Carotenoids biosynthesis and cleavage related genes from bacteria to plants

Engineering tobacco for efficient astaxanthin production using a linker-free monocistronic dual-protein expression system and interspecific hybridization method

The high-value carotenoid astaxanthin is biosynthesized through a dual-enzyme-catalyzed cascade and is getting increased attention for engineered biosynthesis in plants. When developing astaxanthin-producing tobacco by expressing 2A-peptide-linked CBFD (carotenoid β-ring-4-dehydrogenase) and HBFD (carotenoid 4-hydroxy-β-ring-4-dehydrogenase) from Adonis aestivalis, this work discovered an in-enzyme splicing site at the N-terminus of HBFD that has potentials for multiple protein expression in plant using monocistronic cassette. Based on this finding, we generated astaxanthin-producing tobacco plants expressing a directly fused protein of CBFD and HBFD with a monocistronic cassette. Further integrated IP (immunoprecipitation) and LC-MS/MS assays revealed the presence of an in-enzyme splicing site at the N-terminus of HBFD. Nevertheless, the obtained astaxanthin-producing tobacco plants exhibited a growth retardation as observed by previous researches. Subsequent studies revealed that the astaxanthin-producing caused growth retardation of tobacco was correlated with chloroplast disruption and chlorophyll reduction, and it could be alleviated by expressing a chlorophyll biosynthetic enzyme identified by proteomics. Additionally, crossing the astaxanthin-producing tobacco with a variety having higher chlorophyll content also alleviated the growth retardation caused by astaxanthin production, and improved the total astaxanthin yield per plant by at least threefold along with the biomass increase. This work provides novel approaches for expressing multiple proteins in tobacco and for engineering efficient astaxanthin-producing tobacco.

Elevated accumulation of lutein and zeaxanthin in a novel high-biomass yielding strain Dunaliella sp. ZP-1 obtained through EMS mutagenesis

BACKGROUND

Dunaliella microalgae, such as Dunaliella salina riching in β-carotene and Dunaliella bardawil rich in lutein and α-carotene, have been used in aquaculture, supplements, cosmetics, and feed industries. The genus Dunaliella is diverse; therefore, characterization of novel strains and isolation of new varieties through mutagenesis technology will promote natural carotenoid bioproduction.

RESULTS

Salt stress test demonstrated that the newly isolated microalgae strain ZP-1 was a halotolerant strain. Morphology observation and molecular phylogeny analysis indicated that the unicellular green microalga ZP-1 was a member of the genus Dunaliella. Biomass of ZP-1 in RAM medium was up to 2.45 g/L, showing the advantage over other common Dunaliella microalgae in terms of yield. Furthermore, Ethyl methanesulfonate (EMS) mutant library was generated from this high-biomass strain, aiming to improve natural carotenoid productivity. A mutant strain was selected through morphology observation combining with carotenoid quantification by HPLC, which was nominated as turn yellow dunaliella 4 (tyd4). The mutant tyd4 displayed an increased lutein productivity by 28.55% and an increased zeaxanthin productivity by 22.19%. Biomass of tyd4 was promoted by 17.40% through continuous culture under red light. Application of exogenous 1.0 μM melatonin on the mutant tyd4 led to increased cell density and improved biomass.

CONCLUSIONS

Results in this study support that EMS mutagenesis is an effective breeding approach for further improvement of Dunaliella sp. ZP-1, which is a high-biomass microalgae exhibiting potential to overcome the bottleneck of low biomass of current commercial Dunaliella strains. The mutant tyd4 had higher contents of both lutein and zeaxanthin, whose yield could be further elevated by red light and melatonin. This study provided new microalgae sources for scientific research and technical reference for the bioproduction of natural carotenoids.

Integrated Multi-Omics Analysis Reveals Glycosylation Involving 2-O-β-D-Glucopyranosyl-L-Ascorbic Acid Biosynthesis in Lycium barbarum

L-ascorbic acid (vitamin C, AA) is widely present in plants, but humans lack the ability to synthesize it independently. As a potent reducing agent, AA is susceptible to oxidation, making the enhancement of its stability crucial. 2-O-β-D-glucopyranosyl-L-ascorbic acid (AA-2βG) is a stable natural derivative of AA with glycosylation, initially discovered in the fruits of Lycium barbarum. Understanding the biosynthesis of AA-2βG is crucial for enhancing its production in L. barbarum. While the established biosynthesis pathway of AA constitutes the upstream of AA-2βG biosynthesis, the conclusive step of β-glycosylation remains unclear. We identified a L. barbarum cultivar by UPLC, ZN01, with a high content of AA-2βG, and compared its leaves, immature fruits, and mature fruits to a normal AA-2βG content L. barbarum cultivar for metabolomic and transcriptomic analysis. The RNA-seq and RT-qPCR analysis revealed that the expression levels of genes involved in the AA biosynthesis pathway did not consistently correlate with AA-2βG content, suggesting that the final glycosylation step may be a key determinant of AA-2βG accumulation. Subsequently, utilizing phylogenetic and co-expression analysis, we identified ten UDP-glycosyltransferases (UGTs) and three β-glucosidases (BGLUs) which may be involved in the crucial step of the conversion from AA to AA-2βG, and the UGTs' activities were predicted through molecular docking. Lastly, we speculated that the presence of the glycosylation process of AA might have a crucial role in maintaining AA homeostasis in L. barbarum, and deliberated on potential correlations between AA, carotenoids, and anthocyanins. Our integrated multi-omics analysis provides valuable insights into AA-2βG biosynthesis in L. barbarum, identifying thirteen candidate genes and highlighting the complex interplay between AA, carotenoids, and anthocyanins. These findings have implications for improving AA-2βG content in L. barbarum.

Natural pigments derived from plants and microorganisms: classification, biosynthesis, and applications

Pigments, as coloured secondary metabolites, endow the world with a rich palette of colours. They primarily originate from plants and microorganisms and play crucial roles in their survival and adaptation processes. In this article, we categorize pigments based on their chemical structure into flavonoids, carotenoids, pyrroles, quinones, azaphilones, melanins, betalains, flavins, and others. We further meticulously describe the colours, sources, and biosynthetic pathways, including key enzymatic steps and regulatory networks that control pigment production, in both plants and microorganisms. In particular, we highlight the role of transport proteins and transcription factors in fine-tuning these pathways. Finally, we introduce the use of pigments in practical production and research, aiming to provide new insights and directions for the application of coloured compounds in diverse fields, such as agriculture, industry, and medicine.

Characterization of lycopene β-cyclase from Dunaliella bardawil for enhanced β-carotene production and salt tolerance

Dunaliella can accumulate more β-carotene (10 % or even more of the dry weight of cells) than any other species. Lycopene β-cyclase (LcyB) is the key enzyme in the catalysis of lycopene to β-carotene. In the present research, we used Escherichia coli BL21 (DE3) as host to construct two different types of engineering bacteria, one expressing the D. bardawil LcyB and the other expressing the orthologue Erwinia uredovora crtY. The catalytic ability of LcyB and CrtY were evaluated by comparing the β-carotene yields of the two E. coli BL21(DE3) strains, whose salt tolerance was simultaneously compared by cultivated them under different NaCl concentrations (1 %, 2 %, and 4 %). We also interfered with the LcyB gene to investigate the effect of LcyB in D. bardawil. Results displayed that the β-carotene yield of the LcyB-transformant significantly increased by about 48 % compared with the crtY-transformant. Additionally, LcyB was verified to be able to enhance the salt tolerance of E. coli BL21 (DE3). It is concluded that D. bardawil LcyB not only has better catalytic ability but also is able to confer salt tolerance to cells. Interfering D. bardawil LcyB induced the low expression of LcyB and the changes of growth and carotenoids metabolism in D. bardawil.

