Dissecting the chloroplast proteome of chickpea ( Cicer arietinum L.) provides new insights into classical and non-classical functions

Canopy light distribution effects on light use efficiency in wheat and its mechanism

Optimizing canopy light distribution (CLD) has manifested improved light utility and yield without modifying other inputs. Nonetheless, molecular mechanisms working at cellular and organelle level remain to be elucidated. The current study aimed to assess the effect of CLD on photosynthetic performance and yield of wheat, and to investigate into the molecular mechanism underlying the photosynthetically active radiation (PAR)–use efficiency (PUE) at optimized CLD. Wheat was planted in two rows having different spacing [R1 (15 cm) and R2 (25 cm)] to simulate different CLD. Flag and penultimate leaves were subjected to chloroplast proteomics analysis. An increase in row spacing positively affects CLD. A decrease (16.64%) of PAR interception in the upper layer, an increase (19.76%) in the middle layer, improved PUE (12.08%), and increased yield (9.38%) were recorded. The abundance of proteins associated with photosynthetic electron transport, redox state, and carbon-nitrogen assimilation was differentially altered by CLD optimization. In the penultimate leaves, R2 reduced the abundance of photosystem II (PSII) light-harvesting proteins, PSII-subunits, and increased the photosystem I (PSI) light-harvesting proteins, NAD(P)H quinone oxidoreductase (NQO) and enzymes involved in carbon assimilation compared to R1. Additionally, leaf stomatal conductance increased. Altogether, these findings demonstrated that the regulation of chloroplast proteome is intimately linked to light utilization, which provide basis for genetic manipulation of crop species for better adaptation and improvement of cultivation strategies.

1-Methylcyclopropene Preserves the Quality of Chive (Allium schoenoprasum L.) by Enhancing Its Antioxidant Capacities and Organosulfur Profile during Storage

The quality, antioxidant capacities, and organosulfur profile of chives (Allium schoenoprasum L.) treated with 1-methylcyclopropene (1-MCP) during storage were investigated in this study. The 1-MCP treatment (100 μL/L, fumigation 12 h at 20 °C) effectively inhibited tissue respiration and H₂O₂ production, enhanced the ascorbic acid (ASA) and glutathione (GSH) content, and promoted the activity of antioxidant enzymes (superoxide dismutase SOD, Catalase CAT, and ascorbic peroxidase APX) during the 5-day storage period at 20 °C. The result further showed that the 1-MCP treatment inhibited chlorophyll degradation, alleviated cell membrane damage, and delayed the chive senescence, with the yellowing rate being reduced by 67.8% and 34.5% in the 1-MCP treated chives on days 4 and 5 of storage at 20 °C, respectively. The free amino acid content of the chive was not affected by the 1-MCP treatment at 20 °C. However, the senescence rate of the chive was not reduced by the 1-MCP treatment when stored at 3 °C. The liquid chromatography data further showed that the 1-MCP treatment induced a 15.3% and 13.9% increase in the isoalliin and total S-alk(en)ylcysteine sulfoxides (ACSOs) content of the chive on day 2 at 20 °C, respectively. Furthermore, there was a strong positive correlation between ACSOs content and CAT/APX activity, indicating that ACSOs probably played a key role in enhancing the antioxidant capacities of the chive during storage at 20 °C. Thus the study efficiently demonstrates that 1-methylcyclopropene preserves the quality of chive (Allium schoenoprasum L.) by enhancing its antioxidant capacities and organosulfur profile during storage.

Wheat 2-Cys peroxiredoxin plays a dual role in chlorophyll biosynthesis and adaptation to high temperature

