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Glazenburg MM, Hettema NM, Laan L, Remy O, Laloux G, Brunet T, Chen X, Tee YH, Wen W, Rizvi MS, Jolly MK, Riddell M. Perspectives on polarity - exploring biological asymmetry across scales. J Cell Sci 2024; 137:jcs261987. [PMID: 38441500 DOI: 10.1242/jcs.261987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024] Open
Abstract
In this Perspective, Journal of Cell Science invited researchers working on cell and tissue polarity to share their thoughts on unique, emerging or open questions relating to their field. The goal of this article is to feature 'voices' from scientists around the world and at various career stages, to bring attention to innovative and thought-provoking topics of interest to the cell biology community. These voices discuss intriguing questions that consider polarity across scales, evolution, development and disease. What can yeast and protists tell us about the evolution of cell and tissue polarity in animals? How are cell fate and development influenced by emerging dynamics in cell polarity? What can we learn from atypical and extreme polarity systems? How can we arrive at a more unified biophysical understanding of polarity? Taken together, these pieces demonstrate the broad relevance of the fascinating phenomenon of cell polarization to diverse fundamental biological questions.
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Affiliation(s)
- Marieke Margaretha Glazenburg
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, 2629 HZ, The Netherlands
| | - Nynke Marije Hettema
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, 2629 HZ, The Netherlands
| | - Liedewij Laan
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, 2629 HZ, The Netherlands
| | - Ophélie Remy
- Institut de Duve, UCLouvain, 75 avenue Hippocrate, 1200 Brussels, Belgium
| | - Géraldine Laloux
- Institut de Duve, UCLouvain, 75 avenue Hippocrate, 1200 Brussels, Belgium
| | - Thibaut Brunet
- Institut Pasteur, Université Paris-Cité, CNRS UMR 3691, Evolutionary Cell Biology and Evolution of Morphogenesis Unit, 25-28 rue du docteur Roux, 75015 Paris, France
| | - Xin Chen
- Howard Hughes Medical Institute and Department of Biology, Johns Hopkins University, Levi Hall 137, 3400 North Charles Street, Baltimore, MD 21218-2685, USA
| | - Yee Han Tee
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore
| | - Wenyu Wen
- Department of Neurosurgery, Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Mohd Suhail Rizvi
- Department of Biomedical Engineering, Indian Institute of Technology Hyderabad, Sangareddy 502284, India
| | - Mohit Kumar Jolly
- Department of Bioengineering, Indian Institute of Science, Bangalore 560012, India
| | - Meghan Riddell
- Department of Physiology and Department of Obstetrics and Gynecology, University of Alberta, Edmonton, AB, T6G 2S2, Canada
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2
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Updegrove TB, D'Atri D, Ramamurthi KS. Assembling the Bacillus subtilis Spore Coat Basement Layer on Spherical Supported Lipid Bilayers. Methods Mol Biol 2024; 2727:215-225. [PMID: 37815720 DOI: 10.1007/978-1-0716-3491-2_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
Micro- and nanoparticles are often designed by mimicking naturally occurring structures. Bacterial spores are dormant cells elaborated by some Gram-positive bacteria during poor growth conditions to protect their genetic material from harsh environmental stresses. In Bacillus subtilis, this protection is, in part, conferred by a proteinaceous shell, the "coat", which is composed of ~80 different proteins. The basement layer of the coat contains two unusual proteins, which we have recently reconstituted around silica beads to generate synthetic spore-like particles termed "SSHELs". Here, we describe the protocol for generating SSHEL particles, and describe the procedure to covalently link molecules of interest (in this case an anti-HER2 affibody) to SSHEL surfaces. SSHELs therefore represent a versatile platform for the display of ligands or antigens for the site-specific delivery of cargo or vaccines.
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Affiliation(s)
- Taylor B Updegrove
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Domenico D'Atri
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kumaran S Ramamurthi
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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3
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Badvaram I, Camley BA. Physical limits to membrane curvature sensing by a single protein. Phys Rev E 2023; 108:064407. [PMID: 38243534 DOI: 10.1103/physreve.108.064407] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 09/11/2023] [Indexed: 01/21/2024]
Abstract
Membrane curvature sensing is essential for a diverse range of biological processes. Recent experiments have revealed that a single nanometer-sized septin protein has different binding rates to membrane-coated glass beads of 1-µm and 3-µm diameters, even though the septin is orders of magnitude smaller than the beads. This sensing ability is especially surprising since curvature-sensing proteins must deal with persistent thermal fluctuations of the membrane, leading to discrepancies between the bead's curvature and the local membrane curvature sensed instantaneously by a protein. Using continuum models of fluctuating membranes, we investigate whether it is feasible for a protein acting as a perfect observer of the membrane to sense micron-scale curvature either by measuring local membrane curvature or by using bilayer lipid densities as a proxy. To do this, we develop algorithms to simulate lipid density and membrane shape fluctuations. We derive physical limits to the sensing efficacy of a protein in terms of protein size, membrane thickness, membrane bending modulus, membrane-substrate adhesion strength, and bead size. To explain the experimental protein-bead association rates, we develop two classes of predictive models: (i) for proteins that maximally associate to a preferred curvature and (ii) for proteins with enhanced association rates above a threshold curvature. We find that the experimentally observed sensing efficacy is close to the theoretical sensing limits imposed on a septin-sized protein. Protein-membrane association rates may depend on the curvature of the bead, but the strength of this dependence is limited by the fluctuations in membrane height and density.
