Duchenne muscular dystrophy (DMD) is an X-linked recessive disorder resulting in progressive degeneration of the muscle. It affects about 1 in 3,500 male children. Becker's muscular dystrophy is a less severe disease allelic to DMD. Some 30% of DMD patients suffer from various degrees of mental retardation. The giant DMD gene spans about 2,000 kilobases and codes for a 14-kilobase messenger RNA and a protein of molecular weight 427,000. DMD mRNA is most abundant in skeletal and cardiac muscle and less so in smooth muscle. We reported that the expression of the gene is developmentally regulated during the differentiation of primary muscle cultures and in myogenic cell lines in a way similar to the expression of muscle-specific genes such as myosin light chain 2 and skeletal muscle actin. Similar results have been obtained with human primary myogenic cells. Significant levels of DMD mRNA are found in brain tissue. Here we show that the transcript of the DMD gene and the amino terminal of the encoded protein differ in brain and muscle. The 5' ends of these mRNA species are derived from different exons. The results suggest that the two mRNA types are transcribed from different promoters.

A cDNA library was derived from the poly(A)(+) RNA of young tomato leaves. The library was cloned in a λgt11 system and screened by synthetic oligonucleotide probes having sequences that match the codes of conserved regions of amino acid sequences of Cu,Zn superoxide dismutase (SOD) proteins from a wide range of eukaryotic organisms. Two cDNAs were isolated, cloned and sequenced. One of the cDNAs, P31, had a full-size open reading frame of 456 bp with a deduced amino acid sequence having an 80% homology with the deduced amino acid sequence of the cytosolic SOD-2 cDNA of maize. The other cDNA, T10 (extended by T1), had a 651 bp open reading frame that revealed, upon computer translation, 90% homology to the amino acid sequence of mature spinach chloroplast SOD. The 5' end of the reading frame seems to code for a putative transit peptide. This work thus suggests for the first time an amino acid sequence for the transit peptide of chloroplast SOD. Northern hybridizations indicated that each of the P31 and T10 clones hybridized to a blotted poly(A)(+) RNA species. These two species are differentially expressed in the plant organs: e.g., the species having the T10 sequence was detected in the leaves but not in roots, while the one with the P31 sequence was expressed in both leaves and roots. The cDNA clones P31 and T10 were also hybridized to Southern blots of endonuclease fragmented tomato DNA. The clones hybridized to specific fragments and no cross hybridization between the two clones was revealed under stringent hybridization conditions; the hybridization pattern indicated that, most probably, only one locus is coding for each of the two mRNA species.

The molecular events leading to the second template switch during reverse transcription of the HIV genome were studied in a defined in-vitro system. In order to investigate displacement of the tRNA(lys) primer from the primer binding site (PBS) of the viral genomic RNA, following DNA synthesis, we produced an HIV RNA/DNA substrate that resembles the intermediate reverse transcription complex formed prior to the second template switch. Partial tRNA(lys) primer displacement was observed during plus (+) strand DNA synthesis and during minus (-) strand DNA elongation. We found two determinants that may serve as a stop signal for (+) DNA strong stop synthesis, the A(m) at position 19 of the natural tRNA(lys) and the secondary structure at the PBS sequence. The later signal appears to constitute a stronger terminator in-vitro. The 3' end of the nascent (-) DNA strand prior to the second template switch was also determined. It was mapped to the U5-PBS junction at the site for the first endonucleolytic cut introduced by the RNase H activity of the HIV reverse transcriptase (RT). Thus, different signals dictate the arrest of (-) and (+) nascent DNA synthesis. These stop signals appear to be required for the subsequent second template switch. However, an excess of (-) DNA "acceptor" molecules, having a 18-base sequence complementary to the (+) DNA "donor" template, was required to demonstrate the actual template switch in the in-vitro system. Taken together these results indicate that the reverse transcriptase can catalyze all the steps leading to the second template switch and auxiliary viral proteins may act to enhance the efficiency of this step during the reverse transcription process.

