The influence of signals from chilled roots on the proteome of shoot tissues in rice seedlings

Chemoproteomic identification of CO2-dependent lysine carboxylation in proteins

Carbon dioxide is an omnipresent gas that drives adaptive responses within organisms from all domains of life. The molecular mechanisms by which proteins serve as sensors of CO₂ are, accordingly, of great interest. Because CO₂ is electrophilic, one way it can modulate protein biochemistry is by carboxylation of the amine group of lysine residues. However, the resulting CO₂-carboxylated lysines spontaneously decompose, giving off CO₂, which makes studying this modification difficult. Here we describe a method to stably mimic CO₂-carboxylated lysine residues in proteins. We leverage this method to develop a quantitative approach to identify CO₂-carboxylated lysines of proteins and explore the lysine 'carboxylome' of the CO₂-responsive cyanobacterium Synechocystis sp. We uncover one CO₂-carboxylated lysine within the effector binding pocket of the metabolic signaling protein PII. CO₂-carboxylatation of this lysine markedly lowers the affinity of PII for its regulatory effector ligand ATP, illuminating a negative molecular control mechanism mediated by CO₂.

Root responses of contrasting rice genotypes to low temperature stress

Rice (Oryza sativa L.) ssp. indica is the most cultivated species in the South of Brazil. However, these plants face low temperature stress from September to November, which is the period of early sowing, affecting plant development during the initial stages of growth, and reducing rice productivity. This study aimed to characterize the root response to low temperature stress during the early vegetative stage of two rice genotypes contrasting in their cold tolerance (CT, cold-tolerant; and CS, cold-sensitive). Root dry weight and length, as well as the number of root hairs, were higher in CT than CS when exposed to cold treatment. Histochemical analyses indicated that roots of CS genotype present higher levels of lipid peroxidation and H₂O₂ accumulation, along with lower levels of plasma membrane integrity than CT under low temperature stress. RNAseq analyses revealed that the contrasting genotypes present completely different molecular responses to cold stress. The number of over-represented functional categories was lower in CT than CS under cold condition, suggesting that CS genotype is more impacted by low temperature stress than CT. Several genes might contribute to rice cold tolerance, including the ones related with cell wall remodeling, cytoskeleton and growth, signaling, antioxidant system, lipid metabolism, and stress response. On the other hand, high expression of the genes SRC2 (defense), root architecture associated 1 (growth), ACC oxidase, ethylene-responsive transcription factor, and cytokinin-O-glucosyltransferase 2 (hormone-related) seems to be related with cold sensibility. Since these two genotypes have a similar genetic background (sister lines), the differentially expressed genes found here can be considered candidate genes for cold tolerance and could be used in future biotechnological approaches aiming to increase rice tolerance to low temperature.

Biochemical responses of rice roots to cold stress

BACKGROUND

Cold stress is the main factor that reduces rice yield in subtropical areas, especially at the seedling stage. Most of the current studies on cold stress focus the responses of rice shoots to cold stress. Limited studies are available on that of rice roots to cold stress. This study aimed to illustrate the biochemical responses of rice root under cold treatment, and subject to the establishment of cold stress-related biochemical traits for rice breeding or cropping-adjustment.

RESULTS

Our results showed that the growth of rice seedling diminished under cold stress with difference extents among eight rice cultivars of most productive in Taiwan. Under cold treatments, the tested cultivars with higher growth rate had a higher level of hydrogen peroxide (H₂O₂) in the shoots but had a lower level in the roots. In contrast, the tested cultivates with low growth rate had higher levels of H₂O₂ in the roots but a lower level in the shoots. Meanwhile, higher MDA contents and higher cell-damage related electrolyte leakage were also found in the roots not in the shoots, suggesting that cold stress might induce oxidative stress in the roots, not in the shoots. Furthermore, the activity analysis of four antioxidant enzymes, namely superoxide dismutase (SOD), catalase (CAT), ascorbic peroxidase (APX), and glutathione reductase (GR), revealed that cold stress could increase SOD and CAT activities in the roots.

CONCLUSIONS

In summary, low H₂O₂ and low MDA contents along with lower SOD and CAT activities in rice root could be the biochemical traits of cold responses in rice seedlings. The results are hoping to have a contribution to the rice breeding or cropping-adjustment on cold tolerance.

