Carotenoid Biosynthesis Research Articles

Distribution of C30 carotenoid biosynthesis genes suggests habitat adaptation function in insect-adapted and nomadic Lactobacillaceae

Carotenoids are membrane-bound pigments that are essential for photosynthesizing plants and algae, widely applied in food, feed and cosmetics due to their antioxidant and anti-inflammatory properties. The production of carotenoids, particularly C30 forms, has been documented in some non-photosynthetic prokaryotes. However, their function, distribution and ecology beyond photosynthesizing organisms remains understudied. In this study, we performed an eco-evolutionary analysis of terpenoid biosynthetic gene clusters in the Lactobacillaceae family, screening 4203 dereplicated genomes for terpenoid biosynthesis genes, and detected crtMN genes in 28/361 (7.7%) species across 14/34 (41.2%) genera. These genes encode key enzymes for producing the C30 carotenoid 4,4′-diaponeurosporene. crtMN genes appeared to be convergently gained within Fructilactobacillus and horizontally transferred across species and genera, including Lactiplantibacillus to Levilactobacillus. The phenotype was confirmed in 87% of the predicted crtMN gene carriers (27/31). Nomadic and insect-adapted species, particularly those isolated from vegetable fermentations, e.g., Lactiplantibacillus, and floral habitats, e.g., Fructilactobacillus, contained crtMN genes, while vertebrate-associated species, including vaginal associated species, lacked this trait. This habitat association aligned with the observations that C30 carotenoid-producing strains were more resistant to UV-stress. In summary, C30 carotenoid biosynthesis plays a role in habitat adaptation and is scattered across Lactobacillaceae in line with this habitat adaptation.

Origin and evolution of yeast carotenoid pathways.

Carotenoid pathways exist in nature in all domains. Comparison of the genes involved and their distribution allowed the elucidation of the origin and evolution of carotenoid biosynthesis from an early common ancestor of prokaryotes to Bacteria and Archaea. From the latter domain, carotenogenic genes are inherited by fungi as the only phylum of Eukarya. Carotenoid biosynthesis in the algal-plant lineage emerged independently by endosymbiotic gene transfer from an engulfed carotenogenic cyanobacterium. The early set of carotenogenic genes included crtB of phytoene synthase, the desaturase gene crtI, and the lycopene cyclase gene crtYcd for the synthesis of β-carotene. This carotenoid is further metabolised either to zeaxanthin and retinal due to the presence of crtZ and ccd or elongated to a C50 carotenoids by the crtEb gene product. The diversified pathways, especially in bacteria and fungi, result from gene modifications altering the substrate and product specificities of the corresponding enzymes or from the acquisition of novel genes. This was highlighted in more detail for the carotenoid pathways in the red yeasts of Basidiomycota leading to torularhodin, 2'-plectaniaxanthin, and astaxanthin.

Integrated metabolome and transcriptome analysis provides clues to fruit color formation of yellow, orange, and red bell pepper

Fruit color is a crucial trait for bell pepper. To investigate the mechanism of color formation, three bell pepper lines with different color (yellow, orange and red) were used as materials to conduct comprehensive targeted metabolomic and transcriptomic analyses. During the process of fruit development, 54 carotenoids metabolites were discovered, exhibiting unique accumulation patterns and notable variety specificity. The types and content of carotenoids in orange fruit (OM) were notably greater compared to the other two varieties. Red pigment (capsanthin and capsorubin) was specifically enriched in red fruit (RM), and yellow pigment (lutein and zeaxanthin) is the highest in yellow fruit (YM) and OM. Five modules positively correlated with carotenoid accumulation and one negative module was determined by weighted gene co-expression network analysis (WGCNA). Additionally, transcription factors (TFs) and hub genes related to carotenoid synthesis were predicted. By elucidating the regulation of 7 key carotenoid metabolites by 14 critical genes and 5 key TFs, we constructed a comprehensive carotenoid biosynthesis metabolic network that comprehensively explains the pigment changes observed in green and mature pepper fruit. Overall, the results not only provide important insights into carotenoid synthesis pathway, but also lay a solid base for revealing the mechanism of bell pepper color transformation.

