A computational bioinformatics approach to identifying possible LINE1 reverse transcriptase-like domains in Aplysia californica

Abstract:

Recent research uncovered LINE1 (Long-Interspersed Nuclear Elements) or L1’s, a group of retrotransposons, as a key contributor to neural genome diversity, and playing a role in learning and memory. L1 is a class I retrotransposon that encodes two open reading frames: ORF1 encoding a RNA chaperone protein; and ORF2, which encodes an endonuclease and reverse transcriptase. Further, inhibiting L1 retrotransposition in mice blocked long-term fear conditioning memories via the use of lamivudine, a common nucleoside reverse transcriptase inhibitor that also inhibits L1 activity. Determining the presence of L1 transposable elements in other organisms presents a novel research program in understanding the fundamental mechanisms involved in long-term memory. L1 reverse transcriptase (RT)-like domains were located in the sea slug ​Aplysia californica​ using the NCBI Conserved Domains Database and NCBI Blastx programs. Pairwise comparisons were performed between the nucleotide and peptide sequences of a known ORF2 L1 RT element in ​Mus musculus ​and uncharacterized L1 RT-like domains in ​A. californica​. Pairwise comparison data showed percent identities in nucleotide L1 RT-like domains to be higher than 40% and peptide comparison values higher than 20%. These analyses may support the claim that L1 RT-like domains in ​A. californica​ can be manipulated by lamivudine and other reverse transcriptase drugs to elucidate the contribution of L1 retrotransposition to the expression of memory.