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Affiliation(s)
- Indrajit Badvaram
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Brian A Camley
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA
- William H. Miller III Department of Physics & Astronomy, Johns Hopkins University, Baltimore, Maryland 21218, USA
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4
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Delerue T, Chareyre S, Anantharaman V, Gilmore MC, Popham DL, Cava F, Aravind L, Ramamurthi KS. Bacterial cell surface nanoenvironment requires a specialized chaperone to activate a peptidoglycan biosynthetic enzyme. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.06.561273. [PMID: 37986874 PMCID: PMC10659427 DOI: 10.1101/2023.10.06.561273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Bacillus subtilis spores are produced inside the cytosol of a mother cell. Spore surface assembly requires the SpoVK protein in the mother cell, but its function is unknown. Here, we report that SpoVK is a dedicated chaperone from a distinct higher-order clade of AAA+ ATPases that activates the peptidoglycan glycosyltransferase MurG during sporulation, even though MurG does not normally require activation by a chaperone during vegetative growth. MurG redeploys to the spore surface during sporulation, where we show that the local pH is reduced and propose that this change in cytosolic nanoenvironment necessitates a specific chaperone for proper MurG function. Further, we show that SpoVK participates in a developmental checkpoint in which improper spore surface assembly inactivates SpoVK, which leads to sporulation arrest. The AAA+ ATPase clade containing SpoVK includes other dedicated chaperones involved in secretion, cell-envelope biosynthesis, and carbohydrate metabolism, suggesting that such fine-tuning might be a widespread feature of different subcellular nanoenvironments.
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Affiliation(s)
- Thomas Delerue
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Sylvia Chareyre
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Vivek Anantharaman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Michael C. Gilmore
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Science for Life Laboratory (SciLifeLab), Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - David L. Popham
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - Felipe Cava
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Science for Life Laboratory (SciLifeLab), Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - L. Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Kumaran S. Ramamurthi
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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5
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Paracini N, Gutfreund P, Welbourn R, Gonzalez-Martinez JF, Zhu K, Miao Y, Yepuri N, Darwish TA, Garvey C, Waldie S, Larsson J, Wolff M, Cárdenas M. Structural Characterization of Nanoparticle-Supported Lipid Bilayer Arrays by Grazing Incidence X-ray and Neutron Scattering. ACS APPLIED MATERIALS & INTERFACES 2023; 15:3772-3780. [PMID: 36625710 PMCID: PMC9880997 DOI: 10.1021/acsami.2c18956] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Arrays of nanoparticle-supported lipid bilayers (nanoSLB) are lipid-coated nanopatterned interfaces that provide a platform to study curved model biological membranes using surface-sensitive techniques. We combined scattering techniques with direct imaging, to gain access to sub-nanometer scale structural information on stable nanoparticle monolayers assembled on silicon crystals in a noncovalent manner using a Langmuir-Schaefer deposition. The structure of supported lipid bilayers formed on the nanoparticle arrays via vesicle fusion was investigated using a combination of grazing incidence X-ray and neutron scattering techniques complemented by fluorescence microscopy imaging. Ordered nanoparticle assemblies were shown to be suitable and stable substrates for the formation of curved and fluid lipid bilayers that retained lateral mobility, as shown by fluorescence recovery after photobleaching and quartz crystal microbalance measurements. Neutron reflectometry revealed the formation of high-coverage lipid bilayers around the spherical particles together with a flat lipid bilayer on the substrate below the nanoparticles. The presence of coexisting flat and curved supported lipid bilayers on the same substrate, combined with the sub-nanometer accuracy and isotopic sensitivity of grazing incidence neutron scattering, provides a promising novel approach to investigate curvature-dependent membrane phenomena on supported lipid bilayers.
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Affiliation(s)
- Nicolò Paracini
- Department
for Biomedical Science and Biofilms − Research Center for Biointerfaces,
Faculty of Health and Society, Malmö
University, 205 06Malmö, Sweden
| | | | - Rebecca Welbourn
- ISIS
Neutron & Muon Source, STFC, Rutherford
Appleton Laboratory, Harwell, OxfordshireOX11 0QX, U.K.
| | - Juan Francisco Gonzalez-Martinez
- Department
for Biomedical Science and Biofilms − Research Center for Biointerfaces,
Faculty of Health and Society, Malmö
University, 205 06Malmö, Sweden
| | - Kexin Zhu
- School
of Biological Sciences, Nanyang Technological
University, 639798Singapore
| | - Yansong Miao
- School
of Biological Sciences, Nanyang Technological
University, 639798Singapore
| | - Nageshwar Yepuri
- National
Deuteration Facility, Australian Nuclear
Science and Technology Organization (ANSTO), Lucas Heights, NSW2234, Australia
| | - Tamim A. Darwish
- National
Deuteration Facility, Australian Nuclear
Science and Technology Organization (ANSTO), Lucas Heights, NSW2234, Australia
| | - Christopher Garvey
- Heinz
Maier-Leibnitz
Zentrum (MLZ), Technische Universität
München, Lichtenbergstraβe 1, 85748Garching, Germany
| | - Sarah Waldie
- Department
for Biomedical Science and Biofilms − Research Center for Biointerfaces,
Faculty of Health and Society, Malmö
University, 205 06Malmö, Sweden
| | - Johan Larsson
- Department
for Biomedical Science and Biofilms − Research Center for Biointerfaces,
Faculty of Health and Society, Malmö
University, 205 06Malmö, Sweden
| | - Max Wolff
- Department
of Physics and Astronomy, Uppsala University, Box 516, 751 20Uppsala, Sweden
| | - Marité Cárdenas
- Department
for Biomedical Science and Biofilms − Research Center for Biointerfaces,
Faculty of Health and Society, Malmö
University, 205 06Malmö, Sweden
- School
of Biological Sciences, Nanyang Technological
University, 639798Singapore
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6
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Lipid flip-flop and desorption from supported lipid bilayers is independent of curvature. PLoS One 2020; 15:e0244460. [PMID: 33378379 PMCID: PMC7773258 DOI: 10.1371/journal.pone.0244460] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 12/09/2020] [Indexed: 01/10/2023] Open
Abstract
Flip-flop of lipids of the lipid bilayer (LBL) constituting the plasma membrane (PM) plays a crucial role in a myriad of events ranging from cellular signaling and regulation of cell shapes to cell homeostasis, membrane asymmetry, phagocytosis, and cell apoptosis. While extensive research has been conducted to probe the lipid flip flop of planar lipid bilayers (LBLs), less is known regarding lipid flip-flop for highly curved, nanoscopic LBL systems despite the vast importance of membrane curvature in defining the morphology of cells and organelles and in maintaining a variety of cellular functions, enabling trafficking, and recruiting and localizing shape-responsive proteins. In this paper, we conduct molecular dynamics (MD) simulations to study the energetics, structure, and configuration of a lipid molecule undergoing flip-flop and desorption in a highly curved LBL, represented as a nanoparticle-supported lipid bilayer (NPSLBL) system. We compare our findings against those of a planar substrate supported lipid bilayer (PSSLBL). Our MD simulation results reveal that despite the vast differences in the curvature and other curvature-dictated properties (e.g., lipid packing fraction, difference in the number of lipids between inner and outer leaflets, etc.) between the NPSLBL and the PSSLBL, the energetics of lipid flip-flop and lipid desorption as well as the configuration of the lipid molecule undergoing lipid flip-flop are very similar for the NPSLBL and the PSSLBL. In other words, our results establish that the curvature of the LBL plays an insignificant role in lipid flip-flop and desorption.