A Comprehensive Analysis of the 9-Cis Epoxy Carotenoid Dioxygenase Gene Family and Their Responses to Salt Stress in Hordeum vulgare L

Barley (Hordeum vulgare L.) is among the earliest crops to be cultivated and is also considered a crucial staple crop. Nevertheless, the negative effects of abiotic stress on both the quality and productivity of barley are significant. Nine-cis-epoxycarotenoid dioxygenases (NCEDs) are rate-limiting enzymes in plants that cleave carotenoids and produce abscisic acid (ABA). The poor utilization of barley NCEDs in stress-resistant genetic breeding is due to the lack of appropriate information about their potential function in abiotic stress. The current study revealed five NCED genes in the barley genome (HvNCED1-HvNCED5), which are distributed unevenly on barley chromosomes. The PF03055 domain is present in all HvNCEDs, and they encode 413~643 amino acids. Phylogenetic analysis showed that NCED genes were categorized into three distinct clades, confirming the homology of NCED genes between H. vulgare L., Arabidopsis thaliana L., and Oryza sativa L. Expression analysis revealed that HvNCED1 is significantly upregulated under high salt stress, indicating its potential role in enhancing salt tolerance. In contrast, HvNCED3 and HvNCED4 exhibited downregulation, suggesting a complex regulatory mechanism in response to varying salt stress levels. These findings will enhance our comprehension of the genetic composition and evolutionary development of the HvNCED gene family and provide a basis for future research on their role in response to salt-induced stress.

Genome editing in ubiquitous freshwater Actinobacteria

Development of genome-editing tools in diverse microbial species is an important step both in understanding the roles of those microbes in different environments, and in engineering microbes for a variety of applications. Freshwater-specific clades of Actinobacteria are ubiquitous and abundant in surface freshwaters worldwide. Here, we show that Rhodoluna lacicola and Aurantimicrobium photophilum, which represent widespread clades of freshwater Actinobacteria, are naturally transformable. We also show that gene inactivation via double homologous recombination and replacement of the target gene with antibiotic selection markers can be used in both strains, making them convenient and broadly accessible model organisms for freshwater systems. We further show that in both strains, the predicted phytoene synthase is the only phytoene synthase, and its inactivation prevents the synthesis of all pigments. The tools developed here enable targeted modification of the genomes of some of the most abundant microbes in freshwater communities. These genome-editing tools will enable hypothesis testing about the genetics and (eco)physiology of freshwater Actinobacteria and broaden the available model systems for engineering freshwater microbial communities.

IMPORTANCE

To advance bioproduction or bioremediation in large, unsupervised environmental systems such as ponds, wastewater lagoons, or groundwater systems, it will be necessary to develop diverse genetically amenable microbial model organisms. Although we already genetically modify a few key species, tools for engineering more microbial taxa, with different natural phenotypes, will enable us to genetically engineer multispecies consortia or even complex communities. Developing genetic tools for modifying freshwater bacteria is particularly important, as wastewater, production ponds or raceways, and contaminated surface water are all freshwater systems where microbial communities are already deployed to do work, and the outputs could potentially be enhanced by genetic modifications. Here, we demonstrate that common tools for genome editing can be used to inactivate specific genes in two representatives of a very widespread, environmentally relevant group of Actinobacteria. These Actinobacteria are found in almost all tested surface freshwater environments, where they co-occur with primary producers, and genome-editing tools in these species are thus a step on the way to engineering microbial consortia in freshwater environments.

Morphology, behavior, and phylogenomics of Oxytoxum lohmannii, Dinoflagellata

Dinoflagellates are an abundant and diverse group of protists representing a wealth of unique biology and ecology. While many dinoflagellates are photosynthetic or mixotrophic, many taxa are heterotrophs, often with complex feeding strategies. Compared to their photosynthetic counterparts, heterotrophic dinoflagellates remain understudied, as they are difficult to culture. One exception, a long-cultured isolate originally classified as Amphidinium but recently reclassified as Oxytoxum, has been the subject of a number of feeding, growth, and chemosensory studies. This lineage was recently determined to be closely related to Prorocentrum using phylogenetics of ribosomal RNA gene sequences, but the exact nature of this relationship remains unresolved. Using transcriptomes sequenced from culture and three single cells from the environment, we produce a robust phylogeny of 242 genes, revealing Oxytoxum is likely sister to the Prorocentrum clade, rather than nested within it. Molecular investigations uncover evidence of a reduced, nonphotosynthetic plastid and proteorhodopsin, a photoactive proton pump acquired horizontally from bacteria. We describe the ultrastructure of O. lohmannii, including densely packed trichocysts, and a new type of mucocyst. We observe that O. lohmannii feeds preferentially on cryptophytes using myzocytosis, but can also feed on various phytoflagellates using conventional phagocytosis. O. lohmannii is amenable to culture, providing an opportunity to better study heterotrophic dinoflagellate biology and feeding ecology.

'Altruistic' cooperation among the prokaryotic community of Atlantic salterns assessed by metagenomics

Hypersaline environments are extreme habitats with a limited prokaryotic diversity, mainly restricted to halophilic or halotolerant archaeal and bacterial taxa adapted to highly saline conditions. This study attempts to analyze the taxonomic and functional diversity of the prokaryotes that inhabit a solar saltern located at the Atlantic Coast, in Isla Cristina (Huelva, Southwest Spain), and the influence of salinity on the diversity and metabolic potential of these prokaryotic communities, as well as the interactions and cooperation among the individuals within that community. Brine samples were obtained from different saltern ponds, with a salinity range between 19.5 % and 39 % (w/v). Total prokaryotic DNA was sequenced using the Illumina shotgun metagenomic strategy and the raw sequence data were analyzed using supercomputing services following the MetaWRAP and SqueezeMeta protocols. The most abundant phyla at moderate salinities (19.5-22 % [w/v]) were Methanobacteriota (formerly "Euryarchaeota"), Pseudomonadota and Bacteroidota, followed by Balneolota and Actinomycetota and Uroviricota in smaller proportions, while at high salinities (36-39 % [w/v]) the most abundant phylum was Methanobacteriota, followed by Bacteroidota. The most abundant genera at intermediate salinities were Halorubrum and the bacterial genus Spiribacter, while the haloarchaeal genera Halorubrum, Halonotius, and Haloquadratum were the main representatives at high salinities. A total of 65 MAGs were reconstructed from the metagenomic datasets and different functions and pathways were identified in them, allowing to find key taxa in the prokaryotic community able to synthesize and supply essential compounds, such as biotin, and precursors of other bioactive molecules, like β-carotene, and bacterioruberin, to other dwellers in this habitat, lacking the required enzymatic machinery to produce them. This work shed light on the ecology of aquatic hypersaline environments, such as the Atlantic Coast salterns, and on the dynamics and factors affecting the microbial populations under such extreme conditions.

LC-MS/MS-based targeted carotenoid and anthocyanidin metabolic profile of Auricularia cornea under blue and red LED light exposure

Light exposure significantly impacted the coloration and metabolism of Auricularia cornea, although the underlying mechanisms remain unclear. This study aimed to test the apparent color and pigment metabolic profiles of A. cornea in response to red (λp = 630 nm) and blue (λp = 463 nm) visible light exposure. Colorimeter analysis showed that fruiting bodies appeared bright-white under red-light and deeper-red under blue-light, both with a yellow tinge. On the 40th day of light-exposure, bodies were collected for metabolite detection. A total of 481 metabolites were targeted analysis, resulting in 18 carotenoids and 11 anthocyanins. Under red and blue light exposure, the total carotenoids levels were 1.1652 μg/g and 1.1576 μg/g, the total anthocyanins levels were 0.0799 μg/g and 0.1286 μg/g, respectively. Four differential metabolites and three putative gene linked to the visual coloration of A. cornea were identified. This pioneering study provides new insights into the role of light in regulating A. cornea pigmentation and metabolic profile.

