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Kwiatkowski W, Greenwald J, Murzakhmetov L, Robinson RC, Riek R. Short Peptide Amyloids Are a Potential Sequence Pool for the Emergence of Proteins. J Mol Biol 2024; 436:168495. [PMID: 38360090 DOI: 10.1016/j.jmb.2024.168495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 01/15/2024] [Accepted: 02/10/2024] [Indexed: 02/17/2024]
Abstract
Under prebiotic conditions, peptides are capable of self-replication through a structure-based template-assisted mechanism when they form amyloids. Furthermore, peptide amyloids can spontaneously form inside fatty acid vesicles creating membrane enclosed complex structures of variable morphologies. This is possible because fatty acid vesicle membranes act as filters allowing passage of activated amino acids while some amino acids derived from the activated species become non-permeable and trapped in the vesicles. Similarly, nascent peptides derived from the condensation of the activated amino acids are also trapped in the vesicles. It is hypothesized that such preselected peptide amyloids become a sequence pool for the emergence of proteins in life and that after billions of years of cellular evolution, the sequences in the current proteome have diverged significantly from these original seed peptides. If this hypothesis is correct, it could be possible to detect the traces of these seed sequences in current proteomes. Here, we show for all possible 3, 6, 7, 8 or 9 residue sequence motifs that those motifs that are most amyloidogenic/aggregation prone are over-represented in extant proteomes compared to a sequence-randomized proteome. Furthermore, we find that there is a greater proportion of amyloidogenic sequence motifs in archaea proteomes than in the larger primate proteomes. This suggests that the evolution towards larger proteomes leads to smaller proportion of amyloidogenic sequences.
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Affiliation(s)
| | | | | | - Robert C Robinson
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Thailand; Research Institute for Interdisciplinary Science, Okayama University, Japan
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2
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Tran LT, Akıl C, Senju Y, Robinson RC. The eukaryotic-like characteristics of small GTPase, roadblock and TRAPPC3 proteins from Asgard archaea. Commun Biol 2024; 7:273. [PMID: 38472392 DOI: 10.1038/s42003-024-05888-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 02/06/2024] [Indexed: 03/14/2024] Open
Abstract
Membrane-enclosed organelles are defining features of eukaryotes in distinguishing these organisms from prokaryotes. Specification of distinct membranes is critical to assemble and maintain discrete compartments. Small GTPases and their regulators are the signaling molecules that drive membrane-modifying machineries to the desired location. These signaling molecules include Rab and Rag GTPases, roadblock and longin domain proteins, and TRAPPC3-like proteins. Here, we take a structural approach to assess the relatedness of these eukaryotic-like proteins in Asgard archaea, the closest known prokaryotic relatives to eukaryotes. We find that the Asgard archaea GTPase core domains closely resemble eukaryotic Rabs and Rags. Asgard archaea roadblock, longin and TRAPPC3 domain-containing proteins form dimers similar to those found in the eukaryotic TRAPP and Ragulator complexes. We conclude that the emergence of these protein architectures predated eukaryogenesis, however further adaptations occurred in proto-eukaryotes to allow these proteins to regulate distinct internal membranes.
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Affiliation(s)
- Linh T Tran
- Research Institute for Interdisciplinary Science, Okayama University, Okayama, 700-8530, Japan
| | - Caner Akıl
- Research Institute for Interdisciplinary Science, Okayama University, Okayama, 700-8530, Japan
- Division of Structural Biology, University of Oxford, Oxford, England
| | - Yosuke Senju
- Research Institute for Interdisciplinary Science, Okayama University, Okayama, 700-8530, Japan
| | - Robert C Robinson
- Research Institute for Interdisciplinary Science, Okayama University, Okayama, 700-8530, Japan.
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, 21210, Thailand.
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3
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Zhou Y, Wannapaiboon S, Prongjit M, Pornsuwan S, Sucharitakul J, Kamonsutthipaijit N, Robinson RC, Suginta W. Structural and binding studies of a new chitin-active AA10 lytic polysaccharide monooxygenase from the marine bacterium Vibrio campbellii. Acta Crystallogr D Struct Biol 2023; 79:479-497. [PMID: 37259836 DOI: 10.1107/s2059798323003261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 04/10/2023] [Indexed: 06/02/2023] Open
Abstract
Vibrio spp. play a crucial role in the global recycling of the highly abundant recalcitrant biopolymer chitin in marine ecosystems through their ability to secrete chitin-degrading enzymes to efficiently hydrolyse chitinous materials and use them as their major carbon source. In this study, the first crystal structures of a complete four-domain chitin-active AA10 lytic polysaccharide monooxygenase from the chitinolytic bacterium Vibrio campbellii type strain ATCC BAA-1116 are reported. The crystal structures of apo and copper-bound VhLPMO10A were resolved as homodimers with four distinct domains: an N-terminal AA10 catalytic (CatD) domain connected to a GlcNAc-binding (GbpA_2) domain, followed by a module X domain and a C-terminal carbohydrate-binding module (CBM73). Size-exclusion chromatography and small-angle X-ray scattering analysis confirmed that VhLPMO10A exists as a monomer in solution. The active site of VhLPMO10A is located on the surface of the CatD domain, with three conserved residues (His1, His98 and Phe170) forming the copper(II)-binding site. Metal-binding studies using synchrotron X-ray absorption spectroscopy and X-ray fluorescence, together with electron paramagnetic resonance spectroscopy, gave consistently strong copper(II) signals in the protein samples, confirming that VhLPMO10A is a copper-dependent enzyme. ITC binding data showed that VhLPMO10A could bind various divalent cations but bound most strongly to copper(II) ions, with a Kd of 0.1 ± 0.01 µM. In contrast, a Kd of 1.9 nM was estimated for copper(I) ions from redox-potential measurements. The presence of ascorbic acid is essential for H2O2 production in the reaction catalysed by VhLPMO10A. MALDI-TOF MS identified VhLPMO10A as a C1-specific LPMO, generating oxidized chitooligosaccharide products with different degrees of polymerization (DP2ox-DP8ox). This new member of the chitin-active AA10 LPMOs could serve as a powerful biocatalyst in biofuel production from chitin biomass.
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Affiliation(s)
- Yong Zhou
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology, Rayong 21210, Thailand
| | | | - Methinee Prongjit
- Department of Biochemistry, Chulalongkorn University, Bangkok 10330, Thailand
| | - Soraya Pornsuwan
- Department of Chemistry, Mahidol University, Bangkok 10400, Thailand
| | - Jeerus Sucharitakul
- Department of Biochemistry, Chulalongkorn University, Bangkok 10330, Thailand
| | | | - Robert C Robinson
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology, Rayong 21210, Thailand
| | - Wipa Suginta
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology, Rayong 21210, Thailand
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4
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Ponlachantra K, Suginta W, Robinson RC, Kitaoku Y. AlphaFold2: A versatile tool to predict the appearance of functional adaptations in evolution: Profilin interactions in uncultured Asgard archaea: Profilin interactions in uncultured Asgard archaea. Bioessays 2023; 45:e2200119. [PMID: 36461738 DOI: 10.1002/bies.202200119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 11/07/2022] [Accepted: 11/09/2022] [Indexed: 12/05/2022]
Abstract
The release of AlphaFold2 (AF2), a deep-learning-aided, open-source protein structure prediction program, from DeepMind, opened a new era of molecular biology. The astonishing improvement in the accuracy of the structure predictions provides the opportunity to characterize protein systems from uncultured Asgard archaea, key organisms in evolutionary biology. Despite the accumulation in metagenomics-derived Asgard archaea eukaryotic-like protein sequences, limited structural and biochemical information have restricted the insight in their potential functions. In this review, we focus on profilin, an actin-dynamics regulating protein, which in eukaryotes, modulates actin polymerization through (1) direct actin interaction, (2) polyproline binding, and (3) phospholipid binding. We assess AF2-predicted profilin structures in their potential abilities to participate in these activities. We demonstrate that AF2 is a powerful new tool for understanding the emergence of biological functional traits in evolution.
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Affiliation(s)
- Khongpon Ponlachantra
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Wipa Suginta
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Robert C Robinson
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand.,Research Institute for Interdisciplinary Science (RIIS), Okayama University, Okayama, Japan
| | - Yoshihito Kitaoku
- Research Institute for Interdisciplinary Science (RIIS), Okayama University, Okayama, Japan
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5
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Akıl C, Ali S, Tran LT, Gaillard J, Li W, Hayashida K, Hirose M, Kato T, Oshima A, Fujishima K, Blanchoin L, Narita A, Robinson RC. Structure and dynamics of Odinarchaeota tubulin and the implications for eukaryotic microtubule evolution. Sci Adv 2022; 8:eabm2225. [PMID: 35333570 PMCID: PMC8956254 DOI: 10.1126/sciadv.abm2225] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 02/03/2022] [Indexed: 06/14/2023]
Abstract
Tubulins are critical for the internal organization of eukaryotic cells, and understanding their emergence is an important question in eukaryogenesis. Asgard archaea are the closest known prokaryotic relatives to eukaryotes. Here, we elucidated the apo and nucleotide-bound x-ray structures of an Asgard tubulin from hydrothermal living Odinarchaeota (OdinTubulin). The guanosine 5'-triphosphate (GTP)-bound structure resembles a microtubule protofilament, with GTP bound between subunits, coordinating the "+" end subunit through a network of water molecules and unexpectedly by two cations. A water molecule is located suitable for GTP hydrolysis. Time course crystallography and electron microscopy revealed conformational changes on GTP hydrolysis. OdinTubulin forms tubules at high temperatures, with short curved protofilaments coiling around the tubule circumference, more similar to FtsZ, rather than running parallel to its length, as in microtubules. Thus, OdinTubulin represents an evolutionary stage intermediate between prokaryotic FtsZ and eukaryotic microtubule-forming tubulins.
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Affiliation(s)
- Caner Akıl
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan
- Tokyo Institute of Technology, Earth-Life Science Institute (ELSI), Tokyo 152-8551, Japan
| | - Samson Ali
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Linh T. Tran
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan
| | - Jérémie Gaillard
- University of Grenoble-Alpes, CEA, CNRS, INRA, Interdisciplinary Research Institute of Grenoble, Laboratoire de Physiologie Cellulaire & Végétale, CytoMorpho Lab, 38054 Grenoble, France
| | - Wenfei Li
- National Laboratory of Solid State Microstructure, Department of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, 210093 Nanjing, China
| | - Kenichi Hayashida
- Cellular and Structural Physiology Institute (CeSPI), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Mika Hirose
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Takayuki Kato
- Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Atsunori Oshima
- Cellular and Structural Physiology Institute (CeSPI), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
- Department of Basic Medicinal Sciences, Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
- Institute for Glyco-core Research (iGCORE), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Kosuke Fujishima
- Tokyo Institute of Technology, Earth-Life Science Institute (ELSI), Tokyo 152-8551, Japan
- Graduate School of Media and Governance, Keio University, Fujisawa 252-0882, Japan
| | - Laurent Blanchoin
- University of Grenoble-Alpes, CEA, CNRS, INRA, Interdisciplinary Research Institute of Grenoble, Laboratoire de Physiologie Cellulaire & Végétale, CytoMorpho Lab, 38054 Grenoble, France
- Université de Paris, INSERM, CEA, Institut de Recherche Saint Louis, U 976, CytoMorpho Lab, 75010 Paris, France
| | - Akihiro Narita
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Robert C. Robinson
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong 21210, Thailand
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6
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Boiero Sanders M, Toret CP, Guillotin A, Antkowiak A, Vannier T, Robinson RC, Michelot A. Specialization of actin isoforms derived from the loss of key interactions with regulatory factors. EMBO J 2022; 41:e107982. [PMID: 35178724 PMCID: PMC8886540 DOI: 10.15252/embj.2021107982] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 01/19/2022] [Accepted: 01/21/2022] [Indexed: 11/09/2022] Open
Abstract
A paradox of eukaryotic cells is that while some species assemble a complex actin cytoskeleton from a single ortholog, other species utilize a greater diversity of actin isoforms. The physiological consequences of using different actin isoforms, and the molecular mechanisms by which highly conserved actin isoforms are segregated into distinct networks, are poorly known. Here, we sought to understand how a simple biological system, composed of a unique actin and a limited set of actin‐binding proteins, reacts to a switch to heterologous actin expression. Using yeast as a model system and biomimetic assays, we show that such perturbation causes drastic reorganization of the actin cytoskeleton. Our results indicate that defective interaction of a heterologous actin for important regulators of actin assembly limits certain actin assembly pathways while reinforcing others. Expression of two heterologous actin variants, each specialized in assembling a different network, rescues cytoskeletal organization and confers resistance to external perturbation. Hence, while species using a unique actin have homeostatic actin networks, actin assembly pathways in species using several actin isoforms may act more independently.
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Affiliation(s)
| | - Christopher P Toret
- CNRS, IBDM, Turing Centre for Living Systems, Aix Marseille Univ, Marseille, France
| | - Audrey Guillotin
- CNRS, IBDM, Turing Centre for Living Systems, Aix Marseille Univ, Marseille, France
| | - Adrien Antkowiak
- CNRS, IBDM, Turing Centre for Living Systems, Aix Marseille Univ, Marseille, France
| | - Thomas Vannier
- CNRS, IBDM, Turing Centre for Living Systems, Aix Marseille Univ, Marseille, France
| | - Robert C Robinson
- Research Institute for Interdisciplinary Science (RIIS), Okayama University, Okayama, Japan.,School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Alphée Michelot
- CNRS, IBDM, Turing Centre for Living Systems, Aix Marseille Univ, Marseille, France
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7
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Koronfel M, Kounatidis I, Mwangangi DM, Vyas N, Okolo C, Jadhav A, Fish T, Chotchuang P, Schulte A, Robinson RC, Harkiolaki M. Correlative cryo-imaging of the cellular universe with soft X-rays and laser light used to track F-actin structures in mammalian cells. Acta Crystallogr D Struct Biol 2021; 77:1479-1485. [PMID: 34866605 PMCID: PMC8647181 DOI: 10.1107/s2059798321010329] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 10/06/2021] [Indexed: 11/16/2022] Open
Abstract
Imaging of actin filaments is crucial due to the integral role that they play in many cellular functions such as intracellular transport, membrane remodelling and cell motility. Visualizing actin filaments has so far relied on fluorescence microscopy and electron microscopy/tomography. The former lacks the capacity to capture the overall local ultrastructure, while the latter requires rigorous sample preparation that can lead to potential artefacts, and only delivers relatively small volumes of imaging data at the thinnest areas of a cell. In this work, a correlative approach utilizing in situ super-resolution fluorescence imaging and cryo X-ray tomography was used to image bundles of actin filaments deep inside cells under near-native conditions. In this case, fluorescence 3D imaging localized the actin bundles within the intracellular space, while X-ray tomograms of the same areas provided detailed views of the local ultrastructure. Using this new approach, actin trails connecting vesicles in the perinuclear area and hotspots of actin presence within and around multivesicular bodies were observed. The characteristic prevalence of filamentous actin in cytoplasmic extensions was also documented.
