1
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Unnikrishnan M, Wang Y, Gruebele M, Murphy CJ. Nanoparticle-assisted tubulin assembly is environment dependent. Proc Natl Acad Sci U S A 2024; 121:e2403034121. [PMID: 38954547 PMCID: PMC11252952 DOI: 10.1073/pnas.2403034121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 05/30/2024] [Indexed: 07/04/2024] Open
Abstract
Nanomaterials acquire a biomolecular corona upon introduction to biological media, leading to biological transformations such as changes in protein function, unmasking of epitopes, and protein fibrilization. Ex vivo studies to investigate the effect of nanoparticles on protein-protein interactions are typically performed in buffer and are rarely measured quantitatively in live cells. Here, we measure the differential effect of silica nanoparticles on protein association in vitro vs. in mammalian cells. BtubA and BtubB are a pair of bacterial tubulin proteins identified in Prosthecobacter strains that self-assemble like eukaryotic tubulin, first into dimers and then into microtubules in vitro or in vivo. Förster resonance energy transfer labeling of each of the Btub monomers with a donor (mEGFP) and acceptor (mRuby3) fluorescent protein provides a quantitative tool to measure their binding interactions in the presence of unfunctionalized silica nanoparticles in buffer and in cells using fluorescence spectroscopy and microscopy. We show that silica nanoparticles enhance BtubAB dimerization in buffer due to protein corona formation. However, these nanoparticles have little effect on bacterial tubulin self-assembly in the complex mammalian cellular environment. Thus, the effect of nanomaterials on protein-protein interactions may not be readily translated from the test tube to the cell in the absence of particle surface functionalization that can enable targeted protein-nanoparticle interactions to withstand competitive binding in the nanoparticle corona from other biomolecules.
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Affiliation(s)
- Mahima Unnikrishnan
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL61801
| | - Yuhan Wang
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL61801
| | - Martin Gruebele
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL61801
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL61801
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, IL61801
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL61801
| | - Catherine J. Murphy
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL61801
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL61801
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2
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Radler P, Loose M. A dynamic duo: Understanding the roles of FtsZ and FtsA for Escherichia coli cell division through in vitro approaches. Eur J Cell Biol 2024; 103:151380. [PMID: 38218128 DOI: 10.1016/j.ejcb.2023.151380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 12/22/2023] [Accepted: 12/24/2023] [Indexed: 01/15/2024] Open
Abstract
Bacteria divide by binary fission. The protein machine responsible for this process is the divisome, a transient assembly of more than 30 proteins in and on the surface of the cytoplasmic membrane. Together, they constrict the cell envelope and remodel the peptidoglycan layer to eventually split the cell into two. For Escherichia coli, most molecular players involved in this process have probably been identified, but obtaining the quantitative information needed for a mechanistic understanding can often not be achieved from experiments in vivo alone. Since the discovery of the Z-ring more than 30 years ago, in vitro reconstitution experiments have been crucial to shed light on molecular processes normally hidden in the complex environment of the living cell. In this review, we summarize how rebuilding the divisome from purified components - or at least parts of it - have been instrumental to obtain the detailed mechanistic understanding of the bacterial cell division machinery that we have today.
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Affiliation(s)
- Philipp Radler
- Institute for Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria; University of Vienna, Djerassiplatz 1, 1030 Wien, Austria.
| | - Martin Loose
- Institute for Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria.
