Mayer M, Berg HC, Whitesides GM. Using ratchets and sorters to fractionate motile cells of Escherichia coli by length. Lab Chip 2008; 8:1888-1895. [PMID: 18941690 DOI: 10.1039/b809892a] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
This paper describes the fabrication of a composite agar/PDMS device for enriching short cells in a population of motile Escherichia coli. The device incorporated ratcheting microchannels, which directed the motion of swimming cells of E. coli through the device, and three sorting junctions, which isolated successively shorter populations of bacteria. The ratcheting microchannels guided cells through the device with an average rate of displacement of (32 +/- 9) microm s(-1). Within the device, the average length of the cells decreased from 3.8 microm (Coefficient of Variation, CV: 21%) at the entrance, to 3.4 microm (CV: 16%) after the first sorting junction, to 3.2 mum (CV: 19%) after the second sorting junction, to 3.0 mum (CV: 19%) after the third sorting junction.
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Affiliation(s)
- S Elizabeth Hulme
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
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30
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Affiliation(s)
- Howard C Berg
- Departments of Molecular and Cellular Biology and of Physics, Harvard University, Cambridge, Massachusetts 02138, USA.
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31
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Abstract
Cells swimming in confined environments are attracted by surfaces. We measure the steady-state distribution of smooth-swimming bacteria (Escherichia coli) between two glass plates. In agreement with earlier studies, we find a strong increase of the cell concentration at the boundaries. We demonstrate theoretically that hydrodynamic interactions of the swimming cells with solid surfaces lead to their reorientation in the direction parallel to the surfaces, as well as their attraction by the closest wall. A model is derived for the steady-state distribution of swimming cells, which compares favorably with our measurements. We exploit our data to estimate the flagellar propulsive force in swimming E. coli.
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Affiliation(s)
- Allison P Berke
- Department of Mathematics, Massachusetts Institute of Technology, 77 Mass. Avenue, Cambridge, Massachusetts 02139, USA
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32
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Abstract
Biofilms are multicellular aggregates of sessile bacteria encased by an extracellular matrix and are important medically as a source of drug-resistant microbes. In Bacillus subtilis, we found that an operon required for biofilm matrix biosynthesis also encoded an inhibitor of motility, EpsE. EpsE arrested flagellar rotation in a manner similar to that of a clutch, by disengaging motor force-generating elements in cells embedded in the biofilm matrix. The clutch is a simple, rapid, and potentially reversible form of motility control.
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Affiliation(s)
- Kris M Blair
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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33
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Abstract
Members of the bacterial phylum Spirochaetes are generally helical cells propelled by periplasmic flagella. The spirochete Treponema primitia is interesting because of its mutualistic role in the termite gut, where it is believed to cooperate with protozoa that break down cellulose and produce H(2) as a by-product. Here we report the ultrastructure of T. primitia as obtained by electron cryotomography of intact, frozen-hydrated cells. Several previously unrecognized external structures were revealed, including bowl-like objects decorating the outer membrane, arcades of hook-shaped proteins winding along the exterior and tufts of fibrils extending from the cell tips. Inside the periplasm, cone-like structures were found at each pole. Instead of the single peptidoglycan layer typical of other Gram-negative bacteria, two distinct periplasmic layers were observed. These layers formed a central open space that contained two flagella situated adjacent to each other. In some areas, the inner membrane formed flattened invaginations that protruded into the cytoplasm. High-speed light microscopic images of swimming T. primitia cells showed that cell bodies remained rigid and moved in a helical rather than planar motion. Together, these findings support the 'rolling cylinder' model for T. primitia motility that posits rotation of the protoplasmic cylinder within the outer sheath.
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Affiliation(s)
- Gavin E Murphy
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
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34
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Abstract
We compared the abilities of media from agar plates surrounding swarming and nonswarming cells of Salmonella enterica serovar Typhimurium to wet a nonpolar surface by measuring the contact angles of small drops. The swarming cells were wild type for chemotaxis, and the nonswarming cells were nonchemotactic mutants with motor biases that were counterclockwise (cheY) or clockwise (cheZ). The latter strains have been shown to be defective for swarming because the agar remains dry (Q. Wang, A. Suzuki, S. Mariconda, S. Porwollik, and R. M. Harshey, EMBO J. 24:2034-2042, 2005). We found no differences in the abilities of the media surrounding these cells, either wild type or mutant, to wet a low-energy surface (freshly prepared polydimethylsiloxane); although, their contact angles were smaller than that of the medium harvested from the underlying agar. So the agent that promotes wetness produced by wild-type cells is not a surfactant; it is an osmotic agent.
