N2-guanine specific transfer RNA methyltransferase I from rat liver and leukemic rat spleen

N2-Methylation of Guanosine at Position 10 in tRNA Is Catalyzed by a THUMP Domain-containing, S-Adenosylmethionine-dependent Methyltransferase, Conserved in Archaea and Eukaryota

In sequenced genomes, genes belonging to the cluster of orthologous group COG1041 are exclusively, and almost ubiquitously, found in Eukaryota and Archaea but never in Bacteria. The corresponding gene products exhibit a characteristic Rossmann fold, S-adenosylmethionine-dependent methyltransferase domain in the C terminus and a predicted RNA-binding THUMP (thiouridine synthases, RNA methyltransferases, and pseudouridine synthases) domain in the N terminus. Recombinant PAB1283 protein from the archaeon Pyrococcus abyssi GE5, a member of COG1041, was purified and shown to behave as a monomeric 39-kDa entity. This protein (EC 2.1.1.32), now renamed (Pab)Trm-G10, which is extremely thermostable, forms a 1:1 complex with tRNA and catalyzes the adenosylmethionine-dependent methylation of the exocyclic amino group (N(2)) of guanosine located at position 10. Depending on the experimental conditions used, as well as the tRNA substrate tested, the enzymatic reaction leads to the formation of either N(2)-monomethyl (m(2)G) or N(2)-dimethylguanosine (m(2)(2)G). Interestingly, (Pab)Trm-G10 exhibits different domain organization and different catalytic site architecture from another, earlier characterized, tRNA-dimethyltransferase from Pyrococcus furiosus ((Pfu)Trm-G26, also known as (Pfu)Trm1, a member of COG1867) that catalyzes an identical two-step dimethylation of guanosine but at position 26 in tRNAs and is also conserved among all sequenced Eukaryota and Archaea. The co-occurrence of these two guanosine dimethyltransferases in both Archaea and Eukaryota but not in Bacteria is a hallmark of distinct tRNAs maturation strategies between these domains of life.

Characterisation and enzymatic properties of tRNA(guanine 26, N (2), N (2))-dimethyltransferase (Trm1p) from Pyrococcus furiosus

The structural gene TRM1 encoding tRNA(guanine 26, N (2), N (2))-dimethyltransferase (Trm1p) of the hyperthermophilic archaeon Pyrococcus furiosus was cloned and expressed in Escherichia coli. The corresponding recombinant enzyme (pfTrm1p) with a His6-tag at the N terminus was purified to homogeneity in three steps. The enzyme has a native molecular mass of 49 kDa (as determined by gel filtration) and is very stable to heat denaturation (t1/2at 95 degrees C is two hours). pfTrm1p is a monomer and forms a one to one complex with T7 transcripts of yeast tRNA(Phe). It methylates a single guanine residue at position 26 using S -adenosyl- l -methionine as donor of the methyl groups. Depending on the incubation temperature, the type of tRNA transcript and the ratio of enzyme to tRNA, m(2)G26 or m(2)2G26 was the main product. The addition of the second methyl group to N (2)guanine 26 takes place in vitro through a monomethylated intermediate, and the enzyme dissociates from its tRNA substrate between the two consecutive methylation reactions. Identity elements in tRNA for mono- and dimethylation reactions by the recombinant pfTrm1p were identified using in vitro T7 transcripts of 33 variants of tRNA(Asp)and tRNA(Phe)from yeast. The efficient dimethylation of G26 requires the presence of base-pairs C11.G24 and G10.C25 and a variable loop of five bases within a correct 3D-core of the tRNA molecule. These identity elements probably ensure the correct presentation of monomethylated m(2)G26 to the enzyme for the attachment of the second methyl group. In contrast, the structural requirements for monomethylation of the same guanine 26 are much more relaxed and tolerate variations in the base-pairs of the D-stem, in the size of the variable loop or distortions of the 3D-architecture of the tRNA molecule.

