Studies on Agrobacterium tumefaciens. IV. Nonreplication of the bacterial DNA in mung beam (Phaseolus aureus).

DNA·DNA filter hybridization and DNA solution enrichment reassociation experiments showed that no $\text{Agrobacterium tumefaciens}$ DNA was replicated in mung bean seedlings under the conditions specified in published reports for the uptake, integration, and replication of bacterial DNA in higher plants. Residual presumptive DNA hybrids that formed in a few instances were characterized by thermal chromatography on hydroxylapatite. The Tm and melting profiles of these hybrids from DNA-treated plants were the same as those from untreated control plants. The sensitivities of these procedures were sufficient to detect $\text{A. tumefaciens}$ DNA in the order of 0.005% to 0.01% of the plant genome. These results do not concur with previous reports that large pieces of DNA (at least 30%) of the plant genome of bacterial-DNA-treated-plants is made up of bacterial donor DNA.     

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.     

Uptake and aminoacylation of exogenous Escherichia coli tRNA by mouse fibroblasts.

Mouse fibroblasts (L-cells) in suspension culture take up exogenous $\text{Escherichia coli}$ tRNA in the presence of DEAE-Dextran. Tritium-labeled formylmethionine tRNA and valine tRNA are both taken up at very low levels. Tritium activity is associated solely with 4S material as judged by chromatography of cell extracts on Sephadex G-100. Further analysis of this material on a dihydroxyboryl-substituted cellulose indicates that a small portion of the tRNA taken up is acylated by the L-cells.     

Determination of the multiplicity of the silk fibroin gene and detection of fibroin gene-related DNA in the genome of Bombyx mori.

The number of silk fibroin genes per genome in the silkworm Bombyx mori has been determined by hybridization using fibroin [¹²⁵I]mRNA. The purified [¹²⁵I]mRNA had an oligonucleotide pattern after RNAase T₁ digestion which was characteristic of fibroin mRNA (Suzuki &; Brown, 1972) and it hybridized specifically to DNA with a G + C content expected for a fibroin gene. Thermal denaturations indicated that these hybrids were mismatched by about 3%, which probably indicates some variation among the sequences encoding the internal repetitions of the fibroin protein.The concentration of fibroin gene sequences in B. mori DNA was measured by saturation hybridization of [¹²⁵I]mRNA to filter bound DNA. The same saturation level of 1.8 × 10^?5 μg mRNA per μg DNA was calculated from data obtained with unfractionated DNA and with fibroin gene sequences which had been separated from bulk B. mori DNA by actinomycin $\text{D}\text{CsCl}$ centrifugation. Scatchard plots of the subsaturation data extrapolated to an identical saturation value. Internal reiteration of the fibroin mRNA molecule was apparent from the high association constant of hybridization. An exhaustive hybridization experiment showed that such repetitions comprise at least 90% of each mRNA molecule. The saturation value, in conjunction with the genome DNA content and the mRNA size, indicated the presence of only one fibroin gene per haploid B. mori genome.Hybridization of actinomycin $\text{D}\text{CsCl}$ fractionated DNA indicated that fibroin mRNA can form hybrids with DNA that bands with bulk B. mori DNA. These hybrids appear to involve DNA which is related to, but distinguishable from, true fibroin gene sequences. The fibroin gene-related sequences form mismatched hybrids with the mRNA, are much shorter than the fibroin gene and are dispersed in B. mori DNA of much lower G + C content, and there are many copies of these sequences per B. mori genome.     

Studies on invitro DNA synthesis: II. Isolation of a protein which stimulates deoxynucleotide incorporation catalyzed by DNA polymerases of E.coli

Purified RNA polymerase, DNA polymerase III and unwinding protein of $\text{Escherichia}\text{coli}$ catalyze limited rifampicin sensitive fd or ØX 174 DNA-dependent DNA synthesis. A protein has been partially purified from $\text{E.}\text{coli}$ which stimulates rifampicin sensitive dXMP incorporation in this system 20 to 30 fold. This protein also stimulates DNA synthesis catalyzed by DNA polymerases I and II; the stimulation occurs in reactions primed with natural and synthetic DNAs as well as RNA-DNA hybrids. The protein is not a product of the known dna genes. In contrast to the above system of purified enzymes, rifampicin sensitive dXMP incorporation in crude extracts of $\text{E.}\text{coli}$ is specifically dependent on fd but not ØX 174 DNA. An additional factor has been isolated from extracts of $\text{E.}\text{coli}$ which restores specificity to the purified rifampicin sensitive system by preventing ØX 174 DNA from serving as a template.     

Anomalies in 5'-end [32P] labelling of transfer RNA and partial sequence of a tRNAGlu from Scenedesmus obliquus

A chloroplast tRNA_m^Met species from $\text{Scenedesmus}\text{obliquus}$ is very poorly 5′-end [${}^{32}\text{P}$] labelled using [γ-³²P]ATP and T4 polynucleotide kinase. In sequencing the tRNA using standard 5′-labelled methods a very minor contaminating tRNA is preferentially labelled. The partial tRNA sequence determined by this method has an anticodon (CUC) for tRNA^Glu.     

