Detection of queuosine and queuosine precursors in tRNAs by direct RNA sequencing.

Queuosine (Q) is a complex tRNA modification found in bacteria and eukaryotes at position 34 of four tRNAs with a GUN anticodon, and it regulates the translational efficiency and fidelity of the respective codons that differ at the Wobble position. In bacteria, the biosynthesis of Q involves two precursors, preQ0 and preQ1, whereas eukaryotes directly obtain Q from bacterial sources. The study of queuosine has been challenging due to the limited availability of high-throughput methods for its detection and analysis. Here, we have employed direct RNA sequencing using nanopore technology to detect the modification of tRNAs with Q and Q precursors. These modifications were detected with high accuracy on synthetic tRNAs as well as on tRNAs extracted from Schizosaccharomyces pombe and Escherichia coli by comparing unmodified to modified tRNAs using the tool JACUSA2. Furthermore, we present an improved protocol for the alignment of raw sequence reads that gives high specificity and recall for tRNAs ex cellulo that, by nature, carry multiple modifications. Altogether, our results show that 7-deazaguanine-derivatives such as queuosine are readily detectable using direct RNA sequencing. This advancement opens up new possibilities for investigating these modifications in native tRNAs, furthering our understanding of their biological function.

Probing Queuosine Modifications of Transfer RNA in Single Living Cells via Plasmonic Affinity Sandwich Assay.

Queuosine (Q) modification on tRNA plays an essential role in protein synthesis, participating in many tRNA functions such as folding, stability, and decoding. Appropriate analytical tools for the measurement of tRNA Q modifications are essential for the exploration of new roles of Q-modified tRNAs and the rationalization of their exact mechanisms. However, conventional methods for Q modification analysis suffer from apparent disadvantages, such as destructive cells, tedious procedure, and low sensitivity, which much hamper in-depth studies of Q modification-related biological questions. In this study, we developed a new approach called plasmonic affinity sandwich assay that allows for facile and sensitive determination of Q-modified tRNAs in single living cells. This method relies on the combination of plasmon-enhanced Raman scattering detection, base-paring affinity in-cell microextraction, and a set of boronate affinity and molecularly imprinted labeling nanotags for selective recognition of individual Q modifications, including queuosine, galactosyl queuosine (Gal-Q), and mannosyl queuosine (Man-Q). The developed method exhibited high affinity extraction and high specificity recognition. It allowed for the measurement of tRNA Q modifications in not only Q-rich cultured tumor cells but also Q-deficient primary tumor cells. Usefulness of this approach for investigation of the change of the Q modification level in single cells under oxidative stress was demonstrated. Because of its significant advantages over conventional methods, this approach provides a promising analytical tool for the exploration of more roles of Q-modified tRNAs and elucidation of their mechanisms.

Determination of queuosine derivatives by reverse-phase liquid chromatography for the hypomodification study of Q-bearing tRNAs from various mammal liver cells.

Three queuosine derivatives (Q-derivatives) have been found at position 34 of four mammalian so-called Q-tRNAs: queuosine (Q) in tRNA(Asn) and tRNA(His), mannosyl-queuosine (manQ) in tRNA(Asp), and galactosyl-queuosine (galQ) in tRNA(Tyr). An analytical procedure based on the combined means of purified tRNA isolation from liver cells and ribonucleoside analysis by reverse-phase high performance liquid chromatography coupled with real-time UV-spectrometry (RPLC-UV) was developed for the quantitative analysis of the three Q-derivatives present in total tRNA from liver tissues and liver cell cultures. Using this analytical procedure, the rates of Q-tRNA modification were studied in total tRNAs from various mammalian hepatic cells. Our results show that the four Q-tRNAs are fully modified in liver tissues from adult mammals, regardless of the mammal species. However, a lack in the Q-modification level was observed in Q-tRNAs from newborn rat liver, as well in Q-tRNAs from normal rat liver cell cultures growing in a low queuine content medium, and from a rat hepatoma cell line. It is noteworthy that in all cases of Q-tRNA hypomodification, our analytical procedure showed that tRNA(Asp) is always the least affected by the hypomodification. The biological significance of this phenomenon is discussed.

Q-modification of tRNAs in human brain tumors.

Queuosine (Q nucleoside) is a highly modified guanosine analog and is present only in the first position of the anticodons of tRNA(Tyr), tRNA(His), tRNA(Asn) and tRNA(Asp). The levels of Q in normal human brain and two different types of human brain tumors (meningiomas and astrocytomas) were determined by using an enzymatic assay method. tRNAs isolated from tumor tissues contained decrease amounts of Q when compared to tRNAs from normal (i.e. non-tumor) brain tissue. There was a relationship between the levels of Q nucleoside and the tumor malignancy in the sense that the deficiency was greater in the highly malignant astrocytomas compared to meningiomas which are usually benign tumors. Increased Q deficiency was also observed in higher grade tumors.

Isolation and structure elucidation of an epoxide derivative of the hypermodified nucleoside queuosine from Escherichia coli transfer RNA.

A new nucleoside has been identified in tRNATyr from Escherichia coli MRE 600, where it replaces the highly modified nucleoside queuosine. The nucleoside is also present in a large amount relative to queuosine in mixed tRNA from E. coli strains MRE 600 and W (from which it was isolated for characterization). The new nucleoside has been characterized as an epoxy derivative of queuosine: 7-(5-[(2,3-epoxy-4,5-dihydroxycyclopent-1-yl)amino]methyl)-7-de azaguanosine, oQ, based on data from directly combined liquid chromatography/mass spectrometry, high resolution mass spectrometry, and proton NMR spectroscopy. Nucleoside oQ is also present in small amounts in mixed tRNA from E. coli B. Isomerization of oQ occurs readily under alkaline conditions to give a rearranged product, oQ', characterized as 7-(5-[(3,4-epoxy-2,5-dihydroxycyclopent-1-yl)amino]methyl)-7-deaza guanosine. The present finding constitutes the first report of epoxide formation during post-transcriptional processing of RNA.

