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Journal ArticleDOI

Novel mechanism of post-transcriptional modification of tRNA: insertion of base of Q precursor into tRNA by tRNA transglycosidase reaction

01 Jan 1978-Nucleic Acids Research (Oxford University Press)-Vol. 1
About: This article is published in Nucleic Acids Research.The article was published on 1978-01-01 and is currently open access. It has received 12 citations till now. The article focuses on the topics: T arm & RNase P.
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Journal ArticleDOI
TL;DR: It is discussed that not only RNA viruses, but also the eukaryotic host organism might gain some profit from cellular suppressor tRNAs.
Abstract: Translational stop codon readthrough provides a regulatory mechanism of gene expression that is extensively utilised by positive-sense ssRNA viruses. The misreading of termination codons is achieved by a variety of naturally occurring suppressor tRNAs whose structure and function is the subject of this survey. All of the nonsense suppressors characterised to date (with the exception of selenocysteine tRNA) are normal cellular tRNAs that are primarily needed for reading their cognate sense codons. As a consequence, recognition of stop codons by natural suppressor tRNAs necessitates unconventional base pairings in anticodon–codon interactions. A number of intrinsic features of the suppressor tRNA contributes to the ability to read non-cognate codons. Apart from anticodon–codon affinity, the extent of base modifications within or 3′ of the anticodon may up- or down-regulate the efficiency of suppression. In order to out-compete the polypeptide chain release factor an absolute prerequisite for the action of natural suppressor tRNAs is a suitable nucleotide context, preferentially at the 3′ side of the suppressed stop codon. Three major types of viral readthrough sites, based on similar sequences neighbouring the leaky stop codon, can be defined. It is discussed that not only RNA viruses, but also the eukaryotic host organism might gain some profit from cellular suppressor tRNAs.

227 citations


Cites background from "Novel mechanism of post-transcripti..."

  • ...The highly modified Q nucleoside is synthesised as the free queuosine base (Q), which is then inserted into tRNA by a transglycosylase to replace guanine (33)....

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Journal ArticleDOI
01 Apr 2008-RNA
TL;DR: It is shown that a representative of the COG4708 RNA motif from Streptococcus pneumoniae R6 also binds preQ(1), indicating that natural aptamers utilizing different structures to bind the same metabolite may be more common than is currently known.
Abstract: Bioinformatics searches of eubacterial genomes have yielded many riboswitch candidates where the identity of the ligand is not immediately obvious on examination of associated genes. One of these motifs is found exclusively in the family Streptococcaceae within the 59 untranslated regions (UTRs) of genes encoding the hypothetical membrane protein classified as COG4708 or DUF988. While the function of this protein class is unproven, a riboswitch binding the queuosine biosynthetic intermediate pre-queuosine1 (preQ1) has been identified in the 59 UTR of homologous genes in many Firmicute species of bacteria outside of Streptococcaceae. Here we show that a representative of the COG4708 RNA motif from Streptococcus pneumoniae R6 also binds preQ1. Furthermore, representatives of this RNA have structural and molecular recognition characteristics that are distinct from those of the previously described preQ1 riboswitch class. PreQ1 is the second metabolite for which two or more distinct classes of natural aptamers exist, indicating that natural aptamers utilizing different structures to bind the same metabolite may be more common than is currently known. Additionally, the association of preQ1 binding RNAs with most genes encoding proteins classified as COG4708 strongly suggests that these proteins function as transporters for preQ1 or another queuosine biosynthetic intermediate.

124 citations


Cites background from "Novel mechanism of post-transcripti..."

  • ...PreQ1 is preferentially exchanged for a specific guanine in tRNA (Noguchi et al. 1982), and the remaining biosynthetic steps take place in situ (Okada et al. 1979; Slany et al. 1993)....

    [...]

Journal ArticleDOI
TL;DR: In this article, molecular analysis of 10 menadione-sensitive mutants, obtained by insertional mutagenesis, was undertaken to better understand the defense mechanism of Streptococcus thermophilus against superoxide stress.
Abstract: To better understand the defense mechanism of Streptococcus thermophilus against superoxide stress, molecular analysis of 10 menadione-sensitive mutants, obtained by insertional mutagenesis, was undertaken. This analysis allowed the identification of 10 genes that, with respect to their putative functions, were classified into five categories: (i) those involved in cell wall metabolism, (ii) those involved in exopolysaccharide translocation, (iii) those involved in RNA modification, (iv) those involved in iron homeostasis, and (v) those whose functions are still unknown. The behavior of the 10 menadione-sensitive mutants exposed to heat shock was investigated. Data from these experiments allowed us to distinguish genes whose action might be specific to oxidative stress defense (tgt, ossF, and ossG) from those whose action may be generalized to other stressful conditions (mreD, rodA, pbp2b, cpsX, and iscU). Among the mutants, two harbored an independently inserted copy of pGh9:ISS1 in two loci close to each other. More precisely, these two loci are homologous to the sufD and iscU genes, which are involved in the biosynthesis of iron-sulfur clusters. This region, called the suf region, was further characterized in S. thermophilus CNRZ368 by sequencing and by construction of DeltasufD and iscU(97) nonpolar mutants. The streptonigrin sensitivity levels of both mutants suggest that these two genes are involved in iron metabolism.

73 citations

Journal ArticleDOI
TL;DR: The structural diversity of 7-deazapurine containing compounds is illustrated and the current state of knowledge on the biosynthetic pathways that give rise to them is reviewed.

71 citations

Journal ArticleDOI
TL;DR: Results link the production of a tRNA-modified base to primary metabolism and further clarify the biosynthetic pathway for these complex modified nucleosides.
Abstract: Queuosine (Q) and archaeosine (G+) are hypermodified ribonucleosides found in tRNA. Q is present in the anticodon region of tRNAGUN in Eukarya and Bacteria, while G+ is found at position 15 in the D-loop of archaeal tRNA. Prokaryotes produce these 7-deazaguanosine derivatives de novo from GTP through the 7-cyano-7-deazaguanine (pre-Q0) intermediate, but mammals import the free base, queuine, obtained from the diet or the intestinal flora. By combining the results of comparative genomic analysis with those of genetic studies, we show that the first enzyme of the folate pathway, GTP cyclohydrolase I (GCYH-I), encoded in Escherichia coli by folE, is also the first enzyme of pre-Q0 biosynthesis in both prokaryotic kingdoms. Indeed, tRNA extracted from an E. coli ΔfolE strain is devoid of Q and the deficiency is complemented by expressing GCYH-I-encoding genes from different bacterial or archaeal origins. In a similar fashion, tRNA extracted from a Haloferax volcanii strain carrying a deletion of the GCYH-I-encoding gene contains only traces of G+. These results link the production of a tRNA-modified base to primary metabolism and further clarify the biosynthetic pathway for these complex modified nucleosides.

69 citations