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Affiliation(s)
- Mohamed Koronfel
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Ilias Kounatidis
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Dennis M. Mwangangi
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138673, Singapore
| | - Nina Vyas
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Chidinma Okolo
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Archana Jadhav
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Tom Fish
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Phatcharin Chotchuang
- Research Institute for Interdisciplinary Science (RIIS), Okayama University, Okayama 700-8530, Japan
| | - Albert Schulte
- Research Institute for Interdisciplinary Science (RIIS), Okayama University, Okayama 700-8530, Japan
| | - Robert C. Robinson
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138673, Singapore
- Research Institute for Interdisciplinary Science (RIIS), Okayama University, Okayama 700-8530, Japan
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong 21210, Thailand
| | - Maria Harkiolaki
- Beamline B24, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
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8
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Kitaoku Y, Fukamizo T, Kumsaoad S, Ubonbal P, Robinson RC, Suginta W. A structural model for (GlcNAc) 2 translocation via a periplasmic chitooligosaccharide-binding protein from marine Vibrio bacteria. J Biol Chem 2021; 297:101071. [PMID: 34400168 PMCID: PMC8449061 DOI: 10.1016/j.jbc.2021.101071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 08/04/2021] [Accepted: 08/10/2021] [Indexed: 11/25/2022] Open
Abstract
VhCBP is a periplasmic chitooligosaccharide-binding protein mainly responsible for translocation of the chitooligosaccharide (GlcNAc)2 across the double membranes of marine bacteria. However, structural and thermodynamic understanding of the sugar-binding/-release processes of VhCBP is relatively less. VhCBP displayed the greatest affinity toward (GlcNAc)2, with lower affinity for longer-chain chitooligosaccharides [(GlcNAc)3–4]. (GlcNAc)4 partially occupied the closed sugar-binding groove, with two reducing-end GlcNAc units extending beyond the sugar-binding groove and barely characterized by weak electron density. Mutation of three conserved residues (Trp363, Asp365, and Trp513) to Ala resulted in drastic decreases in the binding affinity toward the preferred substrate (GlcNAc)2, indicating their significant contributions to sugar binding. The structure of the W513A–(GlcNAc)2 complex in a ‘half-open’ conformation unveiled the intermediary step of the (GlcNAc)2 translocation from the soluble CBP in the periplasm to the inner membrane–transporting components. Isothermal calorimetry data suggested that VhCBP adopts the high-affinity conformation to bind (GlcNAc)2, while its low-affinity conformation facilitated sugar release. Thus, chitooligosaccharide translocation, conferred by periplasmic VhCBP, is a crucial step in the chitin catabolic pathway, allowing Vibrio bacteria to thrive in oceans where chitin is their major source of nutrients.
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Affiliation(s)
- Yoshihito Kitaoku
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Tamo Fukamizo
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand.
| | - Sawitree Kumsaoad
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Prakayfun Ubonbal
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Robert C Robinson
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand; Research Institute of Interdisciplinary Science (RIIS), Okayama University, Okayama, Japan.
| | - Wipa Suginta
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand.
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9
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Tan YQ, Ali S, Xue B, Teo WZ, Ling LH, Go MK, Lv H, Robinson RC, Narita A, Yew WS. Structure of a Minimal α-Carboxysome-Derived Shell and Its Utility in Enzyme Stabilization. Biomacromolecules 2021; 22:4095-4109. [PMID: 34384019 DOI: 10.1021/acs.biomac.1c00533] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Bacterial microcompartments are proteinaceous shells that encase specialized metabolic processes in bacteria. Recent advances in simplification of these intricate shells have encouraged bioengineering efforts. Here, we construct minimal shells derived from the Halothiobacillus neapolitanus α-carboxysome, which we term Cso-shell. Using cryogenic electron microscopy, the atomic-level structures of two shell forms were obtained, reinforcing notions of evolutionarily conserved features in bacterial microcompartment shell architecture. Encapsulation peptide sequences that facilitate loading of heterologous protein cargo within the shells were identified. We further provide a first demonstration in utilizing minimal bacterial microcompartment-derived shells for hosting heterologous enzymes. Cso-shells were found to stabilize enzymatic activities against heat shock, presence of methanol co-solvent, consecutive freeze-thawing, and alkaline environments. This study yields insights into α-carboxysome assembly and advances the utility of synthetic bacterial microcompartments as nanoreactors capable of stabilizing enzymes with varied properties and reaction chemistries.
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Affiliation(s)
- Yong Quan Tan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), 8 Medical Drive, Singapore 117597.,NUS Synthetic Biology for Clinical and Technological Innovation, 28 Medical Drive, Singapore 117456.,Graduate School for Integrative Sciences and Engineering, NUS, Singapore 119077
| | - Samson Ali
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.,Research Institute for Interdisciplinary Science (RIIS), Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Bo Xue
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), 8 Medical Drive, Singapore 117597.,NUS Synthetic Biology for Clinical and Technological Innovation, 28 Medical Drive, Singapore 117456.,Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599
| | - Wei Zhe Teo
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), 8 Medical Drive, Singapore 117597.,NUS Synthetic Biology for Clinical and Technological Innovation, 28 Medical Drive, Singapore 117456.,Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599
| | - Lay Hiang Ling
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), 8 Medical Drive, Singapore 117597.,NUS Synthetic Biology for Clinical and Technological Innovation, 28 Medical Drive, Singapore 117456.,Graduate School for Integrative Sciences and Engineering, NUS, Singapore 119077
| | - Maybelle Kho Go
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), 8 Medical Drive, Singapore 117597.,NUS Synthetic Biology for Clinical and Technological Innovation, 28 Medical Drive, Singapore 117456.,Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599
| | - Hong Lv
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai 200438, People's Republic of China.,State Key Laboratory of Genetic Engineering, School of Life Science, Fudan University, Shanghai 200438, People's Republic of China
| | - Robert C Robinson
- Research Institute for Interdisciplinary Science (RIIS), Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan.,School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong 21210, Thailand
| | - Akihiro Narita
- Structural Biology Research Center, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Wen Shan Yew
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), 8 Medical Drive, Singapore 117597.,NUS Synthetic Biology for Clinical and Technological Innovation, 28 Medical Drive, Singapore 117456.,Graduate School for Integrative Sciences and Engineering, NUS, Singapore 119077.,Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore 117599
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10
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Chee SMQ, Wongsantichon J, Yi LS, Sana B, Frosi Y, Robinson RC, Ghadessy FJ. Functional display of bioactive peptides on the vGFP scaffold. Sci Rep 2021; 11:10127. [PMID: 33980885 PMCID: PMC8115314 DOI: 10.1038/s41598-021-89421-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 04/27/2021] [Indexed: 11/24/2022] Open
Abstract
Grafting bioactive peptides into recipient protein scaffolds can often increase their activities by conferring enhanced stability and cellular longevity. Here, we describe use of vGFP as a novel scaffold to display peptides. vGFP comprises GFP fused to a bound high affinity Enhancer nanobody that potentiates its fluorescence. We show that peptides inserted into the linker region between GFP and the Enhancer are correctly displayed for on-target interaction, both in vitro and in live cells by pull-down, measurement of target inhibition and imaging analyses. This is further confirmed by structural studies highlighting the optimal display of a vGFP-displayed peptide bound to Mdm2, the key negative regulator of p53 that is often overexpressed in cancer. We also demonstrate a potential biosensing application of the vGFP scaffold by showing target-dependent modulation of intrinsic fluorescence. vGFP is relatively thermostable, well-expressed and inherently fluorescent. These properties make it a useful scaffold to add to the existing tool box for displaying peptides that can disrupt clinically relevant protein–protein interactions.
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Affiliation(s)
- Sharon Min Qi Chee
- p53 Laboratory, A*STAR, 8A Biomedical Grove, Singapore, 138648, Singapore
| | - Jantana Wongsantichon
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Lau Sze Yi
- p53 Laboratory, A*STAR, 8A Biomedical Grove, Singapore, 138648, Singapore
| | - Barindra Sana
- p53 Laboratory, A*STAR, 8A Biomedical Grove, Singapore, 138648, Singapore
| | - Yuri Frosi
- p53 Laboratory, A*STAR, 8A Biomedical Grove, Singapore, 138648, Singapore
| | - Robert C Robinson
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, 21210, Thailand.,Research Institute for Interdisciplinary Science, Okayama University, Okayama, 700-8530, Japan
| | - Farid J Ghadessy
- p53 Laboratory, A*STAR, 8A Biomedical Grove, Singapore, 138648, Singapore.
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11
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Mwangangi DM, Manser E, Robinson RC. The structure of the actin filament uncapping complex mediated by twinfilin. Sci Adv 2021; 7:eabd5271. [PMID: 33571120 PMCID: PMC7840138 DOI: 10.1126/sciadv.abd5271] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 12/08/2020] [Indexed: 05/25/2023]
Abstract
Uncapping of actin filaments is essential for driving polymerization and depolymerization dynamics from capping protein-associated filaments; however, the mechanisms of uncapping leading to rapid disassembly are unknown. Here, we elucidated the x-ray crystal structure of the actin/twinfilin/capping protein complex to address the mechanisms of twinfilin uncapping of actin filaments. The twinfilin/capping protein complex binds to two G-actin subunits in an orientation that resembles the actin filament barbed end. This suggests an unanticipated mechanism by which twinfilin disrupts the stable capping of actin filaments by inducing a G-actin conformation in the two terminal actin subunits. Furthermore, twinfilin disorders critical actin-capping protein interactions, which will assist in the dissociation of capping protein, and may promote filament uncapping through a second mechanism involving V-1 competition for an actin-binding surface on capping protein. The extensive interactions with capping protein indicate that the evolutionary conserved role of twinfilin is to uncap actin filaments.
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Affiliation(s)
- Dennis M Mwangangi
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138673, Singapore
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Edward Manser
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138673, Singapore
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Robert C Robinson
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138673, Singapore.
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong 21210, Thailand
- Research Institute for Interdisciplinary Science (RIIS), Okayama University, Okayama 700-8530, Japan
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12
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Shrestha MM, Lim CY, Bi X, Robinson RC, Han W. Tmod3 Phosphorylation Mediates AMPK-Dependent GLUT4 Plasma Membrane Insertion in Myoblasts. Front Endocrinol (Lausanne) 2021; 12:653557. [PMID: 33959097 PMCID: PMC8095187 DOI: 10.3389/fendo.2021.653557] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 03/22/2021] [Indexed: 12/28/2022] Open
Abstract
Insulin and muscle contractions mediate glucose transporter 4 (GLUT4) translocation and insertion into the plasma membrane (PM) for glucose uptake in skeletal muscles. Muscle contraction results in AMPK activation, which promotes GLUT4 translocation and PM insertion. However, little is known regarding AMPK effectors that directly regulate GLUT4 translocation. We aim to identify novel AMPK effectors in the regulation of GLUT4 translocation. We performed biochemical, molecular biology and fluorescent microscopy imaging experiments using gain- and loss-of-function mutants of tropomodulin 3 (Tmod3). Here we report Tmod3, an actin filament capping protein, as a novel AMPK substrate and an essential mediator of AMPK-dependent GLUT4 translocation and glucose uptake in myoblasts. Furthermore, Tmod3 plays a key role in AMPK-induced F-actin remodeling and GLUT4 insertion into the PM. Our study defines Tmod3 as a key AMPK effector in the regulation of GLUT4 insertion into the PM and glucose uptake in muscle cells, and offers new mechanistic insights into the regulation of glucose homeostasis.
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Affiliation(s)
- Man Mohan Shrestha
- Laboratory of Metabolic Medicine, Singapore Bioimaging Consortium, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Chun-Yan Lim
- Laboratory of Metabolic Medicine, Singapore Bioimaging Consortium, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Xuezhi Bi
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Robert C. Robinson
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Weiping Han
- Laboratory of Metabolic Medicine, Singapore Bioimaging Consortium, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- *Correspondence: Weiping Han,
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13
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Amornloetwattana R, Robinson RC, Soysa HSM, van den Berg B, Suginta W. Chitoporin from Serratia marcescens: recombinant expression, purification and crystallization. Acta Crystallogr F Struct Biol Commun 2020; 76:536-543. [PMID: 33135672 PMCID: PMC7605108 DOI: 10.1107/s2053230x20013874] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 10/18/2020] [Indexed: 11/10/2022] Open
Abstract
Serratia marcescens is an opportunistic pathogen that commonly causes hospital-acquired infections and can utilize chitin-enriched nutrients as an alternative energy source. This study reports the identification of a chitoporin (ChiP), termed SmChiP, from the outer membrane of S. marcescens. Sequence alignment with genetically characterized ChiPs suggests that SmChiP is more closely related to the monomeric EcChiP from Escherichia coli than to the trimeric VhChiP from Vibrio campbellii. A single crystal of SmChiP grown under the condition 22%(w/v) PEG 8000, 0.1 M calcium acetate, 0.1 M MES pH 6.0 diffracted X-ray synchrotron radiation to 1.85 Å resolution. SmChiP co-crystallized with chitohexaose under the condition 19%(w/v) PEG 1500, 2 M ammonium phosphate monobasic, 0.1 M HEPES pH 7.0 diffracted X-rays to 2.70 Å resolution. Preliminary crystallographic analysis shows that both SmChiP crystal forms contain one molecule per asymmetric unit and that they belong to the tetragonal space groups P42212 and P41212, respectively. The SmChiP crystal has unit-cell parameters a = 82.97, b = 82.97, c = 189.53 Å, α = β = γ = 90°, while the crystal of SmChiP in complex with chitohexaose has unit-cell parameters a = 73.24, b = 73.24, c = 213.46 Å, α = β = γ = 90°. Initial assessment of the complex structure clearly revealed electron density for the sugar ligand. Structure determination of SmChiP in the absence and presence of chitohexaose should reveal the molecular basis of chitin utilization by S. marcescens.
