Transcriptional basis of enhanced photoinduction of carotenoid biosynthesis at low temperature in the fungus Neurospora crassa

Ketocarotenoids adonirubin and adonixanthin: Properties, health benefits, current technologies, and emerging challenges

Given their multifaceted roles, carotenoids have garnered significant scientific interest, resulting in a comprehensive and intricate body of literature that occasionally presents conflicting findings concerning the proper characterization, quantification, and bioavailability of these compounds. Nevertheless, it is undeniable that the pursuit of novel carotenoids remains a crucial endeavor, as their diverse properties, functionalities and potential health benefits make them invaluable natural resources in agri-food and health promotion through the diet. In this framework, particular attention is given to ketocarotenoids, viz., astaxanthin (one of them) stands out for its possible multifunctional role as an antioxidant, anticancer, and antimicrobial agent. It has been widely explored in the market and utilized in different applications such as nutraceuticals, food additives, among others. Adonirubin and adonixanthin can be naturally found in plants and microorganisms. Due to the increasing significance of natural-based products and the remarkable opportunity to introduce these ketocarotenoids to the market, this review aims to provide an expert overview of the pros and cons associated with adonirubin and adonixanthin.

Low temperature promotes the production and efflux of terpenoids in yeast

Altering the fermentation environment provides an effective approach to optimizing the production efficiency of microbial cell factories globally. Here, lower fermentation temperatures of yeast were found to significantly improve the synthesis and efflux of terpenoids, including glycyrrhetinic acid (GA), β-caryophyllene, and α-amyrin. The production of GA at 22°C increased by 5.5 times compared to 30°C. Yeast subjected to lower temperature showed substantial changes at various omics levels. Certain genes involved in maintaining cellular homeostasis that were upregulated under the low temperature conditions, leading to enhanced GA production. Substituting Mvd1, a thermo-unstable enzyme in mevalonate pathway identified by transcriptome and proteome, with a thermo-tolerant isoenzyme effectively increased GA production. The lower temperature altered the composition of phospholipids and increased the unsaturation of fatty acid chains, which may influence GA efflux. This study presents a strategy for optimizing the fermentation process and identifying key targets of cell factories for terpenoid production.

Light regulation of secondary metabolism in fungi

Fungi have evolved unique metabolic regulation mechanisms for adapting to the changing environments. One of the key features of fungal adaptation is the production of secondary metabolites (SMs), which are essential for survival and beneficial to the organism. Many of these SMs are produced in response to the environmental cues, such as light. In all fungal species studied, the Velvet complex transcription factor VeA is a central player of the light regulatory network. In addition to growth and development, the intensity and wavelength of light affects the formation of a broad range of secondary metabolites. Recent studies, mainly on species of the genus Aspergillus, revealed that the dimer of VeA-VelB and LaeA does not only regulate gene expression in response to light, but can also be involved in regulating production of SMs. Furthermore, the complexes have a wide regulatory effect on different types of secondary metabolites. In this review, we discussed the role of light in the regulation of fungal secondary metabolism. In addition, we reviewed the photoreceptors, transcription factors, and signaling pathways that are involved in light-dependent regulation of secondary metabolism. The effects of transcription factors on the production of secondary metabolites, as well as the potential applications of light regulation for the production of pharmaceuticals and other products were discussed. Finally, we provided an overview of the current research in this field and suggested potential areas for future research.

Hybrid histidine kinase HisK2301 modulates carotenoid production to counteract cold-induced oxidative stress in Rhodosporidium kratochvilovae YM25235 under low temperature

Hybrid histidine kinases (HHKs) are major sensor proteins for fungi that contribute to stress tolerance. In the present work, we investigated the roles and mechanisms of the HHK HisK2301 in cold-adapted Rhodosporidium kratochvilovae strain YM25235. The HisK2301 deletion strain was constructed by homologous recombination method and arranged for multiple stress tests. We analysed the content of carotenoid using UV-Vis and HPLC. Relative transcript levels of genes phytoene desaturase (RKCrtI) and phytoene synthase and lycopene cyclase (RKCrtYB) were analysed by RT-qPCR. Intracellular reactive oxygen species (ROS) generation was measured using 2',7'-dichlorodihydrofluorescein diacetate (DCFH-DA). Our results clearly indicated that YM25235 produces γ-carotene, torulene, β-carotene and torularhodin, with the latter two components strongly related to adapt to cold. HisK2301 is crucial for YM25235 adaptation to different types of stress such as cold, salt, osmotic and oxidative stress. Growth at low temperature clearly induced oxidative stress in YM25235, as more ROS accumulated at cold. During cold stress, HisK2301 is suggested to sense cold-induced ROS signals and then promote carotenoid production partially by RKCrtI and RKCrtYB to scavenge excessive ROS production. Such an inducible protective system may confer YM25235 fast response and better adaptation to cold stress. To conclude, our findings give the first insight into the effect of HisK2301 on carotenoid biosynthesis and cold-induced oxidative stress in fungi under low temperature and suggest the potential use of the cold-adapted HHK HisK2301 in industrial production of carotenoid.

