A relation between inhibition of protein synthesis and conformation of 5'-phosphorylated 7-methylguanosine derivatives

Additive CHARMM force field for naturally occurring modified ribonucleotides

More than 100 naturally occurring modified nucleotides have been found in RNA molecules, in particular in tRNAs. We have determined molecular mechanics force field parameters compatible with the CHARMM36 all‐atom additive force field for all these modifications using the CHARMM force field parametrization strategy. Emphasis was placed on fine tuning of the partial atomic charges and torsion angle parameters. Quantum mechanics calculations on model compounds provided the initial set of target data, and extensive molecular dynamics simulations of nucleotides and oligonucleotides in aqueous solutions were used for further refinement against experimental data. The presented parameters will allow for computational studies of a wide range of RNAs containing modified nucleotides, including the ribosome and transfer RNAs. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

Emerging therapeutics targeting mRNA translation

A defining feature of many cancers is deregulated translational control. Typically, this occurs at the level of recruitment of the 40S ribosomes to the 5'-cap of cellular messenger RNAs (mRNAs), the rate-limiting step of protein synthesis, which is controlled by the heterotrimeric eukaryotic initiation complex eIF4F. Thus, eIF4F in particular, and translation initiation in general, represent an exploitable vulnerability and unique opportunity for therapeutic intervention in many transformed cells. In this article, we discuss the development, mode of action and biological activity of a number of small-molecule inhibitors that interrupt PI3K/mTOR signaling control of eIF4F assembly, as well as compounds that more directly block eIF4F activity.

Targeting translation dependence in cancer

A challenge in cancer therapy is to selectively target activities that are essential for survival of malignant cells while sparing normal cells. Translational control represents a potential anti-neoplastic target because it is exerted by major signaling pathways that are often usurped in cancers. Herein we describe approaches being developed that target eukaryotic initiation factor (eIF) 4F, a heterotrimeric complex that integrates multiple signaling inputs to the translation apparatus.

Ribavirin is not a functional mimic of the 7-methyl guanosine mRNA cap

Ribavirin is a guanosine ribonucleoside analog that displays broad-spectrum anti-viral activity and is currently used for the treatment of some viral infections. Ribavirin has recently been proposed to also be a mimic of the 7-methyl guanosine cap found at the 5' end of mRNAs. To obtain supporting functional data for this hypothesis, we assessed the ability of ribavirin triphosphate to interfere with the interaction between eIF4E and 7-methyl guanosine capped mRNA. In chemical cross-linking assays, cap-affinity chromatography, and cap-dependent translation assays, ribavirin was unable to function as a cap analog.

Quantitative assessment of mRNA cap analogues as inhibitors of in vitro translation

Fifty-eight analogues of the 5'-terminal 7-methylguanosine-containing cap of eukaryotic messenger RNA were synthesized and tested for their ability to inhibit in vitro protein synthesis. A new algorithm was developed for extracting KI, the dissociation constant for the cap analogue.eIF4E complex, from protein synthesis data. The results indicated that addition of a methyl group to the N2 of guanine produced more inhibitory compounds, but addition of a second methyl group to N2 decreased the level of inhibition dramatically. Aryl substitution at N7 improved the efficacy of guanine nucleoside monophosphate analogues. Substitution of the aromatic ring at the para position with methyl or NO2 groups abolished this effect, but substitution with Cl or F enhanced it. By contrast, aryl substitution at N7 in nucleoside di- or triphosphate analogues produced only minor effects, both positive and negative. By far the strongest determinants of inhibitory activity for cap analogues were phosphate residues. The beneficial effect of more phosphate residues was related more to anionic charge than to the number of phosphate groups per se. The second nucleotide residue in analogues of the form m7GpppN affected inhibitory activity in the order G > C > U > A, but there was no effect of 2'-O-modification. Opening the first ribose ring of m7GpppG analogues dramatically decreased activity, but alterations at the 2'-position of this ribose had no effect. Non-nucleotide-based cap analogues containing benzimidazole derivatives were inhibitory, though less so than those containing 7-methylguanine.

