Comparative proteomics analysis of Tibetan hull-less barley under osmotic stress via data-independent acquisition mass spectrometry

Abstract

Background Tibetan hull-less barley (Hordeum vulgare L. var. nudum) is one of the primary crops cultivated in the mountains of Tibet and encounters low temperature, high salinity, and drought. Specifically, drought is one of the major abiotic stresses that affect and limit Tibetan barley growth. Osmotic stress is often simultaneously accompanied by drought conditions. Thus, to improve crop yield, it is critical to explore the molecular mechanism governing the responses of hull-less barley to osmotic/drought stress conditions. Findings In this study, we used quantitative proteomics by data-independent acquisition mass spectrometry to investigate protein abundance changes in tolerant (XL) and sensitive (DQ) cultivars. A total of 6,921 proteins were identified and quantified in all samples. Two distinct strategies based on pairwise and time-course comparisons were utilized in the comprehensive analysis of differentially abundant proteins. Further functional analysis of differentially abundant proteins revealed that some hormone metabolism–associated and phytohormone abscisic acid–induced genes are primarily affected by osmotic stress. Enhanced regulation of reactive oxygen species (may promote the tolerance of hull-less barley under osmotic stress. Moreover, we found that some regulators, such as GRF, PR10, MAPK, and AMPK, were centrally positioned in the gene regulatory network, suggesting that they may have a dominant role in the osmotic stress response of Tibetan barley. Conclusions Our findings highlight a subset of proteins and processes that are involved in the alleviation of osmotic stress. In addition, this study provides a large-scale and multidimensional proteomic data resource for the further investigation and improvement of osmotic/drought stress tolerance in hull-less barley or other plant species.

Contribution of functional genomics to identify the genetic basis of water‐deficit tolerance in barley and the related molecular mechanisms

“…Consistently, when performing proteomics of two contrasted barley hull‐less cultivars exposed to osmotic stress, Wang et al. (2020) found higher abundance in leaves of various proteins participating in ABA‐induced signalling in the tolerant genotype. Zeng et al, (2016) highlighted the critical role of ABA in the drought tolerance of barley genotypes by performing transcriptome analysis using RNA‐seq of a Tibetan hull‐less cultivar exhibiting strong adaptation to dry environment.…”

“…(2018) and Wang et al. (2020) noticed higher expression of PRX genes compared to sensitive ones. They also noticed in the former increased expression for two genes encoding glutaredoxins.…”

“…Consistently, glutathione reductase, which allows regeneration of the reduced form of this compound, was found to be more abundant in a tolerant barley genotype than in a sensitive one, whereas an increased level of ascorbate peroxidase (APX) was recorded in both lines (Chmielewska et al., 2016). Higher activities of APX and MDHAR, enzymes involved in ascorbate‐related antioxidant mechanisms, have been noticed in drought‐tolerant wild genotypes compared to sensitive ones (Wang et al., 2015, 2020). Of note, the gene encoding another key enzyme in redox homeostasis, alternative oxidase, which is a part of the mitochondrial electron transport chain, is up‐regulated in response to drought in a tolerant wild barley genotype (Ashoub et al., 2018).…”

Application of Mass Spectrometry-Based Proteomics to Barley Research

“…In a closer examination, it was found that MAPK and PR10 showed a higher abundance in the treatment group over all time points of drought-tolerant and drought-sensitive cultivars, highlighting that these genes might play essential roles in plant defense responses to osmotic stress. 148 …”

Data-Independent Acquisition Proteomics Unravels the Effects of Iron Ions on Coronatine Synthesis in Pseudomonas syringae pv. tomato DC3000

“…Recently, a new mass spectrometry (MS) analysis approach called data-independent acquisition (DIA) was proposed for analyzing proteins; DIA is considered a promising approach for high-throughput quantitative proteome profiling ( Gillet et al, 2012 ). It has been demonstrated that DIA can be used to identify and quantify thousands of proteins without the need for fractionation, and only a few micrograms of a protein sample is needed ( Fan et al, 2019 ; Lou et al, 2020 ; Wang et al, 2020 ). The main purpose of the present study was to gain insight into the proteomics of COR biosynthesis in response to iron ion addition in fermentation.…”