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Patchouli is a species of plant from the family Lamiaceae, commonly called the "mint" or "deadnettle" family. The plant grows as a bushy herb, with erect stems.
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Issue 3, Previous Article Next Article. From the journal: RSC Advances. The extraction of essential oils from patchouli leaves Pogostemon cablin Benth using a microwave air-hydrodistillation method as a new green technique. This article is Open Access. Please wait while we load your content Something went wrong. Try again? Cited by. Back to tab navigation Download options Please wait Article type: Paper. DOI: The extraction of essential oils from patchouli leaves Pogostemon cablin Benth using a microwave air-hydrodistillation method as a new green technique H.
Kusuma and M.
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Furthermore, we noticed that three photosynthesis-related pathways, photosynthesis, carbon fixation in photosynthesis, and photosynthesis-antenna proteins, were significantly enriched, implicating the underlying regulatory roles of lysine succinylation in patchouli plant photosynthesis. The majority of the remaining dramatically enriched pathways were related to the metabolism or biosynthesis of diverse secondary metabolites, such as glyoxylate, dicarboxylate, isoquinoline alkaloid, propanoate, glutathione, ascorbate and various amino acids tyrosine, arginine, glycine, serine, threonine, lysine, tryptophan, alanine, aspartate, glutamate, valine, leucine and isoleucine.
These markedly enriched diverse amino acid metabolism-related pathways were a noticeable phenomenon. Domain analysis indicated that both of the top two significantly enriched domains were related to ATPase subunit structure Supporting Figure S2. To investigate the interactions among various succinylated proteins and their involvement in diverse interacting pathways, we carried out protein interaction network PPI analysis with all the identified succinylation proteins.
In total, proteins carrying various succinylation sites were matched to the PPI network Fig. The majority of the succinylated proteins were clustered into three highly interconnected networks, namely, citrate cycle TCA cycle , oxidative phosphorylation and photosynthesis, suggesting the role of protein succinylation in modulating these biological processes. In addition, we noticed that the three internetworks were linked to each other through some succinylated proteins, implying that crosslinks were present among these biological processes and that succinylation may regulate these crosslinks.
The circle size represents mode degree and the color represents succinylation site number on the nodes. The node codes in the network correspond to the gene ID in the supporting information Table S4. The node degree is a key parameter to assess the importance and correlation of proteins in the network. The computed degree information for all succinylated proteins can be seen in Supporting Table S4 , and the result showed that there were 20 succinylated proteins with a degree over 40 in the network, among which Cytochrome b6-f complex iron-sulfur subunit, chloroplastic had the highest degree.
Moreover, some important nodes with a relatively higher degree displayed more than one succinylation site in the network, such as Dihydrolipoyl dehydrogenase 1, mitochondrial 12 sites , ADP, ATP carrier protein 1, mitochondrial 10 sites , Oxygen-evolving enhancer protein , chloroplastic 8 sites and oxygen-evolving enhancer protein 1, chloroplastic 7 sites. The constructed PPI network information indicated that lysine succinylation was relatively active in the TCA cycle, oxidative phosphorylation and photosynthesis processes, and participated in protein—protein interactions that likely influenced the coordination of these processes in this traditional Chinese medicine plant.
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In the present study, with an immunoprecipitation affinity enrichment technique combined with advanced mass spectrometry-based proteomics, we first obtained data of the lysine succinylome in patchouli plants. A previous study on plant succinylomes was mostly concentrated on Gramineae plants, among which the model plant rice has the most succinylation data available succinylation sites in proteins 8 , 16 , 17 , In some horticultural species, including strawberry, tomato, tea, Taxus and D.
Among medicinal herbs, only D. In our study, a total of succinylation sites corresponding to proteins were identified in patchouli plants, among which succinylation sites corresponding to proteins were repeatedly identified in three repeated experiments Fig. Obviously, there is some variation in succinylation site numbers and succinylation protein numbers in different reported plant species, which may be related to the differential intrinsic succinylation levels of proteins in various plant species. In addition, variation in plant growth stages, tissues selected for experiments and culture conditions may also contribute to this difference.
Our study expanded the species and scope of lysine succinylation in plants, especially in medicinal plants. It may help uncover the potential important role of lysine succinylation in herb growth, development, and physiology. To demonstrate the nature of the succinylated lysines in patchouli plants, motif and heat map analyses were conducted, and four consensus sequence motifs were obtained Fig.
It seemed that succinylation was preferred at lysine residues adjacent to residues bearing relatively small side chain groups, such as G and V. Moreover, in the succinylome analysis of silkworm and Candida albicans , the significantly enriched conserved motifs were all G or A-containing motifs.
Furthermore, G and A were overrepresented in the heat map analysis of the amino acid compositions surrounding the succinylated lysine sites 9 , Succinylation introduces a relatively larger structural moiety to the lysine sites than acetylation and methylation, whose steric hindrance effect would be more significant 6. We speculate that amino acids with small side chain groups may be more compatible with succinyl groups because their steric hindrance effects are relatively weak.
Thus G and A were overrepresented surrounding the succinylated lysine sites. Functional characterization and subcellular location analysis of lysine succinylated proteins in patchouli plants indicated that protein succinylation was involved in various metabolic and biological processes and occurred in diverse cellular compartments Fig.
