Predicting protein phosphorylation sites in soybean using interpretable deep tabular learning network.

Phosphorylation of proteins is one of the most significant post-translational modifications (PTMs) and plays a crucial role in plant functionality due to its impact on signaling, gene expression, enzyme kinetics, protein stability and interactions. Accurate prediction of plant phosphorylation sites (p-sites) is vital as abnormal regulation of phosphorylation usually leads to plant diseases. However, current experimental methods for PTM prediction suffers from high-computational cost and are error-prone. The present study develops machine learning-based prediction techniques, including a high-performance interpretable deep tabular learning network (TabNet) to improve the prediction of protein p-sites in soybean. Moreover, we use a hybrid feature set of sequential-based features, physicochemical properties and position-specific scoring matrices to predict serine (Ser/S), threonine (Thr/T) and tyrosine (Tyr/Y) p-sites in soybean for the first time. The experimentally verified p-sites data of soybean proteins are collected from the eukaryotic phosphorylation sites database and database post-translational modification. We then remove the redundant set of positive and negative samples by dropping protein sequences with >40% similarity. It is found that the developed techniques perform >70% in terms of accuracy. The results demonstrate that the TabNet model is the best performing classifier using hybrid features and with window size of 13, resulted in 78.96 and 77.24% sensitivity and specificity, respectively. The results indicate that the TabNet method has advantages in terms of high-performance and interpretability. The proposed technique can automatically analyze the data without any measurement errors and any human intervention. Furthermore, it can be used to predict putative protein p-sites in plants effectively. The collected dataset and source code are publicly deposited at https://github.com/Elham-khalili/Soybean-P-sites-Prediction.

Effective biosorption of Al ions from drinking water by lignocellulosic biomass rice straw.

High concentration of aluminum (Al) in drinking water is a major intake source of it and can result in serious diseases. Rice straw (RS) as lignocellulosic biomasses has great potential to peak up metal ions from aqueous environment, however, feasibility of Al3+ removal by RS has not been investigated yet. The present study aimed to evaluate the capacity of RS as a novel biosorbent for Al3+ from drinking water. Biosorption characteristics of RS were surveyed through several biological and physiochemical techniques. Additionally, isotherm, kinetic and thermodynamic studies were evaluated using various common models. BET profiles revealed the presence of textural mesoporosity on heterogeneous surface, which leading to improve the biosorption capacity. SEM-EDS analysis confirmed the morphological changes as irregularly particles of Al3+ on external surface via physical mechanism. The results of bioassays and FTIR analysis showed carboxylic and hydroxyl groups in lignin and pectin as the main Al3+ binding site. The batch experimental results showed the maximum biosorption capacity of 283.09 mg/g and removal efficiency of 94.86% for Al3+ at biosorbent dosage of 0.05 g/100 mL, contact time of 50 min, pH 7.5, and temperature of 30 °C. The Freundlich model has the best match and suggests the biosorption process as a multi-layer. According to the results of free activation energy, biosorption process was also physical. As thermodynamic result, the biosorption behavior was found spontaneous and endothermic. Consequently, results showed RS as an economical biosorbent for reducing Al3+ of drinking water. Meanwhile, it can be considered as one of the most appropriate methods for management of rice paddies waste.

This article provides a new interdisciplinary horizon at the border of plant biochemistry, agriculture, water treatment industry, and environmental protection. This study covers different aspects including biosorption, cell wall network as well as the usefulness of agricultural by-products in biosorption of Al-polluted drinking water. Findings of the present study revealed that rice straw cell wall polysaccharides have specific Al³⁺ binding sites, therefore can be effectively used in water treatment and reduce Al³⁺ content below the standard permissible limit of WHO (0.2 mg/L). This can be a foundation for future research to evaluate agricultural wastes management in the industry of water as natural biosorbent. This method also effectively converts RS from an unwanted agricultural waste to high-value products.

Increase in lipid productivity and photosynthetic activities during distillery wastewater decolorization by Chlorella vulgaris cultures.

