Studies on the ribothymidine content of specific rat and human tRNAs: a postulated role for 5-methyl cytosine in the regulation of ribothymidine biosynthesis.

Total mammalian tRNAs contain on the average less than one mole of ribothymidine per mole of tRNA. Mammalian tRNAs can be grouped into at least four classes, depending upon their ribothymidine content at position 23 from the 3′ terminus. Class A contains tRNA in which a nucleoside other than uridine replaces ribothymidine (tRNA_i^Met); Class B contains tRNA in which one mole of a modified uridine (rT, ψ, or 2′-O-methylribothymidine) is found per mole of tRNA (tRNA^Ser, tRNA^Trp, and tRNA^Lys, respectively). Class C contains tRNA in which there is a partial conversion of uridine to ribothymidine (tRNA^Phe, tRNA₁^Gly, tRNA₂^Gly); Class D contains tRNA which totally lacks ribothymidine (tRNA^Val). Only those tRNAs in Class C are acceptable substrates for $\text{E.}\text{coli}$ uridine methylase, under the conditions used in these studies. These observations cannot be adequately explained solely on the basis of the presence or absence of a specific “universal” nucleoside other than U or rT at position 23 from the 3′ terminus. However, correlations can be made between the ribothymidine and 5-methylcytosine content of eucaryotic tRNA. We postulate that the presence of one or more 5-methylcytosines in and adjacent to loop III (minor loop) in individual tRNAs act to regulate the amount of ribothymidine formed by uridine methylase. Several experiments are proposed as tests for this hypothesis.     

Salvage of the nucleic acid base queuine from queuine-containing TRNA by animal cells

The incorporation of queuine into tRNA and its fate upon tRNA turnover has been studied in the Vero and L-M cell lines. An assay was developed using [³H]dihydroqueuine to detect the queuine acceptance and, thus, the queuine content of tRNA in intact cells. While L-M cells can use only queuine, Vero cells can use either queuine or its nucleoside, queuosine, to form queunine-containing tRNA. Since queuosine is not a substrate for the enzyme which incorporates queuine into tRNA, Vero cells must generate queuine from its nucleoside. When Vero cells are labelled with [³H]dihydroqueuine, the half life of acid insoluble radioactivity is 52 days in queuine-free medium and 3.1 days in queuine-containing medium, indicating that [³H]dihydroqueuine is salvaged from tRNA and reused by Vero cells, but that exogenous queuine can compete with the salvaged [³H]dihydroqueuine. When L-M cells are labelled with [³H]dihydroqueuine, the half life of the acid insoluble radioactivity is 1.2 days in the presence or absence of queuine, indicating the absence of queuine salvage in L-M cells.     

The absence of ribothymidine in specific eukaryotic transfer RNAs. I. Glycine and threonine tRNAs of wheat embryo

Ribothymidine, generally considered a universal nucleotide in tRNA, is completely absent in five specific wheat embryo tRNAs. These consist of two species of glycine tRNA and three species of threonine tRNA. These tRNAs, all extensively purified, are acceptable substrates for $\text{E. coli}$ - ribothymidine forming-uracil methylase, which produces one mole of ribothymidine per mole of tRNA. These five tRNAs account for about 90% of the wheat embryo tRNAs which are substrates for this methylase. Nucleotide sequence analysis of one of these tRNAs, tRNA^Gly_I, confirmed both the complete absence of ribothymidine at position 23 from the 3′end, and the presence of uridine at that site instead. In addition, it is shown that methylation with $\text{E. coli}$ uracil methylase quantitatively converts uridine at position 23 to ribothymidine, while no other uridine in the molecule is affected.Using $\text{E. coli}$ uracil methylase as an assay we have detected this class of ribothymidine lacking tRNA, in each case consisting of a few specific species, in other higher organisms, such as wheat seedling, fetal calf liver and beef liver, in addition to wheat embryo. We could not detect this class of tRNA in $\text{E. coli}$ or yeast tRNA.     

