17 results on '"Satoru, Horiya"'
Search Results
2. Large-Scale Synthesis of Man9GlcNAc2 High-Mannose Glycan and the Effect of the Glycan Core on Multivalent Recognition by HIV Antibody 2G12
- Author
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Mahesh Neralkar, Bokai Xu, Satoru Horiya, and Isaac J. Krauss
- Subjects
Infectious Diseases - Published
- 2022
3. The Impact of Sustained Immunization Regimens on the Antibody Response to Oligomannose Glycans
- Author
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Isaac J. Krauss, J. Sebastian Temme, Jennifer K. Bailey, Celia C. LaBranche, Satoru Horiya, Avital A. Rodal, ShiYu Wang, Dung N. Nguyen, Robyn L. Stanfield, Ian A. Wilson, David C. Montefiori, Bokai Xu, and Richard L Redman
- Subjects
0301 basic medicine ,Glycan ,animal structures ,Glycosylation ,Protein Conformation ,Oligosaccharides ,HIV Infections ,HIV Antibodies ,HIV Envelope Protein gp120 ,01 natural sciences ,Biochemistry ,Small Molecule Libraries ,03 medical and health sciences ,Mannosidases ,Medicine ,Animals ,Humans ,AIDS Vaccines ,Binding Sites ,Vaccines, Conjugate ,biology ,010405 organic chemistry ,business.industry ,Vaccination ,Glycopeptides ,virus diseases ,General Medicine ,HIV envelope protein ,Articles ,Virology ,Antibodies, Neutralizing ,Glycopeptide ,3. Good health ,0104 chemical sciences ,Regimen ,030104 developmental biology ,Antibody response ,Immunization ,Antibody Formation ,biology.protein ,Molecular Medicine ,High mannose ,Rabbits ,Antibody ,business ,Protein Binding - Abstract
The high mannose patch (HMP) of the HIV envelope protein (Env) is the structure most frequently targeted by broadly neutralizing antibodies; therefore, many researchers have attempted to use mimics of this region as a vaccine immunogen. In our previous efforts, vaccinating rabbits with evolved HMP mimic glycopeptides containing Man9 resulted in an overall antibody response targeting the glycan core and linker rather than the full glycan or Manα1→2Man tips of Man9 glycans. A possible reason could be processing of our immunogen by host serum mannosidases. We sought to test whether more prolonged dosing could increase the antibody response to intact glycans, possibly by increasing the availability of intact Man9 to germinal centers. Here, we describe a study investigating the impact of immunization regimen on antibody response by testing immunogen delivery through bolus, an exponential series of mini doses, or a continuously infusing mini-osmotic pump. Our results indicate that, with our glycopeptide immunogens, standard bolus immunization elicited the strongest HIV Env-binding antibody response, even though higher overall titers to the glycopeptide were elicited by the exponential and pump regimens. Antibody selectivity for intact glycan was, if anything, slightly better in the bolus-immunized animals.
- Published
- 2020
4. Synthesis of multivalent glycopeptide conjugates that mimic an HIV epitope
- Author
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Satoru Horiya, Dung N. Nguyen, Isaac J. Krauss, and Jennifer K. Bailey
- Subjects
0301 basic medicine ,biology ,Organic Chemistry ,Directed evolution ,Biochemistry ,Combinatorial chemistry ,Article ,Glycopeptide ,Epitope ,03 medical and health sciences ,chemistry.chemical_compound ,030104 developmental biology ,chemistry ,Antigen ,Drug Discovery ,Click chemistry ,Peptide synthesis ,biology.protein ,HIV vaccine ,Antibody - Abstract
Recently, we reported a directed evolution method which enabled us to discover sequences of glycopeptides that bind with picomolar affinity to HIV antibody 2G12 and are of interest as HIV vaccine candidates. In this manuscript, we describe the syntheses of several of these large (~11-12 kDa) glycopeptides by a combination of fast flow peptide synthesis and click chemistry. We also discuss the optimization of their attachment to carrier protein CRM197, affording antigenic and immunogenic conjugates ready for animal vaccination.
