1
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Cowan QT, Gu S, Gu W, Ranzau BL, Simonson TS, Komor AC. Development of multiplexed orthogonal base editor (MOBE) systems. Nat Biotechnol 2024:10.1038/s41587-024-02240-0. [PMID: 38773305 DOI: 10.1038/s41587-024-02240-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 04/10/2024] [Indexed: 05/23/2024]
Abstract
Base editors (BEs) enable efficient, programmable installation of point mutations while avoiding the use of double-strand breaks. Simultaneous application of two or more different BEs, such as an adenine BE (which converts A·T base pairs to G·C) and a cytosine BE (which converts C·G base pairs to T·A), is not feasible because guide RNA crosstalk results in non-orthogonal editing, with all BEs modifying all target loci. Here we engineer both adenine BEs and cytosine BEs that can be orthogonally multiplexed by using RNA aptamer-coat protein systems to recruit the DNA-modifying enzymes directly to the guide RNAs. We generate four multiplexed orthogonal BE systems that enable rates of precise co-occurring edits of up to 7.1% in the same DNA strand without enrichment or selection strategies. The addition of a fluorescent enrichment strategy increases co-occurring edit rates up to 24.8% in human cells. These systems are compatible with expanded protospacer adjacent motif and high-fidelity Cas9 variants, function well in multiple cell types, have equivalent or reduced off-target propensities compared with their parental systems and can model disease-relevant point mutation combinations.
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Affiliation(s)
- Quinn T Cowan
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Sifeng Gu
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Wanjun Gu
- Department of Medicine, Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, University of California San Diego, La Jolla, CA, USA
| | - Brodie L Ranzau
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - Tatum S Simonson
- Department of Medicine, Division of Pulmonary, Critical Care, Sleep Medicine, and Physiology, University of California San Diego, La Jolla, CA, USA
| | - Alexis C Komor
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA.
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2
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Tumban E. Bacteriophage Virus-Like Particles: Platforms for Vaccine Design. Methods Mol Biol 2024; 2738:411-423. [PMID: 37966612 DOI: 10.1007/978-1-0716-3549-0_24] [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] [Indexed: 11/16/2023]
Abstract
Virus-like particles (VLPs) derived from bacteriophages have many applications in biomedical sciences, especially in the development of candidate vaccines against viral and bacterial infections. Bacteriophage VLPs can be manufactured cheaply and in large quantities in bacteria compared to eukaryotic expression systems. In addition to this, bacteriophage VLPs are excellent platforms for vaccine design for the following reason: Humans do not have preexisting antibodies against bacteriophage VLPs. Thus, antigens displayed on bacteriophage VLP platforms are expected to be highly immunogenic. As such, VLPs derived from MS2, PP7, Qβ, AP205, P22 bacteriophages, etc. have been used to develop candidate vaccines against human infectious and noninfectious agents. This mini-review summarizes data from some of the candidate bacteriophage-based VLP peptide vaccines that have been developed. The review also highlights some strategies used to develop the candidate bacteriophage-based VLP peptide vaccines.
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Affiliation(s)
- Ebenezer Tumban
- School of Veterinary Medicine, Texas Tech University, Amarillo, TX, USA.
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3
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Thongchol J, Zhang J. Purification of Single-Stranded RNA Bacteriophages and Host Receptors for Structural Determination Using Cryo-Electron Microscopy. Methods Mol Biol 2024; 2793:185-204. [PMID: 38526732 DOI: 10.1007/978-1-0716-3798-2_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Single-stranded RNA bacteriophages (ssRNA phages) are small viruses with a compact genome (~3-4 kb) that infect gram-negative bacteria via retractile pili. These phages have been applied in various fields since their discovery approximately 60 years ago. To understand their biology, it is crucial to analyze the structure of mature virions. Cryo-electron microscopy (cryo-EM) has been employed to determine the structures of two ssRNA phages, MS2 and Qβ. This chapter presents a method for purifying these two phages and their receptor, the F-pilus, to allow examination using cryo-EM.
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Affiliation(s)
- Jirapat Thongchol
- Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Junjie Zhang
- Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA.
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4
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Keshavarz-Joud P, Zhao L, Bobe D, Hernandez C, Kopylov M, Yen LY, Djeddar N, Thompson B, Connors C, Gibson G, Bryksin A, Finn M. Exploring the Landscape of the PP7 Virus-like Particle for Peptide Display. ACS NANO 2023; 17:18470-18480. [PMID: 37669408 PMCID: PMC10540251 DOI: 10.1021/acsnano.3c06178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 08/29/2023] [Indexed: 09/07/2023]
Abstract
Self-assembling virus-like particles (VLPs) can tolerate a wide degree of genetic and chemical manipulation to their capsid protein to display a foreign molecule polyvalently. We previously reported the successful incorporation of foreign peptide sequences in the junction loop and onto the C-terminus of PP7 dimer VLPs, as these regions are accessible for surface display on assembled capsids. Here, we report the implementation of a library-based approach to test the assembly tolerance of PP7 dimer capsid proteins to insertions or terminal extensions of randomized 15-mer peptide sequences. By performing two iterative rounds of assembly-based selection, we evaluated the degree of favorability of all 20 amino acids at each of the 15 randomized positions. Deep sequencing analysis revealed a distinct preference for the inclusion of hydrophilic peptides and negatively charged amino acids (Asp and Glu) and the exclusion of positively charged peptides and bulky and hydrophobic amino acid residues (Trp, Phe, Tyr, and Cys). Within the libraries tested here, we identified 4000 to 22,000 unique 15-mer peptide sequences that can successfully be displayed on the surface of the PP7 dimer capsid. Overall, the use of small initial libraries consisting of no more than a few million members yielded a significantly larger number of unique and assembly-competent VLP sequences than have been previously characterized for this class of nucleoprotein particle.
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Affiliation(s)
- Parisa Keshavarz-Joud
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30306, United States
| | - Liangjun Zhao
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30306, United States
| | - Daija Bobe
- New
York Structural Biology Center, New York, New York 10027, United States
| | - Carolina Hernandez
- New
York Structural Biology Center, New York, New York 10027, United States
| | - Mykhailo Kopylov
- New
York Structural Biology Center, New York, New York 10027, United States
| | - Laura Y. Yen
- New
York Structural Biology Center, New York, New York 10027, United States
| | - Naima Djeddar
- Parker
H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30306, United States
| | - Brianna Thompson
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30306, United States
| | - Caleb Connors
- School
of Biological Sciences, Georgia Institute
of Technology, Atlanta, Georgia 30306, United States
| | - Greg Gibson
- School
of Biological Sciences, Georgia Institute
of Technology, Atlanta, Georgia 30306, United States
| | - Anton Bryksin
- Parker
H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30306, United States
| | - M.G. Finn
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30306, United States
- School
of Biological Sciences, Georgia Institute
of Technology, Atlanta, Georgia 30306, United States
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5
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Lu S, Hou Y, Zhang XE, Gao Y. Live cell imaging of DNA and RNA with fluorescent signal amplification and background reduction techniques. Front Cell Dev Biol 2023; 11:1216232. [PMID: 37342234 PMCID: PMC10277805 DOI: 10.3389/fcell.2023.1216232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 05/24/2023] [Indexed: 06/22/2023] Open
Abstract
Illuminating DNA and RNA dynamics in live cell can elucidate their life cycle and related biochemical activities. Various protocols have been developed for labeling the regions of interest in DNA and RNA molecules with different types of fluorescent probes. For example, CRISPR-based techniques have been extensively used for imaging genomic loci. However, some DNA and RNA molecules can still be difficult to tag and observe dynamically, such as genomic loci in non-repetitive regions. In this review, we will discuss the toolbox of techniques and methodologies that have been developed for imaging DNA and RNA. We will also introduce optimized systems that provide enhanced signal intensity or low background fluorescence for those difficult-to-tag molecules. These strategies can provide new insights for researchers when designing and using techniques to visualize DNA or RNA molecules.
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Affiliation(s)
- Song Lu
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Yu Hou
- Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xian-En Zhang
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yunhua Gao
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
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6
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Suh D, Jin H, Park H, Lee C, Cho YH, Baek Y. Effect of protein fouling on filtrate flux and virus breakthrough behaviors during virus filtration process. Biotechnol Bioeng 2023. [PMID: 37144573 DOI: 10.1002/bit.28407] [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: 02/15/2023] [Revised: 04/13/2023] [Accepted: 04/13/2023] [Indexed: 05/06/2023]
Abstract
Virus filtration process is used to ensure viral safety in the biopharmaceutical downstream processes with high virus removal capacity (i.e., >4 log10 ). However, it is still constrained by protein fouling, which results in reduced filtration capacity and possible virus breakthrough. This study investigated the effects of protein fouling on filtrate flux and virus breakthrough using commercial membranes that had different symmetricity, nominal pore size, and pore size gradients. Flux decay tendency due to protein fouling was influenced by hydrodynamic drag force and protein concentration. As the results of prediction with the classical fouling model, standard blocking was suitable for most virus filters. Undesired virus breakthrough was observed in the membranes having relatively a large pore diameter of the retentive region. The study found that elevated levels of protein solution reduced virus removal performance. However, the impact of prefouled membranes was minimal. These findings shed light on the factors that influence protein fouling during the virus filtration process of biopharmaceutical production.