Plasmid cDNA-directed protein synthesis in a coupled eukaryotic in vitro transcription-translation system

A system is described in which transcription of cDNA clones by bacteriophage T7 RNA polymerase is coupled to translation in the micrococcal nuclease treated rabbit reticulocyte lysate in a single reaction of coupled transcription-translation. The monovalent and divalent cation requirements for translation are dominant for optimum expression in this coupled system, so that transcription is relatively inefficient. Nevertheless, the use of appropriate DNA concentrations leads to the synthesis of sufficient RNA to saturate the protein synthesis capacity of the system. The fidelity and efficiency of expression in this coupled system are high, and the degree of purification of the plasmid DNA is relatively uncritical. The system therefore offers very considerable advantages for rapid screening of 'mini-preparations' of cDNA plasmid constructs for retention of the correct reading frame and expression of the desired protein product.

Preferred translation of human hepatitis B virus polymerase from core protein- but not from precore protein-specific transcript

In the human hepatitis B virus (HBV) genome, the 5' end of the polymerase coding sequence overlaps with the 3' end of the core protein coding sequence. Recent results obtained from genetic studies have suggested that translation of HBV polymerase initiates from the first ATG codon of the polymerase reading frame and is not a result of frameshift translation from the core protein reading frame, as in the case of retroviruses. By using in vitro-synthesized SP6 RNA transcripts, we now demonstrate that HBV core protein-specific mRNA can direct the synthesis of polymerase from the internal polymerase ATG codon in rabbit reticulocyte lysates and Xenopus oocytes. A related message with an additional 60 nucleotides at the 5' end (pre-core protein mRNA) was not as efficient as the core protein mRNA for translation of polymerase. Furthermore, translation of polymerase from the core protein mRNA was not inhibited by the cap analog m7GpppG. This result, together with the results described above, indicates that translation of HBV polymerase occurs in a novel, cap-independent manner.

A spectroscopic study of the binding of N-7-substituted cap analogues to human protein synthesis initiation factor 4E

The binding of N-7-substituted cap analogues to eIF-4E from human erythrocytes is described. Data presented here indicate that there is a correlation between the tightness of binding of these cap analogues to eIF-4E and their potency as inhibitors of protein synthesis. This result indicates that the inhibitory activity of the cap analogues is strictly a function of the affinity of the analogue for eIF-4E under equilibrium conditions. The pH dependence of binding of the cap analogues to eIF-4E indicates that the enolate form of the cap is preferred, as originally postulated by Rhoads et al. [(1983) Biochemistry 22, 6084-6088]. Data indicate that there are differences in the mode of binding of alkyl-substituted and aryl-substituted cap analogues to eIF-4E arising from favorable interactions of the phenyl ring with the guanosine moiety. These differences may explain the enhanced recognition of the aryl-substituted cap analogues by eIF-4E.

A spectroscopic study of the binding of m7GTP and m7GpppG to human protein synthesis initiation factor 4E

The binding of analogues of the 7-methylguanosine-containing cap, m7GTP and m7GpppG, to eIF-4E from human erythrocytes as a function of pH, temperature, and ionic strength is described. From the pH-dependent binding of m7GTP and m7GpppG to eIF-4E, a new model describing the nature of the cap.eIF-4E interaction is proposed. The thermodynamic values and ionic strength dependence of binding are consistent with a binding site which is primarily hydrophobic. Fluorescence and circular dichroism data indicate that tryptophan residues may be involved in base-stacking interactions with the cap in a somewhat buried environment. The model presented here confirms the earlier proposal [Rhoads et al. (1983) Biochemistry 22, 6084-6088] that the enolate tautomer of the cap is preferred for interaction and further proposes that the interaction is with a protonated amino acid residue, such as histidine, while stacking with an aromatic amino acid, such as tryptophan.

