Characterization of retrotransposons present in virus-like particles extracted from plant tissues

Transposable elements (TEs) are major component of genome. They are fragments of DNA that can insert themselves into new chromosomal locations, and often make duplicate copies of themselves in the process. Among the other TEs, retrotransposons are most active in eukaryotic genome and significantly contribute to shaping genome evolution. Retrotransposons resemble retroviruses but have complete intracellular lifecycle. Retrotransposons are further classified into two major groups-Long Terminal Repeat (LTR) Retrotransposons and Non Long Terminal Repeat (Non LTR). The LTR retrotransposons complete their lifecycle by forming Virus Like Particles (VLPs). The lifecycle of a LTR retrotransposon starts with the transcription of its mRNA and followed by translation where proteins are processed to complete its lifecycle. The proteins are the capsid protein (GAG), aspartic proteinase (AP), integrase (INT), and reverse transcriptase (RT-RH). Like retroviruses, the GAG forms a shell, the virus-like particle (VLP), which packages the nucleic acids of the element and transports them to the nucleus. The proteinase cleaves the polyprotein into the functional proteins, the reverse transcriptase copies the RNA into complementary cDNA, and the integrase inserts the cDNA back into the genome in a new position. The goal of my research work was to extract these VLPs from plant tissues to identify the active retrotransposons. To identify the TEs, my work was divided in two steps-first step was to work with model VLP system in Hordeum vulgare (Barley) to establish a proper protocol for extracting VLPs and second step was to implement that protocol to other plant species. Through my study, we established a working protocol for extracting VLPs from plant tissues and identify BARE 1 retrotransposons and other elements from both copia and gypsy super family of LTR retrotransposons. My work also showed several LINE element products of Non LTR retrotransposons group in the VLPs of Liliaceae plant family. These interesting findings from my thesis work supports that the VLPs are important stage in life cycle of retrotransposons which are significant contributors to the growth in genome size.