Cap-dependent binding of mRNA to the 40 S ribosomal subunit during translational initiation requires the association of eukaryotic initiation factor 4G (eIF4G; formerly eIF-4γ and p220) with other initiation factors, notably eIF4E, eIF4A, and eIF3. Infection of cells by picornaviruses results in proteolytic cleavage of eIF4G and generation of a cap-independent translational state. Rhinovirus 2A protease and foot-and-mouth-disease virus L protease were used to analyze the association of eIF4G with eIF4A, eIF4E, and eIF3. Both proteases bisect eIF4G into N-and C-terminal fragments termed cp N and cp c . cp N was shown to contain the eIF4E-binding site, as judged by retention on m 7 GTP-Sepharose, whereas cp c was bound to eIF3 and eIF4A, based on ultracentrifugal co-sedimentation. Further proteolysis of cp N by L protease produced an 18-kDa polypeptide termed cp N2 which retained eIF4E binding activity and corresponded to amino acid residues 319-479 of rabbit eIF4G. Further proteolysis of cp c yielded several smaller fragments. cp C2 (~887-1402) contained the eIF4A binding site, whereas cp C3 (~480-886) contained the eIF3 binding site. These results suggest that cleavage by picornaviral proteases at residues 479-486 separates eIF4G into two domains, one required for recruiting capped mRNAs and one for attaching mRNA to the ribosome and directing helicase activity. Only the latter would appear to be necessary for internal initiation of picornaviral RNAs.

A method is presented for choosing optimal oligodeoxyribonucleotides as probes for filter hybridization, primers for sequencing, or primers for DNA amplification. Three main factors that determine the quality of a probe are considered: stability of the duplex formed between the probe and target nucleic acid, specificity of the probe for the intended target sequence, and self-complementarity. DNA duplex stability calculations are based on the nearest-neighbor thermodynamic values determined by Breslauer et al. [Proc. Natl. Acad. Sci. U.S.A. (1986), 83: 3746]. Temperatures of duplex dissociation predicted by the method described here were within 0.4 degrees C of the values obtained experimentally for ten oligonucleotides. Calculations for specificity of the probe and its self-complementarity are based on a simple dynamic algorithm.

Enteroviruses such as Coxsackievirus B3 can cause dilated cardiomyopathy, but the mechanism of this pathology is unknown. Mutations in cytoskeletal proteins such as dystrophin cause hereditary dilated cardiomyopathy, but it is unclear if similar mechanisms underlie acquired forms of heart failure. We demonstrate here that purified Coxsackievirus protease 2A cleaves dystrophin in vitro as predicted by computer analysis. Dystrophin is also cleaved during Coxsackievirus infection of cultured myocytes and in infected mouse hearts, leading to impaired dystrophin function. In vivo, dystrophin and the dystrophin-associated glycoproteins alpha-sarcoglycan and beta-dystroglycan are morphologically disrupted in infected myocytes. We suggest a molecular mechanism through which enteroviral infection contributes to the pathogenesis of acquired forms of dilated cardiomyopathy.