Inhibition of eukaryotic translation by nucleoside 5'-monophosphate analogues of mRNA 5'-cap: changes in N7 substituent affect analogue activity

Nucleotide cap analogues of 7-methylguanosine 5'-monophosphate (m7GMP) were synthesized in which the 7-methyl moiety was replaced with 7-ethyl (e7), 7-propyl (p7), 7-isopropyl (ip7), 7-butyl (b7), 7-isobutyl (ib7), 7-cyclopentyl (cp7), 7-(carboxymethyl) (cm7), 7-benzyl (bn7), 7-(2-phenylethyl) [7-(2-PhEt)], and 7-(1-phenylethyl) [7-(1-PhEt)]. These derivatives were assayed as competitive inhibitors of capped mRNA translation in reticulocyte lysate. We observed that N7 alkyl and alicyclic substituents larger than ethyl significantly decreased the inhibitory activity of these cap analogues presumably by decreasing their affinity for cap binding proteins, which participate in the initiation of translation. This result defined a maximum size for this class of N7 substituents in the nucleotide binding domain of cap binding proteins. Like m7GMP, the N7-substituted GMP derivatives synthesized in this study were found to be predominantly in the anti conformation as determined by proton NMR analyses. However, bn7GMP and 7-(2-PhEt)GMP, which have aromatic N7 substituents, were more effective than m7GMP as competitive inhibitors of translation. The increased affinity of bn7GMP for cap binding proteins was further examined by synthesis of beta-globin mRNA containing 5'-bn7G, 5'-m7G, or 5'-e7G cap structures. These modified mRNAs were tested as translation templates. Messenger RNA capped with bn7G was observed to increase the translation activity of the template 1.8-fold relative to that of its m7G-capped mRNA counterpart. By contrast, e7G-capped mRNA was 25% less active than m7G-capped mRNA.2+V photo-cross-linking of m7G-capped mRNA to cap binding proteins

A selective recognition mode of a nucleic acid base by an aromatic amino acid: L-phenylalanine-7-methylguanosine 5'-monophosphate stacking interaction

The conformation of 7-methylguanosine 5'-monophosphate (m7GMP) and its interaction with L-phenylalanine (Phe) have been investigated by X-ray crystallographic, 1H-nuclear magnetic resonance, and energy calculation methods. The N(7) methylation of the guanine base shifts m7GMP toward an anti--gauche, gauche conformation about the glycosyl and exocyclic C(4')-C(5') bonds, respectively. The prominent stacking observed between the benzene ring of Phe and guanine base of m7GMP is primarily due to the N(7) guarternization of the guanine base. The formation of a hydrogen bonding pair between the anionic carboxyl group and the guanine base further stabilizes this stacking interaction. The present results imply the importance of aromatic amino acids as a hallmark for the selective recognition of a nucleic acid base.

Stacking and hydrogen bonding interactions between phenylalanine and guanine nucleotide: crystal structure of L-phenylalanine-7-methylguanosine-5'-monophosphate complex

The crystal structure of title complex has been analyzed by X-ray diffraction method as a model for elucidating the possible interaction between the phenylalanyl residue of proteins and the N7-protonated or methylated guanine base of nucleic acids. The guanine base is associated with the benzene ring of phenylalanine by stacking interaction, and further connected with the carboxyl group by the formation of a pair of hydrogen bonds. These two interaction modes are suggested to be responsible for the specific recognition of base sequence by protein.

Indole ring binds to 7-methylguanine base by pi-pi stacking interaction. Crystal structure of 7-methylguanosine 5'-monophosphate-tryptamine complex

Strong pi-pi stacking interaction between the indole ring and 7-methylguanine base was shown by X-ray crystal analysis of the 7-methylguanosine 5'-monophosphate-tryptamine complex. This interaction appears to be strengthened by the attachment of ribose and phosphate groups to the base.

Cap-dependent RNA splicing in a HeLa nuclear extract

We have studied the involvement of the 5' cap structure in the splicing of precursor mRNAs in a HeLa nuclear extract. We show that precursor mRNAs are spliced efficiently only when they possess a cap structure and that preincubation of a HeLa nuclear extract rendered the splicing reaction highly sensitive to inhibition by cap analogues. This sensitization was dependent on exogenous Mg2+ but not exogenous ATP or GTP. These results demonstrate that splicing in a nuclear extract is highly dependent on the cap structure, as was demonstrated for the splicing process in a HeLa whole-cell extract [Konarska, M. M., Padget, R. A. & Sharp, P. A. (1984) Cell 38, 731-736], and thus support the contention that cap recognition is an important feature of eukaryotic mRNA biogenesis.