- Published
- 2016
5. Recent strategies targeting HIV glycans in vaccine design
- Author
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Isaac J. Krauss, Satoru Horiya, and Iain S. MacPherson
- Subjects
Models, Molecular ,Glycan ,Molecular Sequence Data ,HIV Infections ,HIV Envelope Protein gp120 ,Antibodies, Viral ,Article ,Immune system ,Viral envelope ,Polysaccharides ,Humans ,Amino Acid Sequence ,HIV vaccine ,Molecular Biology ,Peptide sequence ,Glycoproteins ,AIDS Vaccines ,chemistry.chemical_classification ,biology ,Cell Biology ,Antibodies, Neutralizing ,Virology ,Carbohydrate Sequence ,chemistry ,Drug Design ,Immunology ,HIV-1 ,biology.protein ,Antibody ,Glycoprotein - Abstract
Although efforts to develop a vaccine against HIV have so far met with little success, recent studies of HIV-positive patients with strongly neutralizing sera have shown that the human immune system is capable of producing potent and broadly-neutralizing antibodies (bnAbs), some of which neutralize up to 90 % of HIV strains. These antibodies bind to conserved vulnerable sites on the viral envelope glycoprotein gp120, and identification of these sites has provided tantalizing clues about the design of potentially effective vaccines. Carbohydrates play a key role in this field, as a large fraction of bnAbs bind to carbohydrates or combinations of carbohydrate and peptide elements on gp120. Additionally, carbohydrates partially mask some peptide surfaces recognized by bnAbs. The use of engineered glycoproteins and other glycostructures as vaccines to elicit antibodies with broad neutralizing activity is therefore a key area of interest in HIV vaccine design.
- Published
- 2014
6. Directed Evolution of Glycopeptides Using mRNA Display
- Author
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Isaac J. Krauss, Satoru Horiya, and Jennifer K. Bailey
- Subjects
0301 basic medicine ,Glycan ,Glycosylation ,medicine.drug_class ,HIV Envelope Protein gp120 ,010402 general chemistry ,Monoclonal antibody ,01 natural sciences ,Epitope ,Article ,03 medical and health sciences ,chemistry.chemical_compound ,Epitopes ,Polysaccharides ,Yeasts ,medicine ,Escherichia coli ,mRNA display ,Humans ,Amino Acid Sequence ,RNA, Messenger ,Glycoproteins ,chemistry.chemical_classification ,biology ,Glycobiology ,Glycopeptides ,Directed evolution ,0104 chemical sciences ,030104 developmental biology ,chemistry ,Biochemistry ,biology.protein ,HIV-1 ,Directed Molecular Evolution ,Glycoprotein - Abstract
Directed evolution is a useful method for the discovery of nucleic acids, peptides, or proteins that have desired binding abilities or functions. Because of the abundance and importance of glycosylation in nature, directed evolution of glycopeptides and glycoproteins is also highly desirable. However, common directed evolution platforms such as phage-, yeast-, or mammalian-cell display are limited for these applications by several factors. Glycan structure at each glycosylation site is not genetically encoded, and yeast and mammalian cells produce a heterogeneous mixture of glycoforms at each site on the protein. Although yeast, mammalian and Escherichia coli cells can be engineered to produce a homogenous glycoform at all glycosylation sites, there are just a few specific glycan structures that can readily be accessed in this manner. Recently, we reported a novel system for the directed evolution of glycopeptide libraries, which could in principle be decorated with any desired glycan. Our method combines in vitro peptide selection by mRNA display with unnatural amino acid incorporation and chemical attachment of synthetic oligosaccharides. Here, we provide an updated and optimized protocol for this method, which is designed to create glycopeptide mRNA display libraries containing ~ 10 13 sequences and select them for target binding. The target described here is the HIV broadly neutralizing monoclonal antibody 2G12; 2G12 binds to cluster of high-mannose oligosaccharides on the HIV envelope glycoprotein gp120; and glycopeptides that mimic this epitope may be useful in HIV vaccine applications. This method is expected to be readily applicable for other types of glycans and targets of interest in glycobiology.