Biosynthesis and Extraction of Chlorophyll, Carotenoids, Anthocyanins, and Betalaine In Vivo and In Vitro

As natural bioactive compounds, plant pigments play crucial roles not only in plant phenotype, growth, development, and adaptation to stress but also hold unique value in biotechnology, healthcare, and industrial applications. There is growing interest in the biosynthesis and acquisition of plant pigments. Thus, this paper explores emerging extraction methods of natural pigments and elucidates the biosynthesis pathways of four key plant pigments, chlorophylls, carotenoids, anthocyanins, and betalaine in vivo and in vitro. We comprehensively discuss the application of solvent, supercritical fluid [extraction], ultrasonic, and microwave-assisted extraction techniques, as well as introducing key enzymes, precursors, and synthetic pathways involved in pigment synthesis. δ-Aminolevulinic acid represents a pivotal initiating enzyme for chlorophyll synthesis, whereas isopentenylpyrophosphate, (IPP) and dimethylallyl pyrophosphate, (DMAPP) are closely associated with carotenoid biosynthesis. Phenylalanine and tyrosine are critical substances for anthocyanin and betalaine synthesis, respectively. Hence, crucial genes such as chlI, crtB, PGT8, CYP76AD1, and BvDODA can be employed for heterologous biosynthesis in vitro to meet the demand for increased plant pigment amount. As a pivotal determinant of plant coloration, an in-depth exploration into the high-quality acquisition of plant pigments can provide a basis for developing superior pigments and offer new insights into increasing pigment yield.

Nuclear Receptors and the Hidden Language of the Metabolome

Nuclear hormone receptors (NHRs) are a family of ligand-regulated transcription factors that control key aspects of development and physiology. The regulation of NHRs by ligands derived from metabolism or diet makes them excellent pharmacological targets, and the mechanistic understanding of how NHRs interact with their ligands to regulate downstream gene networks, along with the identification of ligands for orphan NHRs, could enable innovative approaches for cellular engineering, disease modeling and regenerative medicine. We review recent discoveries in the identification of physiologic ligands for NHRs. We propose new models of ligand-receptor co-evolution, the emergence of hormonal function and models of regulation of NHR specificity and activity via one-ligand and two-ligand models as well as feedback loops. Lastly, we discuss limitations on the processes for the identification of physiologic NHR ligands and emerging new methodologies that could be used to identify the natural ligands for the remaining 17 orphan NHRs in the human genome.

Insights into the synthesis, engineering, and functions of microbial pigments in Deinococcus bacteria

The ability of Deinococcus bacteria to survive in harsh environments, such as high radiation, extreme temperature, and dryness, is mainly attributed to the generation of unique pigments, especially carotenoids. Although the limited number of natural pigments produced by these bacteria restricts their industrial potential, metabolic engineering and synthetic biology can significantly increase pigment yield and expand their application prospects. In this study, we review the properties, biosynthetic pathways, and functions of key enzymes and genes related to these pigments and explore strategies for improving pigment production through gene editing and optimization of culture conditions. Additionally, studies have highlighted the unique role of these pigments in antioxidant activity and radiation resistance, particularly emphasizing the critical functions of deinoxanthin in D. radiodurans. In the future, Deinococcus bacterial pigments will have broad application prospects in the food industry, drug production, and space exploration, where they can serve as radiation indicators and natural antioxidants to protect astronauts' health during long-term space flights.

A chromosome-scale genome provides new insights into the typical carotenoid biosynthesis in the important red yeast Rhodotorula glutinis QYH-2023 with anti-inflammatory effects

Rhodotorula spp. has been studied as one powerful source for a novel cell factory with fast growth and its high added-value biomolecules. However, its inadequate genome and genomic annotation have hindered its widespread use in cosmetics and food industries. Rhodotorula glutinis QYH-2023, was isolated from rice rhizosphere soil, and the highest quality of the genome of the strain was obtained at chromosome level (18 chromosomes) than ever before in red yeast in this study. Comparative genomics analysis revealed that there are more key gene copies of carotenoids biosynthesis in R. glutinis QYH-2023 than other species of Rhodotorula spp. Integrated transcriptome and metabolome analysis revealed that lipids and carotenoids biosynthesis was significantly enriched during fermentation. Subsequent investigation revealed that the over-expression of the strain three genes related to carotenoids biosynthesis in Komagataella phaffii significantly promoted the carotenoid production. Furthermore, in vitro tests initially confirmed that the longer the fermentation period, the synthesized metabolites controlled by R. glutinis QYH-2023 genome had the stronger anti-inflammatory properties. All of the findings revealed a high-quality reference genome which highlight the potential of R. glutinis strains to be employed as chassis cells for biosynthesizing carotenoids and other active chemicals.

Functional Characterization of a CruP-Like Isomerase in Dunaliella

Dunaliella bardawil is a marine unicellular green algal that produces large amounts of β-carotene and is a model organism for studying the carotenoid synthesis pathway. However, there are still many mysteries about the enzymes of the D. bardawil lycopene synthesis pathway that have not been revealed. Here, we have identified a CruP-like lycopene isomerase, named DbLyISO, and successfully cloned its gene from D. bardawil. DbLyISO showed a high homology with CruPs. We constructed a 3D model of DbLyISO and performed molecular docking with lycopene, as well as molecular dynamics testing, to identify the functional characteristics of DbLyISO. Functional activity of DbLyISO was also performed by overexpressing gene in both E. coli and D. bardawil. Results revealed that DbLyISO acted at the C-5 and C-13 positions of lycopene, catalyzing its cis-trans isomerization to produce a more stable trans structure. These results provide new ideas for the development of a carotenoid series from engineered bacteria, algae, and plants.

Growth-promoting bacteria and arbuscular mycorrhizal fungus enhance maize tolerance to saline stress

Climate change intensifies soil salinization and jeopardizes the development of crops worldwide. The accumulation of salts in plant tissue activates the defense system and triggers ethylene production thus restricting cell division. We hypothesize that the inoculation of plant growth-promoting bacteria (PGPB) producing ACC (1-aminocyclopropane-1-carboxylate) deaminase favors the development of arbuscular mycorrhizal fungi (AMF), promoting the growth of maize plants under saline stress. We investigated the efficacy of individual inoculation of PGPB, which produce ACC deaminase, as well as the co-inoculation of PGPB with Rhizophagus clarus on maize plant growth subjected to saline stress. The isolates were acquired from the bulk and rhizospheric soil of Mimosa bimucronata (DC.) Kuntze in a temporary pond located in Pernambuco State, Brazil. In the first greenhouse experiment, 10 halophilic PGPB were inoculated into maize at 0, 40 and 80 mM of NaCl, and in the second experiment, the PGPB that showed the best performance were co-inoculated with R. clarus in maize under the same conditions as in the first experiment. Individual PGPB inoculation benefited the number of leaves, stem diameter, root and shoot dry mass, and the photosynthetic pigments. Inoculation with PGPB 28-10 Pseudarthrobacter enclensis, 24-1 P. enclensis and 52 P. chlorophenolicus increased the chlorophyll a content by 138%, 171%, and 324% at 0, 40 and 80 mM NaCl, respectively, comparing to the non-inoculated control. We also highlight that the inoculation of PGPB 28-10, 28-7 Arthrobacter sp. and 52 increased the content of chlorophyll b by 72%, 98%, and 280% and carotenoids by 82%, 98%, and 290% at 0, 40 and 80 mM of NaCl, respectively. Co-inoculation with PGPB 28-7, 46-1 Leclercia tamurae, 70 Artrobacter sp., and 79-1 Micrococcus endophyticus significantly increased the rate of mycorrhizal colonization by roughly 50%. Furthermore, co-inoculation promoted a decrease in the accumulation of Na and K extracted from plant tissue, with an increase in salt concentration, from 40 mM to 80 mM, also favoring the establishment and development of R. clarus. In addition, co-inoculation of these PGPB with R. clarus promoted maize growth and increased plant biomass through osmoregulation and protection of the photosynthetic apparatus. The tripartite symbiosis (plant-fungus-bacterium) is likely to reprogram metabolic pathways that improve maize growth and crop yield, suggesting that the AMF-PGPB consortium can minimize damages caused by saline stress.