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3
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Wang Y, Unnikrishnan M, Ramsey B, El Andlosy D, Keeley AT, Murphy CJ, Gruebele M. In-Cell Association of a Bioorthogonal Tubulin. Biomacromolecules 2024; 25:1282-1290. [PMID: 38251876 DOI: 10.1021/acs.biomac.3c01253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
Studies of proteins from one organism in another organism's cells have shown that such exogenous proteins stick more, pointing toward coevolution of the cytoplasm and protein surface to minimize stickiness. Here we flip this question around by asking whether exogenous proteins can assemble efficiently into their target complexes in a non-native cytoplasm. We use as our model system the assembly of BtubA and BtubB from Prosthecobacter hosted in human U-2 OS cells. BtubA and B evolved from eukaryotic tubulins after horizontal gene transfer, but they have low surface sequence identity with the homologous human tubulins and do not respond to tubulin drugs such as nocodazole. In U-2 OS cells, BtubA and B assemble efficiently into dimers compared to in vitro, and the wild-type BtubA and B proteins subsequently are able to form microtubules as well. We find that generic crowding effects (Ficoll 70 in vitro) contribute significantly to efficient dimer assembly when compared to sticking interactions (U-2 OS cell lysate in vitro), consistent with the notion that a generic mechanism such as crowding can be effective at driving assembly of exogenous proteins, even when protein-cytoplasm quinary structure and sticking have been modified in a non-native cytoplasm. A simple Monte Carlo model of in vitro and in-cell interactions, treating BtubA and B as sticky dipoles in a matrix of sticky or nonsticky crowders, rationalizes all the experimental trends with two adjustable parameters and reveals nucleation as the likely mechanism for the time-scale separation between dimer- and tubule formation in-cell and in vitro.
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Affiliation(s)
- Yuhan Wang
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Mahima Unnikrishnan
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Brooke Ramsey
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Driss El Andlosy
- Computer Science and Technologies Department, Parkland Community College, Champaign, Illinois 61821, United States
| | - Alex T Keeley
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Catherine J Murphy
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Martin Gruebele
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
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4
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Wagstaff JM, Planelles-Herrero VJ, Sharov G, Alnami A, Kozielski F, Derivery E, Löwe J. Diverse cytomotive actins and tubulins share a polymerization switch mechanism conferring robust dynamics. SCIENCE ADVANCES 2023; 9:eadf3021. [PMID: 36989372 PMCID: PMC10058229 DOI: 10.1126/sciadv.adf3021] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 03/01/2023] [Indexed: 06/19/2023]
Abstract
Protein filaments are used in myriads of ways to organize other molecules within cells. Some filament-forming proteins couple the hydrolysis of nucleotides to their polymerization cycle, thus powering the movement of other molecules. These filaments are termed cytomotive. Only members of the actin and tubulin protein superfamilies are known to form cytomotive filaments. We examined the basis of cytomotivity via structural studies of the polymerization cycles of actin and tubulin homologs from across the tree of life. We analyzed published data and performed structural experiments designed to disentangle functional components of these complex filament systems. Our analysis demonstrates the existence of shared subunit polymerization switches among both cytomotive actins and tubulins, i.e., the conformation of subunits switches upon assembly into filaments. These cytomotive switches can explain filament robustness, by enabling the coupling of kinetic and structural polarities required for cytomotive behaviors and by ensuring that single cytomotive filaments do not fall apart.
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Affiliation(s)
- James Mark Wagstaff
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | | | - Grigory Sharov
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Aisha Alnami
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Frank Kozielski
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Emmanuel Derivery
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Jan Löwe
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
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5
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Oliva M, Gago F, Kamimura S, Díaz JF. Alternative Approaches to Understand Microtubule Cap Morphology and Function. ACS OMEGA 2023; 8:3540-3550. [PMID: 36743020 PMCID: PMC9893253 DOI: 10.1021/acsomega.2c06926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 12/26/2022] [Indexed: 06/18/2023]
Abstract
Microtubules (MTs) are essential cellular machines built from concatenated αβ-tubulin heterodimers. They are responsible for two central and opposite functions from the dynamic point of view: scaffolding (static filaments) and force generation (dynamic MTs). These roles engage multiple physiological processes, including cell shape, polarization, division and movement, and intracellular long-distance transport. At the most basic level, the MT regulation is chemical because GTP binding and hydrolysis have the ability to promote assembly and disassembly in the absence of any other constraint. Due to the stochastic GTP hydrolysis, a chemical gradient from GTP-bound to GDP-bound tubulin is created at the MT growing end (GTP cap), which is translated into a cascade of structural regulatory changes known as MT maturation. This is an area of intense research, and several models have been proposed based on information mostly gathered from macromolecular crystallography and cryo-electron microscopy studies. However, these classical structural biology methods lack temporal resolution and can be complemented, as shown in this mini-review, by other approaches such as time-resolved fiber diffraction and computational modeling. Together with studies on structurally similar tubulins from the prokaryotic world, these inputs can provide novel insights on MT assembly, dynamics, and the GTP cap.
