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Kojima M, Abe S, Furuta T, Hirata K, Yao X, Kobayashi A, Kobayashi R, Ueno T. High-throughput structure determination of an intrinsically disordered protein using cell-free protein crystallization. Proc Natl Acad Sci U S A 2024; 121:e2322452121. [PMID: 38861600 PMCID: PMC11194560 DOI: 10.1073/pnas.2322452121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 05/10/2024] [Indexed: 06/13/2024] Open
Abstract
Intrinsically disordered proteins (IDPs) play a crucial role in various biological phenomena, dynamically changing their conformations in response to external environmental cues. To gain a deeper understanding of these proteins, it is essential to identify the determinants that fix their structures at the atomic level. Here, we developed a pipeline for rapid crystal structure analysis of IDP using a cell-free protein crystallization (CFPC) method. Through this approach, we successfully demonstrated the determination of the structure of an IDP to uncover the key determinants that stabilize its conformation. Specifically, we focused on the 11-residue fragment of c-Myc, which forms an α-helix through dimerization with a binding partner protein. This fragment was strategically recombined with an in-cell crystallizing protein and was expressed in a cell-free system. The resulting crystal structures of the c-Myc fragment were successfully determined at a resolution of 1.92 Å and we confirmed that they are identical to the structures of the complex with the native binding partner protein. This indicates that the environment of the scaffold crystal can fix the structure of c-Myc. Significantly, these crystals were obtained directly from a small reaction mixture (30 µL) incubated for only 72 h. Analysis of eight crystal structures derived from 22 mutants revealed two hydrophobic residues as the key determinants responsible for stabilizing the α-helical structure. These findings underscore the power of our CFPC screening method as a valuable tool for determining the structures of challenging target proteins and elucidating the essential molecular interactions that govern their stability.
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Affiliation(s)
- Mariko Kojima
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama226-8501, Japan
| | - Satoshi Abe
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama226-8501, Japan
| | - Tadaomi Furuta
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama226-8501, Japan
| | - Kunio Hirata
- Synchrotron Radiation Life Science Instrumentation Unit, RIKEN/SPring-8 Center, Sayo-cho, Sayo-gun, Hyogo679-5148, Japan
| | - Xinchen Yao
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama226-8501, Japan
| | - Ayako Kobayashi
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama226-8501, Japan
| | - Ririko Kobayashi
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama226-8501, Japan
| | - Takafumi Ueno
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama226-8501, Japan
- Research Center for Autonomous Systems Materialogy (ASMat), Institute of Innovative Research, Tokyo Institute of Technology, Midori-ku, Yokohama226-8501, Japan
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2
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Parwana KAK, Kaur Gill P, Njanike R, Yiu HHP, Adams CF, Chari DM, Jenkins SI. Investigating Internalization of Reporter-Protein-Functionalized Polyhedrin Particles by Brain Immune Cells. MATERIALS (BASEL, SWITZERLAND) 2024; 17:2330. [PMID: 38793398 PMCID: PMC11122724 DOI: 10.3390/ma17102330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/11/2024] [Accepted: 04/26/2024] [Indexed: 05/26/2024]
Abstract
Achieving sustained drug delivery to the central nervous system (CNS) is a major challenge for neurological injury and disease, and various delivery vehicles are being developed to achieve this. Self-assembling polyhedrin crystals (POlyhedrin Delivery System; PODS) are being exploited for the delivery of therapeutic protein cargo, with demonstrated efficacy in vivo. However, to establish the utility of PODS for neural applications, their handling by neural immune cells (microglia) must be documented, as these cells process and degrade many biomaterials, often preventing therapeutic efficacy. Here, primary mouse cortical microglia were cultured with a GFP-functionalized PODS for 24 h. Cell counts, cell morphology and Iba1 expression were all unaltered in treated cultures, indicating a lack of acute toxicity or microglial activation. Microglia exhibited internalisation of the PODS, with both cytosolic and perinuclear localisation. No evidence of adverse effects on cellular morphology was observed. Overall, 20-40% of microglia exhibited uptake of the PODS, but extracellular/non-internalised PODS were routinely present after 24 h, suggesting that extracellular drug delivery may persist for at least 24 h.
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Affiliation(s)
| | | | - Runyararo Njanike
- School of Medicine, Keele University, Keele ST5 5BG, UK; (P.K.G.); (R.N.)
| | - Humphrey H. P. Yiu
- School of Engineering & Physical Sciences, University of Edinburgh, Edinburgh EH14 4AS, UK;
| | - Chris F. Adams
- School of Life Sciences, Keele University, Keele ST5 5BG, UK; (K.A.K.P.); (C.F.A.)
- Neural Tissue Engineering Keele (NTEK), Keele University, Keele ST5 5BG, UK
| | - Divya Maitreyi Chari
- School of Medicine, Keele University, Keele ST5 5BG, UK; (P.K.G.); (R.N.)
- Neural Tissue Engineering Keele (NTEK), Keele University, Keele ST5 5BG, UK
| | - Stuart Iain Jenkins
- School of Medicine, Keele University, Keele ST5 5BG, UK; (P.K.G.); (R.N.)
- Neural Tissue Engineering Keele (NTEK), Keele University, Keele ST5 5BG, UK
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3
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Schönherr R, Boger J, Lahey-Rudolph JM, Harms M, Kaiser J, Nachtschatt S, Wobbe M, Duden R, König P, Bourenkov G, Schneider TR, Redecke L. A streamlined approach to structure elucidation using in cellulo crystallized recombinant proteins, InCellCryst. Nat Commun 2024; 15:1709. [PMID: 38402242 PMCID: PMC10894269 DOI: 10.1038/s41467-024-45985-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 02/02/2024] [Indexed: 02/26/2024] Open
Abstract
With the advent of serial X-ray crystallography on microfocus beamlines at free-electron laser and synchrotron facilities, the demand for protein microcrystals has significantly risen in recent years. However, by in vitro crystallization extensive efforts are usually required to purify proteins and produce sufficiently homogeneous microcrystals. Here, we present InCellCryst, an advanced pipeline for producing homogeneous microcrystals directly within living insect cells. Our baculovirus-based cloning system enables the production of crystals from completely native proteins as well as the screening of different cellular compartments to maximize chances for protein crystallization. By optimizing cloning procedures, recombinant virus production, crystallization and crystal detection, X-ray diffraction data can be collected 24 days after the start of target gene cloning. Furthermore, improved strategies for serial synchrotron diffraction data collection directly from crystals within living cells abolish the need to purify the recombinant protein or the associated microcrystals.
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Affiliation(s)
- Robert Schönherr
- Institute of Biochemistry, University of Lübeck, Lübeck, Germany
| | - Juliane Boger
- Institute of Biochemistry, University of Lübeck, Lübeck, Germany
| | - J Mia Lahey-Rudolph
- Institute of Biochemistry, University of Lübeck, Lübeck, Germany
- Center for Free-Electron Laser Science (CFEL), Hamburg, Germany
- X-ray technology lab, TH Lübeck - University of Applied Sciences Lübeck, Lübeck, Germany
| | - Mareike Harms
- Institute of Biochemistry, University of Lübeck, Lübeck, Germany
| | | | | | - Marla Wobbe
- Institute of Biochemistry, University of Lübeck, Lübeck, Germany
| | - Rainer Duden
- Institute of Biology, University of Lübeck, Lübeck, Germany
| | - Peter König
- Institute of Anatomy, University of Lübeck, Lübeck, Germany
- Airway Research Center North (ARCN), University of Lübeck, German Center for Lung Research (DZL), Lübeck, Germany
| | - Gleb Bourenkov
- European Molecular Biology Laboratory, Hamburg Unit c/o Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Thomas R Schneider
- European Molecular Biology Laboratory, Hamburg Unit c/o Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany
| | - Lars Redecke
- Institute of Biochemistry, University of Lübeck, Lübeck, Germany.
- Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany.
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4
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Tanaka J, Abe S, Hayakawa T, Kojima M, Yamashita K, Hirata K, Ueno T. Crystal structure of the in-cell Cry1Aa purified from Bacillus thuringiensis. Biochem Biophys Res Commun 2023; 685:149144. [PMID: 37922785 DOI: 10.1016/j.bbrc.2023.149144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 10/22/2023] [Indexed: 11/07/2023]
Abstract
In-cell protein crystals which spontaneously crystallize in living cells, have recently been analyzed in investigations of their structures and biological functions. The crystals have been challenging to analyze structurally because of their small size. Therefore, the number of in-cell protein crystals in which the native structure has been determined is limited because most of the structures of in-cell crystals have been determined by recrystallization after dissolution. Some proteins have been reported to form intermolecular disulfide bonds in natural protein crystals that stabilize the crystals. Here, we focus on Cry1Aa, a cysteine-rich protein that crystallizes in Bacillus thuringiensis (Bt) and forms disulfide bonds. Previously, the full-length structure of 135 kDa Cry1Ac, which is the same size as Cry1Aa, was determined by recrystallization of dissolved protein from crystals purified from Bt cells. However, the formation of disulfide bonds has not been investigated because it was necessary to replace cysteine residues to prevent aggregation of the soluble protein. In this work, we succeeded in direct X-ray crystallographic analysis using crystals purified from Bt cells and characterized the cross-linked network of disulfide bonds within Cry1Aa crystals.
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Affiliation(s)
- Junko Tanaka
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, 226-8501, Japan
| | - Satoshi Abe
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, 226-8501, Japan.
| | - Tohru Hayakawa
- Graduate School of Interdisciplinary Science and Engineering in Health Systems, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama, 700-8530, Japan
| | - Mariko Kojima
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, 226-8501, Japan
| | - Keitaro Yamashita
- SR Life Science Instrumentation Unit, RIKEN/SPring-8 Center, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
| | - Kunio Hirata
- SR Life Science Instrumentation Unit, RIKEN/SPring-8 Center, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan
| | - Takafumi Ueno
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, 226-8501, Japan; Living Systems Materialogy (LiSM) Research Group, International Research Frontiers Initiative (IRFI), Tokyo Institute of Technology, Yokohama, 226-8501, Japan.
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5
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Alexander LT, Durairaj J, Kryshtafovych A, Abriata LA, Bayo Y, Bhabha G, Breyton C, Caulton SG, Chen J, Degroux S, Ekiert DC, Erlandsen BS, Freddolino PL, Gilzer D, Greening C, Grimes JM, Grinter R, Gurusaran M, Hartmann MD, Hitchman CJ, Keown JR, Kropp A, Kursula P, Lovering AL, Lemaitre B, Lia A, Liu S, Logotheti M, Lu S, Markússon S, Miller MD, Minasov G, Niemann HH, Opazo F, Phillips GN, Davies OR, Rommelaere S, Rosas‐Lemus M, Roversi P, Satchell K, Smith N, Wilson MA, Wu K, Xia X, Xiao H, Zhang W, Zhou ZH, Fidelis K, Topf M, Moult J, Schwede T. Protein target highlights in CASP15: Analysis of models by structure providers. Proteins 2023; 91:1571-1599. [PMID: 37493353 PMCID: PMC10792529 DOI: 10.1002/prot.26545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 06/15/2023] [Indexed: 07/27/2023]
Abstract
We present an in-depth analysis of selected CASP15 targets, focusing on their biological and functional significance. The authors of the structures identify and discuss key protein features and evaluate how effectively these aspects were captured in the submitted predictions. While the overall ability to predict three-dimensional protein structures continues to impress, reproducing uncommon features not previously observed in experimental structures is still a challenge. Furthermore, instances with conformational flexibility and large multimeric complexes highlight the need for novel scoring strategies to better emphasize biologically relevant structural regions. Looking ahead, closer integration of computational and experimental techniques will play a key role in determining the next challenges to be unraveled in the field of structural molecular biology.