Challenges in Functional Food Products with the Incorporation of Some Microalgae

Much attention has been given to the use of microalgae to produce functional foods that have valuable bioactive chemicals, including essential amino acids, polyunsaturated fatty acids, vitamins, carotenoids, fiber, and minerals. Microalgal biomasses are increasingly being used to improve the nutritional values of foods because of their unique nutrient compositions that are beneficial to human health. Their protein content and amino acid composition are the most important components. The microalgal biomass used in the therapeutic supplement industry is dominated by bio-compounds like astaxanthin, β-carotene, polyunsaturated fatty acids like eicosapentaenoic acid and docosahexaenoic acid, and polysaccharides such as β-glucan. The popularity of microalgal supplements is growing because of the health benefits of their bioactive substances. Moreover, some microalgae, such as Dunaliella, Arthrospira (Spirulina), Chlorella, and Haematococcus, are commonly used microalgal species in functional food production. The incorporation of microalgal biomass leads not only to enhanced nutritional value but also to improved sensory quality of food products without altering their cooking or textural characteristics. Microalgae, because of their eco-friendly potential, have emerged as one of the most promising and novel sources of new functional foods. This study reviews some recent and relevant works, as well as the current challenges for future research, using different methods of chemical modification in foods with the addition of a few commercial algae to allow their use in nutritional and sensory areas. It can be concluded that the production of functional foods through the use of microalgae in foods has become an important issue.

Overexpression of PtVDL1 in Phaeodactylum tricornutum Increases Fucoxanthin Content under Red Light

Phaeodactylum tricornutum is a model diatom with significant biotechnological applications, including enhancing biomass, biofuel, and carotenoid production. Specifically, owing to the capacity of this organism to serve as a valuable source of essential raw materials for pharmaceuticals and nutraceuticals, ongoing research is actively focused on enhancing its productivity. One of the genes involved in various stages of fucoxanthin (Fx) biosynthesis, violaxanthin de-epoxidase like 1 (VDL1), has recently been identified. To validate the intracellular function of this gene and boost Fx production through overexpression, we established and examined three transgenic P. tricornutum lines characterized by elevated P. tricortunum VDL1 ( PtVDL1) expression and evaluate their cell growth and Fx productivity. These transgenic lines exhibited substantially increased PtVDL1 mRNA and protein levels compared to the wild type (WT). Notably, the enzyme substrate violaxanthin was entirely depleted and could not be detected in the transformants, whereas it remained at constant levels in the WT. Interestingly, under standard white light conditions, Fx productivity in the transformants remained unchanged; however, but after 48 h of exposure to red light, it increased by up to 15%. These results indicate that PtVDL1-overexpressing P. tricornutum has industrial potential, particularly for enhancing Fx production under red light conditions.

Astaxanthin from microalgae: A review on structure, biosynthesis, production strategies and application

Astaxanthin is a red-colored secondary metabolite with excellent antioxidant properties, typically finds application as foods, feed, cosmetics, nutraceuticals, and medications. Astaxanthin is usually produced synthetically using chemicals and costs less as compared to the natural astaxanthin obtained from fish, shrimps, and microorganisms. Over the decades, astaxanthin has been naturally synthesized from Haematococcus pluvialis in commercial scales and remains exceptional, attributed to its higher bioactive properties as compared to synthetic astaxanthin. However, the production cost of algal astaxanthin is still high due to several bottlenecks prevailing in the upstream and downstream processes. To that end, the present study intends to review the recent trends and advancements in astaxanthin production from microalgae. The structure of astaxanthin, sources, production strategies of microalgal astaxanthin, and factors influencing the synthesis of microalgal astaxanthin were discussed while detailing the pathway involved in astaxanthin biosynthesis. The study also discusses the relevant downstream process used in commercial scales and details the applications of astaxanthin in various health related issues.

Involvement of Transcription Factors and Regulatory Proteins in the Regulation of Carotenoid Accumulation in Plants and Algae

Carotenoids are essential for photosynthesis and photoprotection in photosynthetic organisms, which are widely used in food coloring, feed additives, nutraceuticals, cosmetics, and pharmaceuticals. Carotenoid biofortification in crop plants or algae has been considered as a sustainable strategy to improve human nutrition and health. However, the regulatory mechanisms of carotenoid accumulation are still not systematic and particularly scarce in algae. This article focuses on the regulatory mechanisms of carotenoid accumulation in plants and algae through regulatory factors (transcription factors and regulatory proteins), demonstrating the complexity of homeostasis regulation of carotenoids, mainly including transcriptional regulation as the primary mechanism, subsequent post-translational regulation, and cross-linking with other metabolic processes. Different organs of plants and different plant/algal species usually have specific regulatory mechanisms for the biosynthesis, storage, and degradation of carotenoids in response to the environmental and developmental signals. In plants and algae, regulators such as MYB, bHLH, MADS, bZIP, AP2/ERF, WRKY, and orange proteins can be involved in the regulation of carotenoid metabolism. And many more regulators, regulatory networks, and mechanisms need to be explored. Our paper will provide a basis for multitarget or multipathway engineering for carotenoid biofortification in plants and algae.

Microbial Pigments: Major Groups and Industrial Applications

Microbial pigments have many structures and functions with excellent characteristics, such as being biodegradable, non-toxic, and ecologically friendly, constituting an important source of pigments. Industrial production presents a bottleneck in production cost that restricts large-scale commercialization. However, microbial pigments are progressively gaining popularity because of their health advantages. The development of metabolic engineering and cost reduction of the bioprocess using industry by-products opened possibilities for cost and quality improvements in all production phases. We are thus addressing several points related to microbial pigments, including the major classes and structures found, the advantages of use, the biotechnological applications in different industrial sectors, their characteristics, and their impacts on the environment and society.

Genome-wide identification and in-silico expression analysis of carotenoid cleavage oxygenases gene family in Oryza sativa (rice) in response to abiotic stress

Rice constitutes a foundational cereal and plays a vital role in the culinary sector. However, the detriments of abiotic stress on rice quality and productivity are noteworthy. Carotenoid cleavage oxygenases (CCO) hold vital importance as they enable the particular breakdown of carotenoids and significantly contribute towards the growth and response to abiotic stress in rice. Due to the insufficient information regarding rice CCOs and their potential role in abiotic stress, their utilization in stress-resistant genetic breeding remains limited. The current research identified 16 CCO genes within the Oryza sativa japonica group. These OsCCO genes can be bifurcated into three categories based on their conserved sequences: NCEDs (9-Cis-epoxycarotenoid dioxygenases), CCDs (Carotenoid cleavage dioxygenases) and CCD-like (Carotenoid cleavage dioxygenases-like). Conserved motifs were found in the OsCCO gene sequence via MEME analysis and multiple sequence alignment. Stress-related cis-elements were detected in the promoter regions of OsCCOs genes, indicating their involvement in stress response. Additionally, the promoters of these genes had various components related to plant light, development, and hormone responsiveness, suggesting they may be responsive to plant hormones and involved in developmental processes. MicroRNAs play a pivotal role in the regulation of these 16 genes, underscoring their significance in rice gene regulation. Transcriptome data analysis suggests a tissue-specific expression pattern for rice CCOs. Only OsNCED6 and OsNCED10 significantly up-regulated during salt stress, as per RNA seq analyses. CCD7 and CCD8 levels were also higher in the CCD group during the inflorescence growth stage. This provides insight into the function of rice CCOs in abiotic stress response and identifies possible genes that could be beneficial for stress-resistant breeding.

The Scent of Change: Sustainable Fragrances Through Industrial Biotechnology

Current environmental and safety considerations urge innovation to address the need for sustainable high-value chemicals that are embraced by consumers. This review discusses the concept of sustainable fragrances, as high-value, everyday and everywhere chemicals. Current and emerging technologies represent an opportunity to produce fragrances in an environmentally and socially responsible way. Biotechnology, including fermentation, biocatalysis, and genetic engineering, has the potential to reduce the environmental footprint of fragrance production while maintaining quality and consistency. Computational and in silico methods, including machine learning (ML), are also likely to augment the capabilities of sustainable fragrance production. Continued innovation and collaboration will be crucial to the future of sustainable fragrances, with a focus on developing novel sustainable ingredients, as well as ethical sourcing practices.

