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Poly (rC) binding protein 2 forms a ternary complex with the 5'-terminal sequences of poliovirus RNA and the viral 3CD proteinase.

Poly(rC) binding protein 2 (PCBP2) forms a specific ribonucleoprotein (RNP) complex with the 5'-terminal sequences of poliovirus genomic RNA, as determined by electrophoretic mobility shift assay. Mutational analysis showed that binding requires the wild-type nucleotide sequence at positions 20-25. This sequence is predicted to localize to a specific stem-loop within a cloverleaf-like secondary structure element at the 5'-terminus of the viral RNA. Addition of purified poliovirus 3CD to the PCBP2/RNA binding reaction results in the formation of a ternary complex, whose electrophoretic mobility is further retarded. These properties are consistent with those described for the unidentified cellular protein in the RNP complex described by Andino et al. (Andino R, Rieckhof GE, Achacoso PL, Baltimore D, 1993, EMBO J 12:3587-3598). Dicistronic RNAs containing mutations in the 5' cloverleaf-like structure of poliovirus that abate PCBP2 binding show a decrease in RNA replication and translation of gene products directed by the poliovirus 5' noncoding region in vitro, suggesting that the interaction of PCBP2 with these sequences performs a dual role in the virus life cycle by facilitating both viral protein synthesis and initiation of viral RNA synthesis.

3C Viral Proteases↗

Replication of subgenomic hepatitis A virus RNAs expressing firefly luciferase is enhanced by mutations associated with adaptation of virus to growth in cultured cells.

Replication of hepatitis A virus (HAV) in cultured cells is inefficient and difficult to study due to its protracted and generally noncytopathic cycle. To gain a better understanding of the mechanisms involved, we constructed a subgenomic HAV replicon by replacing most of the P1 capsid-coding sequence from an infectious cDNA copy of the cell culture-adapted HM175/18f virus genome with sequence encoding firefly luciferase. Replication of this RNA in transfected Huh-7 cells (derived from a human hepatocellular carcinoma) led to increased expression of luciferase relative to that in cells transfected with similar RNA transcripts containing a lethal premature termination mutation in 3D(pol) (RNA polymerase). However, replication could not be confirmed in either FrhK4 cells or BSC-1 cells, cells that are typically used for propagation of HAV. Replication was substantially slower than that observed with replicons derived from other picornaviruses, as the basal luciferase activity produced by translation of input RNA did not begin to increase until 24 to 48 h after transfection. Replication of the RNA was reversibly inhibited by guanidine. The inclusion of VP4 sequence downstream of the viral internal ribosomal entry site had no effect on the basal level of luciferase or subsequent increases in luciferase related to its amplification. Thus, in this system this sequence does not contribute to viral translation or replication, as suggested previously. Amplification of the replicon RNA was profoundly enhanced by the inclusion of P2 (but not 5' noncoding sequence or P3) segment mutations associated with adaptation of wild-type virus to growth in cell culture. These results provide a simple reporter system for monitoring the translation and replication of HAV RNA and show that critical mutations that enhance the growth of virus in cultured cells do so by promoting replication of viral RNA in the absence of encapsidation, packaging, and cellular export of the viral genome.

5' Untranslated Regions↗

A database analysis method identifies an endogenous trans-acting short-interfering RNA that targets the Arabidopsis ARF2, ARF3, and ARF4 genes.

Two classes of small RNAs, microRNAs and short-interfering RNA (siRNAs), have been extensively studied in plants and animals. In Arabidopsis, the capacity to uncover previously uncharacterized small RNAs by means of conventional strategies seems to be reaching its limits. To discover new plant small RNAs, we developed a protocol to mine an Arabidopsis nonannotated, noncoding EST database. Using this approach, we identified an endogenous small RNA, trans-acting short-interfering RNA-auxin response factor (tasiR-ARF), that shares a 21- and 22-nt region of sequence similarity with members of the ARF gene family. tasiR-ARF has characteristics of both short-interfering RNA and microRNA, recently defined as tasiRNA. Accumulation of trans-acting siRNA depends on DICER-LIKE1 and RNA-DEPENDENT RNA POLYMERASE6 but not RNA-DEPENDENT RNA POLYMERASE2. We demonstrate that tasiR-ARF targets three ARF genes, ARF2, ARF3/ETT, and ARF4, and that both the tasiR-ARF precursor and its target genes are evolutionarily conserved. The identification of tasiRNA-ARF as a low-abundance, previously uncharacterized small RNA species proves our method to be a useful tool to uncover additional small regulatory RNAs.