The molecular mechanism of high-temperature stress (HTS) response, in plants, has so far been investigated using transcriptomics, while the dynamics of HTS-responsive proteome remain unexplored. We examined the adaptive responses of the resilient wheat cultivar 'Unnat Halna' and dissected the HTS-responsive proteome landscape. This led to the identification of 55 HTS-responsive proteins (HRPs), which are predominantly involved in metabolism and defense pathways. Interestingly, HRPs included a 2-cysteine peroxiredoxin (2CP), designated Ta2CP, presumably involved in stress perception and adaptation. Complementation of Ta2CP in yeast and heterologous expression in Arabidopsis demonstrated its role in thermotolerance. Both Ta2CP silencing and overexpression inferred the involvement of Ta2CP in plant growth and chlorophyll biosynthesis. We demonstrated that Ta2CP interacts with protochlorophyllide reductase b, TaPORB. Reduced TaPORB expression was found in Ta2cp-silenced plants, while upregulation was observed in Ta2CP-overexpressed plants. Furthermore, the downregulation of Ta2CP in Taporb-silenced plants and reduction of protochlorophyllide in Ta2cp-silenced plants suggested the key role of Ta2CP in chlorophyll metabolism. Additionally, the transcript levels of AGPase1 and starch were increased in Ta2cp-silenced plants. More significantly, HTS-treated Ta2cp-silenced plants showed adaptive responses despite increased reactive oxygen species and peroxide concentrations, which might help in rapid induction of high-temperature acclimation.

Dehydration-induced alterations in chloroplast proteome and reprogramming of cellular metabolism in developing chickpea delineate interrelated adaptive responses

Chloroplast, the energy organelle unique to photosynthetic eukaryotes, executes several crucial functions including photosynthesis. While chloroplast development and function are controlled by the nucleus, environmental stress modulated alterations perceived by the chloroplasts are communicated to the nucleus via retrograde signaling. Notably, coordination of chloroplast and nuclear gene expression is synchronized by anterograde and retrograde signaling. The chloroplast proteome holds significance for stress responses and adaptation. We unraveled dehydration-induced alterations in the chloroplast proteome of a grain legume, chickpea and identified an array of dehydration-responsive proteins (DRPs) primarily involved in photosynthesis, carbohydrate metabolism and stress response. Notably, 12 DRPs were encoded by chloroplast genome, while the rest were nuclear-encoded. We observed a coordinated expression of different multi-subunit protein complexes viz., RuBisCo, photosystem II and cytochrome b6f, encoded by both chloroplast and nuclear genome. Comparison with previously reported stress-responsive chloroplast proteomes showed unique and overlapping components. Transcript abundance of several previously reported markers of retrograde signaling revealed relay of dehydration-elicited signaling events between chloroplasts and nucleus. Additionally, dehydration-triggered metabolic adjustments demonstrated alterations in carbohydrate and amino acid metabolism. This study offers a panoramic catalogue of dehydration-responsive signatures of chloroplast proteome and associated retrograde signaling events, and cellular metabolic reprograming.

Proteomic dissection of the chloroplast: Moving beyond photosynthesis

Chloroplast, the photosynthetic machinery, converts photoenergy to ATP and NADPH, which powers the production of carbohydrates from atmospheric CO₂ and H₂O. It also serves as a major production site of multivariate pro-defense molecules, and coordinate with other organelles for cell defense. Chloroplast harbors 30-50% of total cellular proteins, out of which 80% are membrane residents and are difficult to solubilize. While proteome profiling has illuminated vast areas of biological protein space, a great deal of effort must be invested to understand the proteomic landscape of the chloroplast, which plays central role in photosynthesis, energy metabolism and stress-adaptation. Therefore, characterization of chloroplast proteome would not only provide the foundation for future investigation of expression and function of chloroplast proteins, but would open up new avenues for modulation of plant productivity through synchronizing chloroplastic key components. In this review, we summarize the progress that has been made to build new understanding of the chloroplast proteome and implications of chloroplast dynamicsing generate metabolic energy and modulating stress adaptation.

Dehydration-induced proteomic landscape of mitochondria in chickpea reveals large-scale coordination of key biological processes

