Microalgae are proposed as feedstock organisms useful for producing biofuels and coproducts. However, several limitations must be overcome before algae-based production is economically feasible. Among these is the ability to induce lipid accumulation and storage without affecting biomass yield. To overcome this barrier, a chemical genetics approach was employed in which 43,783 compounds were screened against Chlamydomonas reinhardtii, and 243 compounds were identified that increase triacylglyceride (TAG) accumulation without terminating growth. Identified compounds were classified by structural similarity, and 15 were selected for secondary analyses addressing impacts on growth fitness, photosynthetic pigments, and total cellular protein and starch concentrations. TAG accumulation was verified using gas chromatographymass spectrometry quantification of total fatty acids, and targeted TAG and galactolipid measurements were performed using liquid chromatography-multiple reaction monitoring/mass spectrometry. These results demonstrated that TAG accumulation does not necessarily proceed at the expense of galactolipid. Untargeted metabolite profiling provided important insights into pathway shifts due to five different compound treatments and verified the anabolic state of the cells with regard to the oxidative pentose phosphate pathway, Calvin cycle, tricarboxylic acid cycle, and amino acid biosynthetic pathways. Metabolite patterns were distinct from nitrogen starvation and other abiotic stresses commonly used to induce oil accumulation in algae. The efficacy of these compounds also was demonstrated in three other algal species. These lipid-inducing compounds offer a valuable set of tools for delving into the biochemical mechanisms of lipid accumulation in algae and a direct means to improve algal oil content independent of the severe growth limitations associated with nutrient deprivation.

Microalgae accumulate lipids during stress such as that of nutrient deprivation, concomitant with cessation of growth and depletion of chloroplasts. By contrast, certain small chemical compounds selected by high-throughput screening in Chlamydomonas reinhardtii can induce lipid accumulation during growth, maintaining biomass. Comprehensive pathway analyses using proteomics, transcriptomics, and metabolomics data were acquired from Chlamydomonas cells grown in the presence of one of two structurally distinct lipid activators. WD10784 stimulates both starch and lipid accumulation, whereas WD30030-treated cells accumulate only lipids. The differences in starch accumulation are largely due to differential effects of the two compounds on substrate levels that feed into starch synthesis and on genes encoding starch metabolic enzymes. The compounds had differential effects on photosynthesis, respiration, and oxidative stress pathways. Cells treated with WD10784 showed slowed growth over time and reduced abundance of photosynthetic proteins, decreased respiration, and increased oxidative stress proteins, glutathione, and reactive oxygen species specific to this compound. Both compounds maintained central carbon and nitrogen metabolism, including the tricarboxylic acid cycle, glycolysis, respiration, and the Calvin-Benson-Bassham cycle. There were few changes in proteins and transcripts related to fatty acid biosynthesis, whereas proteins and transcripts for triglyceride production were elevated, suggesting that lipid synthesis is largely driven by substrate availability. This study reports that the compound WD30030 and, to a lesser extent WD10784, increases lipid and lipid droplet synthesis and storage without restricting growth or biomass accumulation by mechanisms that are substantially different from nutrient deprivation.

a b s t r a c tThe use of microalgae as a biofuel feedstock is highly desired, but current methods to induce lipid accumulation cause severe stress responses that limit biomass and, thus oil yield. To address these issues, a high throughput screening (HTS) method was devised to identify chemical inducers of growth and lipid accumulation. Optimization was performed to determine the most effective cell density, DMSO and Nile Red (NR) concentrations to monitor growth and lipid accumulation. The method was tested using 1717 compounds from National Cancer Institute (NCI) Diversity Set III and Natural Products Set II in Chlamydomonas reinhardtii. Cells were inoculated at low density and 10 μM of the test compound was added. After 72 h, cell density was measured at OD 550 and lipid accumulation assessed using NR fluorescence. Primary screening identified 8 compounds with a hit rate of 0.47% and a robust Z′ discrimination factor (0.68 ± 0.1). Of these, Brefeldin A (BFA) was the most successful at inducing lipid accumulation and was used to evaluate secondary screens including measuring levels of fatty acids, photosynthetic pigments, proteins and carbohydrates. The effectiveness of BFA was confirmed in Chlorella sorokiniana UTEX 1230. This study demonstrates the power of chemical genomics approaches in biofuel research.

Methods of measuring the activities of biomolecules and pathways are fundamental to the study and engineering of biological systems. Traditional marker genes that generate light or color are limited in their dynamic range and often require expensive equipment. Here we describe a way to simultaneously detect the identity and measure the activity of each molecular variant within a mixed population of cells using nanopore sequencing. By linking the desired activity to expression of a base editor that induces mutations in a “canvas” adjacent to the DNA encoding the molecule or pathway of interest, we show that a single long-read sequencing step can retrieve identity and activity at numerous timepoints in bacteria, potentially greatly increasing the available dynamic range. Our technique can replace flow cytometry in directed evolution and may be capable of directly mapping biomolecular fitness landscapes.

A large scale in vivo high throughput screen (HTS) was performed to identify small compounds that stimulate lipid production and accumulation using the model organism Chlamydomonas reinhardtii. The HTS employed a 384‐well microplate format in which cells were allowed to grow in the presence of the compounds at 10 μM final concentration for 72 hours. Accumulation of intracellular lipids was assessed using the lipophilic dye Nile Red and growth was monitored at OD600. The screening library included 43,736 compounds (ChemBridge, Corp). A total of 367 active compounds were identified that stimulated lipid accumulation to > 2.5‐fold and did not affect cell viability to give a hit rate of 0.8%. Primary hits were “cherry picked” and the sub‐set of compounds were retested using an 8‐point dose response assay (0.25‐30 µM). Hits were further assessed visually using a Nikon Ti‐inverted microscope (60X) to reconfirm lipid droplet accumulation was induced.. The final set of hits included 306 compounds. These were further compared for structural similarities using Tibco Spotfire Lead Discovery package and resulted in three main structural clusters: compounds with a piperazine, nitrobenzene, and/or adamantine group. The impact of the compounds on cellular metabolism was also characterization by quantifying Chl A, B, starch, protein and toxicity analysis. Currently, we are examining compound effectiveness in additional algal species such as Chlorella sorokiniana UTEX 1230, Tetrachlorella alterans UTEX 2453, C. protothecoides UTEX 29, C. vulgaris UTEX 395, Nannochloropsis sp. Grant Funding Source: Supported by EPSCoR