Affinity electrophoresis for monitoring terminal phosphorylation and the presence of queuosine in RNA. Application of polyacrylamide containing a covalently bound boronic acid.

An affinity electrophoretic method has been developed to study the state of terminal phosphorylation of RNAs and the presence of the hypermodified base Q in tRNA. It is based on the copolymerization of acryloylaminophenylboronic acid into standard polyacrylamide gels and the interaction of this derivative with free cis-diol groups present in the RNA. In the case of terminal phosphorylation, free ribose groups are present either as such, or may be introduced by enzymatic reactions specific for a particular phosphorylation pattern (e.g. using T4 RNA ligase or guanylyltransferase). Additionally, tRNA species containing the Q base may be resolved from Q-lacking tRNAs by boronate affinity electrophoresis. The introduction of a non-destructive, one-step electrophoretic procedure not only offers an alternative to classical analytical methods, but also provides a means of isolating such populations of RNAs for which other methods are unavailable or are less convenient.

Specific lack of the hypermodified nucleoside, queuosine, in hepatoma mitochondrial aspartate transfer RNA and its possible biological significance.

Tumor nucleic acids have frequently been found to be deficient in methylated and other modified nucleotides. In particular, cytoplasmic transfer RNAs (tRNAs) from various neoplasms partially lack the hypermodified nucleoside queuosine, a modification specific for anticodons of histidine-, tyrosine-, asparagine-, and aspartic acid-accepting tRNAs. Using aspartate tRNA as an example, we show here that liver mitochondria contain tRNA fully modified with respect to queuosine, while the corresponding tRNA from mitochondria of Morris hepatoma 5123D completely lacks this constituent. The sequences of these tRNAs, which were determined by a highly sensitive 32P-postlabeling procedure entailing the direct identification of each position of the polynucleotide chains, were found to be (sequence in text) Lack of queuosine in the hepatoma mitochondrial tRNA may be due to the inavailability of queuine in the hepatoma mitochondria for incorporation into tRNA or to inhibition of the modifying enzyme, tRNA (guanine)-transglycosylase, in the tumor. Taking into account results of others indicating a possible involvement of the queuosine modification in differentiation of eukaryotic cells, we hypothesize that the queuosine defect may develop at an early stage of carcinogenesis (i.e., during the promotion phase) and be directly involved in abnormalities of mitochondria which have been observed frequently in transformed cells and tumors.

Nucleoside Q in tRNA of yellow lupin (Lupinus luteus) seeds.

The nucleoside Q, 7-(4,5-cis-dihydroxyl-l-cyclopenten-3-yl-trans-aminomethyl)-7-deazaguanosine, was found in lupin seed tRNA. The nucleoside occurs in only one of the two histidine tRNA species, as proved by their chromatographic properties (RPC-5) following treatment with cyanogen bromide or periodate, and dihydroxyborylphenyl-succinamyl-aminoethyl-cellulose chromatography.

Effect of diet on the queuosine family of tRNAs of germ-free mice.

The transfer RNAs for aspartic acid, asparagine, histidine, and tyrosine respond to codons in the third column of the genetic code and contain a hypermodified nucleoside known as queuosine (Q) in the first position of the anticodon of the major isoacceptor tRNA. Nothing is known about the physiological or biochemical function of Q. Germ-free mice were maintained for a period of nine tRNA half-lives on a chemically defined diet known to contain all essential constituents of the rodent diet but no Q or its base, queuine. The tRNAs for histidine and asparagine contained only 15% of the Q-containing isoacceptor tRNA. On the other hand, the Q-containing isoacceptor comprised 88% of the tRNAHis and 85% of the tRNAAsn in conventional mice and germ-free mice fed commercial mouse chow. Transfer RNAAsp and tRNATyr were completely modified with respect to Q in germ-free mice maintained on the chemically defined diet as well as on normal mouse chow. Germ-free mice fed the chemically defined diet contained normal amounts of the hypermodified base wye in tRNAPhe.

Changes in transfer ribonucleic acid population of Acanthamoeba castellanii during growth and encystment.

Fifteen aminoacyl-transfer ribonucleic acids (tRNA's) from vegetative cells (trophozoites) and mature cysts of Acanthamoeba castellanii were compared by reversed-phase 5 chromatography. Little or no differences were detected in reversed-phase 5 chromatography elution profiles of alanyl-, arginyl-, isoleucyl-, phenylalanyl-, prolyl-, seryl-, threonyl-, tryptophanyl- and valyl-tRNA's. Significant differences in the relative proportions of isoaccepting species of leucyl-, lysyl-, methionyl-, aspartyl-, histidyl-, and tyrosyl-tRNA's were observed. Based upon the criterion of cyanogen bromide reactivity with the modified nucleoside queuosine, the content of queuosine in aspartyl-tRNA of A, castellanii is significantly greater in mature cysts than in trophozoites. The similarity of change in reversed-phase 5 chromatography elution profiles of aspartyl-, histidyl-, and tyrosyl-tRNA suggests that a common mechanism is responsible for alterations in the chromatographic patterns.