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Affiliation(s)
- Dongwoo Suh
- School of Chemical and Biological Engineering, Seoul National University (SNU), Seoul, Republic of Korea
| | - Hoeun Jin
- Department of Biological Engineering, Inha University, Incheon, Republic of Korea
| | - Hosik Park
- Green Carbon Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon, Republic of Korea
- Department of Advanced Materials and Chemical Engineering, University of Science & Technology (UST), Daejeon, Yuseong-gu, Republic of Korea
| | - Changha Lee
- School of Chemical and Biological Engineering, Seoul National University (SNU), Seoul, Republic of Korea
| | - Young Hoon Cho
- Green Carbon Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon, Republic of Korea
- Department of Advanced Materials and Chemical Engineering, University of Science & Technology (UST), Daejeon, Yuseong-gu, Republic of Korea
| | - Youngbin Baek
- Department of Biological Engineering, Inha University, Incheon, Republic of Korea
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7
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Chang JY, Gorzelnik KV, Thongchol J, Zhang J. Structural Assembly of Qβ Virion and Its Diverse Forms of Virus-like Particles. Viruses 2022; 14:225. [PMID: 35215818 PMCID: PMC8880383 DOI: 10.3390/v14020225] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 01/18/2022] [Accepted: 01/21/2022] [Indexed: 02/04/2023] Open
Abstract
The coat proteins (CPs) of single-stranded RNA bacteriophages (ssRNA phages) directly assemble around the genomic RNA (gRNA) to form a near-icosahedral capsid with a single maturation protein (Mat) that binds the gRNA and interacts with the retractile pilus during infection of the host. Understanding the assembly of ssRNA phages is essential for their use in biotechnology, such as RNA protection and delivery. Here, we present the complete gRNA model of the ssRNA phage Qβ, revealing that the 3' untranslated region binds to the Mat and the 4127 nucleotides fold domain-by-domain, and is connected through long-range RNA-RNA interactions, such as kissing loops. Thirty-three operator-like RNA stem-loops are located and primarily interact with the asymmetric A/B CP-dimers, suggesting a pathway for the assembly of the virions. Additionally, we have discovered various forms of the virus-like particles (VLPs), including the canonical T = 3 icosahedral, larger T = 4 icosahedral, prolate, oblate forms, and a small prolate form elongated along the 3-fold axis. These particles are all produced during a normal infection, as well as when overexpressing the CPs. When overexpressing the shorter RNA fragments encoding only the CPs, we observed an increased percentage of the smaller VLPs, which may be sufficient to encapsidate a shorter RNA.
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Affiliation(s)
| | | | | | - Junjie Zhang
- Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; (J.-Y.C.); (K.V.G.); (J.T.)
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8
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Rūmnieks J, Liekniņa I, Kalniņš G, Šišovs M, Akopjana I, Bogans J, Tārs K. Three-dimensional structure of 22 uncultured ssRNA bacteriophages: Flexibility of the coat protein fold and variations in particle shapes. SCIENCE ADVANCES 2020; 6:6/36/eabc0023. [PMID: 32917600 PMCID: PMC7467689 DOI: 10.1126/sciadv.abc0023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 07/20/2020] [Indexed: 06/11/2023]
Abstract
The single-stranded RNA (ssRNA) bacteriophages are among the simplest known viruses with small genomes and exceptionally high mutation rates. The number of ssRNA phage isolates has remained very low, but recent metagenomic studies have uncovered an immense variety of distinct uncultured ssRNA phages. The coat proteins (CPs) in these genomes are particularly diverse, with notable variation in length and often no recognizable similarity to previously known viruses. We recombinantly expressed metagenome-derived ssRNA phage CPs to produce virus-like particles and determined the three-dimensional structure of 22 previously uncharacterized ssRNA phage capsids covering nine distinct CP types. The structures revealed substantial deviations from the previously known ssRNA phage CP fold, uncovered an unusual prolate particle shape, and revealed a previously unseen dsRNA binding mode. These data expand our knowledge of the evolution of viral structural proteins and are of relevance for applications such as ssRNA phage-based vaccine design.
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Affiliation(s)
- Jānis Rūmnieks
- Latvian Biomedical Research and Study Center, Rātsupītes 1, LV1067, Riga, Latvia
| | - Ilva Liekniņa
- Latvian Biomedical Research and Study Center, Rātsupītes 1, LV1067, Riga, Latvia
| | - Gints Kalniņš
- Latvian Biomedical Research and Study Center, Rātsupītes 1, LV1067, Riga, Latvia
| | - Mihails Šišovs
- Latvian Biomedical Research and Study Center, Rātsupītes 1, LV1067, Riga, Latvia
| | - Ināra Akopjana
- Latvian Biomedical Research and Study Center, Rātsupītes 1, LV1067, Riga, Latvia
| | - Jānis Bogans
- Latvian Biomedical Research and Study Center, Rātsupītes 1, LV1067, Riga, Latvia
| | - Kaspars Tārs
- Latvian Biomedical Research and Study Center, Rātsupītes 1, LV1067, Riga, Latvia.
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9
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Braselmann E, Rathbun C, Richards EM, Palmer AE. Illuminating RNA Biology: Tools for Imaging RNA in Live Mammalian Cells. Cell Chem Biol 2020; 27:891-903. [PMID: 32640188 PMCID: PMC7595133 DOI: 10.1016/j.chembiol.2020.06.010] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/30/2020] [Accepted: 06/15/2020] [Indexed: 01/06/2023]
Abstract
The central dogma teaches us that DNA makes RNA, which in turn makes proteins, the main building blocks of the cell. But this over simplified linear transmission of information overlooks the vast majority of the genome produces RNAs that do not encode proteins and the myriad ways that RNA regulates cellular functions. Historically, one of the challenges in illuminating RNA biology has been the lack of tools for visualizing RNA in live cells. But clever approaches for exploiting RNA binding proteins, in vitro RNA evolution, and chemical biology have resulted in significant advances in RNA visualization tools in recent years. This review provides an overview of current tools for tagging RNA with fluorescent probes and tracking their dynamics, localization andfunction in live mammalian cells.
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Affiliation(s)
- Esther Braselmann
- Department of Biochemistry, BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Avenue, Boulder, CO 80309, USA
| | - Colin Rathbun
- Department of Biochemistry, BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Avenue, Boulder, CO 80309, USA
| | - Erin M Richards
- Department of Biochemistry, BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Avenue, Boulder, CO 80309, USA
| | - Amy E Palmer
- Department of Biochemistry, BioFrontiers Institute, University of Colorado Boulder, 3415 Colorado Avenue, Boulder, CO 80309, USA.
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10
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Abstract
ssRNA phages belonging to the family Leviviridae are among the tiniest viruses, infecting various Gram-negative bacteria by adsorption to their pilus structures. Due to their simplicity, they have been intensively studied as models for understanding various problems in molecular biology and virology. Several of the studied ssRNA characteristics, such as coat protein–RNA interactions and the ability to readily form virus-like particles in recombinant expression systems, have fueled many practical applications such as RNA labeling and tracking systems and vaccine development. In this chapter, we review the life cycle, structure and applications of these small yet fascinating viruses.
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11
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Meng R, Jiang M, Cui Z, Chang JY, Yang K, Jakana J, Yu X, Wang Z, Hu B, Zhang J. Structural basis for the adsorption of a single-stranded RNA bacteriophage. Nat Commun 2019; 10:3130. [PMID: 31311931 PMCID: PMC6635492 DOI: 10.1038/s41467-019-11126-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 06/24/2019] [Indexed: 12/31/2022] Open
Abstract
Single-stranded RNA bacteriophages (ssRNA phages) infect Gram-negative bacteria via a single maturation protein (Mat), which attaches to a retractile pilus of the host. Here we present structures of the ssRNA phage MS2 in complex with the Escherichia coli F-pilus, showing a network of hydrophobic and electrostatic interactions at the Mat-pilus interface. Moreover, binding of the pilus induces slight orientational variations of the Mat relative to the rest of the phage capsid, priming the Mat-connected genomic RNA (gRNA) for its release from the virions. The exposed tip of the attached Mat points opposite to the direction of the pilus retraction, which may facilitate the translocation of the gRNA from the capsid into the host cytosol. In addition, our structures determine the orientation of the assembled F-pilin subunits relative to the cell envelope, providing insights into the F-like type IV secretion systems.
