Translation of capped and uncapped VSV mRNAs in the presence of initiation factors from poliovirus-infected cells

Initiation factor preparations from poliovirus-infected cells have been shown to support the translation of poliovirus RNA in vitro, but they fail to stimulate initiation of translation of other mRNAs. In this study, the role of the m⁷G cap group on vesicular stomatitis virus (VSV) mRNAs has been evaluated with respect to the ability of initiation factors from poliovirus-infected cells to discriminate against its translation. A series of uncapped and/or unmethylated VSV mRNAs was prepared and their translation in vitro was analyzed. Each was compared with capped and methylated VSV mRNA and with poliovirus RNA for its recognition by initiation factors from uninfected or poliovirus-infected HeLa cells. The results show that the capped 5′ terminus of mRNA is not the sole basis for recognition and discrimination by poliovirus-altered initiation factors.     

The 3' stem loop of the West Nile virus genomic RNA can suppress translation of chimeric mRNAs

Cis-acting elements that regulate translation have been identified in the 3' noncoding regions (NCRs) of cellular and viral mRNAs. As one means of analyzing the effect on translation of the conserved 3' terminal RNA structure of the West Nile virus (WNV) genome, the translation efficiencies of chimeric mRNAs composed of a CAT reporter gene flanked by viral or nonviral 5' and 3' terminal sequences were compared. In vitro, the WNV 3'(+) stem loop (SL) RNA reduced the translation efficiencies of chimeric mRNAs with either viral or nonviral 5' NCRs, suggesting that a specific 3'-5' RNA-RNA interaction was not involved. In contrast, the 3' terminal sequence of a togavirus, rubella virus, enhanced translation efficiency. The WNV 3'(+)SL reduced translation efficiency both in cis and in trans and of both capped and uncapped chimeric mRNAs. We have previously reported that three cellular proteins bind specifically to the WNV 3'(+)SL RNA. Competition between the WNV 3'(+)SL and the 5' terminus of the chimeric mRNAs for proteins involved in translation initiation could explain the translation inhibition observed.     

Cap and polyA tail enhance translation initiation at the hepatitis C virus internal ribosome entry site by a discontinuous scanning, or shunting, mechanism.

OBJECTIVES: Hepatitis C virus (HCV) does not replicate in vitro, suggesting that cultured cells may lack factors that are essential for efficient use of HCV messenger RNAs (mRNAs). Here, we have studied the efficiency of HCV mRNA translation compared with translation of capped and polyadenylated mRNAs in human cells. STUDY DESIGN/METHODS: We have generated noninfectious minivirus mRNAs from an infectious HCV genome. These mRNAs were transfected into human cells, and the translation efficiency was determined. RESULTS: Hepatitis C virus mRNAs under control of the HCV internal ribosome entry site (IRES) were inefficiently translated compared with capped and polyadenylated mRNAs. Addition of a cap and a polyA tail on the HCV mRNAs revealed that these structures interacted with the hepatitis C IRES in a synergistic manner to load ribosomes onto the HCV mRNAs, thereby strongly enhancing translation. The positive effect of the cap and the polyA tail on initiation of translation at the initiator AUG embedded in the HCV IRES was the result of a discontinuous scanning, or shunting, mechanism. CONCLUSIONS: The results demonstrated that recruitment of ribosomes to the HCV mRNAs was inefficient in dividing cultured cells. Factors that are necessary for efficient translation of the HCV mRNAs in hepatocytes may be absent or inactive in cultured cells. This may be one reason for the inefficient replication of the HCV in vitro.     

Poliovirus protease 2A is required for interference with vesicular stomatitis virus-specified protein synthesis

Summary A subunit of eukaryotic initiation factor-4F (eIF-4F) which is a component of the protein complex which binds to the methylated cap structure at the 5 end of most cellular mRNAs, is proteolytically cleaved in poliovirus-infected cells resulting in the shutoff of cellular protein synthesis. Poliovirus mRNA is selectively translated in infected cells, in part, because translation of the uncapped viral mRNA does not require an intact cap binding protein complex. Wild-type poliovirus also inhibits the translation of vesicular stomatitis virus (VSV) mRNAs in coinfected cells, however, it has been unclear whether similar mechanisms are employed by poliovirus to interfere with cellular and VSV protein synthesis. Degradation of eIF-4F appears to be an indirect function of the poliovirus-encoded protease 2A. A poliovirus mutant in 2A failed to mediate eIF-4F cleavage and selectively terminate translation of capped cellular mRNAs. Unlike wild-type poliovirus, 2A-1 does not interfere with VSV-specified protein synthesis. These results indicate that the same viral protein, 2A protease, is required not only to effectively terminate host protein synthesis, but also to interfere with expression of a heterologous virus, VSV. In addition, 2A-1 specifies a function, heretofore undescribed for poliovirus, which interferes with VSV-induced shutoff of protein synthesis.     

Fig mosaic virus mRNAs show generation by cap-snatching

Fig mosaic virus (FMV), a member of the newly described genus Emaravirus, has four negative-sense single-stranded genomic RNAs, and each codes for a single protein in the viral complementary RNA (vcRNA). In this study we show that FMV mRNAs for genome segments 2 and 3 contain short (12-18 nucleotides) heterogeneous nucleotide leader sequences at their 5′ termini. Furthermore, by using the high affinity cap binding protein eIF4E_K119A, we also determined that a 5′ cap is present on a population of the FMV positive-sense RNAs, presumably as a result of cap-snatching. Northern hybridization results showed that the 5′ capped RNA3 segments are slightly smaller than the homologous vcRNA3 and are not polyadenylated. These data suggest that FMV generates 5′ capped mRNAs via cap-snatching, similar to strategies used by other negative-sense multipartite ssRNA viruses.     

