Functional and Integrative Analysis of the Proteomic Profile of Radish Root under Pb Exposure

Abstract

Lead (Pb) is one of the most abundant heavy metal (HM) pollutants, which can penetrate the plant through the root and then enter the food chain causing potential health risks for human beings. Radish is an important root vegetable crop worldwide. To investigate the mechanism underlying plant response to Pb stress in radish, the protein profile changes of radish roots respectively upon Pb(NO3)2 at 500 mg L−1(Pb500) and 1000 mg L−1(Pb1000), were comprehensively analyzed using iTRAQ (Isobaric Tag for Relative and Absolute Quantification). A total of 3898 protein species were successfully detected and 2141 were quantified. Among them, a subset of 721 protein species were differentially accumulated upon at least one Pb treatment, and 135 ones showed significantly abundance changes under both two Pb-stressed conditions. Many critical protein species related to protein translation, processing, and degradation, reactive oxygen species (ROS) scavenging, photosynthesis, and respiration and carbon metabolism were successfully identified. Gene Ontology (GO) and pathway enrichment analysis of the 135 differential abundance protein species (DAPS) revealed that the overrepresented GO terms included “cell wall,” “apoplast,” “response to metal ion,” “vacuole,” and “peroxidase activity,” and the critical enriched pathways were involved in “citric acid (TCA) cycle and respiratory electron transport,” “pyruvate metabolism,” “phenylalanine metabolism,” “phenylpropanoid biosynthesis,” and “carbon metabolism.” Furthermore, the integrative analysis of transcriptomic, miRNA, degradome, metabolomics and proteomic data provided a strengthened understanding of radish response to Pb stress at multiple levels. Under Pb stress, many key enzymes (i.e., ATP citrate lyase, Isocitrate dehydrogenase, fumarate hydratase and malate dehydrogenase) involved in the glycolysis and TCA cycle were severely affected, which ultimately cause alteration of some metabolites including glucose, citrate and malate. Meanwhile, a series of other defense responses including ascorbate (ASA)–glutathione (GSH) cycle for ROS scavenging and Pb-defense protein species (glutaredoxin, aldose 1-epimerase malate dehydrogenase and thioredoxin), were triggered to cope with Pb-induced injuries. These results would be helpful for further dissecting molecular mechanism underlying plant response to HM stresses, and facilitate effective management of HM contamination in vegetable crops by genetic manipulation.

Comparative proteomic analysis provides insight into a complex regulatory network of taproot formation in radish (Raphanus sativus L.)

“…The relatively weak correlation of genes at mRNA and protein level indicates that an alteration in a proportion of transcripts may not be translated into changes in protein abundance. Low congruency of genes in mRNA and protein level was similar with other previous studies 20 , 35 .…”

“…However, it has some limitations in protein abundance identification. More recently, isobaric tags for relative and absolute quantitation (iTRAQ), a new and powerful technology, was used in quantitative proteomics by isotope tagging and high-performance liquid chromatography (HPLC) 19 , 20 . High sensitivity (less than 1 ppm), low detection limit (proteins of less than 10 kD or greater than 200 kD) in identification and quantitation of proteins aspects make iTRAQ a valuable approach for proteomics studies in some plant species including cassava 21 , potato 22 , 23 , and Brassica napus 24 .…”

iTRAQ-Based Quantitative Proteomic Analysis of a Toxigenic Dinoflagellate Alexandrium catenella and Its Non-toxigenic Mutant Exposed to a Cell Cycle Inhibitor Colchicine

“…Proteins were compared between two pairs: ACHK-T vs. colchicine-treated ACHK-T and ACHK-NT vs. colchicine-treated ACHK-NT. A protein was considered to be differentially expressed if it contained at least two unique peptides, had similar and significant ratios of ≥ 1.2 (upregulated) or ≤ 0.83 (downregulated) in both of the replicates ( D’Agostino et al, 2014 ; Li et al, 2016 ; Wang et al, 2016 ).…”

Effect of Irrigation Level and Irrigation Frequency on the Growth of Mini Chinese Cabbage and Residual Soil Nitrate Nitrogen

“…The roots of catch crops such as ryegrass and fodder radish can effectively absorb the remaining NO 3 -N in the soil [19]. Moreover, after harvest, the soil NO 3 -N accumulation of 0-1.0 m deep soil planted with leeks and red beets was lower than that of soil without catch crops [19,20]. After the maize harvest, the loss due to nitrate leaching of the test field could be reduced by 80% by planting rye compared to that in a fallow field [21].…”