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S Uesugi

Publications and source records attributed to S Uesugi.

At least 73 records · Page 4Linked to original sources
PubMed1994

Genetic analysis of equine rotavirus by RNA-RNA hybridization.

Serotype G3 equine rotaviruses isolated in Japan made up a common genogroup and were classified into two different genotypes. The genomes of serotype G3 equine rotaviruses with an identical electropherotype (isolated from 1982 to 1989) were very closely related to each other regardless of the year in which they were isolated. Serotype G3 equine rotavirus BI originating from England belonged to the same genogroup of serotype G3 equine rotaviruses isolated in Japan, although BI was classified as having a different genotype. The genomes of both serotype G10 equine rotavirus R-22 and serotype G10 calf rotavirus were closely related to each other.

Animals↗
PubMed1994

[Molecular diagnosis of infectious diseases].

Application of techniques originally developed for the analyses of nucleic acids to the diagnosis and characterization of infectious diseases is increasingly practiced. This tendency has been intensified after the introduction of the polymerase chain reaction (PCR). With the PCR, the molecular diagnostic assays have achieved a high sensitivity that parallels and often exceeds the sensitivity of various culture methods. This means that we are entering a new era in which a new gold standard is to be established. In this review, we summarized the basic principle of molecular diagnostic methods, presented, as an example, the application of such techniques to the study of rotaviruses, the single most important etiological agent of acute diarrhea in children, and finally discussed briefly possible future trends of molecular diagnostics for infectious diseases at large.

DNA, Viral↗
PubMed1993

NMR studies of G:A mismatches in oligodeoxyribonucleotide duplexes modelled after ribozymes.

The structures of two oligodeoxyribonucleotide duplexes, the base sequences of which were modelled after both a hammerhead ribozyme and a small metalloribozyme, were studied by NMR. Both duplexes contain adjacent G:A mismatches; one has a PyGAPu:PyGAPu sequence and the other a PyGAPy:PuGAPu sequence. It is concluded on the basis of many characteristic NOEs that in both duplexes G:A base pairs are formed in the unique 'sheared' form, where an amino proton instead of an imino proton of G is involved in the hydrogen bonding, and G and A bases are arranged 'side by side' instead of 'head to head'. A photo-CIDNP experiment, which gives unique and independent information on the solvent accessibility of nucleotide bases, also supports G:A base pairing rather than a bulged-out structure of G and A residues. This is the first demonstration that not only the PyGAPu:PyGAPu sequence but also the PyGAPy:PuGAPu sequence can form the unique sheared G:A base pairs. Taking the previous studies on G:A mismatches into account, the idea is suggested that a PyGA:GAPu sequence is a minimum and essential element for the formation of the sheared G:A base pairs. The sheared G:A base pairs in the PyGAPu:PyGAPu sequence are suggested to be more stable than those in the PyGAPy:PuGAPu sequence. This is explained rationally by the idea proposed above.

Base Sequence↗
PubMed1993

Crystal structure of ribonuclease Ms (as a ribonuclease T1 homologue) complexed with a guanylyl-3',5'-cytidine analogue.

A ribonuclease T1 homologue, ribonuclease Ms (RNase Ms) from Aspergillus saitoi, has been crystallized as a complex with a substrate analogue GfpC where the 2'-hydroxyl (2'-OH) group of guanosine in guanylyl-3',5'-cytidine (GpC) is replaced by the 2'-fluorine (2'-F) atom to prevent transesterification. The crystal structure of the complex was solved at 1.8-A resolution to a final R-factor of 0.204. The role of His92 (RNase T1 numbering) as the general acid catalyst was confirmed. Of the two alternative candidates for a general base to abstract a proton from the 2'-OH group, His40 and Glu58 were found close to the 2'-F atom, making the decision between the two groups difficult. We then superposed the active site of the RNase Ms/GfpC complex with that of pancreatic ribonuclease S (RNase S) complexed with a substrate analogue UpcA, a phosphonate analogue of uridylyl-3',5'-adenosine (UpA), and found that His12 and His119 of RNase A almost exactly coincided with Glu58 and His92, respectively, of RNase Ms. Similar superposition with a prokaryotic microbial ribonuclease, RNase St [Nakamura, K. T., Iwahashi, K., Yamamoto, Y., Iitaka, Y., Yoshida, N., & Mitsui, Y. (1982) Nature 299, 564-566], also indicated Glu58 as a general base. Thus the present comparative geometrical studies consistently favor, albeit indirectly, the traditional as well as the most recent notion [Steyaert, J., Hallenga, K., Wyns, L., & Stanssens, P. (1990) Biochemistry 29, 9064-9072] that Glu58, rather than His40, must be the general base catalyst in the intact enzymes of the RNase T1 family.