Finding an eco-friendly process for the decolorization of distillery wastewaters is a major concern. This study shows that the Chlorella vulgaris CCAP 211/19 strain can be used for color removal and direct production of oleaginous biomass. A response surface method was used for determining optimal operating conditions, including the dilution factor of industrial wastewater. The highest daily light supply values were the most efficient for color removal. The analysis of the microalgae physiological status confirmed that these colored waters could have a photoprotective action. Moreover, the increase in photosystem 2 activities of C. vulgaris CCAP 211/19 strain after short-term incubations in the presence of a synthetic melanoidin confirmed that this fraction is involved in the enhancement of lipid-enriched biomass production. The results show for the first time the stimulation effect of a melanoidin fraction on the lipid content and productivity by C. vulgaris. These results suggest that this approach may be used to design a closed loop, including water and CO2 recycling for the wastewater dilution and photosynthetic carbon fixation, respectively, while providing biomass for useful renewable algae-based feedstocks of potential interest for a distillery process. KEY POINTS: • Chlorella vulgaris cultures can be used for decolorization of distillery wastewaters. • Diluted distillery wastewaters stimulate biomass and lipid productivities. • Melanoidins, as well as distillery wastewater, stimulate photosynthetic activities.

The contribution of cell wall composition in the expansion of Camellia sinensis seedlings roots in response to aluminum.

MAIN CONCLUSION: Treatment with aluminum triggers a unique response in tea seedlings resulting in biochemical modification of the cell wall, regulation of the activity of the loosening agents, and elongation of root. Unlike most terrestrial plants, tea (Camellia sinensis L.) responds to aluminum (Al) through the promotion of its root elongation; but the real mechanism(s) behind this phenomenon is not well understood. A plausible relationship between the modifications of the cell wall and the promotion of root elongation was examined in tea seedlings treated for 8 days with 400 µM Al. The mechanical properties of the cell wall, the composition of its polysaccharides and their capacity to absorb Al, the expression of genes, and the activities of the wall-modifying proteins were studied. With 6 h of the treatment, about 40% of the absorbed Al was bound to the cell wall; however, the amount did not increase thereafter. Meanwhile, the activity of pectin methylesterase, the level of pectin demethylation, the amounts and the average molecular mass of xyloglucan in the root apices significantly decreased upon exposure to Al, resulting in the reduction of Al binding sites. On the other hand, the activity and the gene expression of peroxidase decreased, whereas the activity and gene expression of xyloglucan-degrading enzymes, the expression of expansin A and the H +-ATPase4 genes increased in the Al-treated plants. Interestingly, it was accompanied by the increase of elastic and viscous extensibility of the root apices. From the results, it can be suggested that the biochemical modification of the cell walls reduces sites of Al binding to roots and triggers the activity of the loosening agents, thereby increasing the length of tea roots.

Integrated pathway-based and network-based analysis of GC-MS rice metabolomics data under diazinon stress to infer affected biological pathways.

Diazinon insecticide is widely applied in rice (Oryza sativa L.) fields in Iran. However, concerns are now being raised about its potential adverse impacts on rice. In this study, a time-course metabolic change in rice plants was investigated after diazinon treatment using gas chromatography-mass spectrometry (GC-MS) and subsequently three different methods, MetaboAnalyst, MetaboNetwork, and analysis of reporter reactions, as a potential multivariate method were used to find the underlying changes in metabolism with stronger evidence in order to link differentially expressed metabolites to biological pathways. Results clearly showed the similarity of acetylcholinesterase (AChE) of rice plants to that of animals in terms of its inhibitability by diazinon and emphasized that subsequent accumulation of AChE mainly affects the metabolism of osmolites and tricarboxylic acid intermediates subsequent accumulation of ACh mainly affects the metabolism of osmolites and TCA intermediates.

Sound waves alter the viability of tobacco cells via changes in cytosolic calcium, membrane integrity, and cell wall composition.

