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[Preprint].2024 Sep 3:2024.09.03.611062.
doi: 10.1101/2024.09.03.611062.Latent infection of an active giant endogenous virus in a unicellular green alga
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- PMID:39282281
- PMCID: PMC11398304
- DOI: 10.1101/2024.09.03.611062
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Latent infection of an active giant endogenous virus in a unicellular green alga
Maria P Erazo-Garcia et al. bioRxiv..
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Abstract
Latency is a common strategy in a wide range of viral lineages, but its prevalence in giant viruses remains unknown. Here we describe the activity and viral production from a 617 kbp integrated giant viral element in the model green algaChlamydomonas reinhardtii. We resolve the integrated viral region using long-read sequencing and show that viral particles are produced and released in otherwise healthy cultures. A diverse array of viral-encoded selfish genetic elements are expressed during GEVE reactivation and produce proteins that are packaged in virions. In addition, we show that field isolates ofChlamydomonas sp. harbor latent giant viruses related to theC. reinhardtii GEVE that exhibit similar infection dynamics, demonstrating that giant virus latency is prevalent in natural host communities. Our work reports the largest temperate virus documented to date and the first active GEVE identified in a unicellular eukaryote, substantially expanding the known limits of viral latency.
Figures
(A) Line plots representing the tandem repeats (black) and GC fraction (yellow) of the viral contig_536. The TIRs flanking the GEVE are marked and shown with arrows. Regions in the contig with viral signatures are represented by ViralRecall scores >0 (red), while eukaryotic regions represent scores <0 (blue). Synteny blocks between the viral contig and chromosome 15 of the reference genome (C. reinhardtii CC-4532 v6) are shown in gray. The tandem repeats and GC fraction tracks are also shown for this chromosome at the bottom.(B) Alignment of five independent copies of the interspersed repetitive element in which the GEVE is integrated. Only the ends of the TIRs are represented and the 6 bp TSD is highlighted by a box.(C) Integration sites of two putative GEVE relics on chromosomes 16 and 7. The TIRs and TSDs of the insertions in CC- 2937 are shown relative to three divergent strains that do not carry the insertions.
(A) Gel image of a PCR assay targeting the viral major capsid protein (mcp) gene and host ITS region. The assay was performed on DNAse-treated supernatants from four culture replicates, sampled daily for 11 days.(B) Quantification of viral and host cell abundances over 11 days in four culture replicates. Viral abundance in the supernatants was measured by qPCR (red), while host cell density was assessed using flow cytometry (FCM) (blue). Error bars represent the standard deviation.(C) Flow cytometry analysis (left) of concentrated supernatants alongside two positive controls of known large DNA viruses mixed in with the sample. The right panel displays an electron micrograph of the concentrated viral fraction of a 9-day-old culture, showing a virus-like particle (VLP) identified through negative staining.
(A) Heatmap of min-max normalized counts for each GEVE gene, obtained from culture flasks inoculated 3–7 days prior to collection date. Each row corresponds to a GEVE gene, ordered as they appear along viral contig_536. Each pair of columns represents biological replicates of a specific time point. Row annotations indicate the assigned cluster based on gene expression patterns (see Methods for details): before peak viral production (BVP, yellow), and during peak viral production (DVP, red). Non-significantly differentially expressed genes (ns) were excluded from the clustering analysis. Column annotations show cell counts on the day of sampling (top panel).(B) Heatmap of min-max normalized counts specifically for hallmark NCLDV genes [24]. Row annotations indicate the assigned cluster.(C) Gene expression patterns of differentially expressed genes (DEGs), colored by their assigned cluster using self-organizing maps.(D) Shrunken Log2-fold expression changes (Log2FC) of genes along the viral contig, as determined by DESeq2. Day three serves as the reference for all comparisons. Each dot represents a gene in the same position as it appears on contig_536. The horizontal dashed line marks no change in gene expression (Log2FC = 0).
Peptides were identified using LC-MS/MS across three biological replicates, each analyzed in duplicate. Each dot represents a protein identified in a technical replicate, with dot size indicating the number of Peptide Spectrum Matches (PSMs) to reflect relative protein abundance, and dot color representing the predicted functional category. Proteins are arranged based on their Mascot database search scores.
(A) InfectedChlamydomonas sp. cell in early exponential phase (left). The nucleus and chloroplast are not clearly distinguishable.(B) Enlargement of the section delimited by a rectangle showing hexagonal viral particles. Virion production in a clearly delineated, lighter colored area with virions in later stages of completion accumulating at the edges of the production area, i.e. the virus factory/viroplasm. Red and black arrows indicate empty and full capsids, respectively. Yellow arrows indicate partially assembled capsids.(C) Enlarged picture of assembled virions. P – pyrenoid; CW – cell wall; L – lipid vesicle/plastoglobule; S – starch sheath.
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References
- Feschotte C, Gilbert C. Endogenous viruses: insights into viral evolution and impact on host biology. Nat Rev Genet. 2012;13: 283–296. - PubMed
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