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7
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Choukate K, Gupta A, Basu B, Virk K, Ganguli M, Chaudhuri B. Higher order assembling of the mycobacterial polar growth factor DivIVA/Wag31. J Struct Biol 2019; 209:107429. [PMID: 31778770 DOI: 10.1016/j.jsb.2019.107429] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/04/2019] [Accepted: 11/21/2019] [Indexed: 12/26/2022]
Abstract
DivIVA or Wag31, which is an essential pole organizing protein in mycobacteria, can self-assemble at the negatively curved side of the membrane at the growing pole to form a higher order structural scaffold for maintaining cellular morphology and localizing various target proteins for cell-wall biogenesis. The structural organization of polar scaffold formed by polymerization of coiled-coil rich Wag31, which is implicated in the anti-tubercular activities of amino-pyrimidine sulfonamides, remains to be determined. A single-site phosphorylation in Wag31 regulates peptidoglycan biosynthesis in mycobacteria. We report biophysical characterizations of filaments formed by mycobacterial Wag31 using circular dichroism, atomic force microscopy and small angle solution X-ray scattering. Atomic force microscopic images of the wild-type, a phospho-mimetic (T73E) and a phospho-ablative (T73A) form of Wag31 show mostly linear filament formation with occasional curving, kinking and apparent branching. Solution X-ray scattering data indicates that the phospho-mimetic forms of the Wag31 polymers are on average more compact than their phospho-ablative counterparts, which is likely due to the extent of bending/branching. Observed structural features in this first view of Wag31 filaments suggest a basis for higher order Wag31 scaffold formation at the pole.
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Affiliation(s)
- Komal Choukate
- CSIR Institute of Microbial Technology, Chandigarh, India
| | - Aanchal Gupta
- CSIR Institute of Genomics and Integrative Biology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110001, India
| | - Brohmomoy Basu
- CSIR Institute of Microbial Technology, Chandigarh, India
| | - Karman Virk
- CSIR Institute of Microbial Technology, Chandigarh, India
| | - Munia Ganguli
- CSIR Institute of Genomics and Integrative Biology, New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110001, India
| | - Barnali Chaudhuri
- CSIR Institute of Microbial Technology, Chandigarh, India; Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi 110001, India.
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8
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Teo ACK, Lee SC, Pollock NL, Stroud Z, Hall S, Thakker A, Pitt AR, Dafforn TR, Spickett CM, Roper DI. Analysis of SMALP co-extracted phospholipids shows distinct membrane environments for three classes of bacterial membrane protein. Sci Rep 2019; 9:1813. [PMID: 30755655 PMCID: PMC6372662 DOI: 10.1038/s41598-018-37962-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 12/05/2018] [Indexed: 11/24/2022] Open
Abstract
Biological characterisation of membrane proteins lags behind that of soluble proteins. This reflects issues with the traditional use of detergents for extraction, as the surrounding lipids are generally lost, with adverse structural and functional consequences. In contrast, styrene maleic acid (SMA) copolymers offer a detergent-free method for biological membrane solubilisation to produce SMA-lipid particles (SMALPs) containing membrane proteins together with their surrounding lipid environment. We report the development of a reverse-phase LC-MS/MS method for bacterial phospholipids and the first comparison of the profiles of SMALP co-extracted phospholipids from three exemplar bacterial membrane proteins with different topographies: FtsA (associated membrane protein), ZipA (single transmembrane helix), and PgpB (integral membrane protein). The data showed that while SMA treatment per se did not preferentially extract specific phospholipids from the membrane, SMALP-extracted ZipA showed an enrichment in phosphatidylethanolamines and depletion in cardiolipins compared to the bulk membrane lipid. Comparison of the phospholipid profiles of the 3 SMALP-extracted proteins revealed distinct lipid compositions for each protein: ZipA and PgpB were similar, but in FtsA samples longer chain phosphatidylglycerols and phosphatidylethanolamines were more abundant. This method offers novel information on the phospholipid interactions of these membrane proteins.
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Affiliation(s)
- Alvin C K Teo
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry, CV4 7AL, UK
| | - Sarah C Lee
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Naomi L Pollock
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Zoe Stroud
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Stephen Hall
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Alpesh Thakker
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK
| | - Andrew R Pitt
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK
| | - Timothy R Dafforn
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Corinne M Spickett
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK.
| | - David I Roper
- School of Life Sciences, Gibbet Hill Road, University of Warwick, Coventry, CV4 7AL, UK.
