RECENT FINDINGS: STRUCTURAL, FUNCTIONAL & EVOLUTIONARY STUDIES OF ORF1p - ORF1p is one of two L1 encoded proteins that are essential for retrotransposition. We earlier showed that primate ORF1p (like that in mouse) is a coiled coil mediated trimer that has nucleic acid binding and chaperone activity. However, the function of ORF1p in retrotransposition is largely unknown. In 2016 we had shown that L1 retrotranposition requires phosphorylation of ORF1p, reviewed in Furano, A. V. and P. R. Cook (2016). The challenge of ORF1p phosphorylation: Effects on L1 activity and its host. Mob Genet Elements 6(1): e1119927. In 2018, we extended, our collaboration with the Williams laboratory (Northeastern Univ.), which had previously shown that rapid oligimerization of ORF1p trimers on single stranded nucleic acid is essential for retrotransposition - Naufer,(2016) Nucleic Acids Res 44:281. Rapid oligomerization of ORF1p trimers (but not trimer formation per se) can be very sensitive to the amino acid sequence of the coiled coil, and we have generated several paired coiled coil mutants that differ by a single amino acid change, which completely inactivate retrotransposition. We are now examining their polymerization properties by single molecule studie with the Williams laboratory and by cryo-EM with the Hinshaw laboratory in NIDDK. Although the coiled coil can be extraordinarily sensitive to even a single amino acid substitution it nonetheless has been subject to repeated and extensive remodeling during primate evolution most recently during a 30 Myr period that ended about 15 MYA. In order to understand the evolutionary mechanisms and consequences of such dramatic change we carried out extensive phylogenetic and bioinformatic analysis of the ORF1 sequences of the seven L1 families, which emerged and then went extinct, from the onset of this event (45 MYA) until the present time: the L1Pa7-L1Pa1 families, the latter of which is currently active in humans. The results unexpectedly showed that multiple versions of the coiled coil region of ORF1p coexisted during the lifetime of each of the L1Pa7-L1Pa3 families. These results, complemented by direct experimental analysis, showed that most coiled coil amino acid substituions are phenotypically neutral, indicating genetic robustness of the coiled coil. Such robustness is permissive to the accumulation of cryptic genetic variation, i.e., genetic changes whose phenotype is revealed by changes elsewhere in the molecule. We identified four such epistatic residues that were present in the ancestral L1Pa5 ORF1p any one of which inactivated the modern ORF1p. Restoration of ORF1p activity in the presence of this quartet required re-introduction of 18 of the 21 ancestral amino acids elsewhere in the coiled coil that differentiated L1Pa1 and L1pa5 ORF1p. Theoretical and experimental studies by others showed that rather than evolving stepwise through discrete adaptive states, phenotypic change can be achieved by exploring related networks of biological sequences. Phylogenetic and cluster analysis revealed that this mode of evolution characterized coiled coil evolution of L1Pa7L1Pa3, each of which consist of several coexisting related but distinct sequences, with eventually only one surviving as the modern coiled coil in L1Pa1 and its immediate precursor L1Pa2. Mapping active and inactive coiled coil mutants on the relevant coiled co sequence space was consistent with this scenario of coiled coil adaptation. We suggest that this evolutionary scenario, not only rationalizes episodic variation in the coiled coil, but ensures L1 survival despite the exquisite sensitivity of its coiled coil domain to even a single amino acid change. Indeed, rather than being paradoxical, coexisting coiled coil variants could ensure L1 survival by increasing the odds of ORF1p surviving a potentially fatal amino acid substitution.
| Furano, Anthony V; Cook, Pamela R (2016) The challenge of ORF1p phosphorylation: Effects on L1 activity and its host. Mob Genet Elements 6:e1119927 |
| Naufer, M Nabuan; Callahan, Kathryn E; Cook, Pamela R et al. (2016) L1 retrotransposition requires rapid ORF1p oligomerization, a novel coiled coil-dependent property conserved despite extensive remodeling. Nucleic Acids Res 44:281-93 |
| Naufer, M Nabuan; Furano, Anthony V; Williams, Mark C (2015) 12 Oligomerization kinetics of ORF1p is correlated with LINE1 retrotransposition. J Biomol Struct Dyn 33 Suppl 1:7-8 |
| Cook, Pamela R; Jones, Charles E; Furano, Anthony V (2015) Phosphorylation of ORF1p is required for L1 retrotransposition. Proc Natl Acad Sci U S A 112:4298-303 |
| Callahan, Kathryn E; Hickman, Alison B; Jones, Charles E et al. (2012) Polymerization and nucleic acid-binding properties of human L1 ORF1 protein. Nucleic Acids Res 40:813-27 |