Messenger RNA processing sites in Trypanosoma brucei

In Kinetoplastids, protein-coding genes are transcribed polycistronically by RNA polymerase II. Individual mature mRNAs are generated from polycistronic precursors by 5' trans splicing of a 39-nt capped leader RNA and 3' polyadenylation. It was previously known that trans splicing generally occurs at an AG dinucleotide downstream of a polypyrimidine tract, and that polyadenylation is coupled to downstream trans splicing. The few polyadenylation sites that had been examined were 100-400 nt upstream of the polypyrimidine tract which marked the adjacent trans splice site. We wished to define the sequence requirements for trypanosome mRNA processing more tightly and to generate a predictive algorithm. By scanning all available Trypanosoma brucei cDNAs for splicing and polyadenylation sites, we found that trans splicing generally occurs at the first AG following a polypyrimidine tract of 8-25 nt, giving rise to 5'-UTRs of a median length of 68 nt. We also found that in general, polyadenylation occurs at a position with one or more A residues located between 80 and 140 nt from the downstream polypyrimidine tract. These data were used to calibrate free parameters in a grammar model with distance constraints, enabling prediction of polyadenylation and trans splice sites for most protein-coding genes in the trypanosome genome. The data from the genome analysis and the program are available from: .     

Mutation of the AAUAAA polyadenylation signal depresses in vitro splicing of proximal but not distal introns.

To investigate the relationship between splicing and polyadenylation during the production of vertebrate mRNAs, we examined the effect of mutation of a poly(A) site on splicing of upstream introns. Mutation of the AAUAAA polyadenylation consensus sequence inhibited in vitro splicing of an upstream intron. The magnitude of the depression depended on the magnesium concentration. Dependence of splicing on polyadenylation signals suggests the existence of interaction between polyadenylation and splicing factors. In multi-intron precursor RNAs containing duplicated splice sites, mutation of the poly(A) site inhibited removal of the last intron, but not the removal of introns farther upstream. Inhibition of removal of only the last intron suggests segmental recognition of multi-exon precursor RNAs and is consistent with previous suggestions that signals at both ends of an exon are required for effective splicing of an upstream intron.     

Investigation of the 5′ terminal structures of genomic and subgenomic RNAs of potato virus S

Hybrid arrest translation involving an antisense RNA, generated from a cloned cDNA close to the 5 region of potato virus S genomic RNA, blocked the synthesis of genomic encoded products but had little effect on subgenomic RNA encoded products. Similarly, the synthesis of PVS genomic RNA-directed peptides was inhibited by the cap analogue m⁷G⁵ ppp⁵G, suggesting the presence of a cap structure at the 5 terminus whilst subgenomic RNA encoded products remained unaffected, suggesting an uncapped structure. This was confirmed by artificially produced uncapped subgenomic RNAs translating as efficiently in in vitro translation systems as authentic viral subgenomic RNAs.     

Inhibition of translation of mRNAs containing gamma-monomethylphosphate cap structure in frog oocytes and in mammalian cells

The gamma-monomethylphosphate cap structure is found in several eukaryotic small RNAs including nuclear U6, U6atac, 7SK, plant nucleolar U3, and rodent cytoplasmic B2 RNAs. In the case of human U6 snRNA, the 5' end sequence corresponding to nucleotides 1-25 serves as the capping signal and directs the formation of methylphosphate cap structure. In this study, we show that the U6 RNA capping signal, when introduced at the 5' end of RNAs, can efficiently direct the methylphosphate cap formation in RNAs of up to 2.7 kb long, as well as in different mRNAs. These data show that the methylphosphate capping signal functions in mRNAs having different primary sequences and different lengths. Presence of the methylphosphate cap structure on the 5' end of a luciferase mRNA with EMCV 5' noncoding region, which is translated in an IRES-dependent pathway, resulted in a 6- to 100-fold inhibition of translation compared to the same mRNA with a 5' triphosphate when microinjected into frog oocytes or expressed in mouse cells in tissue culture. Thus, conversion of the pppG structure to a methyl-pppG structure on the 5' end of an mRNA, which is translated in an IRES-dependent pathway, results in severe inhibition of translation. These data show that the 5' end motif of mRNAs plays an important role even in the IRES-mediated mRNA translation.     

Different trans RNA splicing events in bloodstream and procyclic Trypanosoma brucei

Most trypanosomatid genes are transcribed into polycistronic precursor RNAs that are processed into monocistronic mRNAs possessing a 39-nucleotide spliced leader (SL) at their 5′-ends and polyadenylation at their 3′-ends. We show here that precursor RNA derived from a luciferase gene integrated in reverse orientation at the rDNA locus of Trypanosoma brucei is processed into three major SL-containing RNAs in bloodstream cells and a single SL-containing RNA in procyclic RNAs. This difference in trans RNA splicing between bloodstream and procyclic cells is independent of the 5′- and 3′-UTRs flanking the luciferase coding region. Thus, bloodstream cells can recognize some sequences in precursor RNA as a SL addition site that procyclic cells do not. These alternative SL addition sites may be aberrant or they might be utilized to expand the number of gene products from individual genes. Future experiments on endogenous genes will be necessary to examine the latter possibility.