Phytochrome B regulates resource allocation in Brassica rapa

Regulation of chloroplast biogenesis, development, and signaling by endogenous and exogenous cues

Chloroplasts are one of the defining features in most plants, primarily known for their unique property to carry out photosynthesis. Besides this, chloroplasts are also associated with hormone and metabolite productions. For this, biogenesis and development of chloroplast are required to be synchronized with the seedling growth to corroborate the maximum rate of photosynthesis following the emergence of seedlings. Chloroplast biogenesis and development are dependent on the signaling to and from the chloroplast, which are in turn regulated by several endogenous and exogenous cues. Light and hormones play a crucial role in chloroplast maturation and development. Chloroplast signaling involves a coordinated two-way connection between the chloroplast and nucleus, termed retrograde and anterograde signaling, respectively. Anterograde and retrograde signaling are involved in regulation at the transcriptional level and downstream modifications and are modulated by several metabolic and external cues. The communication between chloroplast and nucleus is essential for plants to develop strategies to cope with various stresses including high light or high heat. In this review, we have summarized several aspects of chloroplast development and its regulation through the interplay of various external and internal factors. We have also discussed the involvement of chloroplasts as sensors of various external environment stress factors including high light and temperature, and communicate via a series of retrograde signals to the nucleus, thus playing an essential role in plants' abiotic stress response.

Generation of High-Value Genomic Resource in Rice: A “Subgenomic Library” of Low-Light Tolerant Rice Cultivar Swarnaprabha

Rice is the major staple food crop for more than 50% of the world’s total population, and its production is of immense importance for global food security. As a photophilic plant, its yield is governed by the quality and duration of light. Like all photosynthesizing plants, rice perceives the changes in the intensity of environmental light using phytochromes as photoreceptors, and it initiates a morphological response that is termed as the shade-avoidance response (SAR). Phytochromes (PHYs) are the most important photoreceptor family, and they are primarily responsible for the absorption of the red (R) and far-red (FR) spectra of light. In our endeavor, we identified the morphological differences between two contrasting cultivars of rice: IR-64 (low-light susceptible) and Swarnaprabha (low-light tolerant), and we observed the phenological differences in their growth in response to the reduced light conditions. In order to create genomic resources for low-light tolerant rice, we constructed a subgenomic library of Swarnaprabha that expedited our efforts to isolate light-responsive photoreceptors. The titer of the library was found to be 3.22 × 105 cfu/mL, and the constructed library comprised clones of 4–9 kb in length. The library was found to be highly efficient as per the number of recombinant clones. The subgenomic library will serve as a genomic resource for the Gramineae community to isolate photoreceptors and other genes from rice.

Auxin inhibits chlorophyll accumulation through ARF7-IAA14-mediated repression of chlorophyll biosynthesis genes in Arabidopsis

Auxin is a well-known important phytohormone in plant that plays vital roles in almost every development process throughout plant lifecycle. However, the effect of auxin on the metabolism of chlorophyll, one of the most important pigments involved in the photosynthesis, was intertwined and the underlying mechanism remained to be explored. Here, we found the auxin-defective yuc2 yuc6 double mutant displayed dark-green leaf color with higher chlorophyll content than wildtype, suggesting a negative regulatory role of auxin in chlorophyll biosynthesis. The chloroplast number and structure in mesophyll cells were altered and the photosynthetic efficiency was improved in yuc2 yuc6. In addition, the chlorophyll level was significantly improved during seedling de-etiolation in yuc2 yuc6 mutant, and decreased dramatically under IAA treatment, confirming the inhibitory role of auxin in chlorophyll biosynthesis. The analyses of gene expression in mature leaves and de-etiolation seedlings suggested that auxin suppressed the expression of many chlorophyll biosynthesis genes, especially PROTOCHLOROPHYLLIDE OXIDOREDUCTASE A (PORA) and GENOMES UNCOUPLED 5 (GUN5). Yeast-one-hybrid and luciferase assays demonstrated that the AUXIN RESPONSE FACTOR 2 (ARF2) and ARF7 bind to the promoter of PORA and GUN5 to suppress their expression with the help of INDOLE-3-ACETIC ACID14 (IAA14). Collectively, our research explicitly unraveled the direct inhibitory role of auxin in chlorophyll biosynthesis, and provided new insight into the interplay between auxin signaling and chlorophyll metabolism.

Biomolecular Strategies for Vascular Bundle Development to Improve Crop Yield

The need to produce crops with higher yields is critical due to a growing global population, depletion of agricultural land, and severe climate change. Compared with the "source" and "sink" transport systems that have been studied a lot, the development and utilization of vascular bundles (conducting vessels in plants) are increasingly important. Due to the complexity of the vascular system, its structure, and its delicate and deep position in the plant body, the current research on model plants remains basic knowledge and has not been repeated for crops and applied to field production. In this review, we aim to summarize the current knowledge regarding biomolecular strategies of vascular bundles in transport systems (source-flow-sink), allocation, helping crop architecture establishment, and influence of the external environment. It is expected to help understand how to use sophisticated and advancing genetic engineering technology to improve the vascular system of crops to increase yield.