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Affiliation(s)
- Leila T. Alexander
- BiozentrumUniversity of BaselBaselSwitzerland
- Computational Structural BiologySIB Swiss Institute of BioinformaticsBaselSwitzerland
| | - Janani Durairaj
- BiozentrumUniversity of BaselBaselSwitzerland
- Computational Structural BiologySIB Swiss Institute of BioinformaticsBaselSwitzerland
| | | | - Luciano A. Abriata
- School of Life SciencesÉcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Yusupha Bayo
- Department of BiosciencesUniversity of MilanoMilanItaly
- IBBA‐CNR Unit of MilanoInstitute of Agricultural Biology and BiotechnologyMilanItaly
| | - Gira Bhabha
- Department of Cell BiologyNew York University School of MedicineNew YorkNew YorkUSA
| | | | | | - James Chen
- Department of Cell BiologyNew York University School of MedicineNew YorkNew YorkUSA
| | | | - Damian C. Ekiert
- Department of Cell BiologyNew York University School of MedicineNew YorkNew YorkUSA
- Department of MicrobiologyNew York University School of MedicineNew YorkNew YorkUSA
| | - Benedikte S. Erlandsen
- Wellcome Centre for Cell BiologyInstitute of Cell Biology, University of EdinburghEdinburghUK
| | - Peter L. Freddolino
- Department of Biological Chemistry, Computational Medicine and BioinformaticsUniversity of MichiganAnn ArborMichiganUSA
| | - Dominic Gilzer
- Department of ChemistryBielefeld UniversityBielefeldGermany
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery InstituteMonash UniversityClaytonVictoriaAustralia
- Securing Antarctica's Environmental FutureMonash UniversityClaytonVictoriaAustralia
- Centre to Impact AMRMonash UniversityClaytonVictoriaAustralia
- ARC Research Hub for Carbon Utilisation and RecyclingMonash UniversityClaytonVictoriaAustralia
| | - Jonathan M. Grimes
- Division of Structural Biology, Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Rhys Grinter
- Department of Microbiology, Biomedicine Discovery InstituteMonash UniversityClaytonVictoriaAustralia
- Centre for Electron Microscopy of Membrane ProteinsMonash Institute of Pharmaceutical SciencesParkvilleVictoriaAustralia
| | - Manickam Gurusaran
- Wellcome Centre for Cell BiologyInstitute of Cell Biology, University of EdinburghEdinburghUK
| | - Marcus D. Hartmann
- Max Planck Institute for BiologyTübingenGermany
- Interfaculty Institute of Biochemistry, University of TübingenTübingenGermany
| | - Charlie J. Hitchman
- Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical BiologyUniversity of LeicesterLeicesterUK
| | - Jeremy R. Keown
- Division of Structural Biology, Wellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Ashleigh Kropp
- Department of Microbiology, Biomedicine Discovery InstituteMonash UniversityClaytonVictoriaAustralia
| | - Petri Kursula
- Department of BiomedicineUniversity of BergenBergenNorway
- Faculty of Biochemistry and Molecular Medicine & Biocenter OuluUniversity of OuluOuluFinland
| | | | - Bruno Lemaitre
- School of Life SciencesÉcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Andrea Lia
- Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical BiologyUniversity of LeicesterLeicesterUK
- ISPA‐CNR Unit of LecceInstitute of Sciences of Food ProductionLecceItaly
| | - Shiheng Liu
- Department of Microbiology, Immunology, and Molecular GeneticsUniversity of CaliforniaLos AngelesCaliforniaUSA
- California NanoSystems InstituteUniversity of CaliforniaLos AngelesCaliforniaUSA
| | - Maria Logotheti
- Max Planck Institute for BiologyTübingenGermany
- Interfaculty Institute of Biochemistry, University of TübingenTübingenGermany
- Present address:
Institute of BiochemistryUniversity of GreifswaldGreifswaldGermany
| | - Shuze Lu
- Lanzhou University School of Life SciencesLanzhouChina
| | | | | | - George Minasov
- Department of Microbiology‐ImmunologyNorthwestern Feinberg School of MedicineChicagoIllinoisUSA
| | | | - Felipe Opazo
- NanoTag Biotechnologies GmbHGöttingenGermany
- Institute of Neuro‐ and Sensory PhysiologyUniversity of Göttingen Medical CenterGöttingenGermany
- Center for Biostructural Imaging of Neurodegeneration (BIN)University of Göttingen Medical CenterGöttingenGermany
| | - George N. Phillips
- Department of BiosciencesRice UniversityHoustonTexasUSA
- Department of ChemistryRice UniversityHoustonTexasUSA
| | - Owen R. Davies
- Wellcome Centre for Cell BiologyInstitute of Cell Biology, University of EdinburghEdinburghUK
| | - Samuel Rommelaere
- School of Life SciencesÉcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Monica Rosas‐Lemus
- Department of Microbiology‐ImmunologyNorthwestern Feinberg School of MedicineChicagoIllinoisUSA
- Present address:
Department of Molecular Genetics and MicrobiologyUniversity of New MexicoAlbuquerqueNew MexicoUSA
| | - Pietro Roversi
- IBBA‐CNR Unit of MilanoInstitute of Agricultural Biology and BiotechnologyMilanItaly
- Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical BiologyUniversity of LeicesterLeicesterUK
| | - Karla Satchell
- Department of Microbiology‐ImmunologyNorthwestern Feinberg School of MedicineChicagoIllinoisUSA
| | - Nathan Smith
- Department of Biochemistry and the Redox Biology CenterUniversity of NebraskaLincolnNebraskaUSA
| | - Mark A. Wilson
- Department of Biochemistry and the Redox Biology CenterUniversity of NebraskaLincolnNebraskaUSA
| | - Kuan‐Lin Wu
- Department of ChemistryRice UniversityHoustonTexasUSA
| | - Xian Xia
- Department of Microbiology, Immunology, and Molecular GeneticsUniversity of CaliforniaLos AngelesCaliforniaUSA
- California NanoSystems InstituteUniversity of CaliforniaLos AngelesCaliforniaUSA
| | - Han Xiao
- Department of BiosciencesRice UniversityHoustonTexasUSA
- Department of ChemistryRice UniversityHoustonTexasUSA
- Department of BioengineeringRice UniversityHoustonTexasUSA
| | - Wenhua Zhang
- Lanzhou University School of Life SciencesLanzhouChina
| | - Z. Hong Zhou
- Department of Microbiology, Immunology, and Molecular GeneticsUniversity of CaliforniaLos AngelesCaliforniaUSA
- California NanoSystems InstituteUniversity of CaliforniaLos AngelesCaliforniaUSA
| | | | - Maya Topf
- University Medical Center Hamburg‐Eppendorf (UKE)HamburgGermany
- Centre for Structural Systems BiologyLeibniz‐Institut für Virologie (LIV)HamburgGermany
| | - John Moult
- Department of Cell Biology and Molecular Genetics, Institute for Bioscience and Biotechnology ResearchUniversity of MarylandRockvilleMarylandUSA
| | - Torsten Schwede
- BiozentrumUniversity of BaselBaselSwitzerland
- Computational Structural BiologySIB Swiss Institute of BioinformaticsBaselSwitzerland
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6
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Jia X, Gao Y, Huang Y, Sun L, Li S, Li H, Zhang X, Li Y, He J, Wu W, Venkannagari H, Yang K, Baker ML, Zhang Q. Architecture of the baculovirus nucleocapsid revealed by cryo-EM. Nat Commun 2023; 14:7481. [PMID: 37980340 PMCID: PMC10657434 DOI: 10.1038/s41467-023-43284-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 11/03/2023] [Indexed: 11/20/2023] Open
Abstract
Baculovirus Autographa californica multiple nucleopolyhedrovirus (AcMNPV) has been widely used as a bioinsecticide and a protein expression vector. Despite their importance, very little is known about the structure of most baculovirus proteins. Here, we show a 3.2 Å resolution structure of helical cylindrical body of the AcMNPV nucleocapsid, composed of VP39, as well as 4.3 Å resolution structures of both the head and the base of the nucleocapsid composed of over 100 protein subunits. AcMNPV VP39 demonstrates some features of the HK97-like fold and utilizes disulfide-bonds and a set of interactions at its C-termini to mediate nucleocapsid assembly and stability. At both ends of the nucleocapsid, the VP39 cylinder is constricted by an outer shell ring composed of proteins AC104, AC142 and AC109. AC101(BV/ODV-C42) and AC144(ODV-EC27) form a C14 symmetric inner layer at both capsid head and base. In the base, these proteins interact with a 7-fold symmetric capsid plug, while a portal-like structure is seen in the central portion of head. Additionally, we propose an application of AlphaFold2 for model building in intermediate resolution density.
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Affiliation(s)
- Xudong Jia
- State key laboratory of biocontrol, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, China
| | - Yuanzhu Gao
- State key laboratory of biocontrol, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, China
- Cryo-EM Facility Center, Southern University of Science and Technology, Shenzhen, China
| | - Yuxuan Huang
- State key laboratory of biocontrol, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, China
| | - Linjun Sun
- State key laboratory of biocontrol, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, China
| | - Siduo Li
- State key laboratory of biocontrol, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, China
| | - Hongmei Li
- State key laboratory of biocontrol, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, China
| | - Xueqing Zhang
- State key laboratory of biocontrol, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, China
| | - Yinyin Li
- State key laboratory of biocontrol, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, China
| | - Jian He
- State key laboratory of biocontrol, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, China
| | - Wenbi Wu
- State key laboratory of biocontrol, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, China
| | - Harikanth Venkannagari
- Department of Biochemistry and Molecular Biology, McGovern Medical School at the University of Texas Health Science Center, Houston, TX, 77030, USA
| | - Kai Yang
- State key laboratory of biocontrol, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, China
| | - Matthew L Baker
- Department of Biochemistry and Molecular Biology, McGovern Medical School at the University of Texas Health Science Center, Houston, TX, 77030, USA.
| | - Qinfen Zhang
- State key laboratory of biocontrol, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, China.
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7
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Keown JR, Crawshaw AD, Trincao J, Carrique L, Gildea RJ, Horrell S, Warren AJ, Axford D, Owen R, Evans G, Bézier A, Metcalf P, Grimes JM. Atomic structure of a nudivirus occlusion body protein determined from a 70-year-old crystal sample. Nat Commun 2023; 14:4160. [PMID: 37443157 PMCID: PMC10345106 DOI: 10.1038/s41467-023-39819-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
Infectious protein crystals are an essential part of the viral lifecycle for double-stranded DNA Baculoviridae and double-stranded RNA cypoviruses. These viral protein crystals, termed occlusion bodies or polyhedra, are dense protein assemblies that form a crystalline array, encasing newly formed virions. Here, using X-ray crystallography we determine the structure of a polyhedrin from Nudiviridae. This double-stranded DNA virus family is a sister-group to the baculoviruses, whose members were thought to lack occlusion bodies. The 70-year-old sample contains a well-ordered lattice formed by a predominantly α-helical building block that assembles into a dense, highly interconnected protein crystal. The lattice is maintained by extensive hydrophobic and electrostatic interactions, disulfide bonds, and domain switching. The resulting lattice is resistant to most environmental stresses. Comparison of this structure to baculovirus or cypovirus polyhedra shows a distinct protein structure, crystal space group, and unit cell dimensions, however, all polyhedra utilise common principles of occlusion body assembly.
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Affiliation(s)
- Jeremy R Keown
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
| | - Adam D Crawshaw
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Jose Trincao
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Loïc Carrique
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Richard J Gildea
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Sam Horrell
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Anna J Warren
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Danny Axford
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Robin Owen
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Gwyndaf Evans
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
- Rosalind Franklin Institute, Harwell Campus, Didcot, UK
| | - Annie Bézier
- Institut de Recherche sur la Biologie de l'Insecte (IRBI), UMR7261 CNRS-Université de Tours, Tours, France
| | - Peter Metcalf
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - Jonathan M Grimes
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
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8
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Cerrudo CS, Motta LF, Cuccovia Warlet FU, Lassalle FM, Simonin JA, Belaich MN. Protein-Gene Orthology in Baculoviridae: An Exhaustive Analysis to Redefine the Ancestrally Common Coding Sequences. Viruses 2023; 15:v15051091. [PMID: 37243176 DOI: 10.3390/v15051091] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/23/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
Baculoviruses are entomopathogens that carry large, double-stranded circular DNA genomes and infect insect larvae of Lepidoptera, Hymenoptera and Diptera, with applications in the biological control of agricultural pests, in the production of recombinant proteins and as viral vectors for various purposes in mammals. These viruses have a variable genetic composition that differs between species, with some sequences shared by all known members, and others that are lineage-specific or unique to isolates. Based on the analysis of nearly 300 sequenced genomes, a thorough bioinformatic investigation was conducted on all the baculoviral protein coding sequences, characterizing their orthology and phylogeny. This analysis confirmed the 38 protein coding sequences currently considered as core genes, while also identifying novel coding sequences as candidates to join this set. Accordingly, homology was found among all the major occlusion body proteins, thus proposing that the polyhedrin, granulin and CUN085 genes be considered as the 39th core gene of Baculoviridae.
