Identification of mutation sites on Δ5 desaturase genes from Mortierella alpina 1S-4 mutants

Catalytic mechanisms underlying fungal fatty acid desaturases activities

Polyunsaturated fatty acids (PUFAs) have beneficial roles in a variety of human pathologies and disorders. Owing to the limited source of PUFAs in animals and plants, microorganisms, especially fungi, have become a new source of PUFAs. In fungi, fatty acid desaturases (F-FADS) are the main enzymes that convert saturated fatty acids (SFAs) into PUFAs. Their catalytic activities and substrate specificities, which are directly dependent on the structure of the FADS proteins, determine their efficiency to convert SFAs to PUFAs. Catalytic mechanisms underlying F-FADS activities can be determined from the findings of the relationship between their structure and function. In this review, the advances made in the past decade in terms of catalytic activities and substrate specificities of the fungal FADS cluster are summarized. The relationship between the key domain(s) and site(s) in F-FADS proteins and their catalytic activity is highlighted, and the FADS cluster is analyzed phylogenetically. In addition, subcellular localization of F-FADS is discussed. Finally, we provide prospective crystal structures of F-FADSs. The findings may provide a reference for the resolution of the crystal structures of F-FADS proteins and facilitate the increase in fungal PUFA production for human health.

Lipid metabolism research in oleaginous fungus Mortierella alpina: Current progress and future prospects

The oleaginous fungus Mortierella alpina has distinct advantages in long-chain PUFAs production, and it is the only source for dietary arachidonic acid (ARA) certificated by FDA and European Commission. This review provides an overall introduction to M. alpina, including its major research methods, key factors governing lipid biosynthesis, metabolic engineering and omics studies. Currently, the research interests in M. alpina focus on improving lipid yield and fatty acid desaturation degree by enhancing fatty acid precursors and the reducing power NADPH, and genetic manipulation on PUFAs synthetic pathways is carried to optimise fatty acid composition. Besides, multi-omics studies have been applied to elucidate the global regulatory mechanism of lipogenesis in M. alpina. However, research challenges towards achieving a lipid cell factory lie in strain breeding and cost control due to the coenocytic mycelium, long fermentation period and insufficient conversion rate from carbon to lipid. We also proposed future research goals based on a multilevel regulating strategy: obtaining ideal chassis by directional evolution and high-throughput screening; rewiring central carbon metabolism and inhibiting competitive pathways by multi-gene manipulation system to enhance carbon to lipid conversion rate; optimisation of protein function based on post-translational modification; application of dynamic fermentation strategies suitable for different fermentation phases. By reviewing the comprehensive research progress of this oleaginous fungus, we aim to further comprehend the fungal lipid metabolism and provide reference information and guidelines for the exploration of microbial oils from the perspectives of fundamental research to industrial application.

Reconstruction and analysis of a genome-scale metabolic model of the oleaginous fungus Mortierella alpina

Background

Mortierella alpina is an oleaginous fungus used in the industrial scale production of arachidonic acid (ARA). In order to investigate the metabolic characteristics at a systems level and to explore potential strategies for enhanced lipid production, a genome-scale metabolic model of M. alpina was reconstructed.

Results

This model included 1106 genes, 1854 reactions and 1732 metabolites. On minimal growth medium, 86 genes were identified as essential, whereas 49 essential genes were identified on yeast extract medium. A series of sequential desaturase and elongase catalysed steps are involved in the synthesis of polyunsaturated fatty acids (PUFAs) from acetyl-CoA precursors, with concomitant NADPH consumption, and these steps were investigated in this study. Oxygen is known to affect the degree of unsaturation of PUFAs, and robustness analysis determined that an oxygen uptake rate of 2.0 mmol gDW⁻¹ h⁻¹ was optimal for ARA accumulation. The flux of 53 reactions involving NADPH was significantly altered at different ARA levels. Of these, malic enzyme (ME) was confirmed as a key component in ARA production and NADPH generation. When using minimization of metabolic adjustment, a knock-out of ME led to a 38.28% decrease in ARA production.

Conclusions

The simulation results confirmed the model as a useful tool for future research on the metabolism of PUFAs.