Light regulates the degradation of the regulatory protein VE-1 in the fungus Neurospora crassa

BACKGROUND

Fungi use light as an environmental signal to regulate developmental transitions that are key aspects of their biological cycles and that are also relevant for their dispersal and infectivity as plant or animal pathogens. In addition, light regulates the accumulation of photoprotective pigments, like carotenoids, and other secondary metabolites. Most fungal light responses occur after changes in gene transcription and we describe here a novel effect of light in the regulation of degradation of VE-1, a key component of the velvet complex, in the model fungus Neurospora crassa. The velvet complex is a fungal-specific protein complex that coordinates fungal development, secondary metabolism, and light regulation by interacting with other regulators and photoreceptors and modifying gene expression.

RESULTS

We have characterized the role of VE-1 during conidiation in N. crassa. In vegetative mycelia, VE-1 is localized in the cytoplasm and nuclei and is required for light-dependent transcription but does not interact with the photoreceptor and transcription factor WC-1. VE-1 is more stable in light than in darkness during asexual development (conidiation). We have shown that this light effect requires the blue-light photoreceptor WC-1. We have characterized the role of the proteasome, the COP9 signalosome (CSN), and the adaptor component of cullin-RING ubiquitin ligases, FWD-1, in the degradation of VE-1.

CONCLUSIONS

We propose that this new effect of light allows the fungal cell to adapt quickly to changes in light exposure by promoting the accumulation of VE-1 for the regulation of genes that participate in the biosynthesis of photoprotective pigments.

Genome-Wide Transcriptional Changes of Rhodosporidium kratochvilovae at Low Temperature

Rhodosporidium kratochvilovae strain YM25235 is a cold-adapted oleaginous yeast strain that can grow at 15°C. It is capable of producing polyunsaturated fatty acids. Here, we used the Nanopore Platform to first assemble the R. kratochvilovae strain YM25235 genome into a 23.71 Mb size containing 46 scaffolds and 8,472 predicted genes. To explore the molecular mechanism behind the low temperature response of R. kratochvilovae strain YM25235, we analyzed the RNA transcriptomic data from low temperature (15°C) and normal temperature (30°C) groups using the next-generation deep sequencing technology (RNA-seq). We identified 1,300 differentially expressed genes (DEGs) by comparing the cultures grown at low temperature (15°C) and normal temperature (30°C) transcriptome libraries, including 553 significantly upregulated and 747 significantly downregulated DEGs. Gene ontology and pathway enrichment analysis revealed that DEGs were primarily related to metabolic processes, cellular processes, cellular organelles, and catalytic activity, whereas the overrepresented pathways included the MAPK signaling pathway, metabolic pathways, and amino sugar and nucleotide sugar metabolism. We validated the RNA-seq results by detecting the expression of 15 DEGs using qPCR. This study provides valuable information on the low temperature response of R. kratochvilovae strain YM25235 for further research and broadens our understanding for the response of R. kratochvilovae strain YM25235 to low temperature.

Carotenoids from fungi and microalgae: A review on their recent production, extraction, and developments

The demand for carotenoids from natural sources obtained by biological extraction methods is increasing with the development of biotechnology and the continued awareness of food safety. Natural plant-derived carotenoids have a relatively high production cost and are affected by the season, while microbial-derived carotenoids are favored due to their natural, high-efficiency, low production cost, and ease of industrialization. This article reviewed the following aspects of natural carotenoids derived from microorganisms: (1) the structures and properties of main carotenoids; (2) fungal and microalgal sources of the main carotenoids; (3) influencing factors and modes of improvement for carotenoids production; (4) efficient extraction methods for carotenoids; and (5) the commercial value of carotenoids. This review provided a reference and guidance for the development of natural carotenoids derived from microorganisms.