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Affiliation(s)
- Ran Meng
- Department of Biochemistry and Biophysics, Center for Phage Technology, Texas A&M University, College Station, TX, 77843, USA
| | - Mengqiu Jiang
- Department of Biochemistry and Biophysics, Center for Phage Technology, Texas A&M University, College Station, TX, 77843, USA
| | - Zhicheng Cui
- Department of Biochemistry and Biophysics, Center for Phage Technology, Texas A&M University, College Station, TX, 77843, USA
| | - Jeng-Yih Chang
- Department of Biochemistry and Biophysics, Center for Phage Technology, Texas A&M University, College Station, TX, 77843, USA
| | - Kailu Yang
- Department of Biochemistry and Biophysics, Center for Phage Technology, Texas A&M University, College Station, TX, 77843, USA
- Howard Hughes Medical Institute, Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, 94305, USA
| | - Joanita Jakana
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Xinzhe Yu
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Zhao Wang
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Bo Hu
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
| | - Junjie Zhang
- Department of Biochemistry and Biophysics, Center for Phage Technology, Texas A&M University, College Station, TX, 77843, USA.
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12
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Liekniņa I, Kalniņš G, Akopjana I, Bogans J, Šišovs M, Jansons J, Rūmnieks J, Tārs K. Production and characterization of novel ssRNA bacteriophage virus-like particles from metagenomic sequencing data. J Nanobiotechnology 2019; 17:61. [PMID: 31084612 PMCID: PMC6513524 DOI: 10.1186/s12951-019-0497-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 05/04/2019] [Indexed: 12/30/2022] Open
Abstract
Background Protein shells assembled from viral coat proteins are an attractive platform for development of new vaccines and other tools such as targeted bioimaging and drug delivery agents. Virus-like particles (VLPs) derived from the single-stranded RNA (ssRNA) bacteriophage coat proteins (CPs) have been important and successful contenders in the area due to their simplicity and robustness. However, only a few different VLP types are available that put certain limitations on continued developments and expanded adaptation of ssRNA phage VLP technology. Metagenomic studies have been a rich source for discovering novel viral sequences, and in recent years have unraveled numerous ssRNA phage genomes significantly different from those known before. Here, we describe the use of ssRNA CP sequences found in metagenomic data to experimentally produce and characterize novel VLPs. Results Approximately 150 ssRNA phage CP sequences were sourced from metagenomic sequence data and grouped into 14 different clusters based on CP sequence similarity analysis. 110 CP-encoding sequences were obtained by gene synthesis and expressed in bacteria which in 80 cases resulted in VLP assembly. Production and purification of the VLPs was straightforward and compatible with established protocols, with the only exception that a considerable proportion of the CPs had to be produced at a lower temperature to ensure VLP assembly. The VLP morphology was similar to that of the previously studied phages, although a few deviations such as elongated or smaller particles were noted in certain cases. In addition, stabilizing inter-subunit disulfide bonds were detected in six VLPs and several possible candidate RNA structures in the phage genomes were identified that might bind to the coat protein and ensure specific RNA packaging. Conclusions Compared to the few types of ssRNA phage VLPs that were used before, several dozens of new particles representing ten distinct similarity groups are now available with a notable potential for biotechnological applications. It is believed that the novel VLPs described in this paper will provide the groundwork for future development of new vaccines and other applications based on ssRNA bacteriophage VLPs. Electronic supplementary material The online version of this article (10.1186/s12951-019-0497-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ilva Liekniņa
- Latvian Biomedical Research and Study Center, Rātsupītes 1, Riga, LV1067, Latvia
| | - Gints Kalniņš
- Latvian Biomedical Research and Study Center, Rātsupītes 1, Riga, LV1067, Latvia
| | - Ināra Akopjana
- Latvian Biomedical Research and Study Center, Rātsupītes 1, Riga, LV1067, Latvia
| | - Jānis Bogans
- Latvian Biomedical Research and Study Center, Rātsupītes 1, Riga, LV1067, Latvia
| | - Mihails Šišovs
- Latvian Biomedical Research and Study Center, Rātsupītes 1, Riga, LV1067, Latvia
| | - Juris Jansons
- Latvian Biomedical Research and Study Center, Rātsupītes 1, Riga, LV1067, Latvia
| | - Jānis Rūmnieks
- Latvian Biomedical Research and Study Center, Rātsupītes 1, Riga, LV1067, Latvia
| | - Kaspars Tārs
- Latvian Biomedical Research and Study Center, Rātsupītes 1, Riga, LV1067, Latvia.
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13
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Zhao L, Kopylov M, Potter CS, Carragher B, Finn MG. Engineering the PP7 Virus Capsid as a Peptide Display Platform. ACS NANO 2019; 13:4443-4454. [PMID: 30912918 PMCID: PMC6991139 DOI: 10.1021/acsnano.8b09683] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
As self-assembling polyvalent nanoscale structures that can tolerate substantial genetic and chemical modification, virus-like particles are useful in a variety of fields. Here we describe the genetic modification and structural characterization of the Leviviridae PP7 capsid protein as a platform for the presentation of functional polypeptides. This particle was shown to tolerate the display of sequences from 1 kDa (a cell penetrating peptide) to 14 kDa (the Fc-binding double Z-domain) on its exterior surface as C-terminal genetic fusions to the coat protein. In addition, a dimeric construct allowed the presentation of exogenous loops between capsid monomers and the simultaneous presentation of two different peptides at different positions on the icosahedral structure. The PP7 particle is thereby significantly more tolerant of these types of polypeptide additions than Qβ and MS2, the other Leviviridae-derived VLPs in common use.
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Affiliation(s)
- Liangjun Zhao
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332, United States
| | - Mykhailo Kopylov
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Avenue, New York, New York 10027, United States
| | - Clinton S. Potter
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Avenue, New York, New York 10027, United States
| | - Bridget Carragher
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, 89 Convent Avenue, New York, New York 10027, United States
| | - M. G. Finn
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332, United States
- School of Biological Sciences, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332, United States
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14
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Kryshtafovych A, Albrecht R, Baslé A, Bule P, Caputo AT, Carvalho AL, Chao KL, Diskin R, Fidelis K, Fontes CMGA, Fredslund F, Gilbert HJ, Goulding CW, Hartmann MD, Hayes CS, Herzberg O, Hill JC, Joachimiak A, Kohring GW, Koning RI, Lo Leggio L, Mangiagalli M, Michalska K, Moult J, Najmudin S, Nardini M, Nardone V, Ndeh D, Nguyen TH, Pintacuda G, Postel S, van Raaij MJ, Roversi P, Shimon A, Singh AK, Sundberg EJ, Tars K, Zitzmann N, Schwede T. Target highlights from the first post-PSI CASP experiment (CASP12, May-August 2016). Proteins 2018; 86 Suppl 1:27-50. [PMID: 28960539 PMCID: PMC5820184 DOI: 10.1002/prot.25392] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 09/19/2017] [Accepted: 09/25/2017] [Indexed: 12/27/2022]
Abstract
The functional and biological significance of the selected CASP12 targets are described by the authors of the structures. The crystallographers discuss the most interesting structural features of the target proteins and assess whether these features were correctly reproduced in the predictions submitted to the CASP12 experiment.