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Affiliation(s)
- Carolina Susana Cerrudo
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular-Área Virosis de Insectos (LIGBCM-AVI), Instituto de Microbiología Básica y Aplicada, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, Bernal B1876BXD, Buenos Aires, Argentina
| | - Lucas Federico Motta
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular-Área Virosis de Insectos (LIGBCM-AVI), Instituto de Microbiología Básica y Aplicada, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, Bernal B1876BXD, Buenos Aires, Argentina
| | - Franco Uriel Cuccovia Warlet
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular-Área Virosis de Insectos (LIGBCM-AVI), Instituto de Microbiología Básica y Aplicada, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, Bernal B1876BXD, Buenos Aires, Argentina
| | - Fernando Maku Lassalle
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular-Área Virosis de Insectos (LIGBCM-AVI), Instituto de Microbiología Básica y Aplicada, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, Bernal B1876BXD, Buenos Aires, Argentina
| | - Jorge Alejandro Simonin
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular-Área Virosis de Insectos (LIGBCM-AVI), Instituto de Microbiología Básica y Aplicada, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, Bernal B1876BXD, Buenos Aires, Argentina
| | - Mariano Nicolás Belaich
- Laboratorio de Ingeniería Genética y Biología Celular y Molecular-Área Virosis de Insectos (LIGBCM-AVI), Instituto de Microbiología Básica y Aplicada, Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, Bernal B1876BXD, Buenos Aires, Argentina
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Mwanza P, Dealtry G, Lee M, Moore S. Transmission Electron Microscopy Observation of Morphological Changes to Cryptophlebia Leucotreta Granulovirus following Ultraviolet Irradiation. Pathogens 2023; 12:pathogens12040590. [PMID: 37111476 PMCID: PMC10144605 DOI: 10.3390/pathogens12040590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/03/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
Cryptophlebia leucotreta granulovirus (CrleGV), a double-stranded DNA virus (genus Betabaculovirus, family Baculoviridae), is highly infective to the citrus insect pest Thaumatotibia leucotreta. The South African isolate CrleGV-SA is formulated into a commercial biopesticide and registered for use in several countries. In South Africa, it is used as a biopesticide in a multi-faceted integrated pest management approach for citrus crops involving chemical and biological control methods. The virus nucleocapsid is surrounded and protected by an occlusion body (OB) composed of granulin protein in a crystalline matrix. Like all other baculoviruses, CrleGV is susceptible to ultraviolet (UV) radiation from sunlight. This reduces its efficacy as a biopesticide in the field and necessitates frequent respraying. UV damage to baculovirus biopesticides is detected by means of functional bioassays. However, bioassays do not give an indication of whether any structural damage has occurred that may contribute to functional loss. In this study, transmission electron microscopy (TEM) was used to observe damage to the OB and nucleocapsid (NC) of CrleGV-SA, following controlled UV irradiation in the laboratory to mimic field conditions. The resultant images were compared with images of non-irradiated CrleGV-SA virus. TEM images of irradiated CrleGV-SA samples revealed changes to the OB crystalline faceting, a reduction in the size of the OBs, and damage to the NC following UV exposure for 72 h.
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Affiliation(s)
- Patrick Mwanza
- Department of Human Physiology, Nelson Mandela University, Gqeberha 6001, South Africa
| | - Gill Dealtry
- Department of Human Physiology, Nelson Mandela University, Gqeberha 6001, South Africa
| | - Michael Lee
- Centre for HRTEM, Nelson Mandela University, Gqeberha 6001, South Africa
| | - Sean Moore
- Citrus Research International, Gqeberha 6070, South Africa
- Centre for Biological Control, Department of Zoology and Entomology, Rhodes University, Makhanda 6139, South Africa
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10
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Kojima M, Abe S, Furuta T, Tran DP, Hirata K, Yamashita K, Hishikawa Y, Kitao A, Ueno T. Engineering of an in-cell protein crystal for fastening a metastable conformation of a target miniprotein. Biomater Sci 2023; 11:1350-1357. [PMID: 36594419 DOI: 10.1039/d2bm01759h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Protein crystals can be utilized as porous scaffolds to capture exogenous molecules. Immobilization of target proteins using protein crystals is expected to facilitate X-ray structure analysis of proteins that are difficult to be crystallized. One of the advantages of scaffold-assisted structure determination is the analysis of metastable structures that are not observed in solution. However, efforts to fix target proteins within the pores of scaffold protein crystals have been limited due to the lack of strategies to control protein-protein interactions formed in the crystals. In this study, we analyze the metastable structure of the miniprotein, CLN025, which forms a β-hairpin structure in solution, using a polyhedra crystal (PhC), an in-cell protein crystal. CLN025 is successfully fixed within the PhC scaffold by replacing the original loop region. X-ray crystal structure analysis and molecular dynamics (MD) simulation reveal that CLN025 is fixed as a helical structure in a metastable state by non-covalent interactions in the scaffold crystal. These results indicate that modulation of intermolecular interactions can trap various protein conformations in the engineered PhC and provides a new strategy for scaffold-assisted structure determination.
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Affiliation(s)
- Mariko Kojima
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama 226-8501, Japan.
| | - Satoshi Abe
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama 226-8501, Japan.
| | - Tadaomi Furuta
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama 226-8501, Japan.
| | - Duy Phuoc Tran
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama 226-8501, Japan.
| | - Kunio Hirata
- SR Life Science Instrumentation Unit, RIKEN/SPring-8 Center, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan
| | - Keitaro Yamashita
- SR Life Science Instrumentation Unit, RIKEN/SPring-8 Center, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.,MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Yuki Hishikawa
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama 226-8501, Japan.
| | - Akio Kitao
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama 226-8501, Japan.
| | - Takafumi Ueno
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama 226-8501, Japan. .,International Research Frontiers Initiative (IRFI), Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama 226-8501, Japan
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11
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Silva LA, Camargo BR, Araújo AC, Batista TL, Ribeiro BM, Ardisson-Araújo DMP. Easily purified baculovirus/insect-system-expressed recombinant hepatitis B virus surface antigen fused to the N- or C-terminus of polyhedrin. Arch Virol 2021; 167:345-354. [PMID: 34839419 DOI: 10.1007/s00705-021-05305-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 10/05/2021] [Indexed: 11/27/2022]
Abstract
Baculoviruses are circular double-stranded DNA viruses that infect insects and are widely used as the baculoviral expression vectors (BEVs), which provide a eukaryotic milieu for heterologous expression. The most frequently used vector is based on Autographa californica multiple nucleopolyhedrovirus (AcMNPV). However, purification of recombinant proteins produced using BEVs is laborious, time-consuming, and often expensive. Numerous strategies have been explored to facilitate purification of heterologous proteins, such as fusion with occlusion body (OBs)-forming proteins like polyhedrin (Polh). Baculoviruses produce OBs in the late stages of infection to protect the virion in the cellular environment, and the main protein responsible for OB formation is Polh. In this study, we investigated the effect of fusing the gene that encodes the surface antigen (S-HBsAg) of hepatitis B virus (HBV) to either the N- or C-terminus of the AcMNPV Polh. The production of recombinant viruses and recombinant proteins was confirmed, and the ability to form chimeric S-HBsAg-containing OBs was accessed by light and scanning electron microscopy of infected cells. The fusion was found to affect the shape and size of the OBs when compared to wild-type OBs, with the N-terminal fusion producing less-amorphous OBs than the C-terminal construct. In addition, the N-terminal construct gave higher levels of expression than the C-terminal construct. Quantitative and qualitative immunoassays with human serum or plasma antibodies against HBsAg showed that the two forms of the antigen reacted differently. Although both reacted with the antibody, the N-terminal fusion protein reacted with more sensitivity (2.27-fold) and is therefore more suitable for quantitative assays than the C-terminal version. In summary, the BEVs represents a promising tool for the production of reagents for the diagnosis of HBV infection.
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Affiliation(s)
- Leonardo A Silva
- Laboratory of Baculovirus, Cell Biology Department, University of Brasilia, Brasília, DF, 70910-900, Brazil
| | - Brenda R Camargo
- Laboratory of Baculovirus, Cell Biology Department, University of Brasilia, Brasília, DF, 70910-900, Brazil
| | - Ana Carolina Araújo
- Laboratory of Baculovirus, Cell Biology Department, University of Brasilia, Brasília, DF, 70910-900, Brazil
| | - Taylice Leonel Batista
- Laboratory of Insect Virology, Cell Biology Department, University of Brasília, Brasília, DF, 70910900, Brazil
| | - Bergmann M Ribeiro
- Laboratory of Baculovirus, Cell Biology Department, University of Brasilia, Brasília, DF, 70910-900, Brazil.
| | - Daniel M P Ardisson-Araújo
- Laboratory of Baculovirus, Cell Biology Department, University of Brasilia, Brasília, DF, 70910-900, Brazil.
- Laboratory of Insect Virology, Cell Biology Department, University of Brasília, Brasília, DF, 70910900, Brazil.
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12
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Tetreau G, Andreeva EA, Banneville AS, De Zitter E, Colletier JP. Can (We Make) Bacillus thuringiensis Crystallize More Than Its Toxins? Toxins (Basel) 2021; 13:toxins13070441. [PMID: 34206749 PMCID: PMC8309801 DOI: 10.3390/toxins13070441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 06/22/2021] [Accepted: 06/24/2021] [Indexed: 11/16/2022] Open
Abstract
The development of finely tuned and reliable crystallization processes to obtain crystalline formulations of proteins has received growing interest from different scientific fields, including toxinology and structural biology, as well as from industry, notably for biotechnological and medical applications. As a natural crystal-making bacterium, Bacillus thuringiensis (Bt) has evolved through millions of years to produce hundreds of highly structurally diverse pesticidal proteins as micrometer-sized crystals. The long-term stability of Bt protein crystals in aqueous environments and their specific and controlled dissolution are characteristics that are particularly sought after. In this article, we explore whether the crystallization machinery of Bt can be hijacked as a means to produce (micro)crystalline formulations of proteins for three different applications: (i) to develop new bioinsecticidal formulations based on rationally improved crystalline toxins, (ii) to functionalize crystals with specific characteristics for biotechnological and medical applications, and (iii) to produce microcrystals of custom proteins for structural biology. By developing the needs of these different fields to figure out if and how Bt could meet each specific requirement, we discuss the already published and/or patented attempts and provide guidelines for future investigations in some underexplored yet promising domains.
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13
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Abe S, Pham TT, Negishi H, Yamashita K, Hirata K, Ueno T. Design of an In‐Cell Protein Crystal for the Environmentally Responsive Construction of a Supramolecular Filament. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Satoshi Abe
- School of Life Science and Technology Tokyo Institute of Technology Nagatsuta 4259-B-55, Midori-ku Yokohama 226-8501 Japan
| | - Thuc Toan Pham
- School of Life Science and Technology Tokyo Institute of Technology Nagatsuta 4259-B-55, Midori-ku Yokohama 226-8501 Japan
| | - Hashiru Negishi
- School of Life Science and Technology Tokyo Institute of Technology Nagatsuta 4259-B-55, Midori-ku Yokohama 226-8501 Japan
| | - Keitaro Yamashita
- SR Life Science Instrumentation Unit RIKEN/SPring-8 RIKEN/SPring-8 Center 1-1-1, Kouto, Sayo-cho Sayo-gun Hyogo 679-5148 Japan
| | - Kunio Hirata
- SR Life Science Instrumentation Unit RIKEN/SPring-8 RIKEN/SPring-8 Center 1-1-1, Kouto, Sayo-cho Sayo-gun Hyogo 679-5148 Japan
| | - Takafumi Ueno
- School of Life Science and Technology Tokyo Institute of Technology Nagatsuta 4259-B-55, Midori-ku Yokohama 226-8501 Japan
- Tokyo Tech World Research Hub Initiative (WRHI) Tokyo Institute of Technology Japan
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14
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Abe S, Pham TT, Negishi H, Yamashita K, Hirata K, Ueno T. Design of an In‐Cell Protein Crystal for the Environmentally Responsive Construction of a Supramolecular Filament. Angew Chem Int Ed Engl 2021; 60:12341-12345. [DOI: 10.1002/anie.202102039] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/17/2021] [Indexed: 12/20/2022]
Affiliation(s)
- Satoshi Abe
- School of Life Science and Technology Tokyo Institute of Technology Nagatsuta 4259-B-55, Midori-ku Yokohama 226-8501 Japan
| | - Thuc Toan Pham
- School of Life Science and Technology Tokyo Institute of Technology Nagatsuta 4259-B-55, Midori-ku Yokohama 226-8501 Japan
| | - Hashiru Negishi
- School of Life Science and Technology Tokyo Institute of Technology Nagatsuta 4259-B-55, Midori-ku Yokohama 226-8501 Japan
| | - Keitaro Yamashita
- SR Life Science Instrumentation Unit RIKEN/SPring-8 RIKEN/SPring-8 Center 1-1-1, Kouto, Sayo-cho Sayo-gun Hyogo 679-5148 Japan
| | - Kunio Hirata
- SR Life Science Instrumentation Unit RIKEN/SPring-8 RIKEN/SPring-8 Center 1-1-1, Kouto, Sayo-cho Sayo-gun Hyogo 679-5148 Japan
| | - Takafumi Ueno
- School of Life Science and Technology Tokyo Institute of Technology Nagatsuta 4259-B-55, Midori-ku Yokohama 226-8501 Japan
- Tokyo Tech World Research Hub Initiative (WRHI) Tokyo Institute of Technology Japan
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15
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Kokusho R, Katsuma S. Loss of p24 from the Bombyx mori nucleopolyhedrovirus genome results in the formation of cuboidal occlusion bodies. Virology 2021; 559:173-181. [PMID: 33930820 DOI: 10.1016/j.virol.2021.03.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 11/30/2022]
Abstract
Some insect viruses produce the occlusion body (OB), a large crystalline particle comprising a viral protein that occludes virions to protect them from harsh environments. The shapes and sizes of OBs are diverse depending on baculovirus species, but the detailed molecular mechanism determining them has yet to be totally clarified yet. Here we generated Bombyx mori nucleopolyhedrovirus (BmNPV) mutants of the p24 gene that encodes a viral capsid protein and found that p24-mutated BmNPVs produced cuboidal OBs with a slightly larger size than typical truncated octahedral OBs produced by wild-type BmNPVs. Meanwhile, p24 disruption has no significant impact on progeny virus production and viral pathogenicity. In addition, we experimentally demonstrated that a single amino acid substitution found in the P24 protein of the BmNPV Cubic isolate caused cuboidal OB production. These results suggest that p24 has a crucial role in generating the typical shape of OBs.