Phytohormone augmented biomass and lipid production in Dunaliella salina under two-stage cultivation strategy: A comprehensive characterization of biomass and lipid using DLS, FTIR, CHNS and NMR for bioenergy prospects

Increasing population, climatic shifts, and decreasing fossil-fuels worldwide led scientists to explore microalgae as a renewable energy resource. The present study unravels the impact of gibberellic acid (GA3) on biomass production, enzymatic activities, macromolecular synthesis, and metabolome analysis of Dunaliella salina using two-stage cultivation strategy. The results indicated a marked increase in biomass (1.44-fold), photosynthetic yield (Fv/Fm 0.68), along with RuBisCO activity (1.66-fold), with an increased in absolute value of zeta potential(ζ) in cultures treated with 10 µM GA3 compared to controls (Stage I). Interestingly, 15 µM GA3-treated cells significantly enhanced lipid content (42.36 %), and carbohydrates (16.56 %) with elevated antioxidative enzymes (SOD, CAT, and APX) activities (Stage II). Enhanced lipid content was further confirmed through FTIR spectra (2928 cm-1, and 1740 cm-1) and 1H NMR signals (1.0– 2, 3.5–4.5 ppm), indicating an increase in both saturated (SFA) and polyunsaturated fatty acids (PUFAs). Elemental analysis demonstrated higher carbon and hydrogen percentages, reflected in higher heating value (HHV) and H/C ratio at 15 µM GA3. The increased lipid content was found to be significantly correlated with ACCase and GPAT activities, suggesting the allocation of carbon flux toward lipid biosynthesis pathways. To substantiate the carbon flux, HR-MS-based metabolomic analysis was performed, indicating a reduction in TCA and Calvin cycle intermediates with a significant rise in carotenoid biosynthesis, as well as metabolic shift towards fatty acid biosynthesis reflecting in the enhanced SFA and PUFAs. Thus, these findings highlighted GA3 significant role in the carbon flux allocation towards the neutral lipid biosynthesis for bioenergy prospects.

CsCBF2 contributes to cold repression of chlorophyll and carotenoid biosynthesis in albino Camellia sinensis cv. Baiye 1.

C-repeat binding factors (CBFs) play a pivotal role in regulating cold response in higher plants. Camellia sinensis cv. Baiye 1, a representative albino tea cultivar, has been identified as temperature-sensitive based on long-term observations by tea farmers. However, it remains unclear whether CsCBFs are involved in temperature-mediated albinism and seasonal greening in 'Baiye 1', and the mechanisms by which CBFs regulate cold responses in albino leaves are unknown. In this study, we demonstrate that CsCBF2 suppresses the seasonal greening of albino leaves by inhibiting chlorophyll and carotenoid biosynthesis under cold stress. In tea plantations, the accumulation of chlorophylls and carotenoids in the albino shoots of 'Baiye 1' is closely correlated with the effective accumulated temperature during its seasonal greening process. Weighted Gene Co-expression Network Analysis revealed negative associations between CsCBF expression and chlorophylls, carotenoids, as well as their biosynthetic genes REVEILLE 1 (CsRVE1) and Zeaxanthin epoxidase 1 (CsZEP1) under temperature fluctuations during seasonal greening. Cold-induced upregulation of CsCBF2 expression and decreased chlorophylls and carotenoids under controlled climate conditions. Transient suppression of CsCBF2 by antisense oligodeoxynucleotide elevated expressions of target genes, and increased chlorophylls and carotenoids. CBF-binding cis-elements were identified in CsRVE1, Protochlorophyllide oxidoreductase A (CsPORA), and CsZEP1 promoters. Luciferase assays suggested CsCBF2 binding to the CRT/DRE cis-elements and repressing expression of CsRVE1, CsPORA, and CsZEP1. These findings highlight CsCBF2 as a key transcriptional repressor involved in the seasonal greening of albino 'Baiye 1' under cold stress, by modulating cold responses and inhibiting genes associated with chlorophyll and carotenoid biosynthesis.