Proteome-wide analyses reveal diverse functions of acetylation proteins in Neurospora crassa

Quantitative acetyl-proteomics, a newly identified post-translational modification, is known to regulate transcriptional activity in different organisms. Neurospora crassa is a model ascomycete fungus maintained for biochemistry and molecular biology research; however, extensive studies of the functions of its acylation proteins have yet to be performed. In this study, using LC-MS/MS qualitative proteomics strategies, we identified 1909 modification sites on 940 proteins in N. crassa and analysed the functions of these proteins using GO enrichment, KEGG pathway, and subcellular location experiments. We classified the acetylation protein involvement in diverse pathways, and protein-protein interaction (PPI) network analysis further demonstrated that these proteins participate in diverse biological processes. In summary, our study comprehensively profiles the crosstalk of modified sites, and PPI among these proteins may form a complex network with both similar and distinct regulatory mechanisms, providing improved understanding of their biological functions in N. crassa.

A novel gene, CaATHB-12, negatively regulates fruit carotenoid content under cold stress in Capsicum annuum

Background

Carotenoids, the secondary metabolites terpenoids, are the largest factors that form the fruit color. Similar to flavonoids, they are not only safe and natural colorants of fruits but also play a role as stress response biomolecules.

Methods

To study the contribution of the key genes in carotenoids biosynthesis, fruit-color formation, and in response to cold stress, we characterized the key regulatory factor CaATHB-12 from the HD-ZIP I sub-gene family members in pepper.

Results

Cold stress enhanced carotenoid accumulation as compared with the normal condition. CaATHB-12 silencing through virus-induced gene silencing changed the fruit color by regulating the carotenoid contents. CaATHB-12 silencing increased the antioxidant enzyme activities in the fruits of pepper, exposed to cold stress, whereas CaATHB-12 overexpression decreased the activities of antioxidant enzymes in the transgenic Arabidopsis lines, exposed to cold stress, suggesting that CaATHB-12 is involved in the regulation of cold stress in the pepper fruits.

Conclusion

Our research will provide insights into the formation of fruit color in pepper and contribution of CaATHB-12 in response to cold stress. Further study should be focused on the interaction between CaATHB-12 and its target gene.

Engineering Photosensory Modules of Non-Opsin-Based Optogenetic Actuators

Optogenetic (photo-responsive) actuators engineered from photoreceptors are widely used in various applications to study cell biology and tissue physiology. In the toolkit of optogenetic actuators, the key building blocks are genetically encodable light-sensitive proteins. Currently, most optogenetic photosensory modules are engineered from naturally-occurring photoreceptor proteins from bacteria, fungi, and plants. There is a growing demand for novel photosensory domains with improved optical properties and light-induced responses to satisfy the needs of a wider variety of studies in biological sciences. In this review, we focus on progress towards engineering of non-opsin-based photosensory domains, and their representative applications in cell biology and physiology. We summarize current knowledge of engineering of light-sensitive proteins including light-oxygen-voltage-sensing domain (LOV), cryptochrome (CRY2), phytochrome (PhyB and BphP), and fluorescent protein (FP)-based photosensitive domains (Dronpa and PhoCl).

Light Regulation of Two New Manganese Peroxidase-Encoding Genes in Trametes polyzona KU-RNW027

To better understand the light regulation of ligninolytic systems in Trametes polyzona KU-RNW027, ligninolytic enzymes-encoding genes were identified and analyzed to determine their transcriptional regulatory elements. Elements of light regulation were investigated in submerged culture. Three ligninolytic enzyme-encoding genes, mnp1, mnp2, and lac1, were found. Cloning of the genes encoding MnP1 and MnP2 revealed distinct deduced amino acid sequences with 90% and 86% similarity to MnPs in Lenzites gibbosa, respectively. These were classified as new members of short-type hybrid MnPs in subfamily A.2 class II fungal secretion heme peroxidase. A light responsive element (LRE), composed of a 5′-CCRCCC-3′ motif in both mnp promoters, is reported. Light enhanced MnP activity 1.5 times but not laccase activity. The mnp gene expressions under light condition increased 6.5- and 3.8-fold, respectively. Regulation of laccase gene expression by light was inconsistent with the absence of LREs in their promoter. Blue light did not affect gene expressions but impacted their stability. Reductions of MnP and laccase production under blue light were observed. The details of the molecular mechanisms underlying enzyme production in this white-rot fungus provide useful knowledge for wood degradation relative to illumination condition. These novel observations demonstrate the potential of enhancing ligninolytic enzyme production by this fungus for applications with an eco-friendly approach to bioremediation.

