N-4-methyl-2'-O-methyl cytidine and other methyl-substituted nucleoside constituents of Escherichia coli ribosomal and soluble RNA

Novel dual methylation of cytidines in the RNA of mammals

RNA modifications play critical roles in regulating a variety of physiological processes. Methylation is the most prevalent modification occurring in RNA. Three isomeric cytidine methylation modifications have been reported in RNA, including 3-methylcytidine (m³C), N4-methylcytidine (m⁴C), and 5-methylcytidine (m⁵C), in mammals. Aside from the single methylation on the nucleobase of cytidines, dual methylation modifications occurring in both the 2′ hydroxyl of ribose and the nucleobase of cytidines also have been reported, including N4,2′-O-dimethylcytidine (m⁴Cm) and 5,2′-O-dimethylcytidine (m⁵Cm). m⁴Cm has been found in the 16S rRNA of E. coli, while m⁵Cm has been found in the tRNA of terminal thermophilic archaea and mammals. However, unlike m⁴Cm and m⁵Cm, the presumed dual methylation of 3,2′-O-dimethylcytidine (m³Cm) has never been discovered in living organisms. Thus, the presence of m³Cm in RNA remains an open question. In the current study, we synthesized m³Cm and established a liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) method to determine the dimethylation of cytidines, m³Cm, m⁴Cm and m⁵Cm. Under optimized analytical conditions, m³Cm, m⁴Cm and m⁵Cm can be clearly distinguished. Using the method, we discovered the existence of m³Cm in the RNA of mammals. The identified m³Cm is a novel modification that hasn't been reported in the three-domain system, including archaea, bacteria, and eukaryotes. We confirmed that m³Cm mainly existed in the small RNA (<200 nt) of mammals. In addition, we identified, for the first time, the presence of m⁴Cm in the 18S rRNA of mammalian cells. The stable isotope tracing monitored by mass spectrometry demonstrated that S-adenosyl-l-methionine was a methyl donor for all three dimethylations of cytidines in RNA. The discovery of m³Cm broadens the diversity of RNA modifications in living organisms. In addition, the discovery of m³Cm and m⁴Cm in mammals opens new directions in understanding RNA modification-mediated RNA processing and gene expression regulation.

We synthesized 3,2′-O-dimethylcytidine (m³Cm) and determined the dimethylation of cytidines in mammals by mass spectrometry analysis. We discovered m³Cm in small RNA and N4,2′-O-dimethylcytidine (m⁴Cm) in 18S rRNA of mammals.

METTL15 introduces N4-methylcytidine into human mitochondrial 12S rRNA and is required for mitoribosome biogenesis

Post-transcriptional RNA modifications, the epitranscriptome, play important roles in modulating the functions of RNA species. Modifications of rRNA are key for ribosome production and function. Identification and characterization of enzymes involved in epitranscriptome shaping is instrumental for the elucidation of the functional roles of specific RNA modifications. Ten modified sites have been thus far identified in the mammalian mitochondrial rRNA. Enzymes responsible for two of these modifications have not been characterized. Here, we identify METTL15, show that it is the main N4-methylcytidine (m⁴C) methyltransferase in human cells and demonstrate that it is responsible for the methylation of position C839 in mitochondrial 12S rRNA. We show that the lack of METTL15 results in a reduction of the mitochondrial de novo protein synthesis and decreased steady-state levels of protein components of the oxidative phosphorylation system. Without functional METTL15, the assembly of the mitochondrial ribosome is decreased, with the late assembly components being unable to be incorporated efficiently into the small subunit. We speculate that m⁴C839 is involved in the stabilization of 12S rRNA folding, therefore facilitating the assembly of the mitochondrial small ribosomal subunits. Taken together our data show that METTL15 is a novel protein necessary for efficient translation in human mitochondria.