5'-Terminal caps of snRNAs are reactive with antibodies specific for 2,2,7-trimethylguanosine in whole cells and nuclear matrices. Double-label immunofluorescent studies with anti-m3G antibodies and with anti-RNP and anti-Sm autoantibodies

Antibodies specific for 2,2,7-trimethylguanosine (m3G), which do not cross-react with m7G-capped RNA molecules were used to study, by immunofluorescence microscopy, the reactivity of the m3G-containing cap structures of the snRNAs U1 to U5 in situ. In interphase cells, immunofluorescent sites were restricted to the nucleus, whilst nucleoli were free of fluorescence. This indicates that the 5' terminal of most of the nucleoplasmic snRNAs are not protected by an m3G cap-recognizing protein and that the snRNA caps are not necessarily required for the binding of snRNPs to subnuclear structures. The snRNAs in the nucleoplasm appeared as distinct units in the light microscope, and this allowed the comparison of the distribution of snRNP proteins by double label studies with anti-RNP or anti-Sm antibodies within the same cell. The three antibody classes produced superimposable fluorescent patterns. Taking into account that the various IgGs react with antigenic sites on snRNAs or snRNP proteins not shared by all the snRNP species, these data suggest that U1 snRNP particles are distributed in the same way as the other snRNPs in the nucleus. Qualitatively the same results were obtained with DNase-treated nuclear matrices indicating that intact snRNPs are part of the nuclear matrix. Our data are consistent with proposals that the various snRNPs may be involved in processing of hnRNA and that this may take place at the nuclear matrix.

Messenger RNA regulation during compensatory renal growth

The normal pattern of mRNA metabolism almost certainly becomes altered after uninephrectomy, especially during the first day when ribosomes accumulate in the proximal tubular cells of the remaining kidney. For example, within the first hour after nephrectomy, the fraction of newly synthesized poly(A)-deficient mRNA increases relative to poly(A)-containing mRNA. Investigation of other growth-specific regulatory changes in renal mRNA has been complicated by its heterogeneity with respect to translational activity, polyadenylate content, membrane association, and cytoplasmic distribution. In general, analysis of kidney mRNA metabolism during growth has not been sufficiently thorough in that few timepoints have been examined after nephrectomy and the techniques used have been suited primarily to the study of only abundant mRNA sequences. Application of recombinant DNA methods should eliminate these difficulties and permit quantitative measurement of growth-specific genetic events during compensatory growth of the kidney.

Design and preparation of affinity columns for the purification of eukaryotic messenger ribonucleic acid cap binding protein

2',3'-O-[1-(2-Carboxyethyl) ethylidene]-7-methylguanosine 5'-diphosphate (5) and 7-(5-carboxypentyl) guanosine 5'-diphosphate (13) have been synthesized and immobilized on AH-Sepharose 4B to the extent of 17.4 and 36.6 mumol of ligand/g of gel, respectively. The affinity resins thus derives were employed in columns for the purificaton of 24K cap binding protein (CBP) from rabbit reticulocytes. Each resin was found to retain the protein of interest; elution of 24K CBP could then be effected by washing with 70 microM m7GDP. The 24K CBPs released from both columns were found to be active, both as judged by a cross-linking assay that utilized 10(4)-oxidized methyl-3H-labeled reovirus mRNA as a substrate for the protein and also by the ability of the isolated 24K CBP to stimulate the translocation of capped Sindbis virus mRNA in HeLa cell extracts.