Transcriptomic and metabolomic analysis reveal differentially expressed genes and metabolic pathways in bermudagrass under drought stress

AbstractDrought stress poses a significant challenge to turfgrass growth, particularly in the regions like southern United States, where bermudagrass (Cynodon sp.) is widely used for lawns and sports fields. Drought stress disrupts physiological processes, leading to reduced water availability, impaired photosynthesis, and oxidative stress. To understand the bermudagrass response to drought, we investigated the physiological differences and characterized the gene expression and metabolite profiles in two bermudagrass genotypes, TifTuf and Premier. Physiological measurements showed significant variations in green cover percentage, visual quality, and relative water content between the two genotypes. RNA sequencing revealed extensive gene expression changes, with differentially expressed genes that were upregulated in both genotypes. Gene ontology (GO) analysis highlighted biological processes such as transcription regulation, lipid metabolism, and cellular structure development pathways. KEGG pathway analysis indicated that TifTuf had significant changes in galactose metabolism, carotenoid biosynthesis, and plant hormone signal transduction pathways, while Premier showed enrichment in plant hormone signaling, lipid metabolism, and secondary metabolite biosynthesis pathways. Metabolomic analysis provided insights into metabolic reprogramming due to drought stress. Principal component analysis revealed distinct metabolic patterns between control and drought‐stressed samples, with both genotypes showing substantial alterations. Differential metabolite analysis identified key metabolites associated with stress adaptation, including the phytohormone ABA and various amino acids. This analysis elucidates the intricate physiological and molecular mechanisms underlying drought tolerance in bermudagrass genotypes. These findings enhance the understanding of drought stress adaptation strategies in bermudagrass and offer valuable insights for the development of drought‐tolerant genotypes.

Altered Photoprotective Mechanisms and Pigment Synthesis in Torreya grandis with Leaf Color Mutations: An Integrated Transcriptome and Photosynthesis Analysis

Torreya grandis is a widely cultivated fruit species in China that is valued for its significant economic and agricultural importance. The molecular mechanisms underlying pigment formation and photosynthetic performance in Torreya leaf color mutants remain to be fully elucidated. In this study, we performed transcriptome sequencing and measured photosynthetic performance indicators to compare mutant and normal green leaves. The research results indicate that the identified Torreya mutant differs from previously reported mutants, exhibiting a weakened photoprotection mechanism and a significant reduction in carotenoid content of approximately 33%. Photosynthetic indicators, including the potential maximum photosynthetic capacity (Fv/Fm) and electron transport efficiency (Ψo, φEo), decreased significantly by 32%, 52%, and 49%, respectively. While the quantum yield for energy dissipation (φDo) increased by 31%, this increase was not statistically significant, which may further reduce PSII activity. A transcriptome analysis revealed that the up-regulation of chlorophyll degradation-related genes—HCAR and NOL—accelerates chlorophyll breakdown in the Torreya mutant. The down-regulation of carotenoid biosynthesis genes, such as LCY1 and ZEP, is strongly associated with compromised photoprotective mechanisms and the reduced stability of Photosystem II. Additionally, the reduced expression of the photoprotective gene psbS weakened the mutant’s tolerance to photoinhibition, increasing its susceptibility to photodamage. These changes in gene expression accelerate chlorophyll degradation and reduce carotenoid synthesis, which may be the primary cause of the yellowing in Torreya. Meanwhile, the weakening of photoprotective mechanisms further impairs photosynthetic efficiency, limiting the growth and adaptability of the mutants. This study emphasizes the crucial roles of photosynthetic pigments and photosystem structures in regulating the yellowing phenotype and the environmental adaptability of Torreya. It also provides important insights into the genetic regulation of leaf color in relation to photosynthesis and breeding.

Effect of Fluridone on Roots and Leaf Buds Development in Stem Cuttings of Salix babylonica (L.) 'Tortuosa' and Related Metabolic and Physiological Traits.