RNA ribose methylation (2'-O-methylation): Occurrence, biosynthesis and biological functions

Methylation of riboses at 2'-OH group is one of the most common RNA modifications found in number of cellular RNAs from almost any species which belong to all three life domains. This modification was extensively studied for decades in rRNAs and tRNAs, but recent data revealed the presence of 2'-O-methyl groups also in low abundant RNAs, like mRNAs. Ribose methylation is formed in RNA by two alternative enzymatic mechanisms: either by stand-alone protein enzymes or by complex assembly of proteins associated with snoRNA guides (sno(s)RNPs). In that case one catalytic subunit acts at various RNA sites, the specificity is provided by base pairing of the sno(s)RNA guide with the target RNA. In this review we compile available information on 2'-OH ribose methylation in different RNAs, enzymatic machineries involved in their biosynthesis and dynamics, as well as on the physiological functions of these modified residues.

Probing the stabilizing effects of modified nucleotides in the bacterial decoding region of 16S ribosomal RNA

The bacterial decoding region of 16S ribosomal RNA has multiple modified nucleotides. In order to study the role of N(4),2'-O-dimethylcytidine (m(4)Cm), the corresponding phosphoramidite was synthesized utilizing 5'-silyl-2'-ACE chemistry. Using solid-phase synthesis, m(4)Cm, 5-methylcytidine (m(5)C), 3-methyluridine (m(3)U), and 2'-O-methylcytidine (Cm) were site-specifically incorporated into small RNAs representing the decoding regions of different bacterial species. Biophysical studies were then used to provide insight into the stabilizing roles of the modified nucleotides. These studies reveal that methylation of cytidine and uridine has different effects. The same modifications at different positions or sequence contexts within similar RNA constructs also have contrasting roles, such as stabilizing or destabilizing the RNA helix.

Selecting Molecular Recognition. What Can Existing Aptamers Tell Us about Their Inherent Recognition Capabilities and Modes of Interaction?

The use of nucleic acid derived aptamers has rapidly expanded since the introduction of SELEX in 1990. Nucleic acid aptamers have demonstrated their ability to target a broad range of molecules in ways that rival antibodies, but advances have been very uneven for different biochemical classes of targets, and clinical applications have been slow to emerge. What sets different aptamers apart from each other and from rivaling molecular recognition platforms, specifically proteins? What advantages do aptamers as a reagent class offer, and how do the chemical properties and selection procedures of aptamers influence their function? Do the building blocks of nucleic acid aptamers dictate inherent limitations in the nature of molecular targets, and do existing aptamers give us insight in how these challenges might be overcome? This review is written as an introduction for potential endusers of aptamer technology who are evaluating the advantages of aptamers as a versatile, affordable, yet highly expandable platform to target a broad range of biological processes or interactions.

Complete modification maps for the cytosolic small and large subunit rRNAs of Euglena gracilis: functional and evolutionary implications of contrasting patterns between the two rRNA components

In the protist Euglena gracilis, the cytosolic small subunit (SSU) rRNA is a single, covalently continuous species typical of most eukaryotes; in contrast, the large subunit (LSU) rRNA is naturally fragmented, comprising 14 separate RNA molecules instead of the bipartite (28S+5.8S) eukaryotic LSU rRNA typically seen. We present extensively revised secondary structure models of the E. gracilis SSU and LSU rRNAs and have mapped the positions of all of the modified nucleosides in these rRNAs (88 in SSU rRNA and 262 in LSU rRNA, with only 3 LSU rRNA modifications incompletely characterized). The relative proportions of ribose-methylated nucleosides and pseudouridine (∼60% and ∼35%, respectively) are closely similar in the two rRNAs; however, whereas the Euglena SSU rRNA has about the same absolute number of modifications as its human counterpart, the Euglena LSU rRNA has twice as many modifications as the corresponding human LSU rRNA. The increased levels of rRNA fragmentation and modification in E. gracilis LSU rRNA are correlated with a 3-fold increase in the level of mispairing in helical regions compared to the human LSU rRNA. In contrast, no comparable increase in mispairing is seen in helical regions of the SSU rRNA compared to its homologs in other eukaryotes. In view of the reported effects of both ribose-methylated nucleoside and pseudouridine residues on RNA structure, these correlations lead us to suggest that increased modification in the LSU rRNA may play a role in stabilizing a 'looser' structure promoted by elevated helical mispairing and a high degree of fragmentation.

