Metabolic engineering of oleaginous fungus Mortierella alpina for high production of oleic and linoleic acids

Advanced Fungal Biotechnologies in Accomplishing Sustainable Development Goals (SDGs): What Do We Know and What Comes Next?

The present era has witnessed an unprecedented scenario with extreme climate changes, depleting natural resources and rising global food demands and its widespread societal impact. From providing bio-based resources to fulfilling socio-economic necessities, tackling environmental challenges, and ecosystem restoration, microbes exist as integral members of the ecosystem and influence human lives. Microbes demonstrate remarkable potential to adapt and thrive in climatic variations and extreme niches and promote environmental sustainability. It is important to mention that advances in fungal biotechnologies have opened new avenues and significantly contributed to improving human lives through addressing socio-economic challenges. Microbe-based sustainable innovations would likely contribute to the United Nations sustainable development goals (SDGs) by providing affordable energy (use of agro-industrial waste by microbial conversions), reducing economic burdens/affordable living conditions (new opportunities by the creation of bio-based industries for a sustainable living), tackling climatic changes (use of sustainable alternative fuels for reducing carbon footprints), conserving marine life (production of microbe-based bioplastics for safer marine life) and poverty reduction (microbial products), among other microbe-mediated approaches. The article highlights the emerging trends and future directions into how fungal biotechnologies can provide feasible and sustainable solutions to achieve SDGs and address global issues.

Focus and Insights into the Synthetic Biology-Mediated Chassis of Economically Important Fungi for the Production of High-Value Metabolites

Substantial progress has been achieved and knowledge gaps addressed in synthetic biology-mediated engineering of biological organisms to produce high-value metabolites. Bio-based products from fungi are extensively explored in the present era, attributed to their emerging importance in the industrial sector, healthcare, and food applications. The edible group of fungi and multiple fungal strains defines attractive biological resources for high-value metabolites comprising food additives, pigments, dyes, industrial chemicals, and antibiotics, including other compounds. In this direction, synthetic biology-mediated genetic chassis of fungal strains to enhance/add value to novel chemical entities of biological origin is opening new avenues in fungal biotechnology. While substantial success has been achieved in the genetic manipulation of economically viable fungi (including Saccharomyces cerevisiae) in the production of metabolites of socio-economic relevance, knowledge gaps/obstacles in fungal biology and engineering need to be remedied for complete exploitation of valuable fungal strains. Herein, the thematic article discusses the novel attributes of bio-based products from fungi and the creation of high-value engineered fungal strains to promote yield, bio-functionality, and value-addition of the metabolites of socio-economic value. Efforts have been made to discuss the existing limitations in fungal chassis and how the advances in synthetic biology provide a plausible solution.

Engineering the Lipid and Fatty Acid Metabolism in Yarrowia lipolytica for Sustainable Production of High Oleic Oils

Oleic acid is widely applied in the chemical, material, nutritional, and pharmaceutical industries. However, the current production of oleic acid via high oleic plant oils is limited by the long growth cycle and climatic constraints. Moreover, the global demand for high oleic plant oils, especially the palm oil, has emerged as the driver of tropical deforestation causing tropical rainforest destruction, climate change, and biodiversity loss. In the present study, an alternative and sustainable strategy for high oleic oil production was established by reprogramming the metabolism of the oleaginous yeast Yarrowia lipolytica using a two-layer "push-pull-block" strategy. Specifically, the fatty acid synthesis pathway was first engineered to increase oleic acid proportion by altering the fatty acid profiles. Then, the content of storage oils containing oleic acid was boosted by engineering the synthesis and degradation pathways of triacylglycerides. The strain resulting from this two-layer engineering strategy produced the highest titer of high oleic microbial oil reaching 56 g/L with 84% oleic acid in fed-batch fermentation, representing a remarkable improvement of a 110-fold oil titer and 2.24-fold oleic acid proportion compared with the starting strain. This alternative and sustainable method for high oleic oil production shows the potential of substitute planting.