The herbicide fluridone (1-methyl-3-phenyl-5-[3-trifluoromethyl (phenyl)]-4(1H)-pyridone) interferes with carotenoid biosynthesis in plants by inhibiting the conversion of phytoene to phytofluene. Fluridone also indirectly inhibits the biosynthesis of abscisic acid and strigolactones, and therefore, our study indirectly addresses the effect of reduced ABA on the roots and leaf buds development in stem cuttings of Salix babylonica L. 'Tortuosa'. The stem cuttings were kept in distilled water (control) or in a solution of fluridone (10 mg/L) in natural greenhouse light and temperature conditions. During the experiments, morphological observations were carried out on developing roots and leaf buds, as well as their appearance and growth. After three weeks of continuous treatments, adventitious roots and leaf buds were collected and analysed. Identification and analysis of anthocyanins were carried out using micro-HPLC-MS/MS-TOF, while HPLC-MS/MS was used to analyse phenolic acids, flavonoids and salicinoids. The fluridone applied significantly inhibited root growth, but the number or density of roots was higher compared to the control. Contents of salicortin and salicin were several dozen times higher in leaf buds than in roots of willow. Fluridone increased the content of salicortin in roots and leaf buds and declined the level of salicin in buds. Fluridone also declined the content of most anthocyanins in roots but enhanced their content in buds, especially cyanidin glucoside, cyanidin galactoside and cyanidin rutinoside. Besides, fluridone markedly decreased the level of chlorophylls and carotenoids in the leaf buds. The results indicate that applied fluridone solution reduced root growth, caused bleaching of leaf buds, and markedly affected the content of secondary metabolites in the adventitious roots and leaf buds of S. babylonica stem cuttings. The paper presents and discusses in detail the significance of fluridone's effects on physiological processes and secondary metabolism.

The transcription factor CaBBX10 promotes chlorophyll and carotenoid pigment accumulation in Capsicum annuum fruit.

Chlorophylls and carotenoids are two pivotal photosynthetic pigments directly influencing the economic value of pepper (Capsicum annuum L.) fruits. However, the coordinated regulatory mechanisms governing the accumulation of both chlorophylls and carotenoids during pepper fruit development remain elusive. In this study, pepper B-box 10 (CaBBX10), a candidate hub transcription factor, was found to play dual roles in the early development of pepper fruit. CaBBX10 virus-induced gene silencing and overexpression experiments demonstrated that the encoded transcription factor promotes both chlorophyll and carotenoid accumulation in pepper fruit. Further comprehensive analyses showed that CaBBX10 directly binds to the promoter of magnesium chelatase subunit D subunit (CaCHLD) and phytoene synthase 1 (CaPSY1), thereby activating their expression in the chlorophyll and carotenoid biosynthesis pathways, respectively. Additionally, the photomorphogenic factor CaCOP1 was found to physically interact with CaBBX10 and lead to its degradation. Therefore, CaBBX10 may serve as a critical link connecting chlorophyll and carotenoid biosynthesis to light signaling. Altogether, our findings reveal a mechanism for the complex transcriptional regulation that simultaneously promotes chlorophyll and carotenoid accumulation in pepper fruit.

Nostoxanthin Biosynthesis by Sphingomonas Species (COS14-R2): Isolation, Identification, and Optimization of Culture Conditions

Nostoxanthin, a yellow pigment, belongs to the xanthophyll group of carotenoids found in various species of bacteria and cyanobacteria. Several species of Sphingomonas can produce appropriate carotenoids for survive in various environments. This comprise nostoxanthin, a significant carotenoid. The study isolated the Sphingomonas species strain COS14-R2 from the Cosmos bipinnatus and identified it through the whole-genome sequence. The strain consists of a circular chromosome with a length of 3,677,457 base pairs.s ecThe genome consists of three carotenoid biosynthesis genes, specifically crtB (phytoene synthase), crtI (phytoene desaturase), and crtY (Lycopene beta-cyclase), which are involved in the synthesis of nostoxanthin. The strain has a circular, undulated colony morphology with a deep yellow color. It demonstrates optimal growth in liquid media at 25 to 35 °C and exhibits a high tolerance for pH levels between 5 and 11 and requires adequate quantities of carbon and nitrogen. We observed the highest concentration of nostoxanthin was recorded at 35 °C, pH of 7.5, glucose concentration of 40 g L−1, and a yeast extract concentration of 5 g L−1 during dark incubation. The fed-batch fermentation process produced nostoxanthin at a concentration of 217.22 ± 9.60 mg L−1, with a selectivity of 72.32% and a productivity of 2.59 g/L/h. The dry biomass extract was purified using column chromatography. The LC–MS/MS analysis of the purified fraction indicated that the molecular weight of nostoxanthin is 600.5098 m/z. The DPPH assay result of 75.5 ± 0.33% indicates nostoxanthin is highly effective in scavenging free radicals.