Fine-tuning of the ribosomal decoding center by conserved methyl-modifications in the Escherichia coli 16S rRNA

In bacterial 16S rRNAs, methylated nucleosides are clustered within the decoding center, and these nucleoside modifications are thought to modulate translational fidelity. The N⁴, 2′-O-dimethylcytidine (m⁴Cm) at position 1402 of the Escherichia coli 16S rRNA directly interacts with the P-site codon of the mRNA. The biogenesis and function of this modification remain unclear. We have identified two previously uncharacterized genes in E. coli that are required for m⁴Cm formation. mraW (renamed rsmH) and yraL (renamed rsmI) encode methyltransferases responsible for the N⁴ and 2′-O-methylations of C1402, respectively. Recombinant RsmH and RsmI proteins employed the 30S subunit (not the 16S rRNA) as a substrate to reconstitute m⁴Cm1402 in the presence of S-adenosylmethionine (Ado-Met) as the methyl donor, suggesting that m⁴Cm1402 is formed at a late step during 30S assembly in the cell. A luciferase reporter assay indicated that the lack of N⁴ methylation of C1402 increased the efficiency of non-AUG initiation and decreased the rate of UGA read-through. These results suggest that m⁴Cm1402 plays a role in fine-tuning the shape and function of the P-site, thus increasing decoding fidelity.

Synthesis and solution conformation studies of the modified nucleoside N(4),2'-O-dimethylcytidine (m(4)Cm) and its analogues

The dimethylated ribosomal nucleoside m(4)Cm and its monomethylated analogues Cm and m(4)C were synthesized. The conformations (syn vs anti) of the three modified nucleosides and cytidine were determined by CD and 1D NOE difference spectroscopy. The ribose sugar puckers were determined by the use of proton coupling constants. The position of modification (e.g., O vs N methylation) was found to have an effect on the sugar pucker of cytidine.

Mutational analysis of the conserved bases C1402 and A1500 in the center of the decoding domain of Escherichia coli 16 S rRNA reveals an important tertiary interaction

Interactions within the decoding center of the 30 S ribosomal subunit have been investigated by constructing all 15 possible mutations at nucleotides C1402 and A1500 in helix 44 of 16 S rRNA. As expected, most of the mutations resulted in highly deleterious phenotypes, consistent with the high degree of conservation of this region and its functional importance. A total of seven mutants were viable under conditions where the mutant ribosomes comprised 100 % of the ribosomal pool. A suppressor mutation specific for the C1402U-A1500G mutant was isolated at position 1520 in helix 45 of 16 S rRNA. In addition, lack of dimethylation of A1518/A1519 caused by mutation of the ksgA methylase enhanced the deleterious effect of many of the 1402/1500 mutations. These data suggest that a higher-order interaction between helices 44 and 45 in 16 S rRNA is important for the proper functioning of the ribosome. This is consistent with the recent high-resolution crystal structures of the 30 S subunit, which show a tertiary interaction between the 1402/1500 region of helix 44 and the dimethyl A stem loop.

Participation of acetylpseudouridine in the synthesis of a peptide bond in vitro

Uracil, uridine, and pseudouridine were acetylated by refluxing in acetic anhydride, and the products of acetylation were incubated with a synthetic peptide (1-21) that corresponds to the N-terminal 21 amino acid residues of human myelin basic protein. Peptide bond formation, at the N alpha terminus in peptide 1-21, was obtained with acetyluracil and acetylpseudouridine, but not with acetyluridine. Transfer of an acetyl group from acetyluracil and acetylpseudouridine depended on acetylation in the N-heterocycle. X-ray crystallographic analysis definitively established N-1 as the site of acetylation in acetyluracil. Mass spectrometry of the acetylation products showed that one acetyl group was transferred to peptide 1-21, in water, by either acetyluracil or acetylpseudouridine at pH approximately 6. Release of the acetyl group by acylaminopeptidase regenerated peptide 1-21 (mass spectrometry) and automated sequencing (for five cycles) of the regenerated (deacetylated) peptide demonstrated that the N terminus was intact. The findings are discussed in the context of a possible role for pseudouridine in ribosome-catalyzed peptidyltransfer, with particular reference being made to similarities between the possible mechanism of acyl transfer by acetyluracil/pseudouridine and the mechanism of carboxyl transfer by carboxylbiotin in acetyl CoA carboxylase. The possibility that idiosyncratic appearance of a wide range of acyl substituents in myelin basic protein could be related to a peculiar involvement of ribosomal pseudouridine is mentioned.