ABSTRACT

Eukaryotic translation initiation factor eIF-4E plays a central role in the recognition of the 7-methylguanosine-containing cap structure of mRNA and the formation of initiation complexes during protein synthesis. eIF-4E exists in both phosphorylated and nonphosphorylated forms, and the primary site of phosphorylation has been identified. Previous studies have suggested that eIF-4E phosphorylation facilitates its participation in protein synthesis. However, the biochemical basis for the functional difference between the two forms of eIF-4E is unknown. To address this directly, we have developed a method for the separation of phosphorylated and nonphosphorylated eIF-4E from rabbit reticulocytes by chromatography on rRNA-Sepharose. Using the resultant purified forms, we have studied the protein's interaction with the cap analogs m7GTP and m7GpppG and with the cap of globin mRNA by fluorescence quenching of tryptophan residues. It was found that phosphorylated eIF-4E had 3-to 4-fold greater affinity for cap analogs and mRNA than nonphosphorylated eIF-4E. The equilibrium binding constants (x 105, expressed as M-1) for the interaction of phosphorylated eIF-4E with m7GTP, m7GpppG, and globin mRNA were 20.0 ± 0.1, 16.4 ± 0.1, and 31.0 ± 0.1, respectively, whereas those for the nonphosphorylated form were 5.5 ± 0.4, 4.3 ± 0.4, and 10.0 ± 0.1, respectively. Treatment with potato acid phosphatase converted the phosphorylated form to the nonphosphorylated form and decreased the binding constant for m7GTP by a factor of3. The increased affinity for mRNA caps may account for the in vivo and in vitro correlations between eIF-4E phosphorylation and accelerated protein synthesis and cell growth.Except in unusual circumstances such as virus infection, cellular stress, or deprivation of nutrients, the overall rate of protein synthesis in eukaryotic cells is thought to be determined by the rate of formation of 48S initiation complexes. This is based on the observations that 48S complexes are present at very low steady-state levels compared with other initiation complexes (1), usually being detected only in the presence of inhibitors (2), and that the ATP-dependent step ofinitiation is rate-limiting (3). Formation ofthe 48S initiation complex involves the binding of mRNA to the 43S initiation complex and is catalyzed by group 4 initiation factors (reviewed in refs. 4-6). The four polypeptides of the eIF-4 group-eIF-4A, eIF-4B, eIF-4E, and eIF-41-collectively bind to the m7GTP-containing cap, unwind mRNA secondary structure at the expense of ATP, and facilitate the movement of the 40S ribosomal subunit along the mRNA until the initiation codon is reached. Various complexes of the eIF-4 polypeptides have been isolated, the best studied of which is termed eIF-4F. eIF-4F isolated from mammalian cells was originally shown to contain the polypeptides eIF-4A, eIF-4E, and eIF-4y (7, 8), but other purifications yield a twocomponent factor consisting of eIF-4E and eIF-4y (9-11). Similarly, eIF-4F and eIF(iso)-4F from plants (12) and ...

Recognition of the 5-cap structure of mRNA by eIF4E is a critical step in the recruitment of most mRNAs to the ribosome. In Caenorhabditis elegans, ϳ70% of mRNAs contain an unusual 2,2,7-trimethylguanosine cap structure as a result of trans-splicing onto the 5 end of the pre-mRNA. The characterization of three eIF4E isoforms in C. elegans (IFE-1, IFE-2, and IFE-3) was reported previously. The present study describes two more eIF4E isoforms expressed in C. elegans, IFE-4 and IFE-5. We analyzed the requirement of each isoform for viability by RNA interference. IFE-3, the most closely related to mammalian eIF4E-1, binds only 7-methylguanosine caps and is essential for viability. In contrast, three closely related isoforms (IFE-1, IFE-2, and IFE-5) bind 2,2,7-trimethylguanosine caps and are partially redundant, but at least one functional isoform is required for viability. IFE-4, which binds only 7-methylguanosine caps, is most closely related to an unusual eIF4E isoform found in plants (nCBP) and mammals (4E-HP) and is not essential for viability in any combination of IFE knockout. ife-2, ife-3, ife-4, and ife-5 mRNAs are themselves trans-spliced to SL1 spliced leaders. ife-1 mRNA is transspliced to an SL2 leader, indicating that its gene resides in a downstream position of an operon.Eukaryotic mRNAs and small nuclear RNAs synthesized by RNA polymerase II are posttranscriptionally modified to form a 5Ј-5Ј GpppN linkage (1). The 5Ј-terminal G is methylated at N7 while still in the nucleus to yield an MMG 1 cap. The cap of small nuclear RNAs is then further methylated at N2 in the cytoplasm to yield a TMG cap (2). Methylation of small nuclear RNAs is dependent upon the binding of Sm proteins to form small nuclear ribonucleoproteins. Formation of the TMG cap is the targeting signal for import of small nuclear ribonucleoproteins back into the nucleus to take part in pre-mRNA splicing (3, 4). mRNAs, on the other hand, which possess only the MMG cap, remain in the cytoplasm.In some primative eukaryotes, including Caenorhabditis elegans, mRNAs acquire a TMG cap through the process of trans-splicing (5). Primary transcripts from approximately 70% of protein-coding genes are trans-spliced to 22-nt SL sequences, such that the original MMG caps are replaced with the TMG caps from the SL small nuclear RNAs (6, 7). Also common in C. elegans is the organization of genes into operons that are transcribed from a single promotor into a polycistronic RNA (8). trans-Splicing results in the processing of these primary transcripts into monocistronic mRNAs. Generally, the mRNA from the first cistron is trans-spliced to SL1,whereas mRNAs from downstream cistrons are trans-spliced to SL2 or SL2 variants (8). mRNAs that are not trans-spliced retain the original MMG cap. Thus, both MMG-and TMG-capped mRNAs are found in the cytoplasm of C. elegans. Both types of mRNA enter polyribosomes and are translated, indicating that they are competent to interact with the translational machinery (9).The recruitment of mRNAs to ribosomes is catalyzed by...