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Affiliation(s)
- María
Ángela Oliva
- Unidad
de Desarrollo de Fármacos Biológicos, Inmunológicos
y Químicos, Centro de Investigaciones
Biológicas Margarita Salas - Consejo Superior de Investigaciones
Científicas, E-28040 Madrid, Spain
| | - Federico Gago
- Department
of Biomedical Sciences and IQM-UAH Associate Unit, University of Alcalá, E-28805 Alcalá de Henares, Spain
| | - Shinji Kamimura
- Department
of Biological Sciences, Faculty of Science and Engineering, Chuo University, 112-8551 Tokyo, Japan
| | - J. Fernando Díaz
- Unidad
de Desarrollo de Fármacos Biológicos, Inmunológicos
y Químicos, Centro de Investigaciones
Biológicas Margarita Salas - Consejo Superior de Investigaciones
Científicas, E-28040 Madrid, Spain
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6
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Santana-Molina C, del Saz-Navarro DM, Devos DP. Early origin and evolution of the FtsZ/tubulin protein family. Front Microbiol 2023; 13:1100249. [PMID: 36704558 PMCID: PMC9871819 DOI: 10.3389/fmicb.2022.1100249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 12/16/2022] [Indexed: 01/12/2023] Open
Abstract
The origin of the FtsZ/tubulin protein family was extremely relevant for life since these proteins are present in nearly all organisms, carrying out essential functions such as cell division or forming a major part of the cytoskeleton in eukaryotes. Therefore, investigating the early evolution of the FtsZ/tubulin protein family could reveal crucial aspects of the diversification of the three domains of life. In this study, we revisited the phylogenies of the FtsZ/tubulin protein family in an extensive prokaryotic diversity, focusing on the main evolutionary events that occurred during its evolution. We found evidence of its early origin in the last universal common ancestor since FtsZ was present in the last common ancestor of Bacteria and Archaea. In bacteria, ftsZ genes are genomically associated with the bacterial division gene cluster, while in archaea, ftsZ duplicated prior to archaeal diversification, and one of the copies is associated with protein biosynthesis genes. Archaea have expanded the FtsZ/tubulin protein family with sequences closely related to eukaryotic tubulins. In addition, we report novel CetZ-like groups in Halobacterota and Asgardarchaeota. Investigating the C-termini of prokaryotic paralogs basal to eukaryotic tubulins, we show that archaeal CetZ, as well as the plasmidic TubZ from Firmicutes, most likely originated from archaeal FtsZ. Finally, prokaryotic tubulins are restricted to Odinarchaeaota and Prosthecobacter species, and they seem to belong to different molecular systems. However, their phylogenies suggest that they are closely related to α/β-tubulins pointing to a potential ancestrality of these eukaryotic paralogs of tubulins.
