Regulation of flavonoid biosynthesis in representatives of the tribe Phaseoleae DC.

Flavonoids play a crucial role in plant metabolism. Many of them have antioxidant activity, and they are also pigments that render a variety of colors to plant tissues. Foods rich in flavonoid compounds are considered as functional components of a healthy diet. Currently, there is an increased interest in studying genetic mechanisms underlying the coloration of plants. Flavonoid biosynthesis pathways are controlled by two groups of genes. Structural genes encode enzymes, while regulatory genes are responsible for transcription factors that activate the expression of structural genes. Transcription factors that belong to R2R3-Myb, bHLH-Myc and WDR families form the ternary MBW complex, which is involved in regulating the expression of structural genes of flavonoid biosynthesis. The mechanisms of regulation of the anthocyanins and proanthocyanidin biosynthesis by the MBW complex are described in detail for the model plant Arabidopsis thaliana L. This review summarizes data on the regulation of phenolic pigment biosynthesis and the features of phenolic pigment accumulation in plant tissues in the main representatives of the Phaseoleae tribe: soybean Glycine max (L.) Merr., common bean Phaseolus vulgaris L., adzuki bean Vigna angularis (Willd.) Ohwi & Ohashi, and cowpea V. unguiculata (L.) Walp. The species discussed in this review are the most important food legumes in many countries of the world and they comprise the staple food in diets of millions of people. Identification and characterization of the genes controlling the flavonoid biosynthesis pathways are necessary for successful breeding of modern varieties with an increased dietary value. Identification of the flavonoid accumulation patterns is essential for solving the problem of broadening the diversity of plant products.

Conserved and newly acquired roles of PIF1 homologs in tomato (Solanum lycopersicum)

PHYTOCHROME INTERACTING FACTORs (PIFs) are transcription factors that interact with the photoreceptors phytochromes and integrate multiple signaling pathways related to light, temperature, defense and hormone responses. PIFs have been extensively studied in Arabidopsis thaliana, but less is known about their roles in other species. Here, we investigate the role of the two homologs of PIF1 found in tomato (Solanum lycopersicum), namely PIF1a and PIF1b. Analysis of gene expression showed very different patterns, indicating a potential evolutionary divergence in their roles. At the protein level, light regulated the stability of PIF1a, but not PIF1b, further supporting a functional divergence. Phenotypic analyses of CRISPR-Cas9-generated tomato mutants defective in PIF1a or PIF1b or both revealed conserved and newly acquired roles compared to Arabidopsis PIF1. Both PIF1a or PIF1b were found to regulate seed germination, photosynthetic pigment biosynthesis and fruit production. However, only PIF1a-defective mutants showed defects on root hair elongation, flowering time and fruit growth and softening. We did not identify any process altered only in plants lacking PIF1b. Together, these data show that neofunctionalization has taken place in tomato, illustrating the potential of these transcription factors to acquiring new roles in different species.

Improving Drought Tolerance in Tobacco By Application of Salicylic Acid

Drought causes not only the decrease of tobacco yield and quality, but also the lowering of net photosynthetic rate, leading to reactive oxygen species accumulation and even the death of plants. Salicylic Acid is involved in regulating many plant physiological processes and has increasingly been applied to improve tolerance in plants exposed to drought stress. To explore the regulating mechanism of SA, flue-cured tobacco K326 was used in the hydroponic experiments to design PEG drought stress. The photosynthetic characteristics, antioxidant enzymes activities and osmotic regulatory substances contents of tobacco seedlings under drought stress were investigated after 0.3 mmol L-1 SA treatment. Transcriptome sequencing and GO/KEGG analysis were also performed. The main results showed that SA-applied greatly increased the activities of SOD, POD, CAT activity, Pn, proline and soluble protein by 44.27%, 50.18%, 26.23%, 45.74%, 34.67% and 24.91% while reduced the MDA content by 23.89%. GO and KEGG analysis showed that SA treatment was able to up-regulate the genes involved in photosynthesis, carbon metabolism, porphyrin and chlorophyll metabolism, photosynthesis-antenna proteins. The conclusion is that SA application would effectively improve the ability of pigment biosynthesis and photosystem repair of tobacco under drought conditions, thus enhance the photosynthesis, reduce the accumulation of ROS and increase drought resistance, which would provide a measure for alleviating the damage of tobacco caused by drought stress.

Light Harvesting-like Protein 3 Interacts with Phytoene Synthase and Is Necessary for Carotenoid and Chlorophyll Biosynthesis in Rice

Background Carotenoid biosynthesis is essential for the generation of photosynthetic pigments, phytohormone production, and flower color development. The light harvesting like 3 (LIL3) protein, which belongs to the light-harvesting complex protein family in photosystems, interacts with geranylgeranyl reductase (GGR) and protochlorophyllide oxidoreductase (POR) both of which are known to regulate terpenoid and chlorophyll biosynthesis, respectively, in both rice and Arabidopsis. Results In our study, a CRISPR-Cas9 generated 4-bp deletion mutant oslil3 showed aberrant chloroplast development, growth defects, low fertility rates and reduced pigment contents. A comparative transcriptomic analysis of oslil3 suggested that differentially expressed genes (DEGs) involved in photosynthesis, cell wall modification, primary and secondary metabolism are differentially regulated in the mutant. Protein-protein interaction assays indicated that LIL3 interacts with phytoene synthase (PSY) and in addition the gene expression of PSY genes are regulated by LIL3. Subcellular localization of LIL3 and PSY suggested that both are thylakoid membrane anchored proteins in the chloroplast. We suggest that LIL3 directly interacts with PSY to regulate carotenoid biosynthesis. Conclusion This study reveals a new role of LIL3 in regulating pigment biosynthesis through interaction with the rate limiting enzyme PSY in carotenoid biosynthesis in rice presenting it as a putative target for genetic manipulation of pigment biosynthesis pathways in crop plants.

