Nucleotide sequences of the mitochondrial genes trnS(TGA) encoding tRNA(TGASer) in Oenothera berteriana and Arabidopsis thaliana

The genes encoding tRNA(TGASer) have been investigated in the mitochondrial (mt) genomes of Oenothera berteriana and Arabidopsis thaliana. Sequence analysis shows four nucleotide (nt) differences between the two dicots, but only two differences between each dicot and the available monocot sequences. Similarity comparisons identify these genes as encoding a native mt tRNA(TGASer), with less than 77% of the nt identical to the corresponding chloroplast tRNAs.     

An Extensive Study of Mutation and Selection on the Wobble Nucleotide in tRNA Anticodons in Fungal Mitochondrial Genomes

Two alternative hypotheses aim to predict the wobble nucleotide of tRNA anticodons in mitochondrion. The codon-anticodon adaptation hypothesis predicts that the wobble nucleotide of tRNA anticodon should evolve toward maximizing the Watson-Crick base pairing with the most frequently used codon within each synonymous codon family. In contrast, the wobble versatility hypothesis argues that the nucleotide at the wobble site should be occupied by a nucleotide most versatile in wobble pairing, i.e., the wobble site of the tRNA anticodon should be G for NNY codon families and U for NNR and NNN codon families (where Y stands for C or U, R for A or G, and N for any nucleotide). We examined codon usage and anticodon wobble sites in 36 fungal genomes to evaluate these two alternative hypotheses and identify exceptional cases that deserve new explanations. While the wobble versatility hypothesis is generally supported, there are interesting exceptions involving tRNA(Arg) translating the CGN codon family, tRNA(Trp) translating the UGR codon family, and tRNA(Met) translating the AUR codon family. Our results suggest that the potential to suppress stop codons, the historical inertia, and the conflict between translation initiation and elongation can all contribute to determining the wobble nucleotide of tRNA anticodons.     

Nucleotide sequences of yeast genes for tRNA(2), tRNA(2) and tRNA(1): homology blocks occur in the vicinity of different tRNA genes

Three members of a collection of pBR322-yeast DNA recombinant plasmids containing yeast tRNA genes have been analyzed and sequenced. Each plasmid carries a single tRNA gene: pY44, tRNA^Ser₂; pY41, tRNA^Arg₂; pY7, tRNA^Val₁. All three genes are intronless and terminate in a cluster of Ts in the non-coding strand. The sequence information here and previously determined sequences allow an extensive comparison of the regions flanking several yeast tRNA genes. This analysis has revealed novel features in tRNA gene arrangement. Blocks of homology in the flanking regions were found between the tRNA genes of an isoacceptor family but, more interestingly, also between genes coding for tRNAs of different amino-acid specificities. Particularly, three examples are discussed in which sequence elements in the neighborhood of different tRNA genes have been conserved to a high degree and over long distances.     

Archaeal Tuc1/Ncs6 Homolog Required for Wobble Uridine tRNA Thiolation Is Associated with Ubiquitin-Proteasome,Translation, and RNA Processing System Homologs

While cytoplasmic tRNA 2-thiolation protein 1 (Tuc1/Ncs6) and ubiquitin-related modifier-1 (Urm1) are important in the 2-thiolation of 5-methoxycarbonylmethyl-2-thiouridine (mcm⁵s²U) at wobble uridines of tRNAs in eukaryotes, the biocatalytic roles and properties of Ncs6/Tuc1 and its homologs are poorly understood. Here we present the first report of an Ncs6 homolog of archaea (NcsA of Haloferax volcanii) that is essential for maintaining cellular pools of thiolated tRNA^Lys_UUU and for growth at high temperature. When purified from Hfx. volcanii, NcsA was found to be modified at Lys204 by isopeptide linkage to polymeric chains of the ubiquitin-fold protein SAMP2. The ubiquitin-activating E1 enzyme homolog of archaea (UbaA) was required for this covalent modification. Non-covalent protein partners that specifically associated with NcsA were also identified including UbaA, SAMP2, proteasome activating nucleotidase (PAN)-A/1, translation elongation factor aEF-1α and a β-CASP ribonuclease homolog of the archaeal cleavage and polyadenylation specificity factor 1 family (aCPSF1). Together, our study reveals that NcsA is essential for growth at high temperature, required for formation of thiolated tRNA^Lys_UUU and intimately linked to homologs of ubiquitin-proteasome, translation and RNA processing systems.     

Viral Genome-Linked Protein (VPg) Is Essential for Translation Initiation of Rabbit Hemorrhagic Disease Virus (RHDV)

Rabbit hemorrhagic disease virus (RHDV), the causative agent of rabbit hemorrhagic disease, is an important member of the caliciviridae family. Currently, no suitable tissue culture system is available for proliferating RHDV, limiting the study of the pathogenesis of RHDV. In addition, the mechanisms underlying RHDV translation and replication are largely unknown compared with other caliciviridae viruses. The RHDV replicon recently constructed in our laboratory provides an appropriate model to study the pathogenesis of RHDV without in vitro RHDV propagation and culture. Using this RHDV replicon, we demonstrated that the viral genome-linked protein (VPg) is essential for RHDV translation in RK-13 cells for the first time. In addition, we showed that VPg interacts with eukaryotic initiation factor 4E (eIF4E) in vivo and in vitro and that eIF4E silencing inhibits RHDV translation, suggesting the interaction between VPg and eIF4E is involved in RHDV translation. Our results support the hypothesis that VPg serves as a novel cap substitute during the initiation of RHDV translation.     

O6-(4-Nitrophenyl)inosine and -Guanosine as Chromogenic Substrates for Adenosine Deaminase

Abstract

O⁶-(4-Nitrophenyl)inosine (la), O⁶ -(4-nitrophenyl)guanosine (1c) and O⁶ -(4-methylumbelliferonyl)inosine (2) were obtained by reaction of 6-chloro-9-(β-D-ribofuranosyl)purine (3a) or 2-amino-6-chloro-9-(β-D-ribofuranosyl)purine (3c) with sodium salts of 4-nitrophenol or 4-methylumbelliferone in N,N-dimethylformamide. Similarly, 6-chloro-9-(β-D-2,3-isopropylideneribofuranosyl)purine (3b) was transformed to 2′,3′-O-isopropylidene-O⁶-(4-nitrophenyl)inosine (1b). Deprotection of 1b with CF₃COOH gave compound la and O⁶ -(4-nitrophenyl)hypoxanthine (4). Compounds 1a and 1c are substrates for adenosine deaminase releasing 4-nitrophenol which is readily detected visually or spectrophotomemcally. Rate and extent of hydrolysis of la are significantly increased in the presence of purine nucleoside phosphorylase but xanthine oxidase has no influence. A potential fluorogenic analogue 2 is not a substrate for adenosine deaminase.

     

Nucleotide sequence of the Escherichia coli tRNA(3Leu) gene

A 300-nucleotide sequence was determined which includes the tRNA(3Leu) coding region and the flanking sequences.