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. 2022 Aug 27;14(9):1892.
doi: 10.3390/v14091892.

Characterization of Transcriptional Responses to Genomovirus Infection of the White Mold Fungus, Sclerotinia sclerotiorum

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Characterization of Transcriptional Responses to Genomovirus Infection of the White Mold Fungus, Sclerotinia sclerotiorum

Connor J Pedersen et al. Viruses. .

Abstract

Soybean leaf-associated gemygorvirus-1 (SlaGemV-1) is a CRESS-DNA virus classified in the family Genomoviridae, which causes hypovirulence and abolishes sclerotia formation in infected fungal pathogens under the family Sclerotiniaceae. To investigate the mechanisms involved in the induction of hypovirulence, RNA-Seq was compared between virus-free and SlaGemV-1-infected Sclerotinia sclerotiorum strain DK3. Overall, 4639 genes were differentially expressed, with 50.5% up regulated and 49.5% down regulated genes. GO enrichments suggest changes in integral membrane components and transmission electron microscopy images reveal virus-like particles localized near the inner cell membrane. Differential gene expression analysis focused on genes responsible for cell cycle and DNA replication and repair pathways, ubiquitin proteolysis, gene silencing, methylation, pathogenesis-related, sclerotial development, carbohydrate metabolism, and oxalic acid biosynthesis. Carbohydrate metabolism showed the most changes, with two glycoside hydrolase genes being the most down regulated by -2396.1- and -648.6-fold. Genes relating to pathogenesis showed consistent down regulation with the greatest being SsNep1, SsSSVP1, and Endo2 showing, -4555-, -14.7-, and -12.3-fold changes. The cell cycle and DNA replication/repair pathways were almost entirely up regulated including a putative cyclin and separase being up regulated 8.3- and 5.2-fold. The oxalate decarboxylase genes necessary for oxalic acid catabolism and oxalic acid precursor biosynthesis genes and its metabolism show down regulations of -17.2- and -12.1-fold changes. Sclerotial formation genes also appear differentially regulated including a melanin biosynthesis gene Pks1 and a sclerotia formation gene Sl2 with fold changes of 3.8 and -2.9.

Keywords: RNA-Seq; Sclerotinia sclerotiorum; genomovirus; hypovirulence; mycovirus.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Differential expression analysis of DK3 vs. DK3-V where DK3 and DK3-V represent virus-free S. sclerotiorum strain DK3 and SlaGemV−1-infected DK3, respectively. (A) Variance stabilization of the normalized mean used for further DESeq2 analysis. (B) log2 fold change vs. mean of normalized counts found by variance stabilization. Initial visualization of padj ≤ 0.1 (Benjamin-Hochberg) where positive log change indicates genes which have been up regulated in the virus-infected samples shows an abundance of differentially expressed genes. (C) Principal component analysis of variance between DK3 and DK3-V with principal components of 88% and 6% showing the clustering of DK3 and DK3V samples together. (D). Distance matrix displayed as a heatmap of total gene expression between DK3 and DK3-V shows clear differences in expression between samples DK3 and DK3-V.
Figure 2
Figure 2
Transmission electron microscopy images of virus-free S. sclerotiorum DK3 (AC) and SlaGemV−1-infected S. sclerotiorum DK3 (DF). (A,D) show an apparent change in morphology of the fungal cell with SlaGemV−1 infection. In (E,F), 20–30 nm icosahedral particles can be seen and contained in vesicles along the inner cell membrane. These particles and vesicles are absent in virus-free samples in (B,C).
Figure 3
Figure 3
(A) Cell cycle and DNA replication/repair (B) and ubiquitin proteolysis genes were investigated for potential differential regulation in presence of SlaGemV−1 infection in S. sclerotiorum. Distance matrices of the differential expression analysis were visualized as heatmaps. Genes relating to cell cycle controls and DNA replication and repair are seen largely up regulated in presence of SlaGemV−1. Likewise, genes relating to the up regulation of ubiquitin proteolysis pathway are also up regulated during viral infection.
Figure 4
Figure 4
RNAi silencing (A) and methylation-related (B) genes were investigated for potential differential regulation in presence of SlaGemV−1 infection in S. sclerotiorum. Distance matrices of the differential expression analysis were visualized as heatmaps. Neither dicer nor argonaut-2 show differential expression, while argonaut-4 is upregulated and all 3 RdRps are downregulated. The S-Adenosyl-L-methionine biosynthesis protein ADK is down regulated in SlaGemV−1-infected samples as well as SAHH, which has been shown as a target of plant geminiviruses to prevent viral genome methylation. Other methylation genes, including SAM-dependent methyltransferases, show differential expression.
Figure 5
Figure 5
(A) Pathogenesis-related, (B) Carbohydrate biosynthesis and metabolism, (C) oxalic acid biosynthesis, metabolism, and citric acid synthesis, (D) and Sclerotial formation genes were investigated for potential differential regulation in presence of SlaGemV−1 infection in S. sclerotiorum. Distance matrices of the differential expression analysis were visualized as heatmaps. Pathogenesis-related genes identified were all down regulated, while most sclerotiral formation genes appear down regulated.

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References

    1. Peltier A.J., Bradley C.A., Chilvers M.I., Malvick D.K., Mueller D.S., Wise K.A., Esker P.D. Biology, Yield loss and Control of Sclerotinia Stem Rot of Soybean. J. Integr. Pest Manag. 2012;3:B1–B7. doi: 10.1603/IPM11033. - DOI
    1. Zhang H., Xie J., Fu Y., Cheng J., Qu Z., Zhao Z., Cheng S., Chen T., Li B., Wang Q. A 2-kb Mycovirus Converts a Pathogenic Fungus into a Beneficial Endophyte for Brassica Protection and Yield Enhancement. Mol. Plant. 2020;13:1420–1433. doi: 10.1016/j.molp.2020.08.016. - DOI - PubMed
    1. Milgroom M.G., Cortesi P. Biological control of chestnut blight with hypovirulence: A critical analysis. Annu. Rev. Phytopathol. 2004;42:311–338. doi: 10.1146/annurev.phyto.42.040803.140325. - DOI - PubMed
    1. Xie J., Jiang D. New insights into mycoviruses and exploration for the biological control of crop fungal diseases. Annu. Rev. Phytopathol. 2014;52:45–68. doi: 10.1146/annurev-phyto-102313-050222. - DOI - PubMed
    1. Nuss D.L. Mycoviruses. Cell. Mol. Biol. Filam. Fungi. 2010:145–152. doi: 10.1128/9781555816636.ch12. - DOI

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This research was funded by the National Sclerotinia Initiative (3060-21220-031-00D; accession#: 0432211) and the United States Department of Agriculture/Agricultural Research Service CRIS (5082-21000-001-000D; accession#: 0438340) to Shin-Yi Marzano.

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