Mining Natural Product Biosynthesis in Eukaryotic Algae

Genomic analysis of Coccomyxa viridis, a common low-abundance alga associated with lichen symbioses

Lichen symbiosis is centered around a relationship between a fungus and a photosynthetic microbe, usually a green alga. In addition to their main photosynthetic partner (the photobiont), lichen symbioses can contain additional algae present in low abundance. The biology of these algae and the way they interact with the rest of lichen symbionts remains largely unknown. Here we present the first genome sequence of a non-photobiont lichen-associated alga. Coccomyxa viridis was unexpectedly found in 12% of publicly available lichen metagenomes. With few exceptions, members of the Coccomyxa viridis clade occur in lichens as non-photobionts, potentially growing in thalli endophytically. The 45.7 Mbp genome of C. viridis was assembled into 18 near chromosome-level contigs, making it one of the most contiguous genomic assemblies for any lichen-associated algae. Comparing the C. viridis genome to its close relatives revealed the presence of traits associated with the lichen lifestyle. The genome of C. viridis provides a new resource for exploring the evolution of the lichen symbiosis, and how symbiotic lifestyles shaped evolution in green algae.

Assessment of the marine microalga Chrysochromulina rotalis as bioactive feedstock cultured in an easy-to-deploy light-emitting-diode-based tubular photobioreactor

Marine microalgae have potential to be low-cost raw materials. This depends on the exploitation of different biomass fractions for high-value products, including unique compounds. Chrysochromulina rotalis, an under-explored haptophyte with promising properties, was the focus of this study. For the first time, C. rotalis was successfully cultivated in an 80 L tubular photobioreactor, illuminated by an easy-to-use light-emitting-diode-based system. C. rotalis grew without certain trace elements and showed adaptability to different phosphorus sources, allowing a significant reduction in the N:P ratio without compromising biomass yield and productivity. The design features of the photobioreactor provided a protective environment that ensured consistent biomass production from this shear-sensitive microalgae. Carotenoid analysis showed fucoxanthin and its derivatives as major components, with essential fatty acids making up a significant proportion of the total. The study emphasizes the tubular photobioreactor's role in sustainable biomass production for biorefineries, with C. rotalis as a valuable bioactive feedstock.

Biosynthetic Potential of Hypogymnia Holobionts: Insights into Secondary Metabolite Pathways

Lichens are symbiotic associations consisting of a photobiont (algae or cyanobacteria) and a mycobiont (fungus). They are known to produce a variety of unique secondary metabolites. To access this biosynthetic potential for biotechnological applications, deeper insights into the biosynthetic pathways and corresponding gene clusters are necessary. Here we provide a comprehensive view of the biosynthetic gene clusters of all organisms comprising a lichen thallus: fungi, green algae, and bacteria. We present two high-quality PacBio metagenomes, in which we identified a total of 460 biosynthetic gene clusters. Lichen mycobionts yielded 73-114 clusters, other lichen associated ascomycetes 8-40, green algae of the genus Trebouxia 14-19, and lichen-associated bacteria 101-105 clusters. The mycobionts contained mainly T1PKSs, followed by NRPSs, and terpenes; Trebouxia reads harbored mainly clusters linked to terpenes, followed by NRPSs and T3PKSs. Other lichen-associated ascomycetes and bacteria contained a mix of diverse biosynthetic gene clusters. In this study, we identified for the first time the biosynthetic gene clusters of entire lichen holobionts. The yet untapped biosynthetic potential of two species of the genus Hypogymnia is made accessible for further research.

Plant biosynthetic gene clusters in the context of metabolic evolution

Covering: up to 2022Plants produce a wide range of structurally and biosynthetically diverse natural products to interact with their environment. These specialised metabolites typically evolve in limited taxonomic groups presumably in response to specific selective pressures. With the increasing availability of sequencing data, it has become apparent that in many cases the genes encoding biosynthetic enzymes for specialised metabolic pathways are not randomly distributed on the genome. Instead they are physically linked in structures such as arrays, pairs and clusters. The exact function of these clusters is debated. In this review we take a broad view of gene arrangement in plant specialised metabolism, examining types of structures and variation. We discuss the evolution of biosynthetic gene clusters in the wider context of metabolism, populations and epigenetics. Finally, we synthesise our observations to propose a new hypothesis for biosynthetic gene cluster formation in plants.

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

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

Antifouling Activity of Halogenated Compounds Derived from the Red Alga Sphaerococcus coronopifolius: Potential for the Development of Environmentally Friendly Solutions

Nowadays, biofouling is responsible for enormous economic losses in the maritime sector, and its treatment with conventional antifouling paints is causing significant problems to the environment. Biomimetism and green chemistry approaches are very promising research strategies for the discovery of new antifouling compounds. This study focused on the red alga Sphaerococcus coronopifolius, which is known as a producer of bioactive secondary metabolites. Fifteen compounds, including bromosphaerol (1), were tested against key marine biofoulers (five marine bacteria and three microalgae) and two enzymes associated with the adhesion process in macroalgae and invertebrates. Each metabolite presented antifouling activity against at least one organism/enzyme. This investigation also revealed that two compounds, sphaerococcinol A (4) and 14R-hydroxy-13,14-dihydro-sphaerococcinol A (5), were the most potent compounds without toxicity towards oyster larvae used as non-target organisms. These compounds are of high potential as they are active towards key biofoulers and could be produced by a cultivable alga, a fact that is important from the green chemistry point of view.

Gene cluster from plant to microbes: Their role in genome architecture, organism's development, specialized metabolism and drug discovery

Plants and microbes fulfil our daily requirements through different high-value chemicals, e.g., nutraceuticals, pharmaceuticals, cosmetics, and through varieties of fruits, crops, vegetables, and many more. Utmost care would therefore be taken for growth, development and sustainability of these important crops and medicinal plants and microbes. Homeobox genes and HOX clusters and their recently characterized expanded family members, including newly discovered homeobox, WOX gene from medicinal herb, Panax ginseng, significantly contributes in the growth and development of these organisms. On the other hand, secondary metabolites produced through secondary metabolism of plants and microbes are used as organisms defense as well as drugs/drug-like molecules for humans. Both the developmental HOX cluster and the biosynthetic gene-cluster (BGC) for secondary metabolites are organised in organisms genome. Genome mining and genomewide analysis of these clusters will definitely identify and characterize many more important molecules from unexplored plants and microbes and underexplored human microbiota and the evolution studies of these clusters will indicate their source of origin. Although genomics revolution now continues at a pace, till date only few hundred plant genome sequences are available. However, next-generation sequencing (NGS) technology now in market and may be applied even for plants with recalcitrant genomes, eventually may discover genomic potential towards production of secondary metabolites of diverse plants and micro-organisms present in the environment and microbiota. Additionally, the development of tools for genome mining e.g., antiSMASH, plantiSMASH, and more and more computational approaches that predicts hundreds of secondary metabolite BGCs will be discussed.