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Affiliation(s)
- Andriy Kryshtafovych
- Genome Center, University of California, Davis, 451 Health Sciences Drive, Davis, California, 95616
| | - Reinhard Albrecht
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany
| | - Arnaud Baslé
- Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Pedro Bule
- CIISA - Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477, Portugal, Lisboa
| | - Alessandro T Caputo
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England, United Kingdom
| | - Ana Luisa Carvalho
- UCIBIO, REQUIMTE, Departamento de Química, Faculdade de Cien⁁cias e Tecnologia, Universidade Nova de Lisboa, Caparica, 2829-516, Portugal
| | - Kinlin L Chao
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, 20850
| | - Ron Diskin
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Krzysztof Fidelis
- Genome Center, University of California, Davis, 451 Health Sciences Drive, Davis, California, 95616
| | - Carlos M G A Fontes
- CIISA - Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477, Portugal, Lisboa
| | - Folmer Fredslund
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen Ø, Denmark
| | - Harry J Gilbert
- Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Celia W Goulding
- Department of Molecular Biology and Biochemistry/Pharmaceutical Sciences, University of California Irvine, Irvine, California, 92697
| | - Marcus D Hartmann
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany
| | - Christopher S Hayes
- Department of Molecular, Cellular and Developmental Biology/Biomolecular Science and Engineering Program, University of California, Santa Barbara, Santa Barbara, California, 93106
| | - Osnat Herzberg
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland, 20850
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, 20742
| | - Johan C Hill
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England, United Kingdom
| | - Andrzej Joachimiak
- Argonne National Laboratory, Midwest Center for Structural Genomics/Structural Biology Center, Biosciences Division, Argonne, Illinois, 60439
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, 60637
| | - Gert-Wieland Kohring
- Microbiology, Saarland University, Campus Building A1.5, Saarbrücken, Saarland, D-66123, Germany
| | - Roman I Koning
- Netherlands Centre for Electron Nanoscopy, Institute of Biology Leiden, Leiden University, 2333, CC Leiden, The Netherlands
- Department of Molecular Cell Biology, Leiden University Medical Center, 2300 RC, Leiden, The Netherlands
| | - Leila Lo Leggio
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen Ø, Denmark
| | - Marco Mangiagalli
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano, 20126, Italy
| | - Karolina Michalska
- Argonne National Laboratory, Midwest Center for Structural Genomics/Structural Biology Center, Biosciences Division, Argonne, Illinois, 60439
| | - John Moult
- Department of Cell Biology and Molecular genetics, University of Maryland, 9600 Gudelsky Drive, Institute for Bioscience and Biotechnology Research, Rockville, Maryland, 20850
| | - Shabir Najmudin
- CIISA - Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477, Portugal, Lisboa
| | - Marco Nardini
- Department of Biosciences, University of Milano, Milano, 20133, Italy
| | - Valentina Nardone
- Department of Biosciences, University of Milano, Milano, 20133, Italy
| | - Didier Ndeh
- Institute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Thanh-Hong Nguyen
- Department of Macromolecular Structures, Centro Nacional de Biotecnologia (CSIC), calle Darwin 3, Madrid, 28049, Spain
| | - Guido Pintacuda
- Université de Lyon, Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), Villeurbanne, 69100, France
| | - Sandra Postel
- University of Maryland School of Medicine, Institute of Human Virology, Baltimore, Maryland, 21201
| | - Mark J van Raaij
- Department of Macromolecular Structures, Centro Nacional de Biotecnologia (CSIC), calle Darwin 3, Madrid, 28049, Spain
| | - Pietro Roversi
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England, United Kingdom
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Henry Wellcome Building, University Road, Leicester, LE1 7RN, UK
| | - Amir Shimon
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Abhimanyu K Singh
- School of Biosciences, University of Kent, Canterbury, Kent, CT2 7NJ, United Kingdom
| | - Eric J Sundberg
- Department of Medicine and Department of Microbiology and Immunology, University of Maryland School of Medicine, Institute of Human Virology, Baltimore, Maryland, 21201
| | - Kaspars Tars
- Latvian Biomedical Research and Study Center, Rātsupītes 1, Riga, LV1067, Latvia
- Faculty of Biology, Department of Molecular Biology, University of Latvia, Jelgavas 1, Riga, LV-1004, Latvia
| | - Nicole Zitzmann
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England, United Kingdom
| | - Torsten Schwede
- Biozentrum/SIB Swiss Institute of Bioinformatics, Klingelbergstrasse 50, Basel, 4056, Switzerland
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15
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Roszyk L, Kollenda S, Hennig S. Using a Specific RNA-Protein Interaction To Quench the Fluorescent RNA Spinach. ACS Chem Biol 2017; 12:2958-2964. [PMID: 29058870 DOI: 10.1021/acschembio.7b00332] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
RNAs are involved in interaction networks with other biomolecules and are crucial for proper cell function. Yet their biochemical analysis remains challenging. For Förster Resonance Energy Transfer (FRET), a common tool to study such interaction networks, two interacting molecules have to be fluorescently labeled. "Spinach" is a genetically encodable RNA aptamer that starts to fluoresce upon binding of an organic molecule. Therefore, it is a biological fluorophore tag for RNAs. However, spinach has never been used in a FRET assembly before. Here, we describe how spinach is quenched when close to acceptors. We used RNA-DNA hybridization to bring quenchers or red organic dyes in close proximity to spinach. Furthermore, we investigate RNA-protein interactions quantitatively on the example of Pseudomonas aeruginosa phage coat protein 7 (PP7) and its interacting pp7-RNA. We utilize spinach quenching as a fully genetically encodable system even under lysate conditions. Therefore, this work represents a direct method to analyze RNA-protein interactions by quenching the spinach aptamer.
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Affiliation(s)
- Laura Roszyk
- Chemical
Genomics Centre of the Max-Planck Society, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
| | - Sebastian Kollenda
- Institute
for Inorganic Chemistry, University of Duisburg Essen, Universitätsstrasse 7, 45141 Essen, Germany
| | - Sven Hennig
- Chemical
Genomics Centre of the Max-Planck Society, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
- Division
of Organic Chemistry, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, Netherlands
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16
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VLP-based vaccine induces immune control of Staphylococcus aureus virulence regulation. Sci Rep 2017; 7:637. [PMID: 28377579 PMCID: PMC5429642 DOI: 10.1038/s41598-017-00753-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 03/09/2017] [Indexed: 12/12/2022] Open
Abstract
Staphylococcus aureus is the leading cause of skin and soft tissue infections (SSTIs) and mounting antibiotic resistance requires innovative treatment strategies. S. aureus uses secreted cyclic autoinducing peptides (AIPs) and the accessory gene regulator (agr) operon to coordinate expression of virulence factors required for invasive infection. Of the four agr alleles (agr types I-IV and corresponding AIPs1-4), agr type I isolates are most frequently associated with invasive infection. Cyclization via a thiolactone bond is essential for AIP function; therefore, recognition of the cyclic form of AIP1 may be necessary for antibody-mediated neutralization. However, the small sizes of AIPs and labile thiolactone bond have hindered vaccine development. To overcome this, we used a virus-like particle (VLP) vaccine platform (PP7) for conformationally-restricted presentation of a modified AIP1 amino acid sequence (AIP1S). Vaccination with PP7-AIP1S elicited AIP1-specific antibodies and limited agr-activation in vivo. Importantly, in a murine SSTI challenge model with a highly virulent agr type I S. aureus isolate, PP7-AIP1S vaccination reduced pathogenesis and increased bacterial clearance compared to controls, demonstrating vaccine efficacy. Given the contribution of MRSA agr type I isolates to human disease, vaccine targeting of AIP1-regulated virulence could have a major clinical impact in the fight against antibiotic resistance.
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17
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18
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Pumpens P, Renhofa R, Dishlers A, Kozlovska T, Ose V, Pushko P, Tars K, Grens E, Bachmann MF. The True Story and Advantages of RNA Phage Capsids as Nanotools. Intervirology 2016; 59:74-110. [DOI: 10.1159/000449503] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 08/30/2016] [Indexed: 11/19/2022] Open
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19
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Shishovs M, Rumnieks J, Diebolder C, Jaudzems K, Andreas LB, Stanek J, Kazaks A, Kotelovica S, Akopjana I, Pintacuda G, Koning RI, Tars K. Structure of AP205 Coat Protein Reveals Circular Permutation in ssRNA Bacteriophages. J Mol Biol 2016; 428:4267-4279. [PMID: 27591890 DOI: 10.1016/j.jmb.2016.08.025] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 08/18/2016] [Accepted: 08/27/2016] [Indexed: 12/18/2022]
Abstract
AP205 is a single-stranded RNA bacteriophage that has a coat protein sequence not similar to any other known single-stranded RNA phage. Here, we report an atomic-resolution model of the AP205 virus-like particle based on a crystal structure of an unassembled coat protein dimer and a cryo-electron microscopy reconstruction of the assembled particle, together with secondary structure information from site-specific solid-state NMR data. The AP205 coat protein dimer adopts the conserved Leviviridae coat protein fold except for the N-terminal region, which forms a beta-hairpin in the other known single-stranded RNA phages. AP205 has a similar structure at the same location formed by N- and C-terminal beta-strands, making it a circular permutant compared to the other coat proteins. The permutation moves the coat protein termini to the most surface-exposed part of the assembled particle, which explains its increased tolerance to long N- and C-terminal fusions.
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Affiliation(s)
- Mihails Shishovs
- Latvian Biomedical Research and Study Center, Rātsupītes 1, LV1067 Riga, Latvia
| | - Janis Rumnieks
- Latvian Biomedical Research and Study Center, Rātsupītes 1, LV1067 Riga, Latvia
| | - Christoph Diebolder
- Netherlands Centre for Electron Nanoscopy, Institute of Biology Leiden, Leiden University Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Kristaps Jaudzems
- Université de Lyon, Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), 69100 Villeurbanne, France
| | - Loren B Andreas
- Université de Lyon, Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), 69100 Villeurbanne, France
| | - Jan Stanek
- Université de Lyon, Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), 69100 Villeurbanne, France
| | - Andris Kazaks
- Latvian Biomedical Research and Study Center, Rātsupītes 1, LV1067 Riga, Latvia
| | - Svetlana Kotelovica
- Latvian Biomedical Research and Study Center, Rātsupītes 1, LV1067 Riga, Latvia
| | - Inara Akopjana
- Latvian Biomedical Research and Study Center, Rātsupītes 1, LV1067 Riga, Latvia
| | - Guido Pintacuda
- Université de Lyon, Centre de RMN à Très Hauts Champs, Institut des Sciences Analytiques (UMR 5280 - CNRS, ENS Lyon, UCB Lyon 1), 69100 Villeurbanne, France
| | - Roman I Koning
- Netherlands Centre for Electron Nanoscopy, Institute of Biology Leiden, Leiden University Einsteinweg 55, 2333 CC Leiden, The Netherlands; Department of Cell Biology, Leiden University Medical Center, Postal Zone S1-P, P.O.Box 9600, 2300 RC Leiden, The Netherlands
| | - Kaspars Tars
- Latvian Biomedical Research and Study Center, Rātsupītes 1, LV1067 Riga, Latvia; Faculty of Biology, Department of Molecular Biology, University of Latvia, Jelgavas 1, LV-1004 Riga, Latvia.
