Molecular Phylogenies and Evolution ofcrtGenes in Algae

Synthetic biology in microalgae towards fucoxanthin production for pharmacy and nutraceuticals

Synthetic biology has emerged as a powerful tool for engineering biological systems to produce valuable compounds, including pharmaceuticals and nutraceuticals. Microalgae, in particular, offer a promising platform for the production of bioactive compounds due to their high productivity, low land and water requirements, and ability to perform photosynthesis. Fucoxanthin, a carotenoid pigment found predominantly in brown seaweeds and certain microalgae, has gained significant attention in recent years due to its numerous health benefits, such as antioxidation, antitumor effect and precaution osteoporosis. This review provides an overview of the principles and applications of synthetic biology in the microbial engineering of microalgae for enhanced fucoxanthin production. Firstly, the fucoxanthin bioavailability and metabolism in vivo was introduced for the beneficial roles, followed by the biological functions of anti-oxidant activity, anti-inflammatory activity, antiapoptotic role antidiabetic and antilipemic effects. Secondly, the cultivation condition and strategy were summarized for fucoxanthin improvement with low production costs. Thirdly, the genetic engineering of microalgae, including gene overexpression, knockdown and knockout strategies were discussed for further improving the fucoxanthin production. Then, synthetic biology tools of CRISPR-Cas9 genome editing, transcription activator-like effector nucleases as well as modular assembly and chassis engineering were proposed to precise modification of microalgal genomes to improve fucoxanthin production. Finally, challenges and future perspectives were discussed to realize the industrial production and development of functional foods of fucoxanthin from microalgae.

Screening of Structurally Distinct Lycopene β-Cyclases for Production of the Cyclic C40 Carotenoids β-Carotene and Astaxanthin by Corynebacterium glutamicum

Lycopene β-cyclase (EC 5.5.1.19) is one of the key enzymes in the biosynthesis of β-carotene and derived carotenoids. It catalyzes isomerase reactions to form β-carotene from lycopene by β-cyclization of both of its ψ-ends. Lycopene β-cyclases are widespread in nature. We systematically analyzed the phylogeny of lycopene β-cyclases from all kingdoms of life and predicted their transmembrane structures. To this end, a collection of previously characterized lycopene β-cyclase polypeptide sequences served as bait sequences to identify their closest homologues in a range of bacteria, archaea, fungi, algae, and plant species. Furthermore, a DeepTMHMM scan was applied to search for the presence of transmembrane domains. A phylogenetic tree suggests at least five distinct clades, and the DeepTMHMM scan revealed that lycopene β-cyclases are a group of structurally different proteins: membrane-bound and cytosolic enzymes. Representative lycopene β-cyclases were screened in the lycopene-overproducing Corynebacterium glutamicum strain for β-carotene and astaxanthin production. This systematic screening facilitates the identification of new enzymes for carotenoid production. Higher astaxanthin production and less reduction of total carotenoids were achieved with the cytosolic lycopene β-cyclase CrtL from Synechococcus elongatus and the membrane-bound heterodimeric lycopene β-cyclase CrtYcd from Brevibacterium linens.

Brown Algae as Functional Food Source of Fucoxanthin: A Review

Fucoxanthin is an algae-specific xanthophyll of aquatic carotenoid. It is prevalent in brown seaweed because it functions as a light-harvesting complex for algal photosynthesis and photoprotection. Its exceptional chemical structure exhibits numerous biological activities that benefit human health. Due to these valuable properties, fucoxanthin's potential as a potent source for functional food, feed, and medicine is being explored extensively today. This article has thoroughly reviewed the availability and biosynthesis of fucoxanthin in the brown seaweed, as well as the mechanism behind it. We included the literature findings concerning the beneficial bioactivities of fucoxanthin such as antioxidant, anti-inflammatory, anti-obesity, antidiabetic, anticancer, and other potential activities. Last, an additional view on its potential as a functional food ingredient has been discussed to facilitate a broader application of fucoxanthin as a promising bioactive compound.