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Affiliation(s)
- Carlos Santana-Molina
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas, Junta de Andalucía, Universidad Pablo de Olavide, Seville, Spain
- Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research (NIOZ), University of Utrecht, Utrecht, Netherlands
| | - DMaría del Saz-Navarro
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas, Junta de Andalucía, Universidad Pablo de Olavide, Seville, Spain
| | - Damien P. Devos
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas, Junta de Andalucía, Universidad Pablo de Olavide, Seville, Spain
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7
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Kattan J, Doerr A, Dogterom M, Danelon C. Shaping Liposomes by Cell-Free Expressed Bacterial Microtubules. ACS Synth Biol 2021; 10:2447-2455. [PMID: 34585918 PMCID: PMC8524656 DOI: 10.1021/acssynbio.1c00278] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Genetic control over
a cytoskeletal network inside lipid vesicles
offers a potential route to controlled shape changes and DNA segregation
in synthetic cell biology. Bacterial microtubules (bMTs) are protein
filaments found in bacteria of the genus Prosthecobacter. They are formed by the tubulins BtubA and BtubB, which polymerize
in the presence of GTP. Here, we show that the tubulins BtubA/B can
be functionally expressed from DNA templates in a reconstituted transcription-translation
system, thus providing a cytosol-like environment to study their biochemical
and biophysical properties. We found that bMTs spontaneously interact
with lipid membranes and display treadmilling. When compartmentalized
inside liposomes, de novo synthesized BtubA/B tubulins
self-organize into cytoskeletal structures of different morphologies.
Moreover, bMTs can exert a pushing force on the membrane and deform
liposomes, a phenomenon that can be reversed by a light-activated
disassembly of the filaments. Our work establishes bMTs as a new building
block in synthetic biology. In the context of creating a synthetic
cell, bMTs could help shape the lipid compartment, establish polarity
or directional transport, and assist the division machinery.
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Affiliation(s)
- Johannes Kattan
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Anne Doerr
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Marileen Dogterom
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Christophe Danelon
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
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8
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Gruebele M. Protein folding and surface interaction phase diagrams in vitro and in cells. FEBS Lett 2021; 595:1267-1274. [PMID: 33576021 DOI: 10.1002/1873-3468.14058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 02/07/2021] [Accepted: 02/08/2021] [Indexed: 11/11/2022]
Abstract
Protein stability is subject to environmental perturbations such as pressure and crowding, as well as sticking to other macromolecules and quinary structure. Thus, the environment inside and outside the cell plays a key role in how proteins fold, interact, and function on the scale from a few molecules to macroscopic ensembles. This review discusses three aspects of protein phase diagrams: first, the relevance of phase diagrams to protein folding and function in vitro and in cells; next, how the evolution of protein surfaces impacts on interaction phase diagrams; and finally, how phase separation plays a role on much larger length-scales than individual proteins or oligomers, when liquid phase-separated regions form to assist protein function and cell homeostasis.
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Affiliation(s)
- Martin Gruebele
- Department of Chemistry and Physics, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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9
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Collective effects of XMAP215, EB1, CLASP2, and MCAK lead to robust microtubule treadmilling. Proc Natl Acad Sci U S A 2020; 117:12847-12855. [PMID: 32457163 PMCID: PMC7293651 DOI: 10.1073/pnas.2003191117] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Treadmilling is a complex behavior of active polymers characterized by polymerization at one polymer end and simultaneous depolymerization at the other end. Treadmilling is an essential feature of cytoskeletal filaments driving actin-based cell motility, bacterial cell division and transport, and reorganization of microtubule arrays in plants. Although microtubule treadmilling occurs in many cellular contexts, how cells coordinate growth at microtubule plus ends and shrinkage at microtubule minus ends to achieve treadmilling is not understood. Here, we employ predictive computational modeling and a multiprotein in vitro assay to reconstitute cellular-like microtubule treadmilling. Our work provides a deeper understanding of how active polymer systems can be tuned to give rise to robust yet dynamic cytoskeletal architectures. Microtubule network remodeling is essential for fundamental cellular processes including cell division, differentiation, and motility. Microtubules are active biological polymers whose ends stochastically and independently switch between phases of growth and shrinkage. Microtubule treadmilling, in which the microtubule plus end grows while the minus end shrinks, is observed in cells; however, the underlying mechanisms are not known. Here, we use a combination of computational and in vitro reconstitution approaches to determine the conditions leading to robust microtubule treadmilling. We find that microtubules polymerized from tubulin alone can treadmill, albeit with opposite directionality and order-of-magnitude slower rates than observed in cells. We then employ computational simulations to predict that the combinatory effects of four microtubule-associated proteins (MAPs), namely EB1, XMAP215, CLASP2, and MCAK, can promote fast and sustained plus-end-leading treadmilling. Finally, we experimentally confirm the predictions of our computational model using a multi-MAP, in vitro microtubule dynamics assay to reconstitute robust plus-end-leading treadmilling, consistent with observations in cells. Our results demonstrate how microtubule dynamics can be modulated to achieve a dynamic balance between assembly and disassembly at opposite polymer ends, resulting in treadmilling over long periods of time. Overall, we show how the collective effects of multiple components give rise to complex microtubule behavior that may be used for global network remodeling in cells.