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Affiliation(s)
- Rawiporn Amornloetwattana
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology, Payupnai, Wangchan, Rayong 21210, Thailand
| | - Robert C. Robinson
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology, Payupnai, Wangchan, Rayong 21210, Thailand
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan
| | - Hannadige Sasimali Madusanka Soysa
- Department of Physical Sciences and Technology, Faculty of Applied Sciences, Sabaragamuwa University of Sri Lanka, Belihuloya 70140, Sri Lanka
| | - Bert van den Berg
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Wipa Suginta
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology, Payupnai, Wangchan, Rayong 21210, Thailand
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14
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Szatmári D, Sárkány P, Kocsis B, Nagy T, Miseta A, Barkó S, Longauer B, Robinson RC, Nyitrai M. Author Correction: Intracellular ion concentrations and cation-dependent remodelling of bacterial MreB assemblies. Sci Rep 2020; 10:18185. [PMID: 33082458 PMCID: PMC7576133 DOI: 10.1038/s41598-020-74830-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Dávid Szatmári
- Department of Biophysics, Medical School, University of Pécs, Pécs, Hungary
| | - Péter Sárkány
- Department of Biophysics, Medical School, University of Pécs, Pécs, Hungary
| | - Béla Kocsis
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
| | - Tamás Nagy
- Department of Laboratory Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Attila Miseta
- Department of Laboratory Medicine, Medical School, University of Pécs, Pécs, Hungary.,Szentágothai Research Center, University of Pécs, Pécs, Hungary
| | - Szilvia Barkó
- Department of Biophysics, Medical School, University of Pécs, Pécs, Hungary
| | - Beáta Longauer
- Department of Biophysics, Medical School, University of Pécs, Pécs, Hungary
| | - Robert C Robinson
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand.,Research Institute for Interdisciplinary Science (RIIS), University of Okayama, Okayama, Japan
| | - Miklós Nyitrai
- Department of Biophysics, Medical School, University of Pécs, Pécs, Hungary. .,MTA-PTE Nuclear-Mitochondrial Interactions Research Group, Pécs, Hungary. .,Szentágothai Research Center, University of Pécs, Pécs, Hungary.
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15
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Akıl C, Kitaoku Y, Tran LT, Liebl D, Choe H, Muengsaen D, Suginta W, Schulte A, Robinson RC. Mythical origins of the actin cytoskeleton. Curr Opin Cell Biol 2020; 68:55-63. [PMID: 33049465 DOI: 10.1016/j.ceb.2020.08.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/13/2020] [Accepted: 08/17/2020] [Indexed: 10/23/2022]
Abstract
The origin of the eukaryotic cell is one of the greatest mysteries in modern biology. Eukaryotic-wide specific biological processes arose in the lost ancestors of eukaryotes. These distinctive features, such as the actin cytoskeleton, define what it is to be a eukaryote. Recent sequencing, characterization, and isolation of Asgard archaea have opened an intriguing window into the pre-eukaryotic cell. Firstly, sequencing of anaerobic sediments identified a group of uncultured organisms, Asgard archaea, which contain genes with homology to eukaryotic signature genes. Secondly, characterization of the products of these genes at the protein level demonstrated that Asgard archaea have related biological processes to eukaryotes. Finally, the isolation of an Asgard archaeon has produced a model organism in which the morphological consequences of the eukaryotic-like processes can be studied. Here, we consider the consequences for the Asgard actin cytoskeleton and for the evolution of a regulated actin system in the archaea-to-eukaryotic transition.
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Affiliation(s)
- Caner Akıl
- Institute of Molecular and Cell Biology, A∗STAR (Agency for Science, Technology and Research), Biopolis, 138673, Singapore; Tokyo Institute of Technology, Earth-Life Science Institute (ELSI), Tokyo 152-8551, Japan
| | - Yoshihito Kitaoku
- Research Institute for Interdisciplinary Science (RIIS), Okayama University, Okayama 700-8530, Japan
| | - Linh T Tran
- Research Institute for Interdisciplinary Science (RIIS), Okayama University, Okayama 700-8530, Japan
| | - David Liebl
- A∗STAR Microscopy Platform, Research Support Center, A∗STAR, Biopolis 138673, Singapore
| | - Han Choe
- Department of Physiology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, 05505, South Korea
| | - Duangkamon Muengsaen
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong 21210, Thailand
| | - Wipa Suginta
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong 21210, Thailand
| | - Albert Schulte
- School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong 21210, Thailand
| | - Robert C Robinson
- Institute of Molecular and Cell Biology, A∗STAR (Agency for Science, Technology and Research), Biopolis, 138673, Singapore; Research Institute for Interdisciplinary Science (RIIS), Okayama University, Okayama 700-8530, Japan; School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong 21210, Thailand.
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16
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Miyata M, Robinson RC, Uyeda TQP, Fukumori Y, Fukushima SI, Haruta S, Homma M, Inaba K, Ito M, Kaito C, Kato K, Kenri T, Kinosita Y, Kojima S, Minamino T, Mori H, Nakamura S, Nakane D, Nakayama K, Nishiyama M, Shibata S, Shimabukuro K, Tamakoshi M, Taoka A, Tashiro Y, Tulum I, Wada H, Wakabayashi KI. Tree of motility - A proposed history of motility systems in the tree of life. Genes Cells 2020; 25:6-21. [PMID: 31957229 PMCID: PMC7004002 DOI: 10.1111/gtc.12737] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 11/11/2019] [Accepted: 11/17/2019] [Indexed: 12/27/2022]
Abstract
Motility often plays a decisive role in the survival of species. Five systems of motility have been studied in depth: those propelled by bacterial flagella, eukaryotic actin polymerization and the eukaryotic motor proteins myosin, kinesin and dynein. However, many organisms exhibit surprisingly diverse motilities, and advances in genomics, molecular biology and imaging have showed that those motilities have inherently independent mechanisms. This makes defining the breadth of motility nontrivial, because novel motilities may be driven by unknown mechanisms. Here, we classify the known motilities based on the unique classes of movement‐producing protein architectures. Based on this criterion, the current total of independent motility systems stands at 18 types. In this perspective, we discuss these modes of motility relative to the latest phylogenetic Tree of Life and propose a history of motility. During the ~4 billion years since the emergence of life, motility arose in Bacteria with flagella and pili, and in Archaea with archaella. Newer modes of motility became possible in Eukarya with changes to the cell envelope. Presence or absence of a peptidoglycan layer, the acquisition of robust membrane dynamics, the enlargement of cells and environmental opportunities likely provided the context for the (co)evolution of novel types of motility.
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Affiliation(s)
- Makoto Miyata
- Department of Biology, Graduate School of Science, Osaka City University, Osaka, Japan.,The OCU Advanced Research Institute for Natural Science and Technology (OCARINA), Osaka City University, Osaka, Japan
| | - Robert C Robinson
- Research Institute for Interdisciplinary Science, Okayama University, Okayama, Japan.,School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Taro Q P Uyeda
- Department of Physics, Faculty of Science and Technology, Waseda University, Tokyo, Japan
| | - Yoshihiro Fukumori
- Faculty of Natural System, Institute of Science and Engineering, Kanazawa University, Kanazawa, Japan.,WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Japan
| | - Shun-Ichi Fukushima
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan
| | - Shin Haruta
- Department of Biological Sciences, Graduate School of Science and Engineering, Tokyo Metropolitan University, Tokyo, Japan
| | - Michio Homma
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Kazuo Inaba
- Shimoda Marine Research Center, University of Tsukuba, Shizuoka, Japan
| | - Masahiro Ito
- Graduate School of Life Sciences, Toyo University, Gunma, Japan
| | - Chikara Kaito
- Laboratory of Microbiology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Kentaro Kato
- Laboratory of Sustainable Animal Environment, Graduate School of Agricultural Science, Tohoku University, Miyagi, Japan
| | - Tsuyoshi Kenri
- Laboratory of Mycoplasmas and Haemophilus, Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
| | | | - Seiji Kojima
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Tohru Minamino
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Hiroyuki Mori
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Shuichi Nakamura
- Department of Applied Physics, Graduate School of Engineering, Tohoku University, Miyagi, Japan
| | - Daisuke Nakane
- Department of Physics, Gakushuin University, Tokyo, Japan
| | - Koji Nakayama
- Department of Microbiology and Oral Infection, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Masayoshi Nishiyama
- Department of Physics, Faculty of Science and Engineering, Kindai University, Osaka, Japan
| | - Satoshi Shibata
- Molecular Cryo-Electron Microscopy Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Katsuya Shimabukuro
- Department of Chemical and Biological Engineering, National Institute of Technology, Ube College, Yamaguchi, Japan
| | - Masatada Tamakoshi
- Department of Molecular Biology, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Azuma Taoka
- Faculty of Natural System, Institute of Science and Engineering, Kanazawa University, Kanazawa, Japan.,WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Japan
| | - Yosuke Tashiro
- Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Isil Tulum
- Department of Botany, Faculty of Science, Istanbul University, Istanbul, Turkey
| | - Hirofumi Wada
- Department of Physics, Graduate School of Science and Engineering, Ritsumeikan University, Shiga, Japan
| | - Ken-Ichi Wakabayashi
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Kanagawa, Japan
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17
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Martin ER, Barbieri A, Ford RC, Robinson RC. In vivo crystals reveal critical features of the interaction between cystic fibrosis transmembrane conductance regulator (CFTR) and the PDZ2 domain of Na +/H + exchange cofactor NHERF1. J Biol Chem 2020; 295:4464-4476. [PMID: 32014995 DOI: 10.1074/jbc.ra119.012015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/17/2020] [Indexed: 12/23/2022] Open
Abstract
Crystallization of recombinant proteins has been fundamental to our understanding of protein function, dysfunction, and molecular recognition. However, this information has often been gleaned under extremely nonphysiological protein, salt, and H+ concentrations. Here, we describe the development of a robust Inka1-Box (iBox)-PAK4cat system that spontaneously crystallizes in several mammalian cell types. The semi-quantitative assay described here allows the measurement of in vivo protein-protein interactions using a novel GFP-linked reporter system that produces fluorescent readouts from protein crystals. We combined this assay with in vitro X-ray crystallography and molecular dynamics studies to characterize the molecular determinants of the interaction between the PDZ2 domain of Na+/H+ exchange regulatory cofactor NHE-RF1 (NHERF1) and cystic fibrosis transmembrane conductance regulator (CFTR), a protein complex pertinent to the genetic disease cystic fibrosis. These experiments revealed the crystal structure of the extended PDZ domain of NHERF1 and indicated, contrary to what has been previously reported, that residue selection at positions -1 and -3 of the PDZ-binding motif influences the affinity and specificity of the NHERF1 PDZ2-CFTR interaction. Our results suggest that this system could be utilized to screen additional protein-protein interactions, provided they can be accommodated within the spacious iBox-PAK4cat lattice.
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Affiliation(s)
- Eleanor R Martin
- School of Biological Sciences, Faculty of Biology Medicine and Health, Michael Smith Building, The University of Manchester, Manchester, M13 9PL, United Kingdom.,Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis 138673, Singapore
| | - Alessandro Barbieri
- School of Biological Sciences, Faculty of Biology Medicine and Health, Michael Smith Building, The University of Manchester, Manchester, M13 9PL, United Kingdom.,Bioinformatics Institute (BII), A*STAR (Agency for Science, Technology and Research), Biopolis 138671, Singapore
| | - Robert C Ford
- School of Biological Sciences, Faculty of Biology Medicine and Health, Michael Smith Building, The University of Manchester, Manchester, M13 9PL, United Kingdom
| | - Robert C Robinson
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis 138673, Singapore .,School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong 21210, Thailand.,Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Japan
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18
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Brändén G, Hammarin G, Harimoorthy R, Johansson A, Arnlund D, Malmerberg E, Barty A, Tångefjord S, Berntsen P, DePonte DP, Seuring C, White TA, Stellato F, Bean R, Beyerlein KR, Chavas LMG, Fleckenstein H, Gati C, Ghoshdastider U, Gumprecht L, Oberthür D, Popp D, Seibert M, Tilp T, Messerschmidt M, Williams GJ, Loh ND, Chapman HN, Zwart P, Liang M, Boutet S, Robinson RC, Neutze R. Coherent diffractive imaging of microtubules using an X-ray laser. Nat Commun 2019; 10:2589. [PMID: 31197138 PMCID: PMC6565740 DOI: 10.1038/s41467-019-10448-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 05/02/2019] [Indexed: 01/09/2023] Open
Abstract
X-ray free electron lasers (XFELs) create new possibilities for structural studies of biological objects that extend beyond what is possible with synchrotron radiation. Serial femtosecond crystallography has allowed high-resolution structures to be determined from micro-meter sized crystals, whereas single particle coherent X-ray imaging requires development to extend the resolution beyond a few tens of nanometers. Here we describe an intermediate approach: the XFEL imaging of biological assemblies with helical symmetry. We collected X-ray scattering images from samples of microtubules injected across an XFEL beam using a liquid microjet, sorted these images into class averages, merged these data into a diffraction pattern extending to 2 nm resolution, and reconstructed these data into a projection image of the microtubule. Details such as the 4 nm tubulin monomer became visible in this reconstruction. These results illustrate the potential of single-molecule X-ray imaging of biological assembles with helical symmetry at room temperature.
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Affiliation(s)
- Gisela Brändén
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530, Gothenburg, Sweden.
| | - Greger Hammarin
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530, Gothenburg, Sweden
| | - Rajiv Harimoorthy
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530, Gothenburg, Sweden
| | - Alexander Johansson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530, Gothenburg, Sweden
| | - David Arnlund
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530, Gothenburg, Sweden
| | - Erik Malmerberg
- Molecular Biophysics and Integrated Bio-Imaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, 94720, Berkeley, CA, USA
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany
| | - Stefan Tångefjord
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530, Gothenburg, Sweden
| | - Peter Berntsen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530, Gothenburg, Sweden
| | - Daniel P DePonte
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Carolin Seuring
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany.,The Hamburg Center for Ultrafast Imaging, 22761, Hamburg, Germany
| | - Thomas A White
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany
| | - Francesco Stellato
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany
| | - Richard Bean
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany
| | - Kenneth R Beyerlein
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany
| | - Leonard M G Chavas
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany
| | - Holger Fleckenstein
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany
| | - Cornelius Gati
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany
| | - Umesh Ghoshdastider
- Institute of Molecular and Cell Biology, Biopolis, A*STAR (Agency for Science, Technology and Research), 138673, Singapore, Singapore
| | - Lars Gumprecht
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany
| | - Dominik Oberthür
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany
| | - David Popp
- Institute of Molecular and Cell Biology, Biopolis, A*STAR (Agency for Science, Technology and Research), 138673, Singapore, Singapore
| | - Marvin Seibert
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Thomas Tilp
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany
| | - Marc Messerschmidt
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Garth J Williams
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - N Duane Loh
- Department of Physics, National University of Singapore, 117551, Singapore, Singapore
| | - Henry N Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany.,The Hamburg Center for Ultrafast Imaging, 22761, Hamburg, Germany.,Department of Physics, University of Hamburg, 22761, Hamburg, Germany
| | - Peter Zwart
- Molecular Biophysics and Integrated Bio-Imaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, 94720, Berkeley, CA, USA
| | - Mengning Liang
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, 22607, Hamburg, Germany.,Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Robert C Robinson
- Institute of Molecular and Cell Biology, Biopolis, A*STAR (Agency for Science, Technology and Research), 138673, Singapore, Singapore.,Department of Biochemistry, National University of Singapore, 117597, Singapore, Singapore.,Research Institute for Interdisciplinary Science, Okayama University, Okayama, 700-8530, Japan
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530, Gothenburg, Sweden.