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Affiliation(s)
- Ryuhei Kokusho
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan; Division of Life Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan.
| | - Susumu Katsuma
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
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16
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Tang Y, Saul J, Nagaratnam N, Martin-Garcia JM, Fromme P, Qiu J, LaBaer J. Construction of gateway-compatible baculovirus expression vectors for high-throughput protein expression and in vivo microcrystal screening. Sci Rep 2020; 10:13323. [PMID: 32770037 PMCID: PMC7414197 DOI: 10.1038/s41598-020-70163-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 07/20/2020] [Indexed: 12/14/2022] Open
Abstract
Baculovirus mediated-insect cell expression systems have been widely used for producing heterogeneous proteins. However, to date, there is still the lack of an easy-to-manipulate system that enables the high-throughput protein characterization in insect cells by taking advantage of large existing Gateway clone libraries. To resolve this limitation, we have constructed a suite of Gateway-compatible pIEx-derived baculovirus expression vectors that allow the rapid and cost-effective construction of expression clones for mass parallel protein expression in insect cells. This vector collection also supports the attachment of a variety of fusion tags to target proteins to meet the needs for different research applications. We first demonstrated the utility of these vectors for protein expression and purification using a set of 40 target proteins of various sizes, cellular localizations and host organisms. We then established a scalable pipeline coupled with the SONICC and TEM techniques to screen for microcrystal formation within living insect cells. Using this pipeline, we successfully identified microcrystals for ~ 16% of the tested protein set, which can be potentially used for structure elucidation by X-ray crystallography. In summary, we have established a versatile pipeline enabling parallel gene cloning, protein expression and purification, and in vivo microcrystal screening for structural studies.
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Affiliation(s)
- Yanyang Tang
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, AZ, 85281, USA
| | - Justin Saul
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, AZ, 85281, USA
| | - Nirupa Nagaratnam
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85281, USA
| | - Jose M Martin-Garcia
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85281, USA
| | - Petra Fromme
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ, 85281, USA
| | - Ji Qiu
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, AZ, 85281, USA.
| | - Joshua LaBaer
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA.
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute, Arizona State University, Tempe, AZ, 85281, USA.
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17
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Thompson MC, Yeates TO, Rodriguez JA. Advances in methods for atomic resolution macromolecular structure determination. F1000Res 2020; 9:F1000 Faculty Rev-667. [PMID: 32676184 PMCID: PMC7333361 DOI: 10.12688/f1000research.25097.1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/25/2020] [Indexed: 12/13/2022] Open
Abstract
Recent technical advances have dramatically increased the power and scope of structural biology. New developments in high-resolution cryo-electron microscopy, serial X-ray crystallography, and electron diffraction have been especially transformative. Here we highlight some of the latest advances and current challenges at the frontiers of atomic resolution methods for elucidating the structures and dynamical properties of macromolecules and their complexes.
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Affiliation(s)
- Michael C. Thompson
- Department of Chemistry and Chemical Biology, University of California, Merced, CA, USA
| | - Todd O. Yeates
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA, USA
| | - Jose A. Rodriguez
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA, USA
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18
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Cruz-Reséndiz A, Zepeda-Cervantes J, Sampieri A, Bastián-Eugenio C, Acero G, Sánchez-Betancourt JI, Gevorkian G, Vaca L. A self-aggregating peptide: implications for the development of thermostable vaccine candidates. BMC Biotechnol 2020; 20:1. [PMID: 31959159 PMCID: PMC6971912 DOI: 10.1186/s12896-019-0592-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 12/06/2019] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The use of biomaterials has been expanded to improve the characteristics of vaccines. Recently we have identified that the peptide PH(1-110) from polyhedrin self-aggregates and incorporates foreign proteins to form particles. We have proposed that this peptide can be used as an antigen carrying system for vaccines. However, the immune response generated by the antigen fused to the peptide has not been fully characterized. In addition, the adjuvant effect and thermostability of the particles has not been evaluated. RESULTS In the present study we demonstrate the use of a system developed to generate nano and microparticles carrying as a fusion protein peptides or proteins of interest to be used as vaccines. These particles are purified easily by centrifugation. Immunization of animals with the particles in the absence of adjuvant result in a robust and long-lasting immune response. Proteins contained inside the particles are maintained for over 1 year at ambient temperature, preserving their immunological properties. CONCLUSION The rapid and efficient production of the particles in addition to the robust immune response they generate position this system as an excellent method for the rapid response against emerging diseases. The thermostability conferred by the particle system facilitates the distribution of the vaccines in developing countries or areas with no electricity.
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Affiliation(s)
- Adolfo Cruz-Reséndiz
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, CDMX 04510, Mexico City, Mexico
| | - Jesús Zepeda-Cervantes
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, CDMX 04510, Mexico City, Mexico
| | - Alicia Sampieri
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, CDMX 04510, Mexico City, Mexico
| | - Carlos Bastián-Eugenio
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, CDMX 04510, Mexico City, Mexico
| | - Gonzalo Acero
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, CDMX 04510, Mexico City, Mexico
| | - J Iván Sánchez-Betancourt
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, CDMX 04510, Mexico City, Mexico
| | - Goar Gevorkian
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, CDMX 04510, Mexico City, Mexico
| | - Luis Vaca
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, CDMX 04510, Mexico City, Mexico. .,Department of Physiology and Biophysics, University of Washington School of Medicine, Seattle, WA, 98124, USA.
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19
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Fabre ML, Masson T, Haase S, Ferrelli ML, Romanowski V. A simplified strategy to package foreign proteins into baculovirus occlusion bodies without engineering the viral genome. J Biotechnol 2020; 307:175-181. [PMID: 31715205 DOI: 10.1016/j.jbiotec.2019.10.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 10/08/2019] [Accepted: 10/26/2019] [Indexed: 11/25/2022]
Abstract
Polyhedron envelope protein (PEP) is the major component of the calyx that surrounds the baculovirus occlusion body (OB). PEP has been associated with the stabilization and resistance of polyhedra in the environment. Due to the abundant levels of PEP in OBs, we decided to use this protein as a fusion partner to redirect foreign proteins to baculovirus polyhedra. In this study we developed a strategy that involves the generation of a monoclonal transformed insect cell line expressing a protein of interest fused to the the Anticarsia gemmatalis multiple nucleopolyhedrovirus (AgMNPV) N-terminus of PEP that enables the packaging of foreign proteins into the OBs without generating a recombinant baculovirus. This proved to be an efficient platform that could be exploited to improve wild type baculovirus for their use as bioinsecticides without facing the concerns of releasing genetically modified DNA to the environment and bypassing the associated regulatory issues. We demonstrated, using immunological, proteomic and microscopy techniques, that the envelope of AgMNPV OBs can effectively trap chimeric proteins in an infected insect cell line expressing AgMNPV PEP fused to the enhanced green fluorescent protein (eGFP). Furthermore, packaging of chimeric PEP also took place with heterologous OBs such as those of Autographa californica multiple nucleopolyhedrovirus (AcMNPV), another group I alphabaculovirus.
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Affiliation(s)
- María Laura Fabre
- Instituto de Biotecnología y Biología Molecular (IBBM, UNLP-CONICET), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Tomás Masson
- Instituto de Biotecnología y Biología Molecular (IBBM, UNLP-CONICET), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Santiago Haase
- Instituto de Biotecnología y Biología Molecular (IBBM, UNLP-CONICET), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - María Leticia Ferrelli
- Instituto de Biotecnología y Biología Molecular (IBBM, UNLP-CONICET), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Víctor Romanowski
- Instituto de Biotecnología y Biología Molecular (IBBM, UNLP-CONICET), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina.
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20
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Mudogo CN, Falke S, Brognaro H, Duszenko M, Betzel C. Protein phase separation and determinants of in cell crystallization. Traffic 2019; 21:220-230. [DOI: 10.1111/tra.12711] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 10/21/2019] [Accepted: 10/27/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Celestin N. Mudogo
- Laboratory for Structural Biology of Infection and InflammationInstitute of Biochemistry and Molecular Biology, University of Hamburg Hamburg Germany
- Department of Basic Sciences, School of MedicineUniversity of Kinshasa Kinshasa Democratic Republic of Congo
| | - Sven Falke
- Laboratory for Structural Biology of Infection and InflammationInstitute of Biochemistry and Molecular Biology, University of Hamburg Hamburg Germany
| | - Hévila Brognaro
- Laboratory for Structural Biology of Infection and InflammationInstitute of Biochemistry and Molecular Biology, University of Hamburg Hamburg Germany
- Centre for Free‐Electron‐Laser Science Hamburg Germany
| | - Michael Duszenko
- Institute of Neurophysiology, University of Tübingen Tübingen Germany
| | - Christian Betzel
- Laboratory for Structural Biology of Infection and InflammationInstitute of Biochemistry and Molecular Biology, University of Hamburg Hamburg Germany
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21
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Yuasa H, Kotani E, Mori H, Takaki K. New method for immobilising diverse proteins onto cubic micro-protein polyhedrin crystals. Protein Expr Purif 2019; 167:105531. [PMID: 31734266 DOI: 10.1016/j.pep.2019.105531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 10/28/2019] [Accepted: 11/07/2019] [Indexed: 11/29/2022]
Abstract
Cypovirus is an insect virus that is encapsulated in stable cubic protein crystals composed of polyhedrin protein produced in virus-infected cells. Molecular technology developed over the last decade is now able to immobilise proteins of interest on polyhedrin crystals. Modified polyhedrin crystals can be used in cell cultures for implantation in animals and vaccines, among other applications. However, this technique does not work for some proteins. Here, we developed and tested an alternative approach for immobilising foreign proteins in polyhedrin crystals using a linker method; diverse proteins, such as fluorescent proteins, enzymes, antibodies, and streptavidin were successfully contained. The immobilised antibodies retained their binding activity on filter paper, implying their potential for new immunochromatography applications. Moreover, this immobilisation method allows enzymes to be collected from one reaction reagent and transferred to another reagent. These results demonstrate the potential of this immobilisation method and the likelihood of expanding the applications of polyhedrin crystals using this approach.
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Affiliation(s)
- Haruna Yuasa
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan.
| | - Eiji Kotani
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan.
| | - Hajime Mori
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan.
| | - Keiko Takaki
- Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto, 606-8585, Japan.
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22
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Coulibaly F. Polyhedra, spindles, phage nucleus and pyramids: Structural biology of viral superstructures. Adv Virus Res 2019; 105:275-335. [PMID: 31522707 DOI: 10.1016/bs.aivir.2019.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Viral infection causes comprehensive rearrangements of the cell that reflect as much host defense mechanisms as virus-induced structures assembled to facilitate infection. Regardless of their pro- or antiviral role, large intracellular structures are readily detectable by microscopy and often provide a signature characteristic of a specific viral infection. The structural features and localization of these assemblies have thus been commonly used for the diagnostic and classification of viruses since the early days of virology. More recently, characterization of viral superstructures using molecular and structural approaches have revealed very diverse organizations and roles, ranging from dynamic viral factories behaving like liquid organelles to ultra-stable crystals embedding and protecting virions. This chapter reviews the structures, functions and biotechnological applications of virus-induced superstructures with a focus on assemblies that have a regular organization, for which detailed structural descriptions are available. Examples span viruses infecting all domains of life including the assembly of virions into crystalline arrays in eukaryotic and bacterial viruses, nucleus-like compartments involved in the replication of large bacteriophages, and pyramid-like structures mediating the egress of archaeal viruses. Among these superstructures, high-resolution structures are available for crystalline objects produced by insect viruses: viral polyhedra which function as the infectious form of occluded viruses, and spindles which are potent virulence factors of entomopoxviruses. In turn, some of these highly symmetrical objects have been used to develop and validate advanced structural approaches, pushing the boundary of structural biology.