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Affiliation(s)
- Bryan G Chen
- Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Ave., Cambridge, MA 02138, USA
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35
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Abstract
Many bacteria swim by rotating thin helical filaments that extend into the external medium, as with common bacteria, or run beneath the outer membrane, as with spirochetes. Each filament is driven at its base by a motor that turns alternately clockwise and counterclockwise. The motor-filament complex is called a flagellum. Other kinds of bacteria glide, but their organelles of locomotion are not known. Since bacteria are microscopic and live in an aqueous environment, they swim at low Reynolds' number; cyclic motion works (e.g. rotation of a helix) but reciprocal motion does not (e.g. stroking of a singly hinged oar). By measuring concentrations of certain chemicals as they move through their environment, making temporal comparisons and modulating the direction of flagellar rotation, bacteria accumulate in regions that they find more favourable. Studies of bacterial chemotaxis are highly advanced, particularly for the peritrichously flagellated species Escherichia coli. A great deal is known about chemoreception, receptor-flagellar coupling and adaptation. Recently it has been found that E. coli can aggregate in response to signals generated by the cells themselves. Complex patterns form with remarkable symmetries.
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Affiliation(s)
- H C Berg
- Department of Cellular & Developmental Biology, Harvard University, Cambridge, MA 02138
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36
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Abstract
The two-component pathway in Escherichia coli chemotaxis has become a paradigm for bacterial signal processing. Genetics and biochemistry of the pathway as well as physiological responses have been studied in detail. Despite its relative simplicity, the chemotaxis pathway is renowned for its ability to amplify and integrate weak signals and for its robustness against various kinds of perturbations. All this information inspired multiple attempts at mathematical analysis and computer modeling, but a quantitative understanding of the pathway was hampered by our inability to follow the signal processing in vivo. To address this problem, we developed assays based on fluorescence resonance energy transfer (FRET) and bioluminescence resonance energy transfer (BRET) that enabled us to monitor activity-dependent protein interactions in real time directly in living cells. Here, we describe quantitative applications of these assays in cell populations and on a single-cell level to study the interaction of the phosphorylated response regulator CheY with its phosphatase CheZ. Since this interaction defines the rate of CheY dephosphorylation, which at steady state equals the rate of CheY phosphorylation, it can be used to characterize intracellular kinase activity and thus to analyze properties of the chemotaxis signaling network.
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Affiliation(s)
- Victor Sourjik
- ZMBH (Center for Molecular Biology Heidelberg), University of Heidelberg, Heidelberg, Germany
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37
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Abstract
Bacteria swim by rotating long thin helical filaments, each driven at its base by a reversible rotary motor. When the motors of peritrichous cells turn counterclockwise (CCW), their filaments form bundles that drive the cells forward. We imaged fluorescently labeled cells of Escherichia coli with a high-speed charge-coupled-device camera (500 frames/s) and measured swimming speeds, rotation rates of cell bodies, and rotation rates of flagellar bundles. Using cells stuck to glass, we studied individual filaments, stopping their rotation by exposing the cells to high-intensity light. From these measurements we calculated approximate values for bundle torque and thrust and body torque and drag, and we estimated the filament stiffness. For both immobilized and swimming cells, the motor torque, as estimated using resistive force theory, was significantly lower than the motor torque reported previously. Also, a bundle of several flagella produced little more torque than a single flagellum produced. Motors driving individual filaments frequently changed directions of rotation. Usually, but not always, this led to a change in the handedness of the filament, which went through a sequence of polymorphic transformations, from normal to semicoiled to curly 1 and then, when the motor again spun CCW, back to normal. Motor reversals were necessary, although not always sufficient, to cause changes in filament chirality. Polymorphic transformations among helices having the same handedness occurred without changes in the sign of the applied torque.
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38
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Abstract
Bacterial flagella can adopt several different helical shapes in response to varying environmental conditions. A geometric model by Calladine ascribes these discrete shape changes to cooperative transitions between two stable tertiary structures of the constituent protein, flagellin, and predicts an ordered set of 12 helical states called polymorphic forms. Using long polymers of purified flagellin, we demonstrate controlled, reversible transformations between different polymorphic forms. While pulling on a single filament using an optical tweezer, we record the progressive transformation of the filament and also measure the force-extension curve. Both normal and coiled polymorphic forms stretch elastically with a bending stiffness of 3.5 pN x microm(2). At a force threshold of 4-7 pN or 3-5 pN (for normal and coiled forms, respectively), a fraction of the filament suddenly transforms to the next, longer, polymorphic form. This transformation is not deterministic because the force and amount of transformation vary from pull to pull. In addition, the force is highly dependent on stretching rate, suggesting that polymorphic transformation is associated with an activation energy.
