Genomic adaptations of the green alga Dunaliella salina to life under high salinity

Enhancing astaxanthin accumulation through the expression of the plant-derived astaxanthin biosynthetic pathway in Dunaliella salina

Dunaliella salina, a microalga that thrives under high-saline conditions, is notable for its high β-carotene content and the absence of a polysaccharide cell wall. These unique characteristics render it a prime candidate as a cellular platform for astaxanthin production. In this study, our initial tests in an E. coli revealed that β-ring-4-dehydrogenase (CBFD) and 4-hydroxy-β-ring-4-dehydrogenase (HBFD) genes from Adonis aestivalis outperformed β-carotene hydroxylase (BCH) and β-carotene ketolase (BKT) from Haematococcus pluvialis counterparts by two-fold in terms of astaxanthin biosynthesis efficiency. Subsequently, we utilized electroporation to integrate either the BKT gene or the CBFD and HBFD genes into the genome of D. salina. In comparison to wild-type D. salina, strains transformed with BKT or CBFD and HBFD exhibited inhibited growth, underwent color changes to shades of red and yellow, and saw a nearly 50% decline in cell density. HPLC analysis confirmed astaxanthin synthesis in engineered D. salina strains, with CBFD + HBFD-D. salina yielding 134.88 ± 9.12 μg/g of dry cell weight (DCW), significantly higher than BKT-D. salina (83.58 ± 2.40 μg/g). This represents the largest amount of astaxanthin extracted from transgenic D. salina, as reported to date. These findings have significant implications, opening up new avenues for the development of specialized D. salina-based microcell factories for efficient astaxanthin production.

Deciphering the β-carotene hyperaccumulation in Dunaliella by the comprehensive analysis of Dunaliella salina and Dunaliella tertiolecta under high light conditions

The green microalga Dunaliella salina hyperaccumulates β-carotene in the chloroplast, which turns its cells orange. This does not occur in the sister species Dunaliella tertiolecta. However, the molecular mechanisms of β-carotene hyperaccumulation were still unclear. Here, we discovered the reasons for β-carotene hyperaccumulation by comparing the morphology, physiology, genome, and transcriptome between the carotenogenic D. salina and the noncarotenogenic D. tertiolecta after transfer to high light. The differences in photosynthetic capacity, cell growth, and the concentration of stored carbon suggest that these species regulate the supply and utilization of carbon differently. The number of β-carotene-containing plastid lipid globules increased in both species, but much faster and to a greater extent in D. salina than in D. tertiolecta. Consistent with the accumulation of plastid lipid globules, the expression of the methyl-erythritol-phosphate and carotenoid biosynthetic pathways increased only in D. salina, which explains the de novo synthesis of β-carotene. In D. salina, the concomitantly upregulated expression of the carotene globule proteins suggests that hyperaccumulation of β-carotene also requires a simultaneous increase in its sink capacity. Based on genomic analysis, we propose that D. salina has genetic advantages for routing carbon from growth to carotenoid metabolism.

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.

The Time-Resolved Salt Stress Response of Dunaliella tertiolecta-A Comprehensive System Biology Perspective

Algae-driven processes, such as direct CO2 fixation into glycerol, provide new routes for sustainable chemical production in synergy with greenhouse gas mitigation. The marine microalgae Dunaliella tertiolecta is reported to accumulate high amounts of intracellular glycerol upon exposure to high salt concentrations. We have conducted a comprehensive, time-resolved systems biology study to decipher the metabolic response of D. tertiolecta up to 24 h under continuous light conditions. Initially, due to a lack of reference sequences required for MS/MS-based protein identification, a high-quality draft genome of D. tertiolecta was generated. Subsequently, a database was designed by combining the genome with transcriptome data obtained before and after salt stress. This database allowed for detection of differentially expressed proteins and identification of phosphorylated proteins, which are involved in the short- and long-term adaptation to salt stress, respectively. Specifically, in the rapid salt adaptation response, proteins linked to the Ca2+ signaling pathway and ion channel proteins were significantly increased. While phosphorylation is key in maintaining ion homeostasis during the rapid adaptation to salt stress, phosphofructokinase is required for long-term adaption. Lacking β-carotene, synthesis under salt stress conditions might be substituted by the redox-sensitive protein CP12. Furthermore, salt stress induces upregulation of Calvin-Benson cycle-related proteins.

Insights into Leishmania donovani potassium channel family and their biological functions

Leishmania donovani is the causative organism for visceral leishmaniasis. Although this parasite was discovered over a century ago, nothing is known about role of potassium channels in L. donovani. Potassium channels are known for their crucial roles in cellular functions in other organisms. Recently the presence of a calcium-activated potassium channel in L. donovani was reported which prompted us to look for other proteins which could be potassium channels and to investigate their possible physiological roles. Twenty sequences were identified in L. donovani genome and subjected to estimation of physio-chemical properties, motif analysis, localization prediction and transmembrane domain analysis. Structural predictions were also done. The channels were majorly α-helical and predominantly localized in cell membrane and lysosomes. The signature selectivity filter of potassium channel was present in all the sequences. In addition to the conventional potassium channel activity, they were associated with gene ontology terms for mitotic cell cycle, cell death, modulation by virus of host process, cell motility etc. The entire study indicates the presence of potassium channel families in L. donovani which may have involvement in several cellular pathways. Further investigations on these putative potassium channels are needed to elucidate their roles in Leishmania.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03692-y.