In vitro translation of avian myeloblastosis virus RNA

Avian myeloblastosis virus (AMV)-infected cells contain two viral mRNA's, a genome-sized 34S (7.5-kilobase) mRNA and a 21S (2.5-kilobase) subgenomic mRNA, which contains the AMV-specific sequences (myb sequences). We found that AMV virions packaged both the 7.5-kilobase full-length genomic RNA and the 2.5-kilobase subgenomic RNA. In vitro translation of AMV virion RNA sized by sucrose density gradient centrifugation yielded 76,000-, 56,000-, 48,500-, 47,000-, and 32,000-dalton products. The 76,000-dalton protein was coded for by RNA throughout the gradient, but the peak of activity was at 34S to 35S. The 56,000-, and 48,500-, and 32,000-dalton proteins were encoded in a 21S RNA, and 47,000-dalton protein was encoded in an RNA of approximately 24S. The 76,000-dalton protein was identified as Pr76gag, based upon immunoprecipitation with specific antiserum and the presence of the 19* dipeptide. 7-Methylguanosine triphosphate inhibited the syntheses of Pr76gag and the 56,000-, 48,500-, and 32,000-dalton proteins, but not the synthesis of the 47,000-dalton protein. The 56,000-, 48,500-, 47,000-, and 32,000-dalton proteins were not immunoprecipitated by anti-gag, anti-reverse transcriptase, or anti-gp85 antiserum. Two-dimensional peptide maps of the 56,000- and 48,500-dalton proteins indicated that they were unique. In vitro translational products of myeloblastosis-associated virus 1 were also analyzed to aid in the identification of the AMV myb gene product(s); the translational products analyzed included Pr76gag, p60env, and a 56,000-dalton polypeptide which apparently was not identical to the 56,000-dalton AMV translational product, as determined by two-dimensional peptide mapping. Our data indicated that one of these proteins (56,000, 48,500, or 32,000 daltons) may represent the product of the AMV myb gene and, therefore, the putative transforming protein(s) of AMV.

Initiation of reovirus transcription by inosine 5'-triphosphate and properties of 7-methylinosine-capped, inosine-substituted messenger ribonucleic acids

Inosine 5'-triphosphate (ITP) can be utilized in place of guanosine 5'-triphosphate (GTP) for both the initiation and the elongation steps of reovirus transcription, resulting in the synthesis of mRNAs containing 5'-terminal m7IpppIm and internal pI. The apparent molecular weights of the I-substituted products were altered as a consequence of the absence of G-C base pairs and accompanying loss of ordered structure. The migration of I-substituted RNAs in agarose gels and glycerol gradients was similar to glyoxal-treated transcripts; i.e., it decreased 2-fold as compared to the corresponding untreated G-containing mRNAs. 7-Methylinosine-capped (m7I-capped), I-substituted transcripts readily attached to wheat germ 80S ribosomes. Unlike native G-containing mRNAs, they also formed heavier complexes that sedimented faster than 80S complexes even in the presence of the nonhydrolyzable ATP analogue AMPP(NH)P and elongation inhibitor sparsomycin. I-substituted molecules that were capped posttranscriptionally to form m7G-capped 5' ends yielded mostly 80S monosomes, consistent with a strong influence of 5'-terminal structure on initiation of translation. Under limited conditions of initiation, I-substituted RNAs outcompeted G-containing transcripts for ribosome attachment. Although the results are consistent with enhanced binding and freer movement of ribosomes on unstructured templates, synthesis of acid-precipitable polypeptides in wheat germ extract directed by I-substituted RNAs was 15-fold less than with G-containing mRNAs.

Ribosome binding site analysis of ovalbumin messenger ribonucleic acid

The region of the ovalbumin messenger ribonucleic acid (mRNAov) molecule bound to the 40S ribosomal subunit and its associated initiation factors in the wheat germ cell-free translation system were isolated and characterized. Two mRNAov fragments, 87 and 92 nucleotides in length, were protected from T1 ribonuclease digestion by binding of guanosine 5',beta,gamma-methylenetriphosphate and were shown by hybridization and fingerprint mapping to be derived from the 5' end of mRNAov. Both these mRNAov fragments were of sufficient length to contain both the cap structure and the AUG initiation codon. Four T1-resistant oligonucleotides, prepared by direct digestion of mRNAov with T1 ribonuclease were also found to bind to the wheat germ 40S ribosomal subunit. Nucleotide sequence analysis of these oligonucleotides revealed (1) that they were not a subset of the ribosome binding fragments described above, (2) that they were derived from within the mRNAov molecule (one from within the coding region and three from the noncoding region at the 3' end of the mRNAov molecule), and (3) that three of the four mRNAov nucleotides contained 3'-terminal AUG trinucleotides. These data suggested that features of the mRNAov molecule in addition to the nucleotide sequence might be important in specifying the correct ribosome binding site for the initiation of protein synthesis. The amount of mRNAov bound to the wheat germ 40S ribosomal subunit in a preinitiation complex was found to vary inversely with the potassium ion concentration. Lowering the potassium concentration to levels suboptimal for translation also resulted in the protection of larger fragments of the mRNAov molecule derived from the same 5'-end region as the ribosome binding fragments described above. The ability of the cap analogue 7-methylguanosine 5'-phosphate (m7G5'p) to reduce the amount of mRNAov bound to the wheat germ 40S ribosomal subunit was found to depend directly on thepotassium concentration. Interestingly, the effects of potassium on the amount of mRNAov bound in a preinitiation complex and the inhibition of this binding by m7G5'p could be observed by changing the potassium concentration after binding had occurred. These data suggested that the interaction between the wheat germ 40S ribosomal subunit and mRNAov was very sensitive to the ionic environment.