One-Cell Metabolic Phenotyping and Sequencing of Soil Microbiome by Raman-Activated Gravity-Driven Encapsulation (RAGE)

Soil harbors arguably the most metabolically and genetically heterogeneous microbiomes on Earth, yet establishing the link between metabolic functions and genome at the precisely one-cell level has been difficult. Here, for mock microbial communities and then for soil microbiota, we established a Raman-activated gravity-driven single-cell encapsulation and sequencing (RAGE-Seq) platform, which identifies, sorts, and sequences precisely one bacterial cell via its anabolic (incorporating D from heavy water) and physiological (carotenoid-containing) functions. We showed that (i) metabolically active cells from numerically rare soil taxa, such as Corynebacterium spp., Clostridium spp., Moraxella spp., Pantoea spp., and Pseudomonas spp., can be readily identified and sorted based on D₂O uptake, and their one-cell genome coverage can reach ∼93% to allow high-quality genome-wide metabolic reconstruction; (ii) similarly, carotenoid-containing cells such as Pantoea spp., Legionella spp., Massilia spp., Pseudomonas spp., and Pedobacter spp. were identified and one-cell genomes were generated for tracing the carotenoid-synthetic pathways; and (iii) carotenoid-producing cells can be either metabolically active or inert, suggesting culture-based approaches can miss many such cells. As a Raman-activated cell sorter (RACS) family member that can establish a metabolism-genome link at exactly one-cell resolution from soil, RAGE-Seq can help to precisely pinpoint “who is doing what” in complex ecosystems.

IMPORTANCE Soil is home to an enormous and complex microbiome that features arguably the highest genomic diversity and metabolic heterogeneity of cells on Earth. Their in situ metabolic activities drive many natural processes of pivotal ecological significance or underlie industrial production of numerous valuable bioactivities. However, pinpointing “who is doing what” in a soil microbiome, which consists of mainly yet-to-be-cultured species, has remained a major challenge. Here, for soil microbiota, we established a Raman-activated gravity-driven single-cell encapsulation and sequencing (RAGE-Seq) method, which identifies, sorts, and sequences at the resolution of precisely one microbial cell via its catabolic and anabolic functions. As a Raman-activated cell sorter (RACS) family member that can establish a metabolism-genome link at one-cell resolution from soil, RAGE-Seq can help to precisely pinpoint “who is doing what” in complex ecosystems.

Diversity and Evolution of Carotenoid Biosynthesis from Prokaryotes to Plants

Carotenoids exist in pro- and eukaryotic organisms, but not in animals (with one exception). Their biosynthesis evolved from a common ancestor of Archaea and Bacteria and via the latter by endosymbiosis to algae and plants. The formation of carotenoids in fungi can be regarded as a lineage from the archaea. This review highlights the distribution and evolution of carotenogenic pathways in taxonomic groups of prokaryotes and eukaryotes with a special emphasis on the evolutionary aspects of prominent carotenogenic genes in relation to the assigned function of their corresponding enzymes. The latter aspect includes a focus on paralogs of gene families evolving novel functions and unrelated genes encoding enzymes with the same function.

Biotechnological Advances in Lycopene β-Cyclases

Lycopene β-cyclase is one of the key enzymes in the biosynthesis of carotenoids, which catalyzes the β-cyclization of both ends of lycopene to produce β-carotene. Lycopene β-cyclases are found in a wide range of sources, mainly plants and microorganisms. Lycopene β-cyclases have been extensively studied for their important catalytic activity, including for use in genetic engineering to modify plants and microorganisms, as a blocking target for lycopene industrial production strains, and for their genetic and physiological effects related to microorganic and plant biological traits. This review of lycopene β-cyclases summarizes the major studies on their basic classification, functional activity, metabolic engineering, and plant science.

