Transcriptomics of the interaction between the monopartite phloem-limited geminivirus tomato yellow leaf curl Sardinia virus and Solanum lycopersicum highlights a role for plant hormones, autophagy and plant immune system fine tuning during infection

Abstract

Tomato yellow leaf curl Sardinia virus (TYLCSV), a DNA virus belonging to the genus Begomovirus, causes severe losses in tomato crops. It infects only a limited number of cells in the vascular tissues, making difficult to detect changes in host gene expression linked to its presence. Here we present the first microarray study of transcriptional changes induced by the phloem-limited geminivirus TYLCSV infecting tomato, its natural host. The analysis was performed on the midrib of mature leaves, a material naturally enriched in vascular tissues. A total of 2206 genes were up-regulated and 1398 were down-regulated in infected plants, with an overrepresentation of genes involved in hormone metabolism and responses, nucleic acid metabolism, regulation of transcription, ubiquitin-proteasome pathway and autophagy among those up-regulated, and in primary and secondary metabolism, phosphorylation, transcription and methylation-dependent chromatin silencing among those down-regulated. Our analysis showed a series of responses, such as the induction of GA- and ABA-responsive genes, the activation of the autophagic process and the fine tuning of the plant immune system, observed only in TYLCSV-tomato compatible interaction so far. On the other hand, comparisons with transcriptional changes observed in other geminivirus-plant interactions highlighted common host responses consisting in the deregulation of biotic stress responsive genes, key enzymes in the ethylene biosynthesis and methylation cycle, components of the ubiquitin proteasome system and DNA polymerases II. The involvement of conserved miRNAs and of solanaceous- and tomato-specific miRNAs in geminivirus infection, investigated by integrating differential gene expression data with miRNA targeting data, is discussed.

Figure 1. Southern blot analysis of TYLCSV DNA.

DNA was extracted from the apex (A), the first leaf (L1) and the midrib of the third (M3) and the fifth (M5) leaves of infected tomato plants. Mock-inoculated tomato plants were used as negative control (C). A Rep gene specific probe was used for TYLCSV detection. Viral DNA forms are open circular double-stranded DNA (oc), covalently closed double-stranded DNA (ds) and single-stranded DNA (ss).

Figure 2. Correlation between microarray and qRT-PCR data.

Expression values are expressed in fold changes (FC) in TYLCSV-infected plants in respect to mock inoculated ones

Figure 3. Over-represented GO categories (P<0.001) in genes differentially expressed in TYLCSV-infected plants in respect to mock-inoculated controls.

Bars represent the percentage of regulated genes in addition to those expected by chance. GO categories were organized in five groups. Numbers of genes associated with each GO category are indicated in brackets.

Figure 4. Comparison of the genes differentially expressed in TYLCSV-tomato, CabLCV-Arabidopsis and SACMV-Arabidopsis (36 dpi).

(A) Venn diagram. Values in brackets indicates the number of genes regulated in the same direction. (B) Hierarchical clustering.

Figure 5. Hypothetical role of miR159 in ethylene regulation during geminivirus infection.

Green and red arrows indicate the regulation of genes during TYLCSV infection according to microarray data. Numbers indicate literature references, and dashed line prediction of miR159 targeting of 1-aminocyclopropane-1-carboxylate synthase 8 (ACS8). ACCO: 1-aminocyclopropane-1-carboxylate oxidase.