Arabidopsis↗

Relationship between structure of the 5' noncoding region of viral mRNA and efficiency in the initiation step of protein synthesis in a eukaryotic system.

To determine whether the rate of protein synthesis is controlled by the structure of mRNA near its 5' terminus, protein-synthesizing ability, especially in its initial stage, was compared among RNAs of plant viruses. Those viruses used here contain several definite pieces of single-stranded RNA. Each of these RNAs acts as a messenger. Cucumber mosaic virus (CMV) RNA 5 synthesizes a small amount of a protein, Mr 7000, in an in vitro protein-synthesizing system from wheat germ or reticulocyte. Brome mosaic virus (BMV) RNA 4 synthesizes a large amount of a coat protein under the same conditions. Both RNAs have the same 5'-cap structure and a short noncoding region (10 nucleotides in CMV RNA 5 and 9 in BMV RNA 4) between the 5' terminus and the initiation codon AUG. A sequence complementary to the 3' terminal of 18S ribosomal RNA is contained in BMV RNA 4 but is not apparent in CMV RNA 5. Formation of the initiation complex for protein synthesis by the 5'-terminal-labeled mRNA of cytoplasmic polyhedrosis virus was inhibited by the addition of unlabeled BMV RNA 4 whereas it was only slightly inhibited by unlabeled CMV RNA 5. BMV RNA 4, which has a sequence complementary to rRNA, can form the initiation complex more easily than CMV RNA5. It is concluded that an apparent complementary sequence in the 3' terminal of 18S rRNA in the 5' noncoding region of eukaryotic mRNA and the 5'-cap structure enhance the rate of initiation complex formation in protein synthesis.

Base Sequence↗

Intrafamilial transmission of hepatitis-C virus among the population of an endemic area of Japan.

OBJECTIVES: To assess the role of intrafamilial transmission of hepatitis C virus (HCV) among general populations. DESIGN AND SETTING: Cross-sectional study in an HCV-endemic area of Japan. PARTICIPANTS: A total of 1122 residents (mean age, 41.7 years; range, 0 to 80 years), including 359 mother-child pairs and 234 pairs of spouses. MAIN OUTCOME MEASURES: Antibody to HCV (anti-HCV) was examined using second-generation anti-HCV testing by passive hemagglutination assay. Hepatitis C virus RNA was detected by polymerase chain reaction with primers deduced from the 5'-noncoding region and HCV genotypes by reaction with type-specific primers deduced from the HCV core gene. RESULTS: Prevalence of anti-HCV was 14.1% (158/1122), and HCV RNA was detected in 82.9% of those who tested positive for anti-HCV. Prevalence of anti-HCV increased with advancing age, but no anti-HCV was found among 312 persons younger than 20 years. Of the 53 children with anti-HCV-positive mothers, three were positive for anti-HCV, all were older than 20 years, and all had a history of surgical treatment. Hepatitis C virus RNA was found in one mother-child pair but with different HCV genotypes. Both spouses were positive for anti-HCV in 17 of 234 pairs. Of the 11 pairs of spouses in whom the HCV genotypes of both were determined, five had different HCV genotypes. CONCLUSIONS: While HCV is highly endemic in this area, neither vertical nor horizontal transmission between spouses seems to play an important role in its spread. The incidence of intrafamilial transmission of HCV seems to be low.

Adolescent↗

Cloning of mouse carbonic anhydrase mRNA and its induction in mouse erythroleukemic cells.