- Published
- 2017
7. Directed Evolution of Multivalent Glycopeptides Tightly Recognized by HIV Antibody 2G12
- Author
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Isaac J. Krauss, J. Sebastian Temme, Yollete V. Guillen Schlippe, Jennifer K. Bailey, and Satoru Horiya
- Subjects
AIDS Vaccines ,Glycan ,Molecular Structure ,biology ,Chemistry ,Glycopeptides ,General Chemistry ,HIV Antibodies ,Directed evolution ,Biochemistry ,Combinatorial chemistry ,Article ,Catalysis ,Glycopeptide ,3. Good health ,Colloid and Surface Chemistry ,biology.protein ,Click chemistry ,mRNA display ,Click Chemistry ,Antibody ,HIV vaccine - Abstract
Herein, we report a method for in vitro selection of multivalent glycopeptides, combining mRNA display with incorporation of unnatural amino acids and "click" chemistry. We have demonstrated the use of this method to design potential glycopeptide vaccines against HIV. From libraries of ~10(13) glycopeptides containing multiple Man9 glycan(s), we selected variants that bind to HIV broadly neutralizing antibody 2G12 with picomolar to low nanomolar affinity. This is comparable to the strength of the natural 2G12-gp120 interaction, and is the strongest affinity achieved to date with constructs containing 3-5 glycans. These glycopeptides are therefore of great interest in HIV vaccine design.
- Published
- 2014
8. RNA LEGO
- Author
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Ryota Saito, Satoru Horiya, Kazuo Harada, Koh Kobayashi, Xianglan Li, Akira Katoh, and Gota Kawai
- Subjects
Pharmacology ,Clinical Biochemistry ,RNA ,Nanotechnology ,General Medicine ,Biology ,Biochemistry ,Nucleic acid secondary structure ,Complementarity (molecular biology) ,Drug Discovery ,Biophysics ,Nucleic acid ,Molecular Medicine ,Rna folding ,Linker ,Molecular Biology ,Macromolecule - Abstract
The high affinity and specificity of nucleic acid base complementarity has been proven to be a powerful method for constructing specific molecular assemblies. On the other hand, recent structural studies of RNA have revealed the wide range of tertiary interactions utilized in RNA folding, which may potentially be used as tools for the design of specific macromolecular assemblies. Here, RNA building blocks containing two hairpin loops, based on the dimerization initiation site (DIS) of HIV RNA, connected by a short linker were used to construct large RNA assemblies through hairpin loop-loop ("kissing") interactions. We show that specific linear and circular assemblies can be constructed in a magnesium-dependent manner using several non-self-complementary loop-loop interactions designed in this study. These results show that the use of RNA tertiary interactions may broaden the reportoire of nucleic acid-based nanostructures.
- Published
- 2003
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9. Selection of RRE RNA binding peptides using a kanamycin antitermination assay
- Author
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Alan D. Frankel, Chandreyee Das, Kazuo Harada, Satoru Horiya, and Hadas Peled-Zehavi
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chemistry.chemical_classification ,Genetics ,Kanamycin Resistance ,RNA-Binding Proteins ,Method ,RNA ,Peptide ,RNA-binding protein ,Biology ,Genes, env ,Transcription antitermination ,HIV Rev response element ,chemistry ,Biochemistry ,Genes, Reporter ,Kanamycin ,Peptide Library ,Antitermination ,HIV-1 ,Biological Assay ,Peptides ,Peptide library ,Molecular Biology - Abstract
The arginine-rich domains of several RNA-binding proteins have been shown to bind their cognate RNAs with high affinities and specificities as isolated peptides, adopting different conformations within different complexes. The sequence simplicity and structural diversity of the arginine-rich motif has made it a good framework for constructing combinatorial libraries and identifying novel RNA-binding peptides, including those targeted to the HIV Rev response element (RRE). Here we describe a modified transcription antitermination reporter assay engineered with kanamycin resistance that enables larger in vivo screens (∼109 sequences) than previously possible. We show that the assay detects only specific RNA–protein complexes, and that binders are enriched at least 300-fold per round of selection. We screened a large peptide library in which amino acids with charged, polar, and small side chains were randomly distributed within a polyarginine framework and identified a set of high affinity RRE-binding peptides. Most contain glutamine at one particular peptide position, and the best peptides display significantly higher antitermination activities than Rev or other previously described high-affinity RRE-binding peptides. The kanamycin antitermination (KAN) assay should be useful for screening relatively large libraries and thereby facilitate identification of novel RNA binders.