Alfalfa as a vegetable source of β-carotene: The change mechanism of β-carotene during fermentation

The objectives of this study were to explore the β-carotene-producing bacteria and ascertain the main factors affecting β-carotene content via investigating the effects of various additives on β-carotene content, bacterial community succession, and quality of fermented alfalfa, using single-molecule real-time (SMRT) sequencing technology. Fresh alfalfa was fermented without (CON) or with squalene (SQ), the combination of Lactobacillus plantarum and cellulase (LPEN), and the combination of SQ and LPEN (SQLPEN) for 3, 45, and 90 d. The results showed that relative to the fresh alfalfa, extensive β-carotene loss in all groups occurred in the early fermentation phase (3 d) since epiphytic Pantoea agglomerans with the ability to produce β-carotene disappeared and β-carotene was oxidized by lipoxygenase and peroxidase. With the prolonged fermentation days, β-carotene content in all groups increased due to bacterial community succession in the middle and late phases of fermentation (45 and 90 d). The species L. parabuchneri, L. kunkeei, and L. kullabergensis (r = 0.591, 0.366, 0.341, orderly) had positive correlations with β-carotene content (P < 0.05). Bacterial functional potential prediction showed that species L. kunkeei, L. helsingborgensis, and L. kullabergensis had positive (r = 0.478, 0.765, 0.601) correlations with C10-C20 isoprenoid biosynthesis (P < 0.01), and L. helsingborgensis and L. kullabergensis had positive (r = 0.805, 0.522) correlations with β-carotene biosynthesis (P < 0.01). Additionally, the pH and propionic acid (r = -0.567, -0.504) had negative correlations with β-carotene content (P < 0.01). The CON group was preserved well after 90 d, LPEN and SQLPEN further improved fermentation quality. In conclusion, certain Lactobacillus had the potential for β-carotene biosynthesis, and high pH and propionic acid content were the unbenefited factors for β-carotene retention in fermented alfalfa.

The apocarotenoid production in microbial biofactories: An overview

Carotenoids are a vast group of natural pigments that come in a variety of colors ranging from red to orange. Apocarotenoids are derived from these carotenoids, which are hormones, pigments, retinoids, and volatiles employed in the textiles, cosmetics, pharmaceutical, and food industries. Due to the high commercial value and poor natural host abundance, they are significantly undersupplied. Microbes like Saccharomyces cerevisiae and Escherichia coli act as heterologous hosts for apocarotenoid production. This article briefly reviews categories of apocarotenoids, their biosynthetic pathway commencing from the MVA and MEP, its significance, the tool enzymes for apocarotenoid biosynthesis like CCDs, their biotechnological production in microbial factories, and future perspectives.

Color-Tuning Mechanism of the Lit Form of Orange Carotenoid Protein

Orange carotenoid protein (OCP) of photosynthetic cyanobacteria binds to ketocarotenoids noncovalently and absorbs excess light to protect the host organism from light-induced oxidative damage. Herein, we found that mutating valine 40 in the α3 helix of Gloeocapsa sp. PCC 7513 (GlOCP1) resulted in blue- or red-shifts of 6-20 nm in the absorption maxima of the lit forms. We analyzed the origins of absorption maxima shifts by integrating X-ray crystallography, homology modeling, molecular dynamics simulations, and hybrid quantum mechanics/molecular mechanics calculations. Our analysis suggested that the single residue mutations alter the polar environment surrounding the bound canthaxanthin, thereby modulating the degree of charge transfer in the photoexcited state of the chromophore. Our integrated investigations reveal the mechanism of color adaptation specific to OCPs and suggest a design principle for color-specific photoswitches.

Insights into vitamin A in bladder cancer, lack of attention to gut microbiota?

Vitamin A has long been associated with bladder cancer, and many exogenous vitamin A supplements, vitamin A derivatives, and synthetic drugs have been investigated over the years. However, the effectiveness of these strategies in clinical practice has not met expectations, and they have not been widely adopted. Recent medical research on intestinal flora has revealed that bladder cancer patients exhibit reduced serum vitamin A levels and an imbalance of gut microbiota. In light of the close relationship between gut microbiota and vitamin A, one can speculate that a complex regulatory mechanism exists between the two in the development and occurrence of bladder cancer. As such, further exploration of their interaction in bladder cancer may help guide the use of vitamin A for preventive purposes. During the course of this review, attention is paid to the influence of intestinal microbiota on the vitamin A metabolism and the RA signaling pathway, as well as the mutual promotion relationships between them in the prevention of bladder cancer, In addition, it emphasizes the importance of intestinal microbiota for bladder cancer prevention and treatment.

Roles of Two Phytoene Synthases and Orange Protein in Carotenoid Metabolism of the β-Carotene-Accumulating Dunaliella salina

Phytoene synthase (PSY) is a key enzyme in carotenoid metabolism and often regulated by orange protein. However, few studies have focused on the functional differentiation of the two PSYs and their regulation by protein interaction in the β-carotene-accumulating Dunaliella salina CCAP 19/18. In this study, we confirmed that DsPSY1 from D. salina possessed high PSY catalytic activity, whereas DsPSY2 almost had no activity. Two amino acid residues at positions 144 and 285 responsible for substrate binding were associated with the functional variance between DsPSY1 and DsPSY2. Moreover, orange protein from D. salina (DsOR) could interact with DsPSY1/2. DbPSY from Dunaliella sp. FACHB-847 also had high PSY activity, but DbOR could not interact with DbPSY, which might be one reason why it could not highly accumulate β-carotene. Overexpression of DsOR, especially the mutant DsORHis, could significantly improve the single-cell carotenoid content and change cell morphology (with larger cell size, bigger plastoglobuli, and fragmented starch granules) of D. salina. Overall, DsPSY1 played a dominant role in carotenoid biosynthesis in D. salina, and DsOR promoted carotenoid accumulation, especially β-carotene via interacting with DsPSY1/2 and regulating the plastid development. Our study provides a new clue for the regulatory mechanism of carotenoid metabolism in Dunaliella. IMPORTANCE Phytoene synthase (PSY) as the key rate-limiting enzyme in carotenoid metabolism can be regulated by various regulators and factors. We found that DsPSY1 played a dominant role in carotenogenesis in the β-carotene-accumulating Dunaliella salina, and two amino acid residues critical in the substrate binding were associated with the functional variance between DsPSY1 and DsPSY2. Orange protein from D. salina (DsOR) can promote carotenoid accumulation via interacting with DsPSY1/2 and regulating the plastid development, which provides new insights into the molecular mechanism of massive accumulation of β-carotene in D. salina.

DbMADS regulates carotenoid metabolism by repressing two carotenogenic genes in the green alga Dunaliella sp. FACHB-847

MADS transcription factors are involved in the regulation of fruit development and carotenoid metabolism in plants. However, whether and how carotenoid accumulation is regulated by algal MADS are largely unknown. In this study, we first used functional complementation to confirm the functional activity of phytoene synthase from the lutein-rich Dunaliella sp. FACHB-847 (DbPSY), the key rate-limiting enzyme in the carotenoid biosynthesis. Promoters of DbPSY and DbLcyB (lycopene β-cyclase) possessed multiple cis-acting elements such as light-, UV-B-, dehydration-, anaerobic-, and salt-responsive elements, W-box, and C-A-rich-G-box (MADS-box). Meanwhile, we isolated one nucleus-localized MADS transcription factor (DbMADS), belonging to type I MADS gene. Three carotenogenic genes, DbPSY, DbLcyB, and DbBCH (β-carotene hydroxylase) genes were upregulated at later stages, which was well correlated with the carotenoid accumulation. In contrast, DbMADS gene was highly expressed at lag phase with low carotenoid accumulation. Yeast one-hybrid assay and dual-luciferase reporter assay demonstrated that DbMADS could directly bind to the promoters of two carotenogenic genes, DbPSY and DbLcyB, and repress their transcriptions. This study suggested that DbMADS may act as a negative regulator of carotenoid biosynthesis by repressing DbPSY and DbLcyB at the lag phase, which provide new insights into the regulatory mechanisms of carotenoid metabolism in Dunaliella.

