Different Metabolic Pathways Are Involved in Response of Saccharomyces cerevisiae to L-A and M Viruses

Abstract

Competitive and naturally occurring yeast killer phenotype is governed by coinfection with dsRNA viruses. Long-term relationship between the host cell and viruses appear to be beneficial and co-adaptive; however, the impact of viral dsRNA on the host gene expression has barely been investigated. Here, we determined the transcriptomic profiles of the host Saccharomyces cerevisiae upon the loss of the M-2 dsRNA alone and the M-2 along with the L-A-lus dsRNAs. We provide a comprehensive study based on the high-throughput RNA-Seq data, Gene Ontology and the analysis of the interaction networks. We identified 486 genes differentially expressed after curing yeast cells of the M-2 dsRNA and 715 genes affected by the elimination of both M-2 and L-A-lus dsRNAs. We report that most of the transcriptional responses induced by viral dsRNAs are moderate. Differently expressed genes are related to ribosome biogenesis, mitochondrial functions, stress response, biosynthesis of lipids and amino acids. Our study also provided insight into the virus-host and virus-virus interplays.

Keywords: RNA-Seq; Saccharomyces cerevisiae; dsRNA viruses; host gene expression.

Figure 1

Distribution of expression fold differences induced by the loss of viral dsRNA(s). Distribution of expression fold changes induced by elimination: of M-2 dsRNA (L+M−) (A); or of both L-A-lus and M-2 dsRNAs (L−M−) (B). Range of represented fold changes is from −4 to 4. Red dashed lines mark the threshold of significant fold change value (1.5-fold change) in our analyses. Bar heights represent percentage of genes showing corresponding fold change compared to the S. cerevisiae S288C reference genome (6008 genes in total).

Figure 2

Statistically significant enriched gene ontology terms associated with the functioning of M-2 virus. Fold enrichment (F.E.) was calculated by dividing the frequency of specific gene cluster to the total frequency for each GO term, according to the data presented in Tables S2–S4: (A) enriched GO terms associated with biological processes; (B) functions; and (C) cellular components. Color coding is as follows: red, upregulated genes; blue, downregulated. snoRNA: small nucleolar RNA; rRNA: ribosomal RNA; SSU: small ribosome subunit; LSU: large ribosome subunit; TM: transmembrane; IMS: intermembrane space; Cytc-cytochrome c.

Figure 3

Statistically significant enriched gene ontology terms associated with the functioning of both M-2 and L-A-lus viruses: (A) statistically significant enriched GO terms associated with biological process; and (B) functioning and cellular components. Red color represents upregulated genes in both virus-free cells, blue-downregulated genes. Fold enrichment (F.E.) was calculated by dividing the frequency of specific gene cluster to the total frequency for each GO term, according to the data presented in Tables S2–S4. Trx: thioredoxin; CW: cell wall; IMS: intermembrane space; TM: transmembrane; UDP-NAG: UDP-N-acetylglucosamine; L-Gln: L-glutamine.

Figure 4

Networks of interconnected gene products involved in viral M-2 dsRNA biology. Networks of physically and/or functionally interacting gene products were established with STRING (see Materials and Methods). Gene products are depicted as color-coded nodes, according to cellular processes, and are connected by edges. Color coding is as follows: blue, ribosomal biogenesis; yellow, oxidation-reduction processes and energy generation; orange, lipid metabolism. (A) Gene products upregulated in response to loss of M2 virus; and (B) downregulated gene products in M2 virus-free cells.

Figure 5

Networks of interconnected gene products involved in biology of L-A-lus and M-2 dsRNAs. Physical and/or functional networks were established with STRING (see Materials and Methods). Gene products are depicted as color-coded nodes, according to cellular processes, and are connected by edges. Color coding is as follows: green, oxidation-reduction and stress response; purple, transmembrane transport; red, amino acid biosynthesis. (A) Gene products upregulated in response to loss of M2 and L-A-lus viruses; and (B) downregulated gene products in M2 and L-A-lus-free cells.

Figure 6

Number of genes differently expressed in virus-free cells: (A) Response to the loss of M2 dsRNA (L+M−) or both L-A-lus and M2 dsRNA’s (L−M−). Red color represents set of upregulated genes, blue-downregulated. (B) Overlap of genes impacted by L-A-1/M1 (green color) and L-A-lus/M2 viruses (yellow).