pGp as the main product of bovine tRNA kinase

One of the Ser-tRNAs, Ser-tRNA^Sec, is converted to Sec-tRNA^Sec by Sec synthase. This Ser-tRNA^Sec is also converted to phosphoser-tRNA^Sec by tRNA kinase. In this study, we analyzed of the products of phosphorylation with tRNA kinase. [³H]Ser-tRNA^Sec purified on Sephacryl S-200 was phosphorylated with [-³²P]ATP by tRNA kinase. The product [³²P][³H]phosphoser-tRNA was purified on Sephacryl S-200 and hydrolyzed with ribonuclease T2. The chromatogram of this hydrolyzate on DEAE-cellulose in 7M urea buffer showed four peaks. The first peak of the pass-through fraction was seryl-adenosine liberated from the 3-terminal of the tRNA. The second peak, eluted before the third peak containing inorganic phosphate, was phosphoseryl-adenosine. The major compound in the fourth peak was pGp. As a control experiment, non-acylated tRNA^Sec was used as a substrate of phosphorylation and the product was analyzed. The chromatogram of the digest with ribonuclease T2 showed no peak of phosphoseryl-adenosine, but a peak of pGp was seen with the peak of inorganic phosphate. Thus, the major product in the presence of tRNA kinase was pGp, and a small but significant proportion of the radioactivity was found as phosphoserine in the presence of seryl residue on the 3-CCA terminal of tRNA^Sec. These results indicated that tRNA kinase phosphorylates not only Ser-tRNA to phosphoser-tRNA but also Gp of the 5-termini of tRNA to pGp. This study gives a new role to mammalian tRNA kinase.     

The nucleotide sequence of rat liver tRNAAsn

The major species of asparagine specific tRNA was isolated from rat liver, degraded to oligonucleotides, and shown to have the nucleotide sequence pG-U-C-U-C-U-G-U-m¹G-m²G-C-G-C- A-A-D-C-G-G-D-X-A-G-C-G-C-m²G-ψ-ψ-C-G-G-C-U-Q-U-U-t⁶A-A-C-C-G- A-A-A-G-m⁷G-D-U-G-G-U-G-G-Z-ψ-C-G-m¹A-G-C-C-C-A-C-C-C-A-G-G-G- A-C-G-C-C-A_OH. Although this tRNA contains several modified nucleotides in their expected positions, it is unique in having X, 3-(3-Amino-3-carboxy-n-propyl)uridine in loop I rather than in loop III; Q, 7-(4,5-cis-dihydroxyl-1-cyclopenten-3-yl-aminomethyl)-7-deazaguanosine in the wobble position of loop II; and Z, an unknown, and presently uncharacterized nucleoside, at position 23 from the 3′ terminus usually occupied by ribothymidine.     

Plant tRNA suppressors: In vivo readthrough properties and nucleotide sequence of yellow lupin seeds tRNA

Transfer RNAs isolated from yellow lupin seeds were screened for tRNA dependent nonsense suppression in Xenopus laevis oocyte system. No opal (UGA) suppressor activity could be detected. However, a tRNA^Tyr isoacceptor species stimulates readthrough of the leaky UAG tobacco mosaic virus (TMV)-RNA stop codon. This natural suppressor tRNA was purified to homogeneity and its sequence was determined to be: pC---C---g--- A---C---C---U---U---A---m²G---c---U---C---A---G---D---G---Gm--- G---U---A---G---A---G---Cm₂²G---G---A---G---G---A---C---U---G--- ψ---A---m¹G---A---ψ---C---C---U---U---A---G---m⁷G---acp³U---C--- A---C---U---G---G---U---ψ---C---G---m¹A---A---Uz.sbnd;C---C---G--- G---U---A---G---G---U---C---G---G---A---C---C---A_OH. The GψA anticodon seqeunce, the presence of the modified nucleoside 3-(3-amino-3-carboxypropyl)uridine (acp³U) in the extra loo p and the absence of ribothymidine are of special interest.     

Effect of griseofulvin on lipid composition and membrane integrity inMicrosporum gypseum

The effect of griseofulvin on lipid constituents and membrane permeability ofMicrosporum gypseum has been investigated. Mycelia grown in medium containing griseofulvin (IC₅₀ concentration) possessed a lower content of total lipids, phospholipids and sterols. This inhibitory effect was further supported by decreased incorporation of [¹⁴C] acetate in total lipids, total phospholipids and sterols. Decrease in total phospholipids was also reflected to a varying extent in all individual phospholipids. An increase in the unsaturated to saturated fatty acid ratio was observed in mycelia grown in medium containing griseofulvin. Membrane permeability was affected by griseofulvin as shown by increased K⁺-efflux and greater leakage of intracellular [³²P] labelled components from prelabelled cells. Our results suggest that the antifungal activity of griseofulvin is partially due to its secondary effect on lipid constituents ofMicrosporum gypseum.     