S1 and some model plants, such as rice and Brachypodium distachyon L. By comparing the succinylome data from this study and in studies on other species Supporting Fig. S1 at the functional and subcellular location levels, we determined that tissue and organ differences may result in relatively higher variation in succinylation protein functions and subcellular distributions than plant species differences. In addition, the same tissues and organs leaves among various plant species showed similar succinylation protein function and subcellular location distribution, which is an interesting phenomenon.
The TCA cycle and oxidative phosphorylation are critical in living organisms because they are major energy production processes In addition, the TCA cycle results in various substrates and intermediates for diverse primary metabolism and secondary metabolism pathways The succinylated proteins are labeled in red. Previous studies in bacteria E.
Patchouli Essential Oil
Consistent with this previous study, 15 protein components or subunits belonging to TCA cycle-related enzymes or enzyme complexes were succinylation modified succinylated with variation in succinylation site number in patchouli plants Supporting Table S3 , suggesting that lysine succinylation may participate in TCA cycle regulation in this herb. Notably, some enzymes and enzyme complexes involved in the TCA cycle were succinylated at different components or subunits, such as in the pyruvate dehydrogenase complex, 3 sites in the dihydrolipoyllysine-residue acetyltransferase, 12 sites in dihydrolipoyl dehydrogenase 1 and 6 sites at pyruvate dehydrogenase E1.
In addition, a similar phenomenon was observed in the pyruvate dehydrogenase complex in rice and in the Brachypodium distachyon L.
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However, more biochemical experiments are necessary to verify this assumption. Oxidative phosphorylation results in ATP production through aerobic respiration in higher animals and higher plants are of vital importance for biological activities. The various lysine succinylation sites at the submits of complex I NADH dehydrogenase , complex II succinate dehydrogenase , complex III cytochrome bc1 complex , complex IV cytochrome c oxidase and complex V ATP synthase may regulate the protein—protein interaction among these subunits and further influence ATP production, as a significantly enriched internetwork was obtained in the PPI analysis, and several proteins with a relatively high degree exhibited multisite succinylation Fig.
Previous studies in other plant species, including rice, Brachypodium distachyon L. Our study demonstrated lysine succinylation on other electron transport chain complexes and expanded the study of succinylation-regulated oxidative phosphorylation. Photosynthesis in chloroplasts is an important biochemical reaction in plants because it converts light energy into chemical energy to support plant life.
Previous global lysine succinylation analyses in Taxus , tea plant, Brachypodium distachyon L. Protein succinylation may be a conserved approach in photosynthesis regulation among different plant species. Consistent with previous studies, our study of patchouli plants also identified many photosynthesis-related lysine succinylated proteins. Moreover, three photosynthesis-related pathways, photosynthesis, photosynthesis-antenna proteins and carbon fixation in photosynthetic organisms, were significantly enriched in the KEGG pathway analysis Fig.
The PPI analysis further validated this hypothesis because a significantly enriched photosynthesis-related subnetwork was obtained in the contrasting network Fig. Then, water is split by an oxygen-evolving complex OEC through the light-induced oxidation of water, resulting in the generation of molecular oxygen, reduced plastoquinone, and a transmembrane proton gradient Electron and hydrogen proton transport is an active event in the light reaction, which could be influenced by the charge states of the involved proteins. We hypothesize that the molecular mechanisms of succinylation-regulated light reaction processes may be related to succinylation-induced charge state alterations in addition to succinylation-induced steric hindrance effects 6.
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Carbon fixation in the Calvin—Benson cycle is the primary carbon assimilation pathway in plants In our study, many Calvin—Benson cycle-related enzymes harbored succinylation sites, such as ribulose bisphosphate carboxylase Rubisco , phosphoglycerate kinase, fructose-bisphosphate aldolase, glyceraldehydephosphate dehydrogenase, sedoheptulose-1,7-bisphosphatase, and glutamate-glyoxylate aminotransferase Supporting Table S3. A previous study also reported lysine succinylation in carbon fixation-related proteins, among which Rubisco exhibited the most succinylation sites 16 , 17 , 18 , Our study revealed a similar phenomenon and identified seven succinylation sites in Rubisco, of which five were in the Rubisco large subunit and two were in the Rubisco small subunit.
The increased identification of succinylation sites in Rubisco may be related to the large size of this enzyme and the high abundance of Rubisco in plant leaf tissues. In addition, it is the most abundant leaf tissue-distributed protein, accounting for approximately half of the soluble protein in plant leaves Its large size is indicative of more potential lysine sites, which are the preferred sites of succinylation modification, while its high abundance is indicative of increased chances of interacting with enzymes or cofactors responsible for intracellular succinylation modifications 6 , Both factors resulted in more Rubisco-related peptides being enriched in immunoprecipitation affinity in the sample preparation stage.
The identified succinylation sites in Rubisco and other carbon fixation-related enzymes indicate that succinylation is a crucial PTM in the photosynthetic carbon assimilation regulation in patchouli plants.
Amino acids are structural units of proteins in living organisms. In the pathway enrichment analyses, we noticed as many as ten amino acid metabolism pathways, especially amino acid biosynthesis-related pathways, were significantly enriched, and the metabolism of at least 13 amino acids was affected by these pathways Fig. We propose that lysine succinylation may play a role in amino acid metabolism in patchouli plants.