Comparative Genomics of Mortierellaceae Provides Insights into Lipid Metabolism: Two Novel Types of Fatty Acid Synthase

Abstract

Fungal species in the family Mortierellaceae are important for their remarkable capability to synthesize large amounts of polyunsaturated fatty acids, especially arachidonic acid (ARA). Although many genomes have been published, the quality of these data is not satisfactory, resulting in an incomplete understanding of the lipid pathway in Mortierellaceae. We provide herein two novel and high-quality genomes with 55.32% of syntenic gene pairs for Mortierella alpina CGMCC 20262 and M. schmuckeri CGMCC 20261, spanning 28 scaffolds of 40.22 Mb and 25 scaffolds of 49.24 Mb, respectively. The relative smaller genome for the former is due to fewer protein-coding gene models (11,761 vs. 13,051). The former yields 45.57% of ARA in total fatty acids, while the latter 6.95%. The accumulation of ARA is speculated to be associated with delta-5 desaturase (Delta5) and elongation of very long chain fatty acids protein 3 (ELOVL3). A further genomic comparison of 19 strains in 10 species in three genera in the Mortierellaceae reveals three types of fatty acid synthase (FAS), two of which are new to science. The most common type I exists in 16 strains of eight species of three genera, and was discovered previously and consists of a single unit with eight active sites. The newly revealed type II exists only in M. antarctica KOD 1030 where the unit is separated into two subunits α and β comprised of three and five active sites, respectively. Another newly revealed type III exists in M. alpina AD071 and Dissophora globulifera REB-010B, similar to type II but different in having one more acyl carrier protein domain in the α subunit. This study provides novel insights into the enzymes related to the lipid metabolism, especially the ARA-related Delta5, ELOVL3, and FAS, laying a foundation for genetic engineering of Mortierellaceae to modulate yield in polyunsaturated fatty acids.

Keywords: Mucoromyceta; arachidonic acid; microbial lipids; phylogenomics; polyunsaturated fatty acids.

Figure 1

Lipids of Mortierella alpina CGMCC 20262 and M. schmuckeri CGMCC 20261. (a) Lipid characters: dry cell weight (DCW, g/L), total lipid weight (TLW, g/L), and total lipid content (TLC); (b) fatty acid profiles: others include C10:0, C12:0, C15:0, C20:0, and C20:1.

Figure 2

A Maximum Likelihood phylogenomic tree illustrating the placements of Mortierella alpina CGMCC 20262 and M. schmuckeri CGMCC 20261 based on 192 clusters of orthologous proteins. New genomes obtained in this study are in bold. Maximum Likelihood bootstrap values (MLBV ≥ 50%) are indicated along branches. A scale bar in the upper left indicates substitutions per site.

Figure 3

Genomic synteny of Mortierella alpina CGMCC 20262 and M. schmuckeri CGMCC 20261 based on protein-coding gene models of the 10 largest scaffolds.

Figure 4

The polyunsaturated fatty acid synthesis mechanism in Mortierellaceae. EMP: Glycolytic pathway; TCA cycle: Tricarboxylic acid cycle; ME: Malate dehydrogenase; NADPH: Nicotinamide adenine dinucleotide phosphate; ACC: Acetyl-CoA carboxylase; ACL: ATP citrate (pro-S)-lyase; FAS: Fatty acid synthase; ELO2: Fatty acid elongase 2; Delta5: delta-5 desaturase; Delta6: delta-6 desaturase; Delta9: delta-9 desaturase; Delta12: delta-12 desaturase; ELOVL: Elongation of very long chain fatty acids protein.

Figure 5

Fatty acid synthases in Mortierellaceae. AT: Acyl transferase domain; ER: Enoyl reductase domain; DH: dehydratase; MPT: Malonyl CoA-acyl carrier protein transacylase; ACP: Acyl carrier protein domain; KR: β-ketoacyl reductase; KS: β-ketoacyl synthase; PPT: Phosphopantetheinyl transferase.

Figure 6

A Maximum Likelihood phylogenetic tree of the gene encoding delta-5 desaturase in the family Mortierellaceae. A scale bar in the upper left indicates substitutions per site.