Immunospecific binding of capped mRNA of reovirus by an antibody to a cap structure; m7G(5′)pppGm

Antibody specific for m⁷G(5′)pppGm was elicited in rabbits. Binding of capped RNA by the antibody and specificity of the binding were assessed by radioimmunoassay using capped and uncapped mRNA of reovirus. More than 50% of capped mRNA, whereas less than 2% of uncapped mRNA were bound by the antibody. The ratios of the amount of competitor to that of m⁷G(5′)pppGm required for 50% inhibition of binding of capped mRNA was 1; 180; 430; 28,600; and 114,000 for m⁷G(5′)pppG, G(5′)pppGm, G(5′)pppG, yeast tRNA and rabbit rRNA respectively. Poly(A) showed no competition. By immunoaffinity chromatography, a 15-fold enrichment of capped mRNA was attained from the mixture of the RNA in a vast excess of rRNA.     

Enzymatic characterization of mRNA cap adenosine-N6 methyltransferase PCIF1 activity on uncapped RNAs

The phosphorylated RNA polymerase II CTD interacting factor 1 (PCIF1) is a methyltransferase that adds a methyl group to the N6-position of 2′O-methyladenosine (A_m), generating N6, 2′O-dimethyladenosine (m⁶A_m) when A_m is the cap-proximal nucleotide. In addition, PCIF1 has ancillary methylation activities on internal adenosines (both A and A_m), although with much lower catalytic efficiency relative to that of its preferred cap substrate. The PCIF1 preference for 2′O-methylated A_m over unmodified A nucleosides is due mainly to increased binding affinity for A_m. Importantly, it was recently reported that PCIF1 can methylate viral RNA. Although some viral RNA can be translated in the absence of a cap, it is unclear what roles PCIF1 modifications may play in the functionality of viral RNAs. Here we show, using in vitro assays of binding and methyltransfer, that PCIF1 binds an uncapped 5′-A_m oligonucleotide with approximately the same affinity as that of a cap analog (K_M = 0.4 versus 0.3 μM). In addition, PCIF1 methylates the uncapped 5′-A_m with activity decreased by only fivefold to sixfold compared with its preferred capped substrate. We finally discuss the relationship between PCIF1-catalyzed RNA methylation, shown here to have broader substrate specificity than previously appreciated, and that of the RNA demethylase fat mass and obesity-associated protein (FTO), which demonstrates PCIF1-opposing activities on capped RNAs.     

Hydrolysis of some mRNA 5′-Cap Analogs Catalyzed by the Human Fhit Protein - and Lupin ApppA Hydrolases

Abstract

Hydrolysis of the following four cap analogs: m⁷G(5′)ppp(5′)A, m⁷G(5′)ppp(5′)m⁶A, m⁷G(5′)ppp(5′)m^2′OG and m⁷G(5′)ppp(5′)2′dG catalyzed by homogeneous human Fhit protein and yellow lupin Ap₃A hydrolase has been investigated. The hydrolysis products were identified by HPLC analysis and the K_m and V_max values calculated based on the data obtained by the fluorimetric method.     

SYNTHESIS AND BIOCHEMICAL PROPERTIES OF NOVEL mRNA 5′ CAP ANALOGS RESISTANT TO ENZYMATIC HYDROLYSIS

A series of new dinucleotide cap analogs with methylene groups replacing oxygens within the pyrophosphate moieties have been synthesized. All the compounds were resistant to the human scavenger decapping hydrolase, DcpS. Binding constants of the modified caps to eIF4E are comparable to those obtained for m⁷GpppG. This suggests these methylene modifications in the pyrophosphate chain do not significantly affect cap-binding at least for eIF4E. These cap analogs are also good inhibitors of in vitro translation. mRNAs capped with novel analogs were translated similarly to the mRNA capped with the parent m⁷GpppG.     

Inhibition of noncapped mRNA translation by the cap analogue, 7-methylguanosine-5'-phosphate.

The cap analogue, 7-methylguanosine-5′-phosphate (pm⁷G), inhibits the translation of the noncapped STNV (satellite tobacco necrosis virus) RNA and CPMV (cowpea mosaic virus) RNA in the $\text{in vitro}$ wheat germ protein synthesizing system. While the translation of some capped mRNAs is inhibited more strongly by the analogue, other capped mRNAs have a level of sensitivity similar to that of the noncapped RNAs. Evidence is presented demonstrating that the effect of the analogue is exerted at a cap binding site even when it is inhibiting noncapped mRNAs. These results therefore indicate that the cap binding site of the translational system is either part of or is closely linked to another mRNA binding component, this component being specific for a site on the mRNA other than the 5′ cap. The observations also suggest caution in the use of pm⁷G inhibition to indicate the presence of a 5′ cap on a particular mRNA.     