Advances in improving the biotechnological application of oleaginous fungus Mortierella alpina

Mortierella alpina is an oleaginous filamentous fungus with considerable lipid productivity, and it has been widely used for industrial production of arachidonic acid. The fermentation process of M. alpina is complicated and can be affected by various factors; therefore, a comprehensive knowledge of its metabolic characteristics and key factors governing lipid biosynthesis is required to further improve its industrial performance. In this review, we discuss the metabolic features and extracellular factors that affect lipid biosynthesis in M. alpina. The current progress in fermentation optimisation and metabolic engineering to improve lipid yield are also summarised. Moreover, we review the applications of M. alpina in the food industry and propose fermentation strategies for better utilisation of this genus in the future. In our opinion, the economic performance of M. alpina should be enhanced from multiple levels, including strains with ideal traits, efficient fermentation strategies, controllable fermentation costs, and competitive products of both high value and productivity. By reviewing the peculiarities of M. alpina and current progress to improve its suitability for biotechnological production, we wish to provide more efficient strategies for future development of M. alpina as a high-value lipid cell factory. KEY POINTS: • Understanding M. alpina metabolism is helpful for rational design of its fermentation processes. • Nitrogen source is a key point that affects PUFA's component and fermentation cost in M. alpina. • Dynamic fermentation strategy combined with breeding is needed to increase lipid yield in M. alpina.

Functional characterization and overexpression of Δ12-desaturase in the oleaginous yeast Rhodotorula toruloides for production of linoleic acid-rich lipids

Linoleic acid (LA) has garnered much attention due to its potential applications in the oleochemical and nutraceutical industries. The oleaginous yeast Rhodotorula toruloides has outstanding lipogenecity, and is considered a potential alternative to the current plant-based platforms for LA production. Δ12-fatty acid desaturases (Δ12-Fads) are involved in LA synthesis in various fungi and yeasts, but their functions in R. toruloides remain poorly understood. To achieve the production of LA-rich lipids in R. toruloides, we investigated the function of the native Δ12-FAD (RtFAD2). First, the overexpression of RtFAD2 and its co-overexpression with RtFAD1 (encoding R. toruloides Δ9-Fad) and their effects on LA production in R. toruloides were investigated. The function of RtFad2 was confirmed by heterologous expression in Saccharomyces cerevisiae. Overexpression of RtFAD2 significantly elevated the LA contents and titers in the wild-type strain R. toruloides DMKU3-TK16 (TK16) and in a thermotolerant derivative of TK16 (L1-1). Additionally, overexpression of RtFAD2 in R. toruloides strains also increased the lipid titer and content. Overexpression of RtFAD1 was down-regulated in the RtFAD1 and RtFAD2 co-overexpressing strains, suggesting that the elevated LA content may function as a key regulator of RtFAD1 expression to control C18 fatty-acid synthesis in R. toruloides. We characterized the function of RtFAD2 and showed that its overexpression in R. toruloides increased the lipid and LA production. These findings may assist in the rational design of metabolic engineering related to LA or polyunsaturated fatty acid production in R. toruloides.

Microbial lipids from organic wastes: Outlook and challenges

Microbial lipids have recently drawn a lot of attention as renewable sources for biochemicals production. Strong research efforts have been addressed to efficiently use organic wastes as carbon source for microbial lipids, which would definitively increase the profitability of the production process and boost a bio-based economy. This review compiles interesting traits of oleaginous microorganisms and highlights current trends on microbial- and process-oriented approaches to maximize microbial oil production from inexpensive substrates like lignocellulosic sugars, volatile fatty acids and glycerol. Furthermore, downstream processes such as cell harvesting or lipid extraction, that are decisive for the cost-effectiveness of the process, are discussed. To underpin microbial oils within the so demanded circular economy, associated challenges, recent advances and possible industrial applications that are also identified in this review.

Δ6 fatty acid desaturases in polyunsaturated fatty acid biosynthesis: insights into the evolution, function with substrate specificities and biotechnological use

Δ6 fatty acid desaturases (FADS6) have different substrate specificities that impact the ratio of omega-6/omega-3 polyunsaturated fatty acids, which are involved in regulating multiple signalling pathways associated with various diseases. For decades, FADS6 with different substrate specificities have been characterized and the functions of these crucial enzymes have been investigated, while it remains enigmatic that the substrate specificities of FADS6 from various species have a huge difference. This review summarizes the substrate specificities of FADS6 in different species and reveals the underlying relationship. Further evaluation of biochemical properties has revealed that the FADS6 prefer linoleic acid that is more hydrophilic and stable. Domain-swapping and site-directed mutagenesis have been employed to delineate the regions and sites that affect the substrate specificities of FADS6. These analyses improve our understanding of the functions of FADS6 and offer information for the discovery of novel biological resources. KEY POINTS: • Outline of the excavation and identification of Δ6 fatty acid desaturases. • Overview of methods used to determine the pivotal resides of desaturases. • Application of substrate properties to generate specific fatty acids.