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20
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Huynh NT, Hesketh EL, Saxena P, Meshcheriakova Y, Ku YC, Hoang LT, Johnson JE, Ranson NA, Lomonossoff GP, Reddy VS. Crystal Structure and Proteomics Analysis of Empty Virus-like Particles of Cowpea Mosaic Virus. Structure 2016; 24:567-575. [PMID: 27021160 DOI: 10.1016/j.str.2016.02.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 02/12/2016] [Accepted: 02/22/2016] [Indexed: 11/24/2022]
Abstract
Empty virus-like particles (eVLPs) of Cowpea mosaic virus (CPMV) are currently being utilized as reagents in various biomedical and nanotechnology applications. Here, we report the crystal structure of CPMV eVLPs determined using X-ray crystallography at 2.3 Å resolution and compare it with previously reported cryo-electron microscopy (cryo-EM) of eVLPs and virion crystal structures. Although the X-ray and cryo-EM structures of eVLPs are mostly similar, there exist significant differences at the C terminus of the small (S) subunit. The intact C terminus of the S subunit plays a critical role in enabling the efficient assembly of CPMV virions and eVLPs, but undergoes proteolysis after particle formation. In addition, we report the results of mass spectrometry-based proteomics analysis of coat protein subunits from CPMV eVLPs and virions that identify the C termini of S subunits undergo proteolytic cleavages at multiple sites instead of a single cleavage site as previously observed.
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Affiliation(s)
- Nhung T Huynh
- Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Emma L Hesketh
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Pooja Saxena
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
| | - Yulia Meshcheriakova
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
| | - You-Chan Ku
- Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Linh T Hoang
- Scripps Center for Metabolics and Mass Spectrometry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - John E Johnson
- Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - George P Lomonossoff
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
| | - Vijay S Reddy
- Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
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21
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Pérez-Cano L, Fernández-Recio J. Dissection and prediction of RNA-binding sites on proteins. Biomol Concepts 2015; 1:345-55. [PMID: 25962008 DOI: 10.1515/bmc.2010.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
RNA-binding proteins are involved in many important regulatory processes in cells and their study is essential for a complete understanding of living organisms. They show a large variability from both structural and functional points of view. However, several recent studies performed on protein-RNA crystal structures have revealed interesting common properties. RNA-binding sites usually constitute patches of positively charged or polar residues that make most of the specific and non-specific contacts with RNA. Negatively charged or aliphatic residues are less frequent at protein-RNA interfaces, although they can also be found either forming aliphatic and positive-negative pairs in protein RNA-binding sites or contacting RNA through their main chains. Aromatic residues found within these interfaces are usually involved in specific base recognition at RNA single-strand regions. This specific recognition, in combination with structural complementarity, represents the key source for specificity in protein-RNA association. From all this knowledge, a variety of computational methods for prediction of RNA-binding sites have been developed based either on protein sequence or on protein structure. Some reported methods are really successful in the identification of RNA-binding proteins or the prediction of RNA-binding sites. Given the growing interest in the field, all these studies and prediction methods will undoubtedly contribute to the identification and comprehension of protein-RNA interactions.
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22
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Dent KC, Thompson R, Barker AM, Hiscox JA, Barr JN, Stockley PG, Ranson NA. The asymmetric structure of an icosahedral virus bound to its receptor suggests a mechanism for genome release. Structure 2014; 21:1225-34. [PMID: 23810697 PMCID: PMC3701328 DOI: 10.1016/j.str.2013.05.012] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 04/23/2013] [Accepted: 05/07/2013] [Indexed: 11/23/2022]
Abstract
Simple, spherical RNA viruses have well-understood, symmetric protein capsids, but little structural information is available for their asymmetric components, such as minor proteins and their genomes, which are vital for infection. Here, we report an asymmetric structure of bacteriophage MS2, attached to its receptor, the F-pilus. Cryo-electron tomography and subtomographic averaging of such complexes result in a structure containing clear density for the packaged genome, implying that the conformation of the genome is the same in each virus particle. The data also suggest that the single-copy viral maturation protein breaks the symmetry of the capsid, occupying a position that would be filled by a coat protein dimer in an icosahedral shell. This capsomere can thus fulfill its known biological roles in receptor and genome binding and suggests an exit route for the genome during infection. The asymmetric structure of a virus receptor complex is described The density for ordered genomic RNA was observed in the structure Viral maturation protein was visualized
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Affiliation(s)
- Kyle C Dent
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
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23
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Stockley PG, Ranson NA, Twarock R. A new paradigm for the roles of the genome in ssRNA viruses. Future Virol 2013. [DOI: 10.2217/fvl.12.84] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Recent work with RNA phages and an ssRNA plant satellite virus challenges the widely held view that the sequences and structures of genomic RNAs are unimportant for virion assembly. In the T=3 phages, RNA–coat protein interactions occur throughout the genome, defining the quasiconformers of their protein shells. In the plant virus, there are multiple packaging signals dispersed throughout the genome that overcome electrostatic barriers to protein self-assembly. Both viral coat proteins cause the solution structures of their cognate genomes to collapse into a form that is readily encapsidated in a two-stage assembly process. Such similar behavior in two structurally unrelated viral protein folds implies that this might be a conserved feature of many viral assembly reactions. These results suggest a highly defined structure for the RNA in the virions, consistent with recent structural studies. They also have implications both for subsequent genome release during infection and for the evolution of viral sequences.
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Affiliation(s)
- Peter G Stockley
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.
| | - Neil A Ranson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Reidun Twarock
- Departments of Biology & Mathematics, York Centre for Complex Systems Analysis, University of York, York, YO10 5DD, UK
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24
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Persson M, Tars K, Liljas L. PRR1 coat protein binding to its RNA translational operator. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:367-72. [DOI: 10.1107/s0907444912047464] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 11/19/2012] [Indexed: 11/10/2022]
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25
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Abstract
Bacteriophages have been a model system to study assembly processes for over half a century. Formation of infectious phage particles involves specific protein-protein and protein-nucleic acid interactions, as well as large conformational changes of assembly precursors. The sequence and molecular mechanisms of phage assembly have been elucidated by a variety of methods. Differences and similarities of assembly processes in several different groups of bacteriophages are discussed in this review. The general principles of phage assembly are applicable to many macromolecular complexes.
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26
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Caldeira JDC, Medford A, Kines RC, Lino CA, Schiller JT, Chackerian B, Peabody DS. Immunogenic display of diverse peptides, including a broadly cross-type neutralizing human papillomavirus L2 epitope, on virus-like particles of the RNA bacteriophage PP7. Vaccine 2010; 28:4384-93. [PMID: 20434554 DOI: 10.1016/j.vaccine.2010.04.049] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2010] [Revised: 04/12/2010] [Accepted: 04/15/2010] [Indexed: 12/27/2022]
Abstract
The immunogenicity of an antigen can be dramatically increased by displaying it in a dense, multivalent context, such as on the surface of a virus or virus-like particle (VLP). Here we describe a highly versatile VLP platform for peptide display based on VLPs of the RNA bacteriophage PP7. We show that this platform can be used for the engineered display of specific peptide sequences as well as for the construction of random peptide libraries. Peptides representing the FLAG epitope, the V3 loop of HIV gp120, and a broadly cross-type neutralizing epitope from L2, the minor capsid protein of Human Papillomavirus type 16 (HPV16), were inserted into an exposed surface loop of a form of PP7 coat protein in which the two identical polypeptides of coat were fused together to form a single-chain dimer. The recombinant proteins assembled into VLPs, displayed these peptides on their surfaces, and induced high-titer antibody responses. The single-chain dimer was also highly tolerant of random 6-, 8-, and 10-amino acid insertions. PP7 VLPs displaying the HPV16 L2 epitope generated robust anti-HPV16 L2 serum antibodies after intramuscular injection that protected mice from genital infection with HPV16 pseudovirus as well as a heterologous HPV pseudovirus type, HPV45. Thus, PP7 VLPs are well-suited for the display of a wide diversity of peptides in a highly immunogenic format.