Mitochondria play crucial roles in regulating multiple biological processes particularly electron transfer and energy metabolism in eukaryotic cells. Exposure to water-deficit or dehydration may affect mitochondrial function, and dehydration response may dictate cell fate decisions. iTRAQ-based quantitative proteome of a winter legume, chickpea, demonstrated the central metabolic alterations in mitochondria, presumably involved in dehydration adaptation. Three-week-old chickpea seedlings were subjected to progressive dehydration and the magnitude of dehydration-induced compensatory physiological responses was monitored in terms of physicochemical characteristics and mitochondrial architecture. The proteomics analysis led to the identification of 40 dehydration-responsive proteins whose expressions were significantly modulated by dehydration. The differentially expressed proteins were implicated in different metabolic processes, with obvious functional tendencies toward purine-thiamine metabolic network, pathways of carbon fixation and oxidative phosphorylation. The linearity of dehydration-induced proteome alteration was examined with transcript abundance of randomly selected candidates under multivariate stress conditions. The differentially regulated proteins were validated through sequence analysis. An extensive sequence based localization prediction revealed >62.5% proteins to be mitochondrial resident by, at least, one prediction algorithm. The results altogether provide intriguing insights into the dehydration-responsive metabolic pathways and useful clues to identify crucial proteins linked to stress tolerance. BIOLOGICAL SIGNIFICANCE: Investigation on plant mitochondrial proteome is of significance because it would allow a better understanding of mitochondrial function in plant adaptation to stress. Mitochondria are the unique organelles, which play a crucial role in energy metabolism and cellular homeostasis, particularly when exposed to stress conditions. Chickpea is one of the cultivated winter legumes, which enriches soil nitrogen and has very low water footprint and thus contributes to fortification of sustainable agriculture. We therefore examined the dehydration-responsive mitochondrial proteome landscape of chickpea and queried whether molecular interplay of mitochondrial proteins modulate dehydration tolerance. A total of 40 dehydration-induced mitochondrial proteins were identified, predicted to be involved in key metabolic processes. Our future efforts would focus on understanding both posttranslational modification and processing for comprehensive characterization of mitochondrial protein function. This approach will facilitate mining of more biomarkers linked to the tolerance trait and contribute to crop adaptation to climate change.

Proteomic analysis for phenanthrene-elicited wheat chloroplast deformation

The exposure of polycyclic aromatic hydrocarbons (PAHs) can cause wheat leaf chlorosis. Thus, we hypothesize that chloroplast inner structure damage is the reason for leaf chlorosis. This study was conducted with the wheat seedlings exposed to Hoagland nutrient solution containing 1.0 mg L^-1 phenanthrene for 9 days. Subcellular observation showed that chloroplast turns round and loses its structural integrity. Herein, iTRAQ (isobaric tag for relative and absolute quantification) was applied to analyze the changes of protein profile in chloroplast exposed to phenanthrene. A total of 517 proteins are identified, 261 of which are up-regulated. Eight proteins related with thylakoid (the structural component of chloroplast) are down-regulated and the expression of related genes further confirms the proteomic results through real-time PCR under phenanthrene treatment, suggesting that the thylakoid destruction is the reason for chloroplast deformation. Four proteins related with envelope and stroma are up-regulated, and this is the reason why chloroplast remains round. This study is useful in discussing the carcinogenic and teratogenic effects of PAHs in plant cells in the environment, and provides necessary knowledge for improving crop resistance to PAH pollution.

Dehydration-responsive nuclear proteome landscape of chickpea (Cicer arietinum L.) reveals phosphorylation-mediated regulation of stress response

Nonavailability of water or dehydration remains recurring climatic disorder affecting yield of major food crops, legumes in particular. Nuclear proteins (NPs) and phosphoproteins (NPPs) execute crucial cellular functions that form the regulatory hub for coordinated stress response. Phosphoproteins hold enormous influence over cellular signalling. Four-week-old seedlings of a grain legume, chickpea, were subjected to gradual dehydration, and NPs were extracted from unstressed control and from 72- and 144-hr stressed tissues. We identified 4,832 NPs and 478 phosphosites, corresponding to 299 unique NPPs involved in multivariate cellular processes including protein modification and gene expression regulation, among others. The identified proteins included several novel kinases, phosphatases, and transcription factors, besides 660 uncharacterized proteins. Spliceosome complex and splicing related proteins were dominant among differentially regulated NPPs, indicating their dehydration modulated regulation. Phospho-motif analysis revealed stress-induced enrichment of proline-directed serine phosphorylation. Association mapping of NPPs revealed predominance of differential phosphorylation of spliceosome and splicing associated proteins. Also, regulatory proteins of key processes viz., protein degradation, regulation of flowering time, and circadian clock were observed to undergo dehydration-induced dephosphorylation. The characterization of novel regulatory proteins would provide new insights into stress adaptation and enable directed genetic manipulations for developing climate-resilient crops.