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9
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Nandi SK, Safran SA. Protein gradients in single cells induced by their coupling to "morphogen"-like diffusion. J Chem Phys 2018; 148:205101. [PMID: 29865807 DOI: 10.1063/1.5021086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
One of the many ways cells transmit information within their volume is through steady spatial gradients of different proteins. However, the mechanism through which proteins without any sources or sinks form such single-cell gradients is not yet fully understood. One of the models for such gradient formation, based on differential diffusion, is limited to proteins with large ratios of their diffusion constants or to specific protein-large molecule interactions. We introduce a novel mechanism for gradient formation via the coupling of the proteins within a single cell with a molecule, that we call a "pronogen," whose action is similar to that of morphogens in multi-cell assemblies; the pronogen is produced with a fixed flux at one side of the cell. This coupling results in an effectively non-linear diffusion degradation model for the pronogen dynamics within the cell, which leads to a steady-state gradient of the protein concentration. We use stability analysis to show that these gradients are linearly stable with respect to perturbations.
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Affiliation(s)
- Saroj Kumar Nandi
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sam A Safran
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 7610001, Israel
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10
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Hutchison E, Yager NA, Taw MN, Taylor M, Arroyo F, Sannino DR, Angert ER. Developmental stage influences chromosome segregation patterns and arrangement in the extremely polyploid, giant bacterium Epulopiscium sp. type B. Mol Microbiol 2017; 107:68-80. [PMID: 29024073 DOI: 10.1111/mmi.13860] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 10/05/2017] [Accepted: 10/06/2017] [Indexed: 12/19/2022]
Abstract
Few studies have described chromosomal dynamics in bacterial cells with more than two complete chromosome copies or described changes with respect to development in polyploid cells. We examined the arrangement of chromosomal loci in the very large, highly polyploid, uncultivated intestinal symbiont Epulopiscium sp. type B using fluorescent in situ hybridization. We found that in new offspring, chromosome replication origins (oriCs) are arranged in a three-dimensional array throughout the cytoplasm. As development progresses, most oriCs become peripherally located. Siblings within a mother cell have similar numbers of oriCs. When chromosome orientation was assessed in situ by labeling two chromosomal regions, no specific pattern was detected. The Epulopiscium genome codes for many of the conserved positional guide proteins used for chromosome segregation in bacteria. Based on this study, we present a model that conserved chromosomal maintenance proteins, combined with entropic demixing, provide the forces necessary for distributing oriCs. Without the positional regulation afforded by radial confinement, chromosomes are more randomly oriented in Epulopiscium than in most small rod-shaped cells. Furthermore, we suggest that the random orientation of individual chromosomes in large polyploid cells would not hamper reproductive success as it would in smaller cells with more limited genomic resources.
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Affiliation(s)
- Elizabeth Hutchison
- Department of Biology, SUNY Geneseo, Geneseo, NY, USA.,Department of Microbiology, Cornell University, Ithaca, NY, USA
| | | | - May N Taw
- Department of Microbiology, Cornell University, Ithaca, NY, USA
| | | | - Francine Arroyo
- Department of Microbiology, Cornell University, Ithaca, NY, USA
| | - David R Sannino
- Department of Microbiology, Cornell University, Ithaca, NY, USA
| | - Esther R Angert
- Department of Microbiology, Cornell University, Ithaca, NY, USA
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11
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Dissection of membrane-binding and -remodeling regions in two classes of bacterial phospholipid N-methyltransferases. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:2279-2288. [PMID: 28912104 DOI: 10.1016/j.bbamem.2017.09.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 08/25/2017] [Accepted: 09/10/2017] [Indexed: 01/08/2023]
Abstract
Bacterial phospholipid N-methyltransferases (Pmts) catalyze the formation of phosphatidylcholine (PC) via successive N-methylation of phosphatidylethanolamine (PE). They are classified into Sinorhizobium-type and Rhodobacter-type enzymes. The Sinorhizobium-type PmtA protein from the plant pathogen Agrobacterium tumefaciens is recruited to anionic lipids in the cytoplasmic membrane via two amphipathic helices called αA and αF. Besides its enzymatic activity, PmtA is able to remodel membranes mediated by the αA domain. According to the Heliquest program, αA- and αF-like amphipathic helices are also present in other Sinorhizobium- and Rhodobacter-type Pmt enzymes suggesting a conserved architecture of α-helical membrane-binding regions in these methyltransferases. As representatives of the two Pmt families, we investigated the membrane binding and remodeling capacity of Bradyrhizobium japonicum PmtA (Sinorhizobium-type) and PmtX1 (Rhodobacter-type), which act cooperatively to produce PC in consecutive methylation steps. We found that the αA regions in both enzymes bind anionic lipids similar to αA of A. tumefaciens PmtA. Membrane binding of PmtX1 αA is enhanced by its substrate monomethyl-PE indicating a substrate-controlled membrane association. The αA regions of all investigated enzymes remodel spherical liposomes into tubular filaments suggesting a conserved membrane-remodeling capacity of bacterial Pmts. Based on these results we propose that the molecular details of membrane-binding and remodeling are conserved among bacterial Pmts.
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12
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Updegrove TB, Ramamurthi KS. Geometric protein localization cues in bacterial cells. Curr Opin Microbiol 2017; 36:7-13. [PMID: 28110195 DOI: 10.1016/j.mib.2016.12.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 12/15/2016] [Accepted: 12/17/2016] [Indexed: 10/20/2022]
Abstract
Bacterial cells are highly organized at a molecular level. Understanding how specific proteins localize to their proper subcellular address has been a major challenge in bacterial cell biology. One mechanism, which appears to be increasingly more common, is the use of 'geometric cues' for protein localization. In this model, certain shape-sensing proteins recognize, and preferentially embed into, either negatively or positively curved (concave or convex, respectively) membranes. Here, we review examples of bacterial proteins that reportedly localize by sensing geometric cues and highlight emerging mechanistic understandings of how proteins may recognize subtle differences in membrane curvature.
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Affiliation(s)
- Taylor B Updegrove
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States
| | - Kumaran S Ramamurthi
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States.