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19
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Musiani D, Bok J, Massignani E, Wu L, Tabaglio T, Ippolito MR, Cuomo A, Ozbek U, Zorgati H, Ghoshdastider U, Robinson RC, Guccione E, Bonaldi T. Proteomics profiling of arginine methylation defines PRMT5 substrate specificity. Sci Signal 2019; 12:12/575/eaat8388. [PMID: 30940768 DOI: 10.1126/scisignal.aat8388] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Protein arginine methyltransferases (PRMTs) catalyze arginine methylation on both chromatin-bound and cytoplasmic proteins. Accumulating evidence supports the involvement of PRMT5, the major type II PRMT, in cell survival and differentiation pathways that are important during development and in tumorigenesis. PRMT5 is an attractive drug target in various cancers, and inhibitors are currently in oncological clinical trials. Nonetheless, given the complex biology of PRMT5 and its multiple nonhistone substrates, it is paramount to fully characterize these dynamic changes in methylation and to link them to the observed anticancer effects to fully understand the functions of PRMT5 and the consequences of its inhibition. Here, we used a newly established pipeline coupling stable isotope labeling with amino acids in cell culture (SILAC) with immunoenriched methyl peptides to globally profile arginine monomethylation and symmetric dimethylation after PRMT5 inhibition by a selective inhibitor. We adopted heavy methyl SILAC as an orthogonal validation method to reduce the false discovery rate. Through in vitro methylation assays, we validated a set of PRMT5 targets identified by mass spectrometry and provided previously unknown mechanistic insights into the preference of the enzyme to methylate arginine sandwiched between two neighboring glycines (a Gly-Arg-Gly, or "GRG," sequence). Our analysis led to the identification of previously unknown PRMT5 substrates, thus both providing insight into the global effects of PRMT5 and its inhibition in live cells, beyond chromatin, and refining our knowledge of its substrate specificity.
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Affiliation(s)
- Daniele Musiani
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Jabez Bok
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore
| | - Enrico Massignani
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Liling Wu
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
| | - Tommaso Tabaglio
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
| | - Marica Rosaria Ippolito
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Alessandro Cuomo
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Umut Ozbek
- Department of Population Health Science and Policy, Mount Sinai, New York, NY 10029, USA.,Tisch Cancer Institute, Icahn School of Medicine, Mount Sinai, New York, NY 10029, USA
| | - Habiba Zorgati
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
| | - Umesh Ghoshdastider
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore
| | - Robert C Robinson
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
| | - Ernesto Guccione
- Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore. .,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore.,Department of Oncological Sciences and Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Pharmacological Sciences and Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy.
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20
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Saisawang C, Wongsantichon J, Robinson RC, Ketterman AJ. Glutathione transferase Omega 1‐1 (GSTO1‐1) modulates Akt and MEK1/2 signaling in human neuroblastoma cell SH‐SY5Y. Proteins 2019; 87:588-595. [DOI: 10.1002/prot.25683] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 01/21/2019] [Accepted: 03/13/2019] [Indexed: 01/13/2023]
Affiliation(s)
- Chonticha Saisawang
- Institute of Molecular BiosciencesMahidol University Salaya Nakhon Pathom Thailand
| | - Jantana Wongsantichon
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR) Singapore Singapore
- Mahidol‐Oxford Tropical Medicine Research Unit (MORU) Bangkok Thailand
| | - Robert C. Robinson
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR) Singapore Singapore
- Research Institute for Interdisciplinary ScienceOkayama University Okayama Japan
| | - Albert J. Ketterman
- Institute of Molecular BiosciencesMahidol University Salaya Nakhon Pathom Thailand
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21
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Kis-Bicskei N, Bécsi B, Erdődi F, Robinson RC, Bugyi B, Huber T, Nyitrai M, Talián GC. Tropomyosins Regulate the Severing Activity of Gelsolin in Isoform-Dependent and Independent Manners. Biophys J 2019; 114:777-787. [PMID: 29490240 PMCID: PMC5984974 DOI: 10.1016/j.bpj.2017.11.3812] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 11/16/2017] [Accepted: 11/29/2017] [Indexed: 12/16/2022] Open
Abstract
The actin cytoskeleton fulfills numerous key cellular functions, which are tightly regulated in activity, localization, and temporal patterning by actin binding proteins. Tropomyosins and gelsolin are two such filament-regulating proteins. Here, we investigate how the effects of tropomyosins are coupled to the binding and activity of gelsolin. We show that the three investigated tropomyosin isoforms (Tpm1.1, Tpm1.12, and Tpm3.1) bind to gelsolin with micromolar or submicromolar affinities. Tropomyosin binding enhances the activity of gelsolin in actin polymerization and depolymerization assays. However, the effects of the three tropomyosin isoforms varied. The tropomyosin isoforms studied also differed in their ability to protect pre-existing actin filaments from severing by gelsolin. Based on the observed specificity of the interactions between tropomyosins, actin filaments, and gelsolin, we propose that tropomyosin isoforms specify which populations of actin filaments should be targeted by, or protected from, gelsolin-mediated depolymerization in living cells.
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Affiliation(s)
| | - Bálint Bécsi
- Department of Medical Chemistry, University of Debrecen, Faculty of Medicine, Debrecen, Hungary; MTA-DE Cell Biology and Signaling Research Group, University of Debrecen, Faculty of Medicine, Debrecen, Hungary
| | - Ferenc Erdődi
- Department of Medical Chemistry, University of Debrecen, Faculty of Medicine, Debrecen, Hungary; MTA-DE Cell Biology and Signaling Research Group, University of Debrecen, Faculty of Medicine, Debrecen, Hungary
| | - Robert C Robinson
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore; Research Institute for Interdisciplinary Science, Okayama University, Okayama, Japan
| | - Beáta Bugyi
- Department of Biophysics, Medical School, University of Pécs, Pécs, Hungary; Szentágothai Research Center, University of Pécs, Pécs, Hungary
| | - Tamás Huber
- Department of Biophysics, Medical School, University of Pécs, Pécs, Hungary
| | - Miklós Nyitrai
- Department of Biophysics, Medical School, University of Pécs, Pécs, Hungary; MTA-PTE Nuclear-Mitochondrial Interactions Research Group, Pécs, Hungary.
| | - Gábor Csaba Talián
- Department of Biophysics, Medical School, University of Pécs, Pécs, Hungary
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22
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Sana B, Chee SMQ, Wongsantichon J, Raghavan S, Robinson RC, Ghadessy FJ. Development and structural characterization of an engineered multi-copper oxidase reporter of protein-protein interactions. J Biol Chem 2019; 294:7002-7012. [PMID: 30770473 PMCID: PMC6497955 DOI: 10.1074/jbc.ra118.007141] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 02/10/2019] [Indexed: 12/13/2022] Open
Abstract
Protein–protein interactions (PPIs) are ubiquitous in almost all biological processes and are often corrupted in diseased states. A detailed understanding of PPIs is therefore key to understanding cellular physiology and can yield attractive therapeutic targets. Here, we describe the development and structural characterization of novel Escherichia coli CueO multi-copper oxidase variants engineered to recapitulate protein–protein interactions with commensurate modulation of their enzymatic activities. The fully integrated single-protein sensors were developed through modular grafting of ligand-specific peptides into a highly compliant and flexible methionine-rich loop of CueO. Sensitive detection of diverse ligand classes exemplified by antibodies, an E3 ligase, MDM2 proto-oncogene (MDM2), and protease (SplB from Staphylococcus aureus) was achieved in a simple mix and measure homogeneous format with visually observable colorimetric readouts. Therapeutic antagonism of MDM2 by small molecules and peptides in clinical development for treatment of cancer patients was assayed using the MDM2-binding CueO enzyme. Structural characterization of the free and MDM2-bound CueO variant provided functional insight into signal-transducing mechanisms of the engineered enzymes and highlighted the robustness of CueO as a stable and compliant scaffold for multiple applications.
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Affiliation(s)
- Barindra Sana
- From the p53 Laboratory, Agency for Science, Technology, and Research (A*STAR), 8A Biomedical Grove, Singapore 138648, Singapore
| | - Sharon M Q Chee
- From the p53 Laboratory, Agency for Science, Technology, and Research (A*STAR), 8A Biomedical Grove, Singapore 138648, Singapore
| | - Jantana Wongsantichon
- the Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok 10400, Thailand, and.,the Institute of Molecular and Cellular Biology, A*STAR, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Sarada Raghavan
- From the p53 Laboratory, Agency for Science, Technology, and Research (A*STAR), 8A Biomedical Grove, Singapore 138648, Singapore
| | - Robert C Robinson
- the Institute of Molecular and Cellular Biology, A*STAR, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Farid J Ghadessy
- From the p53 Laboratory, Agency for Science, Technology, and Research (A*STAR), 8A Biomedical Grove, Singapore 138648, Singapore,
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23
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Szatmári D, Xue B, Kannan B, Burtnick LD, Bugyi B, Nyitrai M, Robinson RC. ATP competes with PIP2 for binding to gelsolin. PLoS One 2018; 13:e0201826. [PMID: 30086165 PMCID: PMC6080781 DOI: 10.1371/journal.pone.0201826] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 07/23/2018] [Indexed: 01/08/2023] Open
Abstract
Gelsolin is a severing and capping protein that targets filamentous actin and regulates filament lengths near plasma membranes, contributing to cell movement and plasma membrane morphology. Gelsolin binds to the plasma membrane via phosphatidylinositol 4,5-bisphosphate (PIP2) in a state that cannot cap F-actin, and gelsolin-capped actin filaments are uncapped by PIP2 leading to filament elongation. The process by which gelsolin is removed from PIP2 at the plasma membrane is currently unknown. Gelsolin also binds ATP with unknown function. Here we characterize the role of ATP on PIP2-gelsolin complex dynamics. Fluorophore-labeled PIP2 and ATP were used to study their interactions with gelsolin using steady-state fluorescence anisotropy, and Alexa488-labeled gelsolin was utilized to reconstitute the regulation of gelsolin binding to PIP2-containing phospholipid vesicles by ATP. Under physiological salt conditions ATP competes with PIP2 for binding to gelsolin, while calcium causes the release of ATP from gelsolin. These data suggest a cycle for gelsolin activity. Firstly, calcium activates ATP-bound gelsolin allowing it to sever and cap F-actin. Secondly, PIP2-binding removes the gelsolin cap from F-actin at low calcium levels, leading to filament elongation. Finally, ATP competes with PIP2 to release the calcium-free ATP-bound gelsolin, allowing it to undergo a further round of severing.
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Affiliation(s)
- Dávid Szatmári
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore, Singapore
- University of Pécs, Medical School, Department of Biophysics, Pécs, Hungary
| | - Bo Xue
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore, Singapore
- Department of Biochemistry, National University of Singapore, Singapore, Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Balakrishnan Kannan
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore, Singapore
| | - Leslie D. Burtnick
- Department of Chemistry and Centre for Blood Research, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
| | - Beáta Bugyi
- University of Pécs, Medical School, Department of Biophysics, Pécs, Hungary
- Szentágothai Research Center, Pécs, Hungary
| | - Miklós Nyitrai
- University of Pécs, Medical School, Department of Biophysics, Pécs, Hungary
- Szentágothai Research Center, Pécs, Hungary
| | - Robert C. Robinson
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore, Singapore
- Department of Biochemistry, National University of Singapore, Singapore, Singapore
- Research Institute for Interdisciplinary Science, Okayama University, Okayama, Japan
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24
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Hatano T, Alioto S, Roscioli E, Palani S, Clarke ST, Kamnev A, Hernandez-Fernaud JR, Sivashanmugam L, Chapa-Y-Lazo B, Jones AME, Robinson RC, Sampath K, Mishima M, McAinsh AD, Goode BL, Balasubramanian MK. Rapid production of pure recombinant actin isoforms in Pichia pastoris. J Cell Sci 2018. [PMID: 29535210 PMCID: PMC5976186 DOI: 10.1242/jcs.213827] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Actins are major eukaryotic cytoskeletal proteins, and they are involved in many important cell functions, including cell division, cell polarity, wound healing and muscle contraction. Despite obvious drawbacks, muscle actin, which is easily purified, is used extensively for biochemical studies of the non-muscle actin cytoskeleton. Here, we report a rapid and cost-effective method to purify heterologous actins expressed in the yeast Pichia pastoris. Actin is expressed as a fusion with the actin-binding protein thymosin β4 and purified by means of an affinity tag introduced in the fusion. Following cleavage of thymosin β4 and the affinity tag, highly purified functional full-length actin is liberated. We purify actins from Saccharomycescerevisiae and Schizosaccharomycespombe, and the β- and γ-isoforms of human actin. We also report a modification of the method that facilitates expression and purification of arginylated actin, a form of actin thought to regulate dendritic actin networks in mammalian cells. The methods we describe can be performed in all laboratories equipped for molecular biology, and should greatly facilitate biochemical and cell biological studies of the actin cytoskeleton. Summary:Here, we describe a method to purify recombinant actin to homogeneity by expression in Pichia pastoris. The purified actin is polymerisation competent and should facilitate biochemical and cell biological studies of the actin cytoskeleton.
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Affiliation(s)
- Tomoyuki Hatano
- Centre for Mechanochemical Cell Biology and Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
| | - Salvatore Alioto
- Department of Biology, Brandeis University, Waltham, MA 02454, USA
| | - Emanuele Roscioli
- Centre for Mechanochemical Cell Biology and Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
| | - Saravanan Palani
- Centre for Mechanochemical Cell Biology and Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
| | - Scott T Clarke
- Centre for Mechanochemical Cell Biology and Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
| | - Anton Kamnev
- Centre for Mechanochemical Cell Biology and Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
| | | | - Lavanya Sivashanmugam
- Centre for Mechanochemical Cell Biology and Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
| | - Bernardo Chapa-Y-Lazo
- Centre for Mechanochemical Cell Biology and Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
| | | | - Robert C Robinson
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology, and Research), Singapore 138673, Singapore.,Department of Biochemistry, National University of Singapore, Singapore 117597, Singapore.,Research Institute for Interdisciplinary Science, Okayama University, Okayama, 700-8530, Japan
| | - Karuna Sampath
- Centre for Mechanochemical Cell Biology and Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
| | - Masanori Mishima
- Centre for Mechanochemical Cell Biology and Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
| | - Andrew D McAinsh
- Centre for Mechanochemical Cell Biology and Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
| | - Bruce L Goode
- Department of Biology, Brandeis University, Waltham, MA 02454, USA
| | - Mohan K Balasubramanian
- Centre for Mechanochemical Cell Biology and Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
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25
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Popp D, Koh F, Scipion CPM, Ghoshdastider U, Narita A, Holmes KC, Robinson RC. Advances in Structural Biology and the Application to Biological Filament Systems. Bioessays 2018; 40:e1700213. [PMID: 29484695 DOI: 10.1002/bies.201700213] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 01/10/2018] [Indexed: 11/10/2022]
Abstract
Structural biology has experienced several transformative technological advances in recent years. These include: development of extremely bright X-ray sources (microfocus synchrotron beamlines and free electron lasers) and the use of electrons to extend protein crystallography to ever decreasing crystal sizes; and an increase in the resolution attainable by cryo-electron microscopy. Here we discuss the use of these techniques in general terms and highlight their application for biological filament systems, an area that is severely underrepresented in atomic resolution structures. We assemble a model of a capped tropomyosin-actin minifilament to demonstrate the utility of combining structures determined by different techniques. Finally, we survey the methods that attempt to transform high resolution structural biology into more physiological environments, such as the cell. Together these techniques promise a compelling decade for structural biology and, more importantly, they will provide exciting discoveries in understanding the designs and purposes of biological machines.