Natural overexpression of CAROTENOID CLEAVAGE DIOXYGENASE 4 in tomato alters carotenoid flux

Carotenoids and apocarotenoids function as pigments and flavor volatiles in plants that enhance consumer appeal and offer health benefits. Tomato (Solanum lycopersicum.) fruit, especially those of wild species, exhibit a high degree of natural variation in carotenoid and apocarotenoid contents. Using positional cloning and an introgression line (IL) of Solanum habrochaites "LA1777', IL8A, we identified carotenoid cleavage dioxygenase 4 (CCD4) as the factor responsible for controlling the dark orange fruit color. CCD4b expression in ripe fruit of IL8A plants was ∼8,000 times greater than that in the wild type, presumably due to 5' cis-regulatory changes. The ShCCD4b-GFP fusion protein localized in the plastid. Phytoene, ζ-carotene, and neurosporene levels increased in ShCCD4b-overexpressing ripe fruit, whereas trans-lycopene, β-carotene, and lutein levels were reduced, suggestive of feedback regulation in the carotenoid pathway by an unknown apocarotenoid. Solid-phase microextraction-gas chromatography-mass spectrometry analysis showed increased levels of geranylacetone and β-ionone in ShCCD4b-overexpressing ripe fruit coupled with a β-cyclocitral deficiency. In carotenoid-accumulating Escherichia coli strains, ShCCD4b cleaved both ζ-carotene and β-carotene at the C9-C10 (C9'-C10') positions to produce geranylacetone and β-ionone, respectively. Exogenous β-cyclocitral decreased carotenoid synthesis in the ripening fruit of tomato and pepper (Capsicum annuum), suggesting feedback inhibition in the pathway. Our findings will be helpful for enhancing the aesthetic and nutritional value of tomato and for understanding the complex regulatory mechanisms of carotenoid and apocarotenoid biogenesis.

Zeaxanthin epoxidase is involved in the carotenoid biosynthesis and light-dependent growth of the marine alga Nannochloropsis oceanica

BACKGROUND

The marine alga Nannochloropsis oceanica, an emerging model belonging to Heterokont, is considered as a promising light-driven eukaryotic chassis for transforming carbon dioxide to various compounds including carotenoids. Nevertheless, the carotenogenic genes and their roles in the alga remain less understood and to be further explored.

RESULTS

Here, two phylogenetically distant zeaxanthin epoxidase (ZEP) genes from N. oceanica (NoZEP1 and NoZEP2) were functionally characterized. Subcellular localization experiment demonstrated that both NoZEP1 and NoZEP2 reside in the chloroplast yet with differential distribution patterns. Overexpression of NoZEP1 or NoZEP2 led to increases of violaxanthin and its downstream carotenoids at the expense of zeaxanthin in N. oceanica, with the extent of changes mediated by NoZEP1 overexpression being greater as compared to NoZEP2 overexpression. Suppression of NoZEP1 or NoZEP2, on the other hand, caused decreases of violaxanthin and its downstream carotenoids as well as increases of zeaxanthin; similarly, the extent of changes mediated by NoZEP1 suppression was larger than that by NoZEP2 suppression. Interestingly, chlorophyll a dropped following violaxanthin decrease in a well-correlated manner in response to NoZEP suppression. The thylakoid membrane lipids including monogalactosyldiacylglycerol also correlated with the violaxanthin decreases. Accordingly, NoZEP1 suppression resulted in more attenuated algal growth than NoZEP2 suppression did under either normal light or high light stage.

CONCLUSIONS

The results together support that both NoZEP1 and NoZEP2, localized in the chloroplast, have overlapping roles in epoxidating zeaxanthin to violaxanthin for the light-dependent growth, yet with NoZEP1 being more functional than NoZEP2 in N. oceanica. Our study provides implications into the understanding of carotenoid biosynthesis and future manipulation of N. oceanica for carotenoid production.

Computational Insight into Intraspecies Distinctions in Pseudoalteromonas distincta: Carotenoid-like Synthesis Traits and Genomic Heterogeneity

Advances in the computational annotation of genomes and the predictive potential of current metabolic models, based on more than thousands of experimental phenotypes, allow them to be applied to identify the diversity of metabolic pathways at the level of ecophysiology differentiation within taxa and to predict phenotypes, secondary metabolites, host-associated interactions, survivability, and biochemical productivity under proposed environmental conditions. The significantly distinctive phenotypes of members of the marine bacterial species Pseudoalteromonas distincta and an inability to use common molecular markers make their identification within the genus Pseudoalteromonas and prediction of their biotechnology potential impossible without genome-scale analysis and metabolic reconstruction. A new strain, KMM 6257, of a carotenoid-like phenotype, isolated from a deep-habituating starfish, emended the description of P. distincta, particularly in the temperature growth range from 4 to 37 °C. The taxonomic status of all available closely related species was elucidated by phylogenomics. P. distincta possesses putative methylerythritol phosphate pathway II and 4,4'-diapolycopenedioate biosynthesis, related to C30 carotenoids, and their functional analogues, aryl polyene biosynthetic gene clusters (BGC). However, the yellow-orange pigmentation phenotypes in some strains coincide with the presence of a hybrid BGC encoding for aryl polyene esterified with resorcinol. The alginate degradation and glycosylated immunosuppressant production, similar to brasilicardin, streptorubin, and nucleocidines, are the common predicted features. Starch, agar, carrageenan, xylose, lignin-derived compound degradation, polysaccharide, folate, and cobalamin biosynthesis are all strain-specific.

Effect of ultrasonic pretreatment on tocochromanol and carotenoid biofortification in maize (Zea mays L.) seedlings

BACKGROUND

Maize is a sought-after food crop because it is micronutrient-rich and affordable. It is an excellent source of carotenoids and tocochromanols. To investigate ways to enhance the micronutrients in maize, we grew maize seedlings with ultrasonic pretreatment to study the effect of ultrasound pretreatment on the biofortification of tocochromanols and carotenoids using high-performance liquid chromatography and real-time quantitative polymerase chain reaction.

RESULTS

Four tocopherol isomers, three tocotrienol isomers and six carotenoid components were measured in maize seedlings. Compared with the untreated maize seedlings, carotenoid content increased and reached the highest level at 8 min ultrasonic pretreatment (19.21 ± 0.44 μg g^-1 fresh weight (FW)), but tocotrienol content evidently decreased. Tocopherol dropped at first but began to rise after 8 min ultrasonic pretreatment (258.1 ± 6.4 μg g^-1 FW). In particular, zeaxanthin in maize seedlings doubled after pre-sonication, while lutein was boosted to 11.81 ± 0.20 μg g^-1 FW. Ultrasonic pretreatment changed the predominant component of tocochromanols in maize seedlings from γ-tocotrienol to α-tocopherol, with the latter content being 1.3 times higher than in the untreated group. Up-regulation of key genes involved in the biosynthesis of tocopherols and carotenoids in maize seedlings occurred as a result of both 2 min and 6 min sonication pretreatment. In particular, _Zm HPPD, _Zm ZE, _Zm ZDS and _Zm MPBQ-MT could partly explain the changes in these phytochemicals.

CONCLUSION

Wet ultrasonic pretreatment could increase tocopherol and carotenoid accumulation in maize seedlings but decrease tocotrienol synthesis. Some up-regulating genes are related to relevant syntheses, such as _Zm HPPD, _Zm ZE, _Zm ZDS and _Zm MPBQ-MT, which could influence the accumulation of tocopherols and carotenoids after ultrasonic pretreatment. © 2022 Society of Chemical Industry.

