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S. Nishimura

Bio: S. Nishimura is an academic researcher from National Cancer Research Institute. The author has contributed to research in topics: Transfer RNA & Escherichia coli. The author has an hindex of 10, co-authored 11 publications receiving 552 citations.

Papers
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Journal ArticleDOI
TL;DR: The structure of Q is unique since it is a derivative of 7-deazaguanosine having cyclopentenediol in the side chain at the C-7 position, which is the first example of purine skeleton modification in a nucleoside from tRNA.
Abstract: The structure of the unknown modified nucleoside Q, which is present in the first position of the anticodons of Escherichia coli tRNA Tyr, tRNA His, tRNA Asn, tRNA Asp, is proposed to be 7-(4,5-cis-dihydroxy-1-cyclopenten-3-ylaminomethyl)-7-deazaguanosine (1). The structure of Q was deduced by means of its uv absorption, mass spectrometry, proton magnetic resonance spectroscopy, and studies of its chemical reactivity. The structure of Q is unique since it is a derivative of 7-deazaguanosine having cyclopentenediol in the side chain at the C-7 position. This is the first example of purine skeleton modification in a nucleoside from tRNA.

192 citations

Journal ArticleDOI
TL;DR: Evidence is provided that yeast N-formylmethionyl-tRNA I serves as an initiator of protein synthesis programmed with the natural messenger in an E. coli system in vitro.

81 citations

Journal ArticleDOI
TL;DR: This is the first demonstration of the presence of 2-methyladenosine in purified tRNA's, isolated from Escherichia coli tRNA Glu 2, tRNA Asp 1 , tRNA His 1 and tRNA Arg and identified as 2- methyladenosines.

52 citations

Journal ArticleDOI
TL;DR: An unknown minor component present in the first position of the anticodon of Escherichia coli tRNAMet has been characterized as N 4 - acetylcytidine, established by comparison of its ultraviolet absorption spectrum and thinlayer chromatographic mobility.

48 citations


Cited by
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Journal ArticleDOI
TL;DR: This Review will begin by summarizing unifying features of radical SAM enzymes, and in subsequent sections delve further into the biochemical, spectroscopic, structural, and mechanistic details for those enzymes that catalyze an amazingly diverse set of reactions.
Abstract: It was once widely held that nearly all reactions in biology were catalyzed via mechanisms involving paired electron species. Beginning approximately 40 years ago, this paradigm was repeatedly challenged as examples of enzymatic reactions involving organic radical intermediates began to emerge, and it is now well accepted that biochemical reactions often involve organic radicals. Indeed, some of the most intensely studied metalloenzymes, including cytochrome P450, methane monooxygenase, ribonucleotide reductase, and the adenosylcobalamin (B12) enzymes, catalyze reactions employing organic radical intermediates. As a general rule, enzymes utilizing radical mechanisms catalyze reactions that would be difficult or impossible to catalyze by polar mechanisms, most often involving H-atom abstraction from an unactivated C–H bond. Among the more recent additions to the enzymes that catalyze radical reactions are the radical S-adenosylmethionine (radical SAM) enzymes, which were first classified as a superfamily in 2001.1 These enzymes utilize a [4Fe–4S] cluster and SAM to initiate a diverse set of radical reactions, in most or all cases via generation of a 5′-deoxyadenosyl radical (dAdo•) intermediate. Although 2001 marked the identification of this superfamily largely through bioinformatics, the discovery of iron metalloenzymes utilizing SAM to initiate radical reactions precedes this date by more than a decade. For example, early studies on the activation of pyruvate formate-lyase showed that it involved the generation of a stable protein radical,2 and was stimulated by the presence of iron, SAM, and an “activating component” from the cell extract now known to be the pyruvate-formate lyase activating enzyme (PFL-AE).3 The radical on PFL was ultimately shown to be located on a specific glycine residue,4 and was one of the first stable protein radicals characterized. PFL-AE was ultimately shown to contain a catalytically essential iron–sulfur cluster,5 and to use SAM as an essential component of PFL activation.6 The anaerobic ribonucleotide reductase, similar to PFL, contains a stable glycyl radical that was shown in early work to require an iron–sulfur cluster and SAM for activation.7 Likewise, preliminary investigations on lysine 2,3-aminomutase (LAM) published in 1970 demonstrated activation by ferrous ion and a strict requirement for SAM.8 Like PFL-AE, LAM was ultimately found to contain a catalytically essential iron–sulfur cluster.9 Work in Perry Frey’s lab showed that LAM used the adenosyl moiety of SAM to mediate hydrogen transfer in a manner similar to adenosylcobalamin-dependent rearrangements, implicating radical intermediates.10 Biotin synthase was first reported to require iron and SAM in 1995,11 and was subsequently shown to contain iron–sulfur clusters and to catalyze a radical reaction.12 These four enzyme systems (PFL/PFL-AE, aRNR, LAM, and biotin synthase) provided early indications of a new type of biological cofactor consisting of an iron–sulfur cluster and SAM, which initiate radical reactions using a fundamental new mechanism of catalysis.13 What none of us in the field in the early days probably anticipated, however, was just how ubiquitous these enzymes would turn out to be. The initial report of the superfamily by Sofia et al. identified ∼600 members;1 however, now that number is ∼48 100 members.14 These enzymes are found across the phylogenetic kingdom and catalyze an amazingly diverse set of reactions, the vast majority of which have yet to be characterized. This Review will begin by summarizing unifying features of radical SAM enzymes, and in subsequent sections delve further into the biochemical, spectroscopic, structural, and mechanistic details for those enzymes that have been characterized. In most cases, these enzymes are grouped by reaction type; however, in two cases (syntheses of modified tetrapyrroles and complex metal cluster cofactors), we have chosen to group together several radical SAM enzymes that catalyze different reaction types but which act together in the same or related metabolic pathways.

