Global Analysis of Differentially Expressed Genes and Proteins in the Wheat Callus Infected by Agrobacterium tumefaciens

Abstract

Agrobacterium-mediated plant transformation is an extremely complex and evolved process involving genetic determinants of both the bacteria and the host plant cells. However, the mechanism of the determinants remains obscure, especially in some cereal crops such as wheat, which is recalcitrant for Agrobacterium-mediated transformation. In this study, differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) were analyzed in wheat callus cells co-cultured with Agrobacterium by using RNA sequencing (RNA-seq) and two-dimensional electrophoresis (2-DE) in conjunction with mass spectrometry (MS). A set of 4,889 DEGs and 90 DEPs were identified, respectively. Most of them are related to metabolism, chromatin assembly or disassembly and immune defense. After comparative analysis, 24 of the 90 DEPs were detected in RNA-seq and proteomics datasets simultaneously. In addition, real-time RT-PCR experiments were performed to check the differential expression of the 24 genes, and the results were consistent with the RNA-seq data. According to gene ontology (GO) analysis, we found that a big part of these differentially expressed genes were related to the process of stress or immunity response. Several putative determinants and candidate effectors responsive to Agrobacterium mediated transformation of wheat cells were discussed. We speculate that some of these genes are possibly related to Agrobacterium infection. Our results will help to understand the interaction between Agrobacterium and host cells, and may facilitate developing efficient transformation strategies in cereal crops.

Proteomic Analysis of the Defense Response of Wheat to the Powdery Mildew Fungus, Blumeria graminis f. sp. tritici

“…They are thought to play important roles in homeostasis, detoxification, and biosynthesis of many secondary compounds. Several studies have suggested that glycosyltransferase activity is linked to the activation of defense signaling in wheat and other plants under biotic stress [55][56][57]. Two other proteins related to secondary metabolism were glyoxylate reductase (spot 22), which may contribute to the redox balance in plants under stress [58], and inactive purple acid phosphatase (spot 37), which is thought to play a role in pathogen-resistance responses [59].…”

Genome-wide analysis of differentially expressed genes and the modulation of PEDV infection in Vero E6 cells

“…i, N and n representing the number of successes, the number of genes with GO annotation, and the number of DEGs in N, respectively. M is the number of all genes which are annotated to the certain GO terms while m is the number of DEGs in M. GO terms in agreement with the condition P ≤ 0.05 were defined as significantly enriched GO terms in DEGs [27].…”

TRA1: a locus responsible for controllingAgrobacterium-mediated transformability in barley

“…Agrobacterium showed that 24 genes were differentially expressed at the RNA and protein levels 319 (Zhou et al, 2013). Of these 24 wheat genes, 17 have 1-to-1 orthologs in barley but none are in TRA1 320 region (data not shown).…”

“…transfer-competent, but not transfer-incompetent, Agrobacterium strains suppress plant defence genes 421 during infection in Arabidopsis (Veena et al 2003). In wheat, there have been attempts to identify 422 the genes responsible for transformability by comparing gene expression in embryos cultured in the 423 presence or absence of Agrobacterium (Zhou et al, 2013). A set of twenty-four genes were found to 424 be differentially expressed at both the RNA and protein levels and most of these genes had roles in 425 stress or immunity-response.…”