- Published
- 2003
10. Identification of antisense RNA stem-loops that inhibit RNA-protein interactions using a bacterial reporter system
- Author
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Eri Haneda, Kazuo Harada, Satoru Horiya, Takako Minami, Makiko Ikeda, and Akiko Yano
- Subjects
Genetics ,Bacteria ,RNA-dependent RNA polymerase ,RNA ,Nuclease protection assay ,Biology ,Regulatory Sequences, Ribonucleic Acid ,Non-coding RNA ,Cell biology ,Antisense RNA ,Ribonucleoprotein, U1 Small Nuclear ,RNA silencing ,Genes, Reporter ,Antitermination ,RNA, Small Nuclear ,Sense (molecular biology) ,Mutation ,Synthetic Biology and Chemistry ,Nucleic Acid Conformation ,RNA, Antisense ,Viral Regulatory and Accessory Proteins - Abstract
Many well-characterized examples of antisense RNAs from prokaryotic systems involve hybridization of the looped regions of stem-loop RNAs, presumably due to the high thermodynamic stability of the resulting loop-loop and loop-linear interactions. In this study, the identification of RNA stem-loops that inhibit U1A protein binding to the hpII RNA through RNA-RNA interactions was attempted using a bacterial reporter system based on phage lambda N-mediated antitermination. As a result, loop sequences possessing 7-8 base complementarity to the 5' region of the boxA element important for functional antitermination complex formation, but not the U1 hpII loop, were identified. In vitro and in vivo mutational analysis strongly suggested that the selected loop sequences were binding to the boxA region, and that the structure of the antisense stem-loop was important for optimal inhibitory activity. Next, in an attempt to demonstrate the ability to inhibit the interaction between the U1A protein and the hpII RNA, the rational design of an RNA stem-loop that inhibits U1A-binding to a modified hpII was carried out. Moderate inhibitory activity was observed, showing that it is possible to design and select antisense RNA stem-loops that disrupt various types of RNA-protein interactions.
- Published
- 2010
11. Replacement of the lambda boxB RNA-N peptide with heterologous RNA-peptide interactions relaxes the strict spatial requirements for the formation of a transcription anti-termination complex
- Author
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Senya Matsufuji, Naomi Masui, Kazuo Harada, Masaya Ishibashi, Misa Mizuguchi, Satoru Horiya, Hiroaki Uehara, Chang-Song Koh, and Mitsuru Inaba
- Subjects
chemistry.chemical_classification ,Binding Sites ,biology ,Transcription, Genetic ,Heterologous ,RNA ,RNA-Binding Proteins ,Peptide ,biology.organism_classification ,Microbiology ,Bacteriophage lambda ,Cell biology ,Bacteriophage ,chemistry.chemical_compound ,Biochemistry ,chemistry ,Transcription (biology) ,RNA polymerase ,Codon, Terminator ,Nucleic Acid Conformation ,RNA, Viral ,Viral Regulatory and Accessory Proteins ,Molecular Biology ,Host factor ,Ribonucleoprotein - Abstract
Summary In bacteriophage λ, formation of a transcriptional anti-termination complex involving the elongating RNA polymerase is mediated by the interaction of boxB RNA with the RNA-binding domain of the N protein (N peptide). In an attempt to understand the spatial requirements for boxB/N peptide interaction within the anti-termination complex, the effects of changes in the distance between boxA and boxB RNA, the length of the boxB stem, and the distance between the N peptide and remainder of the N protein were examined using a bacterial reporter system. It was found that the requirements for boxB stem length and the distance between N peptide and the remainder of N were optimized and strict. In contrast, replacement of the boxB/N interaction by heterologous RNA–peptide interactions appeared to relax the strict requirement for RNA stem length and the orientation of the RNA-binding peptide, presumably due to the absence of the cooperative interaction between boxB/N and the host factor NusA. In addition, the decrease in activity upon stem lengthening could be partially suppressed by simultaneous lengthening of the RNA spacer. A further understanding of the structural organization of the anti-termination complex may provide insights into how functional ribonucleoprotein complexes may be engineered.