High-performance chemical- and light-inducible recombinases in mammalian cells and mice

Site-specific DNA recombinases are important genome engineering tools. Chemical- and light-inducible recombinases, in particular, enable spatiotemporal control of gene expression. However, inducible recombinases are scarce due to the challenge of engineering high performance systems, thus constraining the sophistication of genetic circuits and animal models that can be created. Here we present a library of >20 orthogonal inducible split recombinases that can be activated by small molecules, light and temperature in mammalian cells and mice. Furthermore, we engineer inducible split Cre systems with better performance than existing systems. Using our orthogonal inducible recombinases, we create a genetic switchboard that can independently regulate the expression of 3 different cytokines in the same cell, a tripartite inducible Flp, and a 4-input AND gate. We quantitatively characterize the inducible recombinases for benchmarking their performances, including computation of distinguishability of outputs. This library expands capabilities for multiplexed mammalian gene expression control.

Carotenoid Production by Rhodotorula mucilaginosa in Batch and Fed-Batch Fermentation Using Agroindustrial Byproducts

Carotenoids are natural pigments that can be produced through biotechnological processes. However, the costs are relatively high and can be minimized by using lower-cost substrates as alternative nutrient sources. The fed-batch fermentation is one of the techniques used to obtain a high biomass concentration and/or maximum production. Thus, the aim of this work is to produce carotenoids in batch and fed-batch fermentation with the yeast Rhodotorula mucilaginosa CCT 7688 using agroindustrial byproducts in the culture medium. Carotenoid production was increased using experimental designs, which modified the concentration of the agroindustrial medium. In batch production the highest concentrations of total carotenoids (1248.5 μg/L) and biomass (7.9 g/L) were obtained in the medium containing 70 g/L sugar cane molasses and 3.4 g/L corn steep liquor at 25 °C and 180 rpm in 168 h, demonstrating an increase of 17% when compared to the standard yeast malt medium (1200 μg/L). In the fed-batch production, different feeding strategies were tested with 30 g/L sugar cane molasses and 6.5 g/L corn steep liquor, reaching a total carotenoid production of 3726 μg/L and biomass concentration of 16 g/L. Therefore, the strategy of the fed-batch process resulted in an increase in the carotenoid production of approx. 400% compared to that in the batch process (740.3 μg/L). Thus, the R. mucilaginosa strain has the potential to produce carotenoids in agroindustrial medium.

Control of Development, Secondary Metabolism and Light-Dependent Carotenoid Biosynthesis by the Velvet Complex of Neurospora crassa

Neurospora crassa is an established reference organism to investigate carotene biosynthesis and light regulation. However, there is little evidence of its capacity to produce secondary metabolites. Here, we report the role of the fungal-specific regulatory velvet complexes in development and secondary metabolism (SM) in N. crassa Three velvet proteins VE-1, VE-2, VOS-1, and a putative methyltransferase LAE-1 show light-independent nucleocytoplasmic localization. Two distinct velvet complexes, a heterotrimeric VE-1/VE-2/LAE-1 and a heterodimeric VE-2/VOS-1 are found in vivo The heterotrimer-complex, which positively regulates sexual development and represses asexual sporulation, suppresses siderophore coprogen production under iron starvation conditions. The VE-1/VE-2 heterodimer controls carotene production. VE-1 regulates the expression of >15% of the whole genome, comprising mainly regulatory and developmental features. We also studied intergenera functions of the velvet complex through complementation of Aspergillus nidulans veA, velB, laeA, vosA mutants with their N. crassa orthologs ve-1, ve-2, lae-1, and vos-1, respectively. Expression of VE-1 and VE-2 in A. nidulans successfully substitutes the developmental and SM functions of VeA and VelB by forming two functional chimeric velvet complexes in vivo, VelB/VE-1/LaeA and VE-2/VeA/LaeA, respectively. Reciprocally, expression of veA restores the phenotypes of the N. crassa ve-1 mutant. All N. crassa velvet proteins heterologously expressed in A. nidulans are localized to the nuclear fraction independent of light. These data highlight the conservation of the complex formation in N. crassa and A. nidulans However, they also underline the intergenera similarities and differences of velvet roles according to different life styles, niches and ontogenetic processes.