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13
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Homeoviscous Adaptation and the Regulation of Membrane Lipids. J Mol Biol 2016; 428:4776-4791. [DOI: 10.1016/j.jmb.2016.08.013] [Citation(s) in RCA: 207] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 08/05/2016] [Accepted: 08/08/2016] [Indexed: 11/23/2022]
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14
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Matsumoto K, Hara H, Fishov I, Mileykovskaya E, Norris V. The membrane: transertion as an organizing principle in membrane heterogeneity. Front Microbiol 2015; 6:572. [PMID: 26124753 PMCID: PMC4464175 DOI: 10.3389/fmicb.2015.00572] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 05/25/2015] [Indexed: 01/05/2023] Open
Abstract
The bacterial membrane exhibits a significantly heterogeneous distribution of lipids and proteins. This heterogeneity results mainly from lipid-lipid, protein-protein, and lipid-protein associations which are orchestrated by the coupled transcription, translation and insertion of nascent proteins into and through membrane (transertion). Transertion is central not only to the individual assembly and disassembly of large physically linked groups of macromolecules (alias hyperstructures) but also to the interactions between these hyperstructures. We review here these interactions in the context of the processes in Bacillus subtilis and Escherichia coli of nutrient sensing, membrane synthesis, cytoskeletal dynamics, DNA replication, chromosome segregation, and cell division.
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Affiliation(s)
- Kouji Matsumoto
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, SaitamaJapan
| | - Hiroshi Hara
- Department of Biochemistry and Molecular Biology, Graduate School of Science and Engineering, Saitama University, SaitamaJapan
| | - Itzhak Fishov
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-ShevaIsrael
| | - Eugenia Mileykovskaya
- Department of Biochemistry and Molecular Biology, University of Texas Medical School at HoustonHouston, TX, USA
| | - Vic Norris
- Laboratory of Microbiology Signals and Microenvironment EA 4312, Department of Science, University of Rouen, Mont-Saint-AignanFrance
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15
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Oswald F, L M Bank E, Bollen YJM, Peterman EJG. Imaging and quantification of trans-membrane protein diffusion in living bacteria. Phys Chem Chem Phys 2015; 16:12625-34. [PMID: 24760126 DOI: 10.1039/c4cp00299g] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The cytoplasmic membrane forms the barrier between any cell's interior and the outside world. It contains many proteins that enable essential processes such as the transmission of signals, the uptake of nutrients, and cell division. In the case of prokaryotes, which do not contain intracellular membranes, the cytoplasmic membrane also contains proteins for respiration and protein folding. Mutual interactions and specific localization of these proteins depend on two-dimensional diffusion driven by thermal fluctuations. The experimental investigation of membrane-protein diffusion in bacteria is challenging due to their small size, only a few times larger than the resolution of an optical microscope. Here, we review fluorescence microscopy-based methods to study diffusion of membrane proteins in living bacteria. The main focus is on data-analysis tools to extract diffusion coefficients from single-particle tracking data obtained by single-molecule fluorescence microscopy. We introduce a novel approach, IPODD (inverse projection of displacement distributions), to obtain diffusion coefficients from the usually obtained 2-D projected diffusion trajectories of the highly 3-D curved bacterial membrane. This method provides, in contrast to traditional mean-squared-displacement methods, correct diffusion coefficients and allows unravelling of heterogeneously diffusing populations.
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Affiliation(s)
- Felix Oswald
- LaserLaB Amsterdam, VU University, De Boelelaan 1081, 1081 HV, Amsterdam, Netherlands.
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16
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Wu IL, Narayan K, Castaing JP, Tian F, Subramaniam S, Ramamurthi KS. A versatile nano display platform from bacterial spore coat proteins. Nat Commun 2015; 6:6777. [PMID: 25854653 PMCID: PMC4396682 DOI: 10.1038/ncomms7777] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 02/26/2015] [Indexed: 12/20/2022] Open
Abstract
Dormant bacterial spores are encased in a thick protein shell, the ‘coat', which contains ∼70 different proteins. The coat protects the spore from environmental insults, and is among the most durable static structures in biology. Owing to extensive cross-linking among coat proteins, this structure has been recalcitrant to detailed biochemical analysis, so molecular details of how it assembles are largely unknown. Here, we reconstitute the basement layer of the coat atop spherical membranes supported by silica beads to create artificial spore-like particles. We report that these synthetic spore husk-encased lipid bilayers (SSHELs) assemble and polymerize into a static structure, mimicking in vivo basement layer assembly during sporulation in Bacillus subtilis. In addition, we demonstrate that SSHELs may be easily covalently modified with small molecules and proteins. We propose that SSHELs may be versatile display platforms for drugs and vaccines in clinical settings, or for enzymes that neutralize pollutants for environmental remediation. The densely crosslinked protein coats of bacterial spores are among the most durable static structures in biology. Wu et al. reconstitute the basement layer of a bacterial spore coat on membrane-coated beads, and generate covalently-modified spore-like particles with therapeutic potential.
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Affiliation(s)
- I-Lin Wu
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Kedar Narayan
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Jean-Philippe Castaing
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Fang Tian
- Department of Biochemistry and Molecular Biology, College of Medicine, Pennsylvania State University, Hershey, Pennsylvania 17033, USA
| | - Sriram Subramaniam
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Kumaran S Ramamurthi
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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17
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Structural basis for the geometry-driven localization of a small protein. Proc Natl Acad Sci U S A 2015; 112:E1908-15. [PMID: 25825747 DOI: 10.1073/pnas.1423868112] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In bacteria, certain shape-sensing proteins localize to differently curved membranes. During sporulation in Bacillus subtilis, the only convex (positively curved) surface in the cell is the forespore, an approximately spherical internal organelle. Previously, we demonstrated that SpoVM localizes to the forespore by preferentially adsorbing onto slightly convex membranes. Here, we used NMR and molecular dynamics simulations of SpoVM and a localization mutant (SpoVM(P9A)) to reveal that SpoVM's atypical amphipathic α-helix inserts deeply into the membrane and interacts extensively with acyl chains to sense packing differences in differently curved membranes. Based on binding to spherical supported lipid bilayers and Monte Carlo simulations, we hypothesize that SpoVM's membrane insertion, along with potential cooperative interactions with other SpoVM molecules in the lipid bilayer, drives its preferential localization onto slightly convex membranes. Such a mechanism, which is distinct from that used by high curvature-sensing proteins, may be widely conserved for the localization of proteins onto the surface of cellular organelles.
