m7G5'ppp5'GmptcpUp at the 5' terminus of reovirus messenger RNA

The identity and methylation status of the first transcribed nucleotide in eukaryotic mRNA 5' cap modulates protein expression in living cells

7-Methylguanosine 5' cap on mRNA is necessary for efficient protein expression in vitro and in vivo. Recent studies revealed structural diversity of endogenous mRNA caps, which carry different 5'-terminal nucleotides and additional methylations (2'-O-methylation and m6A). Currently available 5'-capping methods do not address this diversity. We report trinucleotide 5' cap analogs (m7GpppN(m)pG), which are utilized by RNA polymerase T7 to initiate transcription from templates carrying Φ6.5 promoter and enable production of mRNAs differing in the identity of the first transcribed nucleotide (N = A, m6A, G, C, U) and its methylation status (±2'-O-methylation). HPLC-purified mRNAs carrying these 5' caps were used to study protein expression in three mammalian cell lines (3T3-L1, HeLa and JAWS II). The highest expression was observed for mRNAs carrying 5'-terminal A/Am and m6Am, whereas the lowest was observed for G and Gm. The mRNAs carrying 2'-O-methyl at the first transcribed nucleotide (cap 1) had significantly higher expression than unmethylated counterparts (cap 0) only in JAWS II dendritic cells. Further experiments indicated that the mRNA expression characteristic does not correlate with affinity for translation initiation factor 4E or in vitro susceptibility to decapping, but instead depends on mRNA purity and the immune state of the cells.

Dinucleotide Sequences at the 5' Ends of Vaccinia Virus mRNA's Synthesized In Vitro

The diversity of dinucleotide sequences at the 5' ends of vaccinia virus mRNA's was determined by a two-dimensional electrophoresis procedure. RNA labeled with S-adenosyl[methyl-(3)H]methionine was synthesized in vitro by enzymes present in vaccinia virus cores. The RNA, ending in m(7)G(5')pppN(m)pN-, was beta-eliminated and treated with alkaline phosphatase. After digestion with RNases T(2), T(1), and A, all eight possible dinucleotides containing G(m) and A(m) were identified. They are, in decreasing order of abundance: G(m)pUp (22%), A(m)pCp (18%), G(m)pAp (16%), G(m)pCp (15%), A(m)pAp (11%), A(m)pUp (10%), A(m)pGp (7%), and G(m)pGp (2%).

Genetic analysis of resistance to viral infection

As machines that reprogramme eukaryotic cells to suit their own purposes, viruses present a difficult problem for multicellular hosts, and indeed, have become one of the central pre-occupations of the immune system. Unable to permanently outpace individual viruses in an evolutionary footrace, higher eukaryotes have evolved broadly active mechanisms with which to sense viruses and suppress their proliferation. These mechanisms have recently been elucidated by a combination of forward and reverse genetic methods. Some of these mechanisms are clearly ancient, whereas others are relatively new. All are remarkably adept at discriminating self from non-self, and allow the host to cope with what might seem an impossible predicament.

Methylation: a regulator of HIV-1 replication?

Recent characterizations of methyl transferases as regulators of cellular processes have spurred investigations into how methylation events might influence the HIV-1 life cycle. Emerging evidence suggests that protein-methylation can positively and negatively regulate HIV-1 replication. How DNA- and RNA- methylation might impact HIV-1 is also discussed.

Gene-specific inhibition of reovirus replication by RNA interference

Mammalian reoviruses contain a genome of 10 segments of double-stranded RNA (dsRNA). Reovirus replication and assembly occur within distinct structures called viral inclusions, which form in the cytoplasm of infected cells. Viral nonstructural proteins muNS and sigmaNS and core protein mu2 play key roles in forming viral inclusions and recruiting other viral proteins and RNA to these structures for replication and assembly. However, the precise functions of these proteins in viral replication are poorly defined. Therefore, to better understand the functions of reovirus proteins associated with formation of viral inclusions, we used plasmid-based vectors to establish 293T cell lines stably expressing small interfering RNAs (siRNAs) specific for transcripts encoding the mu2, muNS, and sigmaNS proteins of strain type 3 Dearing (T3D). Infectivity assays revealed that yields of T3D, but not those of strain type 1 Lang, were significantly decreased in 293T cells stably expressing mu2, muNS, or sigmaNS siRNA. Stable expression of siRNAs specific for any one of these proteins substantially diminished viral dsRNA, protein synthesis, and inclusion formation, indicating that each is a critical component of the viral replication machinery. Using cell lines stably expressing muNS siRNA, we developed a complementation system to rescue viral replication by transient transfection with recombinant T3D muNS in which silent mutations were introduced into the sequence targeted by the muNS siRNA. Furthermore, we demonstrated that muNSC, which lacks the first 40 amino residues of muNS, is incapable of restoring reovirus growth in the complementation system. These results reveal interdependent functions for viral inclusion proteins and indicate that cell lines stably expressing reovirus siRNAs are useful tools for the study of viral protein structure-function relationships.

