Mechanisms and effective control of physiological browning phenomena in plant cell cultures

Physiology, Biochemistry, and Transcriptomics Jointly Reveal the Phytotoxicity Mechanism of Acetochlor on Pisum sativum L

Acetochlor, as a commonly used pre-emergent herbicide, can be toxic to crops and affect production if used improperly. However, the toxic mechanism of acetochlor on plants is not fully understood. The present study used a combination of transcriptomic analysis and physiological measurements to investigate the effects of short-term (15-day) exposure to different concentrations of acetochlor (1, 10, 20 mg/kg) on the morphology, physiology, and transcriptional levels of pea seedlings, aiming to elucidate the toxic response and resistance mechanisms in pea seedlings under herbicide stress. The results showed that the toxicity of acetochlor to pea seedlings was dose-dependent, manifested as dwarfing and stem base browning with increasing concentrations, especially at 10 mg/kg and above. Analysis of the antioxidant system showed that from the 1 mg/kg treatment, malondialdehyde, superoxide dismutase, peroxidase, and glutathione peroxidase in peas increased with increasing concentrations of acetochlor, indicating oxidative damage. Analysis of the glutathione (GSH) metabolism system showed that under 10 mg/kg treatment, the GSH content of pea plants significantly increased, and GSH transferase activity and gene expression were significantly induced, indicating a detoxification response in plants. Transcriptomic analysis showed that after acetochlor treatment, differentially expressed genes in peas were significantly enriched in the phenylpropane metabolic pathway, and the levels of key metabolites (flavonoids and lignin) were increased. In addition, we found that acetochlor-induced dwarfing of pea seedlings may be related to gibberellin signal transduction. Environ Toxicol Chem 2024;00:1-15. © 2024 SETAC.

Metabolome and transcriptome integration explored the mechanism of browning in Glycyrrhiza uralensis Fisch cells

Introduction

Glycyrrhiza uralensis Fisch, a traditional Chinese medicinal herb known for its diverse pharmacological effects including heat-clearing, detoxification, phlegm dissolving, and cough relief, has experienced an exponential increase in demand due to its expanding clinical use and development prospects. Currently, large-scale cell culture stands out as one of the most promising biotechnological approaches for producing bioactive compounds from medicinal plants. However, the problem of cell browning represents a significant bottleneck in industrial applications of cell culture.

Methods

This study focuses on the Glycyrrhiza uralensis Fisch cells from the Ordos plateau, aiming to elucidate the enzymatic browning process during plant cell culture. Key substrates and genes involved in enzymatic browning were identified by metabolome and transcriptome analysis of normal and browning cells.

Results

Metabolome analysis reveals significant changes in the levels of chalcone, isoflavone, imidazole-pyrimidine, purine nucleosides, organic oxides, carboxylic acids and their derivatives, benzene and its derivatives, flavonoids, 2-arylated benzofuran flavonoids, diazanaphthalenes and fatty acyls within browning cells. In particular, chalcones, isoflavones, and flavones compounds account for a higher proportion of these changes. Furthermore, these compounds collectively show enrichment in four metabolic pathways: Isoflavone biosynthesis pathway; Cutin suberine and wax biosynthesis pathway; Aminoacyl-tRNA biosynthesis pathway; Isoquinoline alkaloid biosynthesis pathway; Transcriptome analysis revealed that the MYB transcription factor is a key regulator of flavonoid synthesis during the browning process in cells. In addition, 223 differentially expressed genes were identified, including phenylpropane, shikimic acid, glycolysis, and pentose phosphate pathways. Among these genes, 23 are directly involved in flavonoid biosynthesis; qPCR validation showed that eight genes (GlPK, GlPAL, Gl24CL, Gl1PDT, Gl3CHI, GlC4H, Gl2F3'H, and Gl2CCR) were up-regulated in browning cells compared to normal cells. These findings corroborate the sequencing results and underscore the critical role of these genes in cellular browning.

Discussion

Consequently, modulation of their expression offers promising strategies for effective control of cellular browning issues.