Concurrent Production of α- and β-Carotenes with Different Stoichiometries Displaying Diverse Antioxidative Activities via Lycopene Cyclases-Based Rational System

α- and β-carotenes belong to the most essential carotenoids in the human body and display remarkable pharmacological value for health due to their beneficial antioxidant activities. Distinct high α-/β-carotene stoichiometries have gained increasing attention for their effective preventions of Alzheimer’s disease, cardiovascular disease, and cancer. However, it is extremely difficult to obtain α-carotene in nature, impeding the accumulations of high α-/β-carotene stoichiometries and excavation of their antioxidant activities. Herein, we developed a dynamically operable strategy based on lycopene cyclases (LCYB and LCYE) for concurrently enriching α- and β-carotenes along with high stoichiometries in E. coli. Membrane-targeted and promoter-centered approaches were firstly implemented to spatially enhance catalytic efficiency and temporally boost expression of TeLCYE to address its low competitivity at the starting stage. Dynamically temperature-dependent regulation of TeLCYE and TeLCYB was then performed to finally achieve α-/β-carotene stoichiometries of 4.71 at 37 °C, 1.65 at 30 °C, and 1.06 at 25 °C, respectively. In the meantime, these α-/β-carotene ratios were confirmed to result in diverse antioxidative activities. According to our knowledge, this is the first time that both the widest range and antioxidant activities of high α/β-carotene stoichiometries were reported in any organism. Our work provides attractive potentials for obtaining natural products with competitivity and a new insight on the protective potentials of α-/β-carotenes with high ratios for health supply.

Study on the Interaction between Four Typical Carotenoids and Human Gut Microflora Using an in Vitro Fermentation Model

Recent studies indicated a strong relationship between carotenoids and gut microflora. However, their structure-activity relationship remains unclear. This study evaluated the interaction between four typical carotenoids (β-carotene, lutein, lycopene, and astaxanthin) and gut microflora using an in vitro fermentation model. After 24 h of fermentation, the retention rates of the four carotenoids were 1.40, 1.38, 1.46, and 5.63 times lower than those of their without gut microflora control groups, respectively. All four carotenoid treated groups significantly increased total short-chain fatty acids (SCFAs) production. All carotenoid supplements significantly promoted the abundance of Roseburia and Parasutterella and inhibited the abundance of Collinsella, while β-carotene, lutein, lycopene, and astaxanthin significantly promoted the abundance of Ruminococcus, Sutterella, Subdoligranulum, and Megamonas, respectively. Furthermore, xanthophylls have a more significant impact on gut microflora than carotenes. This study provides a new way to understand how carotenoids work in the human body with the existing gut microflora.

Advances in the synthesis of three typical tetraterpenoids including β-carotene, lycopene and astaxanthin

Carotenoids are natural pigments that widely exist in nature. Due to their excellent antioxidant, anticancer and anti-inflammatory properties, carotenoids are commonly used in food, medicine, cosmetic and other fields. At present, natural carotenoids are mainly extracted from plants, algae and microorganisms. With the rapid development of metabolic engineering and molecular biology as well as the continuous in-depth study of carotenoids synthesis pathways, industrial microorganisms have showed promising applications in the synthesis of carotenoids. In this review, we introduced the properties of several carotenoids and their biosynthetic metabolism process. Then, the microorganisms synthesizing carotenoids through the natural and non-natural pathways and the extraction methods of carotenoids were summarized and compared. Meanwhile, the influence of substrates on the carotenoids production was also listed. The methods and strategies for achieving high carotenoid production are categorized to help with future research.

Multi-omics analyses provide insight into the biosynthesis pathways of fucoxanthin in Isochrysis galbana

Isochrysis galbana is considered an ideal bait for functional foods and nutraceuticals of humans because of its high fucoxanthin (Fx) content. However, multi-omics analysis of the regulation networks for Fx biosynthesis in I. galbana has not been reported. In this study, we report a high-quality genome sequence of I. galbana LG007, which has a 92.73 Mb genome size, with a contig N50 of 6.99 Mb and 14,900 protein-coding genes. Phylogenomic inferences confirmed the monophyly of Haptophyta, with I. galbana sister to Emiliania huxleyi and Chrysochromulina tobinii. Evolutionary analysis revealed an estimated divergence time between I. galbana and E. huxleyi of ∼ 133 million years ago (Mya). Gene family analysis indicated that lipid metabolism-related genes exhibited significant expansion, including IgPLMT, IgOAR1, and IgDEGS1. Metabolome analysis showed that the content of carotenoids in I. galbana cultured under green light for 7 days was higher than that of white light, and β-carotene was the main carotenoid, accounting for 79.09% of the total carotenoids. Comprehensive analysis of multi-omics analysis revealed that β-carotene, antheraxanthin, zeaxanthin, and Fx content was increased by green light induction, which was significantly correlated with the expression of IgMYB98, IgZDS, IgPDS, IgLHCX2, IgZEP, IgLCYb, and IgNSY. These findings contribute to understanding Fx biosynthesis and its regulation, providing a valuable reference for food and pharmaceutical applications.

Carotenoids Biosynthesis, Accumulation, and Applications of a Model Microalga Euglenagracilis

The carotenoids, including lycopene, lutein, astaxanthin, and zeaxanthin belong to the isoprenoids, whose basic structure is made up of eight isoprene units, resulting in a C40 backbone, though some of them are only trace components in Euglena. They are essential to all photosynthetic organisms due to their superior photoprotective and antioxidant properties. Their dietary functions decrease the risk of breast, cervical, vaginal, and colorectal cancers and cardiovascular and eye diseases. Antioxidant functions of carotenoids are based on mechanisms such as quenching free radicals, mitigating damage from reactive oxidant species, and hindering lipid peroxidation. With the development of carotenoid studies, their distribution, functions, and composition have been identified in microalgae and higher plants. Although bleached or achlorophyllous mutants of Euglena were among the earliest carotenoid-related microalgae under investigation, current knowledge on the composition and biosynthesis of these compounds in Euglena is still elusive. This review aims to overview what is known about carotenoid metabolism in Euglena, focusing on the carotenoid distribution and structure, biosynthesis pathway, and accumulation in Euglena strains and mutants under environmental stresses and different culture conditions. Moreover, we also summarize the potential applications in therapy preventing carcinogenesis, cosmetic industries, food industries, and animal feed.

Characterization of carotenoid biosynthetic pathway genes in the pea aphid (Acyrthosiphon pisum) revealed by heterologous complementation and RNA interference assays

Carotenoids are involved in many essential physiological functions and are produced from geranylgeranyl pyrophosphate through synthase, desaturase, and cyclase activities. In the pea aphid (Acyrthosiphon pisum), the duplication of carotenoid biosynthetic genes, including carotenoid synthases/cyclases (ApCscA-C) and desaturases (ApCdeA-D), through horizontal gene transfer from fungi has been detected, and ApCdeB has known dehydrogenation functions. However, whether other genes contribute to aphid carotenoid biosynthesis, and its specific regulatory pathway, remains unclear. In the current study, functional analyses of seven genes were performed using heterologous complementation and RNA interference assays. The bifunctional enzymes ApCscA-C were responsible for the synthase of phytoene, and ApCscC may also have a cyclase activity. ApCdeA, ApCdeC, and ApCdeD had diverse dehydrogenation functions. ApCdeA catalyzed the enzymatic conversion of phytoene to neurosporene (three-step product), ApCdeC catalyzed the enzymatic conversion of phytoene to ζ-carotene (two-step product), and ApCdeD catalyzed the enzymatic conversion of phytoene to lycopene (four-step product). Silencing of ApCscs reduced the expression levels of ApCdes, and silencing these carotenoid biosynthetic genes reduced the α-, β-, and γ-carotene levels, as well as the total carotenoid level. The results suggest that these genes were activated and led to carotenoid biosynthesis in the pea aphid.