Pseudouridine and O2'-methylated nucleosides. Significance of their selective occurrence in rRNA domains that function in ribosome-catalyzed synthesis of the peptide bonds in proteins

Pseudouridine (5-ribosyluracil, psi) was the first of a host of modified nucleoside constituents detected in cellular RNA and it remains the most abundant, being broadly distributed in the RNA of archaebacteria, eubacteria and eukaryotes. Like some other modifications, psi is particularly abundant in more complex organisms, reaching 2-3% of the total nucleoside constituents in tRNA, snRNA and rRNA of multicellular plants and animals. Like all other modified nucleosides, psi arises by site-specific, enzymically catalyzed modification of a nucleoside residue in an RNA molecule. Unlike all other modified nucleosides, psi arises by isomerisation (not substitution) of a classical nucleoside, uridine (1-ribosyluracil). There have been suggestions that key processes such as ribosome assembly and peptidyl transfer may rely, more than is generally appreciated, on RNA modifications such as O2'-methylation and pseudouridylation, respectively. However, a persuasive case for the view that secondary modifications are of primary importance in ribosome function has not been convincingly made. Accordingly, we think it is timely to broaden what is generally meant by the 'catalytic properties of rRNA', and to ask, to what extent do modifications contribute to in vivo rates of ribosome assembly and ribosomal peptide-bond synthesis? The first part of this article sets forth the evidence that there is a conspicuous association between modified nucleosides and cellular RNAs that participate in group-transfer reactions. The second part reviews evidence in support of the view that the functions of psi and other modified nucleosides are likely of central importance for understanding the dynamics and stereostructural modeling at functionally significant sites in the ribosome.

Summary: the modified nucleosides of RNA

A comprehensive listing is made of posttranscriptionally modified nucleosides from RNA reported in the literature through mid-1994. Included are chemical structures, common names, symbols, Chemical Abstracts registry numbers (for ribonucleoside and corresponding base), Chemical Abstracts Index Name, phylogenetic sources, and initial literature citations for structural characterization or occurrence, and for chemical synthesis. The listing is categorized by type of RNA: tRNA, rRNA, mRNA, snRNA, and other RNAs. A total of 93 different modified nucleosides have been reported in RNA, with the largest number and greatest structural diversity in tRNA, 79; and 28 in rRNA, 12 in mRNA, 11 in snRNA and 3 in other small RNAs.

Pseudouridine in the large-subunit (23 S-like) ribosomal RNA. The site of peptidyl transfer in the ribosome?

On evolutionary grounds, it has been advocated for more than 40 years that RNA generally, and more recently rRNA in particular, may participate, catalytically, in protein biosynthesis. A specific molecular mechanism has never been proposed. We suggest here that the N-1 position(s) in one or more of the approximately 4 pseudouridine (omega) residues in E. coli 23 S rRNA catalyzes transfer of the aminoacyl moiety from teh 3'-terminus of peptidyl tRNA in the P site to aminoacyl tRNA in the A site of the ribosome. Evidence that supports the proposal in the case of E. coli ribosomes, and relevant information pertaining to eukaryotic ribosomes, is summarized. Essential features of the evidence are that (i) the N-1 position in 1-acetylthymine (a direct analogue of 1-acetylpseudouridine) has an especially high potential for acyl-group transfer, comparable to that found for N-acetylimidazole (Spector, L.B. and Keller, E.B. (1958) J. Biol. Chem. 232, 185-192), (ii) most of the omega residues in prokaryotic 23 S rRNA are confined to the peptidyl transferase center in E. coli ribosomes, and (iii) Um-Gm-omega, the most densely modified sequence in eukaryotic 26 S rRNA, is universally conserved at a fixed site in the putative peptidyl transferase center of all eukaryotic ribosomes.