Reiteration of DNA complementary to a cytoplasmic non-ribosomal RNA

Experimentally induced granulomas, in guinea pigs, were fractionated into a 40,000xg pellet and supernatant, which was further fractionated into a 100,000xg pellet and supernatant. The product of in vitro amino acid incorporation by the 40,000xg pellet was tentatively identified as collagen by its high proline/leucine ratio, its digestibility by bacterial collagenase and its solubility in hot trichloroacetic acid. The 100,000xg pellet incorporated leucine much more efficiently than the 40,000xg pellet and the product was insoluble in hot trichloroacetic acid.Labeled RNA from the 40,000xg pellet formed hybrids with granuloma ($\text{C}{}_{\mathrm{o}}\text{t}\text{1}\text{2}\text{= 100–150}$) and liver ($\text{C}{}_{\mathrm{o}}\text{t}\text{1}\text{2}\text{= 8,000}$) $\text{chromatin}$ DNA, indicating that genes coding for this RNA are repeated about 100-fold in granuloma and less than 5 times in liver DNA. Under conditions of poly(A) binding, 50% of this labeled RNA is retained by filters. Digestion with ribonuclease and ribonuclease T₁, decreases binding efficiency by 75%.     

Destabilization of the secondary structure of RNA by ribosomal protein S1 from escherichia coli

S1 is an acidic protein associated with the 3′ end of 16S RNA; it is indispensable for ribosomal binding of natural mRNA. We find that S1 unfolds single stranded stacked or helical polynucleotides (poly rA, poly rC, poly rU). It prevents the formation of poly (rA + rU) and poly (rI + rC) duplexes at 10–25 mM NaCl but not at 50–100 mM NaCl. Partial, salt reversible denaturation is also seen with coliphage MS2 RNA, $\text{E. coli}$ rRNA and tRNA. Generally, only duplex structures with a Tm greater than about 55° are formed in the presence of S1. The protein unfolds single stranded DNA but not poly d(A·T).     

Separation of aminoacyl-transfer RNAs by polyacrylamide gel electrophoresis

A polyacrylamide gel electrophoresis system for separating $\text{E.}$$\text{coli}$ tRNAs and aminoacyl-tRNAs is described. The tRNA was separated into 6 discrete bands which contained varyin aamounts of tRNA and therefore varying numbers of tRNA species. In order to locate specific tRNAs, tRNA was charged with a ¹⁴C amino acid and the aminoacyl-tRNA was located by autoradiography. With several amino acids, 2 isoaccepting species were found. In total, 30 aminoacyl-tRNAs were located.     

A rapid procedure to detect in situ DNA/RNA hybrids

We developed a new method for detecting DNA/RNA hybrids formed $\text{in}\text{situ}$ using $\text{anti-}\text{DNA}\text{RNA}$ antibodies and the Peroxidase-antiperoxidase immunohistochemical procedure. Using RNA synthesised $\text{in}\text{vitro}$ from cloned $\text{Drosophila}$ histone genes (pDm 500H), we localized by this procedure, the histone genes to the 39 D-E region of the left arm of the second chromosome. This method has several advantages compared to conventional procedures.     

Transcription of a specific product from cloned T4 tRNA genes in Xenopus germinal vesicle extract

An extract, prepared from the germinal vesicles of $\text{Xenopus}$ oocytes, was capable of transcribing cloned T₄ tRNA genes. The major product was identified as tRNA^Ser, with some extra nucleotides from neighboring sequences in the tRNA cluster at both termini.     

Reactions at the 3' terminus of transfer ribonucleic acid. IX. tRNA nucleotidyltransferase activity in bacteriophage T4-infected Escherichia coli

There was no detectable increase in tRNA nucleotidyltransferase activity upon infection of $\text{Escherichia coli}$ A19 with bacteriophage T4. Three mutant strains which contained low levels of tRNA nucleotidyltransferase activity also showed no increase in activity after infection. tRNA nucleotidyltransferase was purified from both uninfected and T4-infected cells and examined for possible modification. It was found that enzyme purified from both types of cells eluted from DEAE cellulose at the same specific conductivity. In addition, the molecular weight of tRNA nucleotidyltransferase purified from both uninfected and T4-infected cells was approximately 45,000 daltons as determined by chromatography on Sephadex G-100. These results suggest that T4-infection does not lead to synthesis of a new virus-specific tRNA nucleotidyltransferase nor does it cause modification of the host enzyme.     

Differences in aminoacylation in vivo and in vitro of lysine isoaccepting tRNAs from virus-transformed cells

When murine sarcoma virus-transformed cells are labeled with [³H]lysine $\text{in}\text{vivo}$ for various periods, 5 of 6 isoaccepting lysine tRNAs separable by RPC-5 chromatography are aminoacylated in 1 hr to the same extent that they are aminoacylated $\text{in}\text{vitro}$. The sixth isoacceptor, tRNA₆^Lys, is not aminoacylated $\text{in}\text{vivo}$ to a measurable extent in 1 hr, although it is present in the tRNA prepared from the cells. All six isoacceptors are aminoacylated with [³H]lysine $\text{in}\text{vivo}$ when the labeling period is 2 or 3 hr. These results further show that $\text{in}\text{vitro}$ correlations of the amount of tRNA₄^Lys with cell division accurately reflect the situation $\text{in}\text{vivo}$. Results of differential centrifugation indicate that tRNA₆^Lys occurs in mitochondria.     