Plant carotenoids: recent advances and future perspectives

Carotenoids are isoprenoid metabolites synthesized de novo in all photosynthetic organisms. Carotenoids are essential for plants with diverse functions in photosynthesis, photoprotection, pigmentation, phytohormone synthesis, and signaling. They are also critically important for humans as precursors of vitamin A synthesis and as dietary antioxidants. The vital roles of carotenoids to plants and humans have prompted significant progress toward our understanding of carotenoid metabolism and regulation. New regulators and novel roles of carotenoid metabolites are continuously revealed. This review focuses on current status of carotenoid metabolism and highlights recent advances in comprehension of the intrinsic and multi-dimensional regulation of carotenoid accumulation. We also discuss the functional evolution of carotenoids, the agricultural and horticultural application, and some key areas for future research.

Cytochrome P450s in algae: Bioactive natural product biosynthesis and light-driven bioproduction

Algae are a large group of photosynthetic organisms responsible for approximately half of the earth's total photosynthesis. In addition to their fundamental ecological roles as oxygen producers and as the food base for almost all aquatic life, algae are also a rich source of bioactive natural products, including several clinical drugs. Cytochrome P450 enzymes (P450s) are a superfamily of biocatalysts that are extensively involved in natural product biosynthesis by mediating various types of reactions. In the post-genome era, a growing number of P450 genes have been discovered from algae, indicating their important roles in algal life-cycle. However, the functional studies of algal P450s remain limited. Benefitting from the recent technical advances in algae cultivation and genetic manipulation, the researches on P450s in algal natural product biosynthesis have been approaching to a new stage. Moreover, some photoautotrophic algae have been developed into “photo-bioreactors” for heterologous P450s to produce high-value added pharmaceuticals and chemicals in a carbon-neutral or carbon-negative manner. Here, we comprehensively review these advances of P450 studies in algae from 2000 to 2021.

Bacterial Carotenoids: Extraction, Characterization, and Applications

Natural carotenoids are secondary metabolites that exhibit antioxidant, anti-inflammatory, and anti-cancer properties. These types of compounds are highly demanded by pharmaceutical, cosmetic, nutraceutical, and food industries, leading to the search for new natural sources of carotenoids. In recent years, the production of carotenoids from bacteria has become of great interest for industrial applications. In addition to carotenoids with C40-skeletons, some bacteria have the ability to synthesize characteristic carotenoids with C30-skeletons. In this regard, a great variety of methodologies for the extraction and identification of bacterial carotenoids has been reported and this is the first review that condenses most of this information. To understand the diversity of carotenoids from bacteria, we present their biosynthetic origin in order to focus on the methodologies employed in their extraction and characterization. Special emphasis has been made on high-performance liquid chromatography-mass spectrometry (HPLC-MS) for the analysis and identification of bacterial carotenoids. We end up this review showing their potential commercial use. This review is proposed as a guide for the identification of these metabolites, which are frequently reported in new bacteria strains.

Asymmetric Cation-Olefin Monocyclization by Engineered Squalene-Hopene Cyclases

Squalene-hopene cyclases (SHCs) have great potential for the industrial synthesis of enantiopure cyclic terpenoids. A limitation of SHC catalysis has been the enzymes' strict (S)-enantioselectivity at the stereocenter formed after the first cyclization step. To gain enantio-complementary access to valuable monocyclic terpenoids, an SHC-wild-type library including 18 novel homologs was set up. A previously not described SHC (AciSHC) was found to synthesize small amounts of monocyclic (R)-γ-dihydroionone from (E/Z)-geranylacetone. Using enzyme and process optimization, the conversion to the desired product was increased to 79 %. Notably, analyzed AciSHC variants could finely differentiate between the geometric geranylacetone isomers: While the (Z)-isomer yielded the desired monocyclic (R)-γ-dihydroionone (>99 % ee), the (E)-isomer was converted to the (S,S)-bicyclic ether (>95 % ee). Applying the knowledge gained from the observed stereodivergent and enantioselective transformations to an additional SHC-substrate pair, access to the complementary (S)-γ-dihydroionone (>99.9 % ee) could be obtained.

Pontibacter cellulosilyticus sp. nov., a carboxymethyl cellulose-hydrolysing bacterium isolated from coastal water

A Gram-stain-negative, rod-shaped, non-motile, red-pink bacterium designated SD6^T was isolated from coastal marine water at Sadong Beach, Ulleung Island, South Korea. Cells of SD6^T grew at 10-42 °C (optimum, 30 °C), pH 5.0-9.0 (optimum, pH 6.0-7.0) and at 0-8.0 % (w/v) NaCl (optimum, 0-3 %). Moreover, 16S rRNA gene sequence analysis indicated that strain SD6^T was a member of the genus Pontibacter, sharing similarities to Pontibacter aydingkolensis XAAS-1^T (98.0 %), Pontibacter amylolyticus 9-2^T (97.3 %), Pontibacter korlensis X14-1^T (97.2 %) and Pontibacter soli HYL7-26^T (96.8 %). The predominant fatty acids of strain SD6^T were identified as iso-C_15 : 0 and summed feature 4 (comprising anteiso-C_17 : 1 B and/or iso-C_17 : 1 I) and the sole respiratory quinone was identified as MK-7 (menaquinone 7). Major polar lipids included phosphatidylethanolamine, one unidentified phosphoglycolipid, two unidentified glycolipids and one unidentified lipid. The average nucleotide identity and in silico DNA-DNA hybridization values of strain SD6^T with its closely related strains were 72.8-79.8 % and 19.2-22.6 %, respectively. The genomic DNA G+C content was 45.4 mol%. In accordance with the results of phenotypic, chemotaxonomic and phylogenetic data, strain SD6^T represents a novel species of the genus Pontibacter, for which the name Pontibacter cellulosilyticus sp. nov. is proposed. The type strain is SD6^T (=KACC 21543^T=NBRC 114313^T=JCM 31022^T).

Bioinformatics Analysis and Identification of Phytoene Synthase Gene in Microalgae

BACKGROUND

Carotenoids are known as lipophilic secondary metabolites with important biological activities, which are mostly used in the food and pharmaceutical industry. They contribute to the colours of many fruits and flowers. Studies on the biosynthetic pathways of isoprenoids and carotenoids are still scarce, especially in microalgae, and are limited to specific groups Dunaliella spp. In the Chlorophyta taxon of algae, the 2-C-methyl-D-erythritol 4-phosphate/1-deoxy-D-xylulose 5-phosphate (DOXP/MEP) is the synthesis pathway of sterols and carotenoids.

OBJECTIVES

In this study, we used 12 Psy gene sequences in Dunaliella sp., also Scenedesmus acutus, and Diospyros kaki to investigate a genome-wide search. The results are useful for better identification of carotenoids metabolisms and increasing the production rate of beta-carotene in pharmaceutical, food, and industrial processes.

METHODS

Phytoene synthase (Psy) from Dunaliella spp. was selected as the first regulatory point in the carotenoids pathway that catalysis the formation of geranylgeranyl pyrophosphate in isoprenoid biosynthesis. Structural, evolutionary, and physics-chemical characteristics were investigated using various bioinformatics tools and computer techniques. Moreover, some recently published patents were also regarded.

RESULTS

The maximum length of the conserved motif was 5167 bp for Dunaliella. sp. (DQ463306.1), and the smallest length of the conserved motif was 416 bp belong to D. salina (JQ762451.1). The average molecular weight of species was 41820.53 Da. The theoretical pI of species varied from 4.87 to 9.65, indicating vernation in the acidic nature. Two strains of D. bardawil (U91900.1 and EU328287.1) showed just a long-distance relationship with all other Dunaliella strains. Whilst, D. parva displayed the furthest vicinity with all the studied strains.

CONCLUSION

Our study highlighted the Psy regulatory mechanism as a key factor in the carotenoids pathway to facilitate genetic and metabolic engineering studies. The obtained three-dimensional arrangement of the amino acids revealed the regional structures and folding of the diverse segments of helices, sheets, turns. This information is a key point to unveil the protein's operation mechanism. Besides, we confirmed the suitability of bioinformatic approaches for analysing the gene structures and identifying the new Psy genes in unstudied microalgal strains.