The effect of sound waves (SWs) on plant cells can be considered as important as other mechanical stimuli like touch, wind, rain, and gravity, causing certain responses associated with the downstream signaling pathways on the whole plant. The objective of the present study was to elucidate the response of suspension-cultured tobacco cells (Nicotiana tabacum L. cv Burley 21) to SW at different intensities. The sinusoidal SW (1,000 Hz) was produced through a signal generator, amplified, and beamed to the one layer floating tobacco cells inside a soundproof chamber at intensities of 60, 75, and 90 dB at the plate level for 15, 30, 45, and 60 min. Calibration of the applied SW intensities, accuracy, and uniformity of SW was performed by a sound level meter, and the cells were treated. The effect of SW on tobacco cells was monitored by quantitation of cytosolic calcium, redox status, membrane integrity, wall components, and the activity of wall modifying enzymes. Cytosolic calcium ions increased as a function of sound intensity with a maximum level of 90 dB. Exposure to 90 dB was also accompanied by a significant increase of H2O2 and membrane lipid peroxidation rate but the reduction of total antioxidant and radical scavenging capacities. The increase of wall rigidity in these cells was attributed to an increase in wall-bound phenolic acids and lignin and the activities of phenylalanine ammonia-lyase and covalently bound peroxidase. In comparison, in 60- and 75 dB, radical scavenging capacity increased, and the activity of wall stiffening enzymes reduced, but cell viability showed no changes. The outcome of the current study reveals that the impact of SW on plant cells is started by an increase in cytosolic calcium. However, upon calcium signaling, downstream events, including alteration of H2O2 and cell redox status and the activities of wall modifying enzymes, determined the extent of SW effects on tobacco cells.

Optimization of the fermentation media, mathematical modeling, and enhancement of paclitaxel production by Alternaria alternata after elicitation with pectin.

Alternaria alternata fungus is a potent paclitaxel producer isolated from Corylus avellana. The major challenge is the lack of optimized media for endophytic fungi productivity. In the effort to maximize the production of taxoids by A. alternata, several fermentation conditions, including pH (pH 4.0-7.0), different types and concentrations of carbon (fructose, glucose, sucrose, mannitol, sorbitol, and malt extract), and nitrogen (urea, ammonium nitrate, potassium nitrate, ammonium phosphate, and ammonium sulfate) were applied step by step. Based on the results, A. alternata in a medium containing sucrose 5% (w/v) and ammonium phosphate 2.5 mM at pH 6.0 showed a rapid and sustainable growth rate, the highest paclitaxel yield (94.8 µg gFW-1 vs 2.8 µg gFW-1 in controls), and the maximum content of amino acids. Additionally, the effect of pectin was evaluated on fungus, and mycelia harvested. Pectin significantly enhanced the growth and taxoid yield on day 21 (respectively 171% and 116% of their corresponding on day 7). The results were checked out by mathematical modeling as well. Accordingly, these findings suggest a low-cost, eco-friendly, and easy-to-produce approach with excellent biotechnological potential for the industrial manufacture of taxoids.

Selective regulation of nicotine and polyamines biosynthesis in tobacco cells by enantiomers of ornithine.

L- and D-amino acids have diverse functions and effects on the metabolism, growth, and development of plants. Ornithine (Orn) plays a main role in the biosynthesis of many amino acids, nicotinic alkaloids, and polyamines in tobacco. This investigation describes the impact of Orn enantiomers on the production and distribution of free, conjugated, and bound polyamines, as well as nicotine in tobacco cells. It was recognized that the biosynthesis of metabolites was differently upregulated by each enantiomer. Putrescine was abundantly produced by exogenous L-ornithine (L-Orn), and both spermidine and spermine were significantly accumulated in D-ornithine (D-Orn)-supplied tobacco cells. Furthermore, nicotine production was highly upregulated by L-Orn, while the addition of D-Orn had no effect on the nicotine content of tobacco cells. It was observed that transcript expression of S-adenosylmethionine decarboxylase, as the key enzyme of spermidine/spermine biosynthesis, is coincident with their metabolic levels and is highly upregulated by D-Orn, as opposed to L-Orn. These results indicate that both enantiomers of Orn can trigger selected biosynthetic pathways in the cells, at the transcript level. Regarding these observations, it is proposed that L- and D-Orn function differently in the same biological pathways in which the latter, D-Orn specifically regulates important polyamines in the plant cells.