Mouse carbonic anhydrase mRNA was detected in poly(A+) RNA of anemic spleens sedimenting as a RNA species at 14 S. Subsequently, poly(A+) RNA (12-16 S) was used as a template for the synthesis of double-stranded cDNA, which was inserted into the PstI site of pBR322 by oligo-dG:dC tailing. A recombinant plasmid containing carbonic anhydrase cDNA was identified by a positive hybridization selection assay and by partial DNA sequencing. Predicted amino acid sequences showed homology with the known sequences of rabbit and human carbonic anhydrase I and II. The clone contained sequences for most of the coding region and 600-700 base pairs at the 3' noncoding region of the mRNA. Hybridization analysis of poly(A+) RNA from uninduced and induced mouse erythroleukemic cells labeled for short and long time periods indicated that induction results in an increase of carbonic anhydrase mRNA in newly synthesized RNA.

Animals↗

Absence of persistent infection with enteroviruses in muscles of patients with inflammatory myopathies.

We searched for enteroviral nucleic acid sequences using the polymerase chain reaction and slot-blot hybridization in coded muscle biopsy specimens from 39 patients with active inflammatory myopathies (polymyositis, dermatomyositis, and inclusion-body myositis) and from 16 patients with other neuromuscular diseases, including patients with postpolio syndrome. For primers, we used sequences of the noncoding region at the 5' end of the viral RNA. We failed to detect specific enteroviral nucleic acid sequences in the muscle biopsy specimens. Because this sensitive technique can amplify even low copy numbers of the viral genome, it appears unlikely that a persistent enteroviral infection is the cause of inflammatory myopathies.

Base Sequence↗

Yellow fever 5' noncoding region as a potential element to improve hepatitis C virus production through modification of translational control.

The lengthy 5' noncoding region (5' NCR) of hepatitis C virus (HCV) RNA forms a highly ordered secondary structure, very conserved among different strains. It includes an internal ribosome entry site (IRES) element, responsible for the cap-independent translation initiation of HCV RNA. Similarly to the IRES of hepatitis A virus (HAV), another human hepatitis virus, HCV IRES, activity in internal initiation of translation is weak. Furthermore, both viruses exhibit a poor growth phenotype that may result at least partially from an inhibitory control of translation. To enhance HCV translation, as a preliminary step in designing constructs for improvement in viral production, we sought to evaluate a chimeric construct containing the yellow fever virus (YFV) 5' NCR fused to the initiation codon of the HCV coding sequence. YF viral RNA, as the majority of eukaryotic messenger RNAs, is translated by a ribosome scanning mechanism in a cap-dependent manner. The efficiency of translation initiation of the parental HCV construct was compared in vitro in rabbit reticulocyte lysates with that of the chimeric construct containing YFV 5' NCR. Surprisingly, the related distanced YFV 5' NCR was fivefold more active than was the wild-type HCV IRES in directing that function. Furthermore, chimeric transcripts were shown to be effective in vivo after transfection of eukaryotic cells. Taken together, these results raise the following question: why has the HCV genus evolved to the acquisition of an IRES element within its 5' NCR among the Flaviviridae family?

5' Untranslated Regions↗

Down-regulation of reduced folate carrier gene (RFC1) expression after exposure to methotrexate in ZR-75-1 breast cancer cells.

Methotrexate (MTX) is administered in intervals of one week or longer in the treatment of cancer and autoimmune disease. Early studies suggested that daily MTX administration was associated with decreased effectiveness and increased toxicity, leading to schedules of administration that include periodic intervals of rest during chronic MTX therapy. We hypothesized that these observations may be the result of the down-regulation of the reduced folate carrier, the major route of cellular uptake of both MTX and the endogenous folates, after MTX exposure. We exposed folate-depleted ZR-75-1 breast cancer cells to low-dose MTX in the presence of hypoxanthine, adenosine and thymidine. After 72 h, the initial rate of MTX uptake had decreased to 22% of the Day 0 value. Western blot analysis showed down-regulation of RFC1 protein expression, and Northern blot analysis showed a corresponding decrease in RFC1 RNA levels. Using an RT-PCR assay, we found that levels of RNA transcripts containing each of the three RFC1 5' noncoding exons were decreased after exposure to MTX, suggesting that MTX exposure causes transcriptional down-regulation of RFC1. Promoter-reporter construct assays demonstrated decreased activity of RFC1 promoter elements upstream of these exons after MTX exposure. Preexposure of the ZR-75-1 cells to 5-azacytidine, a DNA methylation inhibitor, further decreased MTX uptake rather than reverse the inhibition of RFC1 activity, indicating that RFC1 down-regulation after MTX exposure is not the result of methylation of the RFC1 promoter. In summary, these studies demonstrate that MTX exposure can down-regulate RFC1 expression and activity. These acute, inducible, epigenetic changes in RFC1 expression may ultimately be molded into the more permanent genetic changes that result in the transport-mediated MTX resistance that have been observed in MTX-resistant cell lines.