Isolation and Analysis of the Cppsy Gene and Promoter from Chlorella protothecoides CS-41

Phytoene synthase (PSY) catalyzes the condensation of two molecules of geranylgeranyl pyrophosphate to form phytoene, the first colorless carotene in the carotenoid biosynthesis pathway. So it is regarded as the crucial enzyme for carotenoid production, and has unsurprisingly been involved in genetic engineering studies of carotenoid production. In this study, the psy gene from Chlorella protothecoides CS-41, designated Cppsy, was cloned using rapid amplification of cDNA ends. The full-length DNA was 2488 bp, and the corresponding cDNA was 1143 bp, which encoded 380 amino acids. Computational analysis suggested that this protein belongs to the Isoprenoid_Biosyn_C1 superfamily. It contained the consensus sequence, including three predicted substrate-Mg²⁺ binding sites. The Cppsy gene promoter was also cloned and characterized. Analysis revealed several candidate motifs for the promoter, which exhibited light- and methyl jasmonate (MeJA)-responsive characteristics, as well as some typical domains universally discovered in promoter sequences, such as the TATA-box and CAAT-box. Light- and MeJA treatment showed that the Cppsy expression level was significantly enhanced by light and MeJA. These results provide a basis for genetically modifying the carotenoid biosynthesis pathway in C. protothecoides.

Carotenoids and their cleavage products: biosynthesis and functions

This review focuses on plant carotenoids, but it also includes progress made on microbial and animal carotenoid metabolism to better understand the functions and the evolution of these structurally diverse compounds with a common backbone. Plants have evolved isogenes for specific key steps of carotenoid biosynthesis with differential expression profiles, whose characteristic features will be compared. Perhaps the most exciting progress has been made in studies of carotenoid cleavage products (apocarotenoids) with an ever-expanding variety of novel functions being discovered. This review therefore covers structural, molecular genetic and functional aspects of carotenoids and apocarotenoids alike. Apocarotenoids are specifically tailored from carotenoids by a family of oxidative cleavage enzymes, but whether there are contributions to their generation from chemical oxidation, photooxidation or other mechanisms is largely unknown. Control of carotenoid homeostasis is discussed in the context of biosynthetic and degradative reactions but also in the context of subcellular environments for deposition and sequestration within and outside of plastids. Other aspects of carotenoid research, including metabolic engineering and synthetic biology approaches, will only be covered briefly.

Expressed sequence tag (EST) profiling in hyper saline shocked Dunaliella salina reveals high expression of protein synthetic apparatus components

The unicellular, halotolerant, green alga, Dunaliella salina (Chlorophyceae) has the unique ability to adapt and grow in a wide range of salt conditions from about 0.05 to 5.5M. To better understand the molecular basis of its salinity tolerance, a complementary DNA (cDNA) library was constructed from D. salina cells adapted to 2.5M NaCl, salt-shocked at 3.4M NaCl for 5h, and used to generate an expressed sequence tag (EST) database. ESTs were obtained for 2831 clones representing 1401 unique transcripts. Putative functions were assigned to 1901 (67.2%) ESTs after comparison with protein databases. An additional 154 (5.4%) ESTs had significant similarity to known sequences whose functions are unclear and 776 (27.4%) had no similarity to known sequences. For those D. salina ESTs for which functional assignments could be made, the largest functional categories included protein synthesis (35.7%), energy (photosynthesis) (21.4%), primary metabolism (13.8%) and protein fate (6.8%). Within the protein synthesis category, the vast majority of ESTs (80.3%) encoded ribosomal proteins representing about 95% of the approximately 82 subunits of the cytosolic ribosome indicating that D. salina invests substantial resources in the production and maintenance of protein synthesis. The increased mRNA expression upon salinity shock was verified for a small set of selected genes by real-time, quantitative reverse-transcription-polymerase chain reaction (qRT-PCR). This EST collection also provided important new insights into the genetic underpinnings for the biosynthesis and utilization of glycerol and other osmoprotectants, the carotenoid biosynthetic pathway, reactive oxygen-scavenging enzymes, and molecular chaperones (heat shock proteins) not described previously for D. salina. EST discovery also revealed the existence of RNA interference and signaling pathways associated with osmotic stress adaptation. The unknown ESTs described here provide a rich resource for the identification of novel genes associated with the mechanistic basis of salinity stress tolerance and other stress-adaptive traits.

