Won-Sub Shin

CRISPR/Cas9-induced knockout and knock-in mutations in Chlamydomonas reinhardtii

Genome editing is crucial for genetic engineering of organisms for improved traits, particularly in microalgae due to the urgent necessity for the next generation biofuel production. The most advanced CRISPR/Cas9 system is simple, efficient and accurate in some organisms; however, it has proven extremely difficult in microalgae including the model alga Chlamydomonas. We solved this problem by delivering Cas9 ribonucleoproteins (RNPs) comprising the Cas9 protein and sgRNAs to avoid cytotoxicity and off-targeting associated with vector-driven expression of Cas9. We obtained CRISPR/Cas9-induced mutations at three loci including MAA7, CpSRP43 and ChlM, and targeted mutagenic efficiency was improved up to 100 fold compared to the first report of transgenic Cas9-induced mutagenesis. Interestingly, we found that unrelated vectors used for the selection purpose were predominantly integrated at the Cas9 cut site, indicative of NHEJ-mediated knock-in events. As expected with Cas9 RNPs, no off-targeting was found in one of the mutagenic screens. In conclusion, we improved the knockout efficiency by using Cas9 RNPs, which opens great opportunities not only for biological research but also industrial applications in Chlamydomonas and other microalgae. Findings of the NHEJ-mediated knock-in events will allow applications of the CRISPR/Cas9 system in microalgae, including “safe harboring” techniques shown in other organisms.

Optimization of variables affecting the direct transesterification of wet biomass from Nannochloropsis oceanica using ionic liquid as a co-solvent

Ionic liquids have many applications, one of which entails their utilization as powerful solvents. In the present study, various experimental conditions of ionic liquid-mediated direct transesterification were investigated in terms of lipid-extracting ionic liquids, catalyst, reaction time, reaction temperature and volume of methanol to achieve effective FAME conversion with wet microalgal feedstock, Nannochloropsis oceanica. With ionic liquid, [Bmim][CF3SO3], highest fatty acid methyl ester (FAME) yield was shown. Among many experimental parameters, the two most critical factors to enhance FAME conversion were characteristic of ionic liquids and volume of methanol. Optimized ionic liquid-mediated direct transesterification of wet N. oceanica, compared with a control experiment using chloroform and methanol, increased the FAME conversion yield by 11-fold.

Effect of shear stress on the growth of continuous culture of Synechocystis PCC 6803 in a flat-panel photobioreactor

The effect of hydrodynamic forces generated by air bubbles on cell growth of continuous culture of Synechocystis PCC 6803 was studied in a flat-panel photobioreactor. Keeping all relevant parameters constant enables the optimization of individual parameters, for which a continuous cultivation approach has significant advantages. Continuous culture of Synechocystis PCC 6803 was cultivated under different gas velocities from 0.022 m s−1 up to 0.128 m s−1. Based on direct determination of effective growth rate at constant cell densities, cell damage due to shear stress induced by the increasing gas velocity at the sparger was directly observed. A significant decrease of effective growth rate was observed at gas velocity of 0.085 m s−1 generated at the gas flow rate of 200 ml min−1, indicating cell damage by shear stress. Optimization of gas volume and the development of an effective aeration system corresponding to a given reactor setup is important to realize a reliable cell growth.

Enrichment as a screening method for a high-growth-rate microalgal strain under continuous cultivation system

Microalgae are a promising feedstock for renewable biodiesel production. High productivity of biodiesel production from microalgae is directly related to growth rate as well as lipid content of cells. In the present study, an enrichment process in a continuous cultivation system was developed to screen a high-growth-rate microalga from a mixed culture of microalgal species; Chlorella vulgaris, Chlorella protothecoides, and Chlamydomonas reinhardtii were used as test organisms for our experiments. The time-dependent washout of mixed microalgal pool was executed to successfully enrich the C. reinhardtii, which exhibits the higher growth rate than C. vulgaris and C. protothecoides under turbidostat conditions within 75 h. The domination of C. reinhardtii in the mixed culture was validated by on-line monitoring of growth rate and flowcytometric analysis. For the time-efficient production of microalgal biomass, this screening process has a high potential to segregate the fast-growing microalgal strains from the pool of various uncharacterized microalgal species and random mutants.

Use of a triiodide resin for isolation of axenic cultures of microalgal Nannochloropsis gaditana.

Triiodide resin (TR) was used to generate axenic cultures of microalgae by employing the antibacterial capability of triiodide. A Nannochloropsis gaditana culture contaminated with bacteria was passed through a column filled with TR using the gravity flow. Based on analyses of flow cytometry and vital staining using a fluorescent dye SYTOX Green, three cycles of TR treatments remarkably reduced the number of viable bacteria but had little effects on the microalgae. This novel approach is a simple, rapid, and cost-effective method that can be used to isolate axenic cultures of microalgae.

Complementation of a mutation in CpSRP43 causing partial truncation of light-harvesting chlorophyll antenna in Chlorella vulgaris

Photosynthesis of microalgae enables conversion of light energy into chemical energy to produce biomass and biomaterials. However, the efficiency of this process must be enhanced, and truncation of light-harvesting complex (LHC) has been suggested to improve photosynthetic efficiency. We reported an EMS-induced mutant (E5) showing partially reduced LHC in Chlorella vulgaris. We determined the mutation by sequencing the whole genome of WT and E5. Augustus gene prediction was used for determining CDS, and non-synonymous changes in E5 were screened. Among these, we found a point mutation (T to A) in a gene homologous to chloroplast signal recognition particle 43 kDa (CpSRP43). The point mutation changed the 102nd valine to glutamic acid (V102E) located in the first chromodomain. Phylogenetic analyses of CpSRP43 revealed that this amino acid was valine or isoleucine in microalgae and plants, suggesting important functions. Transformation of E5 with WT CpSRP43 showed varying degrees of complementation, which was demonstrated by partial recovery of the LHCII proteins to the WT level, and partially restored photosynthetic pigments, photosynthetic ETR, NPQ, and growth, indicating that the V102E mutation was responsible for the reduced LHC in E5.

Growth medium sterilization using decomposition of peracetic acid for more cost-efficient production of omega-3 fatty acids by Aurantiochytrium

Aurantiochytrium can produce significant amounts of omega-3 fatty acids, specifically docosahexaenoic acid and docosapentaenoic acid. Use of a glucose-based medium for heterotrophic growth is needed to achieve a high growth rate and production of abundant lipids. However, heat sterilization for reliable cultivation is not appropriate to heat-sensitive materials and causes a conversion of glucose via browning (Maillard) reactions. Thus, the present study investigated the use of a direct degradation of Peracetic acid (PAA) for omega-3 production by Aurantiochytrium. Polymer-based bioreactor and glucose-containing media were chemically co-sterilized by 0.04% PAA and neutralized through a reaction with ferric ion (III) in HEPES buffer. Mono-cultivation was achieved without the need for washing steps and filtration, thereby avoiding the heat-induced degradation and dehydration of glucose. Use of chemically sterilized and neutralized medium, rather than heat-sterilized medium, led to a twofold faster growth rate and greater productivity of omega-3 fatty acids.