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Affiliation(s)
- David Popp
- Institute of Molecular and Cell Biology A*STAR (Agency for Science, Technology and Research) Biopolis, Singapore 138673, Singapore
| | - Fujiet Koh
- Institute of Molecular and Cell Biology A*STAR (Agency for Science, Technology and Research) Biopolis, Singapore 138673, Singapore
| | - Clement P M Scipion
- Institute of Molecular and Cell Biology A*STAR (Agency for Science, Technology and Research) Biopolis, Singapore 138673, Singapore.,Department of Biochemistry Yong Loo Lin School of Medicine National University of Singapore, Singapore 117597, Singapore
| | - Umesh Ghoshdastider
- Institute of Molecular and Cell Biology A*STAR (Agency for Science, Technology and Research) Biopolis, Singapore 138673, Singapore
| | - Akihiro Narita
- Nagoya University Graduate School of Science Structural Biology Research Center and Division of Biological Sciences, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Kenneth C Holmes
- Max Planck Institute for Medical Research, D69120 Heidelberg, Germany
| | - Robert C Robinson
- Institute of Molecular and Cell Biology A*STAR (Agency for Science, Technology and Research) Biopolis, Singapore 138673, Singapore.,Department of Biochemistry Yong Loo Lin School of Medicine National University of Singapore, Singapore 117597, Singapore.,Research Institute for Interdisciplinary Science Okayama University, Okayama 700-8530, Japan
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26
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Park HW, Ma Z, Zhu H, Jiang S, Robinson RC, Endow SA. Structural Analysis of a Human Mitotic Kinesin and Its Potential Binding Site for a Small Molecule Inhibitor. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.1087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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27
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Chee SMQ, Wongsantichon J, Siau J, Thean D, Ferrer F, Robinson RC, Lane DP, Brown CJ, Ghadessy FJ. Structure-activity studies of Mdm2/Mdm4-binding stapled peptides comprising non-natural amino acids. PLoS One 2017; 12:e0189379. [PMID: 29228061 PMCID: PMC5724825 DOI: 10.1371/journal.pone.0189379] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 11/24/2017] [Indexed: 11/24/2022] Open
Abstract
As primary p53 antagonists, Mdm2 and the closely related Mdm4 are relevant cancer therapeutic targets. We have previously described a series of cell-permeable stapled peptides that bind to Mdm2 with high affinity, resulting in activation of the p53 tumour suppressor. Within this series, highest affinity was obtained by modification of an obligate tryptophan residue to the non-natural L-6-chlorotryptophan. To understand the structural basis for improved affinity we have solved the crystal structure of this stapled peptide (M011) bound to Mdm2 (residues 6–125) at 1.66 Å resolution. Surprisingly, near identity to the structure of a related peptide (M06) without the 6-chloro modification is observed. Further analysis of linear and stapled peptides comprising 6-Me-tryptophan provides mechanistic insight into dual Mdm2/Mdm4 antagonism and confirms L98 of Mdm4 as a mutable steric gate. The results also highlight a possible role of the flexible hinge region in determining Mdm2/Mdm4 plasticity.
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Affiliation(s)
- Sharon Min Qi Chee
- p53Lab, Agency for Science Technology and Research (A*STAR), Singapore, Singapore
| | | | - Jiawei Siau
- p53Lab, Agency for Science Technology and Research (A*STAR), Singapore, Singapore
| | - Dawn Thean
- p53Lab, Agency for Science Technology and Research (A*STAR), Singapore, Singapore
| | - Fernando Ferrer
- p53Lab, Agency for Science Technology and Research (A*STAR), Singapore, Singapore
| | - Robert C. Robinson
- Institute of Molecular and Cellular Biology, A*STAR, Singapore, Singapore
| | - David P. Lane
- p53Lab, Agency for Science Technology and Research (A*STAR), Singapore, Singapore
| | - Christopher J. Brown
- p53Lab, Agency for Science Technology and Research (A*STAR), Singapore, Singapore
- * E-mail: (CJB); (FJG)
| | - Farid J. Ghadessy
- p53Lab, Agency for Science Technology and Research (A*STAR), Singapore, Singapore
- * E-mail: (CJB); (FJG)
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28
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Chan KH, Xue B, Robinson RC, Hauser CAE. Systematic Moiety Variations of Ultrashort Peptides Produce Profound Effects on Self-Assembly, Nanostructure Formation, Hydrogelation, and Phase Transition. Sci Rep 2017; 7:12897. [PMID: 29018249 PMCID: PMC5635115 DOI: 10.1038/s41598-017-12694-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 09/13/2017] [Indexed: 12/18/2022] Open
Abstract
Self-assembly of small biomolecules is a prevalent phenomenon that is increasingly being recognised to hold the key to building complex structures from simple monomeric units. Small peptides, in particular ultrashort peptides containing up to seven amino acids, for which our laboratory has found many biomedical applications, exhibit immense potential in this regard. For next-generation applications, more intricate control is required over the self-assembly processes. We seek to find out how subtle moiety variation of peptides can affect self-assembly and nanostructure formation. To this end, we have selected a library of 54 tripeptides, derived from systematic moiety variations from seven tripeptides. Our study reveals that subtle structural changes in the tripeptides can exert profound effects on self-assembly, nanostructure formation, hydrogelation, and even phase transition of peptide nanostructures. By comparing the X-ray crystal structures of two tripeptides, acetylated leucine-leucine-glutamic acid (Ac-LLE) and acetylated tyrosine-leucine-aspartic acid (Ac-YLD), we obtained valuable insights into the structural factors that can influence the formation of supramolecular peptide structures. We believe that our results have major implications on the understanding of the factors that affect peptide self-assembly. In addition, our findings can potentially assist current computational efforts to predict and design self-assembling peptide systems for diverse biomedical applications.
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Affiliation(s)
- Kiat Hwa Chan
- Institute of Bioengineering and Nanotechnology, Biopolis, A*STAR (Agency for Science, Technology and Research), Singapore, 138669, Singapore. .,Division of Science, Yale-NUS College, 16 College Avenue West, Singapore, 138527, Singapore.
| | - Bo Xue
- Institute of Molecular and Cell Biology, Biopolis, A*STAR (Agency for Science, Technology and Research), Singapore, 138673, Singapore.,NUS Synthetic Biology for Clinical and Technological Innovation, Centre for Life Sciences, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117597, Singapore
| | - Robert C Robinson
- Institute of Molecular and Cell Biology, Biopolis, A*STAR (Agency for Science, Technology and Research), Singapore, 138673, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117597, Singapore.,Research Institute for Interdisciplinary Science, Okayama University, Okayama, 700-8530, Japan
| | - Charlotte A E Hauser
- Institute of Bioengineering and Nanotechnology, Biopolis, A*STAR (Agency for Science, Technology and Research), Singapore, 138669, Singapore. .,Laboratory for Nanomedicine, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia.
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29
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Popp D, Loh ND, Zorgati H, Ghoshdastider U, Liow LT, Ivanova MI, Larsson M, DePonte DP, Bean R, Beyerlein KR, Gati C, Oberthuer D, Arnlund D, Brändén G, Berntsen P, Cascio D, Chavas LMG, Chen JPJ, Ding K, Fleckenstein H, Gumprecht L, Harimoorthy R, Mossou E, Sawaya MR, Brewster AS, Hattne J, Sauter NK, Seibert M, Seuring C, Stellato F, Tilp T, Eisenberg DS, Messerschmidt M, Williams GJ, Koglin JE, Makowski L, Millane RP, Forsyth T, Boutet S, White TA, Barty A, Chapman H, Chen SL, Liang M, Neutze R, Robinson RC. Flow-aligned, single-shot fiber diffraction using a femtosecond X-ray free-electron laser. Cytoskeleton (Hoboken) 2017; 74:472-481. [PMID: 28574190 DOI: 10.1002/cm.21378] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 05/25/2017] [Accepted: 05/29/2017] [Indexed: 01/26/2023]
Abstract
A major goal for X-ray free-electron laser (XFEL) based science is to elucidate structures of biological molecules without the need for crystals. Filament systems may provide some of the first single macromolecular structures elucidated by XFEL radiation, since they contain one-dimensional translational symmetry and thereby occupy the diffraction intensity region between the extremes of crystals and single molecules. Here, we demonstrate flow alignment of as few as 100 filaments (Escherichia coli pili, F-actin, and amyloid fibrils), which when intersected by femtosecond X-ray pulses result in diffraction patterns similar to those obtained from classical fiber diffraction studies. We also determine that F-actin can be flow-aligned to a disorientation of approximately 5 degrees. Using this XFEL-based technique, we determine that gelsolin amyloids are comprised of stacked β-strands running perpendicular to the filament axis, and that a range of order from fibrillar to crystalline is discernable for individual α-synuclein amyloids.
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Affiliation(s)
- David Popp
- Institute of Molecular and Cell Biology, Biopolis, A*STAR (Agency for Science, Technology and Research), 138673, Singapore
| | - N Duane Loh
- Department of Physics, National University of Singapore, 117557, Singapore.,Centre for BioImaging Sciences, National University of Singapore, 117546, Singapore
| | - Habiba Zorgati
- Institute of Molecular and Cell Biology, Biopolis, A*STAR (Agency for Science, Technology and Research), 138673, Singapore.,Department of Biochemistry, National University of Singapore, 117597, Singapore
| | - Umesh Ghoshdastider
- Institute of Molecular and Cell Biology, Biopolis, A*STAR (Agency for Science, Technology and Research), 138673, Singapore
| | - Lu Ting Liow
- Department of Medicine, National University of Singapore, 119074, Singapore
| | - Magdalena I Ivanova
- Department of Neurology, University of Michigan, 109 Zina Pitcher Pl, Ann Arbor, Michigan, 48109
| | - Mårten Larsson
- Institute of Molecular and Cell Biology, Biopolis, A*STAR (Agency for Science, Technology and Research), 138673, Singapore
| | - Daniel P DePonte
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025
| | - Richard Bean
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg, 22607, Germany
| | - Kenneth R Beyerlein
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg, 22607, Germany
| | - Cornelius Gati
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg, 22607, Germany
| | - Dominik Oberthuer
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg, 22607, Germany.,Institute of Biochemistry and Molecular Biology, University of Hamburg, Hamburg, 22607, Germany
| | - David Arnlund
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Gisela Brändén
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Peter Berntsen
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Duilio Cascio
- Howard Hughes Medical Institute, University of California, Los Angeles, California, 90095
| | - Leonard M G Chavas
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg, 22607, Germany
| | - Joe P J Chen
- Department of Electrical and Computer Engineering, Computational Imaging Group, University of Canterbury, Christchurch, New Zealand
| | - Ke Ding
- Institute of Molecular and Cell Biology, Biopolis, A*STAR (Agency for Science, Technology and Research), 138673, Singapore
| | - Holger Fleckenstein
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg, 22607, Germany
| | - Lars Gumprecht
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg, 22607, Germany
| | - Rajiv Harimoorthy
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Estelle Mossou
- Institut Laue-Langevin, Grenoble, 38000, France.,EPSAM/ISTM, Keele University, Staffordshire, ST5 5BG, United Kingdom
| | - Michael R Sawaya
- Howard Hughes Medical Institute, University of California, Los Angeles, California, 90095
| | - Aaron S Brewster
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Johan Hattne
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Nicholas K Sauter
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Marvin Seibert
- Department of Cell and Molecular Biology, Molecular Biophysics, Uppsala University, Uppsala, 751 24, Sweden
| | - Carolin Seuring
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg, 22607, Germany
| | - Francesco Stellato
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg, 22607, Germany
| | - Thomas Tilp
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg, 22607, Germany
| | - David S Eisenberg
- Howard Hughes Medical Institute, University of California, Los Angeles, California, 90095
| | - Marc Messerschmidt
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025
| | - Garth J Williams
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025
| | - Jason E Koglin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025
| | - Lee Makowski
- Department of Bioengineering, Northeastern University, 360 Huntington Ave, Boston, Massachusetts, 02115
| | - Rick P Millane
- Department of Electrical and Computer Engineering, Computational Imaging Group, University of Canterbury, Christchurch, New Zealand
| | - Trevor Forsyth
- Institut Laue-Langevin, Grenoble, 38000, France.,EPSAM/ISTM, Keele University, Staffordshire, ST5 5BG, United Kingdom
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California, 94025
| | - Thomas A White
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg, 22607, Germany
| | - Anton Barty
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg, 22607, Germany
| | - Henry Chapman
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg, 22607, Germany.,Department of Physics, University of Hamburg, Luruper Chaussee 149, Hamburg, 22607, Germany
| | - Swaine L Chen
- Department of Medicine, National University of Singapore, 119074, Singapore.,Genome Institute of Singapore, Biopolis, A*STAR (Agency for Science, Technology and Research), 138672, Singapore
| | - Mengning Liang
- Center for Free Electron Laser Science, DESY, Notkestrasse 85, Hamburg, 22607, Germany
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Robert C Robinson
- Institute of Molecular and Cell Biology, Biopolis, A*STAR (Agency for Science, Technology and Research), 138673, Singapore.,Department of Biochemistry, National University of Singapore, 117597, Singapore.,Research Institute for Interdisciplinary Science, Okayama University, Okayama, 700-8530, Japan
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30
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Ding WY, Ong HT, Hara Y, Wongsantichon J, Toyama Y, Robinson RC, Nédélec F, Zaidel-Bar R. Plastin increases cortical connectivity to facilitate robust polarization and timely cytokinesis. J Cell Biol 2017; 216:1371-1386. [PMID: 28400443 PMCID: PMC5412556 DOI: 10.1083/jcb.201603070] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Revised: 01/11/2017] [Accepted: 03/08/2017] [Indexed: 01/23/2023] Open
Abstract
Ding et al. characterize the function of the F-actin bundling protein plastin in the Caenorhabditis elegans zygote. They demonstrate that plastin is important for optimal connectivity in the cortical actomyosin network that drives large-scale contractile processes such as polarization and cytokinesis. The cell cortex is essential to maintain animal cell shape, and contractile forces generated within it by nonmuscle myosin II (NMY-2) drive cellular morphogenetic processes such as cytokinesis. The role of actin cross-linking proteins in cortical dynamics is still incompletely understood. Here, we show that the evolutionarily conserved actin bundling/cross-linking protein plastin is instrumental for the generation of potent cortical actomyosin contractility in the Caenorhabditis elegans zygote. PLST-1 was enriched in contractile structures and was required for effective coalescence of NMY-2 filaments into large contractile foci and for long-range coordinated contractility in the cortex. In the absence of PLST-1, polarization was compromised, cytokinesis was delayed or failed, and 50% of embryos died during development. Moreover, mathematical modeling showed that an optimal amount of bundling agents enhanced the ability of a network to contract. We propose that by increasing the connectivity of the F-actin meshwork, plastin enables the cortex to generate stronger and more coordinated forces to accomplish cellular morphogenesis.