BoaCRTISO regulates the color and glossiness of Chinese kale through its effects on pigment, abscisic acid, and cuticular wax biosynthesis

Carotenoid isomerase (CRTISO) is an important enzyme in carotenoid biosynthesis, and it catalyzes the conversion of lycopene precursors to lycopene in several plant species. However, the role of CRTISO in other biochemical processes during plant growth and development remains unclear. Here, we showed that Chinese kale boacrtiso mutants have distinctive characteristics, including a yellow-green hue and glossy appearance, and this contrasts with the dark green and glaucous traits observed in wild-type (WT) plants. Analysis of pigments in mutants revealed that the reduction in the content of carotenoids and chlorophylls contributed to the yellow-green coloration observed in mutants. An examination of cuticular waxes in Chinese kale indicated that there was a decrease in both the total wax content and the content of individual waxes in boacrtiso mutants (bearing a mutation of BoaCRTISO), which may be caused by the decrease of abscisic acid (ABA) content. The expression of carotenoid, chlorophyll, ABA, and wax biosynthesis genes was down-regulated in boacrtiso mutants. This finding confirms that BoaCRTISO regulates the biosynthesis of pigments, ABA, and cuticular waxes in Chinese kale. Our results provide new insights into the interplay between plant pigment and cuticular wax metabolic pathways in Brassica vegetables.

Ultraviolet-diethyl sulfate composite mutagenesis of Rhodosporidium toruloides and culture optimization to improve carotenoid production

Rhodosporidium toruloides is a carotenoid-producing oleaginous yeast, and its carotenoids are of considerable value to food, chemical, and medical industries. In this study, to improve carotenoid production capacity, the parent R. toruloides strain (CK) was compound mutagenized using ultraviolet-diethyl sulfate (UV-DES), and cultivation conditions were simultaneously optimized to enhance the carotenoid synthesis ability of the mutant strain (M5). The carotenoid content was significantly increased following UV-DES compound mutagenesis (CK = 249.34 μg/g, M5 = 535.28 μg/g). The carotenoid content of M5 was increased to 763.85 μg/g under optimal culture conditions. In addition, mutagenesis altered the carotenoid components, and torulene and torularhodin levels were also increased following mutation, leading to changes in antioxidant capacity. Real-time quantitative PCR results showed that expression of six genes (CAR1, CAR2, CrtE, CrtI, ME1, HMG1) related to carotenoid accumulation were significantly upregulated by UV-DES composite mutagenesis. In conclusion, combined UV-DES mutagenesis and optimal culture conditions promoted the biosynthesis of carotenoids in R. toruloides.

Proteomic analysis identified proteins that are differentially expressed in the flavonoid and carotenoid biosynthetic pathways of Camellia Nitidissima flowers