Effect of light on nucleotide modifications in the transfer RNA of cucumber cotyledons

The effect of light on nucleotide modifications in the tRNA of cucumber (Cucumis sativus L. var. Guntur) cotyledons was studied by chromatographic, electrophoretic and immunological methods. The tRNA from light-grown tissue showed the absence of 2-methylguanosine and a decrease in the relative proportions of ribothymidine and cytokinin-active ribonucleosides when compared to those produced from dark-grown tissue. On the other hand, a significant amount of one species of 2′-O-methyldinucleotide was observed in the tRNA of light-grown tissue which was not detected in the dark-grown tissue. Also, tRNA from light-grown tissue had higher levels of another species of 2′-O-methyldinucleotide. The results showed no difference in the amounts of other modified nucleosides in tRNA between tissues grown under the two conditions. 2′-O-Methyl-l-methyladenosine, a nucleotide modified both in the base and the ribose, apparently specific to plant tRNAs, has been found to be present in the RNA of both light- and dark-grown tissues. These results on the variation in modified nucleotides suggest that light has some role in nucleotide modification and, consequently, in cellular functions.     

Erratum

RNA polynucleotide kinase has been shown to transfer [γ³²P] from ATP to 5-OH termini of endogenous nuclear RNA. The products of this reaction have been isolated in RNA larger than 125 after in vitro incubation of mouse L cell nuclei. About 20%–30% of these 5′-OH kinase products are polyadenylated. A sizeable fraction of the [γ³²P] label from ATP is also found in internal phosphodiester bonds after 30-minute nuclear incubation in vitro. The possibility of substantial [³²P] recycling via the α position of nucleoside triphosphate was ruled out because: (1) 2mM nucleoside triphosphates in the incubation medium, (2) limited nearestneighbor distribution 3′ and 5′ to the phosphodiester bond compared with that from [α³²P] UTP, (3) different nearest-neighbor distribution for RNA molecules > 12S and 12-3S, (4) relative insensitivity of the [γ³²P] incorporation to α-amanitin as compared with total RNA synthesis, (5) internal [³²P] appearance in RNA > 12S in less than five minutes of incubation, and (6) < 0.03% to 0.6% of the total [³²P] in the α position of nucleoside triphosphates after 30 minutes of incubation. The [γ³²P] incorporation was dependent on high ATP concentration and was insensitive to competition by inorganic phosphate. These results are consistent with the levels of 5′ RNA polynucleotide kinase activity in L cell nuclei and suggest the presence of an RNA ligase that can utilize the termini generated by the 5′-OH RNA kinase in a ligation reaction.     

Influence of mycoplasma infection on the incorporation of different precursors into RNA components of tissue culture cells

Seven different tissue culture cells have been cultured with and without mycoplasma (M. hyorhinis) in the presence of various precursors of RNA. Total cellular RNA was isolated and analysed by electrophoresis on polyacrylamide gels. The results obtained with mycoplasma-infected cells can be summarized as follows:

1. 1. When cells are labelled with [8-³H]guanosine or [5-³H]uridine there is some incorporation into host cell 28S and 18S rRNA, but it is less than into mycoplasma 23S and 16S rRNA. [8-³H]guanosine or [5-³H]uridine are also incorporated into host cell and mycoplasma tRNA and mycoplasma 4.7S RNA, but the incorporation into host cell 5S rRNA and low molecular weight RNA components (LMW RNA) is reduced.

2. 2. [5-³H]uracil is not incorporated into host cell RNA but into mycoplasma tRNA, 4.7S RNA, a mycoplasma low molecular weight RNA component M₁ and 23S and 16S rRNA.

3. 3. [³H]methyl groups are incorporated into mycoplasma tRNA, 23S and 16S rRNA, but not into host cell 28S, 18S, 5S rRNA nor into mycoplasma 4.7S RNA.