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Affiliation(s)
- Jerri do Carmo Caldeira
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, NM 87131, USA
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27
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Goulet A, Blangy S, Redder P, Prangishvili D, Felisberto-Rodrigues C, Forterre P, Campanacci V, Cambillau C. Acidianus filamentous virus 1 coat proteins display a helical fold spanning the filamentous archaeal viruses lineage. Proc Natl Acad Sci U S A 2009; 106:21155-60. [PMID: 19934032 PMCID: PMC2795548 DOI: 10.1073/pnas.0909893106] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2009] [Indexed: 11/18/2022] Open
Abstract
Acidianus filamentous virus 1 (AFV1), a member of the Lipothrixviridae family, infects the hyperthermophilic, acidophilic crenarchaeaon Acidianus hospitalis. The virion, covered with a lipidic outer shell, is 9,100-A long and contains a 20.8-kb linear dsDNA genome. We have identified the two major coat proteins of the virion (MCPs; 132 and 140 amino acids). They bind DNA and form filaments when incubated with linear dsDNA. A C-terminal domain is identified in their crystal structure with a four-helix-bundle fold. In the topological model of the virion filament core, the genomic dsDNA superhelix wraps around the AFV1-132 basic protein, and the AFV1-140 basic N terminus binds genomic DNA, while its lipophilic C-terminal domain is imbedded in the lipidic outer shell. The four-helix bundle fold of the MCPs from AFV1 is identical to that of the coat protein (CP) of Sulfolobus islandicus rod-shaped virus (SIRV), a member of the Rudiviridae family. Despite low sequence identity between these proteins, their high degree of structural similarity suggests that they could have derived from a common ancestor and could thus define an yet undescribed viral lineage.
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Affiliation(s)
- Adeline Goulet
- Architecture et Fonction des Macromolécules Biologiques, Centre national de la recherche scientifique and Universités Aix-Marseille I & II, Architecture et Fonction des Macromolécules Biologiques, Unité Mixte de Recherche 6098, Case 932, 163 avenue de Luminy, 13288 Marseille Cedex 9, France
| | - Stéphanie Blangy
- Architecture et Fonction des Macromolécules Biologiques, Centre national de la recherche scientifique and Universités Aix-Marseille I & II, Architecture et Fonction des Macromolécules Biologiques, Unité Mixte de Recherche 6098, Case 932, 163 avenue de Luminy, 13288 Marseille Cedex 9, France
| | - Peter Redder
- Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, 28 Rue du Dr Roux, 75724 Paris Cedex 15, France; and
| | - David Prangishvili
- Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, 28 Rue du Dr Roux, 75724 Paris Cedex 15, France; and
| | - Catarina Felisberto-Rodrigues
- Architecture et Fonction des Macromolécules Biologiques, Centre national de la recherche scientifique and Universités Aix-Marseille I & II, Architecture et Fonction des Macromolécules Biologiques, Unité Mixte de Recherche 6098, Case 932, 163 avenue de Luminy, 13288 Marseille Cedex 9, France
| | - Patrick Forterre
- Institut Pasteur, Unité de Biologie Moléculaire du Gène chez les Extrêmophiles, 28 Rue du Dr Roux, 75724 Paris Cedex 15, France; and
- Institut de Génétique et Microbiologie, Université Paris-Sud and Centre national de la recherche scientifique, Unité Mixte de Recherche 8621, 91405 Orsay Cedex, France
| | - Valérie Campanacci
- Architecture et Fonction des Macromolécules Biologiques, Centre national de la recherche scientifique and Universités Aix-Marseille I & II, Architecture et Fonction des Macromolécules Biologiques, Unité Mixte de Recherche 6098, Case 932, 163 avenue de Luminy, 13288 Marseille Cedex 9, France
| | - Christian Cambillau
- Architecture et Fonction des Macromolécules Biologiques, Centre national de la recherche scientifique and Universités Aix-Marseille I & II, Architecture et Fonction des Macromolécules Biologiques, Unité Mixte de Recherche 6098, Case 932, 163 avenue de Luminy, 13288 Marseille Cedex 9, France
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Wang KH, Isidro AL, Domingues L, Eskandarian HA, McKenney PT, Drew K, Grabowski P, Chua MH, Barry SN, Guan M, Bonneau R, Henriques AO, Eichenberger P. The coat morphogenetic protein SpoVID is necessary for spore encasement in Bacillus subtilis. Mol Microbiol 2009; 74:634-49. [PMID: 19775244 DOI: 10.1111/j.1365-2958.2009.06886.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Endospores formed by Bacillus subtilis are encased in a tough protein shell known as the coat, which consists of at least 70 different proteins. We investigated the process of spore coat morphogenesis using a library of 40 coat proteins fused to green fluorescent protein and demonstrate that two successive steps can be distinguished in coat assembly. The first step, initial localization of proteins to the spore surface, is dependent on the coat morphogenetic proteins SpoIVA and SpoVM. The second step, spore encasement, requires a third protein, SpoVID. We show that in spoVID mutant cells, most coat proteins assembled into a cap at one side of the developing spore but failed to migrate around and encase it. We also found that SpoIVA directly interacts with SpoVID. A domain analysis revealed that the N-terminus of SpoVID is required for encasement and is a structural homologue of a virion protein, whereas the C-terminus is necessary for the interaction with SpoIVA. Thus, SpoVM, SpoIVA and SpoVID are recruited to the spore surface in a concerted manner and form a tripartite machine that drives coat formation and spore encasement.
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Affiliation(s)
- Katherine H Wang
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
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29
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The structure of bacteriophage phiCb5 reveals a role of the RNA genome and metal ions in particle stability and assembly. J Mol Biol 2009; 391:635-47. [PMID: 19559027 DOI: 10.1016/j.jmb.2009.06.047] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2009] [Revised: 04/29/2009] [Accepted: 06/17/2009] [Indexed: 11/20/2022]
Abstract
The structure of the Leviviridae bacteriophage phiCb5 virus-like particle has been determined at 2.9 A resolution and the structure of the native bacteriophage phiCb5 at 3.6 A. The structures of the coat protein shell appear to be identical, while differences are found in the organization of the density corresponding to the RNA. The capsid is built of coat protein dimers and in shape corresponds to a truncated icosahedron with T = 3 quasi-symmetry. The capsid is stabilized by four calcium ions per icosahedral asymmetric unit. One is located at the symmetry axis relating the quasi-3-fold related subunits and is part of an elaborate network of hydrogen bonds stabilizing the interface. The remaining calcium ions stabilize the contacts within the coat protein dimer. The stability of the phiCb5 particles decreases when calcium ions are chelated with EDTA. In contrast to other leviviruses, phiCb5 particles are destabilized in solution with elevated salt concentration. The model of the phiCb5 capsid provides an explanation of the salt-induced destabilization of phiCb5, since hydrogen bonds, salt bridges and calcium ions have important roles in the intersubunit interactions. Electron density of three putative RNA nucleotides per icosahedral asymmetric unit has been observed in the phiCb5 structure. The nucleotides mediate contacts between the two subunits forming a dimer and a third subunit in another dimer. We suggest a model for phiCb5 capsid assembly in which addition of coat protein dimers to the forming capsid is facilitated by interaction with the RNA genome. The phiCb5 structure is the first example in the levivirus family that provides insight into the mechanism by which the genome-coat protein interaction may accelerate the capsid assembly and increase capsid stability.
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30
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Persson M, Tars K, Liljas L. The Capsid of the Small RNA Phage PRR1 Is Stabilized by Metal Ions. J Mol Biol 2008; 383:914-22. [DOI: 10.1016/j.jmb.2008.08.060] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2007] [Revised: 06/16/2008] [Accepted: 08/18/2008] [Indexed: 10/21/2022]
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31
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Plevka P, Tars K, Liljas L. Crystal packing of a bacteriophage MS2 coat protein mutant corresponds to octahedral particles. Protein Sci 2008; 17:1731-9. [PMID: 18662904 PMCID: PMC2548359 DOI: 10.1110/ps.036905.108] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A covalent dimer of the bacteriophage MS2 coat protein was created by performing genetic fusion of two copies of the gene while removing the stop codon of the first gene. The dimer was crystallized in the cubic F432 space group. The organization of the asymmetric unit together with the F432 symmetry results in an arrangement of subunits that corresponds to T = 3 octahedral particles. The octahedral particles are probably artifacts created by the particular crystal packing. When it is not crystallized in the F cubic crystal form, the coat protein dimer appears to assemble into T = 3 icosahedral particles indistinguishable from the wild-type particles. To form an octahedral particle with closed surface, the dimer subunits interact at sharper angles than in the icosahedral arrangement. The fold of the covalent dimer is almost identical to the wild-type dimer with differences located in loops and in the covalent linker region. The main differences in the subunit packing between the octahedral and icosahedral arrangements are located close to the fourfold and fivefold symmetry axes where different sets of loops mediate the contacts. The volume of the wild-type virions is 7 times bigger than that of the octahedral particles.