BackgroundCamellia nitidissima Chi is a popular ornamental plant because of its golden flowers, which contain flavonoids and carotenoids. To understand the regulatory mechanism of golden color formation, the metabolites of C. nitidissima petals at five different developmental stages were detected, a proteome map of petals was first constructed via tandem mass tag (TMT) analysis, and the accuracy of the sequencing data was validated via parallel reaction monitoring (PRM).ResultsNineteen color components were detected, and most of these components were carotenoids that gradually accumulated, while some metabolites were flavonoids that were gradually depleted. A total of 97,647 spectra were obtained, and 6,789 quantifiable proteins were identified. Then, 1,319 differentially expressed proteins (DEPs) were found, 55 of which belong to the flavonoid and carotenoid pathways, as revealed by pairwise comparisons of protein expression levels across the five developmental stages. Notably, most DEPs involved in the synthesis of flavonoids, such as phenylalanine ammonium lyase and 4-coumarate-CoA ligase, were downregulated during petal development, whereas DEPs involved in carotenoid synthesis, such as phytoene synthase, 1-deoxy-D-xylulose-5-phosphate synthase, and β-cyclase, tended to be upregulated. Furthermore, protein‒protein interaction (PPI) network analysis revealed that these 55 DEPs formed two distinct PPI networks closely tied to the flavonoid and carotenoid synthesis pathways. Phytoene synthase and chalcone synthase exhibited extensive interactions with numerous other proteins and displayed high connectivity within the PPI networks, suggesting their pivotal biological functions in flavonoid and carotenoid biosynthesis.ConclusionProteomic data on the flavonoid and carotenoid biosynthesis pathways were obtained, and the regulatory roles of the DEPs were analyzed, which provided a theoretical basis for further understanding the golden color formation mechanism of C. nitidissima.

Manipulation of artificial light environment improves plant biomass and fruit nutritional quality in tomato

IntroductionThe yield and quality of tomato (Solanum lycopersicum. L) are often decreased when plants suffer from low light intensity and short-photoperiod in winter. Manipulation of the artificial light environment is a feasible technology to promote off-seasonal production and improve fruit nutritional quality in the greenhouse. ObjectivesHere we aim to investigate the appropriate balance between red (R) and blue (B) light to improve tomato yield and quality traits. MethodsBiochemical, molecular and genetic analysis were used to study the photosynthetic traits, pigments, sugar and volatile accumulation pathway genes. ResultsTomato plants subjected to R1B0.8, a ratio between monochromatic red (R) and blue (B) light, for 16 h photoperiod showed significantly increased chlorophyll and biomass accumulation compared to white (W) light treatment. R1B0.8 light treatment enhanced electron transfer efficiency and photosynthetic capacity by improving the light energy utilization rate and inducing photosystem core subunit genes (SlPsaC, SlPsaB, SlPsaA) and light-harvesting complex genes (SlLHCB/A). Compared to W light, R1B0.8 light also induced carotenoid accumulation and accelerated fruit ripening, which was associated with the upregulation of carotenoid biosynthesis genes (SlPSY1, SlPDS) and ethylene biosynthesis genes (SlACS2, SlACO2) in tomato fruits. Moreover, fruits exposed to R1B0.8 light treatments significantly improved fructose and glucose accumulation and the expression of the volatile-related gene (SlAADC1a) and flavor-related gene (SlGORKY). ConclusionOur results showed that R1B0.8 light with a 16 h photoperiod could prominently promote photosynthetic traits, pigments, sugar and volatile accumulation in tomato. Our findings on the manipulation of artificial light environments in protected horticulture offer possibilities for enhancing crop yield and quality to meet the increasing global demand for food.

Physiological response of microalga Dunaliella parva when treated with MeJA, GA3.

DpAP2 is a transcription factor regulating carotenoid biosynthesis pathway. It was speculated that MeJA significantly decreased expression of DpAP2 gene, then the decreasing DpAP2 expression significantly inhibited expression of some key enzyme genes such as PSY, PDS and GGPS in carotenoid biosynthesis pathway. In contrast, it was speculated that GA3 significantly increased expression of DpAP2 gene, then the increasing DpAP2 expression significantly increased expression of some key enzyme genes such as PDS and GGPS in carotenoid biosynthesis pathway. To increase the content of carotenoid, we evaluated the effect of DpAP2 overexpression on carotenoid accumulation in D. parva. Transgenic D. parva showed a higher carotenoid content (3.18 mg/g DW) compared with control group (2.13 mg/g DW) at 9 d. The dosage effects of exogenous hormones MeJA and GA3 were found in D. parva cells treated with different concentrations of MeJA (10, 20, 50, 100 μM) and GA3 (10, 20, 50, 100 μM). The high concentrations of MeJA (10-100 μM) inhibited the accumulation of carotenoid, and the relative expression of DpAP2, PSY, PDS and GGPS decreased significantly. On the contrary, the relative expression of DpAP2, PDS and GGPS increased significantly when D. parva was treated with 10, 20, 50 and 100 μM GA3, which promoted the biosynthesis of carotenoid. Therefore, we inferred that there was a hierarchical regulation from hormone, transcription factor, key enzyme gene to carotenoid accumulation in carotenoid biosynthesis. Carotenoid biosynthesis was enhanced by DpAP2 overexpression (1.4930 fold of control) and exogenous substances such as GA3 (1.5889 fold of control), which laid a foundation for massive accumulation of carotenoids in microalgae. In the future, further studies were required to demonstrate the complex regulatory network.