Determination of allosteric and active sites responsible for catalytic activity of delta 12 fatty acid desaturase from Geotrichum candidum and Mortierella alpina by domain swapping

Cheese lacks essential fatty acids (EFAs). Delta 12 fatty acid desaturase (FADS12) is a critical enzyme required for EFA biosynthesis in fermentation of the predominant strains of cheese. Previously, we identified the FADS12 gene and characterized its function for the first time in Geotrichum candidum, a dominant strain used to manufacture soft cheese with white rind. In this study, we analyzed the molecular mechanism of FADS12 function by swapping domains from Mortierella alpina and G. candidum that had, respectively, high and low oleic acid conversion rates. The results revealed three regions that are essential to this process, including regions from the end of the second transmembrane domain to the beginning of the third transmembrane domain, from the end of the third transmembrane domain to the beginning of the fourth transmembrane domain, and from the 30-amino acid from the end of the sixth transmembrane domain to the C-terminal end region. Based on our domain swapping analyses, nine pairs of amino acids including H112, S118, H156, Q161, K301, R306, E307, A309 and S323 in MaFADS12 (K123, A129, N167, M172, T302, D307, I308, E310 and D324 in GcFADS12) were identified as having a significantly effect on FADS12 catalytic efficiency, and linoleic acid and its analogues (12,13-cyclopropenoid fatty acid) were found to inhibit the catalytic activity of FADS12 and related recombinant enzymes. Furthermore, the molecular mechanism of FADS12 inhibition was analyzed. The results revealed two allosteric domains, including one domain from the N-terminal region to the beginning of the first transmembrane domain and another from the 31^st amino acid from the end of the sixth transmembrane domain to the C terminus. Y4 and F398 amino acid residues from MaFADS12 and eight pairs of amino acids including G56, L60, L344, G10, Q13, S24, K326 and L344 in MaFADS12 (while Y66, F70, F345, F20, Y23, Y34, F327 and F345 in GcFADS12) played a pivotal role in FADS12 inhibition. Finally, we found that both allosteric and active sites were responsible for the catalytic activity of FADS12 at various temperatures, pH, and times. This study offers a solid theoretical basis to develop preconditioning methods to increase the rate at which GcFADS12 converts oleic and linoleic acids to produce higher levels of EFAs in cheese.

Overexpression of delta-12 desaturase in the yeast Schwanniomyces occidentalis enhances the production of linoleic acid

The oleaginous yeast Schwanniomyces occidentalis was previously isolated because of its excellent suitability to convert lignocellulosic hydrolysates into triacyl glycerides: it is able to use a broad range of sugars and is able to tolerate high concentrations of lignocellulosic hydrolysate inhibitors. Compared to other oleaginous yeasts S. occidentalis however produces a low content of unsaturated fatty acids. We show here that the linoleic acid content can be significantly improved by (over)expression Δ12-desaturases derived from S. occidentalis and Fusarium moniliforme. Expression was stable for the homologous expression but decreased during heterologous expression. Both homologous and heterologous expression of mCherry-Δ12-desaturase led to a 4-fold increase in linoleic acid from 0.02 g/g biomass to 0.08 g/g biomass resulting in the production of 2.23 g/L and 2.05 g/L of linoleic acid.

Arachidonic acid production by the oleaginous fungus Mortierella alpina 1S-4: A review

The filamentous fungus Mortierella alpina 1S-4 is capable of accumulating a large amount of triacylglycerol containing C20 polyunsaturated fatty acids (PUFAs). Indeed, triacylglycerol production by M. alpina 1S-4 can reach 20 g/L of culture broth, and the critical cellular signaling and structural PUFA arachidonic acid (ARA) comprises 30%–70% of the total fatty acid. The demonstrated health benefits of functional PUFAs have in turn encouraged the search for rich sources of these compounds, including fungal strains showing enhanced production of specific PUFAs. Screening for mutants and targeted gene manipulation of M. alpina 1S-4 have elucidated the functions of various enzymes involved in PUFA biosynthesis and established lines with improved PUFA productivity. In some cases, these strains have been used for indistrial-scale production of PUFAs, including ARA. In this review, we described practical ARA production through mutant breeding, functional analyses of genes encoding enzymes involved in PUFA biosynthesis, and recent advances in the production of specific PUFAs through molecular breeding of M. alpina 1S-4.