Proteomic analysis validates previous findings on wounding-responsive plant hormone signaling and primary metabolism contributing to the biosynthesis of secondary metabolites based on metabolomic analysis in harvested broccoli (Brassica oleracea L. var. italica)

Proteomics: An Essential Tool to Study Plant-Specialized Metabolism

Plants are a valuable source of specialized metabolites that provide a plethora of therapeutic applications. They are natural defenses that plants use to adapt and respond to their changing environment. Decoding their biosynthetic pathways and understanding how specialized plant metabolites (SPMs) respond to biotic or abiotic stress will provide vital knowledge for plant biology research and its application for the future sustainable production of many SPMs of interest. Here, we focus on the proteomic approaches and strategies that help with the study of plant-specialized metabolism, including the: (i) discovery of key enzymes and the clarification of their biosynthetic pathways; (ii) study of the interconnection of both primary (providers of carbon and energy for SPM production) and specialized (secondary) metabolism; (iii) study of plant responses to biotic and abiotic stress; (iv) study of the regulatory mechanisms that direct their biosynthetic pathways. Proteomics, as exemplified in this review by the many studies performed to date, is a powerful tool that forms part of omics-driven research. The proteomes analysis provides an additional unique level of information, which is absent from any other omics studies. Thus, an integrative analysis, considered versus a single omics analysis, moves us more closely toward a closer interpretation of real cellular processes. Finally, this work highlights advanced proteomic technologies with immediate applications in the field.

Physio-Metabolic Mechanisms Behind Postharvest Quality Deterioration in Broccoli (Brassica oleracea var. Italica) and Swiss Chard (Beta vulgaris L. var. Cicla): A Review

Leafy vegetables are among the potential foods that can combat food insecurity in developing countries. Their major drawback is a short shelf life, which limits their supply chain and is commonly associated with their high metabolic activities. Leafy vegetables have a high water content, which determines their freshness. Moisture loss through respiration and transpiration at postharvest storage is one quality attribute that leads to rapid quality deterioration. Little has been carried out in studying the mechanisms associated with the quality deterioration of leafy vegetables; however, understanding these mechanisms may aid in developing effective preservation measures. Furthermore, recent literature reviews that focus on discussing the mechanisms that lead to quality loss in leafy vegetables are scarce. The current paper aims to review the physiological and biochemical processes associated with quality deterioration in leafy vegetables. The respiration, ethylene production, moisture loss, colour, and texture are highly associated with the quality deterioration of fresh produce and, thus will be discussed critically in selected leafy vegetables, namely: broccoli and Swiss chard. The findings from this review indicate that the quality deterioration in leafy vegetables is primarily enzymatic. Understanding the mechanisms of quality deterioration involves identifying the specific enzymes responsible for each metabolic process and examining the internal and external factors that influence enzyme activities.

Tea Polyphenols Inhibit the Occurrence of Enzymatic Browning in Fresh-Cut Potatoes by Regulating Phenylpropanoid and ROS Metabolism

During fresh-cut processing, potatoes lose their inherent protective cellular structure, leading to enzymatic browning that compromises sensory and edible quality. Tea polyphenols (TPs), natural preservatives with potent reducing properties, are hypothesized to impact this browning process. However, their influence and regulatory mechanism on the enzymatic browning of fresh-cut potatoes remain poorly understood. This study used the "Holland Seven" potato as the research material to explore the effects of a treatment with different TP concentrations (0.1 g L-1, 0.2 g L-1, and 0.3 g L-1) on the browning phenomenon and quality of fresh-cut potatoes during storage. The results showed that appropriate concentrations of TP treatment had a good preservation effect on the appearance and edible quality of fresh-cut potatoes. Furthermore, exogenous TP treatment reduced the content of enzymatic browning substrates (caffeic acid, p-coumaric acid, and ferulic acid) by regulating phenylpropanoid metabolism. Meanwhile, TP treatment augmented the activities of antioxidative enzymes (superoxide dismutase, catalase, ascorbate peroxidase, and glutathione reductase), maintained higher levels of ascorbic acid (Vc), and reduced glutathione (GSH). Consequently, the TP treatment could inhibit enzymatic browning by regulating reactive oxygen species (ROS) metabolism and the Vc-GSH cycle in fresh-cut potatoes.