Reovirus sigma NS protein localizes to inclusions through an association requiring the mu NS amino terminus

Cells infected with mammalian reoviruses contain phase-dense inclusions, called viral factories, in which viral replication and assembly are thought to occur. The major reovirus nonstructural protein mu NS forms morphologically similar phase-dense inclusions when expressed in the absence of other viral proteins, suggesting it is a primary determinant of factory formation. In this study we examined the localization of the other major reovirus nonstructural protein, sigma NS. Although sigma NS colocalized with mu NS in viral factories during infection, it was distributed diffusely throughout the cell when expressed in the absence of mu NS. When coexpressed with mu NS, sigma NS was redistributed and colocalized with mu NS inclusions, indicating that the two proteins associate in the absence of other viral proteins and suggesting that this association may mediate the localization of sigma NS to viral factories in infected cells. We have previously shown that mu NS residues 1 to 40 or 41 are both necessary and sufficient for mu NS association with the viral microtubule-associated protein mu 2. In the present study we found that this same region of micro NS is required for its association with sigma NS. We further dissected this region, identifying residues 1 to 13 of mu NS as necessary for association with sigma NS, but not with mu 2. Deletion of sigma NS residues 1 to 11, which we have previously shown to be required for RNA binding by that protein, resulted in diminished association of sigma NS with mu NS. Furthermore, when treated with RNase, a large portion of sigma NS was released from mu NS coimmunoprecipitates, suggesting that RNA contributes to their association. The results of this study provide further evidence that mu NS plays a key role in forming the reovirus factories and recruiting other components to them.

Characterization of the reovirus lambda1 protein RNA 5'-triphosphatase activity

Characterization of the phosphohydrolytic activities of recombinant reovirus lambda1 protein demonstrates that, in addition to the previously reported nucleoside triphosphate phosphohydrolase and helicase activities, the protein also possesses RNA 5'-triphosphatase activity. This activity was absolutely dependent on the presence of a divalent cation, Mg2+ or Mn2+, and specifically removes the 5'-gamma-phosphate at the end of triphosphate-terminated RNAs. Kinetic competition analysis showed that nucleoside triphosphate phosphohydrolase and RNA 5'-triphosphatase reactions are carried out at a common active site. These results strongly support the idea that, in addition to its role as an RNA helicase during transcription of the viral genome, lambda1 also participates during formation of the cap structure at the 5' end of newly synthesized reovirus mRNAs. The lambda1 protein represents only the third RNA triphosphatase whose primary structure is known and the first described in a double-stranded RNA virus.

Characterization of the nucleoside triphosphate phosphohydrolase and helicase activities of the reovirus lambda1 protein

Previous studies have shown that the reovirus lambda1 core protein harbors a putative nucleotide-binding motif and exhibits an affinity for nucleic acids. In addition, a nucleoside triphosphate phosphohydrolase activity present in reovirus cores has been recently assigned to lambda1 using gene reassortment analysis. In this study, it was demonstrated that the recombinant lambda1 protein, expressed in the yeast Pichia pastoris, is able to hydrolyze nucleoside 5'-triphosphates or deoxynucleoside 5'-triphosphates. This activity was absolutely dependent on the presence of a divalent cation, Mg2+ or Mn2+. The protein can also unwind double-stranded nucleic acid molecules in the presence of a nucleoside 5'-triphosphate or deoxynucleoside 5'-triphosphate. These results provide the first biochemical evidence that the reovirus lambda1 protein is a nucleoside triphosphate phosphohydrolase/helicase and strongly support the idea that lambda1 participates in transcription of the viral genome.

Reovirus progeny subviral particles synthesize uncapped mRNA

Reovirus progeny subviral particles were isolated from L-cells at late times postinfection. It has been shown (D. Skup and S. Millward, J. Virol. 34: 490--496, 1980) that these progeny subviral particles have masked capping enzymes, indicating that mRNA synthesized by these particles should be uncapped. When progeny subviral particles were used for mRNA synthesis in vitro, they failed to incorporate the beta-phosphate of [beta-32P]GTP into the 5' terminal. Direct analysis of reovirus mRNA synthesized by progeny subviral particles in the presence of either [alpha-32P]GTP or [alpha-32P]CTP indicated that the 5' terminal was uncapped, having the structure pGpC... The implications of this finding to the reovirus replicative cycle are discussed.