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18
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Soga H, Fujii S, Yomo T, Kato Y, Watanabe H, Matsuura T. In vitro membrane protein synthesis inside cell-sized vesicles reveals the dependence of membrane protein integration on vesicle volume. ACS Synth Biol 2014; 3:372-9. [PMID: 24328098 DOI: 10.1021/sb400094c] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Giant unilamellar vesicles (GUVs) are vesicles>1 μm in diameter that provide an environment in which the effect of a confined reaction volume on intravesicular reactions can be investigated. By synthesizing EmrE, a multidrug transporter from Escherichia coli, as a model membrane protein using a reconstituted in vitro transcription-translation system inside GUVs, we investigated the effect of a confined volume on the synthesis and membrane integration of EmrE. Flow cytometry was used to analyze multiple properties of the vesicles and to quantify EmrE synthesis inside GUVs composed of only 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine. We found that EmrE was synthesized and integrated into the GUV membrane in its active form. We also found that the ratio of membrane-integrated EmrE to total synthesized EmrE increased with decreasing vesicle volume; this finding is explained by the effect of an increased surface-area-to-volume ratio in smaller vesicles. In vitro membrane synthesis inside GUVs is a useful approach to study quantitatively the properties of membrane proteins and their interaction with the membrane under cell-mimicking environments.
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Affiliation(s)
- Haruka Soga
- Department
of Biotechnology, Graduate School of Engineering, Osaka University, 2-1
Yamadaoka, Suita, Osaka, Japan
| | - Satoshi Fujii
- Exploratory
Research for Advanced Technology, Japan Science and Technology Agency, 1-5 Yamadaoka, Suita, Osaka, Japan
| | - Tetsuya Yomo
- Exploratory
Research for Advanced Technology, Japan Science and Technology Agency, 1-5 Yamadaoka, Suita, Osaka, Japan
- Department
of Bioinformatic Engineering, Graduate School of Information Science
and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, Japan
| | - Yasuhiko Kato
- Department
of Biotechnology, Graduate School of Engineering, Osaka University, 2-1
Yamadaoka, Suita, Osaka, Japan
| | - Hajime Watanabe
- Department
of Biotechnology, Graduate School of Engineering, Osaka University, 2-1
Yamadaoka, Suita, Osaka, Japan
| | - Tomoaki Matsuura
- Department
of Biotechnology, Graduate School of Engineering, Osaka University, 2-1
Yamadaoka, Suita, Osaka, Japan
- Exploratory
Research for Advanced Technology, Japan Science and Technology Agency, 1-5 Yamadaoka, Suita, Osaka, Japan
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19
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Castaing JP, Lee S, Anantharaman V, Ravilious GE, Aravind L, Ramamurthi KS. An autoinhibitory conformation of the Bacillus subtilis spore coat protein SpoIVA prevents its premature ATP-independent aggregation. FEMS Microbiol Lett 2014; 358:145-53. [PMID: 24810258 DOI: 10.1111/1574-6968.12452] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 04/28/2014] [Indexed: 12/17/2022] Open
Abstract
Spores of Bacillus subtilis are dormant cell types that are formed when the bacterium encounters starvation conditions. Spores are encased in a shell, termed the coat, which is composed of approximately seventy different proteins and protects the spore's genetic material from environmental insults. The structural component of the basement layer of the coat is an exceptional cytoskeletal protein, termed SpoIVA, which binds and hydrolyzes ATP. ATP hydrolysis is utilized to drive a conformational change in SpoIVA that leads to its irreversible self-assembly into a static polymer in vitro. Here, we characterize the middle domain of SpoIVA, the predicted secondary structure of which resembles the chemotaxis protein CheX but, unlike CheX, does not harbor residues required for phosphatase activity. Disruptions in this domain did not abolish ATP hydrolysis, but resulted in mislocalization of the protein and reduction in sporulation efficiency in vivo. In vitro, disruptions in this domain prevented the ATP hydrolysis-driven conformational change in SpoIVA required for polymerization and led to the aggregation of SpoIVA into particles that did not form filaments. We propose a model in which SpoIVA initially assumes a conformation in which it inhibits its own aggregation into particles, and that ATP hydrolysis remodels the protein so that it assumes a polymerization-competent conformation.
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Affiliation(s)
- Jean-Philippe Castaing
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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20
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Karttunen J, Mäntynen S, Ihalainen TO, Lehtivuori H, Tkachenko NV, Vihinen-Ranta M, Ihalainen JA, Bamford JKH, Oksanen HM. Subcellular localization of bacteriophage PRD1 proteins in Escherichia coli. Virus Res 2014; 179:44-52. [PMID: 24291253 DOI: 10.1016/j.virusres.2013.11.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 11/19/2013] [Accepted: 11/19/2013] [Indexed: 11/19/2022]
Abstract
Bacteria possess an intricate internal organization resembling that of the eukaryotes. The complexity is especially prominent at the bacterial cell poles, which are also known to be the preferable sites for some bacteriophages to infect. Bacteriophage PRD1 is a well-known model serving as an ideal system to study structures and functions of icosahedral internal membrane-containing viruses. Our aim was to analyze the localization and interactions of individual PRD1 proteins in its native host Escherichia coli. This was accomplished by constructing a vector library for production of fluorescent fusion proteins. Analysis of solubility and multimericity of the fusion proteins, as well as their localization in living cells by confocal microscopy, indicated that multimeric PRD1 proteins were prone to localize in the cell poles. Furthermore, PRD1 spike complex proteins P5 and P31, as fusion proteins, were shown to be functional in the virion assembly. In addition, they were shown to co-localize in the specific polar area of the cells, which might have a role in the multimerization and formation of viral protein complexes.