Metabolomic and transcriptomic analysis of cold plasma promoting biosynthesis of active substances in broccoli sprouts

INTRODUCTION

Broccoli sprouts have great health and commercial value because they are rich in sulforaphane, a special bioactive compound that helps to prevent chronic diseases, such as cancer and cardiovascular disease.

OBJECTIVE

The aim of this study was to increase the levels of active substances in broccoli sprouts and understand their metabolic mechanisms.

METHODOLOGY

Metabolomics based on liquid chromatography-tandem mass spectrometry and transcriptome analysis were combined to analyse the enrichment of metabolites in broccoli sprouts treated with cold plasma.

RESULTS

After 2 min of cold plasma treatment, the contents of sulforaphane, glucosinolates, total phenols, and flavonoids, as well as myrosinase activity, were greatly improved. Transcriptomics revealed 7460 differentially expressed genes in the untreated and treated sprouts. Metabolomics detected 6739 differential metabolites, including most amino acids, their derivatives, and organic acids. Enrichment analyses of metabolomics and transcriptomics identified the 20 most significantly differentially expressed metabolic pathways.

CONCLUSIONS

Overall, cold plasma treatment can induce changes in the expression and regulation of certain metabolites and genes encoding active substances in broccoli sprouts.

Cross-Talk and Physiological Role of Jasmonic Acid, Ethylene, and Reactive Oxygen Species in Wound-Induced Phenolic Biosynthesis in Broccoli

Wounding induces phenolic biosynthesis in broccoli. However, there is scarce information about the physiological and molecular mechanisms governing this stress response. In the present study, a chemical-genetics approach was used to elucidate the role of reactive oxygen species (ROS), jasmonic acid (JA), and ethylene (ET) as stress-signaling molecules in the wound-induced phenolic biosynthesis in broccoli. Wounding activated the biosynthesis of ET and JA. Likewise, the wound-induced biosynthesis of ET and JA was regulated by ROS. JA activated primary metabolism, whereas the three signaling molecules activated phenylpropanoid metabolism. The signaling molecules inhibited the wound-induced activation of the hydroxycinnamoyl-CoA quinate hydroxycinnamoyl transferase (HQT) gene, which is involved in caffeoylquinic acids biosynthesis, and the main phenolics accumulated in wounded broccoli, suggesting that an alternative caffeoylquinic biosynthesis pathway is activated in the tissue due to wounding. ROS mediated the biosynthesis of most individual phenolic compounds evaluated. In conclusion, ROS, ET, and JA are essential in activating broccoli's primary and secondary metabolism, resulting in phenolic accumulation.

Parallel repair mechanisms in plants and animals

All organisms have acquired mechanisms for repairing themselves after accidents or lucky escape from predators, but how analogous are these mechanisms across phyla? Plants and animals are distant relatives in the tree of life, but both need to be able to efficiently repair themselves, or they will perish. Both have an outer epidermal barrier layer and a circulatory system that they must protect from infection. However, plant cells are immotile with rigid cell walls, so they cannot raise an animal-like immune response or move away from the insult, as animals can. Here, we discuss the parallel strategies and signalling pathways used by plants and animals to heal their tissues, as well as key differences. A more comprehensive understanding of these parallels and differences could highlight potential avenues to enhance healing of patients' wounds in the clinic and, in a reciprocal way, for developing novel alternatives to agricultural pesticides.

Effect of different drying techniques on rose (Rosa rugosa cv. Plena) proteome based on label-free quantitative proteomics

To explore the molecular mechanisms of different processing technologies on rose tea (Rosa rugosa cv. Plena), we investigated the rose tea proteome (fresh rose tea [CS], vacuum freeze-drying rose tea [FD], and vacuum microwave rose tea [VD]) using label-free quantification proteomics (LFQ). A total of 2187 proteins were identified, with 1864, 1905, and 1660 proteins identified in CS, FD, and VD, respectively. Of those, 1500 proteins were quantified. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation and enrichment analysis of differential expression proteins (DEPs) in VD vs. CS, FD vs. CS, and FD vs. VD showed that these pathways were associated with energy metabolism, the metabolic breakdown of energy substances and protein biosynthesis, such as oxidative phosphorylation, citrate cycle, carbon metabolism pathways, and ribosome and protein processing in endoplasmic reticulum. FD could ensure the synthesis of protein translation and energy metabolism, thereby maintaining the high quality of rose tea.