The cyanobacterium Prochlorococcus has divergent light-harvesting antennae and may have evolved in a low-oxygen ocean

Marine picocyanobacteria of the genus Prochlorococcus are the most abundant photosynthetic organisms in the modern ocean, where they exert a profound influence on elemental cycling and energy flow. The use of transmembrane chlorophyll complexes instead of phycobilisomes as light-harvesting antennae is considered a defining attribute of Prochlorococcus. Its ecology and evolution are understood in terms of light, temperature, and nutrients. Here, we report single-cell genomic information on previously uncharacterized phylogenetic lineages of this genus from nutrient-rich anoxic waters of the eastern tropical North and South Pacific Ocean. The most basal lineages exhibit optical and genotypic properties of phycobilisome-containing cyanobacteria, indicating that the characteristic light-harvesting antenna of the group is not an ancestral attribute. Additionally, we found that all the indigenous lineages analyzed encode genes for pigment biosynthesis under oxygen-limited conditions, a trait shared with other freshwater and coastal marine cyanobacteria. Our findings thus suggest that Prochlorococcus diverged from other cyanobacteria under low-oxygen conditions before transitioning from phycobilisomes to transmembrane chlorophyll complexes and may have contributed to the oxidation of the ancient ocean.

Mechanical Cell Disruption Technologies for the Extraction of Dyes and Pigments from Microorganisms: A Review

The production of pigments using single cell microorganisms is gaining traction as a sustainable alternative to conventional syntheses, which rely, in no negligible proportions, on petrochemicals. In addition to depending on petroleum, these syntheses involved the use of toxic organic solvents, which may be inadequately disposed of across a range of industries, thus compounding the deleterious effects of fossil fuel exploitation. Literature suggests that notable research efforts in the area of sustainable pigment production using single cell microorganisms are focused on the production of pigments coveted for their interesting qualities, which transcend their mere capacity to dye various fabrics both natural and synthetic. As interest in sustainable pigment biosynthesis grows, the need to devise effective and efficient cell disruption processes becomes more pressing given that the viability of pigment biosynthesis is not only dependent on microorganisms’ yield in terms of production, but also on researchers’ ability to recover them. This review chiefly reports findings as to mechanical cell disruption methods, used individually or in various combinations, and their aptitude to recover biosynthetic pigments.

Nitrogen Sources and Iron Availability Affect Pigment Biosynthesis and Nutrient Consumption in Anabaena sp. UTEX 2576

Anabaena sp. UTEX 2576 metabolizes multiple nitrogen (N) sources and is deemed a biotechnological platform for chemical production. Cyanobacteria have been identified as prolific producers of biofertilizers, biopolymers, biofuels, and other bioactive compounds. Here, we analyze the effect of different N-sources and Fe availability on the bioproduction of phycobiliproteins and β-carotene. We characterize nutrient demand in modified BG11 media, including data on CO2 fixation rates, N-source consumption, and mineral utilization (e.g., phosphorus (P), and 11 metallic elements). Results suggest that non-diazotrophic cultures grow up to 60% faster than diazotrophic cells, resulting in 20% higher CO2-fixation rates. While the production of β-carotene was maximum in medium with NaNO3, Fe starvation increased the cellular abundance of C-phycocyanin and allophycocyanin by at least 22%. Compared to cells metabolizing NaNO3 and N2, cultures adapted to urea media increased their P, calcium and manganese demands by at least 72%, 97% and 76%, respectively. Variations on pigmentation and nutrient uptake were attributed to changes in phycocyanobilin biosynthesis, light-induced oxidation of carotenoids, and urea-promoted peroxidation. This work presents insights into developing optimal Anabaena culture for efficient operations of bioproduction and wastewater bioremediation with cyanobacteria.

Transcriptome Dynamics during Black and White Sesame (Sesamum indicum L.) Seed Development and Identification of Candidate Genes Associated with Black Pigmentation

Seed coat color is a crucial agronomic trait in sesame (Sesamum indicum L.) since it is strongly linked to seed oil, proteins, and lignans contents, and also influences consumer preferences. In East Asia, black sesame seed is used in the treatment and the prevention of various diseases. However, in sesame, little is known about the establishment of the seed coat color, and only one gene has been reported to control black pigmentation. This study provides an overview of developing seeds transcriptome of two varieties of sesame “Zhongfengzhi No.1” (white seed) and “Zhongzhi No.33” (black seed) and shed light on genes involving in black seed formation. Until eight days post-anthesis (DPA), both the seeds of the two varieties were white. The black sesame seed turned to yellow between 9 and 11 DPA and then black between 12 and 14 DPA. The black and white sesame showed similar trend-expressed genes with the numbers increased at the early stages of seed development. The differentially expressed genes (DEGs) number increased with seed development in the two sesame varieties. We examined the DEGs and uncovered that more were up-regulated at the early stages. The DEGs between the black and white sesame were mainly enriched in 37 metabolic pathways, among which the flavonoid biosynthesis and biosynthesis of secondary metabolites were dominants. Furthermore, we identified 20 candidate genes associated with pigment biosynthesis in black sesame seed, among which 10 were flavonoid biosynthesis and regulatory genes. These genes also include isochorismate and polyphenol oxidase genes. By comparing the phenotypes and genes expressions of the black and white sesame seed at different development stages, this work revealed the important role of 8–14 DPA in black pigment biosynthesis and accumulation. Moreover, it unfolded candidate genes associated with black pigmentation in sesame. These findings provide a vast transcriptome dataset and list of genes that will be targeted for functional studies related to the molecular mechanism involved in biosynthesis and regulation of seed coat color in sesame.