Genome-Wide Characterization and Expression Profiling of ABA Biosynthesis Genes in a Desert Moss Syntrichia caninervis

Syntrichia caninervis can survive under 80-90% protoplasmic water losses, and it is a model plant in desiccation tolerance research. A previous study has revealed that S. caninervis would accumulate ABA under dehydration stress, while the ABA biosynthesis genes in S. caninervis are still unknown. This study identified one ScABA1, two ScABA4s, five ScNCEDs, twenty-nine ScABA2s, one ScABA3, and four ScAAOs genes, indicating that the ABA biosynthesis genes were complete in S. caninervis. Gene location analysis showed that the ABA biosynthesis genes were evenly distributed in chromosomes but were not allocated to sex chromosomes. Collinear analysis revealed that ScABA1, ScNCED, and ScABA2 had homologous genes in Physcomitrella patens. RT-qPCR detection found that all of the ABA biosynthesis genes responded to abiotic stress; it further indicated that ABA plays an important role in S. caninervis. Moreover, the ABA biosynthesis genes in 19 representative plants were compared to study their phylogenetic and conserved motifs; the results suggested that the ABA biosynthesis genes were closely associated with plant taxa, but these genes had the same conserved domain in each plant. In contrast, there is a huge variation in the exon number between different plant taxa; it revealed that ABA biosynthesis gene structures are closely related to plant taxa. Above all, this study provides strong evidence demonstrating that ABA biosynthesis genes were conserved in the plant kingdom and deepens our understanding of the evolution of the phytohormone ABA.

Microalgal Carotenoids: Therapeutic Application and Latest Approaches to Enhance the Production

Microalgae are microscopic photosynthetic organisms frequently found in fresh and marine water ecosystems. Various microalgal species have been considered a reservoir of diverse health-value products, including vitamins, proteins, lipids, and polysaccharides, and are broadly utilized as food and for the treatment of human ailments such as cancer, cardiovascular diseases, allergies, and immunodeficiency. Microalgae-derived carotenoids are the type of accessory pigment that possess light-absorbing potential and play a significant role in metabolic functions. To date, nearly a thousand carotenoids have been reported, but a very less number of microalgae have been used for the commercial production of carotenoids. This review article briefly discussed the carotenoids of microalgal origin and their therapeutic application. In addition, we have briefly compiled the optimization of culture parameters used to enhance microalgal carotenoid production. In addition, the latest biotechnological approaches used to improve the yields of carotenoid has also been discussed.

Salinity fluctuation influences the toxicity of 1-octyl-3-methylimidazolium chloride ([C8mim]Cl) to a marine diatom Phaeodactylum tricornutum

In this work, a marine diatom (Phaeodactylum tricornutum) was exposed to 1-octyl-3-methylimidazolium chloride ([C₈mim]Cl) for 96 h at three different salinities (25, 35, and 45 ‰) for investigating their interactive effects. Results showed that values of EC₁₀ and EC₅₀ at 96 h of exposure were 0.29, 1.06, 2.01 μg L^-1 and 7.21, 7.71, 7.25 mg L^-1 when the salinities were 25, 35, and 45 ‰, respectively, meaning that salinity fluctuation affected the toxicity of [C₈mim]Cl to this diatom. Changes in chlorophyll a contents and chlorophyll fluorescence parameters suggested that [C₈mim]Cl and salinity fluctuation had a significant interactive effect on the algal photosynthesis. In addition, soluble protein content and activities of antioxidant enzymes in algal cells changed significantly. Increased malondialdehyde contents indicated that the combined stresses could induce excessive production of reactive oxygen species leading to oxidative damage to the algal cells.

Plasticity across levels: relating epigenomic, transcriptomic, and phenotypic responses to osmotic stress in a halotolerant microalga

Phenotypic plasticity, the ability of a given genotype to produce alternative phenotypes in response to its environment of development, is an important mechanism for coping with variable environments. While the mechanisms underlying phenotypic plasticity are diverse, their relative contributions need to be investigated quantitatively to better understand the evolvability of plasticity across biological levels. This requires relating plastic responses of the epigenome, transcriptome, and organismal phenotype, and investigating how they vary with the genotype. Here we carried out this approach for responses to osmotic stress in Dunaliella salina, a green microalga that is a model organism for salinity tolerance. We compared two strains that show markedly different demographic responses to osmotic stress, and showed that these phenotypic responses involve strain‐ and environment‐specific variation in gene expression levels, but a relative low—albeit significant—effect of strain × environment interaction. We also found an important genotype effect on the genome‐wide methylation pattern, but little contribution from environmental conditions to the latter. However, we did detect a significant marginal effect of epigenetic variation on gene expression, beyond the influence of genetic differences on epigenetic state, and we showed that hypomethylated regions are correlated with higher gene expression. Our results indicate that epigenetic mechanisms are either not involved in the rapid plastic response to environmental change in this species, or involve only few changes in trans that are sufficient to trigger concerted changes in the expression of many genes, and phenotypic responses by multiple traits.

