The CERV Protein of Cer1, a C. elegans LTR Retrotransposon, is Required for Nuclear Export of Viral Genomic RNA and Can Form Giant Nuclear Rods

Abstract

Retroviruses and closely related LTR retrotransposons export full-length, unspliced genomic RNA (gRNA) for packaging into virions and to serve as the mRNA encoding GAG and POL polyproteins. Because gRNA often includes splice acceptor and donor sequences used to splice viral mRNAs, retroelements must overcome host mechanisms that retain intron-containing RNAs in the nucleus. Here we examine gRNA expression in Cer1, an LTR retrotransposon in C. elegans which somehow avoids silencing and is highly expressed in germ cells. Newly exported Cer1 gRNA associates rapidly with the Cer1 GAG protein, which has structural similarity with retroviral GAG proteins. gRNA export requires CERV (C. elegans regulator of viral expression), a novel protein encoded by a spliced Cer1 mRNA. CERV phosphorylation at S214 is essential for gRNA export, and phosphorylated CERV colocalizes with nuclear gRNA at presumptive sites of transcription. By electron microscopy, tagged CERV proteins surround clusters of distinct, linear fibrils that likely represent gRNA molecules. Single fibrils, or groups of aligned fibrils, also localize near nuclear pores.

Introduction

Long terminal repeat (LTR) retrotransposons are ubiquitous in animals and plants; they comprise about 8% of the human genome and over 70% of plant genomes such as maize and wheat [1,2]. LTR retrotransposons appear to contribute to human aging and to chronic diseases such as autoimmune disorders [3–7], and are pathogens in several plants [8,9]. Conversely, LTR retrotransposons can have positive roles; some elements have been co-opted for host functions such as viral defense, and LTR retrotransposons have had major impacts on the evolution of gene regulatory networks and genome variation [10–13].

Materials and method

Worm culture

Nematode were maintained as described [113] with 15°C as the standard culture temperature unless stated otherwise. Plate media was made using Bactopeptone (Difco) and Bacto-agar (Difco) as described [113]. Culture plates were allowed to dry at room temperature for 2 days in the dark, then seeded with a fresh, overnight culture of E. coli strain OP50. Seeded plates were stored in the dark at room temperature for no more than 5 days. All worm cultures were grown for a minimum of two generations without starving before analysis. All strains used for this study are listed in S1 Table. A minimum of 30–40 animals were analyzed for each experiment reported.

Results

Background

Cer1 viral particles, called GAG particles, are most abundant in adult hermaphrodites cultured at 15°C [24], the temperature used for all experiments in this study unless indicated otherwise; a timeline of development at 15°C is shown for reference (Fig 1A). Hermaphrodites produce and store "self-sperm" during the fourth and final larval stage (L4), then switch to producing oocytes as adults (A). The self-sperm are largely depleted by adult day 4 (A4); thereafter, oocytes can only be fertilized by sperm from males. Each of the two arms of the hermaphrodite gonad resembles an elongated, U-shaped cylinder lined with about 1000 germ cells (Fig 1A; for general reviews of gonad biology see [38,39]).

Discussion

Retroviral gRNA is contained and protected by a protein shell, the capsid, which is assembled from hexamers and pentamers of CA, a subdomain of the GAG polyprotein. Cer1 GAG lacks sequence similarity to CA, but we showed that it contains a CA-like domain with predicted structural similarity to CA and the potential to form hexamers. Thus, Cer1 GAG resembles retroviral GAG proteins in having both CA and NC domains, but lacks sequence or structural similarity with the N-terminal MA (matrix) domain of retroviruses [81]. Most LTR retrotransposons in the Ty3/Gypsy family, which includes Cer1, lack MA proteins and their GAG proteins begin with the CA domain [81]. By contrast, Cer1 GAG has an N-terminal domain which is larger than most retroviral MA proteins (S4 Fig).

Acknowledgments

We thank Ujwal Sheth, who first noticed rods of unknown identify in some germ nuclei; Shannon Dennis for advice on Cer1 gene constructions and gift of the JJ2506 strain; Daniel Durning for advice on APEX2 staining protocols; Steve MacFarlane and Bobbie Schneider for assistance with TEM; and Anne Villeneuve for advice on germ cell biology. We thank Paul Davis and Stavros Diamantakis for providing raw data on CoDing Sequence (CDS) lengths in C. elegans. Some strains were provided by the CGC, which is funded by NIH Office of Research Infrastructure Programs (P40 OD010440).

Citation: Sun B, Kim H, Mello CC, Priess JR (2023) The CERV protein of Cer1, a C. elegans LTR retrotransposon, is required for nuclear export of viral genomic RNA and can form giant nuclear rods. PLoS Genet 19(6): e1010804. https://doi.org/10.1371/journal.pgen.1010804

Editor: Andrew D. Chisholm, University of California San Diego, UNITED STATES

Received: April 10, 2023; Accepted: May 31, 2023; Published: June 29, 2023

Copyright: © 2023 Sun et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Data Availability: All the relevant data are within the manuscript and its Supporting Information files.

Funding: This work was supported by NIH RO1GM098583 grant to J.R.P with salary support for HK and J.R.P; NIH RO1GM58800 and a Howard Hughes Medical Institute award to C.C.M with salary support for B.S. and C.C.M. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests: The authors have declared that no competing interests exist.