The effect of cold acclimation, deacclimation and reacclimation on metabolite profiles and freezing tolerance in winter wheat

Global climate change will cause longer and warmer autumns, thus negatively affecting the quality of cold acclimation (CA) and reducing the freezing tolerance (FT) of winter wheat. Insufficient FT and fluctuating temperatures during winter can accelerate the deacclimation (DEA) process, whereas reacclimation (REA) is possible only while the vernalization requirement is unfulfilled. Six winter wheat genotypes with different winter hardiness profiles were used to evaluate the impact of constant low-temperature (2°C) and prolonged higher low-temperature (28 days at 10°C followed by 2°C until day 49) on shoot biomass and metabolite accumulation patterns in leaf and crown tissues throughout 49 days of CA, 7 days of DEA, and 14 days of REA. The FT of winter wheat was determined as LT₃₀ values by conducting freezing tests after CA, DEA, and REA. Shoot biomass accumulation, projected as the green leaf area (GLA), was investigated by non-destructive RGB imaging-based phenotyping. Dynamics of carbohydrates, hexose phosphates, organic acids, proteins, and amino acids were assessed in leaf and crown tissues. Results revealed that exposure to higher low-temperature induced higher accumulation of shoot biomass and had a negative impact on FT of winter wheat. Prolonged higher low-temperature negatively affected the accumulation of soluble carbohydrates, protein content and amino acids, and had a positive effect on starch accumulation in leaf and crown tissues after CA, in comparison with the constant low-temperature treatment. DEA resulted in significantly reduced FT. Lower concentrations of glucose-6-phosphate, sucrose and proline, as well as higher concentrations of starch in leaves and crowns were found after DEA. The majority of the genotypes regained FT after REA; higher concentrations of glucose and malate in leaves, and sucrose in crown tissue were observed, whereas starch accumulation was decreased in both tissues. Negative correlations were determined between FT and starch concentration in leaves and crowns, while proline and proteins, accumulated in crowns, showed positive correlations with FT. This study broadens the knowledge regarding the effect of different low-temperature regimes on the dynamics of metabolite accumulation in winter wheat throughout CA, DEA, and REA, and its relationship to biomass accumulation and FT.

Does the higher root carbon contribution to soil under cropping cycles following grassland conversion also increase shoot biomass?

This study tested the possible root biomass improvements in crop rotations after the conversion of grasslands, and crop samples from maize, winter wheat, and winter barley were collected during 2011-2013 from a long-term experimental site in Lusignan, France (http://www.soere-acbb). Root biomass C quantification was performed using δ¹³C isotopic signatures to determine the presence of both C3 and C4 plants. We also calculated the recovery rate of maize root biomass C. The results showed that after crop rotations, 0-60 cm root biomass C values were 44.1, 34.2, and 18.7 g C m^-2 for maize, winter wheat, and winter barley respectively. The Root biomass C of crops after conversion to grassland was approximately 2-3 times those observed after crop rotations. However, incorporating ley grassland duration into crop rotations showed limited improvements in shoot biomass C and grain yield of the crops, regardless of the decreased rate of N fertilizer for maize. Moreover, root biomass C had a significant relationship with N supply from residues (P < .05). Nevertheless, shoot biomass C of only maize showed significance in its relationships with N supply and root biomass C. In addition, in each 30 cm soil layer (0-30 cm, 30-60 cm, and 60-90 cm), the recovery rate of maize roots decreased to approximately 15% when root biomass C increased to 10 g C m^-2. However, further increases in root biomass C had little impact on the recovery rate. In conclusion, compared with continuous cropland, incorporating ley grassland duration into crop rotations increases root biomass C of crops, but this change may not be a significant increase of the shoot biomass C or grain yield. This finding simply indicates the improved C input from crops and the potential to increase soil organic C, as well as providing a model for the sustainability of crop rotations.

Auxins, the hidden player in chloroplast development

Throughout decades of plant research, the plant hormones known as auxins have been found to be of vital importance in most plant development processes. Indole-3-acetic acid (IAA) represents the most common auxin in plants and can be synthesized from its tryptophan precursor, which is synthesized in the chloroplast. The chloroplast constitutes an organelle of great relevance to plants since the photosynthesis process by which plants get most of their energy is carried out there. The role of auxins in photosynthesis has been studied for at least 50 years, and in this time, it has been shown that auxins have an effect on several of the essential components and structure of the chloroplast. In recent decades, a high number of genes have been reported to be expressed in the chloroplast and some of their mutants have been shown to alter different auxin-mediated pathways. Genes in signaling pathways such as IAA/AUX, ARF, GH.3, SAUR and TIR, biosynthesis-related genes such as YUCCA and transport-related genes such as PIN have been identified among the most regulated genes in mutants related to alterations in the chloroplast. This review aims to provide a complete and updated summary of the relationship between auxins and several processes that involve the chloroplast, including chloroplast development, plant albinism, redox regulation and pigment synthesis.

