Systematic analysis of the lysine acetylome reveals diverse functions of lysine acetylation in the oleaginous yeast Yarrowia lipolytica

Abstract

Lysine acetylation of proteins, a major post-translational modification, plays a critical regulatory role in almost every aspects in both eukaryotes and prokaryotes. Yarrowia lipolytica, an oleaginous yeast, is considered as a model for bio-oil production due to its ability to accumulate a large amount of lipids. However, the function of lysine acetylation in this organism is elusive. Here, we performed a global acetylproteome analysis of Y. lipolytica ACA-DC 50109. In total, 3163 lysine acetylation sites were identified in 1428 proteins, which account for 22.1% of the total proteins in the cell. Fifteen conserved acetylation motifs were detected. The acetylated proteins participate in a wide variety of biological processes. Notably, a total of 65 enzymes involved in lipid biosynthesis were found to be acetylated. The acetylation sites are distributed in almost every type of conserved domains in the multi-enzymatic complexes of fatty acid synthetases. The provided dataset probably illuminates the crucial role of reversible acetylation in oleaginous microorganisms, and serves as an important resource for exploring the physiological role of lysine acetylation in eukaryotes.

Keywords: Acetylproteome; Lipid biosynthesis; Lysine acetylation; Oleaginous yeast; Yarrowia lipolytica.

Fig. 1

Cell mass, oil content and lipid particles of the yeast strain ACA-DC 50109. a Biomass of the yeast strain. Data are given as mean ± SD, n = 3. b Oil content of the yeast strain. Data are given as mean ± SD, n = 3. c Lipid particles of the yeast strain were taken under fluorescent microscope. d Lipid particles of the yeast strain were taken under phase microscope

Fig. 2

Proteome-wide identification of lysine acetylation sites in Y. lipopytica. a Overview of experimental procedures used in this study. b Mass error distribution of all identified peptides. c Peptide length distribution

Fig. 3

An overview of lysine acetylation in Y. lipolytica as analyzed by SDS-PAGE and Western blotting. a 100 μg of total protein was separated by SDS-PAGE (1) and the acetylated proteins were detected with pan anti-acetyl lysine antibody (2). b The Western blotting signal with anti-histone H2A.Z antibody and anti-H2A.Z (acetyl K7) antibody. c MS/MS spectra of acetylpeptide with an acetylation site at K7 of histone H2A.Z (Q6C341)

Fig. 4

Distribution and motif analysis of lysine acetylation sites. a Pie chart illustrating the number and percentage of lysine acetylation sites per protein. b Heat map of the amino acid compositions around the lysine acetylation sites showing the frequency of different types of amino acids surrounding this residue. c Sequence probability logos of significantly enriched acetylation site motifs for ±10 amino acids around the lysine acetylation sites. d Number of identified peptides contained in each conserved motif

Fig. 5

Secondary structure analysis of acetylated proteins. a Probabilities of lysine acetylation in the structures of alpha-helix, beta-strand and coil. b Predicted surface accessibility of acetylation sites

Fig. 6

Pie charts showing the functional classification of acetylated proteins in Y. lipolytica. a Classification of the acetylated proteins based on biological process. b Classification of the acetylated proteins based on molecular function. c Classification of the acetylated proteins based on cellular component. d Subcellular localization of the acetylated proteins

Fig. 7

Enrichment analysis of the acetylated proteins in Y. lipolytica. a GO-based enrichment analysis in terms of molecular function, cell component and biological process. b KEGG pathway-based enrichment analysis of the acetylated proteins. c Domain-based enrichment analysis of the acetylated proteins

Fig. 8

Working scheme of lysine acetylated enzymes involved in central and triacylglycerols (TAGs) metabolism pathways in oleaginous yeasts. a Reconstruction of central and TAGs metabolism scheme from the KEGG pathway. Identified acetylated enzymes were highlighted in red. Abbreviations for the components, enzyme symbols and annotations are included in Additional file 8: Tables S7. b An overview of acetylation sites in fatty acid synthetase (FAS1). c An overview of acetylation sites in fatty acid synthetase (FAS2)

Fig. 9

Working scheme of lysine acetylation events involved in oxidative phosphorylation. Identified acetylated proteins were highlighted in red

Fig. 10

Interaction networks of the acetylated proteins in oleaginous yeast. Interaction networks of all acetylated proteins with the top five clusters of proteins associated with ribosome (red), aminoacyl-tRNA biosynthesis (blue), RNA transport (light blue), ribosome biogenesis in eukaryotes (light green) and oxidative phosphorylation (green)