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Affiliation(s)
- Jenni Karttunen
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science and Nanoscience Center, P.O. Box 35, 40014 University of Jyväskylä, Finland
| | - Sari Mäntynen
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science and Nanoscience Center, P.O. Box 35, 40014 University of Jyväskylä, Finland
| | - Teemu O Ihalainen
- Nanoscience Center, Department of Biological and Environmental Science, P.O. Box 35, 40014 University of Jyväskylä, Finland
| | - Heli Lehtivuori
- Nanoscience Center, Department of Biological and Environmental Science, P.O. Box 35, 40014 University of Jyväskylä, Finland
| | - Nikolai V Tkachenko
- Department of Chemistry and Bioengineering, Tampere University of Technology, P.O. Box 541, 33101 Tampere, Finland
| | - Maija Vihinen-Ranta
- Nanoscience Center, Department of Biological and Environmental Science, P.O. Box 35, 40014 University of Jyväskylä, Finland
| | - Janne A Ihalainen
- Nanoscience Center, Department of Biological and Environmental Science, P.O. Box 35, 40014 University of Jyväskylä, Finland
| | - Jaana K H Bamford
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science and Nanoscience Center, P.O. Box 35, 40014 University of Jyväskylä, Finland
| | - Hanna M Oksanen
- Institute of Biotechnology and Department of Biosciences, P.O. Box 56, 00014 University of Helsinki, Finland.
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21
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ATP hydrolysis by a domain related to translation factor GTPases drives polymerization of a static bacterial morphogenetic protein. Proc Natl Acad Sci U S A 2012; 110:E151-60. [PMID: 23267091 DOI: 10.1073/pnas.1210554110] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The assembly of static supramolecular structures is a culminating event of developmental programs. One such structure, the proteinaceous shell (called the coat) that surrounds spores of the bacterium Bacillus subtilis, is composed of about 70 different proteins and represents one of the most durable biological structures known. The coat is built atop a basement layer that contains an ATPase (SpoIVA) that forms a platform required for coat assembly. Here, we show that SpoIVA belongs to the translation factors class of P-loop GTPases and has evolutionarily lost the ability to bind GTP; instead, it uses ATP hydrolysis to drive its self-assembly into static filaments. We demonstrate that ATP hydrolysis is required by every subunit for incorporation into the growing polymer by inducing a conformational change that drives polymerization of a nucleotide-free filament. SpoIVA therefore differs from other self-organizing polymers (dynamic cytoskeletal structures and static intermediate filaments) in that it uses ATP hydrolysis to self-assemble, not disassemble, into a static polymer. We further show that polymerization requires a critical concentration that we propose is only achieved once SpoIVA is recruited to the surface of the developing spore, thereby ensuring that SpoIVA polymerization only occurs at the correct subcellular location during spore morphogenesis.
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22
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Vankemmelbeke M, O′Shea P, James R, Penfold CN. Interaction of nuclease colicins with membranes: insertion depth correlates with bilayer perturbation. PLoS One 2012; 7:e46656. [PMID: 23029560 PMCID: PMC3460906 DOI: 10.1371/journal.pone.0046656] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Accepted: 09/05/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Protein transport across cellular membranes is an important aspect of toxin biology. Escherichia coli cell killing by nuclease colicins occurs through DNA (DNases) or RNA (RNases) hydrolysis and to this end their cytotoxic domains require transportation across two sets of membranes. In order to begin to unravel the molecular mechanisms underlying the membrane translocation of colicin nuclease domains, we have analysed the membrane association of four DNase domains (E9, a charge reduction E9 mutant, E8, and E7) and one ribosomal RNase domain (E3) using a biomembrane model system. PRINCIPAL RESULTS We demonstrate, through the use of large unilamellar vesicles composed of synthetic and E. coli lipids and a membrane surface potential sensor, that the colicin nuclease domains bind anionic membranes only, with micromolar affinity and via a cooperative binding mechanism. The evaluation of the nuclease bilayer insertion depth, through a fluorescence quenching analysis using brominated lipids, indicates that the nucleases locate to differential regions in the bilayer. Colicin DNases target the interfacial region of the lipid bilayer, with the DNase E7 showing the deepest insertion, whereas the ribosomal RNase E3 penetrates into the hydrophobic core region of the bilayer. Furthermore, the membrane association of the DNase E7 and the ribosomal RNase E3 induces vesicle aggregation, lipid mixing and content leakage to a much larger extent than that of the other DNases analysed. CONCLUSIONS/SIGNIFICANCE Our results show, for the first time, that after the initial electrostatically driven membrane association, the pleiotropic membrane effects induced by colicin nuclease domains relate to their bilayer insertion depth and may be linked to their in vivo membrane translocation.
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Affiliation(s)
- Mireille Vankemmelbeke
- School of Molecular Medical Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, United Kingdom
- * E-mail:
| | - Paul O′Shea
- School of Biology, University of Nottingham, Nottingham, United Kingdom
| | - Richard James
- School of Molecular Medical Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Christopher N. Penfold
- School of Molecular Medical Sciences, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, United Kingdom
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23
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Govindarajan S, Nevo-Dinur K, Amster-Choder O. Compartmentalization and spatiotemporal organization of macromolecules in bacteria. FEMS Microbiol Rev 2012; 36:1005-22. [DOI: 10.1111/j.1574-6976.2012.00348.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Revised: 06/27/2012] [Accepted: 06/28/2012] [Indexed: 12/18/2022] Open
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24
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Nevo-Dinur K, Govindarajan S, Amster-Choder O. Subcellular localization of RNA and proteins in prokaryotes. Trends Genet 2012; 28:314-22. [DOI: 10.1016/j.tig.2012.03.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Revised: 03/15/2012] [Accepted: 03/19/2012] [Indexed: 10/28/2022]
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25
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Daptomycin-mediated reorganization of membrane architecture causes mislocalization of essential cell division proteins. J Bacteriol 2012; 194:4494-504. [PMID: 22661688 DOI: 10.1128/jb.00011-12] [Citation(s) in RCA: 226] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Daptomycin is a lipopeptide antibiotic used clinically for the treatment of certain types of Gram-positive infections, including those caused by methicillin-resistant Staphylococcus aureus (MRSA). Details of the mechanism of action of daptomycin continue to be elucidated, particularly the question of whether daptomycin acts on the cell membrane, the cell wall, or both. Here, we use fluorescence microscopy to directly visualize the interaction of daptomycin with the model Gram-positive bacterium Bacillus subtilis. We show that the first observable cellular effects are the formation of membrane distortions (patches of membrane) that precede cell death by more than 30 min. Membrane patches are able to recruit the essential cell division protein DivIVA. Recruitment of DivIVA correlates with membrane defects and changes in cell morphology, suggesting a localized alteration in the activity of enzymes involved in cell wall synthesis that could account for previously described effects of daptomycin on cell wall morphology and septation. Membrane defects colocalize with fluorescently labeled daptomycin, DivIVA, and fluorescent reporters of peptidoglycan biogenesis (Bocillin FL and BODIPY FL-vancomycin), suggesting that daptomycin plays a direct role in these events. Our results support a mechanism for daptomycin with a primary effect on cell membranes that in turn redirects the localization of proteins involved in cell division and cell wall synthesis, causing dramatic cell wall and membrane defects, which may ultimately lead to a breach in the cell membrane and cell death. These results help resolve the longstanding questions regarding the mechanism of action of this important class of antibiotics.