Identification, characterization and epitope mapping of proteins encoded by putative allergenic napin genes from Brassica rapa

BACKGROUND

Brassica rapeseed crops contain high concentrations of oil in the seed. The remaining meal, following oil extraction, has a high protein content, but is of low value due to the presence of high amounts of napin seed storage proteins. These 2S albumin-like proteins are difficult to digest and have been identified as major allergens in humans.

OBJECTIVE

To comprehensively characterize the napin gene (NG) family in Brassica rapa and to gain an understanding of the structural basis of allergenicity of the expressed proteins.

METHODS

To identify candidate napin genes in B rapa, 2S albumin-like napin genes of Arabidopsis thaliana were used as query sequences to search for similarity against the B rapa var. pekinensis Chiifu-401 v2 and the var. trilocularis R-o-18 v1.5 genomes. Multiple sequence alignment (MSA) and epitope modelling was carried out to determine structural and evolutionary relationships of NGs and their potential allergenicity.

RESULTS

Four candidate napin genes in R-o-18 and ten in Chiifu-401 were identified with high sequence similarity to A thaliana napin genes. Multiple sequence alignment revealed strong conservation among the candidate genes. An epitope survey indicated high conservation of allergenic epitope motifs with known 2S albumin-like allergens.

CONCLUSION

Napin is thought to be responsible for a  high prevalence of food allergies. Characterization of the napin gene family in B rapa will give important insight into the protein structure, and epitope modelling will help to advance studies into allergenicity including the development of precise diagnostic screenings and therapies for this potential food allergy as well as the possible manipulation of napin levels in the seed by gene editing technology.

Accessions of Brazilian ginseng (Pfaffia glomerata) with contrasting anthocyanin content behave differently in growth, antioxidative defense, and 20-hydroxyecdysone levels under UV-B radiation

Ultraviolet-B (UV-B) radiation is an elicitor of secondary metabolites in plant tissue culture, but the effects on 20-hydroxyecdysone (20E) are still unclear. The 20E may show biotechnological, pharmacological, medical, and agrochemical applicability. Here, we use Pfaffia glomerata, a medically important species, to understand the impacts of UV-B radiation on their physiological performance, the expression of key genes involved in the 20E biosynthesis, and the 20E content. Two accessions (A22 and A43) of plants 20 days old grown in vitro were exposed to 0 (control), 2 (6.84 kJ m^-2), and 4 (13.84 kJ m^-2) h UV-B radiation for 20 consecutive days. Our data showed that UV-B reduced glucose concentration in A22 and A43 under 4 h of exposure (29 and 30%, respectively), while sucrose concentration increased (32 and 57%, respectively). UV-B also differentially impacted the accessions (A22 and A43), where the A22 under 4 h of UV-B had reduced total dry weight (8%) and electron transport rate (31%); in contrast, A43 did not change. Also, only A22 had increased POD activity under 4 h of UV-B (66%), as well as increased gene expression of the 20E pathway and the 20E content under 2 and 4 h of UV-B in leaves (28 and 21%, respectively) and roots (16 and 13%, respectively). This differential performance to UV-B can be explained by the contrasting anthocyanin contents. Notably, A43 displayed 56% more anthocyanin to the former, a possible defense against UV-B. In conclusion, UV-B radiation is a potential elicitor for increasing 20E content in P. glomerata grown in vitro.

Salinity-induced modifications on growth, physiology and 20-hydroxyecdysone levels in Brazilian-ginseng [Pfaffia glomerata (Spreng.) Pedersen]

- Salinity is a major threat to agriculture. However, depending on the concentration of soluble salts in soil, increased secondary metabolite levels can occur with no major damages to plant growth and development. The phytoecdysteroid (PE) 20-hydroxyecdysone (20E) is a secondary metabolite with biotechnological, medicinal, pharmaceutical and agrochemical applicability. Here, we characterize the responses (growth and physiology) of Pfaffia glomerata under different NaCl concentrations and examine the production of 20E as affected by salinity. Forty-day-old plants grown in greenhouse were exposed to 0, 120, 240, 360 or 480 mM of NaCl for 11 days. Moderate salinity (i.e., 120 mM of NaCl) led to increased 20E concentrations in leaves (47%) relative to the control with no significant effect on photosynthesis and biomass accumulation, thus allowing improved 20E contents on a per whole-plant basis. In contrast, plants under high salinity (i.e., 240-480 mM of NaCl) displayed similar 20E concentrations in leaves compared to the control, but with marked impairments to biomass accumulation and photosynthetic performance (coupled with decreased sucrose and starch levels) in parallel to nutritional imbalance. High salinity also strongly increased salicylic acid levels, antioxidant enzyme activities, and osmoregulatory status. Regardless of stress severity, 20E production was accompanied by the upregulation of Spook and Phantom genes. Our findings suggest that P. glomerata cultivation in moderate salinity soils can be considered as a suitable agricultural option to increase 20E levels, since metabolic and structural complexity that makes its artificial synthesis very difficult.