Advances and opportunities in gene editing and gene regulation technology for Yarrowia lipolytica.

Yarrowia lipolytica has emerged as a biomanufacturing platform for a variety of industrial applications. It has been demonstrated to be a robust cell factory for the production of renewable chemicals and enzymes for fuel, feed, oleochemical, nutraceutical and pharmaceutical applications. Metabolic engineering of this non-conventional yeast started through conventional molecular genetic engineering tools; however, recent advances in gene/genome editing systems, such as CRISPR-Cas9, transposons, and TALENs, has greatly expanded the applications of synthetic biology, metabolic engineering and functional genomics of Y. lipolytica. In this review we summarize the work to develop these tools and their demonstrated uses in engineering Y. lipolytica, discuss important subtleties and challenges to using these tools, and give our perspective on important gaps in gene/genome editing tools in Y. lipolytica.

Dual CRISPR-Cas9 Cleavage Mediated Gene Excision and Targeted Integration in Yarrowia lipolytica.

CRISPR-Cas9 technology has been successfully applied in Yarrowia lipolytica for targeted genomic editing including gene disruption and integration; however, disruptions by existing methods typically result from small frameshift mutations caused by indels within the coding region, which usually resulted in unnatural protein. In this study, a dual cleavage strategy directed by paired sgRNAs is developed for gene knockout. This method allows fast and robust gene excision, demonstrated on six genes of interest. The targeted regions for excision vary in length from 0.3 kb up to 3.5 kb and contain both non-coding and coding regions. The majority of the gene excisions are repaired by perfect nonhomologous end-joining without indel. Based on this dual cleavage system, two targeted markerless integration methods are developed by providing repair templates. While both strategies are effective, homology mediated end joining (HMEJ) based method are twice as efficient as homology recombination (HR) based method. In both cases, dual cleavage leads to similar or improved gene integration efficiencies compared to gene excision without integration. This dual cleavage strategy will be useful for not only generating more predictable and robust gene knockout, but also for efficient targeted markerless integration, and simultaneous knockout and integration in Y. lipolytica.

Engineering xylose utilization in Yarrowia lipolytica by understanding its cryptic xylose pathway.

BACKGROUND: The oleaginous yeast, Yarrowia lipolytica, has been utilized as an industrial host for about 60 years for various applications. Recently, the metabolic engineering of this host has become increasingly popular due to its ability to accumulate lipids as well as improvements made toward developing new genetic tools. Y. lipolytica can robustly metabolize glucose, glycerol, and even different lipid classes. However, little is known about its xylose metabolizing capability. Given the desirability of having a robust xylose utilizing strain of Y. lipolytica, we performed a comprehensive investigation and elucidation of the existing components of its xylose metabolic pathway. RESULTS: A quick and efficient means of determining functionality of the candidate xylose pathway genes (XYR, XDH, and XKS) from Y. lipolytica was desirable. We challenged Escherichia coli mutants lacking either the xylose isomerase (xylA) gene or the xylulose kinase (xylB) gene to grow on xylose minimal media by expressing the candidate genes from Y. lipolytica. We showed that the XKS of Y. lipolytica is able to rescue xylose growth of E. coli ΔxylB, and the XDH enabled growth on xylitol, but not on xylose, of E. coli ΔxylA. Overexpression of XKS and XDH in Y. lipolytica improved growth on xylitol, indicating that expression of the native enzymes was limiting. Overexpression of XKS and XDH in Y. lipolytica also enables robust growth on xylose under high nitrogen conditions without the need for adaptation. These results prove that a complete xylose pathway exists in Y. lipolytica, but the pathway is poorly expressed. To elucidate the XYR gene, we applied the E. coli ΔxylA xylose growth challenge with 14 candidate XYR genes and XDH. The XYR2 candidate was able to rescue growth of E. coli ΔxylA xylose on minimal media. CONCLUSIONS: While a native xylose pathway exists in Y. lipolytica, the microorganism's inability to grow robustly on xylose is an effect of cryptic genetic circuits that control expression of key enzymes in the metabolic pathway. We have characterized the key enzymes associated with xylose metabolism and demonstrated that gene regulatory issues can be overcome using strong hybrid promoters to attain robust growth on xylose without adaptation.

Direct quantification of fatty acids in wet microalgal and yeast biomass via a rapid in situ fatty acid methyl ester derivatization approach.