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26
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Wirth SE, Krywy JA, Aldridge B, Fortune S, Fernandez-Suarez M, Gray TA, Derbyshire KM. Polar assembly and scaffolding proteins of the virulence-associated ESX-1 secretory apparatus in mycobacteria. Mol Microbiol 2012; 83:654-64. [PMID: 22233444 PMCID: PMC3277861 DOI: 10.1111/j.1365-2958.2011.07958.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The ESX-1 secretion system is required for pathogenicity of Mycobacterium tuberculosis (Mtb). Despite considerable research, little is known about the structural components of ESX-1, or how these proteins are assembled into the active secretion apparatus. Here, we exploit the functionally related ESX-1 apparatus of Mycobacterium smegmatis (Ms) to show that fluorescently tagged proteins required for ESX-1 activity consistently localize to the cell pole, identified by time-lapse fluoro-microscopy as the non-septal (old) pole. Deletions in Msesx1 prevented polar localization of tagged proteins, indicating the need for specific protein-protein interactions in polar trafficking. Remarkably, expression of the Mtbesx1 locus in Msesx1 mutants restored polar localization of tagged proteins, indicating establishment of the MtbESX-1 apparatus in M. smegmatis. This observation illustrates the cross-species conservation of protein interactions governing assembly of ESX-1, as well as polar localization. Importantly, we describe novel non-esx1-encoded proteins, which affect ESX-1 activity, which colocalize with ESX-1, and which are required for ESX-1 recruitment and assembly. This analysis provides new insights into the molecular assembly of this important determinant of Mtb virulence.
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Affiliation(s)
- Samantha E. Wirth
- Division of Genetics, Wadsworth Center, Center for Medical Science, New York State, Department of Health, Albany, NY 12201, USA
| | - Janet A. Krywy
- Department of Biomedical Sciences, School of Public Health, State University of New York at Albany, Albany, NY 12201-2002, USA
| | - Bree Aldridge
- Department of Immunology and Infectious Disease, Harvard School of Public Health, Boston, MA, USA
| | - Sarah Fortune
- Department of Immunology and Infectious Disease, Harvard School of Public Health, Boston, MA, USA
| | - Marta Fernandez-Suarez
- Department of Immunology and Infectious Disease, Harvard School of Public Health, Boston, MA, USA
| | - Todd A. Gray
- Division of Genetics, Wadsworth Center, Center for Medical Science, New York State, Department of Health, Albany, NY 12201, USA
- Department of Biomedical Sciences, School of Public Health, State University of New York at Albany, Albany, NY 12201-2002, USA
| | - Keith M. Derbyshire
- Division of Genetics, Wadsworth Center, Center for Medical Science, New York State, Department of Health, Albany, NY 12201, USA
- Department of Biomedical Sciences, School of Public Health, State University of New York at Albany, Albany, NY 12201-2002, USA
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27
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Abstract
Prokaryotes are characterized by an extreme flexibility of their respiratory systems allowing them to cope with various extreme environments. To date, supramolecular organization of respiratory systems appears as a conserved evolutionary feature as supercomplexes have been isolated in bacteria, archaea, and eukaryotes. Most of the yet identified supercomplexes in prokaryotes are involved in aerobic respiration and share similarities with those reported in mitochondria. Supercomplexes likely reflect a snapshot of the cellular respiration in a given cell population. While the exact nature of the determinants for supramolecular organization in prokaryotes is not understood, lipids, proteins, and subcellular localization can be seen as key players. Owing to the well-reported supramolecular organization of the mitochondrial respiratory chain in eukaryotes, several hypotheses have been formulated to explain the consequences of such arrangement and can be tested in the context of prokaryotes. Considering the inherent metabolic flexibility of a number of prokaryotes, cellular distribution and composition of the supramolecular assemblies should be studied in regards to environmental signals. This would pave the way to new concepts in cellular respiration.
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28
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Higgins D, Dworkin J. Recent progress in Bacillus subtilis sporulation. FEMS Microbiol Rev 2011; 36:131-48. [PMID: 22091839 DOI: 10.1111/j.1574-6976.2011.00310.x] [Citation(s) in RCA: 314] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Revised: 08/25/2011] [Accepted: 09/02/2011] [Indexed: 11/29/2022] Open
Abstract
The Gram-positive bacterium Bacillus subtilis can initiate the process of sporulation under conditions of nutrient limitation. Here, we review some of the last 5 years of work in this area, with a particular focus on the decision to initiate sporulation, DNA translocation, cell-cell communication, protein localization and spore morphogenesis. The progress we describe has implications not only just for the study of sporulation but also for other biological systems where homologs of sporulation-specific proteins are involved in vegetative growth.
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Affiliation(s)
- Douglas Higgins
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY, USA
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