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10
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Cavalier-Smith T, Chao EEY. Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria). PROTOPLASMA 2020. [PMID: 31900730 DOI: 10.1007/s00709-019-01442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Palaeontologically, eubacteria are > 3× older than neomura (eukaryotes, archaebacteria). Cell biology contrasts ancestral eubacterial murein peptidoglycan walls and derived neomuran N-linked glycoprotein coats/walls. Misinterpreting long stems connecting clade neomura to eubacteria on ribosomal sequence trees (plus misinterpreted protein paralogue trees) obscured this historical pattern. Universal multiprotein ribosomal protein (RP) trees, more accurate than rRNA trees, are taxonomically undersampled. To reduce contradictions with genically richer eukaryote trees and improve eubacterial phylogeny, we constructed site-heterogeneous and maximum-likelihood universal three-domain, two-domain, and single-domain trees for 143 eukaryotes (branching now congruent with 187-protein trees), 60 archaebacteria, and 151 taxonomically representative eubacteria, using 51 and 26 RPs. Site-heterogeneous trees greatly improve eubacterial phylogeny and higher classification, e.g. showing gracilicute monophyly, that many 'rDNA-phyla' belong in Proteobacteria, and reveal robust new phyla Synthermota and Aquithermota. Monoderm Posibacteria and Mollicutes (two separate wall losses) are both polyphyletic: multiple outer membrane losses in Endobacteria occurred separately from Actinobacteria; neither phylum is related to Chloroflexi, the most divergent prokaryotes, which originated photosynthesis (new model proposed). RP trees support an eozoan root for eukaryotes and are consistent with archaebacteria being their sisters and rooted between Filarchaeota (=Proteoarchaeota, including 'Asgardia') and Euryarchaeota sensu-lato (including ultrasimplified 'DPANN' whose long branches often distort trees). Two-domain trees group eukaryotes within Planctobacteria, and archaebacteria with Planctobacteria/Sphingobacteria. Integrated molecular/palaeontological evidence favours negibacterial ancestors for neomura and all life. Unique presence of key pre-neomuran characters favours Planctobacteria only as ancestral to neomura, which apparently arose by coevolutionary repercussions (explained here in detail, including RP replacement) of simultaneous outer membrane and murein loss. Planctobacterial C-1 methanotrophic enzymes are likely ancestral to archaebacterial methanogenesis and β-propeller-α-solenoid proteins to eukaryotic vesicle coats, nuclear-pore-complexes, and intraciliary transport. Planctobacterial chaperone-independent 4/5-protofilament microtubules and MamK actin-ancestors prepared for eukaryote intracellular motility, mitosis, cytokinesis, and phagocytosis. We refute numerous wrong ideas about the universal tree.