Electronic supplementary material

The online version of this article (doi:10.1186/s12918-014-0137-8) contains supplementary material, which is available to authorized users.

Identification of the substrate recognition region in the Δ⁶-fatty acid and Δ⁸-sphingolipid desaturase by fusion mutagenesis

Δ⁸-sphingolipid desaturase and Δ⁶-fatty acid desaturase share high protein sequence identity. Thus, it has been hypothesized that Δ⁶-fatty acid desaturase is derived from Δ⁸-sphingolipid desaturase; however, there is no direct proof. The substrate recognition regions of Δ⁶-fatty acid desaturase and Δ⁸-sphingolipid desaturase, which aid in understanding the evolution of these two enzymes, have not been reported. A blackcurrant Δ⁶-fatty acid desaturase and a Δ⁸-sphingolipid desaturase gene, RnD6C and RnD8A, respectively, share more than 80 % identity in their coding protein sequences. In this study, a set of fusion genes of RnD6C and RnD8A were constructed and expressed in yeast. The Δ⁶- and Δ⁸-desaturase activities of the fusion proteins were characterized. Our results indicated that (1) the exchange of the C-terminal 172 amino acid residues can lead to a significant decrease in both desaturase activities; (2) amino acid residues 114-174, 206-257, and 258-276 played important roles in Δ⁶-substrate recognition, and the last two regions were crucial for Δ⁸-substrate recognition; and (3) amino acid residues 114-276 of Δ⁶-fatty acid desaturase contained the substrate recognition site(s) responsible for discrimination between ceramide (a substrate of Δ⁸-sphingolipid desaturase) and acyl-PC (a substrate of Δ⁶-fatty acid desaturase). Substituting the amino acid residues 114-276 of RnD8A with those of RnD6C resulted in a gain of Δ⁶-desaturase activity in the fusion protein but a loss in Δ⁸-sphingolipid desaturase activity. In conclusion, several regions important for the substrate recognition of Δ⁸-sphingolipid desaturase and Δ⁶-fatty acid desaturase were identified, which provide clues in understanding the relationship between the structure and function in desaturases.

Identification of mutation sites on Delta12 desaturase genes from Mortierella alpina 1S-4 mutants

The mutation sites on the Delta12 desaturase gene in Mortierella alpina Delta12 desaturase-defective mutants SR88, TM912, and Mut48 accumulating Mead acid were identified. Each mutation resulted in an amino acid replacement (H116Y and P166L) in the Delta12 desaturase gene from SR88 and Mut48, respectively.

Identification of mutation sites on omega3 desaturase genes from Mortierella alpina 1S-4 mutants

The mutation sites on omega3 desaturase genes in two omega3 desaturase-defective mutants derived from arachidonic acid-producing Mortierella alpina 1S-4 were identified. The mutations each resulted in an amino acid replacement (W232Stop or W386Stop) which caused a lack of omega3 desaturase activity in these mutants.

Identification and characterization of a novel yeast omega3-fatty acid desaturase acting on long-chain n-6 fatty acid substrates from Pichia pastoris

A cDNA sequence putatively encoding a omega(3)-fatty acid desaturase gene was isolated from methylotrophic yeast Pichia pastoris GS115. The deduced amino acid sequence of this cloned cDNA showed high identity to known fungal omega(3)-fatty acid desaturases. Functional identification of this gene heterologously in Saccharomyces cerevisiae strain INVScl indicated that the deduced amino acid sequence exhibited omega(3)-fatty acid desaturase activity. The newly identified omega(3)-fatty acid desaturase, named Pp-FAD3, is novel because it showed broad n-6 fatty acid substrate specificity by its ability to convert all the 18-carbon and 20-carbon n-6 substrates examined to the corresponding n-3 fatty acids, with an approximately equivalent high conversion rate. Pp-FAD3 is the first known yeast omega(3)-fatty acid desaturase to act on long-chain n-6 fatty acid substrates. Heterologous expression of the newly identified omega(3) desaturase in different hosts will be an alternative method to increase the flow of n-6 fatty acid intermediates into their n-3 derivatives.