Inhibitory effect of methylated derivatives of guanylic acid for protein synthesis with reference to the functional structure of the 5'-'cap' in viral messenger RNA

Guanylic acid modified variously with methyl groups on base or sugar moieties were synthesized chemically and their inhibitory effects on protein synthesis were tesetd in a wheat germ cell-free system using mRNAs from cytoplasmic polyhedrosis virus and tobacco mosaic virus. The confronting dinucleotide m7G5' pppA that corresponds to the most simple 'cap' structure of an eukaryotic mRNA is a strong inhibitor of protein synthesis, but non-methylated G5' pppA or G5' ppA is not inhibitory. The strong inhibitory effect is observed only by 7-methylguanylic acid (pm7G). Among 11 derivatives of pG, the most effective inhibitors are methylated at the 7-position. Further methylation at the other position sometimes cancels the inhibitory effect. Although pm7G carries a positively charged base, other nucleotides which carry a plus charged base (1-methyladenylic acid and 2-methylthio-7-methylinosinic acid) were not inhibitory. Thus, methylation at the 7-position on guanylic acid is specifically required for the inhibitory effect. Addition of pm7G was inhibitory for the formation of the initiation complex for eukaryotic protein synthesis. These results suggest that the 'cap' component containing 7-methylguanylic acid in viral mRNA participates during protein synthesis, especially in its initial steps. Protein synthesis in a bacterial cell-free system was not inhibited by addition of m7GpppA or pm7G when either TMV RNA or phage MS2 RNA was used as an mRNA.

5'-Terminal 7-methylguanosine and mRNA function. The effect of enzymatic decapping and of cap analogs on translation of tobacco-mosaic-virus RNA and globin mRNA in vitro

1. Decapped tobacco mosaic virus (TMV) RNA and rabbit globin mRNA were prepared by enzymic treatment of RNAs with nucleotide pyrophosphatase purified from potato. The extent of removal of 5'-terminal 7-methylguanosine 5'-monophosphate (m7GMP) from TMV RNA was at least 97% as estimated by labeling of the 5' termini in vitro with S-adenosyl[methyl-3H]methionine catalysed by vaccinia virus methyltransferases. 2. The effect of enzymic decapping was compared with the effect of cap analogs on mRNAs translation in a nuclease-treated rabbit reticulocyte lysate and in a wheat germ extract. When translation was studied at low K+ concentration, little or no dependence on 5'-terminal 7-methylguanosine was found with either cell-free system. The importance of the 5'-terminal cap for the efficient translation of TMV RNA and globin mRNA increased as the concentration of K+ in a protein-synthesis system was raised. In a reticulocyte lysate analogs and enzymic decapping had a similar effect on translation. In a wheat germ extract, mRNA decapping resulted in a more pronounced decrease of mRNA activity, presumably due to the increased susceptibility of decapped mRNAs to the nucleases present in this protein synthesis system. 3. The requirement for a 5'-terminal cap was similar for the synthesis of 130,000-Mr and 165,000-Mr polypeptides coded by TMV RNA. This indicates that both proteins may be initiated at the common site close to the 5' terminus.