Differential effects of ornithine enantiomers on the activity of anti-oxidant enzymes, polyamines content, and growth of tobacco cells under osmotic stresses.

Ornithine (Orn) plays an essential role in the metabolism of plant cells through incorporation in polyamines biosynthesis, the urea cycle and nitrogen metabolism. Herein, we show that Orn enantiomers have different effects on anti-oxidant enzymes activities, polyamines and proline biosynthesis and also an alleviation effect of osmotic stresses on tobacco cells. The type of stress has a significant impact on the function of L- and D-Orn for improvement of the stress effect on the cells. Under saline conditions, both enantiomers restored cell growth, though D-Orn was more beneficial to some extent. This was accompanied with a higher biosynthesis of putrescine, proline, and up-regulated activity of certain anti-oxidant enzymes by D-Orn. Under drought stress conditions, a distinct differential behavior emerged and only L-Orn showed an alleviative effect on the cell growth. Regulation of hydrogen peroxide content via the activity of catalase/peroxidase and production of osmolytes, e.g., proline and fructans, was dependent on the type of enantiomers. Activity of anti-oxidant enzymes and production of malondialdehyde from cell membranes were differently regulated following treatment with either Orn enantiomer. The results suggest that management of H2 O2 content is a determining feature of the function of Orn enantiomers in tobacco cells under salinity and drought stress conditions.

Antioxidant capacity of parsley cells (Petroselinum crispum L.) in relation to iron-induced ferritin levels and static magnetic field.

This study was aimed to evaluate antioxidant response of parsley cells to 21 ppm iron and static magnetic field (SMF; 30 mT). The activity of catalase (CAT) and ascorbate peroxidase (APX) and the contents of malonyldialdehyde, iron and ferritin were measured at 6 and 12 h after treatments. Exposure to SMF increased the activity of CAT in treated cells, while combination of iron and SMF treatments as well as iron supply alone decreased CAT activity, compared to that of control cells. Combination of SMF with iron treatment reduced iron content of the cells and ameliorated mal effect of iron on CAT activity. All treatments reduced APX activity; however, the content of total ascorbate increased in response to iron and SMF+iron. The results showed that among the components of antioxidant system of parsley cells, enhanced activity of CAT in SMF-treated cells and increase of ascorbate in SMF+Fe-treated ones were responsible for the maintenance of membranes integrity. Ferritin contents of SMF- and SMF+Fe-treated cells also decreased significantly 12 h after treatments, compared to those of the control cells. These results cast doubt on the proposed functions of ferritin as a putative reactive oxygen species detoxifying molecule.

Increase of seed germination, growth and membrane integrity of wheat seedlings by exposure to static and a 10-KHz electromagnetic field.

There is a large body of experimental data demonstrating various effects of magnetic field (MF) on plants growth and development. Although the mechanism(s) of perception of MF by plants is not yet elucidated, there is a possibility that like other stimuli, MF exerts its effects on plants by changing membrane integrity and conductance of its water channels, thereby influencing growth characteristics. In this study, the seeds of wheat (Triticum aestivum L. cv. Kavir) were imbibed in water overnight and then treated with or without a 30-mT static magnetic field (SMF) and a 10-kHz electromagnetic field (EMF) for 4 days, each 5 h. Water uptake of seeds reduced 5 h of the treatment with EMF but did not show changes in SMF treatment. Exposure to both magnetic fields did not affect germination percent of the seeds but increased the speed of germination, compared to the control group. Treatment with EMF significantly reduced seedling length and subsequently vigor index I, while SMF had no effects on these parameters. Both treatments significantly increased vigor index II, compared to the control group. These treatments also remarkably increased catalase activity and proline contents of seedlings but reduced the activity of peroxidase, the rate of lipid peroxidation and electrolyte leakages of membranes. The results suggest promotional effects of EMFs on membrane integrity and growth characteristics of wheat seedlings.

Agrobacterium rhizogenes transformed soybean roots differ in their nodulation and nitrogen fixation response to genistein and salt stress.

