Ty elements transpose through an RNA intermediate

During these last years, a powerful methodology has been developed to study the secondary and tertiary structure of RNA molecules either free or engaged in complex with proteins. This method allows to test the reactivity of every nucleotide towards chemical or enzymatic probes. The detection of the modified nucleotides and RNase cleavages can be conducted by two different paths which are oriented both by the length of the studied RNA and by the nature of the probes used. The first one uses end-labeled RNA molecule and allows to detect only scissions in the RNA chain. The second approach is based on primer extension by reverse transcriptase and detects stops of transcription at modified or cleaved nucleotides. The synthesized cDNA fragments are then sized by electrophoresis on polyacrylamide:urea gels. In this paper, the various structure probes used so far are described, and their utilization is discussed.

Probing the structure of RNAs in solution

Formation of the pool of covalently closed circular viral DNA in hepadnavirus-infected cells

https://people.healthsciences.ucla.edu/institution/publication-download?publication%5fid=84885

Polyglutamine-Expanded Human Huntingtin Transgenes Induce Degeneration of Drosophila Photoreceptor Neurons

As is the case for some other RNA viruses, the amino acid sequences of retroviral proteins change at an astonishing rate. For example, the proteases of the human immunodeficiency virus (HIV) and the visna lentivirus with which it is often compared are as different as the proteases of fungi and mammals, and those of the human type I leukemia virus are as different from HIV or visna as are the proteins of humans and bacteria. That the sequences of retrovirus proteins can be recognized as sharing common ancestry with non-retroviral proteins implies that the vastly accelerated change has begun only recently or occurs very sporadically. Only a scheme whereby exogenous retroviruses exist as short-lived bursts upon a backdrop of germline-encoded endogenous viruses is consistent with the sequence data. Retroviruses are related to many other reverse transcriptase-bearing entities present in the genomes of eukaryotes. They also have proteins that are homologous with those of some plant and animal DNA viruses, and t...

Origins and evolutionary relationships of retroviruses.

The presence in cultured Drosophila melanogaster cells of retrovirus-like particles containing 5 kilobase RNA molecules homologous to the transposable element copia provides support for the suggested evolutionary relationship between retroviruses and eukaryotic movable genetic elements.

Retrovirus-like particles containing RNA homologous to the transposable element copia in Drosophila melanogaster.

We have shown previously that Drosophila cells contain virus-like particles (VLPs) containing 5-kilobase (kb) RNA that hybridizes to a transposable element, termed copia. We have suggested that VLPs and copia are derivatives of viral particles and proviral forms, respectively, of 'copia' retrovirus, a putative Drosophila retrovirus. To further clarify the relationship between copia and copia-related RNA in VLPs (VLP H-RNA), we determined and compared their nucleotide sequences. VLP H-RNA was found to be an unspliced, genome-sized transcript of copia, and, like retroviral genome RNA, VLP H-RNA is terminally redundant with termini localized in the long terminal repeats (LTRs) of copia. VLP H-RNA contains two long open reading frames (ORFs), one of which includes the coding sequence for a predominant VLP protein of relative molecular mass (Mr) 31,000 (31K). Here we show that, in contrast to 17.6 ORF2, ORFs of copia have no extensive amino-acid sequence homology to the RT region of the reverse transcriptase of retrovirus in vertebrates. Because of a one-base insertion/deletion, the two ORFs in VLP H-RNA are fused and become a single, longer ORF in a genomic copia.

The nucleotide sequences of copia and copia-related RNA in Drosophila virus-like particles.

Drosophila cells contain virus-like particles (VLPs) containing 5 kilobases (kb) of RNA (VLP H-RNA) homologous to the transposable element copia1. The identity between VLP H-RNA and copia DNA has previously been confirmed at the nucleotide sequence level2 and reverse transcriptase activity is also detected in the VLPs1. These results suggest that VLPs and copia are derivatives of viral particle and provirus forms, respectively, of the copia retrovirus-like particle. If the copia retrovirus-like particle replicates by a mechanism similar to the mechanism of vertebrate retroviral replication, a cellular transfer RNA would prime synthesis of the first DNA strand. We show that this is indeed so but that copia retrovirus-like particle has a novel type of priming mechanism; the first DNA extension does not start from the 3′ end of a tRNA, but from an internal site (two nucleotides after the anticodon loop) of the Drosophila initiator methionine tRNA (tRNAiMet)

Unusual priming mechanism of RNA-directed DNA synthesis in copia retrovirus-like particles of Drosophila.

Localization of A protein in the RNA-A protein complex of RNA phage MS2.

PREPARATIONS of the three components of RNA phage—RNA, coat protein and maturation protein (A protein)—have been used in several attempts to reconstitute the particles in vitro1–7. Particles recovered so far have been similar to authentic particles with respect to S value, morphology and other properties. We have now reconstituted a complex, by mixing RNA and A protein only, which can infect Escherichia coli regardless of its small S value, 28S.

Tadayoshi Shiba

Papers

Retrovirus-like particles containing RNA homologous to the transposable element copia in Drosophila melanogaster.

The nucleotide sequences of copia and copia-related RNA in Drosophila virus-like particles.

Unusual priming mechanism of RNA-directed DNA synthesis in copia retrovirus-like particles of Drosophila.

Localization of A protein in the RNA-A protein complex of RNA phage MS2.

New type of infectious complex of E. coli RNA phage.