Protein identification and quantification from riverbank grape, Vitis riparia: Comparing SDS-PAGE and FASP-GPF techniques for shotgun proteomic analysis

Protein sample preparation optimisation is critical for establishing reproducible high throughput proteomic analysis. In this study, two different fractionation sample preparation techniques (in-gel digestion and in-solution digestion) for shotgun proteomics were used to quantitatively compare proteins identified in Vitis riparia leaf samples. The total number of proteins and peptides identified were compared between filter aided sample preparation (FASP) coupled with gas phase fractionation (GPF) and SDS-PAGE methods. There was a 24% increase in the total number of reproducibly identified proteins when FASP-GPF was used. FASP-GPF is more reproducible, less expensive and a better method than SDS-PAGE for shotgun proteomics of grapevine samples as it significantly increases protein identification across biological replicates. Total peptide and protein information from the two fractionation techniques is available in PRIDE with the identifier PXD001399 (http://proteomecentral.proteomexchange.org/dataset/PXD001399).

Quantitative proteomic analysis of cabernet sauvignon grape cells exposed to thermal stresses reveals alterations in sugar and phenylpropanoid metabolism

Grapes (Vitis vinifera) are a valuable fruit crop and wine production is a major industry. Global warming and expanded range of cultivation will expose grapes to more temperature stresses in future. Our study investigated protein level responses to abiotic stresses, with particular reference to proteomic changes induced by the impact of four different temperature stress regimes, including both hot and cold temperatures, on cultured grape cells. Cabernet Sauvignon cell suspension cultures grown at 26°C were subjected to 14 h of exposure to 34 and 42°C for heat stress, and 18 and 10°C for cold stress. Cells from the five temperatures were harvested in biological triplicates and label-free quantitative shotgun proteomic analysis was performed. A total of 2042 non-redundant proteins were identified from the five temperature points. Fifty-five proteins were only detected in extreme heat stress conditions (42°C) and 53 proteins were only detected at extreme cold stress conditions (10°C). Gene Ontology (GO) annotations of differentially expressed proteins provided insights into the metabolic pathways that are involved in temperature stress in grape cells. Sugar metabolism displayed switching between alternative and classical pathways during temperature stresses. Additionally, nine proteins involved in the phenylpropanoid pathway were greatly increased in abundance at extreme cold stress, and were thus found to be cold-responsive proteins. All MS data have been deposited in the ProteomeXchange with identifier PXD000977 (http://proteomecentral.proteomexchange.org/dataset/PXD000977).

Mass spectrometric analysis of the cell surface N-glycoproteome by combining metabolic labeling and click chemistry

Cell surface N-glycoproteins play extraordinarily important roles in cell-cell communication, cell-matrix interactions, and cellular response to environmental cues. Global analysis is exceptionally challenging because many N-glycoproteins are present at low abundances and effective separation is difficult to achieve. Here, we have developed a novel strategy integrating metabolic labeling, copper-free click chemistry, and mass spectrometry (MS)-based proteomics methods to analyze cell surface N-glycoproteins comprehensively and site-specifically. A sugar analog containing an azido group, N-azidoacetylgalactosamine, was fed to cells to label glycoproteins. Glycoproteins with the functional group on the cell surface were then bound to dibenzocyclooctyne-sulfo-biotin via copper-free click chemistry under physiological conditions. After protein extraction and digestion, glycopeptides with the biotin tag were enriched by NeutrAvidin conjugated beads. Enriched glycopeptides were deglycosylated with peptide-N-glycosidase F in heavy-oxygen water, and in the process of glycan removal, asparagine was converted to aspartic acid and tagged with 18O for MS analysis. With this strategy, 144 unique N-glycopeptides containing 152 N-glycosylation sites were identified in 110 proteins in HEK293T cells. As expected, 95% of identified glycoproteins were membrane proteins, which were highly enriched. Many sites were located on important receptors, transporters, and cluster of differentiation proteins. The experimental results demonstrated that the current method is very effective for the comprehensive and site-specific identification of the cell surface N-glycoproteome and can be extensively applied to other cell surface protein studies.

Current perspectives in proteomic analysis of abiotic stress in Grapevines

Grapes are an important crop plant which forms the basis of a globally important industry. Grape and wine production is particularly vulnerable to environmental and climatic fluctuations, which makes it essential for us to develop a greater understanding of the molecular level responses of grape plants to various abiotic stresses. The completion of the initial grape genome sequence in 2007 has led to a significant increase in research on grapes using proteomics approaches. In this article, we discuss some of the current research on abiotic stress in grapevines, in the context of abiotic stress research in other plant species. We also highlight some of the current limitations in grapevine proteomics and identify areas with promising scope for potential future research.