4. 4. With [³²P]orthophosphate or [³H]adenosine as precursors, the labelling is primarily in the host RNA.

Mycoplasma infection influences the labelling of RNA primarily by an effect on the utilization of the exogenously added radioactive RNA precursors, since the generation time of mycoplasma infected cells is about the same as that of uninfected cells. Mycoplasma infection may completely prevent the identification of LMW RNA components.     

Crystallographic and mutational studies on the tRNA thiouridine synthetase TtuA

In thermophilic bacteria, specific 2‐thiolation occurs on the conserved ribothymidine at position 54 (T54) in tRNAs, which is necessary for survival at high temperatures. T54 2‐thiolation is achieved by the tRNA thiouridine synthetase TtuA and sulfur‐carrier proteins. TtuA has five conserved CXXC/H motifs and the signature PP motif, and belongs to the TtcA family of tRNA 2‐thiolation enzymes, for which there is currently no structural information. In this study, we determined the crystal structure of a TtuA homolog from the hyperthermophilic archeon Pyrococcus horikoshii at 2.1 Å resolution. The P. horikoshii TtuA forms a homodimer, and each subunit contains a catalytic domain and unique N‐ and C‐terminal zinc fingers. The catalytic domain has much higher structural similarity to that of another tRNA modification enzyme, TilS (tRNA^Ile₂ lysidine synthetase), than to the other type of tRNA 2‐thiolation enzyme, MnmA. Three conserved cysteine residues are clustered in the putative catalytic site, which is not present in TilS. An in vivo mutational analysis in the bacterium Thermus thermophilus demonstrated that the three conserved cysteine residues and the putative ATP‐binding residues in the catalytic domain are important for the TtuA activity. A positively charged surface that includes the catalytic site and the two zinc fingers is likely to provide the tRNA‐binding site. Proteins 2013; 81:1232–1244. © 2013 Wiley Periodicals, Inc.     

Growth and comparative physiology ofKlebsiella oxytoca attached to granular activated carbon particles and in liquid media

Experiments were performed to evaluate the comparative growth and physiology ofKlebsiella oxytoca grown attached to granular activated carbon particles (GAC) and in liquid medium. Laboratory studies showed that when this organism attached to GAC, the growth rate was enhanced more than 10 times in the presence of glutamate, a substrate that adsorbed to the surface. No differences were observed if the substrate was glucose, which did not adsorb to GAC. Cellular [³H]thymidine uptake was used to estimate DNA biosynthesis. Attached bacteria grown in a minimal nutrient medium containing 20.0 mg/liter glutamate took up 5 times more [³H]thymidine than cells grown in suspension. [³H]uridine was used as a measure of RNA turnover. Attached cells were shown to assimilate 11 times more [³H]uridine than cells in liquid media. Cell size measurements were performed by differential filtration. Cells grown in a minimal medium with 20.0 mg/liter glutamate decreased in size over time, with 62% of the total number passing through a 1.0m filter after 9 days incubation. In the same period, 39% of a cell population that was grown on GAC passed through a 1.0m filter. These studies indicate that GAC provides an interfacial environment for the enhanced growth ofK. oxytoca when glutamate is the substrate.     

Identification of a selenocysteine-specific aminoacyl transfer RNA from rat liver

The aminoacylation of rat liver tRNA with selenocysteine was studied in tissue slices and in a cell-free system with [⁷⁵Se]selenocysteine and [⁷⁵Se]selenite as substrates. [⁷⁵Se]Selenocysteyl tRNA was isolated via phenol extraction, 1 M NaCl extraction and chromatography on DEAE-cellulose. [⁷⁵Se]Selenocysteyl tRNA was purified on columns of DEAE-Sephacel, benzoylated DEAE-cellulose and Sepharose 4B. In a dual-label aminoacylation with [³⁵S]cysteme, the most highly purified ⁷⁵Se-fractions were > 100-fold purified relative to ³⁵S. These fractions contained < 0.7% of the [³⁵S]cysteine originally present in the total tRNA. When [³⁵Se]selenocysteyl tRNA was purified from a mixture of ¹⁴C-labeled amino acids, over 97% of the [¹⁴C]aminoacyl tRNA was removed. The [⁷⁵Se]selenocysteine was associated with the tRNA via an aminoacyl linkage. Criteria used for identification included alkaline hydrolysis and recovery of [⁷⁵Se]selenocysteine, reaction with hydroxylamine and recovery of [⁷⁵Se]selenocysteyl hydroxamic acid and release of ⁷⁵Se by ribonuclease. The specificity of [⁷⁵Se]selenocysteine aminoacylation was demonstrated by resistance to competition by a 125-fold molar excess of either unlabeled cysteine or a mixture of the other 19 amino acids in the cell-free selenocysteine aminoacylation system.     