We evaluated response differences of normal and transformed (so-called 'hairy') roots of soybean (Glycine max L. (Merr.), cv L17) to the Nod-factor inducing isoflavone genistein and salinity by quantifying growth, nodulation, nitrogen fixation and biochemical changes. Composite soybean plants were generated using Agrobacterium rhizogenes-mediated transformation of non-nodulating mutant nod139 (GmNFR5α minus) with complementing A. rhizogenes K599 carrying the wild-type GmNFR5α gene under control of the constitutive CaMV 35S promoter. We used genetic complementation for nodulation ability as only nodulated roots were scored. After hairy root emergence, primary roots were removed and composite plants were inoculated with Bradyrhizobium japonicum (strain CB1809) pre-induced with 10 µM genistein and watered with NaCl (0, 25, 50 and 100 mM). There were significant differences between hairy roots and natural roots in their responses to salt stress and genistein application. In addition, there were noticeable nodulation and nitrogen fixation differences. Composite plants had better growth, more root volume and chlorophyll as well as more nodules and higher nitrogenase activity (acetylene reduction) compared with natural roots. Decreased lipid peroxidation, proline accumulation and catalase/peroxidase activities were found in 'hairy' roots under salinity stress. Genistein significantly increased nodulation and nitrogen fixation and improved roots and shoot growth. Although genistein alleviated lipid peroxidation under salinity stress, it had no significant effect on the activity of antioxidant enzymes. In general, composite plants were more competitive in growth, nodulation and nitrogen fixation than normal non-transgenic even under salinity stress conditions.

Developed network between taxoid and phenylpropanoid pathways in Cryptosporiopsis tarraconensis, taxan-producing endophytic fungus by Debiased Sparse Partial Correlation (DSPC) algorithm.

Although bioproduction of Paclitaxel by endophytic fungi is highly considered as an alternative promising source, but its yield is usually very low in comparison with other taxoids. Different strategies i.e., chemical and physical elicitations have been developed in order to overcome the shortage of Paclitaxel production. Paclitaxel biosynthesis is started with terpenoid pathway followed by phenylpropanoid metabolism where a benzoylphenylisoserine moiety is attached to C13 of baccatin III skeleton. This point which is catalyzed by the function of PAM seems to be a bottleneck that limits the rate of Paclitaxel production. Whether phenylpropanoids pathway regulates the taxanes biosynthesis in Cryptosporiopsis tarraconensis endophytic fungus elicited with benzoic acid (BA) was hypothesized in the present paper. The involvement of certain signal molecules and key enzymes of terpenoid and phenylpropanoid metabolism were investigated. According to the results, application of BA promoted a signaling pathway which was started with increase of H2O2 and ABA and continued by increase of NO and MJ, and finally resulted in increase of both phenylpropanoids and taxanes. However, again the rate of Paclitaxel production was lower than other taxoids, and the latter was much lower than phenolics. Therefore, supplying benzoic acid provided the precursor for the common taxan ring production. It is unlikely that Paclitaxel production is merely controlled by side chain production stage. It is more likely that in C. tarraconensis endophytic fungus, similar to Taxus sp., the competition between phenylpropanoid and taxoid pathways for substrate ended in favor of the former. The interaction network which was constructed based on DSPC algorithm confirmed that most compounds with close proximity have shared metabolic pathway relationships. Therefore, it is unlikely that the feeding with a given precursor directly result in increase of a desired metabolite which is composed of different merits.

Harmonized biochemical modification of cell walls to get permission for entrance of Azospirillum sp. to rice roots.