In the polymerase chain reaction (PCR) technique, DNA is amplified in vitro by a series of polymerization cycles consisting of three temperature-dependent steps: DNA denaturation, primer-template annealing, and DNA synthesis by a thermostable DNA polymerase. The purity and yield of the reaction products depend on several parameters, one of which is the annealing temperature (Ta). At both sub- and super-optimal Ta values, non-specific products may be formed, and the yield of products is reduced. Optimizing the Ta is especially critical when long products are synthesized or when total genomic DNA is the substrate for PCR. In this article we experimentally determine the optimal annealing temperature (TaOPT) values for several primer-template pairs and develop a method for its calculation. The TaOPT is found to be a function of the melting temperatures of the less stable primer-template pair and of the product. The fact that experimental and calculated TaOPT values agree to within 0.7 degree C eliminates the need for determining TaOPT experimentally. Synthesis of DNA fragments shorter than 1 kb is more efficient if a variable Ta is used, such that the Ta is higher in each consecutive cycle.

Insulin rapidly stimulates protein synthesis in a wide variety of tissues. This stimulation is associated with phosphorylation of several translational initiation and elongation factors, but little is known about the signaling pathways leading to these events. To study these pathways, we have used a myeloid progenitor cell line (32D) which is dependent on interleukin 3 but insensitive to insulin because of the very low levels of insulin receptor (IR) and the complete lack of insulin receptor substrate ( Insulin influences a variety of cellular activities. It modulates glucose and amino acid transport; activates key enzymes of intermediary metabolism; increases the rates of protein, DNA, and RNA synthesis; enhances transcription and translation of specific genes; and generally promotes cellular growth and differentiation (53). These actions are mediated through the insulin receptor (IR), which phosphorylates itself as well as substrates such as the insulin receptor substrate (IRS)-signaling proteins (IRS-1 and IRS-2) and Shc (53, 60). The phosphorylated Tyr residues bind directly to proteins containing Src homology 2 domains (SH2 proteins) in a sequence-specific manner, leading to the activation of a wide variety of enzymatic activities. IRS-signaling proteins are required for insulin stimulation of phosphatidylinositol 3-kinase (PI3K), the Tyr phosphatase SH-PTP2, mitogen-activated protein kinase (MAPK), and the 70-kDa S6 kinase (pp70 S6K ). Disruption of the IRS-1 gene in mice is not lethal but causes mild insulin resistance (56), a finding which led to the discovery of a second IRS protein, IRS-2 (55).One of the principal end points of insulin action is the stimulation of protein synthesis. Insulin induces both a general increase in the rate of mRNA translation and preferential increases in the translation of specific mRNAs, e.g., mRNAs with polypyrimidine tracts in their 5Ј untranslated regions (20, 37, 57) and mRNAs rich in secondary structure (32). Such mRNAs encode ''growth-regulated'' proteins which increase disproportionately during rapid growth and include those required for S phase events, components of the translational machinery, and transcription factors (2). Insulin appears to regulate both the initiation and elongation phases of translation (22), presumably by altering the phosphorylation of eukaryotic translation initiation factors (eIF2, eIF2B, eIF3, eIF4B, eIF4E, and eIF4G) and eukaryotic elongation factors (eEF1 and eEF2). (The names of initiation, elongation, and termination factors were revised on 8 April 1995 by an expert panel [Marianne Grunberg-Manago, convener] appointed by the IUBMB Nomenclature Committee. The new names are used in the present article. eIF4G was formerly referred to as either p220, eIF-4␥, or eIF-4F␥.)Despite the large number of protein synthesis factors phosphorylated in response to insulin, the specific effects of these phosphorylations on the overall rate of translation are not known in most cases. One of the best-characterized systems is the phosphorylation of eIF4...