Enhanced activity of tRNA-pseudouridine synthetase in Yoshida ascites sarcoma.

Five days after transplantation of Yoshida ascites sarcoma cells into a rat, specific activity of tRNA-pseudouridine synthetase was extremely high in the supernatant of tumor cells and moderately high in the tumor-bearing rat liver compared with normal rat liver. Enzyme assay was performed at 37°C by determining the release of tritium from heterogeneous [³H] tRNA extracted from $\text{E. coli}$ B grown in the presence of [5,6-³H]-uracil and resulting in the increased ratio of the amount of pseudouridine to uridine residues in [³H] tRNA. Neither [5-³H]-uridine, [5,6-³H]-UTP, nor [5,6-³H]-poly U released tritium in the present assay conditions.     

Pyrimidine metabolism during somatic embryo development in white spruce (Picea glauca)

Pyrimidine metabolism was investigated at various stages ofsomatic embryo development of white spruce (Picea glauca). The contribution of thede novo and the salvage pathways of pyrimidine biosynthesis to nucleotide and nucleic acid formation and the catabolism of pyrimidine was estimated by the exogenously supplied [6-¹⁴C]orotic acid, an intermediate of thede novo pathway, and with [2-¹⁴C]uridine and [2-¹⁴C]uracil, substrates of the salvage pathways. Thede novo pathway was very active throughout embryo development. More than 80 percnt; of [6-¹⁴C]orotic acid taken up by the tissue was utilized for nucleotide and nucleic acid synthesis in all stages of this process. The salvage pathways of uridine and uracil were also operative. Relatively high nucleic acid biosynthesis from uridine was observed, whereas the contribution of uracil salvage to the pyrimidine nucleotide and nucleic acid synthesis was extremely limited. A large proportion of uracil was degraded as ¹⁴CO₂, probably via β-ureidopropionate. Among the enzymes of pyrimidine metabolism, orotate phosphoribosyltransferase was high during the initial phases of embryo development, after which it gradually declined. Uridine kinase, responsible for the salvage of uridine, showed an opposite pattern, since its activity increased as embryos developed. Low activities of uracil phosphoribosyltransferase and non-specific nucleoside phosphotransferase were also detected throughout the developmental period. These results suggest that the flux of thede novo and salvage pathways of pyrimidine nucleotide biosynthesisin vivo is roughly controlled by the amount of these enzymes. However, changing patterns of enzyme activity during embryo development that were measuredin vitro did not exactly correlate with the flux estimated by the radioactive precursors. Therefore, other fine control mechanisms, such as the fluctuation of levels of substrates and/or effectors may also participate to the real control of pyrimidine metabolism during white spruce somatic embryo development.     

Protein synthetic ability of Escherichia coli valine transfer RNA with pseudouridine, ribothymidine, and other uridine-derived residues replaced by 5-fluorouridine

The requirement for pseudouridine and other uridine-derived minor nucleotides for activity of transfer RNA in several of the intermediate steps in protein synthesis was examined using a purified preparation of Escherichia coli valine transfer RNA in which the uridine and uridine-derived nucleotides were replaced by 5-fluorouridine. The degree of substitution was 87% or better for uridine, pseudouridine, ribothymidine, dihydrouridine, and 4-thiouridine, and at least 75% for uridine-5-oxyacetic acid. Each of these nucleotides, except for uridine, occurs only once in this transfer RNA species.The rate and yield of ternary complex formation with elongation factor Tu-GTP of E. coli, the rate and extent of elongation factor-dependent binding to ribosomes at 10 mm-Mg²⁺, and the rate and extent of synthesis of the co-polypeptide (Phe_n,Val) dependent on poly(U₃,G) were all unchanged when the fluorouridine-containing transfer RNA was used in place of the normal control. In all yield assays, the amount of product formed was proportional to the amount of valyl-tRNA added. Non-enzymatic binding to ribosomes in the presence of tetracycline was more efficient for the fluorouridine-substituted tRNA than for the control. At 15 to 20 mm-Mg²⁺ the polynucleotide-dependent binding, as a percentage of tRNA added, was 44% for the control and 65% for the modified tRNA, while at 5 mm-Mg²⁺, the figures were 10% and 40%, respectively.We conclude from these results that there is no essential requirement for pseudouridine or ribothymidine in the GTψC loop of tRNA for its proper functioning in protein synthesis in vitro. Confirming earlier work, dihydrouridine and 4-thiouridine are also not essential.     

