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Search: authors:"Satoru Watanabe"

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Effect of Glu12-His89 Interaction on Dynamic Structures in HIV-1 p17 Matrix Protein Elucidated by NMR

To test the existence of the salt bridge and stability of the HIV-1 p17 matrix protein, an E12A (mutated at helix 1) was established to abolish possible electrostatic interactions. The chemical shift perturbation from the comparison between wild type and E12A suggested the existence of an electrostatic interaction in wild type between E12 and H89 (located in helix 4...

CyanoBase: a large-scale update on its 20th anniversary

The first ever cyanobacterial genome sequence was determined two decades ago and CyanoBase (http://genome.microbedb.jp/cyanobase), the first database for cyanobacteria was simultaneously developed to allow this genomic information to be used more efficiently. Since then, CyanoBase has constantly been extended and has received several updates. Here, we describe a new large-scale...

Intracellular Delivery of Proteins via Fusion Peptides in Intact Plants

In current plant biotechnology, the introduction of exogenous DNA encoding desired traits is the most common approach used to modify plants. However, general plant transformation methods can cause random integration of exogenous DNA into the plant genome. To avoid these events, alternative methods, such as a direct protein delivery system, are needed to modify the plant. Although...

Intensive DNA Replication and Metabolism during the Lag Phase in Cyanobacteria

Unlike bacteria such as Escherichia coli and Bacillus subtilis, several species of freshwater cyanobacteria are known to contain multiple chromosomal copies per cell, at all stages of their cell cycle. We have characterized the replication of multi-copy chromosomes in the cyanobacterium Synechococcus elongatus PCC 7942 (hereafter Synechococcus 7942). In Synechococcus 7942, the...

Solution structures of the DNA-binding domains of immune-related zinc-finger protein ZFAT

ZFAT is a transcriptional regulator, containing eighteen C2H2-type zinc-fingers and one AT-hook, involved in autoimmune thyroid disease, apoptosis, and immune-related cell survival. We determined the solution structures of the thirteen individual ZFAT zinc-fingers (ZF) and the tandemly arrayed zinc-fingers in the regions from ZF2 to ZF5, by NMR spectroscopy. ZFAT has eight...

A new modeling method in feature construction for the HSQC spectra screening problem

Motivation: Large-scale biological analyses produce huge amounts of data. As a consequence, automation in the data analysis process is needed. Sample screening problems in NMR high-throughput protein structure analysis are the typical examples. Especially, screening by protein 1H−15N heteronuclear single quantum coherence (HSQC) spectra must be done quantitatively by a human...

Regulation of nitrate assimilation in cyanobacteria

Nitrate assimilation by cyanobacteria is inhibited by the presence of ammonium in the growth medium. Both nitrate uptake and transcription of the nitrate assimilatory genes are regulated. The major intracellular signal for the regulation is, however, not ammonium or glutamine, but 2-oxoglutarate (2-OG), whose concentration changes according to the change in cellular C/N balance...

T Cell-Mediated Control of Epstein-Barr Virus Infection in Humanized Mice

Humanized NOD/Shi-scid/interleukin-2Rγnull (NOG) mice with full T cell development had significantly longer life span after Epstein-Barr virus (EBV) infection, compared with those with minimal T cell development. Removing CD3+ or CD8+ T cells from EBV-infected humanized mice by administration of anti-CD3 or anti-CD8 antibodies reduced their life span. CD8+ T cells obtained from...

Structural basis for the dual RNA-recognition modes of human Tra2-β RRM

Human Transformer2-β (hTra2-β) is an important member of the serine/arginine-rich protein family, and contains one RNA recognition motif (RRM). It controls the alternative splicing of several pre-mRNAs, including those of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. Accordingly, the RRM of hTra2...

Protection of Macaques with Diverse MHC Genotypes against a Heterologous SIV by Vaccination with a Deglycosylated Live-Attenuated SIV

HIV vaccine development has been hampered by issues such as undefined correlates of protection and extensive diversity of HIV. We addressed these issues using a previously established SIV-macaque model in which SIV mutants with deletions of multiple gp120 N-glycans function as potent live attenuated vaccines to induce near-sterile immunity against the parental pathogenic...

A New Humanized Mouse Model of Epstein-Barr Virus Infection That Reproduces Persistent Infection, Lymphoproliferative Disorder, and Cell-Mediated and Humoral Immune Responses

The functional human immune system, including T, B, and natural killer lymphocytes, is reconstituted in NOD/Shi-scid/IL-2Rγnull (NOG) mice that receive hematopoietic stem cell transplants. Here, we show that these humanized mice can recapitulate key aspects of Epstein-Barr virus (EBV) infection in humans. Inoculation with ∼1 × 103 TD50 (50% transforming dose) of EBV caused B cell...

An RNA Fragment Consisting of the P7 and P9.0 Stems and the 3′-Terminal Guanosine of the Tetrahymena Group I Intron

On the basis of the nucleotide sequence of Tetrahymena group I intron, we constructed a 31 residue RNA that has the P7 stem and the 3′-terminal guanosine residue (3′-G) with a putative stem-loop structure (P9.0) intervening between them. For this model RNA (P7/P9.0/G), four residues around the guanosine binding site (GBS) in the P7 stem were found to exhibit much lower...

NMR signal assignment of the polyuridine tract of the single-stranded RNA complexed with Sxl RBD1-RBD2 by using residue selective [5-2H]uridine substitutions

Using [5-2H]uridine phosphoramidite, we synthesized a series of 2H-labeled Drosophila Sex-lethal (Sxl) target RNAs, in which all the uridine residues except one were specifically replaced by [5-2H]uridine. By observing the H5-H6 cross peaks of RNA in the TOCSY spectra, we unambiguously assigned all the base proton resonences of the target RNA in a Sxl-RNA complex. Furthermore, it...

NMR Analysis of the Hydrogen Bonding Interactions of the RNA-Binding Domains of the Drosophila Sex-Lethal Protein with Target RNA Fragments with Site-Specific [3-15N]Uridine Substitutions

It has been reported that a 183 residue fragment, consisting of the two RNA-binding domains (RBD1-RBD2) of the Drosophila melanogster Sex-lethal (Sxl) protein, strongly binds an oligonucleotide of the target RNA sequence (5′-GUUUUUUUUC-3′) that regulates alternative splicing, and forms four or five hydrogen bonds with the imino groups of the RNA. In the present study, we used...

The guanosine binding mechanism of the Tetrahymena group I intron

The Tetrahymena group I intron catalyzes self-splicing through two consecutive transesterification reactions, using a single guanosine-binding site (GBS). In this study, we constructed a model RNA that contains the GBS and a conserved guanosine nucleotide at the 3′-terminus of the intron (ωG). We determined by NMR the solution structure of this model RNA, and revealed the...