Structure and Function of the First Open Reading Frame (ORF1) Protein Encoded by the Human LINE-1 Retrotransposon

Abstract

L1 is an autonomous retrotransposable element that replicates to high copy number and has generated over 40% of mammalian DNA. L1 retrotransposition in mammals is a significant source of genetic diversity and defects. Since L1 elements are deleterious and have been subject to negative selection, a major question is how does L1 persist despite its genetic load on the host.

The architecture of an active L1 element consists of a promoter in the 5'UTR, two open reading frame proteins (ORF1p and ORF2p), and a 3'UTR with unknown function. The two L1-encoded proteins are required for L1 replication. ORF2p functions as the L1 replicase. Mouse ORF1p was shown to bind nucleic acids with high affinity and has nucleic acid chaperone activity. Paradoxically, nucleic acid chaperones promote the melting and annealing of nucleic acids. The nucleic acid chaperone activity of ORF1p has been proposed to play a role in L1 replication during assembly of the L1 replication complex. However, the mechanism by which ORF1p promotes this process is not understood.

By studying the sequence evolution of the active L1 lineage over the last 25 million years of human evolution, our laboratory identified that ORF1p underwent an episode of adaptive evolution. Specifically, the coiled coil domain, which mediates trimerization of ORF1p monomers, acquired more amino acid substitutions than would be expected by chance, a phenomenon that reflects positive selection. Positive selection often indicates adaption or the adjustment of an organism to its environment, i.e., the host. It is possible that the biochemical properties of ORF1p were altered in response to changes in the host or competition between L1 families.

I examined the biochemical consequences of positive selection by determining if the adaptive changes affected ORF1p function. I found that the adaptive changes did not affect the measurable biochemical properties of the protein. These properties are highly conserved. My results are consistent with the studies published on the mouse protein. However, in studying the biochemistry of human ORF1p I made several unanticipated findings related to nucleic acid chaperone activity, significantly extending our understanding of how this protein functions in L1 replication.