Identification of QTLs responsible for culturability, and fine-mapping of QTL qCBT9 related to callus browning derived from Dongxiang common wild rice (Oryza rufipogon Griff.)

Compared to japonica, the lower genetic transformation efficiency of indica is a technical bottleneck for rice molecular breeding. Specifically, callus browning frequently occurs during the culture of the elite indica variety 93-11, leading to poor culturability and lower genetic transformation efficiency. Here, 67 QTLs related to culturability were detected using 97 introgression lines (designated as 9DILs) derived from Dongxiang common wild rice (DXCWR, Oryza rufipogon Griff.) with 93-11 genetic background, explaining 4% ~12% of the phenotypic variations. The QTL qCBT9 on chromosome 9 was a primary QTL for reducing callus browning derived from DXCWR. Five 9DILs with light callus browning and high differentiation were screened. We evaluated the callus browning index (CBI) of 100 F2 population crossed of 93-11 and 9DIL71 and the recombinant plants screened from 3270 individuals. The qCBT9 was delimited to a ~148kb region between the markers X16 and X23. RNA-seq analysis of DEGs between 9DIL71 and 93-11 showed three upregulated DEGs (Os09g0526500, Os09g0527900, Os09g0528200,) and three downregulated DEGs (Os09g0526700, Os09g0526800, Os09g0527700) were located in the candidate region of qCBT9. Furthermore, callus browning may be involved in cell senescence and death caused by oxidative stress. The differentiation of indica and japonica in this region suggested that qCBT9 was possibly a vital QTL contributed to better culturability of japonica. Our results laid a foundation for further cloning of the gene for reduced callus browning in O. rufipogon, and also provided a new genetic resource and material basis for improving the culturability and genetic transformation efficiency of cultivated rice.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-024-01470-z.

Targeted control of supporting pathways in paclitaxel biosynthesis with CRISPR-guided methylation

Introduction: Plant cell culture biomanufacturing is rapidly becoming an effective strategy for production of high-value plant natural products, such as therapeutic proteins and small molecules, vaccine adjuvants, and nutraceuticals. Many of these plant natural products are synthesized from diverse molecular building blocks sourced from different metabolic pathways. Even so, engineering approaches for increasing plant natural product biosynthesis have typically focused on the core biosynthetic pathway rather than the supporting pathways. Methods: Here, we use both CRISPR-guided DNA methylation and chemical inhibitors to control flux through the phenylpropanoid pathway in Taxus chinensis, which contributes a phenylalanine derivative to the biosynthesis of paclitaxel (Taxol), a potent anticancer drug. To inhibit PAL, the first committed step in phenylpropanoid biosynthesis, we knocked down expression of PAL in Taxus chinensis plant cell cultures using a CRISPR-guided plant DNA methyltransferase (NtDRM). For chemical inhibition of downstream steps in the pathway, we treated Taxus chinensis plant cell cultures with piperonylic acid and caffeic acid, which inhibit the second and third committed steps in phenylpropanoid biosynthesis: cinnamate 4-hydroxylase (C4H) and 4-coumaroyl-CoA ligase (4CL), respectively. Results: Knockdown of PAL through CRISPR-guided DNA methylation resulted in a profound 25-fold increase in paclitaxel accumulation. Further, through the synergistic action of both chemical inhibitors and precursor feeding of exogenous phenylalanine, we achieve a 3.5-fold increase in paclitaxel biosynthesis and a similar reduction in production of total flavonoids and phenolics. We also observed perturbations to both activity and expression of PAL, illustrating the complex transcriptional co-regulation of these first three pathway steps. Discussion: These results highlight the importance of controlling the metabolic flux of supporting pathways in natural product biosynthesis and pioneers CRISPR-guided methylation as an effective method for metabolic engineering in plant cell cultures. Ultimately, this work demonstrates a powerful method for rewiring plant cell culture systems into next-generation chassis for production of societally valuable compounds.