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Affiliation(s)
- Pavel Plevka
- Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
| | - Kaspars Tars
- Latvian Biomedical Research and Study Centre, LV 1067 Riga, Latvia
| | - Lars Liljas
- Department of Cell and Molecular Biology, Uppsala University, SE-751 24 Uppsala, Sweden
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32
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Alcid EA, Jurica MS. A protein-based EM label for RNA identifies the location of exons in spliceosomes. Nat Struct Mol Biol 2008; 15:213-5. [PMID: 18223660 DOI: 10.1038/nsmb.1378] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2007] [Accepted: 01/02/2008] [Indexed: 11/09/2022]
Abstract
To locate key RNA features in the structure of the spliceosome by EM, we fused a sequence-specific RNA binding protein to a protein with a distinct donut-shaped structure. We used this fusion to label spliceosomes assembled on a pre-mRNA that contained the target sequence in the exons. The label is clearly visible in EM images of the spliceosome, and subsequent image processing with averaging shows that the exons sit close to each other in the complex. This labeling strategy will serve as a general tool for analyzing the structures of RNA-containing macromolecular complexes.
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Affiliation(s)
- Eric A Alcid
- Department of Molecular, Cell and Developmental Biology and Center for Molecular Biology of RNA, University of California, 1156 High Street, Santa Cruz, California 95064, USA
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33
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Caldeira JC, Peabody DS. Stability and assembly in vitro of bacteriophage PP7 virus-like particles. J Nanobiotechnology 2007; 5:10. [PMID: 18039380 PMCID: PMC2211308 DOI: 10.1186/1477-3155-5-10] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2007] [Accepted: 11/26/2007] [Indexed: 11/10/2022] Open
Abstract
Background The stability of a virus-like particle (VLP) is an important consideration for its use in nanobiotechnology. The icosahedral capsid of the RNA bacteriophage PP7 is cross-linked by disulfide bonds between coat protein dimers at its 5-fold and quasi-6-fold symmetry axes. This work determined the effects of these disulfides on the VLP's thermal stability. Results Measurements of the thermal denaturation behavior of PP7 VLPs in the presence and absence of a reducing agent show that disulfide cross-links substantially stabilize them against thermal denaturation. Although dimers in the capsid are linked to one another by disulfides, the two subunits of dimers themselves are held together only by non-covalent interactions. In an effort to confer even greater stability a new cross-link was introduced by genetically fusing two coat protein monomers, thus producing a "single-chain dimer" that assembles normally into a completely cross-linked VLP. However, subunit fusion failed to increase the thermal stability of the particles, even though it stabilized the isolated dimer. As a step toward gaining control of the internal composition of the capsid, conditions that promote the assembly of PP7 coat protein dimers into virus-like particles in vitro were established. Conclusion The presence of inter-dimer disulfide bonds greatly stabilizes the PP7 virus-like particle against thermal denaturation. Covalently cross-linking the subunits of the dimers themselves by genetically fusing them through a dipeptide linker sequence, offers no further stabilization of the VLP, although it does stabilize the dimer. PP7 capsids readily assemble in vitro in a reaction that requires RNA.
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Affiliation(s)
- Jerri C Caldeira
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, NM87131, USA.
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34
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Hogg JR, Collins K. RNA-based affinity purification reveals 7SK RNPs with distinct composition and regulation. RNA (NEW YORK, N.Y.) 2007; 13:868-80. [PMID: 17456562 PMCID: PMC1869041 DOI: 10.1261/rna.565207] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Recent studies have uncovered an unanticipated diversity of noncoding RNAs (ncRNAs), although these studies provide limited insight into their biological significance. Numerous general methods for identification and characterization of protein interactions have been developed, but similar approaches for characterizing cellular ncRNA interactions are lacking. Here we describe RNA Affinity in Tandem (RAT), an original, entirely RNA tag-based method for affinity purification of endogenously assembled RNP complexes. We demonstrate the general utility of RAT by isolating RNPs assembled in vivo on ncRNAs transcribed by RNA polymerase II or III. Using RAT in conjunction with protein identification by mass spectrometry and protein-RNA interaction assays, we define and characterize previously unanticipated protein subunits of endogenously assembled human 7SK RNPs. We show that 7SK RNA resides in a mixed population of RNPs with different protein compositions and responses to cellular stress. Depletion of a newly identified 7SK RNP component, hnRNP K, alters the partitioning of 7SK RNA among distinct RNPs. Our results establish the utility of a generalizable RNA-based RNP affinity purification method and provide insight into 7SK RNP dynamics.
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Affiliation(s)
- J Robert Hogg
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720-3200, USA
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35
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Ruokoranta TM, Grahn AM, Ravantti JJ, Poranen MM, Bamford DH. Complete genome sequence of the broad host range single-stranded RNA phage PRR1 places it in the Levivirus genus with characteristics shared with Alloleviviruses. J Virol 2006; 80:9326-30. [PMID: 16940544 PMCID: PMC1563911 DOI: 10.1128/jvi.01005-06] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Single-stranded RNA (ssRNA) bacteriophages of the family Leviviridae infect gram-negative bacteria. They are restricted to a single host genus. Phage PRR1 is an exception, having a broad host range due to the promiscuity of the receptor encoded by the IncP plasmid. Here we report the complete genome sequence of PRR1. Three proteins homologous with those of other ssRNA phages, i.e., maturation, coat, and replicase proteins, were identified. A fourth protein has a lysis function. Comparison of PRR1 with other members of the Leviviridae family places PRR1 in the genus Levivirus with some characteristics more similar to those of members of the genus Allolevivirus.
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Affiliation(s)
- Tanja M Ruokoranta
- Department of Biological and Environmental Sciences, Institute of Biotechnology, Viikki Biocenter 2, P.O. Box 56 (Viikinkaari 5), FIN-00014 University of Helsinki, Finland
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36
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van den Worm SHE, Koning RI, Warmenhoven HJ, Koerten HK, van Duin J. Cryo electron microscopy reconstructions of the Leviviridae unveil the densest icosahedral RNA packing possible. J Mol Biol 2006; 363:858-65. [PMID: 16989861 DOI: 10.1016/j.jmb.2006.08.053] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2006] [Revised: 08/21/2006] [Accepted: 08/21/2006] [Indexed: 11/21/2022]
Abstract
We solved the structures of the single-stranded RNA bacteriophages Qbeta, PP7 and AP205 by cryo-electron microscopy. On the outside, the symmetrized electron density maps resemble the previously described cryo-electron microscopy structure of MS2. RNA density is present inside the capsids, suggesting that the genomic RNA of Qbeta, PP7 and AP205, analogous to MS2, contains many coat protein-binding sites in addition to the hairpin on which assembly and packaging are initiated. All four bacteriophages harbour the same overall arrangement of the RNA, which is a unique combination of both triangles and pentagons. This combination has not been found in other icosahedral viruses, in which the RNA structures are either triangular or pentagonal. Strikingly, the unique RNA packing of the Leviviridae appears to deploy the most efficient method of RNA storage by obeying icosahedral symmetry.
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Affiliation(s)
- Sjoerd H E van den Worm
- Department of Biochemistry, Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA, Leiden, the Netherlands.
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37
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Licis N, van Duin J. Structural constraints and mutational bias in the evolutionary restoration of a severe deletion in RNA phage MS2. J Mol Evol 2006; 63:314-29. [PMID: 16838216 DOI: 10.1007/s00239-005-0012-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2005] [Accepted: 04/12/2006] [Indexed: 11/28/2022]
Abstract
A 4-nucleotide (nt) deletion was made in the 36-nt-long intercistronic region separating the coat and replicase genes of the single-stranded RNA phage MS2. This region is the focus of several RNA structures conferring high fitness. One such element is the operator hairpin, which, in the course of infection, will bind a coat-protein dimer, thereby precluding further replicase synthesis and initiating encapsidation. Another structure is a long-distance base pairing (MJ) controlling replicase expression. The 4-nt deletion does not directly affect the operator hairpin but it disrupts the MJ pairing. Its main effect, however, is a frame shift in the overlapping lysis gene. This gene starts in the upstream coat gene, runs through the 36-nt-long intercistronic region, and ends in the downstream replicase cistron. Here we report and interpret the spectrum of solutions that emerges when the crippled phage is evolved. Four different solutions were obtained by sequencing 40 plaques. Three had cured the frame shift in the lysis gene by inserting one nt in the loop of the operator hairpin causing its inactivation. Yet these low-fitness revertants could further improve themselves when evolved. The inactivated operator was replaced by a substitute and thereafter these revertants found several ways to restore control over the replicase gene. To allow for the evolutionary enrichment of low-probability but high-fitness revertants, we passaged lysate samples before plating. Revertants obtained in this way also restored the frame shift, but not at the expense of the operator. By taking larger and larger lysates samples for such bulk evolution, ever higher-fitness and lower-frequency revertants surfaced. Only one made it back to wild type. As a rule, however, revertants moved further and further away from the wild-type sequence because restorative mutations are, in the majority of cases, selected for their capacity to improve the phenotype by optimizing one of several potential alternative RNA foldings that emerge as a result of the initial deletion. This illustrates the role of structural constraints which limit the path of subsequent restorative mutations.
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Affiliation(s)
- Normunds Licis
- Biomedical Research and Study Centre, University of Latvia, Ratsupites 1, LV 1067, Riga, Latvia.