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Affiliation(s)
| | - Ema E-Yung Chao
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
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11
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Cavalier-Smith T, Chao EEY. Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria). PROTOPLASMA 2020; 257:621-753. [PMID: 31900730 PMCID: PMC7203096 DOI: 10.1007/s00709-019-01442-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 09/19/2019] [Indexed: 05/02/2023]
Abstract
Palaeontologically, eubacteria are > 3× older than neomura (eukaryotes, archaebacteria). Cell biology contrasts ancestral eubacterial murein peptidoglycan walls and derived neomuran N-linked glycoprotein coats/walls. Misinterpreting long stems connecting clade neomura to eubacteria on ribosomal sequence trees (plus misinterpreted protein paralogue trees) obscured this historical pattern. Universal multiprotein ribosomal protein (RP) trees, more accurate than rRNA trees, are taxonomically undersampled. To reduce contradictions with genically richer eukaryote trees and improve eubacterial phylogeny, we constructed site-heterogeneous and maximum-likelihood universal three-domain, two-domain, and single-domain trees for 143 eukaryotes (branching now congruent with 187-protein trees), 60 archaebacteria, and 151 taxonomically representative eubacteria, using 51 and 26 RPs. Site-heterogeneous trees greatly improve eubacterial phylogeny and higher classification, e.g. showing gracilicute monophyly, that many 'rDNA-phyla' belong in Proteobacteria, and reveal robust new phyla Synthermota and Aquithermota. Monoderm Posibacteria and Mollicutes (two separate wall losses) are both polyphyletic: multiple outer membrane losses in Endobacteria occurred separately from Actinobacteria; neither phylum is related to Chloroflexi, the most divergent prokaryotes, which originated photosynthesis (new model proposed). RP trees support an eozoan root for eukaryotes and are consistent with archaebacteria being their sisters and rooted between Filarchaeota (=Proteoarchaeota, including 'Asgardia') and Euryarchaeota sensu-lato (including ultrasimplified 'DPANN' whose long branches often distort trees). Two-domain trees group eukaryotes within Planctobacteria, and archaebacteria with Planctobacteria/Sphingobacteria. Integrated molecular/palaeontological evidence favours negibacterial ancestors for neomura and all life. Unique presence of key pre-neomuran characters favours Planctobacteria only as ancestral to neomura, which apparently arose by coevolutionary repercussions (explained here in detail, including RP replacement) of simultaneous outer membrane and murein loss. Planctobacterial C-1 methanotrophic enzymes are likely ancestral to archaebacterial methanogenesis and β-propeller-α-solenoid proteins to eukaryotic vesicle coats, nuclear-pore-complexes, and intraciliary transport. Planctobacterial chaperone-independent 4/5-protofilament microtubules and MamK actin-ancestors prepared for eukaryote intracellular motility, mitosis, cytokinesis, and phagocytosis. We refute numerous wrong ideas about the universal tree.
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Affiliation(s)
| | - Ema E-Yung Chao
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
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12
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Szewczak‐Harris A, Wagstaff J, Löwe J. Cryo-EM structure of the MinCD copolymeric filament from Pseudomonas aeruginosa at 3.1 Å resolution. FEBS Lett 2019; 593:1915-1926. [PMID: 31166018 PMCID: PMC6771821 DOI: 10.1002/1873-3468.13471] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 06/02/2019] [Accepted: 06/03/2019] [Indexed: 11/07/2022]
Abstract
Positioning of the division site in many bacterial species relies on the MinCDE system, which prevents the cytokinetic Z-ring from assembling anywhere but the mid-cell, through an oscillatory diffusion-reaction mechanism. MinD dimers bind to membranes and, via their partner MinC, inhibit the polymerization of cell division protein FtsZ into the Z-ring. MinC and MinD form polymeric assemblies in solution and on cell membranes. Here, we report the high-resolution cryo-EM structure of the copolymeric filaments of Pseudomonas aeruginosa MinCD. The filaments consist of three protofilaments made of alternating MinC and MinD dimers. The MinCD protofilaments are almost completely straight and assemble as single protofilaments on lipid membranes, which we also visualized by cryo-EM.