Carotenoid biosynthesis in diatoms

Diatoms are ubiquitous and constitute an important group of the phytoplankton community having a major contribution to the total marine primary production. These microalgae exhibit a characteristic golden-brown colour due to a high amount of the xanthophyll fucoxanthin that plays a major role in the light-harvesting complex of photosystems. In the water column, diatoms are exposed to light intensities that vary quickly from lower to higher values. Xanthophyll cycles prevent photodestruction of the cells in excessive light intensities. In diatoms, the diadinoxanthin-diatoxanthin cycle is the most important short-term photoprotective mechanism. If the biosynthetic pathways of chloroplast pigments have been extensively studied in higher plants and green algae, the research on carotenoid biosynthesis in diatoms is still in its infancy. In this study, the data on the biosynthetic pathway of diatom carotenoids are reviewed. The early steps occur through the 2-C-methyl-D: -erythritol 4-phosphate (MEP) pathway. Then a hypothetical pathway is suggested from dimethylallyl diphosphate (DMAPP) and isopentenyl pyrophosphate (IPP). Most of the enzymes of the pathway have not been so far isolated from diatoms, but candidate genes for each of them were identified using protein similarity searches of genomic data.

The metabolomics of carotenoids in engineered cell factory

Carotenoids such as beta-carotene, lycopene, and antheraxanthin have plenty of scientific and commercial value. The comprehensive investigation of carotenoids drives people to improve and develop all kinds of analytical techniques to approach or even achieve "versatile" analysis. The metabolic engineering efforts in plants and algae have progressed rapidly, aiming to enable the use of plants and algae as "cell factories" for producing specific or novel carotenoids, such as beta-carotene (provitamin A) in Gold rice, while the emerging technologies of metabolomics support it by providing comprehensive analysis of carotenoids biochemical characterizations. This review describes metabolomics as a high-throughput platform to study carotenoids, including the engineering methods in the plants or algae, the bioinformatics for metabolomics, and the metabolomics of carotenoids in engineered cell factory. Modern systems biology tools, together with the development of genomics and metabolomics databases, will dramatically facilitate the advancement of our knowledge in gene-to-metabolite networks in plants. Metabolomics accompanying genomics, transcriptomics, and proteomics as well as bioinformatics facilitate metabolic engineering efforts towards designing superior biocatalysts in cell factories. Ongoing advances in biological techniques coupled with crucial metabolic networks will further promote plants and algae as attractive platforms for the production of numerous high-value compounds such as carotenoids.

An update on carotenoid biosynthesis in algae: phylogenetic evidence for the existence of two classes of phytoene synthase

Carotenoids play crucial roles in structure and function of the photosynthetic apparatus of bacteria, algae, and higher plants. The entry-step reaction to carotenoid biosynthesis is catalyzed by the phytoene synthase (PSY), which is structurally and functionally related in all organisms. A comparative genomic analysis regarding the PSY revealed that the green algae Ostreococcus and Micromonas possess two orthologous copies of the PSY genes, indicating an ancient gene duplication event that produced two classes of PSY in algae. However, some other green algae (Chlamydomonas reinhardtii, Chlorella vulgaris, and Volvox carteri), red algae (Cyanidioschyzon merolae), diatoms (Thalassiosira pseudonana and Phaeodactylum tricornutum), and higher plants retained only one class of the PSY gene whereas the other gene copy was lost in these species. Further, similar to the situation in higher plants recent gene duplications of PSY have occurred for example in the green alga Dunaliella salina/bardawil. As members of the PSY gene families in some higher plants are differentially regulated during development or stress, the discovery of two classes of PSY gene families in some algae suggests that carotenoid biosynthesis in these algae is differentially regulated in response to development and environmental stress as well.