Oil accumulation by the oleaginous diatom Fistulifera solaris as revealed by the genome and transcriptome.

Oleaginous photosynthetic organisms such as microalgae are promising sources for biofuel production through the generation of carbon-neutral sustainable energy. However, the metabolic mechanisms driving high-rate lipid production in these oleaginous organisms remain unclear, thus impeding efforts to improve productivity through genetic modifications. We analyzed the genome and transcriptome of the oleaginous diatom Fistulifera solaris JPCC DA0580. Next-generation sequencing technology provided evidence of an allodiploid genome structure, suggesting unorthodox molecular evolutionary and genetic regulatory systems for reinforcing metabolic efficiencies. Although major metabolic pathways were shared with nonoleaginous diatoms, transcriptome analysis revealed unique expression patterns, such as concomitant upregulation of fatty acid/triacylglycerol biosynthesis and fatty acid degradation (ß-oxidation) in concert with ATP production. This peculiar pattern of gene expression may account for the simultaneous growth and oil accumulation phenotype and may inspire novel biofuel production technology based on this oleaginous microalga.

Chloroplast-targeting protein expression in the oleaginous diatom Fistulifera solaris JPCC DA0580 toward metabolic engineering.

The chloroplast plays critical roles in lipid metabolism of microalgae, thus it is recognized as an attractive target of metabolic engineering to enhance biofuel production. It has been well known that recombinant protein expression in microalgal chloroplasts needs specific signal sequence which governs the transition manner of nuclear-encoded polypeptides within the subcellular compartments. However certain microalgae, including diatoms, have complex membrane systems surrounding the chloroplast, and thus chloroplast-targeting protein expression with the signal sequence has rarely been demonstrated except for a few model non-oleaginous diatoms. In this study, we performed recombinant green fluorescence protein (GFP) expression and transportation into the chloroplast of the oleaginous marine diatom, Fistulifera solaris JPCC DA0580. The signal sequence of ATP synthetase gamma subunit, which was predicted to localize in the chloroplast according to a bioinformatics analysis pipeline, was employed as a key factor of this technique. As a result, specific localization of GFP in the chloroplast was observed. It would be useful to engineer the lipid synthesis pathways existing in the chloroplast. Furthermore, intensive gathering of GFP in the rod-like structure was also detected, which has not been observed in model diatom studies. As comparing with electron microscopic observation, the structure was estimated to be a pyrenoid.

Tracking difference in gene expression in a time-course experiment using gene set enrichment analysis.

Fistulifera sp. strain JPCC DA0580 is a newly sequenced pennate diatom that is capable of simultaneously growing and accumulating lipids. This is a unique trait, not found in other related microalgae so far. It is able to accumulate between 40 to 60% of its cell weight in lipids, making it a strong candidate for the production of biofuel. To investigate this characteristic, we used RNA-Seq data gathered at four different times while Fistulifera sp. strain JPCC DA0580 was grown in oil accumulating and non-oil accumulating conditions. We then adapted gene set enrichment analysis (GSEA) to investigate the relationship between the difference in gene expression of 7,822 genes and metabolic functions in our data. We utilized information in the KEGG pathway database to create the gene sets and changed GSEA to use re-sampling so that data from the different time points could be included in the analysis. Our GSEA method identified photosynthesis, lipid synthesis and amino acid synthesis related pathways as processes that play a significant role in oil production and growth in Fistulifera sp. strain JPCC DA0580. In addition to GSEA, we visualized the results by creating a network of compounds and reactions, and plotted the expression data on top of the network. This made existing graph algorithms available to us which we then used to calculate a path that metabolizes glucose into triacylglycerol (TAG) in the smallest number of steps. By visualizing the data this way, we observed a separate up-regulation of genes at different times instead of a concerted response. We also identified two metabolic paths that used less reactions than the one shown in KEGG and showed that the reactions were up-regulated during the experiment. The combination of analysis and visualization methods successfully analyzed time-course data, identified important metabolic pathways and provided new hypotheses for further research.

Oleosome-associated protein of the oleaginous diatom Fistulifera solaris contains an endoplasmic reticulum-targeting signal sequence.

Microalgae tend to accumulate lipids as an energy storage material in the specific organelle, oleosomes. Current studies have demonstrated that lipids derived from microalgal oleosomes are a promising source of biofuels, while the oleosome formation mechanism has not been fully elucidated. Oleosome-associated proteins have been identified from several microalgae to elucidate the fundamental mechanisms of oleosome formation, although understanding their functions is still in infancy. Recently, we discovered a diatom-oleosome-associated-protein 1 (DOAP1) from the oleaginous diatom, Fistulifera solaris JPCC DA0580. The DOAP1 sequence implied that this protein might be transported into the endoplasmic reticulum (ER) due to the signal sequence. To ensure this, we fused the signal sequence to green fluorescence protein. The fusion protein distributed around the chloroplast as like a meshwork membrane structure, indicating the ER localization. This result suggests that DOAP1 could firstly localize at the ER, then move to the oleosomes. This study also demonstrated that the DOAP1 signal sequence allowed recombinant proteins to be specifically expressed in the ER of the oleaginous diatom. It would be a useful technique for engineering the lipid synthesis pathways existing in the ER, and finally controlling the biofuel quality.