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Affiliation(s)
- Andrzej Szewczak‐Harris
- MRC Laboratory of Molecular BiologyCambridgeUK
- Present address:
Department of BiochemistryUniversity of CambridgeUK
| | | | - Jan Löwe
- MRC Laboratory of Molecular BiologyCambridgeUK
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13
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Lawrence EJ, Zanic M. Rescuing microtubules from the brink of catastrophe: CLASPs lead the way. Curr Opin Cell Biol 2019; 56:94-101. [PMID: 30453184 PMCID: PMC6370552 DOI: 10.1016/j.ceb.2018.10.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 10/12/2018] [Accepted: 10/31/2018] [Indexed: 01/11/2023]
Abstract
Microtubules are cytoskeletal polymers that dynamically remodel to perform essential cellular functions. Individual microtubules alternate between phases of growth and shrinkage via sudden transitions called catastrophe and rescue, driven by losing and regaining a stabilizing cap at the dynamic microtubule end. New in vitro studies now show that a conserved family of CLASP proteins specifically modulate microtubule catastrophe and rescue transitions. Further, recent cryo-electron microscopy approaches have elucidated new structural features of the stabilizing cap. Together, these new advances provide a clearer view on the complexity of the microtubule end and its regulation.
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Affiliation(s)
- E J Lawrence
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37240, United States
| | - M Zanic
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37240, United States; Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37240, United States; Department of Biochemistry, Vanderbilt University, Nashville, TN 37240, United States.
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Pospich S, Raunser S. Single particle cryo-EM-an optimal tool to study cytoskeletal proteins. Curr Opin Struct Biol 2018; 52:16-24. [PMID: 30056307 DOI: 10.1016/j.sbi.2018.07.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 07/12/2018] [Accepted: 07/16/2018] [Indexed: 12/01/2022]
Abstract
Cytoskeletal proteins play essential roles in many cellular processes. Knowledge of their structures is important to understand their function and regulation. Since cytoskeletal polymers are difficult to crystallize, cryo-EM has been the predominant method of choice to study their structures. Recent advances in the methodology have enabled reconstructions at near-atomic resolution. In this review, we focus on novel insights gained from high-resolution cryo-EM structures of cytoskeletal polymers. These include eukaryotic proteins such as F-actin and microtubules as well as their prokaryotic homologues. The unprecedented high-resolutions allow identifying small molecules, including nucleotides and drugs, as well as subtle changes at interfaces that are key to complex processes, such as nucleotide hydrolysis in microtubules and actin filaments. While major methodological advances have already promoted the structural analysis of cytoskeletal polymers, there are still specific methodological challenges to overcome and many scientific questions remain to be answered.
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Affiliation(s)
- Sabrina Pospich
- Max Planck Institute of Molecular Physiology, Department of Structural Biochemistry, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
| | - Stefan Raunser
- Max Planck Institute of Molecular Physiology, Department of Structural Biochemistry, Otto-Hahn-Str. 11, 44227 Dortmund, Germany.
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Abstract
We report three high-resolution structures of microtubules in different nucleotide states—GMPCPP, GDP, and GTPγS—in the absence of any binding proteins, allowing us to separate the effects of nucleotide- and microtubule (MT)-associated protein (MAPs) binding on MT structure. End-binding (EB) proteins can bind and induce partial lattice compaction of a preformed GMPCPP-bound MT, a lattice type that is far from EBs’ ideal binding platform. We propose a model in which the MT lattice serves as a platform that integrates internal tubulin signals, such as nucleotide state, with outside signals, such as binding of MAPs. These global lattice rearrangements in turn affect the affinity of other MT partners and result in the exquisite regulation of the MT dynamics. Microtubules (MTs) are polymers assembled from αβ-tubulin heterodimers that display the hallmark behavior of dynamic instability. MT dynamics are driven by GTP hydrolysis within the MT lattice, and are highly regulated by a number of MT-associated proteins (MAPs). How MAPs affect MTs is still not fully understood, partly due to a lack of high-resolution structural data on undecorated MTs, which need to serve as a baseline for further comparisons. Here we report three structures of MTs in different nucleotide states (GMPCPP, GDP, and GTPγS) at near-atomic resolution and in the absence of any binding proteins. These structures allowed us to differentiate the effects of nucleotide state versus MAP binding on MT structure. Kinesin binding has a small effect on the extended, GMPCPP-bound lattice, but hardly affects the compacted GDP-MT lattice, while binding of end-binding (EB) proteins can induce lattice compaction (together with lattice twist) in MTs that were initially in an extended and more stable state. We propose a MT lattice-centric model in which the MT lattice serves as a platform that integrates internal tubulin signals, such as nucleotide state, with outside signals, such as binding of MAPs or mechanical forces, resulting in global lattice rearrangements that in turn affect the affinity of other MT partners and result in the exquisite regulation of MT dynamics.