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Affiliation(s)
- Fasséli Coulibaly
- Infection & Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
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23
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The cysteine-rich region of a baculovirus VP91 protein contributes to the morphogenesis of occlusion bodies. Virology 2019; 535:144-153. [PMID: 31302508 DOI: 10.1016/j.virol.2019.06.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 06/26/2019] [Indexed: 11/21/2022]
Abstract
The baculovirus core gene vp91 has been reported to be essential for nucleocapsid assembly and oral infection. Here, we studied the function of vp91 by analyzing its homologue, ha76, in Helicoverpa armigera nucleopolyhedrovirus (HearNPV). HA76 was expressed at the late stage of HearNPV infection; deletion of ha76 showed that the gene is required for budded virus production. A series of recombinants with truncated ha76 was constructed and analyzed in vitro and in vivo. The results showed that the region encoding the C-terminus of HA76 was essential for nucleocapsid assembly, whereas the N-terminal cysteine-rich region was responsible for oral infection. Electron microscope analyses further showed that the cysteine-rich region contributed to morphogenesis of occlusion bodies (OBs), with amino acids 136-223 of HA76 being critical for this function. The results revealed a novel function of VP91 and suggested that the impact on OB morphogenesis is partially related to oral infectivity.
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24
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Simultaneous induction of distinct protein phase separation events in multiple subcellular compartments of a single cell. Exp Cell Res 2019; 379:92-109. [DOI: 10.1016/j.yexcr.2019.03.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 02/18/2019] [Accepted: 03/05/2019] [Indexed: 01/31/2023]
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25
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Cell-line-dependent crystal morphology and sublocalization of the Thyrinteina arnobia cypovirus polyhedrin expressed from a recombinant baculovirus. Arch Virol 2019; 164:1677-1682. [DOI: 10.1007/s00705-019-04214-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 02/21/2019] [Indexed: 01/30/2023]
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26
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Schönherr R, Rudolph JM, Redecke L. Protein crystallization in living cells. Biol Chem 2019; 399:751-772. [PMID: 29894295 DOI: 10.1515/hsz-2018-0158] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 05/07/2018] [Indexed: 11/15/2022]
Abstract
Protein crystallization in living cells has been observed surprisingly often as a native assembly process during the past decades, and emerging evidence indicates that this phenomenon is also accessible for recombinant proteins. But only recently the advent of high-brilliance synchrotron sources, X-ray free-electron lasers, and improved serial data collection strategies has allowed the use of these micrometer-sized crystals for structural biology. Thus, in cellulo crystallization could offer exciting new possibilities for proteins that do not crystallize applying conventional approaches. In this review, we comprehensively summarize the current knowledge of intracellular protein crystallization. This includes an overview of the cellular functions, the physical properties, and, if known, the mode of regulation of native in cellulo crystal formation, complemented with a discussion of the reported crystallization events of recombinant proteins and the current method developments to successfully collect X-ray diffraction data from in cellulo crystals. Although the intracellular protein self-assembly mechanisms are still poorly understood, regulatory differences between native in cellulo crystallization linked to a specific function and accidently crystallizing proteins, either disease associated or recombinantly introduced, become evident. These insights are important to systematically exploit living cells as protein crystallization chambers in the future.
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Affiliation(s)
- Robert Schönherr
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, D-23562 Lübeck, Germany.,Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, D-22607 Hamburg, Germany
| | - Janine Mia Rudolph
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, D-23562 Lübeck, Germany.,Center for Free-Electron Laser Science (CFEL), DESY, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Lars Redecke
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, D-23562 Lübeck, Germany.,Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, D-22607 Hamburg, Germany
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27
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Banerjee S, Montaville P, Chavas LMG, Ramaswamy S. The New Era of Microcrystallography. J Indian Inst Sci 2018. [DOI: 10.1007/s41745-018-0086-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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28
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López MG, Diez M, Alfonso V, Taboga O. Biotechnological applications of occlusion bodies of Baculoviruses. Appl Microbiol Biotechnol 2018; 102:6765-6774. [DOI: 10.1007/s00253-018-9130-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 05/21/2018] [Accepted: 05/22/2018] [Indexed: 11/29/2022]
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29
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Negishi H, Abe S, Yamashita K, Hirata K, Niwase K, Boudes M, Coulibaly F, Mori H, Ueno T. Supramolecular protein cages constructed from a crystalline protein matrix. Chem Commun (Camb) 2018; 54:1988-1991. [PMID: 29405208 DOI: 10.1039/c7cc08689j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Protein crystals are formed via ordered arrangements of proteins, which assemble to form supramolecular structures. Here, we show a method for the assembly of supramolecular protein cages within a crystalline environment. The cages are stabilized by covalent cross-linking allowing their release via dissolution of the crystal. The high stability of the desiccated protein crystals allows cages to be constructed.
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Affiliation(s)
- Hashiru Negishi
- School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.
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30
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Abe S, Maity B, Ueno T. Design of a confined environment using protein cages and crystals for the development of biohybrid materials. Chem Commun (Camb) 2018; 52:6496-512. [PMID: 27032539 DOI: 10.1039/c6cc01355d] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
There is growing interest in the design of protein assemblies for use in materials science and bionanotechnology. Protein assemblies, such as cages and crystalline protein structures, provide confined chemical environments that allow immobilization of metal complexes, nanomaterials, and proteins by metal coordination, assembly/disassembly reactions, genetic manipulation and crystallization methods. Protein assembly composites can be used to prepare hybrid materials with catalytic, magnetic and optical properties for cellular applications due to their high stability, solubility and biocompatibility. In this feature article, we focus on the recent development of ferritin as the most promising molecular template protein cage and in vivo and in vitro engineering of protein crystals as solid protein materials with functional properties.
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Affiliation(s)
- Satoshi Abe
- Department of Biomolecular Engineering, Graduate School of Bioscience and Biotechonology, Tokyo Institute of Techonology, B-55, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.
| | - Basudev Maity
- Department of Biomolecular Engineering, Graduate School of Bioscience and Biotechonology, Tokyo Institute of Techonology, B-55, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.
| | - Takafumi Ueno
- Department of Biomolecular Engineering, Graduate School of Bioscience and Biotechonology, Tokyo Institute of Techonology, B-55, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan.
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31
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López MG, Pallarés HM, Alfonso V, Carmona SJ, Farber M, Taboga O, Wilkowsky SE. Novel biotechnological platform based on baculovirus occlusion bodies carrying Babesia bovis small antigenic peptides for the design of a diagnostic enzyme-linked immunosorbent assay (ELISA). Appl Microbiol Biotechnol 2017; 102:885-896. [PMID: 29177536 DOI: 10.1007/s00253-017-8662-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 11/15/2017] [Accepted: 11/16/2017] [Indexed: 11/28/2022]
Abstract
Baculoviruses are large DNA virus of insects principally employed in recombinant protein expression. Its ability to form occlusion bodies (OBs), which are composed mainly of polyhedrin protein (POLH), makes them biotechnologically attractive, as these crystals (polyhedra) can incorporate foreign peptides and can be easily isolated. On the other hand, peptide microarrays allow rapid and inexpensive high-throughput serological screening of new candidates to be incorporated to OBs. To integrate these 2 biotechnological approaches, we worked on Babesia bovis, one of the causative agents of bovine babesiosis. Current molecular diagnosis of infection with B. bovis includes enzyme-linked immunosorbent assay (ELISA) techniques, which use merozoite lysate obtained from infected bovine erythrocytes. However, it is important to produce recombinant antigens that replace the use of crude antigens. Here, we describe a new biotechnological platform for the design of indirect ELISAs based on 5 antigenic peptides of 15 amino acid residues of B. bovis (ApBb), selected from a peptide microarray and expressed as a fusion to POLH. An Sf9POLHE44G packaging cell line infected with recombinant baculoviruses carrying POLH-ApBb fusions yielded higher levels of chimeric polyhedra, highlighting the advantage of a trans-contribution of a mutant copy of polyhedrin. Finally, the use of dissolved recombinant polyhedra as antigens was successful in an ELISA assay, as B. bovis-positive sera recognized the fusion POLH-ApBb. Thus, the use of this platform resulted in a promising alternative for molecular diagnosis of relevant infectious diseases.
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Affiliation(s)
- M G López
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires, Argentina. .,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.
| | - H M Pallarés
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires, Argentina
| | - V Alfonso
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - S J Carmona
- Ludwig Cancer Research Center, Department of Fundamental Oncology, University of Lausanne, Epalinges, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - M Farber
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - O Taboga
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - S E Wilkowsky
- Instituto de Biotecnología, Instituto Nacional de Tecnología Agropecuaria (INTA), Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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32
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Three Conserved Regions in Baculovirus Sulfhydryl Oxidase P33 Are Critical for Enzymatic Activity and Function. J Virol 2017; 91:JVI.01158-17. [PMID: 28904203 PMCID: PMC5686738 DOI: 10.1128/jvi.01158-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 08/30/2017] [Indexed: 01/07/2023] Open
Abstract
Baculoviruses encode a conserved sulfhydryl oxidase, P33, which is necessary for budded virus (BV) production and multinucleocapsid occlusion-derived virus (ODV) formation. Here, the structural and functional relationship of P33 was revealed by X-ray crystallography, site-directed mutagenesis, and functional analysis. Based on crystallographic characterization and structural analysis, a series of P33 mutants within three conserved regions, i.e., the active site, the dimer interface, and the R127-E183 salt bridge, were constructed. In vitro experiments showed that mutations within the active site and dimer interface severely impaired the sulfhydryl oxidase activity of P33, while the mutations in the salt bridge had a relatively minor influence. Recombinant viruses containing mutated P33 were constructed and assayed in vivo Except for the active-site mutant AXXA, all other mutants produced infectious BVs, although certain mutants had a decreased BV production. The active-site mutant H114A, the dimer interface mutant H227D, and the salt bridge mutant R127A-E183A were further analyzed by electron microscopy and bioassays. The occlusion bodies (OBs) of mutants H114A and R127A-E183A had a ragged surface and contained mostly ODVs with a single nucleocapsid. The OBs of all three mutants contained lower numbers of ODVs and had a significantly reduced oral infectivity in comparison to control virus. Crystallographic analyses further revealed that all three regions may coordinate with one another to achieve optimal function of P33. Taken together, our data revealed that all the three conserved regions are involved in P33 activity and are crucial for virus morphogenesis and peroral infectivity.IMPORTANCE Sulfhydryl oxidase catalyzes disulfide bond formation of substrate proteins. P33, a baculovirus-encoded sulfhydryl oxidase, is different from other cellular and viral sulfhydryl oxidases, bearing unique features in tertiary and quaternary structure organizations. In this study, we found that three conserved regions, i.e., the active site, dimer interface, and the R127-E183 salt bridge, play important roles in the enzymatic activity and function of P33. Previous observations showed that deletion of p33 results in a total loss of budded virus (BV) production and in morphological changes in occlusion-derived virus (ODV). Our study revealed that certain P33 mutants lead to occlusion bodies (OBs) with a ragged surface, decreased embedded ODVs, and reduced oral infectivity. Interestingly, some P33 mutants with impaired ODV/OB still retained BV productivity, indicating that the impacts on BV and on ODV/OB are two distinctly different functions of P33, which are likely to be performed via different substrate proteins.
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33
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Boudes M, Garriga D, Coulibaly F. Microcrystallography of Protein Crystals and In Cellulo Diffraction. J Vis Exp 2017. [PMID: 28784967 DOI: 10.3791/55793] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The advent of high-quality microfocus beamlines at many synchrotron facilities has permitted the routine analysis of crystals smaller than 10 µm in their largest dimension, which used to represent a challenge. We present two alternative workflows for the structure determination of protein microcrystals by X-ray crystallography with a particular focus on crystals grown in vivo. The microcrystals are either extracted from cells by sonication and purified by differential centrifugation, or analyzed in cellulo after cell sorting by flow cytometry of crystal-containing cells. Optionally, purified crystals or crystal-containing cells are soaked in heavy atom solutions for experimental phasing. These samples are then prepared for diffraction experiments in a similar way by application onto a micromesh support and flash cooling in liquid nitrogen. We briefly describe and compare serial diffraction experiments of isolated microcrystals and crystal-containing cells using a microfocus synchrotron beamline to produce datasets suitable for phasing, model building and refinement. These workflows are exemplified with crystals of the Bombyx mori cypovirus 1 (BmCPV1) polyhedrin produced by infection of insect cells with a recombinant baculovirus. In this case study, in cellulo analysis is more efficient than analysis of purified crystals and yields a structure in ~8 days from expression to refinement.
