Retrotransposons are important forces in genome remodeling and major components of the genome. They resemble retroviruses in their structure and life cycle but are not known to be infectious. Like retroviruses, these genomic components replicate by a cycle of transcription of the integrated copies, as if they were cellular genes, followed by translation of their encoded products and reverse transcription of the RNA into cDNA. The proteins by the retrotransposon are necessary for the classical life cycle of both retrotransposons and retroviruses. The retroelements are Aselfish@ because they replicate independently of the genome, yet exploit the cellular regulatory circuitry, particularly of stress response. One major difference to the retroviruses is that many plant retrotransposons parasitize others for the key proteins needed for their lifecycle. These groups, more than merely having stop codons that result from replication errors, completely lack protein coding domains and therefore differ from the swarm of individual variants or fossils of autonomous elements. Nevertheless, their polymorphic insertion pattern indicates that they are able to move within genomes. Recently, we and other have identified large, structurally uniform retrotransposon groups in which no member contains the Gag, Pol, or Env internal domains. A spectacular example is a novel group of TRIMs, Cassandra elements, which universally carry conserved 5S rRNA sequences and associated RNA polymerase III promoters in their long terminal repeats. Uniquely, the entire Cassandra elements are transcribed by RNA polymerase II and the 5S rRNA sequences are also transcribed by polymerase III. Cassandra elements are widespread throughout the vascular plants. Predicted RNA folding of the 5S Cassandra regions resemble those for cellular 5S rRNA. We propose to: 1) determine how the Cassandra retrotransposons are moving and find which elements are the active partners, by examination of each step of their life cycle;2) track the fate of Cassandra-encoded 5S rRNA and develop a model for its role;3) examine the role of Cassandra in modulating the expression of cellular genes. A combination of bioinformatic, molecular biological, and cell biological methods will be used, with analyses on the DNA, RNA, and protein levels, combined with 1- and 3-hybrid assays in E. coli and yeast and transformation in tobacco, Arabidopsis, and barley. Advances in genomics in recent years have shown that retrotransposons are far from the â??junkâ? they were initially considered. They are a dynamic component of the genome, affecting both gene expression and overall genome structure. Until very recently, the non-autonomous retrotransposons were considered the junk of the junk. We are now establishing that they are, rather, the parasites of the parasites. It will likely prove that the dynamics of their interaction with the autonomous elements affect genes, genomes, and plants on all scales. One must, therefore, invoke a new framework, â??genome ecology,â? as a model for these systems. Newly identified retroelement parasites such as Cassandra have no coding capacity but appear to exploit not only proteins of other retrotransposons but also those of the cell. Furthermore, the plant cell must regulate the replicative capacity of the retrotransposon to prevent unlimited, disruptive integration of new daughter copies. On the applied level, Cassandra elements are proving to be excellent molecular markers. Analysis of their functionality will aid exploitation in mapping and genome diversity studies. As a parasitic element with no coding capacity, they may prove to be excellent carriers of genes in transformation projects, in a way parallel to retroviral therapy for humans. The work is supported by domestic and international collaborations.
Vastaava tutkija
Schulman Alan Hankkeen kesto 2005 - 2011
Asiasanat
valkuaisaineiden vuorovaikutukset, genomin evoluutio, valkuaisaine-DNA, viruksen kaltaisen partikkelin rankentuminen, vuorovaikutukset, retrotransposoni, genomin evoluutio
Hankkeen vaihe: Päättynyt
HUOM! Tämä tutkimushankekuvaus on tuotettu Hankehaaviin Maa- ja elintarviketalouden tutkimuskeskuksen tutkimustietojärjestelmästä, jota ei enää ylläpidetä. Tarkista ajantaiset tutkimushanketiedot Luonnonvarakeskus Luken järjestelmästä.
|