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Affiliation(s)
- Wei Yung Ding
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore
| | - Hui Ting Ong
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore
| | - Yusuke Hara
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore.,Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore
| | - Jantana Wongsantichon
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology, and Research), Singapore 138673, Singapore
| | - Yusuke Toyama
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore.,Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Robert C Robinson
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology, and Research), Singapore 138673, Singapore.,Department of Biochemistry, National University of Singapore, Singapore 117597, Singapore
| | - François Nédélec
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Ronen Zaidel-Bar
- Mechanobiology Institute, National University of Singapore, Singapore 117411, Singapore.,Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore 117583, Singapore
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31
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Singaravelu P, Lee WL, Wee S, Ghoshdastider U, Ding K, Gunaratne J, Grimes JM, Swaminathan K, Robinson RC. Yersinia effector protein (YopO)-mediated phosphorylation of host gelsolin causes calcium-independent activation leading to disruption of actin dynamics. J Biol Chem 2017; 292:8092-8100. [PMID: 28280241 PMCID: PMC5427284 DOI: 10.1074/jbc.m116.757971] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 03/05/2017] [Indexed: 12/21/2022] Open
Abstract
Pathogenic Yersinia bacteria cause a range of human diseases. To modulate and evade host immune systems, these yersiniae inject effector proteins into host macrophages. One such protein, the serine/threonine kinase YopO (YpkA in Yersinia pestis), uses monomeric actin as bait to recruit and phosphorylate host actin polymerization-regulating proteins, including the actin-severing protein gelsolin, to disrupt actin filaments and thus impair phagocytosis. However, the YopO phosphorylation sites on gelsolin and the consequences of YopO-mediated phosphorylation on actin remodeling have yet to be established. Here we determined the effects of YopO-mediated phosphorylation on gelsolin and identified its phosphorylation sites by mass spectrometry. YopO phosphorylated gelsolin in the linker region between gelsolin homology domains G3 and G4, which, in the absence of calcium, are compacted but adopt an open conformation in the presence of calcium, enabling actin binding and severing. Using phosphomimetic and phosphodeletion gelsolin mutants, we found that YopO-mediated phosphorylation partially mimics calcium-dependent activation of gelsolin, potentially contributing to a reduction in filamentous actin and altered actin dynamics in phagocytic cells. In summary, this work represents the first report of the functional outcome of serine/threonine phosphorylation in gelsolin regulation and provides critical insight into how YopO disrupts normal gelsolin function to alter host actin dynamics and thus cripple phagocytosis.
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Affiliation(s)
- Pavithra Singaravelu
- From the Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore 138673.,Department of Biological Sciences, National University of Singapore, Singapore 117543
| | - Wei Lin Lee
- From the Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore 138673,
| | - Sheena Wee
- From the Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore 138673
| | - Umesh Ghoshdastider
- From the Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore 138673
| | - Ke Ding
- From the Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore 138673
| | - Jayantha Gunaratne
- From the Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore 138673
| | - Jonathan M Grimes
- From the Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore 138673.,Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, United Kingdom.,Diamond Light Source Ltd., Diamond House, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom, and
| | | | - Robert C Robinson
- From the Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore 138673
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32
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Lee WL, Singaravelu P, Wee S, Xue B, Ang KC, Gunaratne J, Grimes JM, Swaminathan K, Robinson RC. Mechanisms of Yersinia YopO kinase substrate specificity. Sci Rep 2017; 7:39998. [PMID: 28051168 PMCID: PMC5209680 DOI: 10.1038/srep39998] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 11/30/2016] [Indexed: 02/06/2023] Open
Abstract
Yersinia bacteria cause a range of human diseases, including yersiniosis, Far East scarlet-like fever and the plague. Yersiniae modulate and evade host immune defences through injection of Yersinia outer proteins (Yops) into phagocytic cells. One of the Yops, YopO (also known as YpkA) obstructs phagocytosis through disrupting actin filament regulation processes - inhibiting polymerization-promoting signaling through sequestration of Rac/Rho family GTPases and by using monomeric actin as bait to recruit and phosphorylate host actin-regulating proteins. Here we set out to identify mechanisms of specificity in protein phosphorylation by YopO that would clarify its effects on cytoskeleton disruption. We report the MgADP structure of Yersinia enterocolitica YopO in complex with actin, which reveals its active site architecture. Using a proteome-wide kinase-interacting substrate screening (KISS) method, we identified that YopO phosphorylates a wide range of actin-modulating proteins and located their phosphorylation sites by mass spectrometry. Using artificial substrates we clarified YopO's substrate length requirements and its phosphorylation consensus sequence. These findings provide fresh insight into the mechanism of the YopO kinase and demonstrate that YopO executes a specific strategy targeting actin-modulating proteins, across multiple functionalities, to compete for control of their native phospho-signaling, thus hampering the cytoskeletal processes required for macrophage phagocytosis.
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Affiliation(s)
- Wei Lin Lee
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore
| | - Pavithra Singaravelu
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Sheena Wee
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore
| | - Bo Xue
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore
| | - Khay Chun Ang
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore
| | - Jayantha Gunaratne
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore
- Department of Anatomy, National University of Singapore, Singapore
| | - Jonathan M. Grimes
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, UK
- Diamond Light Source Ltd., UK
| | | | - Robert C. Robinson
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore
- Department of Biochemistry, National University of Singapore, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, 636921, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
- Lee Kong Chan School of Medicine, 50 Nanyang Avenue, 639798, Singapore
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33
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Jiang S, Ghoshdastider U, Narita A, Popp D, Robinson RC. Structural complexity of filaments formed from the actin and tubulin folds. Commun Integr Biol 2016; 9:e1242538. [PMID: 28042378 PMCID: PMC5193048 DOI: 10.1080/19420889.2016.1242538] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 09/21/2016] [Accepted: 09/23/2016] [Indexed: 11/09/2022] Open
Abstract
From yeast to man, an evolutionary distance of 1.3 billion years, the F-actin filament structure has been conserved largely in line with the 94% sequence identity. The situation is entirely different in bacteria. In comparison to eukaryotic actins, the bacterial actin-like proteins (ALPs) show medium to low levels of sequence identity. This is extreme in the case of the ParM family of proteins, which often display less than 20% identity. ParMs are plasmid segregation proteins that form the polymerizing motors that propel pairs of plasmids to the extremities of a cell prior to cell division, ensuring faithful inheritance of the plasmid. Recently, exotic ParM filament structures have been elucidated that show ParM filament geometries are not limited to the standard polar pair of strands typified by actin. Four-stranded non-polar ParM filaments existing as open or closed nanotubules are found in Clostridium tetani and Bacillus thuringiensis, respectively. These diverse architectures indicate that the actin fold is capable of forming a large variety of filament morphologies, and that the conception of the “actin” filament has been heavily influenced by its conservation in eukaryotes. Here, we review the history of the structure determination of the eukaryotic actin filament to give a sense of context for the discovery of the new ParM filament structures. We describe the novel ParM geometries and predict that even more complex actin-like filaments may exist in bacteria. Finally, we compare the architectures of filaments arising from the actin and tubulin folds and conclude that the basic units possess similar properties that can each form a range of structures. Thus, the use of the actin fold in microfilaments and the tubulin fold for microtubules likely arose from a wider range of filament possibilities, but became entrenched as those architectures in early eukaryotes.
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Affiliation(s)
- Shimin Jiang
- Institute of Molecular and Cell Biology, ASTAR (Agency for Science, Technology and Research) , Biopolis, Singapore
| | - Umesh Ghoshdastider
- Institute of Molecular and Cell Biology, ASTAR (Agency for Science, Technology and Research) , Biopolis, Singapore
| | - Akihiro Narita
- Nagoya University Graduate School of Science, Structural Biology Research Center and Division of Biological Sciences , Furo-cho , Chikusa-ku, Nagoya, Japan
| | - David Popp
- Institute of Molecular and Cell Biology, ASTAR (Agency for Science, Technology and Research) , Biopolis, Singapore
| | - Robert C Robinson
- Institute of Molecular and Cell Biology, ASTAR (Agency for Science, Technology and Research), Biopolis, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore; Lee Kong Chan School of Medicine, Singapore
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34
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Sun H, Yeo WL, Lim YH, Chew X, Smith DJ, Xue B, Chan KP, Robinson RC, Robins EG, Zhao H, Ang EL. Directed Evolution of a Fluorinase for Improved Fluorination Efficiency with a Non-native Substrate. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201606722] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Huihua Sun
- Metabolic Engineering Research Laboratory (MERL); Science and Engineering Institutes; Agency for Science, Technology, and Research (A*STAR); 31 Biopolis Way, Nanos #01-01 Singapore 138669 Singapore
| | - Wan Lin Yeo
- Metabolic Engineering Research Laboratory (MERL); Science and Engineering Institutes; Agency for Science, Technology, and Research (A*STAR); 31 Biopolis Way, Nanos #01-01 Singapore 138669 Singapore
| | - Yee Hwee Lim
- Institute of Chemical and Engineering Sciences (ICES); A*STAR; 8 Biomedical Grove, Neuros #07-01/02/03 Singapore 138665 Singapore
| | - Xinying Chew
- Institute of Chemical and Engineering Sciences (ICES); A*STAR; 8 Biomedical Grove, Neuros #07-01/02/03 Singapore 138665 Singapore
| | - Derek John Smith
- Bioinformatics Institute; A*STAR; 30 Biopolis Street, Matrix #07-01 Singapore 138671 Singapore
- Biotransformation Innovation Platform; 61 Biopolis Drive, Proteos #04-14 Singapore 138673 Singapore
| | - Bo Xue
- Institute of Molecular and Cell Biology (IMCB); A*STAR; 61 Biopolis Drive, Proteos #03-15 Singapore 138673 Singapore
| | - Kok Ping Chan
- Institute of Chemical and Engineering Sciences (ICES); A*STAR; 8 Biomedical Grove, Neuros #07-01/02/03 Singapore 138665 Singapore
| | - Robert C. Robinson
- Institute of Molecular and Cell Biology (IMCB); A*STAR; 61 Biopolis Drive, Proteos #03-15 Singapore 138673 Singapore
- Department of Biochemistry; Yong Loo Lin School of Medicine; National University of Singapore; Singapore 117597 Singapore
- NTU Institute of Structural Biology; Nanyang Technological University (NTU); 59 Nanyang Drive Singapore 636921 Singapore
- School of Biological Sciences; NTU; 60 Nanyang Drive Singapore 637551 Singapore
- Lee Kong Chian School of Medicine; 50 Nanyang Avenue Singapore 639798 Singapore
| | - Edward G. Robins
- Singapore Bioimaging Consortium (SBIC); A*STAR; 11 Biopolis way, #02-02 Singapore 138667 Singapore
| | - Huimin Zhao
- Metabolic Engineering Research Laboratory (MERL); Science and Engineering Institutes; Agency for Science, Technology, and Research (A*STAR); 31 Biopolis Way, Nanos #01-01 Singapore 138669 Singapore
- 215 Roger Adams Laboratory, Box C3; University of Illinois at Urbana-Champaign; 600 South Mathews Avenue Urbana IL 61801 USA
| | - Ee Lui Ang
- Metabolic Engineering Research Laboratory (MERL); Science and Engineering Institutes; Agency for Science, Technology, and Research (A*STAR); 31 Biopolis Way, Nanos #01-01 Singapore 138669 Singapore
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35
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Sun H, Yeo WL, Lim YH, Chew X, Smith DJ, Xue B, Chan KP, Robinson RC, Robins EG, Zhao H, Ang EL. Directed Evolution of a Fluorinase for Improved Fluorination Efficiency with a Non-native Substrate. Angew Chem Int Ed Engl 2016; 55:14277-14280. [PMID: 27739177 DOI: 10.1002/anie.201606722] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 08/24/2016] [Indexed: 11/09/2022]
Abstract
Fluorinases offer an environmentally friendly alternative for selective fluorination under mild conditions. However, their diversity is limited in nature and they have yet to be engineered through directed evolution. Herein, we report the directed evolution of the fluorinase FlA1 for improved conversion of the non-native substrate 5'-chloro-5'-deoxyadenosine (5'-ClDA) into 5'-fluoro-5'-deoxyadenosine (5'-FDA). The evolved variants, fah2081 (A279Y) and fah2114 (F213Y, A279L), were successfully applied in the radiosynthesis of 5'-[18 F]FDA, with overall radiochemical conversion (RCC) more than 3-fold higher than wild-type FlA1. Kinetic studies of the two-step reaction revealed that the variants show a significantly improved kcat value in the conversion of 5'-ClDA into S-adenosyl-l-methionine (SAM) but a reduced kcat value in the conversion of SAM into 5'-FDA.
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Affiliation(s)
- Huihua Sun
- Metabolic Engineering Research Laboratory (MERL), Science and Engineering Institutes, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos #01-01, Singapore, 138669, Singapore
| | - Wan Lin Yeo
- Metabolic Engineering Research Laboratory (MERL), Science and Engineering Institutes, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos #01-01, Singapore, 138669, Singapore
| | - Yee Hwee Lim
- Institute of Chemical and Engineering Sciences (ICES), A*STAR, 8 Biomedical Grove, Neuros #07-01/02/03, Singapore, 138665, Singapore
| | - Xinying Chew
- Institute of Chemical and Engineering Sciences (ICES), A*STAR, 8 Biomedical Grove, Neuros #07-01/02/03, Singapore, 138665, Singapore
| | - Derek John Smith
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, Matrix #07-01, Singapore, 138671, Singapore.,Biotransformation Innovation Platform, 61 Biopolis Drive, Proteos #04-14, Singapore, 138673, Singapore
| | - Bo Xue
- Institute of Molecular and Cell Biology (IMCB), A*STAR, 61 Biopolis Drive, Proteos #03-15, Singapore, 138673, Singapore
| | - Kok Ping Chan
- Institute of Chemical and Engineering Sciences (ICES), A*STAR, 8 Biomedical Grove, Neuros #07-01/02/03, Singapore, 138665, Singapore
| | - Robert C Robinson
- Institute of Molecular and Cell Biology (IMCB), A*STAR, 61 Biopolis Drive, Proteos #03-15, Singapore, 138673, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University (NTU), 59 Nanyang Drive, Singapore, 636921, Singapore.,School of Biological Sciences, NTU, 60 Nanyang Drive, Singapore, 637551, Singapore.,Lee Kong Chian School of Medicine, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Edward G Robins
- Singapore Bioimaging Consortium (SBIC), A*STAR, 11 Biopolis way, #02-02, Singapore, 138667, Singapore
| | - Huimin Zhao
- Metabolic Engineering Research Laboratory (MERL), Science and Engineering Institutes, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos #01-01, Singapore, 138669, Singapore. .,215 Roger Adams Laboratory, Box C3, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA.
| | - Ee Lui Ang
- Metabolic Engineering Research Laboratory (MERL), Science and Engineering Institutes, Agency for Science, Technology, and Research (A*STAR), 31 Biopolis Way, Nanos #01-01, Singapore, 138669, Singapore.
