Structure of a Ty1 restriction factor reveals the molecular basis of transposition copy number control

Abstract

Excessive replication of Saccharomyces cerevisiae Ty1 retrotransposons is regulated by Copy Number Control, a process requiring the p22/p18 protein produced from a sub-genomic transcript initiated within Ty1 GAG. In retrotransposition, Gag performs the capsid functions required for replication and re-integration. To minimize genomic damage, p22/p18 interrupts virus-like particle function by interaction with Gag. Here, we present structural, biophysical and genetic analyses of p18m, a minimal fragment of Gag that restricts transposition. The 2.8 Å crystal structure of p18m reveals an all α-helical protein related to mammalian and insect ARC proteins. p18m retains the capacity to dimerise in solution and the crystal structures reveal two exclusive dimer interfaces. We probe our findings through biophysical analysis of interface mutants as well as Ty1 transposition and p18m restriction in vivo. Our data provide insight into Ty1 Gag structure and suggest how p22/p18 might function in restriction through a blocking-of-assembly mechanism.

An interchangeable prion-like domain is required for Ty1 retrotransposition

“…Ty1 Gag contains a 71-amino acid domain with strikingly similar amino acid composition to yeast prions in its disordered N-terminus, comparable to Sup35 and Ure2. This Gag prion-like domain (PrLD) is predicted to be unstructured by AlphaFold (46) and no published structures of the region are available, similar to canonical prions (15,(47)(48)(49)(50) (Fig. S2).…”

“…Ty1 Gag performs the same functions as retroviral capsid and nucleocapsid. Amino acids 159-355 encode NTD and CTD capsid folds, assembling VLPs (15), and a C-terminal domain of Gag displays nucleic acid chaperone (NAC) activity (16, 17). Sequences in the Ty1 RNA encoding the Gag protein are required for packing, dimerization, and reverse transcription (3).…”

“…Fig 1.The Ty1 retrotransposon Gag contains a prion-like domain. Schematic of the Ty1 retrotransposon gene organization, with a detailed view of domains of the Gag protein (A), yeast prion Sup35 (B), yeast prion Ure2 (C), mouse prion protein (PrP) (D), and human amyloid beta (Aβ) (E); PrLD = prion-like domain, capsid domain (CA) and nucleic acid chaperone domain (NAC) are defined in(15). Below are bioinformatic analyses of each protein aligned with the schematic above: yeast prion-like amino acid composition (PLAAC), predicted amyloidogenic regions (ArchCandy), predicted protein disorder (PrDOS), predicted disordered (green) and globular (grey) regions (GlobPlot2.3).…”

Cryo-ET Structural Studies of Ty1 Retrotranspon Capsids

“…The Saccharomyces Ty1 retrotransposon assembles into virus-like particles (VLPs) comprised of the Gag and Gag-Pol proteins, and belongs to the widely-disseminated Ty1/Copia family [1]. Studies of Ty VLP structure and function have provided important insights into the structure, function, and evolution of retrovirus capsids (CA) and eukaryotic retrotransposons [2,3,4,5]. Interestingly, Ty1 VLP assembly is inhibited by a novel self-encoded restriction factor (p22) containing the conserved CA carboxyterminal-domain.…”

“…Interestingly, Ty1 VLP assembly is inhibited by a novel self-encoded restriction factor (p22) containing the conserved CA carboxyterminal-domain. This defense system helps prevent unabated cycles of retrotransposition [2,3,4]. Scanning transmission electron microscopy [6] and cryo-electron microscopy (cryo-EM) studies [6,7] of Ty1 VLPs identified significant variation in particle morphology and size.…”