Biosynthesis of polyunsaturated fatty acids in the oleaginous marine diatom Fistulifera sp. strain JPCC DA0580.

Studies of polyunsaturated fatty acid (PUFA) biosynthesis in microalgae are of great importance for many reasons, including the production of biofuel and variable omega 3-long chain PUFAs. The elucidation of the PUFA biosynthesis pathway is necessary for bioengineering to increase or decrease PUFA content in certain microalgae. In this study, we identified the PUFA synthesis pathway in the oleaginous marine diatom, Fistulifera sp. strain JPCC DA0580, a promising candidate for biodiesel production. The data revealed not only the presence of the desaturases and elongases involved in eicosapentaenoic acid (EPA) synthesis, but also the unexpected localization of ω3-desaturase expression in the chloroplast. This suggests that this microalga might perform the final step of EPA synthesis in the chloroplast and not in the endoplasmic reticulum (ER) like other diatoms. The detailed fatty acid profile suggests that the EPA was synthesized only through the ω6-pathway in this strain, which was also different from other diatoms. Finally, the transcriptome analysis demonstrated an overall down-regulation of desaturases and elongases over incubation time. These genetic features might explain the decrease of PUFA percentage over incubation time in this strain. The important insights into metabolite synthesis acquired here will be useful for future metabolic engineering to control PUFA content in this diatom.

Assessment of the anti-biofouling potentials of a copper iodide-doped nylon mesh.

We propose a copper iodide (CuI)-doped nylon mesh prepared using polyiodide ions as a precursor toward anti-biofouling polymer textile. The CuI-doped nylon mesh was subjected to the prevention of biofouling in marine environments. The attachment of the marine organisms was markedly inhibited on the CuI-doped nylon mesh surface until 249 days. Scanning electron microscopy-energy dispersive X-ray analysis indicated that copper compounds were maintained in the nylon mesh after the field experiment, although copper content in the nylon mesh was reduced. Therefore, the copper ions slowly dissolved from nylon mesh will contribute to the long-term prevention of biofouling. Furthermore, electron spin resonance analysis revealed the generation of reactive oxygen species (ROS) from CuI-doped nylon mesh after the field experiment. One of the possibilities for toxic action of copper ions will be the direct effect of Cu+ -induced ROS on biofilm forming on nylon mesh surface. The proposed polymer textile can be applied to fishing and aquafarming nets, mooring rope for ship, or silt fence to restrict polluted water in marine environments.

Single-cell detection using a thin film transistor photosensor with micro-partitions.

A thin film transistor (TFT) photosensor was applied to single-cell detection by identifying cell surface molecules based on chemiluminescence. Micro-partitions were directly fabricated on the TFT photosensor surface by photolithography. The surface of each pixel was surrounded by 25 µm-height partitions, forming areas of approximately 30 µm × 30 µm for cell entrapment and photosensing. Visualization of individual JM cells, stained with mouse anti-human CD8 IgG1 primary antibody and Horseradish peroxidase (HRP)-labeled anti-mouse IgG1 secondary antibody, as bright-pixels was successfully achieved using the micro-partitioned TFT photosensor integrated into a microfluidic chamber. Furthermore, real-time monitoring of HRP-labeled JM cells was also accomplished. The fabrication of micro-partitions on the surface of the TFT photosensor allows highly efficient single-cell entrapment and chemiluminescence-based detection of JM cells. This is the first report of single-cell entrapment and subsequent signal detection on the photosensing area of individual pixels of TFT photosensor. This system will allow high-throughput and real-time analysis of more than 10(4) cells with minimum optical system requirements.

High-content analysis of single cells directly assembled on CMOS sensor based on color imaging.

A complementary metal oxide semiconductor (CMOS) image sensor was applied to high-content analysis of single cells which were assembled closely or directly onto the CMOS sensor surface. The direct assembling of cell groups on CMOS sensor surface allows large-field (6.66 mm×5.32 mm in entire active area of CMOS sensor) imaging within a second. Trypan blue-stained and non-stained cells in the same field area on the CMOS sensor were successfully distinguished as white- and blue-colored images under white LED light irradiation. Furthermore, the chemiluminescent signals of each cell were successfully visualized as blue-colored images on CMOS sensor only when HeLa cells were placed directly on the micro-lens array of the CMOS sensor. Our proposed approach will be a promising technique for real-time and high-content analysis of single cells in a large-field area based on color imaging.