Utilization of the guanylyltransferase and methyltransferases of vaccinia virus to modify and identify the 5′-terminals of heterologous RNA species

Enzymes extracted from purified vaccinia virus particles were used to catalyze the guanylylation (i.e. capping) and/or methylation of heterologous RNA species containing two or three phosphates or the structure m⁷G(5′)pppN at their 5′-terminals. This procedure provides a novel and specific method of labeling the 5′-terminals with $\text{[}{}^{\mathrm{\alpha -32}}\text{P]GTP}$ or S-adenosyl-[methyl-³H]methionine. Analysis of the RNAs of satellite tobacco necrosis virus and tobacco mosaic virus that were modified in this manner indicated that the original 5′-terminal sequences were (p)ppApGpPy and m⁷G(5′)pppGpU, respectively, which were enzymatically converted to m⁷G(5′)pppA^mpGpPy and m⁷G(5′)pppG^mpU.     

Intrinsic RNA Binding by the Eukaryotic Initiation Factor 4F Depends on a Minimal RNA Length but Not on the m7G Cap

The eukaryotic initiation factor 4F (eIF4F) is thought to be the first factor to bind mRNA during 7-methylguanosine (m⁷G) cap-dependent translation initiation. The multipartite eIF4F contains the cap-binding protein eIF4E, and it is assumed that eIF4F binds mRNAs primarily at the 5′ m⁷G cap structure. We have analyzed equilibrium binding of rabbit eIF4F to a series of diverse RNAs and found no impact of the 5′-cap on the stability of eIF4F-RNA complexes. However, eIF4F preferentially and cooperatively binds to RNAs with a minimum length of ∼60 nucleotides in vitro. Furthermore, translation activity in rabbit reticulocyte lysate is strongly inhibited by RNAs exceeding this length, but not by shorter ones, consistent with the notion that eIF4F in its physiological environment preferentially binds longer RNAs, too. Collectively, our results indicate that intrinsic RNA binding by eIF4F depends on a minimal RNA length, rather than on cap recognition. The nonetheless essential m⁷G cap may either function at steps subsequent to eIF4F-RNA binding, or other factors facilitate preferential binding of eIF4F to the m⁷G cap.     

Translation, stability, and resistance to decapping of mRNAs containing caps substituted in the triphosphate chain with BH3, Se, and NH

Decapping is an essential step in multiple pathways of mRNA degradation. Previously, we synthesized mRNAs containing caps that were resistant to decapping, both to dissect the various pathways for mRNA degradation and to stabilize mRNA for more sustained protein expression. mRNAs containing an α-β CH₂ group are resistant to in vitro cleavage by the decapping enzyme hDcp2 but poorly translated. mRNAs containing an S substitution at the β-phosphate are well translated but only partially resistant to hDcp2. We now describe seven new cap analogs substituted at the β-phosphate with BH₃ or Se, or substituted at either the α-β or β-γ O with NH. The analogs differ in affinity for eIF4E and efficiency of in vitro incorporation into mRNA by T7 RNA polymerase. Luciferase mRNAs capped with these analogs differ in resistance to hDcp2 hydrolysis in vitro, translational efficiency in rabbit reticulocyte lysate and in HeLa cells, and stability in HeLa cells. Whereas mRNAs capped with m₂^7,2′-OGpp_SpG were previously found to have the most favorable properties of translational efficiency and stability in mammalian cells, mRNAs capped with m⁷Gpp_BH3pm⁷G are translated with the same efficiency but are more stable. Interestingly, some mRNAs exhibit a lag of up to 60 min before undergoing first-order decay (t_1/2 ≅ 25 min). Only mRNAs that are efficiently capped, resistant to decapping in vitro, and actively translated have long lag phases.     

Capping of Viral RNA in Cultured Spodoptera frugiperda Cells Infected with Autographa californica Nuclear Polyhedrosis Virus

Viral RNA from fall armyworm (Spodoptera frugiperda) cells infected with Autographa californica nuclear polyhedrosis virus contains cap structures. Most of the cap labeled in vivo with [³H]methionine or ³²P_i cochromatographed on DEAE-cellulose with the −5 charge marker; a minor component appeared at −4 net charge. The former is probably a cap 1 structure (m⁷GpppX^m_pYp), and the latter is probably a cap 0 (m⁷GpppXp). On the basis of relative labeling of the two caps with [³H]adenosine and [³H]guanosine, we concluded that each cap contained at least one adenosine residue in addition to guanosine and, therefore, that cap 0 contained m⁷GpppAp. Cleavage of [³H]methionine-labeled viral RNA with tobacco acid pyrophosphatase released a labeled component that cochromatographed on polyethyleneimine-cellulose with m⁷Gp, confirming the m⁷GpppX linkage in the cap. These results were also seen with host polyadenylated RNA. The caps appeared in nearly equal abundance in viral polyadenylated and non-polyadenylated RNAs. The ratio of ³²P_i incorporated into the cap to that incorporated into mononucleotides suggested average lengths for the polyadenylated and non-polyadenylated RNAs of 1,800 and 1,200 nucleotides, respectively.