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Affiliation(s)
- Nicholas C Darnton
- Rowland Institute at Harvard, Harvard University, Cambridge, Massachusetts 02142, USA
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39
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Abstract
Chemoreceptors of the bacterium Escherichia coli are thought to form trimers of homodimers that undergo conformational changes upon ligand binding and thereby signal a cytoplasmic kinase. We monitored the physical responses of trimers in living cells lacking other chemotaxis proteins by fluorescently tagging receptors and measuring changes in fluorescence anisotropy. These changes were traced to changes in energy transfer between fluorophores on different dimers of a trimer: attractants move these fluorophores farther apart, and repellents move them closer together. These measurements allowed us to define the responses of bare receptor oligomers to ligand binding and compare them to the corresponding response in kinase activity. Receptor responses could be fit by a simple "two-state" model in which receptor dimers are in either active or inactive conformations, from which energy bias and dissociation constants could be estimated. Comparison with responses in kinase-activity indicated that higher-order interactions are dominant in receptor clusters.
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Affiliation(s)
- Ady Vaknin
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
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40
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Shimizu TS, Delalez N, Pichler K, Berg HC. Monitoring bacterial chemotaxis by using bioluminescence resonance energy transfer: absence of feedback from the flagellar motors. Proc Natl Acad Sci U S A 2006; 103:2093-7. [PMID: 16452163 PMCID: PMC1413742 DOI: 10.1073/pnas.0510958103] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We looked for a feedback system in Escherichia coli that might sense the rotational bias of flagellar motors and regulate the activity of the chemotaxis receptor kinase. Our search was based on the assumption that any machinery that senses rotational bias will be perturbed if flagellar rotation stops. We monitored the activity of the kinase in swimming cells by bioluminescence resonance energy transfer (BRET) between Renilla luciferase fused to the phosphatase, CheZ, and yellow fluorescent protein fused to the response regulator, CheY. Then we jammed the flagellar motors by adding an antifilament antibody that crosslinks adjacent filaments in flagellar bundles. At steady state, the rate of phosphorylation of CheY is equal to the rate of dephosphorylation of CheY-P, which is proportional to the degree of association between CheZ and CheY-P, the quantity sensed by BRET. No changes were observed, even upon addition of an amount of antibody that stopped the swimming of >95% of cells within a few seconds. So, the kinase does not appear to be sensitive to motor output. The BRET technique is complementary to one based on FRET, described previously. Its reliability was confirmed by measurements of the response of cells to the addition of attractants.
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Affiliation(s)
- Thomas S. Shimizu
- Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138
| | - Nicolas Delalez
- Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138
| | - Klemens Pichler
- Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138
| | - Howard C. Berg
- Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138
- To whom correspondence should be addressed. E-mail:
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41
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Abstract
Two-component signaling systems play a major role in the long-term adaptation of microorganisms to changes in osmolarity, but how osmoreceptors work is not well understood. Temporal changes in solute concentration are sensed by the chemotaxis system in Escherichia coli, enabling these bacteria to avoid regions of high osmolarity. To study how osmolarity is detected in this system, we fused yellow fluorescent protein (YFP) to the C terminus of the serine or aspartate chemoreceptor, monitored the steady-state fluorescence polarization of YFP, and found that the polarization decreased substantially upon addition of osmotic agents. This decrease was due to an increase in fluorescence resonance energy transfer between YFP fluorophores in adjacent homodimers within trimers of dimers. Thus, changes in homodimer spacing and/or orientation appear to initiate osmotactic signaling.
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Affiliation(s)
- Ady Vaknin
- Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
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42
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Abstract
When grown on a soft agar surface in a rich medium, cells of Salmonella typhimurium elongate, produce extra flagella and move over the surface in a coordinated manner. In mutants with defects in the chemotaxis signaling pathway, the agar plates remain dry and the cells' flagella are short. Recent work shows that the anti-sigma factor controlling late-gene flagellar synthesis is secreted less by flagella when things are dry: the flagellum senses wetness.