The tRNA(guanine-26,N2-N2) methyltransferase (Trm1) from the hyperthermophilic archaeon Pyrococcus furiosus: cloning, sequencing of the gene and its expression in Escherichia coli

The structural gene pfTRM1 (GenBank accession no. AF051912), encoding tRNA(guanine-26, N 2- N 2) methyltransferase (EC 2.1.1.32) of the strictly anaerobic hyperthermophilic archaeon Pyrococcus furiosus, has been identified by sequence similarity to the TRM1 gene of Saccharomyces cerevisiae (YDR120c). The pfTRM1 gene in a 3.0 kb restriction DNA fragment of P.furiosus genomic DNA has been cloned by library screening using a PCR probe to the 5'-part of the corresponding ORF. Sequence analysis revealed an entire ORF of 1143 bp encoding a polypeptide of 381 residues (calculated molecular mass 43.3 kDa). The deduced amino acid sequence of this newly identified gene shares significant similarity with the TRM1- like genes of three other archaea (Methanococcus jannaschii, Methanobacterium thermoautotrophicum and Archaeoglobus fulgidus), one eukaryon (Caenorhabditis elegans) and one hyperthermophilic eubacterium (Aquifex aeolicus). Two short consensus motifs for S-adenosyl-l-methionine binding are detected in the sequence of pfTrm1p. Cloning of the P.furiosus TRM1 gene in an Escherichia coli expression vector allowed expression of the recombinant protein (pfTrm1p) with an apparent molecular mass of 42 kDa. A protein extract from the transformed E.coli cells shows enzymatic activity for the quantitative formation of N 2, N 2-dimethylguanosine at position 26 in a transcript of yeast tRNAPhe used as substrate. The recombinant enzyme was also shown to modify bulk E.coli tRNAs in vivo.

Enzymatic formation of N2,N2-dimethylguanosine in eukaryotic tRNA: importance of the tRNA architecture

In eukaryotic tRNA, guanosine at position 26 in the junction between the D-stem and the anticodon stem is mostly modified to N2,N2-dimethylguanosine (m2(2)G26). Here we review the available information on the enzyme catalyzing the formation of this modified nucleoside, the SAM-dependent tRNA (m2(2)G26)-methyltransferase, and our attemps to identify the parameters in tRNA needed for efficient enzymatic dimethylation of guanosine-26. The required identity elements in yeast tRNA for dimethylation under in vitro conditions by the yeast tRNA(m2(2)G26)-methyltransferase (the TRM1 gene product) are comprised of two G-C base pairs at positions G10-C25 and C11-G24 in the D-stem together with a variable loop of at least five nucleotides. These positive determinants do not seem to act via base specific interactions with the methyltransferase; they instead ensure that G26 is presented to the enzyme in a favorable orientation, within the central 3D-core of the tRNA molecule. The anticodon stem and loop is not involved in such an interaction with the enzyme. In a heterologous in vivo system, consisting of yeast tRNAs microinjected into Xenopus laevis oocytes, the requirements for modification of G26 are less stringent than in the yeast homologous in vitro system. Indeed, G26 in several microinjected tRNAs becomes monomethylated, while in yeast extracts it stays unmethylated, even after extensive incubation. Thus either the X laevis tRNA(m2(2)G26)-methyltransferase has a more relaxed specificity than its yeast homolog, or there exist two distinct G26-methylating activities, one for G26-monomethylation, and one for dimethylation of G26.(ABSTRACT TRUNCATED AT 250 WORDS)

Site specificities of three transfer RNA methyltransferases from yeast

The site specificities of two distinct tRNA(m1G)methyltransferases and one tRNA(m2G)methyltransferase from yeast have been investigated by heterologous methylation and analysis of purified Escherichia coli tRNAs. The two tRNA(m1G)methyltransferases were found to be specific for sites 9 and 37, respectively. The tRNA(m2G)methyltransferase was specific for site 10. Two of the enzymes were purified by affinity chromatography on tRNA-Sepharose.

Partial purification and characterization of a ribonucleic acid N2-guanine methyltransferase associated with avian myeloblastosis virus

A nucleic acid methylase, N2-guanine ribonucleic acid (RNA) methyltransferase, which is associated with type C RNA tumor viruses, has been purified from avian myeloblastosis virions by gel filtration on Sephadex G-200, followed by chromatography on hydroxylapatite. The molecular weight estimated by gel filtration is 220 000, and the methylase activity has a pH optimum of 7.6--7.9. Magnesium and ammonium ions both stimulate activity 1.5-fold at 9.5 mM and 0.36 M, respectively, but apparently neither is essential for activity. Both daunomycin and adriamycin, antineoplastic drugs, also increase activity 1.5-fold at 1 mM. The enzyme was purified 120-fold from the virions and the activity is partially stabilized by dithiothretiol, but large losses were sustained during 24-h dialysis. The purified enzyme retains 75% of its activity on storage at -25 degrees C for 2 months in buffer containing 50% glycerol. Escherichia coli tRNAPhe and tRNAVal are preferred substrates with methylation occurring at position 10 of E. coli tRNAPhe.

