The synthetic future of algal genomes

Abstract

Algae are diverse organisms with significant biotechnological potential for resource circularity. Taking inspiration from fermentative microbes, engineering algal genomes holds promise to broadly expand their application ranges. Advances in genome sequencing with improvements in DNA synthesis and delivery techniques are enabling customized molecular tool development to confer advanced traits to algae. Efforts to redesign and rebuild entire genomes to create fit-for-purpose organisms currently being explored in heterotrophic prokaryotes and eukaryotic microbes could also be applied to photosynthetic algae. Future algal genome engineering will enhance yields of native products and permit the expression of complex biochemical pathways to produce novel metabolites from sustainable inputs. We present a historical perspective on advances in engineering algae, discuss the requisite genetic traits to enable algal genome optimization, take inspiration from whole-genome engineering efforts in other microbes for algal systems, and present candidate algal species in the context of these engineering goals.

Keywords: algal biotechnology; engineering biology; light-driven biotechnology; metabolic engineering; synthetic biology; synthetic genomics.

Graphical abstract

Figure 1

The algal cell is a platform for harnessing energy from photosynthesis to convert basic inputs into more complex chemicals A simplified cellular architecture, illustrated here, shows a primary endosymbiotic alga containing a plastid that was derived from uptake of a cyanobacterium by an ancestral protist. Genomes are present in the nucleus (purple), mitochondria (light gray and white), and plastid (green). Various other subcellular compartments characteristic of eukaryotes are illustrated, including the ER (gray cisternae), Golgi apparatus (light-gray cisternae), lipid droplets (orange), and vacuoles or other microbodies (dark gray). Eukaryotic algae accumulate starch for carbon storage (white). In addition to photosynthetic production of oxygen (O₂), some species can generate molecular hydrogen (H₂) under specific conditions. Algae transform water, CO₂, and inorganic nutrients into biomass containing valuable molecules with diverse applications. Efficient uptake of dissolved nutrients can mitigate eutrophication and yield clean water. Genetic engineering of algal genomes opens possibilities beyond natural products to generate valuable biochemicals and recombinant proteins from minimal inorganic inputs.

Figure 2

Native and engineered algae for biotechnology (A) Algae cultures are scaled up from small volumes in flasks (upper left) to several thousand liters in raceway ponds (upper right) or tubular photobioreactors (lower middle). Photos of outdoor algal cultivation are of the Phase I facilities of Development of Algal Biotechnology in Kingdom of Saudi Arabia (DAB-KSA) – Beacon Development project funded by the Ministry of Environment Water and Agriculture and run by Dr. Claudio Fuentes Grünewald at King Abdullah University of Science & Technology (KAUST) Campus from 2023 (photo credit author K.J.L.). The product of algal cultivation is biomass with species-specific composition of pigments and other compounds; from left to right are dried green algae biomass from Tetraselmis, Chlorella, Haematococcus, and Dunaliella sourced from Algikey, Portugal, in 2022 (photo credit Sergio Gutiérrez). (B) Engineering of algae involves the transformation of designer DNA, followed by the selection of transformant colonies and their subsequent isolation and characterization. The workflow for C. reinhardtii transformant recovery and high-throughput screening on agar plates is shown (top). Scale-up of engineered algae is the same as for wild-type strains, with increasing culture sizes providing the inoculum until production volumes are achieved (bottom) (pictures and images provided by Dr. Mark Seger of Arizona Center for Algae Technology & Innovation). (C) Left: among other compounds, C. reinhardtii has been genetically modified to produce heterologous isoprenoids, including patchoulol,^,, sclareol, bisabolene, casbene,^, and volatile isoprene. Middle: P. moriformis was engineered to make tailored triacylglycerol oils. The images show a high-stability oil (left panel) that remains unfouled after 10 days of continuous deep frying, compared to high-oleic Canola oil (right panel). The relative percentages of major fatty acids in the oils are indicated above the pictures (reproduced from INFORM magazine, with permission). Right: C. reinhardtii (top^34,35), C. merolae (middle³⁶), and A. protothecoides (bottom³⁷) have all been engineered to produce orange-red ketocarotenoids such as canthaxanthin and astaxanthin (structures shown above) using the C. reinhardtii β-carotene ketolase 1 (BKT1). Wild-type strains are on the left, and modified strains are on the right. The C. reinhardtii pictures were provided by Dr. Thomas Baier and Jacop Kneip, Universität Bielefeld. The C. merolae pictures are from Seger et al.A. protothecoides (photo by author J.L.M.) was grown heterotrophically on organic carbon and is non-photosynthetic in this state. The yellow pigmentation in wild-type Auxenochlorella is primarily from lutein.

Figure 3

Algal genomes that are candidates for engineering and resynthesis The nuclear genomes of the algae in this list are substantially smaller than the model Chlorophyta C. reinhardtii, making them more suitable for complete genome redesign. Cartoons representing each genus or species illustrate the relative cell sizes and pigmentation differences. The ploidy of the vegetative state is indicated by paired chromosomes for diploid and single chromosomes for haploid. The total haploid numbers of chromosomes in each nuclear genome, and the sizes of the mitochondrial and plastid genomes, are indicated. Genome data are from the following references: C. reinhardtii,O. tauri,Picochlorum spp.,Prototheca spp.,A. protothecoides (unpublished data), P. purpureum,C. merolae 10D, and Galdieria spp. Plastids (green, except phycoerythrin-containing P. purpureum and heterotrophic Prototheca spp.), nuclei (purple), starch deposits (white), vacuoles and microbodies (gray), lipid bodies (orange), and mitochondria, ER, and Golgi (illustrated cartoons).

Figure 4

The wild-type alga compared to the genome-engineered alga of the future Left: the wild-type alga maintains three separate genomes in the plastid, mitochondria, and nucleus. The nuclear genome may be haploid or diploid in vegetative cells, and genes for all cellular processes are distributed throughout the chromosomes. Genetic loci on any of the genomes may be modified by gene targeting and editing, and transgenes can be integrated and expressed. Simple heterologous pathways can be introduced, but broad genomic alterations, multi-locus targeting, and reliable expression of multiple transgenes of complex biochemical pathways is still challenging. The wild-type or domesticated alga is susceptible to pathogens, represented by blue hexagons, and accumulates both native and engineered products through synthetic biology. Right: the engineered alga of the future will feature completely recoded and redesigned genomes. The nuclear genome, either haploid or diploid, will be dispersed across numerous small autonomously replicating chromosomes, neochromosomes, or episomes. Plastid genomes may be rearranged, with additional gene transfer to the nucleus when advantageous. Redundancies and repetitions in the genome will be eliminated except where necessary to increase gene copy numbers for improved protein expression. Genes will be grouped into neighborhoods according to function to facilitate modular engineering, and recombination elements will be inserted to enable broad-scale genome shuffling on demand. The recoded algal genomes will be intrinsically resistant to pathogen attack and will encode defenses against competitors and grazers, along with biocontainment strategies such as engineered auxotrophy or mating incompatibility. Genome landing pads will streamline the integration of multi-transgene pathways and accelerate the biosynthesis of novel products, symbolized by colored hexagons in the plastid.