Biological nitrogen-fixation is important in increasing crop efficiency. Azospirillum is a nitrogen-fixing microorganism that naturally coexists with grasses roots. The present study was undertaken to clarify the role of rice root cell walls in the acceptance of two Azospirillum species, alone or in combination with indole-3-acetic acid (IAA) and gibberellic acid (GA3) treatments. Rice seedlings were grown in Yoshida solution for 21 days and then inoculated with A. brasilense and A. irakens in the presence of 0, 0.57, and 1.14 mM of IAA or 0, 0.29, and 0.58 mM GA3 or a combination of 1.14 mM of IAA and 0.58 mM of GA3. The results showed that the amount of hydrogen peroxide, lipid peroxidation, total nitrogen and activity of ferulic acid peroxidase, NADPH oxidase, nitrate reductase, pectin methyl esterase, cellulase, mannanase, xylanase and pectinase were significantly increased in inoculated samples treated with or without phytohormones. The highest activity of these enzymes was observed in A. brasilense- inoculated rice roots in auxin+gibberellin treatment. In the latter, the activity of phenylalanine ammonia lyase and wall ferulic acid peroxidase enzymes, the content of cell wall polysaccharide, lignin, and total phenolic compounds were the least, compared to controls and also with those samples which were inoculated with A. irakens. The results indicate an active role of the wall and its enzymes in allowing bacteria to enter the roots. Understanding this mechanism can improve the methods of inoculating bacteria into plants and increase crop efficiency, which will result in reduced use of chemical fertilizers and their destructive environmental effects.

Exogenous melatonin induces phenolic compounds production in Linum album cells by altering nitric oxide and salicylic acid.

Melatonin is a pleiotropic molecule that can influence various aspects of plant performance. Recent studies have exhibited that it mediates plant defensive responses, probably through managing redox homeostasis. We tried to track the regulatory effects of melatonin on the antioxidant machinery of Linum album cell culture. To this, different concentrations of melatonin were applied, and the oxidative status of cells was investigated by measuring the levels of oxidative molecules and antioxidant agents. The results showed that H2O2 content did not change at the low melatonin levels, while it increased at the high concentrations. It can be correlated with the low melatonin dosages capacity to remove excessive amounts of H2O2, while the high melatonin dosages exhibit toxicity effects. In contrast, the NO enhancement occurred at 50 µM melatonin, proposing its role in triggering melatonin-induced defensive responses. The MDA results stated that NO led to oxidative stress in melatonin-treated cells at 50 µM melatonin. Antioxidant enzyme POD was activated by melatonin treatment, while SOD enzyme behaved reversely which can explain the changes in the H2O2 level. In addition, the analysis of the phenolics profile showed that the contents of phenolic acids, flavonoids, and lignans enhanced following an increase in PAL enzyme activity. The increased level of phenolic hormone SA can indicate that melatonin affects the defensive responses in L. album cells through a SA-dependent pathway. In general, it seems that melatonin, by modulating NO and SA levels, can induce the activity of antioxidant enzymes and the production of phenolics, especially lignans, in L. album cells.

Oxidative stress in broad bean (Vicia faba L.) induced by static magnetic field under natural radioactivity.

The investigation was performed to evaluate the influence of the static magnetic field on oxidative stress in Vicia faba cultivated in soil from high background natural radioactivity in Iran. Soil samples were collected from Ramsar, Iran where the annual radiation absorbed dose from background radiation is substantially higher than 20 mSv/year. The soil samples were then divided into 2 separate groups including high and low natural radioactivity. The plants were continuously exposed to static magnetic field of 15 mT for 8 days, each 8h/day. The results showed that in the plants cultivated in soils with high background natural radioactivity and low background natural radioactivity the activity of antioxidant enzymes as well as flavonoid content were lower than those of the control. Treatment of plants with static magnetic field showed similar results in terms of lowering of antioxidant defense system and increase of peroxidation of membrane lipids. Accumulation of ROS also resulted in chromosomal aberration and DNA damage. This phenomenon was more pronounced when a combination of natural radiation and treatment with static magnetic field was applied. The results suggest that exposure to static magnetic field causes accumulation of reactive oxygen species in V. faba and natural radioactivity of soil exaggerates oxidative stress.

Maintenance of membrane integrity and increase of taxanes production in hazel (Corylus avellana L.) cells induced by low-intensity ultrasound.

Suspension-cultured hazel cells were ultrasonicated at power densities of 4 and 455 mW for 4-40 min. Both treatments stimulated the production of major taxanes: Taxol, 10-deacetylbaccatin, and baccatin III. The highest amounts of these taxanes (0.46, 0.26, and 0.07 mg/l, respectively) were obtained at 8 and 20 min of the treatment at 455 mW. Ultrasound had no adverse effects on cell viability, growth, or membrane integrity. Increased release of taxanes by ultrasound resulted not from increased membrane permeability but more likely from stimulation of taxanes biosynthesis.