Reovirus-induced modification of cap-dependent translation in infected L cells

The translational apparatus in cell-free extracts prepared from L cells infected with reovirus undergoes a time-dependent transition from cap dependence to cap independence. Extracts from uninfected L cells translate capped reovirus mRNA at high efficiency and synthesize the expected three size classes of reovirus polypeptides, and the translation is sensitive to m7G(5')ppp. This same extract translates uncapped mRNA at a much lower efficiency. In contrast, extracts from infected L cells translate uncapped reovirus mRNA at high efficiency and synthesize the correct three size classes of polypeptides, and the translation is not sensitive to inhibition by m7G(5')ppp. Infected cell extracts translate capped mRNA at reduced efficiency (a,proximately 25%), the translation is not sensitive to inhibition by m7G(5')ppp, and the correct three size classes of viral polypeptides are not synthesized. These observations may explain how reovirus takes over the host translational apparatus.

Nucleotide sequences at the 5' termini of reovirus mRNA's

During in vitro synthesis of reovirus mRNA by viral cores, methyl groups from S-adenosylmethionine are incorporated only into 5'-terminal cap structures, i.e., m7GpppGmCp.... Thus, mRNA synthesized in the presence of S-adenosyl-[methyl-3H]methionine is 3H labeled specifically at the 5' terminus. This circumstance was exploited in the determination of 5'-terminal nucleotide sequences. Seven 5'-terminal fragments derived by complete RNase T1, digestion of methyl-3Hlabeled mRNA were partially degraded with RNase T2, and the products were separated by electrophoresis-homochromatography. From the patterns formed by the methyl-3H-labeled RNase T2 products, the sequences of the seven RNase T1-generated fragments were deduced. All seven fragments started with the sequence m7GpppGmCUA, after which the sequences diverged, with a tendency to be either U-rich or A-rich. Their chain lengths ranged from 7 to 10 nucleotides (excluding the m7G residue), and none of them contained an initiator AUG triplet. The sequences obtained support the hypothesis that virion-associated oligonucleotides arise through abortive transcription of the viral genome. There is no apparent 5'-terminal sequence feature distinctive of early versus late mRNA species within the small-mRNA size class.

Highly efficient translation of messenger RNA in cell-free extracts prepared from L-cells

Micrococcal nuclease was used to eliminate endogenous protein synthesis in extracts prepared from L cells. The nuclease can be inhibited subsequently with 2'-deoxythymidine-3', 5'-diphosphate. Nuclease-treated extracts primed with exogenous reovirus mRNA, synthesized full length polypeptides with linear kinetics for almost two hours leading to stimulation of the order of 10(4) times over endogenous background. On the average, between 40 and 50 molecules of polypeptide were synthesized per molecule of mRNA.

The RNA of unfertilized sea urchin eggs is "capped"

It is shown that the RNA of unfertilized sea urchin eggs is active in stimulating protein synthesis in a wheat germ cell free system. This activity is not lowered by conditions that inhibit the methylation processes but is inhibited by a treatment that damages the "cap", A difference in activity in a wheat germ cell free system between the RNA of unfertilized eggs and the RNA from early embryos is described.

5' Terminal noncoding sequence heterogeneity in reovirus mRNA

The nucleotide sequences of the mRNAs of reovirus appear to diverge near the 5' termini. Ribonuclease T1 digestion of methylated mRNA synthesized in vitro yielded seven different 5' terminal fragments of the form m7G5'pp5' GmpCpUp(Np)nGp. Chain length analysis showed that the parameter "n" in this structural formula assumes the values 3, 4 and 5.

Methylated constituents of poly(A)- and poly(A)+ polyribosomal RNA of sea urchin embryos

We have examined the poly(A)- and poly(A)+ polyribosomal (Ps) RNAs of developing sea urchin embryos to see whether they contain the capped structures previously observed in the poly(A)+ cytoplasmic RNA (mRNA) of a variety of eucaryotic organisms. We have found that both classes of Ps RNA contain 7-methylguanosine linked to the RNA by a 5'-5' triphosphate bridge. Capped structures derived from either class of Ps RNA appear to be of the type m7G5'ppp5'NmpNp, with only a single sugar-methylated nucleoside per cap, and we have estimated that both classes of Ps RNA are capped to the same extent. The 5' terminal 2'-0-methylated nucleosides have been identified and quantitated. The relative amounts are Am = 78%, Gm = 14%, Cm = 5%, Um = 3% for poly(A)- Ps RNA, and Am = 78%, Gm = 15%, Cm = 5%, Um = 2% for poly (A)+ Ps RNA. In addition, both classes of Ps RNA contain 2-4 internal residues of N6-methyladenylic acid per molecule.