Selective deuteration of 4-N-methylcytosines

A convenient photochemical method of preparation of mono-, di- and trideuterate 4-N-methylcytosines of high isotopic purity is described. These products were obtained by photo-decarboxylation of pyrimidinyl glycines or their alpha, alpha-dideuterated derivatives in water or in deuterium oxide. [2, 2H2]Glycine derivatives were prepared by hydrogen-deuterium exchange in alkaline solution.

Methylation patterns of mycoplasma transfer and ribosomal ribonucleic acid

The methylation patterns of transfer and ribosomal ribonucleic acid (RNA) from two mycoplasmas, Mycoplasma capricolum and Acholeplasma laidlawii, have been examined. The transfer RNA from the two mycoplasmas resembled that of other procaryotes in degree of methylation and general diversity of methylated nucleotides, and bore particular resemblance to Bacillus subtilis transfer RNA. The only unusual feature was the absence of m5U from M. capricolum transfer RNA. The methylation patterns of the mycoplasma 16S RNAs were also typically procaryotic, retaining the methylated residues previously shown to be highly conserved among eubacterial 16S RNAs. The mycoplasma 23S RNA methylation patterns were, on the other hand, quite unusual. M. capricolum 23S RNA contained only four methylated residues in stoichiometric amounts, all of which were ribose methylated. A. laidlawii 23S RNA contained the same ribose-methylated residues, plus in addition approximately six m5U residues. These findings are discussed in relation to the phylogenetic status of mycoplasma, as well as the possible role of RNA methylation.

The 3'-terminal primary structure of five eukaryotic 18S rRNAs determined by the direct chemical method of sequencing. The highly conserved sequences include an invariant region complementary to eukaryotic 5S rRNA

The 3'-terminal sequences of 18S rRNA from chicken reticulocyte, mouse sarcoma, rat liver, rabbit reticulocyte and barley embryo were determined by the direct chemical sequencing method. The regions sequenced show complete homology for the first 73 nucleotides. A sequence 5'-proximal to the m6(2)Am6(2)A residues that is complementary to eukaryotic 5S RNAs is totally conserved. This supports the hypothesis that base-paired interaction between 5S and 18S rRNA, which are present in the large and small ribosomal subunits respectively, may be involved in the reversible association of ribosomal subunits during protein synthesis.

Stacking properties of a highly hydrophobic dinucleotide sequence, N6, N6-dimethyladenylyl(3' leads to 5')N6, N6-dimethyladenosine, occurring in 16--18-S ribosomal RNA

The thermal denaturation ultraviolet absorption spectra of N6,N6-dimethyladenylyl(3' leads to 5')-N6,N6-dimethyladenosine (m2(6)Apm2(6)A), which is a common sequence in 16--18-S ribosomal RNA, in aqueous buffer at pH 7 have been measured over the temperature range 3-90 degrees C. These data have been used to determine the thermodynamic quantitites associated with the intramolecular stacking equilibria. At 25 degrees C in neutral aqueous solution m2(6)Apmw(6)A exists mainly (about 81%) as a stacked form, so that the stacking interactions are stronger than those in the parent unmethylated adenylyl-(3'-5')adenosine (ApA), where about 52% is stacked. From the parameters of delta H and delta S, it is concluded that 'hidden' hydrophobic inteactions are of prime importance in the enhanced stability of m2(6)Apm2(6)A. Transphosphorylation reaction of ApA and m2(6)Apm2(6)A to form the corresponding cyclic 2',3'-phosphates has been studied. First-order rate constants at 25 degrees C for the reactions, which are base-catalyzed, have been obtained. Insertion of two methyl groups at N-6 of ApA reduces the rate of transphosphorylation. Effects of stacking on rates are discussed in the light of reaction mechanisms.