Transcriptomic Analysis Reveals the Mechanism of Color Formation in the Peel of an Evergreen Pomegranate Cultivar 'Danruo No.1' During Fruit Development.

Pomegranate (Punica granatum L.) is an ancient fruit crop that has been cultivated worldwide and is known for its attractive appearance and functional metabolites. Fruit color is an important index of fruit quality, but the color formation pattern in the peel of evergreen pomegranate and the relevant molecular mechanism is still unknown. In this study, the contents of pigments including anthocyanins, carotenoids, and chlorophyll in the peel of 'Danruo No. 1' pomegranate fruit during three developmental stages were measured, and RNA-seq was conducted to screen key genes regulating fruit color formation. The results show that pomegranate fruit turned from green to red during development, with a dramatic increase in a* value, indicating redness and anthocyanins concentration, and a decrease of chlorophyll content. Moreover, carotenoids exhibited a decrease-increase accumulation pattern. Through RNA-seq, totals of 30, 18, and 17 structural genes related to anthocyanin biosynthesis, carotenoid biosynthesis and chlorophyll metabolism were identified from differentially expressed genes (DEGs), respectively. Transcription factors (TFs) such as MYB, bHLH, WRKY and AP2/ERF were identified as key candidates regulating pigment metabolism by K-means analysis and weighted gene co-expression network analysis (WGCNA). The results provide an insight into the theory of peel color formation in evergreen pomegranate fruit.

Diverse and specialized metabolic capabilities of microbes in oligotrophic built environments

BackgroundBuilt environments (BEs) are typically considered to be oligotrophic and harsh environments for microbial communities under normal, non-damp conditions. However, the metabolic functions of microbial inhabitants in BEs remain poorly understood. This study aimed to shed light on the functional capabilities of microbes in BEs by analyzing 860 representative metagenome-assembled genomes (rMAGs) reconstructed from 738 samples collected from BEs across the city of Hong Kong and from the skin surfaces of human occupants. The study specifically focused on the metabolic functions of rMAGs that are either phylogenetically novel or prevalent in BEs.ResultsThe diversity and composition of BE microbiomes were primarily shaped by the sample type, with Micrococcus luteus and Cutibacterium acnes being prevalent. The metabolic functions of rMAGs varied significantly based on taxonomy, even at the strain level. A novel strain affiliated with the Candidatus class Xenobia in the Candidatus phylum Eremiobacterota and two novel strains affiliated with the superphylum Patescibacteria exhibited unique functions compared with their close relatives, potentially aiding their survival in BEs and on human skins. The novel strains in the class Xenobia possessed genes for transporting nitrate and nitrite as nitrogen sources and nitrosative stress mitigation induced by nitric oxide during denitrification. The two novel Patescibacteria strains both possessed a broad array of genes for amino acid and trace element transport, while one of them carried genes for carotenoid and ubiquinone biosynthesis. The globally prevalent M. luteus in BEs displayed a large and open pangenome, with high infraspecific genomic diversity contributed by 11 conspecific strains recovered from BEs in a single geographic region. The versatile metabolic functions encoded in the large accessory genomes of M. luteus may contribute to its global ubiquity and specialization in BEs.ConclusionsThis study illustrates that the microbial inhabitants of BEs possess metabolic potentials that enable them to tolerate and counter different biotic and abiotic conditions. Additionally, these microbes can efficiently utilize various limited residual resources from occupant activities, potentially enhancing their survival and persistence within BEs. A better understanding of the metabolic functions of BE microbes will ultimately facilitate the development of strategies to create a healthy indoor microbiome.Bh9ATT9ssZEtNaJHv1wg7GVideo

Examining Carotenoid Metabolism Regulation and Its Role in Flower Color Variation in Brassica rapa L.