Antimetabolites, Antineoplastic↗

Nucleotide sequence of the Aspergillus niger trpC gene: structural relationship with analogous genes of other organisms.

The nucleotide sequence of the Aspergillus niger tryptophan C (trpC) gene was determined. Northern hybridization and S1-mapping experiments showed the presence of a 2.6 kb trpC poly(A)+ RNA with two very short (5 and 6 nucleotides) noncoding 5'-regions. Comparison of the predicted amino acid sequence with that of trp gene proteins of pro- and eukaryotic organisms revealed three functional domains (G, C, F) in the A. niger TrpC protein which catalyse the glutamine amidotransferase reaction (GAT), the indole-3-glycerol phosphate synthase reaction (IGPS) and the N-(5'-phosphoribosyl) anthranilate isomerase reaction (PRAI), respectively. These domains are highly conserved and bordered by short areas showing less homology. Within the F domain of the trpC gene in A. niger, A. nidulans and Neurospora crassa, a region encoding 30 amino acids was found which is absent in the analogous genes of Saccharomyces cerevisiae and prokaryotic organisms. This region has features of a mutated in-phase intron.

Amino Acid Sequence↗

Sequence analysis of the 5' non coding region of Turkish HCV isolates: implications for PCR diagnosis.

Hepatitis C virus (HCV) is a positive-strand RNA virus related to pestiviruses and flaviviruses. The 5' noncoding region (NCR) of the virus genome consists of 324-341 nucleotides and is generally highly conserved among different HCV isolates which has made this region the choice for primer selection in amplification of HCV sequences by polymerase chain reaction (PCR). In this study, we report the partial nucleotide sequences of the 5'-NCR from type 1a (n = 4), type 1b (n = 6) and type 4 (n = 1) Turkish HCV isolates. Sequence information was obtained by direct sequencing of RT-PCR product using biotinylated primers and single strands were sequenced using T7 DNA polymerase after binding to streptavidin coated magnetic beads. In comparison to prototype type 1a consensus sequence, all type 1b sequences had A-G substitution at position - 99. Nucleotid changes from the prototype 1a sequence were found in 12 of the 174 nucleotide positions. The most variable domain spans 51 nucleotides (positions - 167 to - 117) where nine polymorphic sites were identified. Although the nucleotide sequence of the 5'-noncoding region is highly conserved there are type-specific polymorphic sites within this region that has to be taken into consideration in the design of oligonucleotide primers for reliable amplification of sequences from different HCV genotypes.

Journal Article↗

Norepinephrine transporter splice variants and their interaction with substrates and blockers.

Norepinephrine transporter (NET), a member of the Na+/Cl--dependent neurotransmitter transporter family, displays species-specific isoforms produced by alternative RNA splicing. This occurs at 3'-flanking coding and noncoding regions, resulting in different carboxy-terminals. When these NET splice variants were expressed in cultured cell lines, the characteristics of substrate transport and the sensitivity to uptake inhibitors differed between isoforms. The different functional expression suggests the physiological importance of the action and interaction of NET splice variants in synaptic transmission.

Alternative Splicing↗

Exportin-5 orthologues are functionally divergent among species.