Studies of odd bases in yeast mitochondrial tRNA: II. Characterization of rare nucleosides

The nucleoside composition of tRNA from highly purified yeast mitochondria shows the presence of T, ψ, hU, m¹G, m²G, m₂²G, I and t⁶A whereas neither m⁷G, m⁵C, m³C, m¹A, i⁶A and Y nor O′-methylated nucleosides (which are common in yeast cytoplasmic tRNA) were found. The G+C content is very low (35%). The overall methylation content is 2.7% which is about half the content of yeast cytoplasmic tRNA but similar to that of $\text{E. coli}$ tRNA. Some rare nucleosides however which are found in $\text{E. coli}$ (s⁴U, acp³U, m²A, m⁶A, ms²i⁶A, Q) were not found in yeast mitochondrial tRNA.     

DNA reassociation kinetic analysis of the brine shrimp, Artemia salina

DNA reassociation kinetics have been partly elucidated for the brine shrimp $\text{Artemia salina}$, using calf thymus DNA as a standard. The $\text{Artemia}$ single-copy DNA sequences comprise 45% of the genome; sequences having a repetition frequency of about 2–90 are not detectable. The average repetition frequency of the intermediately redundant DNA component is about 5,000 copies. Reassociation kinetic data are consistent with a unit genome size of 1.5 pg.     

Studies on avian heart pyruvate kinase during development.

The cytokinin-active nucleoside 6-(4-hydroxy-3-methyl-$\text{cis}$-2-butenylamino)-9-β-$\text{D}$-ribofuranosylpurine, i.e. ribosyl-$\text{cis}$-zeatin, has been isolated from an hydrolysate of tRNA from $\text{Corynebacterium fascians}$. The identification of ribosyl-$\text{cis}$-zeatin is based on biological activity, liquid chromatographic mobility and uv spectrum of the purified material as well as the mass spectrum and gas chromatographic mobility of its trimethylsilylated derivative.     

Nondiscrimination of RNA viral message in binding to 30S ribosomes derived from T4 phage infected Escherichia coli

The effect of T4 phage on ribosomes in terms of their ability to bind RNA viral template is examined. It is found that the 30S subunits of T4 ribosomes bind MS2 RNA as efficiently as do the subunits of uninfected $\text{E. coli}$ ribosomes. On the other hand, analyses of the formation of 70S initiation complex, presumably from MS2 RNA-30S ribosome complex, using both labeled MS2 RNA and initiator tRNA, reveal that T4 ribosomes are only about half as active as $\text{E. coli}$ ribosomes. The latter phenomenon has been reported previously. These results suggest that, following T4 infection, ribosomes are modified in such a way that the attachment of fMet-tRNA_f to MS2 RNA-30S subunit complex is impaired.     

DNA strand scission by the antitumor protein neocarzinostatin

The antibiotic protein, neocarzinostatin, induces the scission of DNA strands $\text{in vivo}$ and $\text{in vitro}$. HeLa cell DNA prelabelled with [¹⁴C] thymidine is cut into large pieces with a peak at 80–90S when cells are incubated with 0.5 to 5.0 μg/ml of highly purified neocarzinostatin. Incubation of the antibiotic (0.5 μg/ml) with [³H] SV40 DNA in the presence of 2-mercaptoethanol results in the conversion of superhelical DNA I to nicked circular duplex DNA II. At high levels of drug, smaller fragments of linear DNA are produced. Strand breaks are detected in both neutral and alkaline sucrose gradients, indicating that drug susceptibility is not due to alkali-labile bonds.     

The stimulation of cerebral N2-methyl- and N2-2-dimethyl guanine-specific tRNA methyltransferases by methionine sulfoximine: an in vivo study.

The administration of a single convulsant dose or of multiple subconvulsant doses of L-methionine-dl-sulfoximine (MSO) to 18-day old rats results in a significant elevation of the specific activity of cerebral tRNA methyltransferases, as determined in an $\text{in vitro}$ assay, using heterologous or species-homologous tRNAs as substrates. The increase was detectable as early as 90 min after MSO and persisted throughout the entire 5–6 h preconvulsant period. The ¹⁴[C]-methyl tRNA was purified, and hydrolyzed to its constituent bases and their distribution was quantitated by high performance liquid chromatography. A marked increase in the formation of ¹⁴[C]-N²-methyl- and ¹⁴[C]-N₂²-dimethyl guanine was noted in the MSO-treated animals, demonstrating a specific stimulation by MSO $\text{in vivo}$ of the cerebral N²-methyl and/or N₂²-dimethyl guanine-specific tRNA methyltransferases.