Poly- und Metaphosphate in höheren Pflanzen (Lemnaceae)

Summary After pulse-labelling with [³²P]orthophosphate of higher plants (Lemna perpusilla (Torrey) and Lemna gibba (L.)) which were previously grown in a P-free medium for 24 h, the [³²P]-radioactivity is partially incorporated into condensed inorganic phosphates. The isolation of the latter was achieved by joint extraction with the nucleic acids and fractionation on methylated serum albumin and Kieselgur (MAK). Two-dimensional thin layer chromatography on a mixture of cellulose and microcrystalline cellulose revealed that ³²P-radioactivity was present in linear oligophosphates with 2 to 7 residues as well as in cyclic tri-, tetra-, penta- and hexametaphosphates. Among the low-molecular condensed inorganic phosphates the trimetaphosphate contained significantly more radioactivity than the other compounds. It is supposeded that the condensed phosphates are involved in the regulation of the ATP-ADP-P_i-system.     

Transfer RNA analysis during the reproductive cycle of a freshwater teleost,H. fossilis

Transfer RNA was analyzed qualitatively as well as quantitatively from ovaries of the fresh water teleostHeteropneustes fossilis for twelve months. The tRNA samples were found to be pure and devoid of any high molecular weight RNA or DNA contaminations. The quantity of tRNA as well as its biological activity, assayed byin vitro aminoacylation using homologous aminoacyl tRNA synthetases, were found to be higher during resting and preparatory (pre-vitellogenic) phases, i.e. from November to March, as compared to vitellogenic and spawning phases of the fish, i.e. from April to October. The highest tRNA pool and its activity was found in the month of February, which coincides with the early preparatory phase. The results indicate that the accumulation of active tRNA starts in the resting phase. Such an accumulation of tRNA may be a part of the enrichment of mature eggs with complete translational machinery before ovulation in order to cope with the high rate of protein synthesis after fertilization.Abbreviations aaRS aminoacyl tRNA synthetase - [¹⁴C] APH [¹⁴C]-algal protein hydrolysate - ATP adenosine triphosphate - DTT dithiothreitol - EDTA ethylene diamine tetra acetic acid - GSI gonado somatic index - TCA trichloroacetic acid - tRNA transfer RNA     

Capacity for RNA synthesis in 70S ribosome-deficient plastids of heat-bleached rye leaves

In the leaves of rye seedlings (Secale cereale L.) grown at an elevated temperature of 32°C the formation of plastidic 70S ribosomes is specifically prevented. The resulting plastid ribosome-deficient leaves, which are chlorotic in light, represent a system for the identification of translation products of the 80S ribosomes among the chloroplastic proteins. Searching for the primary heat-sensitive event causing the 70S ribosome-deficiency, the thermostability of the chloroplastic capacity for RNA synthesis was investigated. The RNA polymerase activity of isolated normal chloroplasts from 22°-grown rye leaves was not inactivated in vitro at temperatures between 30° and 40°C. The ribosome-deficient plastids purified from bleached 32°-grown leaf parts contained significant RNA polymerase activity which was, however, lower than in functional chloroplasts. After application of [³H]uridine to intact leaf tissues [³H]uridine incorporation was found in ribosome-deficient plastids of 32°C-grown leaves. The amount of incorporation was similar to that in the control chloroplasts from 22°C-grown leaves. According to these results, it is unlikely that the non-permissive temperature (32°C) causes a general inactivation of the chloroplastic RNA synthesis in rye leaves.