Biological effects of weak electromagnetic field on healthy and infected lime (Citrus aurantifolia) trees with phytoplasma.

Exposure to electromagnetic fields (EMF) has become an issue of concern for a great many people and is an active area of research. Phytoplasmas, also known as mycoplasma-like organisms, are wall-less prokaryotes that are pathogens of many plant species throughout the world. Effects of electromagnetic fields on the changes of lipid peroxidation, content of H(2)O(2), proline, protein, and carbohydrates were investigated in leaves of two-year-old trees of lime (Citrus aurantifolia) infected by the Candidatus Phytoplasma aurantifoliae. The healthy and infected plants were discontinuously exposed to a 10 KHz quadratic EMF with maximum power of 9 W for 5 days, each 5 h, at 25 °C. Fresh and dry weight of leaves, content of MDA, proline, and protein increased in both healthy and infected plants under electromagnetic fields, compared with those of the control plants. Electromagnetic fields decreased hydrogen peroxide and carbohydrates content in both healthy and infected plants compared to those of the controls.

Molecular and biochemical modifications of suspension-cultured tobacco cell walls after exposure to alternative gravity.

The plant cell wall is a flexible physical barrier surrounding the cell which functions in growth and differentiation, signaling, and response to environmental stimuli including the Earth gravity force. In the present study, structural and molecular modifications of cell wall components of cultured tobacco (Nicotiana tabacum cv. Burley 21) cells under alternative gravity conditions induced by 7 days exposure to 2-D clinostat have been investigated. In comparison with the control group, clinorotation significantly increased biomass but reduced the total amounts of wall and the contents of cellulose, pectin, uronic acidic, and xyloglucan. Gene expression of H+-ATPase was not changed but of expansin A reduced in clinostat-treated cells. However, the gene expression and activity of xyloglucan endotransglycosylase/hydrolases (XTH; EC 2.4.1.207) and endo-(1,4)-ß-D-glucanase (EGase; EC 3.2.1.4), the amount of arabinogalactan proteins (AGP), and the expression of wall-associated kinase (WAK) gene significantly increased by clinorotation. Altered gravity also reduced the activity of polyphenol oxidase and covalently bound peroxidase. The results suggest that altered gravity promoted orchestrated changes of wall-modifying genes and proteins which reduced its stiffness and enhanced cell expansion and division potential.

Phenolics and terpenoids change in response to yeast extract and chitosan elicitation in Zataria multiflora cell suspension culture.

Zataria multiflora is an important medicinal plant with antioxidant and anticancer properties attributed to its phytochemicals. To develop a method for bulk production of valuable phytochemicals, cell suspension culture of Z. multiflora were grown in liquid B5 medium and then treated in their log growth phase with chitosan (0, 10, 20, and 40 mg L-1) and yeast extract (0, 400, 800, and 1200 mg L-1) for 3 days. The levels of hydrogen peroxide (H2O2), nitric oxide (NO), malondialdehyde (MDA), and the main terpenoids and phenylpropanoids in the cell extracts were determined by HPLC and spectrophotometric techniques. The H2O2 and MDA levels significantly increased in the cells treated with both yeast extract and chitosan, while the NO level increased in those exposed to yeast extract. At their highest concentrations, both elicitors significantly increased PAL and TAL activities, as well as phenolic acids and flavonoids contents. Chitosan only induced the production of caffeic acid (22 µg g-1 DW), benzoic acid (2 µg g-1 DW), 4-hydroxy benzoic acid (6 µg g-1 DW), epicatechin (63 µg g-1 DW), and apigenin (5 µg g-1 DW) in the cells, while yeast extract increased the contents of phenylpropanoids gallic acid (50 µg g-1 DW), vanillin (35 µg g-1 DW), salicylic acid (24 µg g-1 DW), catechin (130 µg g-1 DW) and terpenoids carvacrol (7 µg g-1 DW) and thymol (24 µg g-1 DW). In conclusion, changes in the production of phenolics and terpenoids are a defensive mechanism in Z. multiflora cells treated by yeast extract and chitosan. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-022-03235-x.