Exportin-5, an evolutionarily conserved nuclear export factor belonging to the importin-beta family of proteins, is known to play a role in the nuclear export of small noncoding RNAs such as precursors of microRNA, viral minihelix RNA and a subset of tRNAs in mammalian cells. In this study, we show that the exportin-5 orthologues from different species such as human, fruit fly and yeast exhibit diverged functions. We found that Msn5p, a yeast exportin-5 orthologue, binds double-stranded RNAs and that it prefers a shorter 22 nt, double-stranded RNA to approximately 80 nt pre-miRNA, even though both of these RNAs share a similar terminal structure. Furthermore, we found that Drosophila exportin-5 binds pre-miRNAs and that amongst the exportin-5 orthologues tested, it shows the highest affinity for tRNAs. The knockdown of Drosophila exportin-5 in cultured cells decreased the amounts of tRNA as well as miRNA, whereas the knock down of human exportin-5 in cultured cells affected only miRNA but not tRNA levels. These results indicate that double-stranded RNA binding ability is an inherited functional characteristic of the exportin-5 orthologues and that Drosophila exportin-5 functions as an exporter of tRNAs as well as pre-miRNAs in the fruit fly that lacks the orthologous gene for exportin-t.

Animals↗

Molecular cloning and characterization of alternatively spliced mRNA isoforms from psoriatic skin encoding a novel member of the S100 family.

In an effort to identify psoriasis-associated genes, we compared gene expression in normal and psoriatic skin, using differential display RT-PCR technique. Sequence analysis of a 650-bp cDNA fragment (clone 110) that was highly up-regulated in lesional skin revealed homology to a noncoding cDNA (NICE-2). By subsequent cDNA cloning, using RNA from psoriatic skin, we have identified two alternatively spliced mRNA-isoforms (0.5 and 4.4 kb), which differ in composition of their untranslated regions. By sequence comparison, we have mapped the novel gene, named S100A15, to the S100 gene cluster within the epidermal differentiation complex (chromosome 1q21). Analysis of the deduced amino acid sequence revealed a protein of 101 amino acids containing two potential EF-hand motifs with high homology to the S100A7. Northern blot hybridization and semiquantitative RT-PCR analysis confirmed the S100A15 overexpression in psoriasis, showing different levels of expression of the S100A15 mRNA isoforms. In situ hybridization of the S100A15 revealed a markedly increased staining of basal and suprabasal epidermal layers of psoriatic skin compared with healthy tissue. Our data suggest an involvement of the novel S100A15 in epidermal differentiation and inflammation and might therefore be important for the pathogenesis of psoriasis and other diseases.

Alternative Splicing↗

Mutational analysis of the promoter required for influenza virus virion RNA synthesis.

An in vitro RNA synthesis system was established in which the influenza virus virion (minus-sense) RNA was made from the synthetic plus-sense RNA (cRNA) template by the purified viral polymerase complex. The cRNA promoter was studied by mutational analysis using the in vitro system, and on the basis of these experiments, the first 11 nucleotides of the 3' noncoding sequence were found to contain the minimum promoter required for virion RNA synthesis. The addition of extra nucleotides at the 3' end decreased the promoter activity of the templates, indicating that the viral polymerase does not recognize an internal promoter efficiently. The wild-type and mutated RNA templates were also tested in vivo by using the ribonucleoprotein transfection system. In contrast to the in vitro system, it was found that the majority of mutations at the 3'-terminal sequence significantly decreased or abolished chloramphenicol acetyltransferase (CAT) expression. These results suggest that the cRNA promoter overlaps other essential cis elements required for chloramphenicol acetyltransferase expression in vivo.

Base Sequence↗

Nucleotide sequence of a cDNA encoding rat protamine and the haploid expression of the gene during rat spermatogenesis.