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Affiliation(s)
- Marion Boudes
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University
| | - Damià Garriga
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University
| | - Fasséli Coulibaly
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University;
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34
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Improving Baculovirus Infectivity by Efficiently Embedding Enhancing Factors into Occlusion Bodies. Appl Environ Microbiol 2017; 83:AEM.00595-17. [PMID: 28500037 DOI: 10.1128/aem.00595-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Accepted: 05/02/2017] [Indexed: 11/20/2022] Open
Abstract
The relatively low infectivity of baculoviruses to their host larvae limits their use as insecticidal agents on a larger scale. In the present study, a novel strategy was developed to efficiently embed foreign proteins into Autographa californica multiple nucleopolyhedrovirus (AcMNPV) occlusion bodies (OBs) to achieve stable expression of foreign proteins and to improve viral infectivity. A recombinant AcMNPV bacmid was constructed by expressing the 150-amino-acid (aa) N-terminal segment of polyhedrin under the control of the p10 promoter and the remaining C-terminal 95-aa segment under the control of the polyhedrin promoter. The recombinant virus formed OBs in Spodoptera frugiperda 9 cells, in which the occlusion-derived viruses were embedded in a manner similar to that for wild-type AcMNPV. Next, the 95-aa polyhedrin C terminus was fused to enhanced green fluorescent protein, and the recombinant AcMNPV formed fluorescent green OBs and was stably passaged in vitro and in vivo The AcMNPV recombinants were further modified by fusing truncated Agrotis segetum granulovirus enhancin or truncated Cydia pomonella granulovirus ORF13 (GP37) to the C-terminal 95 aa of polyhedrin, and both recombinants were able to form normal OBs. Bioactivity assays indicated that the median lethal concentrations of these two AcMNPV recombinants were 3- to 5-fold lower than that of the control virus. These results suggest that embedding enhancing factors in baculovirus OBs by use of this novel technique may promote efficient and stable foreign protein expression and significantly improve baculovirus infectivity.IMPORTANCE Baculoviruses have been used as bioinsecticides for over 40 years, but their relatively low infectivity to their host larvae limits their use on a larger scale. It has been reported that it is possible to improve baculovirus infectivity by packaging enhancing factors within baculovirus occlusion bodies (OBs); however, so far, the packaging efficiency has been low. In this article, we describe a novel strategy for efficiently embedding foreign proteins into AcMNPV OBs by expressing N- and C-terminal (dimidiate) polyhedrin fragments (150 and 95 amino acids, respectively) as fusions to foreign proteins under the control of the p10 and polyhedrin promoters, respectively. When this strategy was used to embed an enhancing factor (enhancin or GP37) into the baculovirus OBs, 3- to 5-fold increases in baculoviral infectivity were observed. This novel strategy has the potential to create an efficient protein expression system and a highly efficient virus-based system for insecticide production in the future.
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35
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Morgado FDS, Ardisson-Araújo DMP, Ribeiro BM. Real-Time Expression Analysis of Selected Anticarsia gemmatalis multiple nucleopolyhedrovirus Gene Promoters during Infection of Permissive, Semipermissive and Nonpermissive Cell Lines. Viruses 2017; 9:E132. [PMID: 28587184 PMCID: PMC5490809 DOI: 10.3390/v9060132] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Revised: 05/22/2017] [Accepted: 05/24/2017] [Indexed: 12/03/2022] Open
Abstract
Baculovirus infection follows a transcriptionally controlled sequence of gene expression that occurs by activation of different viral gene promoter sequences during infection. This sequence of promoter activation may be disrupted by cellular defenses against viral infection, which might interfere with viral progeny formation. In this work, the activity of the ie1, gp64, lef-1, vp39, p6.9 and polh promoters of the Anticarsia gemmatalis multiple nucleopolyhedrovirus was assessed during infection of permissive, semipermissive and nonpermissive cell lines by a novel methodology that detects reporter protein luminescence in real-time. This technique allowed us to characterize in rich detail the AgMNPV promoters in permissive cell lines and revealed differential profiles of expression in cells with limited permissivity that correlate well with limitations in viral DNA replication. Semipermissive and nonpermissive cell lines presented delays and restrictions in late and very late promoter expression. Cells undergoing apoptosis did not inhibit late gene expression; however, viral progeny formation is severely affected. This work demonstrates the application of the real-time luminescence detection methodology and how the promoter expression profile may be used to diagnose cellular permissivity to baculovirus infection.
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Affiliation(s)
- Fabricio da Silva Morgado
- Laboratory of Baculovirus, Cell Biology Department, University of Brasília, 70910-900 Brasília-DF, Brazil.
| | - Daniel Mendes Pereira Ardisson-Araújo
- Laboratory of Insect Virology, Department of Biochemistry and Molecular Biology, Federal University of Santa Maria, 97105-900 Santa Maria-RS, Brazil.
| | - Bergmann Morais Ribeiro
- Laboratory of Baculovirus, Cell Biology Department, University of Brasília, 70910-900 Brasília-DF, Brazil.
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36
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Atomic structure of granulin determined from native nanocrystalline granulovirus using an X-ray free-electron laser. Proc Natl Acad Sci U S A 2017; 114:2247-2252. [PMID: 28202732 DOI: 10.1073/pnas.1609243114] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To understand how molecules function in biological systems, new methods are required to obtain atomic resolution structures from biological material under physiological conditions. Intense femtosecond-duration pulses from X-ray free-electron lasers (XFELs) can outrun most damage processes, vastly increasing the tolerable dose before the specimen is destroyed. This in turn allows structure determination from crystals much smaller and more radiation sensitive than previously considered possible, allowing data collection from room temperature structures and avoiding structural changes due to cooling. Regardless, high-resolution structures obtained from XFEL data mostly use crystals far larger than 1 μm3 in volume, whereas the X-ray beam is often attenuated to protect the detector from damage caused by intense Bragg spots. Here, we describe the 2 Å resolution structure of native nanocrystalline granulovirus occlusion bodies (OBs) that are less than 0.016 μm3 in volume using the full power of the Linac Coherent Light Source (LCLS) and a dose up to 1.3 GGy per crystal. The crystalline shell of granulovirus OBs consists, on average, of about 9,000 unit cells, representing the smallest protein crystals to yield a high-resolution structure by X-ray crystallography to date. The XFEL structure shows little to no evidence of radiation damage and is more complete than a model determined using synchrotron data from recombinantly produced, much larger, cryocooled granulovirus granulin microcrystals. Our measurements suggest that it should be possible, under ideal experimental conditions, to obtain data from protein crystals with only 100 unit cells in volume using currently available XFELs and suggest that single-molecule imaging of individual biomolecules could almost be within reach.
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Banerjee S, Coussens NP, Gallat FX, Sathyanarayanan N, Srikanth J, Yagi KJ, Gray JSS, Tobe SS, Stay B, Chavas LMG, Ramaswamy S. Structure of a heterogeneous, glycosylated, lipid-bound, in vivo-grown protein crystal at atomic resolution from the viviparous cockroach Diploptera punctata. IUCRJ 2016; 3:282-93. [PMID: 27437115 PMCID: PMC4937783 DOI: 10.1107/s2052252516008903] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 06/02/2016] [Indexed: 05/20/2023]
Abstract
Macromolecular crystals for X-ray diffraction studies are typically grown in vitro from pure and homogeneous samples; however, there are examples of protein crystals that have been identified in vivo. Recent developments in micro-crystallography techniques and the advent of X-ray free-electron lasers have allowed the determination of several protein structures from crystals grown in cellulo. Here, an atomic resolution (1.2 Å) crystal structure is reported of heterogeneous milk proteins grown inside a living organism in their functional niche. These in vivo-grown crystals were isolated from the midgut of an embryo within the only known viviparous cockroach, Diploptera punctata. The milk proteins crystallized in space group P1, and a structure was determined by anomalous dispersion from the native S atoms. The data revealed glycosylated proteins that adopt a lipocalin fold, bind lipids and organize to form a tightly packed crystalline lattice. A single crystal is estimated to contain more than three times the energy of an equivalent mass of dairy milk. This unique storage form of nourishment for developing embryos allows access to a constant supply of complete nutrients. Notably, the crystalline cockroach-milk proteins are highly heterogeneous with respect to amino-acid sequence, glycosylation and bound fatty-acid composition. These data present a unique example of protein heterogeneity within a single in vivo-grown crystal of a natural protein in its native environment at atomic resolution.
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Affiliation(s)
- Sanchari Banerjee
- Institute of Stem Cell Biology and Regenerative Medicine, Bellary Road, GKVK Campus, Bangalore, Karnataka 560 065, India
| | - Nathan P. Coussens
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - François-Xavier Gallat
- Structural Biology Research Centre, High Energy Accelerator Research Organization, Tsukuba, Ibaraki 305-0801, Japan
| | - Nitish Sathyanarayanan
- Institute of Stem Cell Biology and Regenerative Medicine, Bellary Road, GKVK Campus, Bangalore, Karnataka 560 065, India
| | - Jandhyam Srikanth
- Centre for Cellular and Molecular Platforms, Bellary Road, GKVK Campus, Bangalore, Karnataka 560 065, India
| | - Koichiro J. Yagi
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
| | - James S. S. Gray
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
- Bio-Research Products Inc., Cherry Street, North Liberty, IA 52317, USA
| | - Stephen S. Tobe
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
| | - Barbara Stay
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Leonard M. G. Chavas
- Structural Biology Research Centre, High Energy Accelerator Research Organization, Tsukuba, Ibaraki 305-0801, Japan
- Experimental Division, Synchrotron SOLEIL, BP 48, L’Orme des Merisiers, 91192 Gif-sur-Yvette, France
| | - Subramanian Ramaswamy
- Institute of Stem Cell Biology and Regenerative Medicine, Bellary Road, GKVK Campus, Bangalore, Karnataka 560 065, India
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
- Centre for Cellular and Molecular Platforms, Bellary Road, GKVK Campus, Bangalore, Karnataka 560 065, India
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Boudes M, Garriga D, Fryga A, Caradoc-Davies T, Coulibaly F. A pipeline for structure determination of in vivo-grown crystals using in cellulo diffraction. Acta Crystallogr D Struct Biol 2016; 72:576-85. [PMID: 27050136 PMCID: PMC4822565 DOI: 10.1107/s2059798316002369] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 02/08/2016] [Indexed: 11/10/2022] Open
Abstract
While structure determination from micrometre-sized crystals used to represent a challenge, serial X-ray crystallography on microfocus beamlines at synchrotron and free-electron laser facilities greatly facilitates this process today for microcrystals and nanocrystals. In addition to typical microcrystals of purified recombinant protein, these advances have enabled the analysis of microcrystals produced inside living cells. Here, a pipeline where crystals are grown in insect cells, sorted by flow cytometry and directly analysed by X-ray diffraction is presented and applied to in vivo-grown crystals of the recombinant CPV1 polyhedrin. When compared with the analysis of purified crystals, in cellulo diffraction produces data of better quality and a gain of ∼0.35 Å in resolution for comparable beamtime usage. Importantly, crystals within cells are readily derivatized with gold and iodine compounds through the cellular membrane. Using the multiple isomorphous replacement method, a near-complete model was autobuilt from 2.7 Å resolution data. Thus, in favourable cases, an in cellulo pipeline can replace the complete workflow of structure determination without compromising the quality of the resulting model. In addition to its efficiency, this approach maintains the protein in a cellular context throughout the analysis, which reduces the risk of disrupting transient or labile interactions in protein-protein or protein-ligand complexes.