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38
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Angelescu DG, Bruinsma R, Linse P. Monte Carlo simulations of polyelectrolytes inside viral capsids. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2006; 73:041921. [PMID: 16711850 DOI: 10.1103/physreve.73.041921] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2005] [Revised: 03/01/2006] [Indexed: 05/09/2023]
Abstract
Structural features of polyelectrolytes as single-stranded RNA or double-stranded DNA confined inside viral capsids and the thermodynamics of the encapsidation of the polyelectrolyte into the viral capsid have been examined for various polyelectrolyte lengths by using a coarse-grained model solved by Monte Carlo simulations. The capsid was modeled as a spherical shell with embedded charges and the genome as a linear jointed chain of oppositely charged beads, and their sizes corresponded to those of a scaled-down T=3 virus. Counterions were explicitly included, but no salt was added. The encapisdated chain was found to be predominantly located at the inner capsid surface, in a disordered manner for flexible chains and in a spool-like structure for stiff chains. The distribution of the small ions was strongly dependent on the polyelectrolyte-capsid charge ratio. The encapsidation enthalpy was negative and its magnitude decreased with increasing polyelectrolyte length, whereas the encapsidation entropy displayed a maximum when the capsid and polyelectrolyte had equal absolute charge. The encapsidation process remained thermodynamically favorable for genome charges ca. 3.5 times the capsid charge. The chain stiffness had only a relatively weak effect on the thermodynamics of the encapsidation.
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39
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Peabody DS. A Viral Platform for Chemical Modification and Multivalent Display. J Nanobiotechnology 2003; 1:5. [PMID: 12890286 PMCID: PMC169181 DOI: 10.1186/1477-3155-1-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2003] [Accepted: 07/15/2003] [Indexed: 11/10/2022] Open
Abstract
The ability to chemically modify the surfaces of viruses and virus-like particles makes it possible to confer properties that make them potentially useful in biotechnology, nanotechnology and molecular electronics applications. RNA phages (e.g. MS2) have characteristics that make them suitable scaffolds to which a variety of substances could be chemically attached in definite geometric patterns. To provide for specific chemical modification of MS2's outer surface, cysteine residues were substituted for several amino acids present on the surface of the wild-type virus particle. Some substitutions resulted in coat protein folding or stability defects, but one allowed the production of an otherwise normal virus-like particle with an accessible sulfhydryl on its surface.
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Affiliation(s)
- David S Peabody
- Department of Molecular Genetics and Microbiology and the Cancer Research and Treatment Center University of New Mexico School of Medicine Albuquerque, New Mexico, USA 87131.
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40
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Brown WL, Mastico RA, Wu M, Heal KG, Adams CJ, Murray JB, Simpson JC, Lord JM, Taylor-Robinson AW, Stockley PG. RNA bacteriophage capsid-mediated drug delivery and epitope presentation. Intervirology 2003; 45:371-80. [PMID: 12602361 DOI: 10.1159/000067930] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE To use our knowledge of the three-dimensional structure and self-assembly mechanism of RNA bacteriophage capsids to develop novel virus-like particles (VLPs) for drug delivery and epitope presentation. METHODS Site-directed mutagenesis of a recombinant MS2 coat protein expression construct has been used to generate translational fusions encompassing short epitope sequences. These chimeric proteins still self-assemble in vivo into T = 3 shells with the foreign epitope in an accessible location. Covalent conjugation has also been used to generate RNA stem-loops attached to the toxin, ricin A chain, or to nucleotide-based drugs, that are still capable of stimulating self-assembly of the capsid in vitro. These packaged drugs can then be directed to specific cells in culture by further covalent decoration of the capsids with targeting molecules. RESULTS Chimeric VLPs are strongly immunogenic when carrying either B or T cell epitopes, the latter generating cytokine profiles consistent with memory responses. Immune responses to the underlying phage epitopes appear to be proportional to the area of the phage surface accessible. Phage shells effectively protect nucleic acid-based drugs and, for the toxin construct, make cell-specific delivery systems with LD50 values in culture sub-nanomolar. CONCLUSION VLP technology has potential for therapeutic and prophylactic intervention in disease.
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Affiliation(s)
- William L Brown
- Ashbury Centre for Structural Molecular Biology, University of Leeds, UK
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41
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Spingola M, Lim F, Peabody DS. Recognition of diverse RNAs by a single protein structural framework. Arch Biochem Biophys 2002; 405:122-9. [PMID: 12176065 DOI: 10.1016/s0003-9861(02)00334-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The coat proteins of different single-strand RNA phages utilize a common structural framework to recognize different RNA targets, making them suitable models for studies of RNA-protein recognition generally, especially for the class of proteins that bind RNA on a beta-sheet surface. Here we show that structurally distinct molecules are capable of satisfying the requirements for binding to Qbeta coat protein. Although the predicted secondary structures of the RNAs differ markedly, we contend that they are approximately equivalent structurally in their complexes with coat protein. Based on our prior observations that the RNA-binding specificities of Qbeta and MS2 coat proteins can be interconverted with as few as one amino acid substitution each, and taking into account details of the structures of complexes of MS2 coat protein with wild-type and aptamer RNAs, we propose a model for the Qbeta coat protein-RNA complex.
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Affiliation(s)
- Marc Spingola
- Department of Molecular Genetics and Microbiology, University of New Mexico School of MedicineAlbuquerque, NM 87131, USA
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42
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Klovins J, Overbeek GP, van den Worm SHE, Ackermann HW, van Duin J. Nucleotide sequence of a ssRNA phage from Acinetobacter: kinship to coliphages. J Gen Virol 2002; 83:1523-1533. [PMID: 12029168 DOI: 10.1099/0022-1317-83-6-1523] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The complete nucleotide sequence of ssRNA phage AP205 propagating in Acinetobacter species is reported. The RNA has three large ORFs, which code for the following homologues of the RNA coliphage proteins: the maturation, coat and replicase proteins. Their gene order is the same as that in coliphages. RNA coliphages or Leviviridae fall into two genera: the alloleviviruses, like Q(beta), which have a coat read-through protein, and the leviviruses, like MS2, which do not have this coat protein extension. AP205 has no read-through protein and may therefore be classified as a levivirus. A major digression from the known leviviruses is the apparent absence of a lysis gene in AP205 at the usual position, overlapping the coat and replicase proteins. Instead, two small ORFs are present at the 5' terminus, preceding the maturation gene. One of these might encode a lysis protein. The other is of unknown function. Other new features concern the 3'-terminal sequence. In all ssRNA coliphages, there are always three cytosine residues at the 3' end, but in AP205, there is only a single terminal cytosine. Distantly related viruses, like AP205 and the coliphages, do not have significant sequence identity; yet, important secondary structural features of the RNA are conserved. This is shown here for the 3' UTR and the replicase-operator hairpin. Interestingly, although AP205 has the genetic map of a levivirus, its 3' UTR has the length and RNA secondary structure of an allolevivirus. Sharing features with both MS2 and Q(beta) suggests that, in an evolutionary sense, AP205 should be placed between Q(beta) and MS2. A phylogenetic tree for the ssRNA phages is presented.
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Affiliation(s)
- J Klovins
- Biomedical Research Centre, University of Latvia, Riga, Latvia2
- Department of Biochemistry, Gorlaeus Laboratories, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands1
| | - G P Overbeek
- Department of Biochemistry, Gorlaeus Laboratories, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands1
| | - S H E van den Worm
- Department of Biochemistry, Gorlaeus Laboratories, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands1
| | - H-W Ackermann
- Félix d'Hérelle Reference Centre for Bacterial Viruses, Department of Microbiology, Medical Faculty, Laval University, Québec, Canada G1K 7P43
| | - J van Duin
- Department of Biochemistry, Gorlaeus Laboratories, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands1
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43
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Lim F, Downey TP, Peabody DS. Translational repression and specific RNA binding by the coat protein of the Pseudomonas phage PP7. J Biol Chem 2001; 276:22507-13. [PMID: 11306589 DOI: 10.1074/jbc.m102411200] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
PP7 is a single-strand RNA bacteriophage of Pseudomonas aeroginosa and a distant relative to coliphages like MS2 and Qbeta. Here we show that PP7 coat protein is a specific RNA-binding protein, capable of repressing the translation of sequences fused to the translation initiation region of PP7 replicase. Its RNA binding activity is specific since it represses the translational operator of PP7, but does not repress the operators of the MS2 or Qbeta phages. Conditions for the purification of coat protein and for the reconstitution of its RNA binding activity from disaggregated virus-like particles were established. Its dissociation constant for PP7 operator RNA in vitro was determined to be about 1 nm. Using a genetic system in which coat protein represses translation of a replicase-beta-galactosidase fusion protein, amino acid residues important for binding of PP7 RNA were identified.
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Affiliation(s)
- F Lim
- Department of Molecular Genetics and Microbiology, University of New Mexico School of Medicine, Albuquerque, New Mexico 87131, USA
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