Ethylene: Management and breeding for postharvest quality in vegetable crops. A review

Ethylene is a two-carbon gaseous plant growth regulator that involved in several important physiological events, including growth, development, ripening and senescence of fruits, vegetables, and ornamental crops. The hormone accelerates ripening of ethylene sensitive fruits, leafy greens and vegetables at micromolar concentrations, and its accumulation can led to fruit decay and waste during the postharvest stage. Several strategies of crops management and techniques of plant breeding have been attempted in the last decades to understand ethylene regulation pathways and ethylene-dependent biochemical and physiological processes, with the final aim to extend the produce shelf-life and improve the postharvest quality of fruits and vegetables. These investigation approaches involve the use of conventional and new breeding techniques, including precise genome-editing. This review paper aims to provide a relevant overview on the state of the art related to the use of modern breeding techniques focused on ethylene and ethylene-related metabolism, as well as on the possible postharvest technological applications for the postharvest management of ethylene-sensitive crops. An updated view and perspective on the implications of new breeding and management strategies to maintain the quality and the marketability of different crops during postharvest are given, with particular focus on: postharvest physiology (ethylene dependent) for mature and immature fruits and vegetables; postharvest quality management of vegetables: fresh and fresh cut products, focusing on the most important ethylene-dependent biochemical pathways; evolution of breeding technologies for facing old and new challenges in postharvest quality of vegetable crops: from conventional breeding and marker assisted selection to new breeding technologies focusing on transgenesis and gene editing. Examples of applied breeding techniques for model plants (tomato, zucchini and brocccoli) are given to elucidate ethylene metabolism, as well as beneficial and detrimental ethylene effects.

Ecological roles of secondary metabolites of Saposhnikovia divaricata in adaptation to drought stress

Saposhnikovia divaricata is a traditional Chinese herb that mainly grows in arid grasslands and strongly adapts to various stresses. Drought is not only a major abiotic stress factor but also a typical feature conducive to producing high-quality medicinal material. The present study investigated by treating S. divaricata plants with polyethylene glycol (PEG-6000). Ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS) identified 146 compounds from the roots of S. divaricata, among which seven primary metabolites and 28 secondary metabolites showed significant changes after drought treatment. UV-Vis spectrophotometer detected the activity of antioxidant enzymes and the content of superoxide anion (O2 -.) and malondialdehyde (MDA). The differential primary metabolites revealed that drought promotes glycolysis, reducing primary metabolism and enhancing secondary metabolism. Meanwhile, the differential secondary metabolites showed an increase in the content of compounds upstream of the secondary metabolic pathway, and other glycosides and increased that of the corresponding aglycones. The activities of antioxidant enzymes and the content of O2 -. and MDA shown different changes duing the drought treatment. These observations indicate that drought promotes the biosynthesis and transformation of the secondary metabolites and activity of antioxidant enzymes, improving plant adaptability. The present study also analyzed a few primary and secondary metabolites of S. divaricata under different degrees and durations of drought and speculated on the metabolic pathways in an arid environment. The findings indicate the biological nature, diversity, and complexity of secondary metabolites and the mechanisms of plant adaptation to ecological stress.

Biosynthesis of Phenolic Compounds and Antioxidant Activity in Fresh-Cut Fruits and Vegetables

Phenolic compounds are secondary metabolites and widely distributed in higher plants. When plants are subjected to injury stress, the rapid synthesis of more phenols is induced to result in injury defense response for wound healing and repair. Fresh-cut fruits and vegetables undergo substantial mechanical injury caused by pre-preparations such as peeling, coring, cutting and slicing. These processing operations lead to activate the biosynthesis of phenolic compounds as secondary metabolite. Phenolic compounds are important sources of antioxidant activity in fresh-cut fruits and vegetables. The wound-induced biosynthesis and accumulation of phenolic compounds in fresh-cut fruits and vegetables have been widely reported in recent years. This article provides a brief overview of research published over the last decade on the phenolic compounds and antioxidant activity in fresh-cut fruits and vegetables. It is suggested that fresh-cut processing as mechanical wounding stress can be used as an effective way to improve the nutritional composition and function of fresh-cut produces.