Recognition of individual procaryotic and eucaryotic transfer-ribonucleic acids by B subtilis adenine-1-methyltransferase specific for the dihydrouridine loop

Bulk tRNA from yeast and Rat liver can be methylated in vitro with -adenosylmethionine and B, subtilis extracts. The sole product formed is 1-methyladenosine (m1A). This tRNA (adenine-1) methyltransferase converts quantitatively the 3'-terminal adenosine-residue in the dihydrouridine-loop of tRNAThr and tRNATyr from yeast into m1A. Out of 16 eucaryotic tRNAs with known sequences 6 accepted methyl groups, all at a molar ratio of 1. These tRNAs have in common an unpaired adenosine-residue at the specific site in the sequence Py-A-A+-G-G-C-m2G. Out of 12 tRNAs from E. coli 6 served as specific substrates. These E. coli tRNAs also have an unpaired adenosine-residue at the 3'-end of the D-loop. Besides restrictions in primary structure intact secondary and tertiary structure is important for recognition of the specific tRNAs by the enzyme.

Purification and characterization of two tRNA-(guanine)-methyltransferases from rat liver

tRNA(guanine-1-)-methyltransferase (EC 2.1.1.31) and tRNA(N2-guanine)-methyltransferase I (EC 2.1.1.32) were isolated from rat liver. The (guanine-1-)-methyltransferase preparation is 6800-fold purified and is free from contaminating methyltransferases or ribonuclease. The molecular weight of (guanine-1-)-methyltransferase is 83 000. Of seven purified Escherichia coli tRNAs examined, only tRNAMetf was utilized as substrate by (guanine-1-)-methyltransferase. The methylation of tRNAMetf is maximally stimulated by 40 mM putrescine with a pH optimum of 8.0. Using E. coli K-12 tRNA, the Km for S-adenosylmethionine is 3 micrometer and Ki for S-adenosylhomocysteine is 0.11 micrometer for (guanine-1-)-methyltransferase. (N2-Guanine-)-methyltransferase is 6200-fold purified and is also free of interfering enzymes. It has a molecular weight of 69 000. E. coli tRNAPhe, tRNAVal and tRNAArg are substrates for this enzyme which introduces a methyl at the 2-amino group of the guanine at position 10 from the 5'-terminus of these tRNAs. The methylation of tRNAPhe is maximally stimulated by 100 micrometer spermidine with a pH optimum of 8.0. (N2-Guanine-)-methyltransferase has a Km for S-adenosylmethionine of 2 micrometer and a Ki for S-adenosylhomocysteine of 23 micrometer with E. coli K-12 tRNA as methyl acceptor.

Recognition of individual Escherichia coli transfer ribonucleic acids by 1-adenine-specific methyltransferase from rat liver

Purified 1-adenine-specific tRNA methyltransferase from rat liver preferentially methylated Escherichia coli tRNA species containing the target adenylate residue in a G-T-psi-C-G-A-A-U-C sequence. The results of methylation of various tRNA species are discussed.

7-Methylguanine specific tRNA-methyltransferase from Escherichia coli

A 7-methylguanine (m7G) specific tRNA methyltransferase from E. coli MRE 600 was purified about 1000 fold by affinity chromatography on Sepharose bound with normal E. coli tRNA. The purified enzyme catalyzes exclusively the formation of m7G in submethylated bulk tRNA of E. coli K12 met- rel-. The purified enzyme transfers the methyl group from S-adenosyl-methionine to initiator tRNA of B. subtilis and 0.8 moles m7G residues are formed per mole tRNA. It is suggested that the enzyme specifically recognizes the extra arm unpaired guanylate residue.