An in situ gel assay was applied to the study of double stranded RNA dependent RNase activity associated with reverse transcriptase (RT) of HIV-1 and murine leukemia virus. Polyacrylamide gels containing [32P] RNA/RNA substrate were used for electrophoresis of proteins under denaturing conditions. The proteins were renatured and in situ enzymatic degradation of 32P-RNA/RNA was followed. E. coli RNaseIII, but not E. coli RNaseH, was active in this in situ gel assay, indicating specificity of the assay to RNA/RNA dependent nucleases. Analysis of purified preparations of HIV-1 RT p66/p51 expressed in E. coli demonstrated an RNA/RNA dependent RNase activity comigrating with the large subunit (p66) of the enzyme. In addition, this activity of the RT was often accompanied by a contaminating RNA/RNA dependent RNase, with a molecular weight approximately 30,000 dalton identical to that of E. coli RNaseIII. As the p51 small subunit of HIV-1 RT and a mutant of RT p66/p51, at Glutamic acid #478, did not exhibit RNA/RNA dependent RNase activity, at least part of the active site of the RNA/RNA dependent RNase activity appeared to reside at the carboxy end of the molecule. As these RT proteins are also deficient of RNaseH, our results suggest overlapping or identical catalytic sites for degradation of the substrates RNA/DNA and RNA/RNA.

Early events in the retroviral replication cycle include the conversion of viral genomic RNA into linear double-stranded DNA. This process is mediated by the reverse transcriptase (RT), a multifunctional enzyme that possesses RNA-dependent DNA polymerase, DNA-dependent DNA polymerase, and RNase H activities. In the course of studies of a recombinant RT of human immunodeficiency virus type 1 (HIV-1), we observed an additional, unexpected activity of the enzyme. The purified RT catalyzes a specifiC cleavage in HIV-1 RNA hybridized to tRNALYS, the primer for HIV-1 reverse transcription. The cleavage at the primer binding site (PBS) of HIV RNA is dependent on the double-stranded structure of the HIV RNA-tRNALys complex. This RNase activity appears to be distinct from the RNase H activity of HIV-1 RT, as the substrate specificity and the products of the two activities are different. Moreover, Escherichia coli RNase H and avian myeloblastosis virus RT are unable to cleave the IIV RNAtRNALYs complex. We refer to this unusual activity as RNase D. Two lines of evidence indicate that the specific RNase D activity is an integral part of recombinant Hil RT. The specific RNase D activity comigrates with the other RT activities, DNA polymerase, and RNase H upon filtration on a Superose 6 gel column or chromatography on a phosphocellulose column. Moreover, three recombinant HIV-1 RT preparations expressed and purified in different laboratories by various procedures exhibit RNase D activity. Sequence analysis indicated that RNase D activity cleaves the substrate HIV-1 RNAtRNALYS at two distinct sites within the PBS sequence 5'-UGGCGCCCGA | ACAG I GGAC-3'. The sequence specificity of RNase D activity suggests that it might be involved in two stages during the reverse transcription process: displacement of the PBS to enable copying of tRNALS sequences into plus-strand DNA or to facilitate the second template switch, which was postulated to occur at the PBS sequence.The reverse transcriptase (RT) of human immunodeficiency virus (HIV), like the enzyme of other retroviruses, exhibits several activities: RNA-and DNA-directed DNA synthesis (1-3), RNase H (4, 5), and tRNALYS binding (6, 7). These well-characterized activities participate in various stages of double-stranded proviral DNA synthesis. The synthesis of the first strand, minus-strand DNA, is primed by a tRNALYS of cellular origin hybridized to the viral genomic RNA at a complementary sequence of 18 nucleotides, the primer binding site (PBS) (8). Synthesis of the plus-strand DNA is primed by an oligoribonucleotide of virus origin hybridized to the nascent minus-strand DNA, which now serves as a template (9, 10). To produce a proviral DNA with two long terminal repeats, the enzyme has to switch templates at two stages of the reverse transcription process: during synthesis of minusstrand DNA the enzyme jumps from the 5' end to the 3' end of the RNA template and, to complete synthesis of the double-stranded proviral DNA, the enzyme switches templates at the region of the...