582 citations

Book ChapterDOI
TL;DR: Further studies of mutation in picornaviruses or their RNAs would be fruitful since these viral RNAs are also messenger RNAs and are directly translated, whereas in vivo studies, definitive information is still lacking as to whether alkylation of DNA, RNA, or perhaps protein is the biologically important event.
Abstract: Publisher Summary This chapter discusses the studies relating to the chemical nature of alkylation, from the products of nucleoside alkylation to in vivo effects of alkylating agents that are oncogenic. The reactions of simple methylating agents with nucleosides, nucleotides, and polynucleotides have also been discussed in the chapter. More recent studies of the mechanism of alkylation by nitroso compounds and ethylating agents have shown that both qualitatively and quantitatively the site of alkylation is a function of both the type of reagent used and the conformation and milieu of the nucleic acid. However, translation of this body of knowledge to an understanding of the biological mechanism of alkylation-induced mutagenesis and carcinogenesis is difficult. Further studies of mutation in picornaviruses or their RNAs would be fruitful since these viral RNAs are also messenger RNAs and are directly translated, whereas in vivo studies, definitive information is still lacking as to whether alkylation of DNA, RNA, or perhaps protein, is the biologically important event.

409 citations

Journal ArticleDOI
TL;DR: This compilation presents in a small space the tRNA sequences so far published in order to enable rapid orientation and comparison and to refer either to the original literature or to other tRNA sequence compilations.
Abstract: This compilation presents in a small space the tRNA sequences so far published in order to enable rapid orientation and comparison. The numbering of tRNAPhe from yeast is used as has been done earlier (1) but following the rules proposed by the participants of the Cold Spring Harbor Meeting on tRNA 1978 (2) (Fig. 1). This numbering allows comparisons with the three dimensional structure of tRNAPhe, the only structure known from X-ray analysis. The secondary structure of tRNAs is indicated by specific underlining. In the primary structure a nucleoside followed by a nucleoside in brackets or a modification in brackets denotes that both types of nucleosides can occupy this position. Part of a sequence in brackets designates a piece of sequence not unambiguously analyzed. Rare nucleosides are named according to the IUPAC-IUB rules (for some more complicated rare nucleosides and their identification see Table 1); those with lengthy names are given with the prefix x and specified in the footnotes. Footnotes are numbered according to the coordinates of the corresponding nucleoside and are indicated in the sequence by an asterisk. The references are restricted to the citation of the latest publication in those cases where several papers deal with one sequence. For additional information the reader is referred either to the original literature or to other tRNA sequence compilations (3--7). Mutant tRNAs are dealt with in a separate compilation prepared by J. Celis (see below). The compilers would welcome any information by the readers regarding missing material or erroneous presentation. On the basis of this numbering system computer printed compilations of tRNA sequences in a linear form and in cloverleaf form are in preparation.

360 citations

Book ChapterDOI
TL;DR: The chapter discusses that it is possible to increase the content of a minor component by separating short chains of oligonucleotides containing the required minor components, and also to correlate the presence of particular minor components with codon recognition of tRNA.
Abstract: Publisher Summary This chapter reviews that the presence of a variety of minor components has been considered to be one of the typical characteristics of tRNA. Elucidation of the primary sequences of numerous tRNA's has established that minor components are located in specific regions of the tRNA molecule, as arranged in a cloverleaf structure. The minor components in tRNA's is classified into three groups depending upon their locations in the molecule, including: (1) minor components located in the first position of the anticodon, (2) minor components located next to the 3´-OH end of the anticodon, and (3) minor components located in other parts of the tRNA molecule. The chapter discusses that it is possible to increase the content of a minor component by separating short chains of oligonucleotides containing the required minor components. This is possibly the only way to be certain that the component is a part of the tRNA and not an impurity carried through the isolation procedure. When unfractionated tRNA is used as a source of minor components, it is impossible to deduce their locations in the tRNA molecule or to be certain that they are indeed in the tRNA molecule at all. The chapter reviews that the availability of numerous tRNA's enabled to characterize several minor components, and also to correlate the presence of particular minor components with codon recognition of tRNA.

332 citations