Formation of phenylalanine transfer RNA lacking the wye base in Vero cells during methionine starvation

Structural significance of hypermodified nucleic acid base hydroxywybutine (OHyW) which occur at 37th position in the anticodon loop of yeast tRNA(Phe)

Conformational preferences of hypermodified nucleic acid base hydroxywybutine (OHyW) have been studied using quantum chemical single point semi-empirical PM3 method. Automated geometry optimization using semi-empirical RM1, molecular mechanics force field (MMFF) along with ab-initio HF-SCF (6-31G** basis set) and DFT (B3LYP/6-31G** basis set) calculations have also been made to compare the salient features. Molecular electrostatic potentials (MEPs) depict the polarities of hydroxywybutine (OHyW) side chain. Another conformational study showed that hydroxywybutosine side chain interacts with adjacent bases within the anticodon loop of tRNA(Phe). The solvent accessible surface area (SASA) calculations revealed the structural role of hydroxywybutine in anticodon loop. Explicit molecular dynamics (MD) simulation has been done over the PM3 most stable structure of OHyW. The hydroxywybutine side chain prefers 'distal' conformation i.e. spreads away from the cyclic five membered imidazole moiety of modified tricyclic guanine base. The predicted preferred conformation of hydroxywybutine may prevent extended Watson-Crick base pairing during protein biosynthesis process. This conformation of OHyW stabilized by intramolecular interactions between O(6)⋯HO(16), O(6)⋯HC(15) and O(20)⋯HC(17). Further stabilization is also expected from interactions between O(22)⋯HC(16) and O(23)⋯HC(15). Explicit molecular dynamics (MD) simulation over the PM3 most stable structure of OHyW support the preferred geometry by preserving the 'distal' orientation of hydroxywybutine side chain and intramolecular hydrogen bonding interactions. MD simulation study revealed the role of hydroxyl group of OHyW to avoid fluctuations and prevent multiple iso-energetic conformations of hydroxywybutine side chain as compared to wybutine (yW).

Variations in tRNA modifications, particularly of their queuine content in higher eukaryotes. Its relation to malignancy grading

Literature references dealing with the variations in the modification level of nucleosides in total eukaryotic tRNAs as a function of different physiological status and after drug administration as well as in sequenced cytoplasmic tRNAs between normal and tumor cells and in SV40-transformed cells are reviewed. In addition, special attention is given to guanine replacement of queuine in the first position of the anticodon of tRNAs. A correlation between the level of this undermodification in cancer tissues and the malignancy grading could be found in human ovarian tumors, confirming the results reported in several laboratories for lymphomas and lung cancer tissues. Indeed tRNAs from primary and metastatic human ovarian malignant tumors are Q deficient as compared to tRNAs from normal tissues or benign tumors: thus queuine deficiency increases with malignancy and grading of differentiation.

Modified nucleosides in body fluids of tumor-bearing patients

The catabolism of nucleic acids, particularly tRNA, produces a variety of modified nucleosides which are not reutilized by mammalian cells. Investigation of these compounds in body fluids, mainly urine, has recently provided evidence of altered metabolic situations in tumor-bearing patients. The factors involved in the alterations of modified nucleosides formation are connected with altered tRNA-modifying enzymes and/or altered turnover of subpopulations of tRNA. A common pattern in tumor cells or tissues is the presence of isoaccepting tRNA species containing aberrant nucleoside modifications. Several modified nucleosides have been detected and quantitated by HPLC analysis of the urine of normal subjects and cancer patients. Results obtained, in the authors' laboratory, among others, indicate a possible correlation between urinary excretion of these compounds and the course of the disease, with implications for the follow-up of therapeutic treatment. Particular reference should be made to psi, which appears to be a suitable marker for monitoring these subjects. The data from the authors' laboratory also show that the analysis of modified nucleosides in blood may be considered a useful tool in the search for proper markers associated with the cancer status. In this respect psi is suggested as a biochemical indicator for cancer patients.

Alterations in post-transcriptional modification of the Y base in phenylalanine tRNA from tumor cells

Various tumor cells contain chromatographically distinct isoacceptor tRNA species. To decide whether the tumor-specific species represent an expression of a separate tRNA gene or only an undermodified form of normal tRNAPhe, nucleotide sequences of tRNAPhe isolated from neuroblastoma and normal mouse liver were determined by postlabeling techniques. The results showed identical sequences except for the changes of post-transcriptional modifications in the anticodon loop. Normal mouse liver tRNAPhe contained Cm32, Gm34, and the hypermodified YOH next to the 3' end of the anticodon. On the contrary, tRNAPhe from neuroblastoma contained C32, G34, and, instead of YOH base m1G. A small proportion of tRNAPhe species contained an undermodified YOH base. For the examination of the conditions leading to the undermodified tRNAPhe, Vero cells derived from the kidney of African green monkey in culture were used. In these cells, deprivation of methionine or lysine resulted in changes in tRNAPhe modification similar to those in tumor cells. Ehrlich ascites tumor cells were examined to determine whether the presence of altered tRNAPhe species in various tumors is also the result of starvation of some nutritional factors. Results obtained with these cells showed that tRNAPhe species lacking the Y base disappeared in tumor-bearing mice after intraperitoneal injection with a mixture of amino acids and vitamins. Thus it is concluded that tumor-specific tRNAPhe species are the products of aberrant post-transcriptional modification, not the transcripts of different, normally repressed genes.

The effect of exogenous nutrients on the biosynthesis of Y base in tRNAPHe from Ehrlich ascites carcinoma

In contrast to normal eukaryotic tissue, which contains a single isoaccepting species of tRNAPhe, the Ehrlich ascites carcinoma contains a spectrum of tRNAPhe species varying in their relative degree of posttranscriptional modification. The occurrence of multiple species involves an incomplete biosynthesis of the Y base, a complex hypermodified nucleoside located adjacent to the 3' end of the anticodon. Following intraperitoneal innoculation of a mixture of essential amino acids and vitamins into these mice, the majority of the tumor tRNAPhe behaved like the single liver tRNAPhe species. This suggests that under these conditions the modification of Y base was completed.

Under-modified Y base in a tRHAPhe isoacceptor observed in tumor cells

A fluorescent wye (Ye) was isolated from tRHAPhe specific to Ehrlich ascites cells. The structure was determined to be alpha-amino-beta-hydroxy-4,9,-dihydro-4,6-dimethyl-9-oxo-1-H-imidazo(1,2-alpha)purine-7-butyric acid: namely the compound lacking methyl carboxyl and methyl groups and thus is an under-modified precursor of hydroxy-Y base present in normal liver tRNAPhe.