The methylation of tRNA

The methylation of tRNA is a post-transcriptional modification which is achieved by specific enzymes, the tRNA methylases, with S adenosylmethionine as a methyl donor. The level and pattern of methylation are characteristic of the tRNA species and origin. Abnormally methylated tRNAs have been obtained, in vivo and in vitro, by a variety of methods, and their properties have been studied. The tRNA methylases are found in all cells and tissues. Their activity varies with the differentiation state of the cells, and under the influence of many internal and external factors ; it is especially elevated in embryonic and cancerous tissues. These enzymes are very unstable, and none of them has been purified to homogeneity. We present here their known properties and we propose a theory concerning their specificity. Finally, after reviewing the few available experimental data, we discuss the current hypotheses and speculations about the roles and functions of tRNA methylation.

tRNA methyltransferases from rat liver. Differences in response of partially purified enzymes to polyamines and inorganic salts

Three tRNA methyltransferases, purified from rat liver, have been compared for their activity in the presence of various amines and Mg2+. The enzymes differ with respect to the ion which permits maximal activity; they also differ with respect to the concentration of a given ion necessary for maximal activity. The methyltransferase which forms N2-methylguanine in the region between the dihydrouridine loop and the acceptor stem (2mG I), when assayed using purified tRNA as substrate, shows high activity with 3--5 mM sperimidine or 20 mM putrescine and significantly lower rates of methylation with 200--350 mM ammonium acetate or 1--10 mM magnesium acetate. The enzyme responsible for forming N2-methylguanine between the dihydrouridine and anticodon loops (2mG II) works well in the presence of 0.2--0.5 mM spermidine, 10 mM putrescine or 200--300 mM ammonium acetate and shows slightly lower activity with 1 mM magnesium acetate. The optimal conditions for assaying 1-adenine methyltransferase (1mA) with purified tRNAs are either 200--300 mM ammonium acetate or 30 mM putrescine; spermidine is slightly less effective and magnesium acetate permits less than 25% of maximal activity. The addition of 10 mM Mg2+, in combination with polyamines or NH4+, depresses slightly the activity of the guanine methyltransferases but completely abolishes the polyamine or ammonium-stimulated activity of the adenine methyltransferase. When unfractionated (Escherichia coli) tRNA is used as substrate, the concentrations of polyamines required for optimal methyltransferase activity are increased but the patterns of response of the three enzymes do not differ significantly from those obtained with purified tRNA substrates. Based on the studies with these three enzymes, unfractionated tRNA and 40 mM putrescine should provide the most reliable system for detecting methylating activity if the nature of the tRNA methyltransferase is unknown.

S-adenosylhomocysteine inhibition of three purified tRNA methyltransferases from rat liver

Three tRNA methyltransferases from rat liver have been fractionated and purified greater than 100-fold. These enzymes have been examined for their sensitivity to inhibition by S-adenosylhomocysteine (SAH). The methyltransferase which forms m2-guanine in the region between the dihydrouridine loop and the acceptor stem of tRNA (m2-guanine methyltransferase I) is least sensitive to SAH inhibition, with a Ki of 8 muM. The enzyme responsible for forming m2-guanine between the dihydrouridine and anticodon loops (m2-guanine methyltransferase II) has a Ki of 0.3 muM, while m1-adenine methyltransferase shows intermediate sensitivity to SAH (Ki = 2.4 muM). All three methyltransferases have similar Km's for the S-adenosylmethionine substrate (1.5-2.0 muM). These results are consistent with the hypothesis that activity of individual tRNA methyltransferases may be controlled by enzyme systems which alter cellular SAH levels.

Two transfer RNA (1-methylguanine) methylases from yeast

Two distinct tRNA (m-1G) methylases have been found in the yeast Saccharomyces cerevisiae. They differ in their chromatographic properties on hydroxyapatite, in their response to spermine, and in their site specificity. Only one of the methylases is active against normal tRNA from Escherichia coli.

N2-guanine specific transfer RNA methyltransferase II from rat liver

N(2)-guanine methyltransferase II was purified from rat liver. This enzyme methylated bulk E. coli tRNA to an extent of 7.6 nmoles of methyl groups/mg tRNA. Oligonucleotide analysis showed that N(2)-methylated guanosines were present in the modified tRNA in two sequences, namely Y-m(2)G-Cp and Y-m(2) (2)G-Cp in the ratio 4:3. Two pure tRNA(Leu) species, and tRNA(Met) (f) from E. coli were methylated with the enzyme to extents of 17, 11, and 8 nmoles of methyl groups incorporated per mg tRNA, respectively. When the methylated tRNAs were analysed no m(2) (2)G was detected and the m(2)G occurred in the tRNAs specific for leucine in a Y-m(2)G-Cp sequence and in the tRNA(Met) (f) in a sequence Y-m(2)G-Up.It is concluded that the mammalian enzyme specifically recognizes the interstem unpaired guanylate residue between the dihydrouridine arm and the anticodon arm. The absence of any detectable m(2) (2)G methylation of individual tRNA species is discussed.