Inhibition of translation of lens mRNAs in a messenger dependent reticulocyte lysate by cap analogues

The nuclease treated reticulocyte lysate forms a highly efficient and completely mRNA-dependent cell-free system. In this system the functioning of the cap on eukaryotic mRNAs was explored by blocking cap recognition with cap analogues. Translation of capped mRNAs was severely inhibited, while translation of uncapped mRNAs was unaffected. It is concluded that this cell-free system can be used for screening cap dependence in the translation of specific mRNAs, like calf lens mRNAs. At 1.2 mM m7G5'p, 0.16 mM m7G5'pp or 0.16 m7G5'ppp5'G, translation of all lens mRNAs was totally inhibited. At lower concentrations the sensitivity to cap analogues was different for the various species of lens crystallin messenger. gamma-Crystallin mRNA showed relatively the lowest response. The translation of added polyribosomes was also inhibited by the cap analogue. It is concluded that translation of all crystallin messengers is cap-dependent.

Partial purification and characterization of rat-liver messenger RNA coding for phosphoenolpyruvate carboxykinase (GTP)

The mRNA coding for the gluconeogenic enzyme phosphoenolpyruvate carboxykinase (GTP) (EC 4.1.1.32) was partially purified from the liver of cyclic-AMP-treated rats by a procedure involving multiple oligo(dT)-cellulose chromatographies and sucrose gradient fractionations. The purification was monitored by translational assay using a wheat germ extract. Relative to RNA bound once to oligo(dT)-cellulose, the final material was enriched 20-fold in template activity for phosphoenolpyruvate carboxykinase synthesis. With this RNA preparation, cell-free enzyme synthesis amounted to 5% of total mRNA-directed protein synthesis. The apparent sedimentation coefficient of phosphoenolpyruvate carboxykinase mRNA in sucrose gradients was between 20 and 22 S, corresponding to an average molecular weight of 0.93 X 10(6). By formamide/polyacrylamide gel electrophoresis the molecular weight of the enzyme mRNA was estimated at between 0.91 X 10(6) and 1.12 X 10(6). From these estimates, it was concluded that considerable non-coding sequence(s) are present in the mRNA. Approximately 20% of the enzyme mRNA in rat liver failed to bind to oligo(dT)-cellulose, presumably because of the absence of a poly(A) segment. The translation of phosphoenolpyruvate carboxykinase mRNA by the wheat germ extract was inhibited in the presence of 7-methylguanosine 5'-phosphate. The enzyme mRNA appears therefore to have a 'cap' at the 5' end.

Modified bases in tRNA: the structures of 5-carbamoylmethyl- and 5-carboxymethyl uridine

The crystal structures of two nucleosides, 5-carbamoylmethyluridine (1) and 5-carboxymethyluridine (2), were determined from three-dimensional x-ray diffraction data, and refined to R = 0.036 and R = 0.047, respectively. Compound 1 is in the C3'-endo conformation with chi +5.2 degrees (anti), psiinfinity = +63.4 degrees and psialpha = +180.0 degrees (tt); 2 is in the C2'endo conformation with chi +49.4 degrees (anti), psiinfinity -60.5 degrees and psialpha +60.0 degrees (gg). For each derivative, the plane of the side chain substituent is skewed with respect to the plane of the nucleobase; for 1, the carboxamide group is on the same side of the uracil plane vis a vis the ribose ring; for 2, the carboxyl group is on the opposite side of this plane. No base pairing is observed for either structure. Incorporation of structure 1 into a 3'-stacked tRNA anticodon appears to place 08 within hydrogen bonding distance of the 02' hydroxyl of ribose 33, which may limit the ability of such a molecule of tRNA to "wobble".

Cleavage of pm7G from mRNA 5' terminal cap structures by pyrophosphatase activity in embryonic chick lens cells

The presence of pyrophosphatase activity in embryonic lens cells which cleaves pm7G and ppGm from m7G(5')pppGm was demonstrated. It was also found that m7G(5')pppG, but not G(5')pppG, was hydrolyzed, and conversion of m7GpppG to m7G*pppG, in which the 5-membered ring of the m7G moiety is open, abolished its hydrolysis. For the caps hydrolyzed, pm7G was released only in the presence of lens cellular fraction; pm7G inhibited cap hydrolysis.

Spatial configuration of mRNA 5'-terminus

Nuclear magnetic resonance investigation has revealed that the 5'-terminus m7G5'ppp5'Am of mRNA displays a spatial configuration in which the bases form stacked arrays. Details of the conformation as derived from coupling constants, shift trends and ring current considerations are discussed.