Accurate determination of fatty acid contents is routinely required in microalgal and yeast biofuel studies. A method of rapid in situ fatty acid methyl ester (FAME) derivatization directly from wet fresh microalgal and yeast biomass was developed in this study. This method does not require prior solvent extraction or dehydration. FAMEs were prepared with a sequential alkaline hydrolysis (15 min at 85 °C) and acidic esterification (15 min at 85 °C) process. The resulting FAMEs were extracted into n-hexane and analyzed using gas chromatography. The effects of each processing parameter (temperature, reaction time, and water content) upon the lipids quantification in the alkaline hydrolysis step were evaluated with a full factorial design. This method could tolerate water content up to 20% (v/v) in total reaction volume, which equaled up to 1.2 mL of water in biomass slurry (with 0.05-25 mg of fatty acid). There were no significant differences in FAME quantification (p>0.05) between the standard AOAC 991.39 method and the proposed wet in situ FAME preparation method. This fatty acid quantification method is applicable to fresh wet biomass of a wide range of microalgae and yeast species.

Regulation of starch and lipid accumulation in a microalga Chlorella sorokiniana.

Microalgae have attracted growing attention due to their potential in biofuel feedstock production. However, current understanding of the regulatory mechanisms for lipid biosynthesis and storage in microalgae is still limited. This study revealed that the microalga Chlorella sorokiniana showed sequential accumulation of starch and lipids. When nitrogen was replete and/or depleted over a short period, starch was the predominant carbon storage form with basal levels of lipid accumulation. After prolonged nitrogen depletion, lipid accumulation increased considerably, which was partially due to starch degradation, as well as the turnover of primary metabolites. Lipid accumulation is also strongly dependent on the linear electron flow of photosynthesis, peaking at lower light intensities. Collectively, this study reveals a relatively clear regulation pattern of starch and lipid accumulation that is basically controlled by nitrogen levels. The mixotrophic growth of C. sorokiniana shows promise for biofuel production in terms of lipid accumulation in the final biomass.

Effects of lignin modification on wheat straw cell wall deconstruction by Phanerochaete chrysosporium.

BACKGROUND: A key focus in sustainable biofuel research is to develop cost-effective and energy-saving approaches to increase saccharification of lignocellulosic biomass. Numerous efforts have been made to identify critical issues in cellulose hydrolysis. Aerobic fungal species are an integral part of the carbon cycle, equip the hydrolytic enzyme consortium, and provide a gateway for understanding the systematic degradation of lignin, hemicelluloses, and cellulose. This study attempts to reveal the complex biological degradation process of lignocellulosic biomass by Phanerochaete chrysosporium in order to provide new knowledge for the development of energy-efficient biorefineries. RESULTS: In this study, we evaluated the performance of a fungal biodegradation model, Phanerochaete chrysosporium, in wheat straw through comprehensive analysis. We isolated milled straw lignin and cellulase enzyme-treated lignin from fungal-spent wheat straw to determine structural integrity and cellulase absorption isotherms. The results indicated that P. chrysosporium increased the total lignin content in residual biomass and also increased the cellulase adsorption kinetics in the resulting lignin. The binding strength increased from 117.4 mL/g to 208.7 mL/g in milled wood lignin and from 65.3 mL/g to 102.4 mL/g in cellulase enzyme lignin. A detailed structural dissection showed a reduction in the syringyl lignin/guaiacyl lignin ratio and the hydroxycinnamate/lignin ratio as predominant changes in fungi-spent lignin by heteronuclear single quantum coherence spectroscopy. CONCLUSION: P. chrysosporium shows a preference for degradation of phenolic terminals without significantly destroying other lignin components to unzip carbohydrate polymers. This is an important step in fungal growth on wheat straw. The phenolics presumably locate at the terminal region of the lignin moiety and/or link with hemicellulose to form the lignin-carbohydrate complex. Findings may inform the development of a biomass hydrolytic enzyme combination to enhance lignocellulosic biomass hydrolysis and modify the targets in plant cell walls.

Improved lipid accumulation by morphology engineering of oleaginous fungus Mortierella isabellina.

