Cryo-electron microscopy structure of yeast Ty retrotransposon virus-like particles

Summary Retrotransposons are ubiquitous and major components of plant genomes, and are characteristically retroviral‐like in their genomic structure and in the major proteins encoded. Nevertheless, few have been directly demonstrated to be transcribed or reverse transcribed. The BARE‐1 retrotransposon family of barley (Hordeum vulgare) is highly prevalent, actively transcribed, and contains well conserved functional regions. Insertion sites for BARE‐1 are highly polymorphic in the barley genome. Here we show that BARE‐1 is translated and the capsid protein (GAG) and integrase (IN) components of the predicted polyprotein are processed into polypeptides of expected size. Some of the GAG sediments as virus‐like particles together with IN and with BARE‐1 cDNA. Reverse transcriptase activity is also present in gradient fractions containing BARE‐1 translation products. Virus‐like particles have also been visualized in fractions containing BARE‐1 components. Thus BARE‐1 components necessary for carrying out the life cycle of an active retrotransposon appear to be present in vivo, and to assemble. This would suggest that post‐translational mechanisms may be at work to prevent rapid genome inflation through unrestricted integration.

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“…The appearance of these shells is virtually identical to negatively stained yeast Ty1 VLPs (Burns et al . 1992; Palmer et al . 1997).…”

Section: Resultsmentioning

confidence: 99%

Retrotransposon BARE‐1: expression of encoded proteins and formation of virus‐like particles in barley cells

et al. 1999

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“…Although members of the Ty1/Copia class can also encode NC, Ty1 itself does not. Ty1 and Ty3 Gag proteins, together with lesser amounts of Gag-Pol, form roughly spherical virus-like particles of variable sizes within cells (36–39) that also undergo proteolytic maturation. In the case of Ty3, Gag3 is cleaved into CA and NC domains (40).…”

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confidence: 99%

Structure of the Ty3/Gypsy retrotransposon capsid and the evolution of retroviruses

Dodonova

Prinz

Bilanchone

et al. 2019

Proc. Natl. Acad. Sci. U.S.A.

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Retroviruses evolved from long terminal repeat (LTR) retrotransposons by acquisition of envelope functions, and subsequently reinvaded host genomes. Together, endogenous retroviruses and LTR retrotransposons represent major components of animal, plant, and fungal genomes. Sequences from these elements have been exapted to perform essential host functions, including placental development, synaptic communication, and transcriptional regulation. They encode a Gag polypeptide, the capsid domains of which can oligomerize to form a virus-like particle. The structures of retroviral capsids have been extensively described. They assemble an immature viral particle through oligomerization of full-length Gag. Proteolytic cleavage of Gag results in a mature, infectious particle. In contrast, the absence of structural data on LTR retrotransposon capsids hinders our understanding of their function and evolutionary relationships. Here, we report the capsid morphology and structure of the archetypal Gypsy retrotransposon Ty3. We performed electron tomography (ET) of immature and mature Ty3 particles within cells. We found that, in contrast to retroviruses, these do not change size or shape upon maturation. Cryo-ET and cryo-electron microscopy of purified, immature Ty3 particles revealed an irregular fullerene geometry previously described for mature retrovirus core particles and a tertiary and quaternary arrangement of the capsid (CA) C-terminal domain within the assembled capsid that is conserved with mature HIV-1. These findings provide a structural basis for studying retrotransposon capsids, including those domesticated in higher organisms. They suggest that assembly via a structurally distinct immature capsid is a later retroviral adaptation, while the structure of mature assembled capsids is conserved between LTR retrotransposons and retroviruses.

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“…For foamy retroviruses and retrovirus-like LTR (long terminal repeat) retrotransposons, reverse transcription occurs in such capsids without leaving the producer cell [32][33][34] . Such capsids contain hundreds 35 to thousands 36 of Gag proteins and approximately 10-20-fold fewer Gag-Pol fusion proteins 28,37 . Retrovirus genomic RNAs are selectively packaged in these capsids by Gag interaction with specific cis-acting signals, often designated as Ψ 38,39 .…”

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confidence: 99%

Parallels among positive-strand RNA viruses, reverse-transcribing viruses and double-stranded RNA viruses

2006

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Viruses are divided into seven classes on the basis of differing strategies for storing and replicating their genomes through RNA and/or DNA intermediates. Despite major differences among these classes, recent results reveal that the non-virion, intracellular RNA-replication complexes of some positive-strand RNA viruses share parallels with the structure, assembly and function of the replicative cores of extracellular virions of reverse-transcribing viruses and double-stranded RNA viruses. Therefore, at least four of seven principal virus classes share several underlying features in genome replication and might have emerged from common ancestors. This has implications for virus function, evolution and control.

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Cryo-electron microscopy structure of yeast Ty retrotransposon virus-like particles

Cited by 32 publications

References 34 publications

Retrotransposon BARE‐1: expression of encoded proteins and formation of virus‐like particles in barley cells

Retrotransposon BARE‐1: expression of encoded proteins and formation of virus‐like particles in barley cells

Structure of the Ty3/Gypsy retrotransposon capsid and the evolution of retroviruses

Parallels among positive-strand RNA viruses, reverse-transcribing viruses and double-stranded RNA viruses

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