Chrysanthemum × grandiflora leaf and root transcript profiling in response to salinity stress

As high soil salinity threatens the growth and development of plants, understanding the mechanism of plants' salt tolerance is critical. The Chrysanthemum × grandiflora is a newly developed species with a strong salt resistance that possesses multiple genes controlling its quantitative salt resistance. Because of this multigene control, we chose to investigate the plant stress genes overall responses at the transcriptome level. C. grandiflora were treated with a 200 mM NaCl solution for 12 h to study its effect on the roots and leaves via Illumina RNA sequencing. PAL, CYP73A, and 4CL in the phenylpropanoid biosynthesis pathway were upregulated in roots and leaves. In the salicylic acid signal transduction pathway, TGA7 was upregulated in the roots and leaves, while in the jasmonic acid signal transduction pathway, TIFY9 was upregulated in the roots and leaves. In the ion transporter gene, we identified HKT1 that showed identical expression patterns in the roots and leaves. The impact of NaCl imposition for 12 h was largely due to osmotic effect of salinity on C. grandiflora, and most likely the transcript abundance changes in this study were due to the osmotic effect. In order to verify the accuracy of the Illumina sequencing data, we selected 16 DEGs for transcription polymerase chain reaction (qRT-PCR) analysis. qRT-PCR and transcriptome sequencing analysis revealed that the transcriptome sequencing results were reliable.

Chemical Genetics Applied to Elucidate the Physiological Role of Stress-Signaling Molecules on the Wound-Induced Accumulation of Glucosinolates in Broccoli

Wounding stress is an effective strategy to induce glucosinolate (GS) biosynthesis in broccoli. However, there is insufficient knowledge on the physiological and molecular mechanisms underlying this stress response. Herein, a chemical-genetic approach was applied to elucidate the role of jasmonic acid (JA), ethylene (ET), and reactive oxygen species (ROS) on the wound-induced biosynthesis of GS. Broccoli was processed into chops to induce wounding stress. Broccoli chops were treated with phenidone (PHEN) and diphenyleneiodonium chloride (DPI) as inhibitors of JA and ROS biosynthesis, respectively, whereas 1-methylcyclopropene (1-MCP) was applied as an inhibitor of ET action. Wounding stress induced the expression of genes related to the biosynthesis of indolic and aliphatic GS, which was correlated with the accumulation of GS and modulated by the inhibitors of signaling molecules applied. Results of gene expression analysis indicated that JA played a key role in the activation of most genes, followed by ROS. Furthermore, except for the CYP79B2 gene, PHEN and 1-MCP synergistically downregulated the expression of GS biosynthetic genes evaluated, showing that the interaction between JA and ET was fundamental to modulate GS biosynthesis. Results presented herein increased our knowledge of the physiological and molecular mechanisms governing the wound-induced biosynthesis of GS in broccoli.

Transcriptome in Combination Proteome Unveils the Phenylpropane Pathway Involved in Garlic (Allium sativum) Greening

Garlic (Allium sativum) is an important vegetable crop that is widely used in cooking and medicine. The greening phenomenon of garlic severely decreases the quality of garlic and hinders garlic processing. To study the mechanism of garlic greening, comprehensive full-length transcript sets were constructed. We detected the differences in greening between Pizhou (PZ) garlic and Laiwu (LW) garlic that were both stored at −2.5°C and protected from light at the same time. The results showed that 60,087 unigenes were respectively annotated to the NR, KEGG, GO, Pfam, eggNOG and Swiss Prot databases, and a total of 30,082 unigenes were annotated. The analysis of differential genes and differential proteins showed that PZ garlic and LW garlic had 923 differentially expressed genes (DEGs), of which 529 genes were up regulated and 394 genes were downregulated. Through KEGG and GO enrichment analysis, it was found that the most significant way of enriching DEGs was the phenylpropane metabolic pathway. Proteomics analysis found that there were 188 differentially expressed proteins (DAPs), 162 up-regulated proteins, and 26 down-regulated proteins between PZ garlic and LW garlic. The content of 10 proteins related to phenylpropanoid biosynthesis in PZ garlic was significantly higher than that of LW garlic. This study explored the mechanisms of garlic greening at a molecular level and further discovered that the formation of garlic green pigment was affected significantly by the phenylpropanoid metabolic pathway. This work provided a theoretical basis for the maintenance of garlic quality during garlic processing and the future development of the garlic processing industries.