Oleaginous fungi capable of accumulating a considerable amount of lipids are promising sources for lipid-based biofuel production. The specific productivities of filamentous fungi in submerged fermentation are often correlated with morphological forms. However, the relationship between morphological development and lipid accumulation is not known. In this study, distinct morphological forms of oleaginous fungus Mortierella isabellina including pellets of different sizes, free dispersed mycelia, and broken hyphal fragments were developed by additions of different concentrations of magnesium silicate microparticles. Different morphological forms led to different levels of lipid accumulation as well as different spatial patterns of lipid distribution within pellets/mycelial aggregates. Significant higher lipid content (0.75 g lipid/g cell biomass) and lipid yield (0.18 g lipid/g glucose consumed) were achieved in free dispersed mycelia than in pellets. Moreover, extracellular metabolite analysis showed that production of undesirable by-product malate was repressed in free dispersed mycelium form. Unveiling the desired morphological form of M. isabellina for lipid accumulation provided insights into molecular mechanism of lipid biosynthesis linked with morphological development, as well as design and optimization of bioprocess to produce lipid-based biofuels.

Microbial lipid production from xylose by Mortierella isabellina.

Culture conditions including nitrogen source and concentration, xylose concentration, and inoculum level were evaluated for the effect on cell growth and lipid production of an oleaginous fungus, Mortierella isabellina, grown on xylose. Yeast extract and ammonium sulfate were found to be the best amongst the organic and inorganic nitrogen sources tested, respectively. Subsequent combination of these two nitrogen sources at a nitrogen ratio of 1:1 further enhanced lipid production. The highest cell biomass 28.8 g L(-1) and lipid 18.5 g L(-1) were obtained on a medium containing 100 g L(-1) xylose and 50.4 mM nitrogen with a spore concentration of 10(8) mL(-1). Specifically, nitrogen concentration and inoculum level were demonstrated to be important for obtaining a high lipid yield on xylose consumed of 0.182 g g(-1). The results suggest that M. isabellina holds great potential to be a candidate for biofuel production from xylose, the second most abundant sugar from lignocellulose.

Lignocellulosic biomass as a carbohydrate source for lipid production by Mortierella isabellina.

Various carbon sources including monosugars, disaccharides and carboxymethyl-cellulose (CMC) were used for single-cell oil production by the filamentous fungus Mortierella isabellina. In addition, the inhibitory effects of lignocellulose-derived compounds (lignin aldehydes, furan aldehydes and weak acid) were investigated. C6 sugars were preferably used for growth compared to C5 sugars. CMC was not an usable substrate, implying the absence of a cellulase system in this fungus. Lignin derivatives showed the most inhibitory effects, but acetic and formic acids at concentrations of 4 g/L improved lipid production, achieving 6.81 ± 0.07 g/L and 6.66 ± 0.33 g/L respectively, which was twice as high as that of the control. A 16.8% lipid yield from hydrolysate suggested that this fungus could be useful for microbial lipid production.

Advanced biorefinery in lower termite-effect of combined pretreatment during the chewing process.

BACKGROUND: Currently the major barrier in biomass utilization is the lack of an effective pretreatment of plant cell wall so that the carbohydrates can subsequently be hydrolyzed into sugars for fermentation into fuel or chemical molecules. Termites are highly effective in degrading lignocellulosics and thus can be used as model biological systems for studying plant cell wall degradation. RESULTS: We discovered a combination of specific structural and compositional modification of the lignin framework and partial degradation of carbohydrates that occurs in softwood with physical chewing by the termite, Coptotermes formosanus, which are critical for efficient cell wall digestion. Comparative studies on the termite-chewed and native (control) softwood tissues at the same size were conducted with the aid of advanced analytical techniques such as pyrolysis gas chromatography mass spectrometry, attenuated total reflectance Fourier transform infrared spectroscopy and thermogravimetry. The results strongly suggest a significant increase in the softwood cellulose enzymatic digestibility after termite chewing, accompanied with utilization of holocellulosic counterparts and an increase in the hydrolysable capacity of lignin collectively. In other words, the termite mechanical chewing process combines with specific biological pretreatment on the lignin counterpart in the plant cell wall, resulting in increased enzymatic cellulose digestibility in vitro. The specific lignin unlocking mechanism at this chewing stage comprises mainly of the cleavage of specific bonds from the lignin network and the modification and redistribution of functional groups in the resulting chewed plant tissue, which better expose the carbohydrate within the plant cell wall. Moreover, cleavage of the bond between the holocellulosic network and lignin molecule during the chewing process results in much better exposure of the biomass carbohydrate. CONCLUSION: Collectively, these data indicate the participation of lignin-related enzyme(s) or polypeptide(s) and/or esterase(s), along with involvement of cellulases and hemicellulases in the chewing process of C. formosanus, resulting in an efficient pretreatment of biomass through a combination of mechanical and enzymatic processes. This pretreatment could be mimicked for industrial biomass conversion.