Multiple cellular compartments engagement in Nicotiana benthamiana-peanut stunt virus-satRNA interactions revealed by systems biology approach

Abstract

PSV infection changed the abundance of host plant's transcripts and proteins associated with various cellular compartments, including ribosomes, chloroplasts, mitochondria, the nucleus and cytosol, affecting photosynthesis, translation, transcription, and splicing. Virus infection is a process resulting in numerous molecular, cellular, and physiological changes, a wide range of which can be analyzed due to development of many high-throughput techniques. Plant RNA viruses are known to replicate in the cytoplasm; however, the roles of chloroplasts and other cellular structures in the viral replication cycle and in plant antiviral defense have been recently emphasized. Therefore, the aim of this study was to analyze the small RNAs, transcripts, proteins, and phosphoproteins affected during peanut stunt virus strain P (PSV-P)-Nicotiana benthamiana interactions with or without satellite RNA (satRNA) in the context of their cellular localization or functional connections with particular cellular compartments to elucidate the compartments most affected during pathogenesis at the early stages of infection. Moreover, the processes associated with particular cell compartments were determined. The 'omic' results were subjected to comparative data analyses. Transcriptomic and small RNA (sRNA)-seq data were obtained to provide new insights into PSV-P-satRNA-plant interactions, whereas previously obtained proteomic and phosphoproteomic data were used to broaden the analysis to terms associated with cellular compartments affected by virus infection. Based on the collected results, infection with PSV-P contributed to changes in the abundance of transcripts and proteins associated with various cellular compartments, including ribosomes, chloroplasts, mitochondria, the nucleus and the cytosol, and the most affected processes were photosynthesis, translation, transcription, and mRNA splicing. Furthermore, sRNA-seq and phosphoproteomic analyses indicated that kinase regulation resulted in decreases in phosphorylation levels. The kinases were associated with the membrane, cytoplasm, and nucleus components.

Keywords: Defense response; Peanut stunt virus; Phosphorylation; Plant–virus interactions; Small RNAs; Virus infection.

Fig. 1

Schematic representation of sRNAs targeting PSV-P positions within viral genomic RNAs. The numbers of targeted potentially transcripts are shown with examples. The transcript accession numbers refer to transcriptome assembly v5.1 (Nakasugi et al. 2014)

Fig. 2

Graphical presentation of the results obtained in this study. Up and down arrows indicate up- or downregulated proteins, phosphoproteins, sRNAs, or transcripts. Orange and brown colored arrows are connected with the treatment of N. benthamiana plants with PSV-P and PSV-P + satRNA, respectively. Arrows are put next to the icons representing differentially regulated proteins, phosphoproteins, sRNAs targeting N. benthamiana transcripts, and transcripts associated with certain cellular components indicating their up- or downregulation. Black asterisk is associated with differentially regulated ta-siRNAs. The figure has been partially created using BioRender. A detailed list of the affected cellular components elements is presented in Table 2

Fig. 3

Biological process (a) and cellular component (b) terms for N. benthamiana PSV-specific sRNAs presented in pie charts. The numbers in parentheses represent the numbers of sRNA-targeted transcripts assigned to the different terms

Fig. 4

a Venn diagram showing the unique and common differentially expressed genes (DEGs) in PSV-P and PSV-P + satRNA plants. The arrows indicate upregulated (↑) and downregulated (↓) DEGs. b Gene Ontology biological process terms for the DEGs of N. benthamiana infected with PSV-P or PSV-P + satRNA presented in pie charts. The distribution of GO terms was analyzed separately for the upregulated and downregulated DEGs. The specific cellular component terms are presented in Table 2