Phytosulfokine contributes to suspension culture of Cunninghamia lanceolata through its impact on redox homeostasis

BACKGROUND

Suspension culture is widely used in the establishment of efficient plant regeneration systems, as well as in the mass production of plant secondary metabolites. However, the establishment of a suspension culture system of Cunninghamia lanceolata is genotype-dependent given that proembryogenic masses (PEMs) are prone to browning during this process in recalcitrant genotypes. Previously, we reported that the plant peptide hormone phytosulfokine (PSK) can tremendously decrease the hydrogen peroxide (H2O2) level and help to initiate somatic embryogenesis (SE) in recalcitrant C. lanceolata genotypes. However, to date, no studies have revealed whether or how PSK may contribute to the establishment of a suspension culture system in these recalcitrant genotypes.

RESULTS

Here, we demonstrated that exogenous application of PSK effectively inhibited PEM browning during suspension culture in a recalcitrant genotype of C. lanceolata. Comparative time-series transcriptome profiling showed that redox homeostasis underwent drastic fluctuations when PEMs were cultured in liquid medium, while additional PSK treatment helped to maintain a relatively stable redox homeostasis. Interestingly, PSK seemed to have a dual effect on peroxidases (PRXs), with PSK simultaneously transcriptionally repressing ROS-producing PRXs and activating ROS-scavenging PRXs. Furthermore, determination of H2O2 and MDA content, as well as cell viability, showed that exogenous PSK treatment inhibited PEM browning and safeguarded PEM suspension culture by decreasing the H2O2 level and increasing PEM activity.

CONCLUSIONS

Collectively, these findings provide a valuable tool for the future establishment of large-scale C. lanceolata PEM suspension culture without genotype limitations.

Harnessing the power of botanical gardens: Evaluating the costs and resources needed for exceptional plant conservation

PREMISE

The effective ex situ conservation of exceptional plants, whether in living collections or cryo-collections, requires more resources than the conservation of other species. Because of their expertise with rare plants, botanical gardens are well positioned to lead this effort, but a well-developed strategy requires a clear understanding of the resources needed.

METHODS

Grant funding was obtained from the Institute of Museum and Library Services to support a three-year project on cryobanking, and to provide smaller grants to 10 other botanical gardens for one-year projects on either (1) seed behavior studies or (2) the development of protocols for in vitro propagation or cryopreservation.

RESULTS

Nine of the partner gardens worked on 19 species (one was unable to continue due to the COVID-19 pandemic), while the larger project focused on 14 species. A point system was developed for tasks accomplished, and the average costs per point of the larger and smaller projects were similar. Labor accounted for half the costs. Projects focused on species in the Asteraceae and Orchidaceae had lower costs per point than other species.

DISCUSSION

Both large and small projects can contribute to a strategy for exceptional plant conservation for similar costs. Prioritizing species with lower costs could help advance the field while allowing time for work on more difficult species to develop.

N-Acetyl-d-glucosamine Inhibition of Hexokinase Results in Downregulation of the Phenylpropanoid Metabolic Pathway and Decreased Resistance to Brown Rot in Peach Fruit

To explore the role of hexokinase (HXK) on disease resistance in peach fruit, peaches were treated with N-acetyl-d-glucosamine (NAG), a known HXK inhibitor, and then inoculated with Monilinia fructicola. We demonstrate that NAG significantly inhibits HXK activity, which in turn results in significantly reduced resistance to M. fructicola infection. In the HXK-inhibited fruit, the sucrose content was higher and the glucose and fructose contents were lower than in the control fruit. By transcriptome analysis, we found 347 differentially expressed genes (DEGs) between NAG-treated and control peaches, most of which were involved in the mitogen-activated protein kinase signaling pathway in plants, plant-pathogen interaction, plant hormone signal transduction, and the phenylpropanoid biosynthesis pathway. In particular, the DEGs related to phenylpropanoid metabolism, such as peroxidase, flavonoid, and isoflavonoid biosynthesis were significantly downregulated. Nontargeted metabolomic analysis revealed 44 differential metabolites, 9 of which were increased and 35 of which were decreased in the NAG-treated fruit. The decreased metabolites were secondary metabolites, including polyphenols, flavonoids, terpenoids, and glycosides. The relationship between HXK and phenylpropanoid metabolism was further investigated, and we found that in HXK-inhibited fruits the activities of phenylalanine ammonia-lyase, 4-coumarate-CoA ligase, and cinnamate 4-hydroxylase were significantly decreased over the control fruit, as well as the total phenol and total flavone contents were also significantly decreased. These results demonstrate that the inhibition of HXK activity decreases the disease resistance of peach fruits by affecting sugar metabolism and the phenylpropanoid pathway.