Amino Acid Sequence↗
PubMed1993

Charged collagen structure mediates the recognition of negatively charged macromolecules by macrophage scavenger receptors.

Macrophage scavenger receptors mediate the recognition of a wide range of negatively charged macromolecules including modified low density lipoproteins (LDL). Truncated bovine receptors lacking residues 330-342, which include the conserved lysine cluster of a collagen-like domain, were unable to degrade modified LDL in spite of their expression on the cell surface. Substitution of lysine 337 into alanine abolished the acetyl-LDL degradation and binding at 37 degrees C, but did not abolish the 4 degrees C binding. In contrast, substitution of more than 2 lysines in this region are needed to abolish the oxidized LDL degradation and 37 degrees C binding. Based on computational modeling of this domain, we propose that a "charged collagen" structure containing a lysine cluster forms a positively charged groove which specifically interacts with negatively charged ligands.

Amino Acid Sequence↗
PubMed1993

Determination of bovine rotavirus G and P serotypes by polymerase chain reaction.

Among bovine rotaviruses there are two major G serotypes (G6 and G10) and three P serotypes (P1, P5, and P11, each of which is defined on the basis of the VP4 antigenic specificity of NCDV, UK and KK-3, respectively). The nucleotide sequence of a P11 gene (KK-3) was determined. The predicted KK-3 VP4 contained 772 amino-acids and showed 96% amino-acid identity with B223 VP4, an American prototype of P11 bovine rotavirus. Comparative analysis of the genes determining the G and P serotypes of bovine rotaviruses allowed us to develop polymerase chain reaction (PCR)-based assays which distinguished two G serotypes and three P serotypes commonly found in bovine rotaviruses. For determination of G serotypes, a 1013 bp fragment of the VP7 gene was first reverse-transcribed and then amplified with a pair of generic primers. In a second PCR amplification, the 5' generic primer and two different typing primers (either G6- or G10-specific) were used to generate fragments whose sizes served to identify the G serotype. Similarly, for determination of P serotypes, an 864 bp fragment of the VP4 gene was first reverse-transcribed and then amplified with another pair of generic primers. In a second PCR amplification, the 5' generic primer and three different typing primers, each one specific to one of the three P serotypes, were used to generate fragments whose sizes served to identify the P serotype. These assays were able to identify the G and P serotypes of six reference bovine rotavirus strains.

Animals↗
PubMed1993

Crystal structure of RNase T1(Y45W) complexed with 3'AMP and GflpA.

We have previously reported the crystallization of a mutant RNase T1(Y45W) with a synthetic modified trinucleotide ApGflpA [Hakoshima, T. et al. (1990) J. Biochem. 108, 695-698]. In the present report, we describe the crystal structure refined at 2.4 A resolution. During the refinement process, we found that the ApGflpA molecule was cleaved at the phosphodiester bond between the 5'-terminal adenosine and the subsequent 2'-fluoroguanosine. At the end of the refinement (R = 17.1%), it was supposed that the resulting molecules, i.e., 3'AMP and GflpA, were separately bound to the enzyme. In the complex structure, the binding-site of the enzyme was occupied by the guanine base of GflpA via a similar interaction to that of the enzyme complexed with 2'GMP, while the phosphate group of GflpA was not bound to the active site. The guanosine adopted the anti orientation on the glycosyl torsion angle with a C2'-endo-C3'-exo sugar pucker. This conformation resulted in the phosphate group protruding from the active site. The phosphate group of 3'AMP was bound to the active site of the enzyme and oriented itself toward the solvent region. This orientation was different from that of 2'AMP bound to the RNase T1(Y45W).

Adenosine↗
PubMed1993

Structural studies of DNA and RNA containing AG base pairs by NMR.