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36
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Awuni Y, Jiang S, Robinson RC, Mu Y. Exploring the A22-Bacterial Actin MreB Interaction through Molecular Dynamics Simulations. J Phys Chem B 2016; 120:9867-74. [PMID: 27600765 DOI: 10.1021/acs.jpcb.6b05199] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
MreB is an actin-like cytoskeleton protein that plays a vital role in the maintenance of the rod-shaped morphology of many bacteria. S-(3,4-Dichlorobenzyl) isothiourea (A22) is an antibiotic-like small molecule that perturbs the rod cell shape and has been suggested to inhibit MreB by targeting ATP hydrolysis. However, without the elucidation of the structure of the ATP-bound state of MreB in the presence of A22, the mechanism of A22 inhibition is still not clear. Here we apply conventional molecular dynamics simulations to explore the dynamics of the active site of MreB in complex with A22 and different nucleotides. We observe that hydrogen bonding between A22 and the catalytic Glu140 residue is not favored in the ATP-A22-bound state of MreB. Water dynamics analysis in the MreB active site reveals that in the presence of A22 water molecules are able to occupy positions suitable for ATP hydrolysis. Overall, our results are consistent with a mechanism in which A22 affects MreB polymerization/depolymerization dynamics in part through slowing phosphate release rather than by inhibiting ATP hydrolysis. These data can be incorporated in the design/development of the next generation of MreB inhibitors.
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Affiliation(s)
- Yaw Awuni
- School of Biological Sciences, Nanyang Technological University , 60 Nanyang Drive, Singapore 637551
| | - Shimin Jiang
- Institute of Molecular and Cell Biology , A*STAR, Biopolis, Singapore 138673
| | - Robert C Robinson
- School of Biological Sciences, Nanyang Technological University , 60 Nanyang Drive, Singapore 637551.,Institute of Molecular and Cell Biology , A*STAR, Biopolis, Singapore 138673.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore , Singapore 117597.,Institute of Structural Biology, Nanyang Technological University , 59 Nanyang Drive, Singapore 636921.,Lee Kong Chian School of Medicine , 50 Nanyang Avenue, Singapore 639798
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University , 60 Nanyang Drive, Singapore 637551
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37
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Barkó S, Szatmári D, Bódis E, Türmer K, Ujfalusi Z, Popp D, Robinson RC, Nyitrai M. Large-scale purification and in vitro characterization of the assembly of MreB from Leptospira interrogans. Biochim Biophys Acta Gen Subj 2016; 1860:1942-52. [PMID: 27297907 DOI: 10.1016/j.bbagen.2016.06.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 05/23/2016] [Accepted: 06/06/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND Weil's syndrome is caused by Leptospira interrogans infections, a Gram negative bacterium with a distinct thin corkscrew cell shape. The molecular basis for this unusual morphology is unknown. In many bacteria, cell wall synthesis is orchestrated by the actin homolog, MreB. METHODS Here we have identified the MreB within the L. interrogans genome and expressed the His-tagged protein product of the synthesized gene (Li-MreB) in Escherichia coli. Li-MreB did not purify under standard nucleotide-free conditions used for MreBs from other species, requiring the continual presence of ATP to remain soluble. Covalent modification of Li-MreB free thiols with Alexa488 produced a fluorescent version of Li-MreB. RESULTS We developed native and denaturing/refolding purification schemes for Li-MreB. The purified product was shown to assemble and disassemble in MgCl2 and KCl dependent manners, as monitored by light scattering and sedimentation studies. The fluorescence spectrum of labeled Li-MreB-Alexa488 showed cation-induced changes in line with an activation process followed by a polymerization phase. The resulting filaments appeared as bundles and sheets under the fluorescence microscope. Finally, since the Li-MreB polymerization was cation dependent, we developed a simple method to measure monovalent cation concentrations within a test case prokaryote, E. coli. CONCLUSIONS We have identified and initially characterized the cation-dependent polymerization properties of a novel MreB from a non-rod shaped bacterium and developed a method to measure cation concentrations within prokaryotes. GENERAL SIGNIFICANCE This initial characterization of Li-MreB will enable future structural determination of the MreB filament from this corkscrew-shaped bacterium.
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Affiliation(s)
- Szilvia Barkó
- Department of Biophysics, Medical School, University of Pécs, Szigeti str. 12, Pécs H-7624, Hungary
| | - Dávid Szatmári
- Department of Biophysics, Medical School, University of Pécs, Szigeti str. 12, Pécs H-7624, Hungary
| | - Emőke Bódis
- Department of Biophysics, Medical School, University of Pécs, Szigeti str. 12, Pécs H-7624, Hungary
| | - Katalin Türmer
- Department of Biophysics, Medical School, University of Pécs, Szigeti str. 12, Pécs H-7624, Hungary
| | - Zoltán Ujfalusi
- Department of Biophysics, Medical School, University of Pécs, Szigeti str. 12, Pécs H-7624, Hungary
| | - David Popp
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis 138673, Singapore
| | - Robert C Robinson
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis 138673, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore
| | - Miklós Nyitrai
- Department of Biophysics, Medical School, University of Pécs, Szigeti str. 12, Pécs H-7624, Hungary; MTA-PTE Nuclear-Mitochondrial Interactions Research Group, Szigeti str. 12, Pécs H-7624, Hungary
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38
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Brichkina A, Nguyen NT, Baskar R, Wee S, Gunaratne J, Robinson RC, Bulavin DV. Proline isomerisation as a novel regulatory mechanism for p38MAPK activation and functions. Cell Death Differ 2016; 23:1592-601. [PMID: 27233083 DOI: 10.1038/cdd.2016.45] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 04/05/2016] [Accepted: 04/15/2016] [Indexed: 12/22/2022] Open
Abstract
The stress-induced p38 mitogen-activated protein kinase (MAPK) pathway plays an essential role in multiple physiological processes, including cancer. In turn, p38MAPK phosphorylation at Thr180 and Tyr182 is a key regulatory mechanism for its activation and functions. Here we show that this mechanism is actively regulated through isomerisation of Pro224. Different cyclophilins can isomerise this proline residue and modulate the ability of upstream kinases to phosphorylate Thr180 and Tyr182. In vivo mutation of Pro224 to Ile in endogenous p38MAPK significantly reduced its phosphorylation and activity. This resulted in attenuation of p38MAPK signalling, which in turn caused an enhanced apoptosis and sensitivity to a DNA-damaging drug, cisplatin. We further found a reduction in size and number of lesions in homozygous mice carrying the p38MAPK P224I substitution in a K-ras model of lung tumorigenesis. We propose that cyclophilin-dependent isomerisation of p38MAPK is an important novel mechanism in regulating p38MAPK phosphorylation and functions. Thus, inhibition of this process, including with drugs that are in clinical trials, may improve the efficacy of current anti-cancer therapeutic regimes.
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Affiliation(s)
- A Brichkina
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138673, Singapore
| | - N Tm Nguyen
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138673, Singapore
| | - R Baskar
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138673, Singapore
| | - S Wee
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138673, Singapore
| | - J Gunaratne
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138673, Singapore
| | - R C Robinson
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138673, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - D V Bulavin
- Institute for Research on Cancer and Aging of Nice (IRCAN), INSERM, U1081-UMR CNRS 7284, University of Nice - Sophia Antipolis, Centre Antoine Lacassagne, Nice, France
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39
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Tankrathok A, Iglesias-Fernández J, Williams RJ, Pengthaisong S, Baiya S, Hakki Z, Robinson RC, Hrmova M, Rovira C, Williams SJ, Ketudat Cairns JR. A Single Glycosidase Harnesses Different Pyranoside Ring Transition State Conformations for Hydrolysis of Mannosides and Glucosides. ACS Catal 2015. [DOI: 10.1021/acscatal.5b01547] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Anupong Tankrathok
- School of Biochemistry, Institute of Science, and Center
for Biomolecular Structure, Function and Application, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
- Department of Biotechnology, Faculty of Agro-Industrial
Technology, Rajamangala University of Technology, Isan, Kalasin Campus, Kalasin 46000, Thailand
| | - Javier Iglesias-Fernández
- Departament de Quı́mica
Orgànica/Institut de Quı́mica Teòrica i
Computacional (IQTCUB), Universitat de Barcelona, Martı́ i Franquès
1, 08028 Barcelona, Spain
| | - Rohan J. Williams
- School of Chemistry and Bio21 Molecular
Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Salila Pengthaisong
- School of Biochemistry, Institute of Science, and Center
for Biomolecular Structure, Function and Application, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Supaporn Baiya
- School of Biochemistry, Institute of Science, and Center
for Biomolecular Structure, Function and Application, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Zalihe Hakki
- School of Chemistry and Bio21 Molecular
Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Robert C. Robinson
- Institute of Molecular
and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138673
- Department of Biochemistry, National University of Singapore, 8 Medical Drive, Singapore 117597
| | - Maria Hrmova
- School of Agriculture, Food and Wine, Australian
Centre for Plant Functional Genomics, University of Adelaide, Waite Campus, Glenn
Osmond, Australia
| | - Carme Rovira
- Departament de Quı́mica
Orgànica/Institut de Quı́mica Teòrica i
Computacional (IQTCUB), Universitat de Barcelona, Martı́ i Franquès
1, 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluı́s Companys, 23, 08018 Barcelona, Spain
| | - Spencer J. Williams
- School of Chemistry and Bio21 Molecular
Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - James R. Ketudat Cairns
- School of Biochemistry, Institute of Science, and Center
for Biomolecular Structure, Function and Application, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
- Laboratory of Biochemistry, Chulabhorn Research Institute, Bangkok 10210, Thailand
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40
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Go MK, Wongsantichon J, Cheung VWN, Chow JY, Robinson RC, Yew WS. Synthetic Polyketide Enzymology: Platform for Biosynthesis of Antimicrobial Polyketides. ACS Catal 2015. [DOI: 10.1021/acscatal.5b00477] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Maybelle Kho Go
- Department of Biochemistry,
Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597,
- NUS
Synthetic Biology for Clinical and Technological Innovation, Life
Sciences Institute, National University of Singapore, 28 Medical
Drive, Singapore 117456,
| | - Jantana Wongsantichon
- Institute
of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138673
| | - Vivian Wing Ngar Cheung
- Department of Biochemistry,
Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597,
- NUS
Synthetic Biology for Clinical and Technological Innovation, Life
Sciences Institute, National University of Singapore, 28 Medical
Drive, Singapore 117456,
| | - Jeng Yeong Chow
- Department of Biochemistry,
Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597,
| | - Robert C. Robinson
- Department of Biochemistry,
Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597,
- Institute
of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138673
| | - Wen Shan Yew
- Department of Biochemistry,
Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597,
- NUS
Synthetic Biology for Clinical and Technological Innovation, Life
Sciences Institute, National University of Singapore, 28 Medical
Drive, Singapore 117456,
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41
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Gunning PW, Ghoshdastider U, Whitaker S, Popp D, Robinson RC. The evolution of compositionally and functionally distinct actin filaments. J Cell Sci 2015; 128:2009-19. [DOI: 10.1242/jcs.165563] [Citation(s) in RCA: 157] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
ABSTRACT
The actin filament is astonishingly well conserved across a diverse set of eukaryotic species. It has essentially remained unchanged in the billion years that separate yeast, Arabidopsis and man. In contrast, bacterial actin-like proteins have diverged to the extreme, and many of them are not readily identified from sequence-based homology searches. Here, we present phylogenetic analyses that point to an evolutionary drive to diversify actin filament composition across kingdoms. Bacteria use a one-filament-one-function system to create distinct filament systems within a single cell. In contrast, eukaryotic actin is a universal force provider in a wide range of processes. In plants, there has been an expansion of the number of closely related actin genes, whereas in fungi and metazoa diversification in tropomyosins has increased the compositional variety in actin filament systems. Both mechanisms dictate the subset of actin-binding proteins that interact with each filament type, leading to specialization in function. In this Hypothesis, we thus propose that different mechanisms were selected in bacteria, plants and metazoa, which achieved actin filament compositional variation leading to the expansion of their functional diversity.
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Affiliation(s)
- Peter W. Gunning
- School of Medical Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Umesh Ghoshdastider
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138673
| | - Shane Whitaker
- School of Medical Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - David Popp
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138673
| | - Robert C. Robinson
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138673
- Department of Biochemistry, National University of Singapore, 8 Medical Drive, Singapore 117597
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42
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Lee WL, Grimes JM, Robinson RC. Yersinia effector YopO uses actin as bait to phosphorylate proteins that regulate actin polymerization. Nat Struct Mol Biol 2015; 22:248-55. [PMID: 25664724 DOI: 10.1038/nsmb.2964] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 12/30/2014] [Indexed: 11/09/2022]
Abstract
Pathogenic Yersinia species evade host immune systems through the injection of Yersinia outer proteins (Yops) into phagocytic cells. One Yop, YopO, also known as YpkA, induces actin-filament disruption, impairing phagocytosis. Here we describe the X-ray structure of Yersinia enterocolitica YopO in complex with actin, which reveals that YopO binds to an actin monomer in a manner that blocks polymerization yet allows the bound actin to interact with host actin-regulating proteins. SILAC-MS and biochemical analyses confirm that actin-polymerization regulators such as VASP, EVL, WASP, gelsolin and the formin diaphanous 1 are directly sequestered and phosphorylated by YopO through formation of ternary complexes with actin. This leads to a model in which YopO at the membrane sequesters actin from polymerization while using the bound actin as bait to recruit, phosphorylate and misregulate host actin-regulating proteins to disrupt phagocytosis.