Conservation of the primary structure at the 3' end of 18S rRNA from eucaryotic cells

DNA sequencing methods have been used to determine a sequence of about 20 nucleotides at the 3' termini of various 18S (small ribosomal subunit) RNA molecules. Polyadenylated rRNA was first synthesized using the enzyme ATP:polynucleotidyl transferase from mainze. Then in the presence of an oligonucleotide primer uniquely complementary to the end of each adenylated rRNA, a cDNA copy was produced using AMV reverse transcriptase. In every case, the cDNA transcript was of finite size, which we ascribe to the appearance of an oligonucleotide containing m62A near the 3' end of the 18S rRNAs. Sequences at the 3' termini of 18S rRNA molecules from the four eucaryotic species examined here (mouse, silk worm, wheat embryo and slime mold) are highly conserved. They also exhibit strong homology to the 3' end of E. coli 16S rRNA. Two important differences, however, are apparent. First, the 16S sequence CCUCC, implicated in mRNA binding by E. coli ribosomes, is absent from each eucaryotic rRNA sequence. Second, a purine-rich region which exhibits extensive complementarity to the 5' noncoding regions of many eucaryotic mRNAs appears consistently.

2'-O-methylation of adenosine, guanosine, uridine, and cytidine in RNA of isolated rat liver nuclei

Nuclei isolated from rat liver, when incubated with methyl-labeled S-adenosylmethionine, incorporated label into 2'-O-methyladenosine, 2'-O-methylguanosine, 2'-O-methyluridine, and 2'-O-methylcytidine of endogenous nuclear RNA. Addition of ribosomal RNA from wheat germ to the reaction markedly stimulated 2'-O-methylation of total RNA. The relative incorporation of label into the four different 2'-O-methyl ribonucleosides was greatly changed by the addition of wheat germ RNA. There was much more 2'-O-methylation of the purine ribonucleosides, relative to the pyrimidine ribonucleosides, in the reaction stimulated by wheat germ RNA.

Preparation, purification and analyses of thirteen alkali-stable dinucleotides from yeast ribonucleic acid

Of the 16 alkali-stable dinucleotides known to be obtained by hydrolysis of commercial yeast RNA with alkali, 13 were prepared in quantities of the order of 10mg or more. The samples, with only one exception, contain at least 90% of dinucleotide, and spectroscopic constants and nucleotide-sequence determinations, although not conclusive, indicate a high degree of purity of these products. The small dinucleotide fraction in 150g of RNA hydrolysed with alkali (1-2% of the total nucleotides) was separated from the mononucleotides by stepwise ion-exchange chromatography on DEAE-cellulose columns and resolved into seven fractions containing from one to four different dinucleotides by electrophoresis on paper at pH3.0. These fractions were resolved into their constituent dinucleotides by chromatography in ammonium sulphate. Contamination of the products by impurities from the paper was minimized by washing it before using it for chromatography or electrophoresis and, by using a thick grade of paper (Whatman no. 17), it was possible to handle and purify relatively large quantities of nucleotides.

The terminal groups of ribonucleate chains in each of the 16S and 23S components of Escherichia coli ribosomal RNA

Ribosomal ribonucleates from Escherichia coli have been resolved into 16S and 28S components by sucrose density-gradient centrifugation, and the chain termini in each of the 16S and 23S RNA components have been analyzed by hydrolysis with alkali. The principal 5′-linked end group of 16S RNA was found to be adenosine, and the principal 5′-linked end group of 23S RNA was found to be uridine. The principal 3′-linked end group of 16S RNA was also found to be adenosine, whereas the principal 3′-linked end group of 23S RNA was found to be guanosine. Quantitative estimates of chain length based on analyses for 5′-iinked terminals indicate that the mean chain length for 16S RNA is about 1.3 × 103nucleotide residues and the mean chain length for 23S RNA is about 2.1 × 103nucleotide residues.