Base pairing between A and G residues has been suggested in some ribozymes and the structure derived from this non-standard base pairing could play a crucial role in enzymatic actions of the ribozymes. We have studied the structures of three DNAs and an RNA that base sequences were modeled after the ribozymes by NMR. It was found that the A and G residues can form a basepair in a very unique fashion both in the DNAs and RNA. "Side" instead of "head to head" alignment of the two bases was found, where an amino proton instead of an imino proton of the G residue is involved in the hydrogen bonding. As a result of the unique basepairing, certain bases stack over the bases of the opposite strand instead of over the ones of the same strand. It was also shown that the formation and thermal stability of this unique AG basepair depend on the neighbouring base sequences. Moreover existence of the unique AG basepairs was suggested in a real small metalloribozyme itself.

Adenine↗
PubMed1993

DNA binding properties of c-Myc-related bHLH/LZ oncoproteins.

Structural features and DNA binding properties of bacterially expressed c-Myc related oncoproteins were examined. The circular dichroism spectra demonstrated highly alpha-helical nature of these proteins. Dimerization and the DNA binding of these proteins were examined by electrophoretic mobility shift assay.

Circular Dichroism↗
PubMed1993

[Automatic analyzing systems for blood chemistry and urinalysis].

We constructed two new automatic analyzing systems for blood chemistry and urinalysis. The blood chemistry system consists of centrifuge station, on-line allotting station, belt line, Hitachi 736 -60, -40, off-line allotting station, storage allotting station and sample stocker, these are connected with belt line. If only specimens are set and switched on, analytical process from serum separation to measurement is advanced automatically, and then printed out the analytical results, it is the highest speed of 1.8 test/sec, in the world. Urinalysis system consists of qualitative analyzing station, quantitative analyzing station and urinary sediment analyzer, two station are logically coupled with belt line. It is a unique system of urinalysis that qualitative and quantitative analysis of urine is logically done by computerizing program.

Blood Chemical Analysis↗
PubMed1992

Deletion of internal sequence on the HDV-ribozyme: elucidation of functionally important single-stranded loop regions.

In elucidating functionally important single-stranded loop regions derived mainly from three models in genomic hepatitis delta virus (HDV) ribozyme possessing self-cleavage activity, we have constructed several internal deletion variants of the HDV133 molecule (654-786 nt on genomic RNA) by oligonucleotide-directed mutagenesis. When self-cleavage activities were compared among variants, the HDV133DI-1 (deletion of 701-718 nt) and HDV133DI-3 (deletion of 740-752 nt) ribozyme could maintain their self-cleavage activity, despite at reduced level. However, the activity could be regained in both mutants by some extent under partially denaturing conditions. These results suggest that the above two single-stranded RNA loop regions in HDV ribozyme are not part of the catalytic core but might be involved in the stability of the molecule. In contrast, deletion mutants such as HDV133DI-2 (deletion of 696-722 nt), HDV88DI-1 (deletion of 701-718 nt), HDV88DI-2 (deletion of 696-722 nt), and HDV88DI-4 (deletion of 733-760 nt) abolished catalytic activity. These results suggest that the remaining single-stranded regions of bases between 726-731 and 762-766 in the HDV88 ribozyme may be the potential regions to interact with Mg2+ ions.

Base Composition↗
PubMed1992

Three-dimensional structure of a mutant ribonuclease T1 (Y45W) complexed with non-cognizable ribonucleotide, 2'AMP, and its comparison with a specific complex with 2'GMP.