The nucleotide sequence of a 342-base cDNA encoding the rat protamine has been determined. This insert, isolated from a rat testis cDNA library, encodes a polypeptide of 50 amino acids of which 29 are arginine 9 are cysteine and 2 are tyrosine. The insert contains the complete 3'-noncoding region of 170 bases and 18 bases of the 5'-noncoding region. Hybridization of the protamine cDNA with the RNA prepared from testes of prepubertal and sexually mature rats revealed that protamine mRNA is first detectable as a 600 nucleotide long molecule in the 35-day old testis containing around 15% of round spermatids but not in testis of younger animals. The RNA of 50-day old and sexually mature rats was found to contain a second protamine mRNA which is around 500 nucleotides in length. Hybridization of the protamine cDNA with the RNA of isolated spermatids of the mature testis resulted in 2 prominent hybridization signals (600 and 500 bp) while the faint signal obtained with the RNA of pachytene spermatocytes (600 bp) was found to be due to contamination of the cell preparation by spermatids. After digestion of the mRNAs with ribonuclease H a single hybridization band even smaller than 500 nucleotides was obtained. As demonstrated on testis sections the transcripts are confined to the central layers of the tubuli seminiferi corresponding to the spatial arrangement of corresponding to the spatial arrangement of postmeiotic cells. The results indicate that the protamine gene in the rat is postmeiotically expressed and that the mRNA undergoes post-transcriptional processing that includes a reduction in molecular size with respect to the poly-(A)+ tail.

Amino Acid Sequence↗

Specific inhibition of hepatitis C viral gene expression by antisense phosphorothioate oligodeoxynucleotides.

The inhibitory effect of antisense phosphorothioate oligodeoxynucleotides (S-ODN) on hepatitis C viral gene expression and analyzed in an in vitro test system and in cell culture. S-ODN were directed against different stem loop structures in the 5'noncoding region (NCR) of the hepatitis C virus, (HCV) RNA and against a nucleotide stretch, including the start codon of the polyprotein precursor. The inhibitory effect of these S-ODN was quantified employing a viral RNA consisting of the first 407 nucleotides of a HCV type 1b genome fused to the coding sequence of the firefly luciferase gene. For in vitro assays this RNA was generated by in vitro transcription and used as a template in a rabbit reticulocyte lysate in vitro translation system. The production of active luciferase in the absence or presence of S-ODN was monitored using an enzymatic assay. The best results were obtained with S-ODN 4 directed against nucleotides 326 to 348, comprising the start AUG of the polyprotein coding sequence. With this oligonucleotide, a specific and dose-dependent effect was observed with a maximal inhibition of 96 +/- 1% at a S-ODN concentration of 4.14 mumol/L. For cell culture experiments, the hepatoblastoma cell line HepG2 was transfected with a plasmid expressing the HCV-luciferase fusion RNA. In this assay system S-ODN 2, complementary to nucleotides 264 to 282 of the HCV RNA, and S-ODN 4 were most efficient and reduced the viral translation by 96 +/- 0.4% and 94 +/- 0.7%, respectively, at a concentration of 0.3 mumol/L. The inhibition was specific (1) because the expression of the HCV-luciferase fusion RNA was not significantly impaired by the control S-ODN and (2) because the expression of an unrelated messenger RNA was not or only slightly downregulated. These data suggest that HCV gene expression can be inhibited effectively by antisense S-ODN. Therefore, this approach represents a promising perspective for the treatment of hepatitis C.

Base Sequence↗

Development of a recombinant RNA technique for the construction of chimeric RNA with a long poly(C) tract.

The murine cardioviruses and bovine aphthoviruses are distinguished from other (+) strand RNA viruses by their long poly(C) tract in the 5'-noncoding region. The presence of this poly(C) tract has long hampered the construction of full-length cDNA with the complete poly(C) tract, because long poly(dC-dG) homopolymer-containing plasmids are difficult to amplify in bacterial systems. To overcome this problem, we constructed a chimeric RNA by joining the poly(C) region of the viral RNA to the 5'-truncated RNA transcript of the encephalomyocarditis (EMC) virus cDNA. The non-chimeric, recombinant EMC virus with a short poly(C) tract produces recombinant progeny virus, but this is not pathogenic in vivo. On the other hand, the EMC viral RNA chimera with the complete poly(C) tract produces recombinant progeny virus that is pathogenic in vivo. This method of viral RNA construction will be invaluable for functional studies of other cardioviruses and aphthoviruses, as well as for recombinant RNA manipulations.

Animals↗