The expression pattern of β-carotene ketolase gene restricts the accumulation of astaxanthin in Dunaliella under salt stress

Dunaliella salina can accumulate a large amount of β-carotene which is generally considered to be its terminal product of carotenoid metabolism. In this study, it was proved that D. salina has the ketolase (DsBKT) of catalyzing the synthesis of astaxanthin, the downstream products of β-carotene. Therefore, the reason why D. salina does not synthesize astaxanthin is the purpose of this study. The enzymatic activity of DsBKT was detected by functional complementation assays in Escherichia coli, results showed that DsBKT had efficient ketolase activity toward β-carotene and zeaxanthin to produce astaxanthin, indicating that there were complete astaxanthin-producing genes in Dunaliella. Unlike the induced expression of Lycopene cyclase (catalyzing β-carotene synthesis) under salt stress, the expression of DsBKT was very low under both normal and stress conditions, which may be the main reason why D. salina cannot accumulate astaxanthin. On the contrary, with the astaxanthin-rich Haematococcus pluvialis as a control, its BKT gene was significantly upregulated under salt stress. Further study showed that DsBKT promoter had strong promoter ability and could stably drive the expression of ble-egfp in D. salina. Obviously, DsBKT promoter is not the reason of DsBKT not being expressed which may be caused by Noncoding RNA.

Fructanogenic traits in halotolerant Bacillus licheniformis OK12 and their predicted functional significance

AIMS

Isolating a novel bacterial source of fructan from a saltern and analysis of its genome to better understand the possible roles of fructans in hypersaline environments.

METHODS AND RESULTS

Bacteria were isolated from crude salt samples originating from Çamaltı Saltern in Western Turkey and screened for fructanogenic traits in high-salt and sucrose-rich selective medium. Exopolysaccharide accumulated in the presence of sucrose by isolate OK12 was purified and chemically characterized via HPLC, FT-IR and NMR, which revealed that it was a levan-type fructan (β-2,6 linked homopolymer of fructose). The isolate was taxonomically classified as Bacillus licheniformis OK12 through 16S rRNA gene and whole-genome sequencing methods. Strain OK12 harbours one levansucrase and two different levanase genes, which altogether were predicted to significantly contribute to intracellular glucose and fructose pools. The isolate could withstand 15% NaCl, and thus classified as a halotolerant.

CONCLUSIONS

Fructanogenic traits in halotolerant B. licheniformis OK12 are significant due to predicted influx of glucose and fructose as a result of levan biosynthesis and levan hydrolysis, respectively.

SIGNIFICANCE AND IMPACT OF THE STUDY

Fructans from the residents of hypersaline habitats are underexplored compounds and are expected to demonstrate physicochemical properties different from their non-halophilic counterparts. Revealing fructanogenic traits in the genome of a halotolerant bacterium brings up a new perspective in physiological roles of fructans.

Weighted gene co-expression network analysis of the salt-responsive transcriptomes reveals novel hub genes in green halophytic microalgae Dunaliella salina

Despite responses to salinity stress in Dunaliella salina, a unicellular halotolerant green alga, being subject to extensive study, but the underlying molecular mechanism remains unknown. Here, Empirical Bayes method was applied to identify the common differentially expressed genes (DEGs) between hypersaline and normal conditions. Then, using weighted gene co-expression network analysis (WGCNA), which takes advantage of a graph theoretical approach, highly correlated genes were clustered as a module. Subsequently, connectivity patterns of the identified modules in two conditions were surveyed to define preserved and non-preserved modules by combining the Zsummary and medianRank measures. Finally, common and specific hub genes in non-preserved modules were determined using Eigengene-based module connectivity or module membership (k_ME) measures and validation was performed by using leave-one-out cross-validation (LOOCV). In this study, the power of beta = 12 (scale-free R2 = 0.8) was selected as the soft-thresholding to ensure a scale-free network, which led to the identification of 15 co-expression modules. Results also indicate that green, blue, brown, and yellow modules are non-preserved in salinity stress conditions. Examples of enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in non-preserved modules are Sulfur metabolism, Oxidative phosphorylation, Porphyrin and chlorophyll metabolism, Vitamin B6 metabolism. Moreover, the systems biology approach was applied here, proposed some salinity specific hub genes, such as radical-induced cell death1 protein (RCD1), mitogen-activated protein kinase kinase kinase 13 (MAP3K13), long-chain acyl-CoA synthetase (ACSL), acetyl-CoA carboxylase, biotin carboxylase subunit (AccC), and fructose-bisphosphate aldolase (ALDO), for the development of metabolites accumulating strains in D. salina.