- Published
- 2009
12. Analysis of the interaction between selected RNA-binding peptides and a target RNA containing a bulge and a GNRA-type tetraloop
- Author
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Kazuo Harada, Chang-Song Koh, Senya Matsufuji, and Satoru Horiya
- Subjects
Messenger RNA ,Base Sequence ,Stereochemistry ,Molecular Sequence Data ,RNA-dependent RNA polymerase ,RNA ,General Medicine ,Biology ,Molecular biology ,Tetraloop ,gag Gene Products, Human Immunodeficiency Virus ,Frameshift mutation ,Molecular recognition ,Bulge ,Peptide Library ,pol Gene Products, Human Immunodeficiency Virus ,HIV-1 ,Nucleic Acid Conformation ,RNA, Viral ,RNA, Messenger ,Purine metabolism ,Peptides - Abstract
We have characterized the interaction between selected novel RNA-binding peptides and their target RNA. The RNA is comprised of two elements, a GCAA tetraloop, a member of the thermodynamically stable GNRA-type (where N is A or G, U, C; R is G or A) tetraloops, and a tri-purine bulge found in the frameshift stimutating structure on the human immunodeficiency virus type 1 (HIV-1) gag-pol mRNA. Peptides that bind specifically to the target RNA were selected from a combinatorial library based on arginine-rich motif (ARM) by a bacterial reporter system. We performed mutational studies using the reporter system and gel shift assays and found that the binding affinity and specificity of the RNA were mainly dependent on the GNRA-type tetraloop, and a modest contribution was also attributed to the bulge structure. Our finding reveals a novel mode of interaction by an RNA-peptide complex and expands our knowledge on the diversity of molecular recognition.
- Published
- 2008
13. An efficient thermally induced RNA conformational switch as a framework for the functionalization of RNA nanostructures
- Author
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Satoru Horiya, Xianglan Li, and Kazuo Harada
- Subjects
Models, Molecular ,Nanostructure ,Hot Temperature ,Molecular Sequence Data ,Nanotechnology ,Plasma protein binding ,Biochemistry ,Genes, env ,Catalysis ,chemistry.chemical_compound ,Colloid and Surface Chemistry ,Circular RNA ,Nucleic acid structure ,Base Sequence ,RNA ,HIV ,General Chemistry ,Non-coding RNA ,Nanostructures ,chemistry ,Biophysics ,Nucleic Acid Conformation ,RNA, Viral ,Isomerization ,DNA ,Protein Binding - Abstract
RNA offers a variety of interactions and dynamic conformational switches not available with DNA that may be exploited for the construction of nanomolecular structures. Here, we show how the RNA loop-loop, or "kissing", interaction can be used to construct specific circular RNA arrangements that are capable of thermal isomerization to alternative structures. We also show how this thermally induced structural rearrangement can be used to unmask a functional RNA structure, in this case, a peptide-binding RNA structure, the Rev-response element (RRE) of HIV, thereby acting as a functional peptide-binding switch. The relative ease with which the RRE could be engineered into the RNA substrates suggested that a variety of functional RNA structures may be introduced. In addition, the structural rearrangement was extremely efficient, showing that the "kissing" complexes described in this study may provide a useful framework for the construction of functional RNA-based nanostructures, as well as aid in our understanding of the way RNA functions in biological systems.
- Published
- 2006
14. Screening in vivo for RNA-binding peptides from combinatorial libraries
- Author
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Kazuo Harada, Hadas Zehavi, Satoru Horiya, and Alan D. Frankel
- Subjects
Kanamycin Resistance ,Reporter gene ,Kanamycin Kinase ,RNA ,RNA-Binding Proteins ,General Medicine ,Computational biology ,Biology ,Molecular biology ,In vivo ,Genes, Reporter ,Peptide Library ,Drug Design ,Combinatorial Chemistry Techniques ,Neomycin Phosphotransferase - Abstract
We have modified a previously developed genetic assay system for RNA-polypeptide interactions in a attempt to more readily identify RNA-binding peptides. The first modification involved the design of a "complex" library that would contain a variety of RNA-binding polypeptides. The second modification involved the use of neomycin phosphotransferase (NPT II) as the reporter gene, therefore allowing "selection" of RNA-binding peptides by kanamycin resistance. The improved screening system should allow the identification of peptides that bind to a variety of RNA structures.