A novel spray bioreactor for the proliferation of plant callus; Hyoscyamus niger and Arnebia pulchra

OBJECTIVE

Unlike plant cell suspension culture, the proliferation of callus in bioreactors has received inadequate attention. The magnificent potential of plant callus becomes more appreciated as the research unfolds and promises interesting applications including the production of valuable metabolites, therapeutic antibodies, bioactive extracts with regenerating effects, and the generation of genetically improved plants. Issues such as the lack of 3D-access of the cells to the nutrients, using an interfering gelling substance as the support matrix, and the changes in the medium formulation during the growth phase were discouraging factors for extending research on this topic. Considering the existing drawbacks, a novel open-flow spray bioreactor (OFSB) was configured to circumvent the associated problems with the solid cell culture and promote the applicability of plant callus culture via improving the feeding strategy.

METHODS

Applying similar subculture conditions, the proliferation of Arnebia pulchra and Hyoscyamus niger calli as the examples of two important plant families (Boraginaceae and Solanaceae) was studied in the OFSB in comparison with similar calli that grew in Petri dishes and jars.

RESULTS

A. pulchra and H. niger calli obtained the weight gains of (%87.3 and %106.7) in the Petri dishes, (%208.7 and %226) in the jars, and (%288.6 and %320.0) in OFSB, respectively, while no significant changes were observed in the productivity indices of the examined calli.

CONCLUSION

The simple design of OFSB bypasses most of the notorious problems associated with solid plant callus culture. OFSB technical features allow the bioreactor to be used for growth optimization of various types of plant calli in a cost-effective manner.

Effect of UV-B Radiation on Flavonoids and Phenols Accumulation in Tempisque (Sideroxylon capiri Pittier) Callus

Tempisque (Sideroxylon capiri Pittier) is classified as a threatened species and has been reported with a high content of phenols and flavonoids in the leaves. The use of abiotic elicitors such as radiation has been reported due to the changes it produces in the metabolism of plants by activating their defense mechanisms and increasing the biosynthesis of bioactive compounds with antioxidant capacity such as phenols and flavonoids. Therefore, the aim of this work was to evaluate the effect of UV-B radiation on growth parameters and the synthesis of bioactive compounds in in vitro culture of tempisque callus. For the callus induction, we used thidiazuron (TDZ) and 2,4-dichlorophenoxyacetic acid (2,4-D) at 0, 0.5 and 1 mg/L. Calluses were exposed to UV-B radiation (0, 1, 2, 3 and 4 h/day) for two and four weeks. The highest callus formation index was obtained with TDZ and 2,4-D at 1 mg/mL. The greatest increase in the concentration of phenols and flavonoids was detected in the fourth week with 4 h of exposure per day. The highest concentrations of quercetin (230 µg/g dry weight), kaempferol (235 µg/g dry weight) and gallic acid (240 µg/g dry weight) were found in callus obtained from leaves explants.

The Effect of Endogenous Hormones, Total Antioxidant and Total Phenol Changes on Regeneration of Barley Cultivars

Background

Barley (Hordeum vulgar L.) is a valuable platform for producing recombinant proteins. Before using different barley cultivars as an efficient platform for molecular farming, optimization of cultural conditions and studying the effective factors on the tissue culture are critical.