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Affiliation(s)
- Marion Boudes
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Damià Garriga
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Andrew Fryga
- Faculty of Medicine, Nursing and Health Sciences, FlowCore, Monash University, Melbourne, VIC 3800, Australia
| | | | - Fasséli Coulibaly
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
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Sajjan DB, Hinchigeri SB. Structural Organization of Baculovirus Occlusion Bodies and Protective Role of Multilayered Polyhedron Envelope Protein. FOOD AND ENVIRONMENTAL VIROLOGY 2016; 8:86-100. [PMID: 26787118 DOI: 10.1007/s12560-016-9227-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 01/09/2016] [Indexed: 06/05/2023]
Abstract
Baculoviruses are the ingenious insect pathogens. Outside the host, baculovirus occlusion bodies (OB) provide stability to occlusion-derived viruses (ODV) embedded within. The OB is an organized structure, chiefly composed of proteins namely polyhedrin, polyhedron envelope protein (PEP) and P10. Currently, the structural organization of OB is poorly understood and the role of OB proteins in conferring the stability to ODV is unknown. Here we have shown that the assembly of polyhedrin unit cells into an OB is a rapid process; the PEP forms in multiple layers; the PEP layers predominantly contribute to ODV viability. Full-grown OBs (n = 36) were found to be 4.0 ± 1.0 µm in diameter and possessed a peculiar geometry of a truncated rhombic dodecahedron. The atomic force microscopy (AFM) study on the structure of OBs at different stages of growth in insect cells revealed polyhedrin assembly and thickness of PEP layers. The thickness of PEP layers at 53 h post-transfection (hpt) ranged from 56 to 80 nm. Mature PEP layers filled up approximately one third of the OB volume. The size of ODV nucleocapsid was found to be 433 ± 10 nm in length. The zeta potential and particle size distribution study of viruses revealed the protective role of PEP layers. The presence of a multilayered PEP confers a viable advantage to the baculoviruses compared to single-layered PEP. Thus, these findings may help in developing PEP layer-based biopolymers for protein-based nanodevices, nanoelectrodes and more stable biopesticides.
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Affiliation(s)
- Dayanand B Sajjan
- Department of Biochemistry, Karnatak University, Dharwad, Karnataka, 580 003, India
| | - Shivayogeppa B Hinchigeri
- Department of Biochemistry, Karnatak University, Dharwad, Karnataka, 580 003, India.
- REVA University, Rukmini Knowledge Park, Adminstrative Block, Kattigenahalli, Yelahanka, Bangalore, Karnataka, 560064, India.
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40
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Jakobi AJ, Passon DM, Knoops K, Stellato F, Liang M, White TA, Seine T, Messerschmidt M, Chapman HN, Wilmanns M. In cellulo serial crystallography of alcohol oxidase crystals inside yeast cells. IUCRJ 2016; 3:88-95. [PMID: 27006771 PMCID: PMC4775156 DOI: 10.1107/s2052252515022927] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/30/2015] [Indexed: 06/05/2023]
Abstract
The possibility of using femtosecond pulses from an X-ray free-electron laser to collect diffraction data from protein crystals formed in their native cellular organelle has been explored. X-ray diffraction of submicrometre-sized alcohol oxidase crystals formed in peroxisomes within cells of genetically modified variants of the methylotrophic yeast Hansenula polymorpha is reported and characterized. The observations are supported by synchrotron radiation-based powder diffraction data and electron microscopy. Based on these findings, the concept of in cellulo serial crystallography on protein targets imported into yeast peroxisomes without the need for protein purification as a requirement for subsequent crystallization is outlined.
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Affiliation(s)
- Arjen J. Jakobi
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory (EMBL), Notkestrasse 85, 22607 Hamburg, Germany
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Daniel M. Passon
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory (EMBL), Notkestrasse 85, 22607 Hamburg, Germany
| | - Kèvin Knoops
- Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Francesco Stellato
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Mengning Liang
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Thomas A. White
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Thomas Seine
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory (EMBL), Notkestrasse 85, 22607 Hamburg, Germany
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Marc Messerschmidt
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Henry N. Chapman
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
- Department of Physics, University of Hamburg, Luruper Chaussee 149, 22607 Hamburg, Germany
- Center for Ultrafast Imaging, Luruper Chaussee 149, 22607 Hamburg, Germany
| | - Matthias Wilmanns
- Hamburg Unit c/o DESY, European Molecular Biology Laboratory (EMBL), Notkestrasse 85, 22607 Hamburg, Germany
- University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany
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41
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Ji X, Axford D, Owen R, Evans G, Ginn HM, Sutton G, Stuart DI. Polyhedra structures and the evolution of the insect viruses. J Struct Biol 2015; 192:88-99. [PMID: 26291392 PMCID: PMC4597613 DOI: 10.1016/j.jsb.2015.08.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 08/07/2015] [Accepted: 08/17/2015] [Indexed: 01/07/2023]
Abstract
Polyhedra represent an ancient system used by a number of insect viruses to protect virions during long periods of environmental exposure. We present high resolution crystal structures of polyhedra for seven previously uncharacterised types of cypoviruses, four using ab initio selenomethionine phasing (two of these required over 100 selenomethionine crystals each). Approximately 80% of residues are structurally equivalent between all polyhedrins (pairwise rmsd ⩽ 1.5 Å), whilst pairwise sequence identities, based on structural alignment, are as little as 12%. These structures illustrate the effect of 400 million years of evolution on a system where the crystal lattice is the functionally conserved feature in the face of massive sequence variability. The conservation of crystal contacts is maintained across most of the molecular surface, except for a dispensable virus recognition domain. By spreading the contacts over so much of the protein surface the lattice remains robust in the face of many individual changes. Overall these unusual structural constraints seem to have skewed the molecule's evolution so that surface residues are almost as conserved as the internal residues.
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Affiliation(s)
- Xiaoyun Ji
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, Oxfordshire OX3 7BN, United Kingdom
| | - Danny Axford
- Diamond House, Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Robin Owen
- Diamond House, Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Gwyndaf Evans
- Diamond House, Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Helen M. Ginn
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, Oxfordshire OX3 7BN, United Kingdom
| | - Geoff Sutton
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, Oxfordshire OX3 7BN, United Kingdom
| | - David I. Stuart
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, Oxfordshire OX3 7BN, United Kingdom,Diamond House, Diamond Light Source, Harwell Science & Innovation Campus, Didcot, Oxfordshire OX11 0DE, United Kingdom,Corresponding author at: Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, Oxfordshire OX3 7BN, United Kingdom.Division of Structural BiologyThe Wellcome Trust Centre for Human GeneticsUniversity of OxfordRoosevelt DriveOxfordOxfordshireOX3 7BNUnited Kingdom
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42
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Evidence of a deep viral host switch event with beak and feather disease virus infection in rainbow bee-eaters (Merops ornatus). Sci Rep 2015; 5:14511. [PMID: 26411487 PMCID: PMC4585972 DOI: 10.1038/srep14511] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 09/02/2015] [Indexed: 11/27/2022] Open
Abstract
Since the characterization of psittacine beak and feather disease (PBFD) in 1984, a wide range of avian circoviruses have been discovered with varying pathogenic effects amongst a diverse range of avian hosts. Until recently these circovirus species were thought to be restricted to within avian Orders such as the Psittaciformes for beak and feather disease virus (BFDV) and Columbiformes for pigeon circovirus with little evidence of cross-family transmission or replication. We report evidence of a naturally occurring novel host switch event with self-limiting BFDV infection in a group of rainbow bee-eaters (Merops ornatus) a species of Coraciiformes unrelated to parrots and not previously known to be susceptible to any avian circovirus. The outbreak highlights important and unexpected aspects of disease emergence and host-switching pertinent to other situations when viruses might cross species boundaries as well as the potential of avian circoviruses to infect disparate host species.
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43
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Duszenko M, Redecke L, Mudogo CN, Sommer BP, Mogk S, Oberthuer D, Betzel C. In vivo protein crystallization in combination with highly brilliant radiation sources offers novel opportunities for the structural analysis of post-translationally modified eukaryotic proteins. Acta Crystallogr F Struct Biol Commun 2015; 71:929-37. [PMID: 26249677 PMCID: PMC4528919 DOI: 10.1107/s2053230x15011450] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 06/12/2015] [Indexed: 11/11/2022] Open
Abstract
During the last decade, the number of three-dimensional structures solved by X-ray crystallography has increased dramatically. By 2014, it had crossed the landmark of 100 000 biomolecular structures deposited in the Protein Data Bank. This tremendous increase in successfully crystallized proteins is primarily owing to improvements in cloning strategies, the automation of the crystallization process and new innovative approaches to monitor crystallization. However, these improvements are mainly restricted to soluble proteins, while the crystallization and structural analysis of membrane proteins or proteins that undergo major post-translational modifications remains challenging. In addition, the need for relatively large crystals for conventional X-ray crystallography usually prevents the analysis of dynamic processes within cells. Thus, the advent of high-brilliance synchrotron and X-ray free-electron laser (XFEL) sources and the establishment of serial crystallography (SFX) have opened new avenues in structural analysis using crystals that were formerly unusable. The successful structure elucidation of cathepsin B, accomplished by the use of microcrystals obtained by in vivo crystallization in baculovirus-infected Sf9 insect cells, clearly proved that crystals grown intracellularly are very well suited for X-ray analysis. Here, methods by which in vivo crystals can be obtained, isolated and used for structural analysis by novel highly brilliant XFEL and synchrotron-radiation sources are summarized and discussed.
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Affiliation(s)
- Michael Duszenko
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Strasse 4, 72076 Tübingen, Germany
| | - Lars Redecke
- Institute of Biochemistry, Center for Structural Biology and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany
| | - Celestin Nzanzu Mudogo
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Strasse 4, 72076 Tübingen, Germany
| | - Benjamin Philip Sommer
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Strasse 4, 72076 Tübingen, Germany
- Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Building 22a, Notkestrasse 85, 22607 Hamburg, Germany
| | - Stefan Mogk
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Strasse 4, 72076 Tübingen, Germany
| | - Dominik Oberthuer
- Center for Free-Electron Laser Science, Deutsches Elektronen Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg, Germany
| | - Christian Betzel
- Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Building 22a, Notkestrasse 85, 22607 Hamburg, Germany
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44
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Schönherr R, Klinge M, Rudolph JM, Fita K, Rehders D, Lübber F, Schneegans S, Majoul IV, Duszenko M, Betzel C, Brandariz-Nuñez A, Martinez-Costas J, Duden R, Redecke L. Real-time investigation of dynamic protein crystallization in living cells. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2015; 2:041712. [PMID: 26798811 PMCID: PMC4711630 DOI: 10.1063/1.4921591] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 05/05/2015] [Indexed: 05/21/2023]
Abstract
X-ray crystallography requires sufficiently large crystals to obtain structural insights at atomic resolution, routinely obtained in vitro by time-consuming screening. Recently, successful data collection was reported from protein microcrystals grown within living cells using highly brilliant free-electron laser and third-generation synchrotron radiation. Here, we analyzed in vivo crystal growth of firefly luciferase and Green Fluorescent Protein-tagged reovirus μNS by live-cell imaging, showing that dimensions of living cells did not limit crystal size. The crystallization process is highly dynamic and occurs in different cellular compartments. In vivo protein crystallization offers exciting new possibilities for proteins that do not form crystals in vitro.
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Affiliation(s)
- R Schönherr
- Institute of Biology, Center for Structural and Cell Biology in Medicine, University of Lübeck , Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - M Klinge
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck , Ratzeburger Allee 160, 23562 Lübeck, Germany
| | | | - K Fita
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck , Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - D Rehders
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck , Ratzeburger Allee 160, 23562 Lübeck, Germany
| | | | | | - I V Majoul
- Institute of Biology, Center for Structural and Cell Biology in Medicine, University of Lübeck , Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - M Duszenko
- Interfaculty Institute of Biochemistry, University of Tübingen , Hoppe-Seyler-Straβe 4, 72076 Tübingen, Germany
| | - C Betzel
- Institute of Biochemistry and Molecular Biology, University of Hamburg , c/o DESY, Notkestr. 85, 22603 Hamburg, Germany
| | - A Brandariz-Nuñez
- Department of Biochemistry and Molecular Biology, Centro de Investigación en Química Biológica y Materiales Moleculares (CIQUS), University Santiago de Compostela , 15782 Santiago de Compostela, Spain
| | - J Martinez-Costas
- Department of Biochemistry and Molecular Biology, Centro de Investigación en Química Biológica y Materiales Moleculares (CIQUS), University Santiago de Compostela , 15782 Santiago de Compostela, Spain
| | - R Duden
- Institute of Biology, Center for Structural and Cell Biology in Medicine, University of Lübeck , Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - L Redecke
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck , Ratzeburger Allee 160, 23562 Lübeck, Germany
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45
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Structural basis for the enhancement of virulence by viral spindles and their in vivo crystallization. Proc Natl Acad Sci U S A 2015; 112:3973-8. [PMID: 25787255 DOI: 10.1073/pnas.1418798112] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The great benefits that chemical pesticides have brought to agriculture are partly offset by widespread environmental damage to nontarget species and threats to human health. Microbial bioinsecticides are considered safe and highly specific alternatives but generally lack potency. Spindles produced by insect poxviruses are crystals of the fusolin protein that considerably boost not only the virulence of these viruses but also, in cofeeding experiments, the insecticidal activity of unrelated pathogens. However, the mechanisms by which spindles assemble into ultra-stable crystals and enhance virulence are unknown. Here we describe the structure of viral spindles determined by X-ray microcrystallography from in vivo crystals purified from infected insects. We found that a C-terminal molecular arm of fusolin mediates the assembly of a globular domain, which has the hallmarks of lytic polysaccharide monooxygenases of chitinovorous bacteria. Explaining their unique stability, a 3D network of disulfide bonds between fusolin dimers covalently crosslinks the entire crystalline matrix of spindles. However, upon ingestion by a new host, removal of the molecular arm abolishes this stabilizing network leading to the dissolution of spindles. The released monooxygenase domain is then free to disrupt the chitin-rich peritrophic matrix that protects insects against oral infections. The mode of action revealed here may guide the design of potent spindles as synergetic additives to bioinsecticides.