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Affiliation(s)
- Wei Lin Lee
- 1] Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore. [2] Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Jonathan M Grimes
- 1] Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK. [2] Diamond Light Source, Oxfordshire, UK
| | - Robert C Robinson
- 1] Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore. [2] Department of Biochemistry, National University of Singapore, Singapore
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43
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Van Overbeke W, Wongsantichon J, Everaert I, Verhelle A, Zwaenepoel O, Loonchanta A, Burtnick LD, De Ganck A, Hochepied T, Haigh J, Cuvelier C, Derave W, Robinson RC, Gettemans J. An ER-directed gelsolin nanobody targets the first step in amyloid formation in a gelsolin amyloidosis mouse model. Hum Mol Genet 2015; 24:2492-507. [PMID: 25601851 DOI: 10.1093/hmg/ddv010] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 01/14/2015] [Indexed: 01/01/2023] Open
Abstract
Hereditary gelsolin amyloidosis is an autosomal dominantly inherited amyloid disorder. A point mutation in the GSN gene (G654A being the most common one) results in disturbed calcium binding by the second gelsolin domain (G2). As a result, the folding of G2 is hampered, rendering the mutant plasma gelsolin susceptible to a proteolytic cascade. Consecutive cleavage by furin and MT1-MMP-like proteases generates 8 and 5 kDa amyloidogenic peptides that cause neurological, ophthalmological and dermatological findings. To this day, no specific treatment is available to counter the pathogenesis. Using GSN nanobody 11 as a molecular chaperone, we aimed to protect mutant plasma gelsolin from furin proteolysis in the trans-Golgi network. We report a transgenic, GSN nanobody 11 secreting mouse that was used for crossbreeding with gelsolin amyloidosis mice. Insertion of the therapeutic nanobody gene into the gelsolin amyloidosis mouse genome resulted in improved muscle contractility. X-ray crystal structure determination of the gelsolin G2:Nb11 complex revealed that Nb11 does not directly block the furin cleavage site. We conclude that nanobodies can be used to shield substrates from aberrant proteolysis and this approach might establish a novel therapeutic strategy in amyloid diseases.
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Affiliation(s)
| | - Jantana Wongsantichon
- Institute of Molecular and Cellular Biology, A*STAR, Biopolis, Singapore 138673, Singapore
| | - Inge Everaert
- Department of Movement and Sport Sciences, Faculty of Medicine and Health Sciences
| | - Adriaan Verhelle
- Department of Biochemistry, Faculty of Medicine and Health Sciences
| | | | - Anantasak Loonchanta
- Department of Chemistry and Centre for Blood Research, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Leslie D Burtnick
- Department of Chemistry and Centre for Blood Research, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ariane De Ganck
- Department of Biochemistry, Faculty of Medicine and Health Sciences
| | - Tino Hochepied
- Department for Molecular Biomedical Research, VIB, Ghent, Belgium, Department of Biomedical Molecular Biology and
| | - Jody Haigh
- Department of Biomedical Molecular Biology and Vascular Cell Biology Unit, VIB Inflammation Research Centre, Ghent, Belgium and Mammalian Functional Genetics Laboratory, Division of Blood Cancers, Australian Centre for Blood Diseases, Department of Clinical Haematology, Monash University and Alfred Health Centre, Melbourne, Australia
| | - Claude Cuvelier
- Department of Pathology, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Wim Derave
- Department of Movement and Sport Sciences, Faculty of Medicine and Health Sciences
| | - Robert C Robinson
- Institute of Molecular and Cellular Biology, A*STAR, Biopolis, Singapore 138673, Singapore, Department of Biochemistry, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore,
| | - Jan Gettemans
- Department of Biochemistry, Faculty of Medicine and Health Sciences,
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44
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Ranok A, Wongsantichon J, Robinson RC, Suginta W. Structural and thermodynamic insights into chitooligosaccharide binding to human cartilage chitinase 3-like protein 2 (CHI3L2 or YKL-39). J Biol Chem 2014; 290:2617-29. [PMID: 25477513 DOI: 10.1074/jbc.m114.588905] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Four crystal structures of human YKL-39 were solved in the absence and presence of chitooligosaccharides. The structure of YKL-39 comprises a major (β/α)8 triose-phosphate isomerase barrel domain and a small α + β insertion domain. Structural analysis demonstrates that YKL-39 interacts with chitooligosaccharides through hydrogen bonds and hydrophobic interactions. The binding of chitin fragments induces local conformational changes that facilitate tight binding. Compared with other GH-18 members, YKL-39 has the least extended chitin-binding cleft, containing five subsites for sugars, namely (-3)(-2)(-1)(+1)(+2), with Trp-360 playing a prominent role in the sugar-protein interactions at the center of the chitin-binding cleft. Evaluation of binding affinities obtained from isothermal titration calorimetry and intrinsic fluorescence spectroscopy suggests that YKL-39 binds to chitooligosaccharides with Kd values in the micromolar concentration range and that the binding energies increase with the chain length. There were no significant differences between the Kd values of chitopentaose and chitohexaose, supporting the structural evidence for the five binding subsite topology. Thermodynamic analysis indicates that binding of chitooligosaccharide to YKL-39 is mainly driven by enthalpy.
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Affiliation(s)
- Araya Ranok
- From the Biochemistry-Electrochemistry Research Unit, School of Biochemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Jantana Wongsantichon
- the Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A*STAR), Biopolis Drive, Singapore 138673, Singapore, and
| | - Robert C Robinson
- the Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A*STAR), Biopolis Drive, Singapore 138673, Singapore, and the Department of Biochemistry, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
| | - Wipa Suginta
- From the Biochemistry-Electrochemistry Research Unit, School of Biochemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand,
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45
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Cheung VWN, Xue B, Hernandez-Valladares M, Go MK, Tung A, Aguda AH, Robinson RC, Yew WS. Identification of polyketide inhibitors targeting 3-dehydroquinate dehydratase in the shikimate pathway of Enterococcus faecalis. PLoS One 2014; 9:e103598. [PMID: 25072253 PMCID: PMC4114755 DOI: 10.1371/journal.pone.0103598] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 07/04/2014] [Indexed: 12/28/2022] Open
Abstract
Due to the emergence of resistance toward current antibiotics, there is a pressing need to develop the next generation of antibiotics as therapeutics against infectious and opportunistic diseases of microbial origins. The shikimate pathway is exclusive to microbes, plants and fungi, and hence is an attractive and logical target for development of antimicrobial therapeutics. The Gram-positive commensal microbe, Enterococcus faecalis, is a major human pathogen associated with nosocomial infections and resistance to vancomycin, the “drug of last resort”. Here, we report the identification of several polyketide-based inhibitors against the E. faecalis shikimate pathway enzyme, 3-dehydroquinate dehydratase (DHQase). In particular, marein, a flavonoid polyketide, both inhibited DHQase and retarded the growth of Enterococcus faecalis. The purification, crystallization and structural resolution of recombinant DHQase from E. faecalis (at 2.2 Å resolution) are also reported. This study provides a route in the development of polyketide-based antimicrobial inhibitors targeting the shikimate pathway of the human pathogen E. faecalis.
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Affiliation(s)
- Vivian Wing Ngar Cheung
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Bo Xue
- Institute of Molecular and Cell Biology, Singapore, Singapore
| | | | - Maybelle Kho Go
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Alvin Tung
- Institute of Molecular and Cell Biology, Singapore, Singapore
| | | | - Robert C. Robinson
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Institute of Molecular and Cell Biology, Singapore, Singapore
- * E-mail: (RCR); (WSY)
| | - Wen Shan Yew
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Synthetic Biology Research Consortium, National University of Singapore, Singapore, Singapore
- * E-mail: (RCR); (WSY)
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46
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Smadbeck J, Chan KH, Khoury GA, Xue B, Robinson RC, Hauser CAE, Floudas CA. De novo design and experimental characterization of ultrashort self-associating peptides. PLoS Comput Biol 2014; 10:e1003718. [PMID: 25010703 PMCID: PMC4091692 DOI: 10.1371/journal.pcbi.1003718] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 05/31/2014] [Indexed: 12/19/2022] Open
Abstract
Self-association is a common phenomenon in biology and one that can have positive and negative impacts, from the construction of the architectural cytoskeleton of cells to the formation of fibrils in amyloid diseases. Understanding the nature and mechanisms of self-association is important for modulating these systems and in creating biologically-inspired materials. Here, we present a two-stage de novo peptide design framework that can generate novel self-associating peptide systems. The first stage uses a simulated multimeric template structure as input into the optimization-based Sequence Selection to generate low potential energy sequences. The second stage is a computational validation procedure that calculates Fold Specificity and/or Approximate Association Affinity (K*association) based on metrics that we have devised for multimeric systems. This framework was applied to the design of self-associating tripeptides using the known self-associating tripeptide, Ac-IVD, as a structural template. Six computationally predicted tripeptides (Ac-LVE, Ac-YYD, Ac-LLE, Ac-YLD, Ac-MYD, Ac-VIE) were chosen for experimental validation in order to illustrate the self-association outcomes predicted by the three metrics. Self-association and electron microscopy studies revealed that Ac-LLE formed bead-like microstructures, Ac-LVE and Ac-YYD formed fibrillar aggregates, Ac-VIE and Ac-MYD formed hydrogels, and Ac-YLD crystallized under ambient conditions. An X-ray crystallographic study was carried out on a single crystal of Ac-YLD, which revealed that each molecule adopts a β-strand conformation that stack together to form parallel β-sheets. As an additional validation of the approach, the hydrogel-forming sequences of Ac-MYD and Ac-VIE were shuffled. The shuffled sequences were computationally predicted to have lower K*association values and were experimentally verified to not form hydrogels. This illustrates the robustness of the framework in predicting self-associating tripeptides. We expect that this enhanced multimeric de novo peptide design framework will find future application in creating novel self-associating peptides based on unnatural amino acids, and inhibitor peptides of detrimental self-aggregating biological proteins.
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Affiliation(s)
- James Smadbeck
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, United States of America
| | - Kiat Hwa Chan
- Institute of Bioengineering and Nanotechnology, Singapore, Singapore
| | - George A. Khoury
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, United States of America
| | - Bo Xue
- Institute of Molecular and Cell Biology, A*STAR (Agency of Science, Technology and Research), Biopolis, Singapore, Singapore
| | - Robert C. Robinson
- Institute of Molecular and Cell Biology, A*STAR (Agency of Science, Technology and Research), Biopolis, Singapore, Singapore
| | | | - Christodoulos A. Floudas
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, United States of America
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Ghoshdastider U, Popp D, Burtnick LD, Robinson RC. The expanding superfamily of gelsolin homology domain proteins. Cytoskeleton (Hoboken) 2013; 70:775-95. [DOI: 10.1002/cm.21149] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 10/11/2013] [Accepted: 10/02/2013] [Indexed: 12/29/2022]
Affiliation(s)
- Umesh Ghoshdastider
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science; Technology and Research); Biopolis 138673 Singapore
| | - David Popp
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science; Technology and Research); Biopolis 138673 Singapore
| | - Leslie D. Burtnick
- Department of Chemistry and Centre for Blood Research; Life Sciences Institute; University of British Columbia; Vancouver British Columbia V6T 1Z1 Canada
| | - Robert C. Robinson
- Institute of Molecular and Cell Biology, A*STAR (Agency for Science; Technology and Research); Biopolis 138673 Singapore
- Department of Biochemistry; National University of Singapore; Singapore 117597 Singapore
- School of Biological Sciences; Nanyang Technological University; Singapore 637551 Singapore
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Tankrathok A, Iglesias-Fernández J, Luang S, Robinson RC, Kimura A, Rovira C, Hrmova M, Ketudat Cairns JR. Structural analysis and insights into the glycon specificity of the rice GH1 Os7BGlu26 β-D-mannosidase. Acta Crystallogr D Biol Crystallogr 2013; 69:2124-35. [DOI: 10.1107/s0907444913020568] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2013] [Accepted: 07/24/2013] [Indexed: 11/10/2022]
Abstract
Rice Os7BGlu26 is a GH1 family glycoside hydrolase with a threefold higherkcat/Kmvalue for 4-nitrophenyl β-D-mannoside (4NPMan) compared with 4-nitrophenyl β-D-glucoside (4NPGlc). To investigate its selectivity for β-D-mannoside and β-D-glucoside substrates, the structures of apo Os7BGlu26 at a resolution of 2.20 Å and of Os7BGlu26 with mannose at a resolution of 2.45 Å were elucidated from isomorphous crystals in space groupP212121. The (β/α)8-barrel structure is similar to other GH1 family structures, but with a narrower active-site cleft. The Os7BGlu26 structure with D-mannose corresponds to a product complex, with β-D-mannose in the1S5skew-boat conformation. Docking of the1S3,1S5,2SOand3S1pyranose-ring conformations of 4NPMan and 4NPGlc substrates into the active site of Os7BGlu26 indicated that the lowest energies were in the1S5and1S3skew-boat conformations. Comparison of these docked conformers with other rice GH1 structures revealed differences in the residues interacting with the catalytic acid/base between enzymes with and without β-D-mannosidase activity. The mutation of Tyr134 to Trp in Os7BGlu26 resulted in similarkcat/Kmvalues for 4NPMan and 4NPGlc, while mutation of Tyr134 to Phe resulted in a 37-fold higherkcat/Kmfor 4NPMan than 4NPGlc. Mutation of Cys182 to Thr decreased both the activity and the selectivity for β-D-mannoside. It was concluded that interactions with the catalytic acid/base play a significant role in glycon selection.
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Dudgeon C, Shreeram S, Tanoue K, Mazur SJ, Sayadi A, Robinson RC, Appella E, Bulavin DV. Genetic variants and mutations of PPM1D control the response to DNA damage. Cell Cycle 2013; 12:2656-64. [PMID: 23907125 DOI: 10.4161/cc.25694] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The Wip1 phosphatase is an oncogene that is overexpressed in a variety of primary human cancers. We were interested in identifying genetic variants that could change Wip1 activity. We identified 3 missense SNPs of the human Wip1 phosphatase, L120F, P322Q, and I496V confer a dominant-negative phenotype. On the other hand, in primary human cancers, PPM1D mutations commonly result in a gain-of-function phenotype, leading us to identify a hot-spot truncating mutation at position 525. Surprisingly, we also found a significant number of loss-of-function mutations of PPM1D in primary human cancers, both in the phosphatase domain and in the C terminus. Thus, PPM1D has evolved to generate genetic variants with lower activity, potentially providing a better fitness for the organism through suppression of multiple diseases. In cancer, however, the situation is more complex, and the presence of both activating and inhibiting mutations requires further investigation to understand their contribution to tumorigenesis.
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Affiliation(s)
- Crissy Dudgeon
- Department of Pediatrics, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
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Nag S, Larsson M, Robinson RC, Burtnick LD. Gelsolin: The tail of a molecular gymnast. Cytoskeleton (Hoboken) 2013; 70:360-84. [DOI: 10.1002/cm.21117] [Citation(s) in RCA: 149] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 05/24/2013] [Indexed: 12/14/2022]
Affiliation(s)
| | - Mårten Larsson
- Institute of Molecular and Cell Biology, A*STAR; Singapore
| | | | - Leslie D. Burtnick
- Department of Chemistry and Centre for Blood Research; Life Sciences Institute, University of British Columbia; Vancouver; British Columbia; Canada
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