Objectives

In this study, we evaluated callus induction, plant regeneration and changes in the levels of total antioxidant, total phenol and endogenous hormones of three Iranian barley cultivars (Reyhan, Yousef and Bahman) and Golden Promise cultivar.

Materials and Methods

We used immature embryos as explants on MS-based medium containing 3 mg.L^-1 2,4-D for callus induction. Calluses were transferred to regeneration media with 2 mg.L^-1 BAP. The levels of endogenous hormones were measured using High-Performance Liquid Chromatography system and total antioxidant and total phenols were determined using a spectrophotometer.

Results

We demonstrated that callus formation was very high in all cultivars (about 91%) and all immature embryo explants had the potential to produce embryogenic calluses. The present study also showed that the regeneration rates among the studied cultivars were very different and the Iranian cultivars showed lower regeneration percentages (about 1.4%) compared to Golden Promise cultivar (about 72.5%). The levels of endogenous hormones in Iranian cultivars and Golden Promise varied distinctly and significant differences in terms of total antioxidants and total phenols were found in the two groups.

Conclusions

Accumulated evidence suggests that for successful regeneration of recalcitrant cultivars, external treatments should be done in a way to reduce the inhibitory effects of internal factors.

Green (cell) factories for advanced production of plant secondary metabolites

For centuries plants have been intensively utilized as reliable sources of food, flavoring, agrochemical and pharmaceutical ingredients. However, plant natural habitats are being rapidly lost due to climate change and agriculture. Plant biotechnology offers a sustainable method for the bioproduction of plant secondary metabolites using plant in vitro systems. The unique structural features of plant-derived secondary metabolites, such as their safety profile, multi-target spectrum and "metabolite likeness," have led to the establishment of many plant-derived drugs, comprising approximately a quarter of all drugs approved by the Food and Drug Administration and/or European Medicinal Agency. However, there are still many challenges to overcome to enhance the production of these metabolites from plant in vitro systems and establish a sustainable large-scale biotechnological process. These challenges are due to the peculiarities of plant cell metabolism, the complexity of plant secondary metabolite pathways, and the correct selection of bioreactor systems and bioprocess optimization. In this review, we present an integrated overview of the possible avenues for enhancing the biosynthesis of high-value marketable molecules produced by plant in vitro systems. These include metabolic engineering and CRISPR/Cas9 technology for the regulation of plant metabolism through overexpression/repression of single or multiple structural genes or transcriptional factors. The use of NMR-based metabolomics for monitoring metabolite concentrations and additionally as a tool to study the dynamics of plant cell metabolism and nutritional management is discussed here. Different types of bioreactor systems, their modification and optimal process parameters for the lab- or industrial-scale production of plant secondary metabolites are specified.

A common wild rice-derived BOC1 allele reduces callus browning in indica rice transformation

Callus browning, a common trait derived from the indica rice cultivar (Oryza sativa L.), is a challenge to transformation regeneration. Here, we report the map-based cloning of BROWNING OF CALLUS1 (BOC1) using a population derived from crossing Teqing, an elite indica subspecies exhibiting callus browning, and Yuanjiang, a common wild rice accession (Oryza rufipogon Griff.) that is less susceptible to callus browning. We show that BOC1 encodes a SIMILAR TO RADICAL-INDUCED CELL DEATH ONE (SRO) protein. Callus browning can be reduced by appropriate upregulation of BOC1, which consequently improves the genetic transformation efficiency. The presence of a Tourist-like miniature inverted-repeat transposable element (Tourist MITE) specific to wild rice in the promoter of BOC1 increases the expression of BOC1 in callus. BOC1 may decrease cell senescence and death caused by oxidative stress. Our study provides a gene target for improving tissue culturability and genetic transformation.

Callus browning heavily affects indica rice transformation regeneration. Here, the authors show transposon insertion in the promoter of BOC1 gene, encoding a SIMILAR TO RADICAL-INDUCED CELL DEATH ONE protein, can upregulate its expression and decrease callus browning in cultivated rice by releasing oxidative stress.