Assessing Global Transcriptome Changes in Response to South African Cassava Mosaic Virus [ZA-99] Infection in Susceptible Arabidopsis thaliana

Abstract

In susceptible plant hosts, co-evolution has favoured viral strategies to evade host defenses and utilize resources to their own benefit. The degree of manipulation of host gene expression is dependent on host-virus specificity and certain abiotic factors. In order to gain insight into global transcriptome changes for a geminivirus pathosystem, South African cassava mosaic virus [ZA:99] and Arabidopsis thaliana, 4×44K Agilent microarrays were adopted. After normalization, a log2 fold change filtering of data (p<0.05) identified 1,743 differentially expressed genes in apical leaf tissue. A significant increase in differential gene expression over time correlated with an increase in SACMV accumulation, as virus copies were 5-fold higher at 24 dpi and 6-fold higher at 36 dpi than at 14 dpi. Many altered transcripts were primarily involved in stress and defense responses, phytohormone signalling pathways, cellular transport, cell-cycle regulation, transcription, oxidation-reduction, and other metabolic processes. Only forty-one genes (2.3%) were shown to be continuously expressed across the infection period, indicating that the majority of genes were transient and unique to a particular time point during infection. A significant number of pathogen-responsive genes were suppressed during the late stages of pathogenesis, while during active systemic infection (14 to 24 dpi), there was an increase in up-regulated genes in several GO functional categories. An adaptive response was initiated to divert energy from growth-related processes to defense, leading to disruption of normal biological host processes. Similarities in cell-cycle regulation correlated between SACMV and Cabbage leaf curl virus (CaLCuV), but differences were also evident. Differences in gene expression between the two geminiviruses clearly demonstrated that, while some global transcriptome responses are generally common in plant virus infections, temporal host-specific interactions are required for successful geminivirus infection. To our knowledge this is the first geminivirus microarray study identifying global differentially expressed transcripts at 3 time points.

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

“…Contrarily to what observed for CabLCV [19] and SACMV [20], we could not detect in our dataset any indication of cell cycle activation probably because of the very low number of infected cells. The inability of the approach to highlight such change underscores the difficulty to investigate cell-autonomous processes, particularly for phloem-limited viruses, and the need to study infected cells instead of cell tissues.…”

SnRK1 Phosphorylation of AL2 Delays Cabbage Leaf Curl Virus Infection in Arabidopsis

“…The extent of these interactions is illustrated by host transcriptome studies that have identified thousands of plant genes that are differentially expressed in response to geminivirus infection (52,53). In contrast, less is known about posttranscriptional regulation in the infection process.…”

RNA-seq-based digital gene expression analysis reveals modification of host defense responses by rice stripe virus during disease symptom development in Arabidopsis

“…qRT-PCR was performed using the SsoFast EvaGreen Supermix (BioRad, Hercules, CA, USA) with the Bio-Rad iQ5 Real-Time PCR system with gene specific primers (Additional file 1), each reaction containing 10 μl SsoFast EvaGreen Supermix, 1 μl cDNA, 1 μl primers and 8 μl water. The expression levels of transcripts are presented relative to the corresponding control samples for each condition, EF1-a and actin2 were used as internal control gene [26, 27]. …”