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Affiliation(s)
- Howard C Berg
- Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts 02138, USA.
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43
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DiLuzio WR, Turner L, Mayer M, Garstecki P, Weibel DB, Berg HC, Whitesides GM. Escherichia coli swim on the right-hand side. Nature 2005; 435:1271-4. [PMID: 15988531 DOI: 10.1038/nature03660] [Citation(s) in RCA: 360] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2005] [Accepted: 04/21/2005] [Indexed: 11/09/2022]
Abstract
The motion of peritrichously flagellated bacteria close to surfaces is relevant to understanding the early stages of biofilm formation and of pathogenic infection. This motion differs from the random-walk trajectories of cells in free solution. Individual Escherichia coli cells swim in clockwise, circular trajectories near planar glass surfaces. On a semi-solid agar substrate, cells differentiate into an elongated, hyperflagellated phenotype and migrate cooperatively over the surface, a phenomenon called swarming. We have developed a technique for observing isolated E. coli swarmer cells moving on an agar substrate and confined in shallow, oxidized poly(dimethylsiloxane) (PDMS) microchannels. Here we show that cells in these microchannels preferentially 'drive on the right', swimming preferentially along the right wall of the microchannel (viewed from behind the moving cell, with the agar on the bottom). We propose that when cells are confined between two interfaces--one an agar gel and the second PDMS--they swim closer to the agar surface than to the PDMS surface (and for much longer periods of time), leading to the preferential movement on the right of the microchannel. Thus, the choice of materials guides the motion of cells in microchannels.
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Affiliation(s)
- Willow R DiLuzio
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
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44
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Altman S, Bassler BL, Beckwith J, Belfort M, Berg HC, Bloom B, Brenchley JE, Campbell A, Collier RJ, Connell N, Cozzarelli NR, Craig NL, Darst S, Ebright RH, Elledge SJ, Falkow S, Galan JE, Gottesman M, Gourse R, Grindley NDF, Gross CA, Grossman A, Hochschild A, Howe M, Hurwitz J, Isberg RR, Kaplan S, Kornberg A, Kustu SG, Landick RC, Landy A, Levy SB, Losick R, Long SR, Maloy SR, Mekalanos JJ, Neidhardt FC, Pace NR, Ptashne M, Roberts JW, Roth JR, Rothman-Denes LB, Salyers A, Schaechter M, Shapiro L, Silhavy TJ, Simon MI, Walker G, Yanofsky C, Zinder N. An Open Letter to Elias Zerhouni. Science 2005; 307:1409-10. [PMID: 15746409 DOI: 10.1126/science.307.5714.1409c] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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45
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Abstract
Two-component signaling systems, in which a receptor-coupled kinase is used to control the phosphorylation level of a response regulator, are commonly used in bacteria to sense their environment. In the chemotaxis system of Escherichia coli, the receptors, and thus the kinase, are clustered on the inner cell membrane. The phosphatase of this system also is recruited to receptor clusters, but the reason for this association is not clear. By using FRET imaging of single cells, we show that in vivo the phosphatase activity is substantially larger at the cluster, indicating that the signaling source (the kinase) and the signaling sink (the phosphatase) tend to be located at the same place in the cell. When this association is disrupted, a gradient in the concentration of the phosphorylated response regulator appears, and the chemotactic response is degraded. Such colocalization is inevitable in systems in which the activity of the kinase and the phosphatase are produced by the same enzyme. Evidently, this design enables a more rapid and spatially uniform response.
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Affiliation(s)
- Ady Vaknin
- Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
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46
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Abstract
Bacterial chemoreceptors are embedded in the inner cell membrane in tight clusters. We show that changes in receptor methylation that generate large changes in kinase activity have relatively little effect on cluster morphology. Thus, changes in receptor activity do not appear to be mediated by changes in receptor-kinase assembly.
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47
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Abstract
We activated a solid-fluid interface by attaching flagellated bacteria to a solid surface. We adsorbed swarmer cells of Serratia marcescens to polydimethylsiloxane or polystyrene. The cell bodies formed a densely packed monolayer while their flagella continued to rotate freely. Motion of the fluid close to an extended flat surface, visualized with tracer beads, was dramatically enhanced compared to the motion farther away. The tracer beads revealed complex ever-changing flow patterns, some linear (rivers), others rotational (whirlpools). Typical features of this flow were small (tens of micro m) and reasonably stable (many minutes). The surface performed active mixing equivalent to diffusion with a coefficient of 2 x 10(-7) cm(2)/s. We call these flat constructs "bacterial carpets". When attached to polystyrene beads or to fragments of polydimethylsiloxane, the bacteria generated both translation and rotation. We call these constructs "auto-mobile beads" or "auto-mobile chips". Given the size and strength of the flow patterns near the carpets, the motion must be generated by small numbers of coordinated flagella. We should be able to produce larger and longer-range effects by increasing coordination.