Carotenoids are vital organic pigments that determine the color of flowers, roots, and fruits in plants, imparting them yellow, orange, and red hues. This study comprehensively analyzes carotenoid accumulation in different tissues of the Brassica rapa mutant "YB1", which exhibits altered flower and root colors. Integrating physiological and biochemical assessments, transcriptome profiling, and quantitative metabolomics, we examined carotenoid accumulation in the flowers, roots, stems, and seeds of YB1 throughout its growth and development. The results indicated that carotenoids continued to accumulate in the roots and stems of YBI, especially in its cortex, throughout plant growth and development; however, the carotenoid levels in the petals decreased with progression of the flowering stage. In total, 54 carotenoid compounds were identified across tissues, with 30 being unique metabolites. Their levels correlated with the expression pattern of 22 differentially expressed genes related to carotenoid biosynthesis and degradation. Tissue-specific genes, including CCD8 and NCED in flowers and ZEP in the roots and stems, were identified as key regulators of color variations in different plant parts. Additionally, we identified genes in the seeds that regulated the conversion of carotenoids to abscisic acid. In conclusion, this study offers valuable insights into the regulation of carotenoid metabolism in B. rapa, which can guide the selection and breeding of carotenoid-rich varieties.

Characteristic of new Phaffia rhodozyma yeast strains isolated from birch slime fluxes in Poland

Three new strains of Phaffia rhodozyma yeast have recently been isolated in Poland. The aim of this study was to phenotypically characterize these strains and to compare them with the properties of the reference strain. The potential for carotenoid biosynthesis in these strains was also determined, depending on temperature, carbon, and nitrogen sources in the medium. Phaffia rhodozyma yeasts were also identified by MALDI-TOF MS. There were minor differences in cell morphology among the strains. All strains reproduced asexually by budding and formed spherical chlamydospores. No ability for sexual reproduction was observed. Physiological tests showed minor variations between the reference strain and the isolates, likely due to the geographical specificity of the habitat from which they were originally isolated. Analysis of protein spectra showed that the tested yeast isolates had seven common peaks of different intensities, with masses at 2200, 2369, 3213, 3628, 3776, 3921, and 4710 m/z. Moreover, additional strain-dependent spectra were found. The amount of synthesized carotenoids varied with the carbon and nitrogen sources used, as well as the temperature. The best producer of carotenoids was the P. rhodozyma CMIFS 102 isolate.

Carotenoid-carbohydrate crosstalk: evidence for genetic and physiological interactions in storage tissues across crop species.

Carotenoids play essential roles in photosynthesis, photoprotection, and human health. Efforts to increase carotenoid content in several staple crops have been successful through both conventional selection and genetic engineering methods. Interestingly, in some cases, altering carotenoid content has had unexpected effects on other aspects of plant metabolism, impacting traits like sugar content, dry matter percentage, fatty acid content, stress tolerance, and phytohormone concentrations. Studies across several diverse crop species have identified negative correlations between carotenoid and starch contents, as well as positive correlations between carotenoids and soluble sugars. Collectively, these reports suggest a metabolic interaction between carotenoids and carbohydrates. We synthesize evidence pointing to four hypothesized mechanisms: (1) direct competition for precursors; (2) physical interactions in plastids; (3) influences of sugar or apocarotenoid signaling networks; and (4) nonmechanistic population or statistical sources of correlations. Though the carotenoid biosynthesis pathway is well understood, the regulation and interactions of carotenoids, especially in nonphotosynthetic tissues, remain unclear. This topic represents an underexplored interplay between primary and secondary metabolism where further research is needed.