Mammalian L1 retrotransposon replication

National Institute Of Diabetes And Digestive And Kidney Diseases

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Abstract

RECENT FINDINGS: EVOLUTIONARY PROCESSES THAT ENSURE L1 SURVIVAL: Despite being seriously deleterious, a single lineage of successive L1 families has persisted in many mammalian genomes, each family amplifying before undergoing extinction and replacement by another active family. During 80 million years of primate evolution this process generated 40% of the human genome where L1 remains active causing genetic defects and rearrangements. Thus, accounting for the persistence of L1 is a major issue for mammalian and human biology. L1 encodes a coiled coil-containing protein (ORF1p) that is essential for retrotransposition, and the emergence of novel primate L1 families has been correlated with episodes of extensive amino acid substitutions in the coiled coil. These bore the signature of positive selection (more amino acid substitutions than expected by chance), which often indicates an adaptive change, implying an arms race between L1 and its host. Determing the contestants in this arms race would reveal a major aspect of L1/host interaction. But our latest findings now suggest an alternate evolutionary model. We experimentally demonstrated that most of the amino acid substitutions which occurred during the last episode of extensive coiled coil change 30-10 MYA during the emergence of primate L1Pa7-L1Pa3 families, had no effect on ORF1p function. Being hidden from selection these substitutions could accumulate cryptically and increase sequence diversity (sequence space) of functional ORF1p. Principal component and phylogenetic analysis showed that this indeed occurred - thus each of the aforementioned L1 families contain three or more distinct coiled coil sequences. The availability of multiple functional ORF1p coiled coil sequences could buffer ORF1p activity from random inactivating epistatic mutations, which we also experimentally demonstrated. Sampling related networks of functional sequences rather than traversing discrete adaptive states characterized the persistence of L1 activity during this evolutionary event a strategy that ensured its survival. By providing a mechanistic explanation for the distinctive evolutionary history of ORF1p coiled coil, our findings represent a major advance in understanding the persistence of the L1 parasite in mammals and are relevant to coiled coil evolution in general, an important motif in at least 10% of all proteins. CURRENT STUDIES: (1) We are preparing a paper with Mark Williams, (Dept. of physics, Northeastern) reporting our latest results using single molecule studies to examine the interaction of L1 ORF1p and nucleic acid (NA). We previously showed (Naufer et al , 2016: doi:10.1093/nar/gkv1342) that the inability of the protein to form stably bound polymers after binding to NA was the only biochemical defect of a coiled coil (CC) mutant that is inactive in retrotransposition. Our current study which included an additional pair of coiled coil active and inactive variants and employed a newly developed single molecule method, confirmed our original findings and provided far more detail and nuance to the interaction between the protein and NA. (2) ORF1p is an obligate coiled coil-mediated trimer. As L1 families with distinct coiled coil sequences have coexisted during primate evolution (2020, PLOS Genetics: e1008991), we are determining whether ORF1ps with distinct coiled coil sequences can become entangled when co-expressed. (3) We are determining the interaction between ORF1p - the main component of the L1 RNP retrotransposition intermediate - and nucleosomes and histone proteins.