- Published
- 2003
15. RNA LEGO: magnesium-dependent assembly of RNA building blocks through loop-loop interactions
- Author
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Ryota Saito, Satoru Horiya, Gota Kawai, Xianglan Li, Kazuo Harada, Koh Kobayashi, and Akira Katoh
- Subjects
chemistry.chemical_classification ,Circular dichroism ,Base Sequence ,Stereochemistry ,Magnesium ,Base pair ,Molecular Sequence Data ,RNA ,chemistry.chemical_element ,General Medicine ,Biology ,Molecular biology ,Loop (topology) ,chemistry ,Nucleic Acid Conformation ,Nucleotide ,Electrophoresis, Polyacrylamide Gel ,Polyacrylamide gel electrophoresis ,Linker - Abstract
We describe the construction of nano-molecular assemblies using RNA building blocks the human immunodeficiency virus type 1 (HIV-1) dimerization initiation site (DIS) RNA, that forms stable base pairing through a magnesium-depe ndent loop-loop interaction ("kissing"). RNA building blocks containing two DIS or DIS-like hairpins connected by a two nucleotide linker self-assembled to form specific structures as observed by non-denaturin g polyacrylamide gel electrophoresis (PAGE). Furthermore, observation of "real time" formation of the molecular assemblies by circular dichroism (CD) spectroscopy was attempted.
- Published
- 2003
16. RNA LEGO: magnesium-dependent formation of specific RNA assemblies through kissing interactions
- Author
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Satoru, Horiya, Xianglan, Li, Gota, Kawai, Ryota, Saito, Akira, Katoh, Koh, Kobayashi, and Kazuo, Harada
- Subjects
Circular Dichroism ,HIV-1 ,Nucleic Acid Conformation ,RNA ,RNA, Viral ,Electrophoresis, Polyacrylamide Gel ,Electrophoretic Mobility Shift Assay ,Magnesium ,DNA-Directed RNA Polymerases ,Dimerization - Abstract
The high affinity and specificity of nucleic acid base complementarity has been proven to be a powerful method for constructing specific molecular assemblies. On the other hand, recent structural studies of RNA have revealed the wide range of tertiary interactions utilized in RNA folding, which may potentially be used as tools for the design of specific macromolecular assemblies. Here, RNA building blocks containing two hairpin loops, based on the dimerization initiation site (DIS) of HIV RNA, connected by a short linker were used to construct large RNA assemblies through hairpin loop-loop ("kissing") interactions. We show that specific linear and circular assemblies can be constructed in a magnesium-dependent manner using several non-self-complementary loop-loop interactions designed in this study. These results show that the use of RNA tertiary interactions may broaden the repertoire of nucleic acid-based nanostructures.
- Published
- 2003
17. Analysis of the spacial requirements for RNA-protein interactions within the N antitermination complex of bacteriophage
- Author
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Mitsuru Inaba, Senya Matsufuji, Kazuo Harada, Satoru Horiya, Hiroaki Uehara, Masaya Ishibashi, Naomi Masui, and Chang-Song Koh
- Subjects
Gene Expression Regulation, Viral ,Base Sequence ,RNA-induced transcriptional silencing ,Termination factor ,Molecular Sequence Data ,RNA-Binding Proteins ,RNA ,RNA-dependent RNA polymerase ,General Medicine ,Biology ,Bacteriophage lambda ,Molecular biology ,chemistry.chemical_compound ,chemistry ,RNA polymerase ,Antitermination ,RNA polymerase I ,Biophysics ,RNA, Viral ,Viral Regulatory and Accessory Proteins ,Small nuclear RNA - Abstract
In bacteriophage lambda, formation of a transcriptional antitermination complex consisting of the lambda N protein, nut RNA transcript (boxA-boxB), host factors, and RNA polymerase is mediated by the interaction of the boxB RNA with the RNA-binding domain of N. In order to understand the spacial requirements of this boxB/N interaction within the complex, the effects of changes in the length of the nut site linker, the boxB stem, and the peptide spacer connecting the RNA-binding domain and activation domain of N were examined using a bacterial reporter system. As a result, we found that the requirements for the boxB stem length and N peptide linker length were optimized and strict. In contrast, when the boxB/N interaction was replaced by heterologous RNA/peptide interactions, the strict requirement for the length of the peptide linker and the RNA stem was relaxed, presumably due to the absence of the interaction between boxB/N and the host factor NusA in the wild-type complex. It was also shown that the decrease in activity upon stem lengthening could be partially suppressed by simultaneous lengthening of the RNA spacer, suggesting that a further understanding of the organization of the antitermination complex may provide insights into the engineering of functional ribonucleoprotein complexes.
- Published
- 2009
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