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46
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Sampieri A, Luz-Madrigal A, Zepeda J, Vaca L. Identification of fragments from Autographa californica polyhedrin protein essential for self-aggregation and exogenous protein incorporation. BMC BIOCHEMISTRY 2015; 16:5. [PMID: 25648249 PMCID: PMC4320575 DOI: 10.1186/s12858-015-0034-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 01/15/2015] [Indexed: 11/10/2022]
Abstract
BACKGROUND Baculoviruses are widely used for the production of recombinant proteins, biopesticides and as gene delivery systems. One of the viral forms called polyhedra has been recently exploited as a scaffold system to incorporate or encapsulate foreign proteins or peptide fragments. However, an efficient strategy for foreign protein incorporation has not been thoroughly studied. RESULTS Based on the crystal structure of polyhedrin, we conducted an in silico analysis of the baculovirus Autographa californica nucleopolyhedrovirus (AcMNPV) polyhedrin protein to select the minimum fragments of polyhedrin that could be incorporated into polyhedra. Using confocal and transmission electron microscopy we analyzed the expression and cellular localization of the different polyhedrin fragments fused to the green fluorescent protein (EGFP) used as reporter. The amino fragment 1-110 contains two repeats formed each of two β sheets followed by a α helix (amino acids 1-58 and 58-110) that are important for the formation and stability of polyhedra. These fragments 1-58, 58-110 and 1-110 could be incorporated into polyhedra. However, only fragments 1-110 and 58-110 can self-aggregate. CONCLUSIONS These results demonstrate that 58-110 is the minimum fragment that contributes to the assembly of the recombinant polyhedra via self-aggregation. This is the minimum sequence that can be used to efficiently incorporate foreign proteins into polyhedra.
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Affiliation(s)
- Alicia Sampieri
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad Universitaria, México, DF, 04510, México.
| | - Agustín Luz-Madrigal
- Department of Biology and Center for Tissue Regeneration and Engineering, University of Dayton (TREND), Dayton, OH, USA. .,Department of Biology, Miami University, Oxford, OH, USA.
| | - Jesus Zepeda
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad Universitaria, México, DF, 04510, México.
| | - Luis Vaca
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad Universitaria, México, DF, 04510, México.
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47
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Gallat FX, Matsugaki N, Coussens NP, Yagi KJ, Boudes M, Higashi T, Tsuji D, Tatano Y, Suzuki M, Mizohata E, Tono K, Joti Y, Kameshima T, Park J, Song C, Hatsui T, Yabashi M, Nango E, Itoh K, Coulibaly F, Tobe S, Ramaswamy S, Stay B, Iwata S, Chavas LMG. In vivo crystallography at X-ray free-electron lasers: the next generation of structural biology? Philos Trans R Soc Lond B Biol Sci 2015; 369:20130497. [PMID: 24914164 DOI: 10.1098/rstb.2013.0497] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The serendipitous discovery of the spontaneous growth of protein crystals inside cells has opened the field of crystallography to chemically unmodified samples directly available from their natural environment. On the one hand, through in vivo crystallography, protocols for protein crystal preparation can be highly simplified, although the technique suffers from difficulties in sampling, particularly in the extraction of the crystals from the cells partly due to their small sizes. On the other hand, the extremely intense X-ray pulses emerging from X-ray free-electron laser (XFEL) sources, along with the appearance of serial femtosecond crystallography (SFX) is a milestone for radiation damage-free protein structural studies but requires micrometre-size crystals. The combination of SFX with in vivo crystallography has the potential to boost the applicability of these techniques, eventually bringing the field to the point where in vitro sample manipulations will no longer be required, and direct imaging of the crystals from within the cells will be achievable. To fully appreciate the diverse aspects of sample characterization, handling and analysis, SFX experiments at the Japanese SPring-8 angstrom compact free-electron laser were scheduled on various types of in vivo grown crystals. The first experiments have demonstrated the feasibility of the approach and suggest that future in vivo crystallography applications at XFELs will be another alternative to nano-crystallography.
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Affiliation(s)
- François-Xavier Gallat
- Photon Factory, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Naohiro Matsugaki
- Photon Factory, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Nathan P Coussens
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, USA
| | - Koichiro J Yagi
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada M5S 3G5
| | - Marion Boudes
- Department of Biochemistry and Molecular Biology, Monash University, Building 76, Clayton, Victoria 3800, Australia
| | - Tetsuya Higashi
- Department of Medicinal Biotechnology, University of Tokushima, 1-78 Sho-machi Tokushima, Tokushima 770-8505, Japan
| | - Daisuke Tsuji
- Department of Medicinal Biotechnology, University of Tokushima, 1-78 Sho-machi Tokushima, Tokushima 770-8505, Japan
| | - Yutaka Tatano
- Deparment of Microbiology and Immunology, School of Medicine, Shimane University, Izumo, Shimane 693-8501, Japan
| | - Mamoru Suzuki
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Eiichi Mizohata
- Division of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kensuke Tono
- Japan Synchrotron Radiation Research Institute, Kouto 1-1-1, Sayo, Hyogo 679-5198, Japan
| | - Yasumasa Joti
- Japan Synchrotron Radiation Research Institute, Kouto 1-1-1, Sayo, Hyogo 679-5198, Japan
| | - Takashi Kameshima
- Japan Synchrotron Radiation Research Institute, Kouto 1-1-1, Sayo, Hyogo 679-5198, Japan
| | - Jaehyun Park
- RIKEN SPring-8 Center, Kouto 1-1-1, Sayo, Hyogo 679-5148, Japan
| | - Changyong Song
- RIKEN SPring-8 Center, Kouto 1-1-1, Sayo, Hyogo 679-5148, Japan
| | - Takaki Hatsui
- RIKEN SPring-8 Center, Kouto 1-1-1, Sayo, Hyogo 679-5148, Japan
| | - Makina Yabashi
- RIKEN SPring-8 Center, Kouto 1-1-1, Sayo, Hyogo 679-5148, Japan
| | - Eriko Nango
- RIKEN SPring-8 Center, Kouto 1-1-1, Sayo, Hyogo 679-5148, Japan
| | - Kohji Itoh
- Department of Medicinal Biotechnology, University of Tokushima, 1-78 Sho-machi Tokushima, Tokushima 770-8505, Japan
| | - Fasséli Coulibaly
- Department of Biochemistry and Molecular Biology, Monash University, Building 76, Clayton, Victoria 3800, Australia
| | - Stephen Tobe
- Department of Cell and Systems Biology, University of Toronto, Toronto, Canada M5S 3G5
| | - S Ramaswamy
- Institute for Stem Cell Biology and Regenerative Medicine, Bellary Road, Bangalore 560065, India
| | - Barbara Stay
- Department of Biology, University of Iowa, Iowa City, IA 52242, USA
| | - So Iwata
- RIKEN SPring-8 Center, Kouto 1-1-1, Sayo, Hyogo 679-5148, Japan
| | - Leonard M G Chavas
- Photon Factory, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan Center for Free-Electron Laser science, Notkestrasse 85, Building 99, Hamburg 22607, Germany
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48
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Gildea RJ, Waterman DG, Parkhurst JM, Axford D, Sutton G, Stuart DI, Sauter NK, Evans G, Winter G. New methods for indexing multi-lattice diffraction data. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:2652-66. [PMID: 25286849 PMCID: PMC4188007 DOI: 10.1107/s1399004714017039] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 07/23/2014] [Indexed: 11/10/2022]
Abstract
A new indexing method is presented which is capable of indexing multiple crystal lattices from narrow wedges of diffraction data. The method takes advantage of a simplification of Fourier transform-based methods that is applicable when the unit-cell dimensions are known a priori. The efficacy of this method is demonstrated with both semi-synthetic multi-lattice data and real multi-lattice data recorded from crystals of ∼1 µm in size, where it is shown that up to six lattices can be successfully indexed and subsequently integrated from a 1° wedge of data. Analysis is presented which shows that improvements in data-quality indicators can be obtained through accurate identification and rejection of overlapping reflections prior to scaling.
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Affiliation(s)
- Richard J. Gildea
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - David G. Waterman
- STFC Rutherford Appleton Laboratory, Didcot OX11 0QX, England
- CCP4, Research Complex at Harwell, Rutherford Appleton Laboratory, Didcot OX11 0FA, England
| | - James M. Parkhurst
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Danny Axford
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Geoff Sutton
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, England
| | - David I. Stuart
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, England
| | - Nicholas K. Sauter
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Gwyndaf Evans
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
| | - Graeme Winter
- Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0DE, England
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49
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Li SN, Wang JY, Yuan MJ, Yang K. Disruption of the baculovirus core gene ac78 results in decreased production of multiple nucleocapsid-enveloped occlusion-derived virions and the failure of primary infection in vivo. Virus Res 2014; 191:70-82. [PMID: 25087880 DOI: 10.1016/j.virusres.2014.07.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 07/19/2014] [Accepted: 07/21/2014] [Indexed: 02/07/2023]
Abstract
The Autographa californica multiple nucleopolyhedrovirus (AcMNPV) ac78 gene is one of the baculovirus core genes. Recent studies showed that ac78 is essential for budded virion (BV) production and the embedding of occlusion-derived virion (ODV) into occlusion body during the AcMNPV life cycle. Here, we report that an ac78-knockout AcMNPV (vAc78KO) constructed in this study had different phenotypes than those described in the previous studies. A few infectious BVs were detected using titer assays, immunoblot analyses and plaque assays, indicating that ac78 is not essential for BV formation. Electron microscopy confirmed that the ac78 deletion did not affect nucleocapsid assembly and ODV formation. However, the numbers of multiple nucleocapsid-enveloped ODVs and ODV-embedded occlusion bodies were significantly decreased. Subsequently, the highly conserved amino acid residues 2-25 and 64-88 of Ac78, which are homologous to an oxidoreductase and cytochrome c oxidase, respectively, were demonstrated to play a crucial role in the morphogenesis of multiple nucleocapsid-enveloped ODV. Immunoblot analysis found that Ac78 was an ODV envelope-associated protein. Consistently, amino acid residues 56-93 of Ac78 were identified as an inner nuclear membrane sorting motif, which may direct the localization of Ac78 to the ODV envelope. In vivo infectivity assays showed that the occlusion bodies of vAc78KO were unable to establish primary infection in the midgut of Trichoplusia ni larvae. Taken together, our results suggest that ac78 plays an important role in BV production and proper multiple nucleocapsid-enveloped ODV formation, as well as AcMNPV primary infection in vivo.
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Affiliation(s)
- Sai-Nan Li
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China; Department of Biology, Zhaoqing University, Zhaoqing 526061, China
| | - Jin-Yu Wang
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Mei-Jin Yuan
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Kai Yang
- State Key Laboratory of Biocontrol, Sun Yat-sen University, Guangzhou 510275, China.
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50
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Axford D, Ji X, Stuart DI, Sutton G. In cellulo structure determination of a novel cypovirus polyhedrin. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:1435-41. [PMID: 24816111 PMCID: PMC4014125 DOI: 10.1107/s1399004714004714] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2013] [Accepted: 03/01/2014] [Indexed: 11/11/2022]
Abstract
This work demonstrates that with the use of a microfocus synchrotron beam the structure of a novel viral polyhedrin could be successfully determined from microcrystals within cells, removing the preparatory step of sample isolation and maintaining a favourable biological environment. The data obtained are of high quality, comparable to that obtained from isolated crystals, and enabled a facile structure determination. A small but significant difference is observed between the unit-cell parameters and the mosaic spread of in cellulo and isolated crystals, suggesting that even these robust crystals are adversely affected by removal from the cell.
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Affiliation(s)
- Danny Axford
- Diamond Light Source Ltd, Harwell Oxford, Didcot OX11 0DE, England
| | - Xiaoyun Ji
- Division of Structural Biology, The Welcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, England
| | - David I. Stuart
- Diamond Light Source Ltd, Harwell Oxford, Didcot OX11 0DE, England
- Division of Structural Biology, The Welcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, England
| | - Geoff Sutton
- Division of Structural Biology, The Welcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, England
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