The crystal structure of a mutant ribonuclease T1 (Y45W) complexed with a non-cognizable ribonucleotide, 2'AMP, has been determined and refined to an R-factor of 0.159 using X-ray diffraction data at 1.7 A resolution. A specific complex of the enzyme with 2'GMP was also determined and refined to an R-factor of 0.173 at 1.9 A resolution. The adenine base of 2'AMP was found at a base-binding site that is far apart from the guanine recognition site, where the guanine base of 2'GMP binds. The binding of the adenine base is mediated by a single hydrogen bond and stacking interaction of the base with the imidazole ring of His92. The mode of stacking of the adenine base with His92 is similar to the stacking of the guanine base observed in complexes of ribonuclease T1 with guanylyl-2',5'-guanosine, reported by Koepke et al., and two guanosine bases, reported by Lenz et al., and in the complex of barnase with d(GpC), reported by Baudet & Janin. These observations suggest that the site is non-specific for base binding. The phosphate group of 2'AMP is tightly locked at the catalytic site with seven hydrogen bonds to the enzyme in a similar manner to that of 2'GMP. In addition, two hydrogen bonds are formed between the sugar moiety of 2'AMP and the enzyme. The 2'AMP molecule adopts the anti conformation of the glycosidic bond and C-3'-exo sugar pucker, whereas 2'GMP is in the syn conformation with C-3'-endo-C'-2'-exo pucker. The mutation enhances the binding of 2'GMP with conformational changes of the sugar ring and displacement of the phosphate group towards the interior of the catalytic site from the corresponding position in the wild-type enzyme complex. Comparison of two crystal structures obtained provides a solution to the problem that non-cognizable nucleotides exhibit unexpectedly strong binding to the enzyme, compared with high specificity in nucleolytic activity. The results indicate that the discrimination of the guanine base from the other nucleotide bases at the guanine recognition site is more effective than that estimated from nucleotide-binding experiments so far.

Adenosine Monophosphate↗
PubMed1992

Thermal degradation of RNA-RNA hybrids during hybridization in solution.

Degradation of single-stranded RNA molecules at high temperatures was examined in relation to the kinetics of RNA-RNA hybridization in solution. Eleven species (ranging from 670 bases to 3300 bases) of single-stranded RNAs transcribed from rotavirus genomic RNAs degraded significantly after 16 h of incubation at 65 degrees C. The hybridization of these 11 RNA molecules to the corresponding genomic RNAs, however, was completed within 30 min of incubation. Partially homologous hybrids that were once formed at an early time of incubation gradually degraded in proportion to the length of incubation at 65 degrees C. Thus, the length of hybridization has a critical effect on the final hybridization results. Furthermore, thermal hydrolysis of single-stranded RNA molecules provides a plausible explanation why the percent of nucleotide sequence mismatch allowed to form a stable hybrid in the RNA-RNA hybridization assays for rotavirus genes is much less than that predicted by calculation.

Base Composition↗
PubMed1992

Properties of hammerhead-type RNA enzyme derivatives which contain a G-to-I replacement in the loop region.

Three hammerhead-type ribozyme derivatives containing a G-to-I replacement in the loop regions were chemically synthesized and their properties were examined. All three complexes showed a markedly reduced RNA-cleaving activity. NMR studies suggested that the complex with mutation at the third guanosine of the longer internal loop region has the greatest influence on the conformation of the loop regions.

Base Sequence↗
PubMed1992

Conformational features of the four successive non-Watson-Crick base pairs in RNA duplex.

A tridecaribonucleotide, r(UGAGCUUCGGCUC) doesn't form hairpin or interior loop and forms a double helix of 12 base pairs including the four successive nonstandard base pairs, U.G-U.C-C.U-G.U, in the crystal. Non-Watson-Crick base pairs, G.U and U.C are nicely incorporated in RNA duplex maintaining the regular A-form backbone. There exist the good overlapping between base pairings, U.G and U.C, so as to stabilize the nonstandard base pair track. Hydrogen bond networks involving water molecules in the major and minor grooves to stabilize this mismatch base pairing array, are observed and its conformational features are described.

Base Composition↗
PubMed1992

Synthesis and properties of oligodeoxyribonucleotides containing a mutagenic base, N4-aminocytosine.

Oligodeoxyribonucleotides containing a mutagenic base analog, N4-aminocytosine, 5'-AATTGC(am)AATT-3' and 5'-AATTAC(am)AATT-3' (C(am); N4-aminocytosine) were prepared by chemical modification of 5'-AATTGCAATT-3' and 5'-AATTACAATT-3', respectively. The values of Tm were 29 degrees C for 5'-AATTGC(am)AATT-3' and 32 degrees C for 5'-AATTGCAATT-3'. In contrast, no melting was observed for 5'-AATTAC(am)AATT-3' and 5'-AATTACAATT-3'. These data show that the stability of C(am)-purine paris is C(am)-G > C(am)-A and that C(am)-G is less stable than C-G. This property is consistent with the incorporation specificity of N4-amino-dCTP during DNA synthesis in vitro.

Base Sequence↗