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Chaaban S, Brouhard GJ. A microtubule bestiary: structural diversity in tubulin polymers. Mol Biol Cell 2018; 28:2924-2931. [PMID: 29084910 PMCID: PMC5662251 DOI: 10.1091/mbc.e16-05-0271] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 08/30/2017] [Accepted: 09/06/2017] [Indexed: 11/11/2022] Open
Abstract
Microtubules are long, slender polymers of αβ-tubulin found in all eukaryotic cells. Tubulins associate longitudinally to form protofilaments, and adjacent protofilaments associate laterally to form the microtubule. In the textbook view, microtubules are 1) composed of 13 protofilaments, 2) arranged in a radial array by the centrosome, and 3) built into the 9+2 axoneme. Although these canonical structures predominate in eukaryotes, microtubules with divergent protofilament numbers and higher-order microtubule assemblies have been discovered throughout the last century. Here we survey these noncanonical structures, from the 4-protofilament microtubules of Prosthecobacter to the 40-protofilament accessory microtubules of mantidfly sperm. We review the variety of protofilament numbers observed in different species, in different cells within the same species, and in different stages within the same cell. We describe the determinants of protofilament number, namely nucleation factors, tubulin isoforms, and posttranslational modifications. Finally, we speculate on the functional significance of these diverse polymers. Equipped with novel tubulin-purification tools, the field is now prepared to tackle the long-standing question of the evolutionary basis of microtubule structure.
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Affiliation(s)
- Sami Chaaban
- Department of Biology, McGill University, Montreal, QC H3A 1B1, Canada
| | - Gary J Brouhard
- Department of Biology, McGill University, Montreal, QC H3A 1B1, Canada
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Wagstaff J, Löwe J. Prokaryotic cytoskeletons: protein filaments organizing small cells. Nat Rev Microbiol 2018; 16:187-201. [PMID: 29355854 DOI: 10.1038/nrmicro.2017.153] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Most, if not all, bacterial and archaeal cells contain at least one protein filament system. Although these filament systems in some cases form structures that are very similar to eukaryotic cytoskeletons, the term 'prokaryotic cytoskeletons' is used to refer to many different kinds of protein filaments. Cytoskeletons achieve their functions through polymerization of protein monomers and the resulting ability to access length scales larger than the size of the monomer. Prokaryotic cytoskeletons are involved in many fundamental aspects of prokaryotic cell biology and have important roles in cell shape determination, cell division and nonchromosomal DNA segregation. Some of the filament-forming proteins have been classified into a small number of conserved protein families, for example, the almost ubiquitous tubulin and actin superfamilies. To understand what makes filaments special and how the cytoskeletons they form enable cells to perform essential functions, the structure and function of cytoskeletal molecules and their filaments have been investigated in diverse bacteria and archaea. In this Review, we bring these data together to highlight the diverse ways that linear protein polymers can be used to organize other molecules and structures in bacteria and archaea.
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Affiliation(s)
- James Wagstaff
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Jan Löwe
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
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