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Affiliation(s)
- Nicholas Darnton
- Rowland Institute at Harvard, Cambridge, Massachusetts 02142, USA
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48
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Jaffe JD, Stange-Thomann N, Smith C, DeCaprio D, Fisher S, Butler J, Calvo S, Elkins T, FitzGerald MG, Hafez N, Kodira CD, Major J, Wang S, Wilkinson J, Nicol R, Nusbaum C, Birren B, Berg HC, Church GM. The complete genome and proteome of Mycoplasma mobile. Genome Res 2004; 14:1447-61. [PMID: 15289470 PMCID: PMC509254 DOI: 10.1101/gr.2674004] [Citation(s) in RCA: 201] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Although often considered "minimal" organisms, mycoplasmas show a wide range of diversity with respect to host environment, phenotypic traits, and pathogenicity. Here we report the complete genomic sequence and proteogenomic map for the piscine mycoplasma Mycoplasma mobile, noted for its robust gliding motility. For the first time, proteomic data are used in the primary annotation of a new genome, providing validation of expression for many of the predicted proteins. Several novel features were discovered including a long repeating unit of DNA of approximately 2435 bp present in five complete copies that are shown to code for nearly identical yet uniquely expressed proteins. M. mobile has among the lowest DNA GC contents (24.9%) and most reduced set of tRNAs of any organism yet reported (28). Numerous instances of tandem duplication as well as lateral gene transfer are evident in the genome. The multiple available complete genome sequences for other motile and immotile mycoplasmas enabled us to use comparative genomic and phylogenetic methods to suggest several candidate genes that might be involved in motility. The results of these analyses leave open the possibility that gliding motility might have arisen independently more than once in the mycoplasma lineage.
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Affiliation(s)
- Jacob D Jaffe
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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49
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Abstract
Mycoplasma mobile glides on surfaces at up to 7 microm/s by an unknown mechanism. We studied the energetics that power gliding by using a novel, growth medium-free system. We found that cells could glide in defined media if the glass substrate is preconditioned by exposure to horse serum. The active component that potentiates gliding is sensitive to proteinase K treatment. We used the defined medium system to test the effect of various inhibitors, ionophores, and poisons on motility of M. mobile. Valinomycin, carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone (FCCP), N,N'-dicyclohexylcarbodiimide, phenamil, amiloride, rifampin, and puromycin had no short-term effects on gliding. We also confirmed that we were able to modulate the membrane potential with valinomycin and FCCP by using a potential-sensitive dye. Shifting the pH likewise had no effect on motility. These results rule out the use of conventional ion motive forces to power gliding. Arsenate had a dramatic inhibitory effect on gliding, and both the speed and the fraction of cells moving tracked ATP levels. Sodium orthovanadate had a slight but significant inhibitory effect on gliding. Taken together, these results suggest that the motor system of M. mobile is likely an ATPase or is directly coupled to an ATPase.
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Affiliation(s)
- Jacob D Jaffe
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
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50
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Abstract
Bacterial chemotaxis is a model system for signal transduction, noted for its relative simplicity, high sensitivity, wide dynamic range and robustness. Changes in ligand concentrations are sensed by a protein assembly consisting of transmembrane receptors, a coupling protein (CheW) and a histidine kinase (CheA). In Escherichia coli, these components are organized at the cell poles in tight clusters that contain several thousand copies of each protein. Here we studied the effects of variation in the composition of clusters on the activity of the kinase and its sensitivity to attractant stimuli, monitoring responses in vivo using fluorescence resonance energy transfer. Our results indicate that assemblies of bacterial chemoreceptors work in a highly cooperative manner, mimicking the behaviour of allosteric proteins. Conditions that favour steep responses to attractants in mutants with homogeneous receptor populations also enhance the sensitivity of the response in wild-type cells. This is consistent with a number of models that assume long-range cooperative interactions between receptors as a general mechanism for signal integration and amplification.
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Affiliation(s)
- Victor Sourjik
- Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts 02138, USA
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