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. 2023 Jan 26:13:1046114.
doi: 10.3389/fmicb.2022.1046114. eCollection 2022.

Regulation of autophagy and lipid accumulation under phosphate limitation in Rhodotorula toruloides

Ya-Nan Wang  1   2 , Fang-Jie Liu  1 , Hong-di Liu  1 , Yue Zhang  1 , Xiang Jiao  1 , Ming-Liang Ye  1   3 , Zong-Bao Kent Zhao  1   4 , Su-Fang Zhang  1   4
Affiliations

Regulation of autophagy and lipid accumulation under phosphate limitation in Rhodotorula toruloides

Ya-Nan Wang et al. Front Microbiol. .

Abstract

Background: It is known that autophagy is essential for cell survival under stress conditions. Inorganic phosphate (Pi) is an essential nutrient for cell growth and Pi-limitation can trigger autophagy and lipid accumulation in oleaginous yeasts, yet protein (de)-phosphorylation and related signaling events in response to Pi limitation and the molecular basis linking Pi-limitation to autophagy and lipid accumulation remain elusive.

Results: Here, we compared the proteome and phosphoproteome of Rhodotorula toruloides CGMCC 2.1389 under Pi-limitation and Pi-repletion. In total, proteome analysis identified 3,556 proteins and the phosphoproteome analysis identified 1,649 phosphoproteins contained 5,659 phosphosites including 4,499 pSer, 978 pThr, and 182 pTyr. We found Pi-starvation-induced autophagy was regulated by autophagy-related proteins, but not the PHO pathway. When ATG9 was knocked down, the engineered strains produced significantly less lipids under Pi-limitation, suggesting that autophagy required Atg9 in R. toruloides and that was conducive to lipid accumulation.

Conclusion: Our results provide new insights into autophagy regulation under Pi-limitation and lipid accumulation in oleaginous yeast, which should be valuable to guide further mechanistic study of oleaginicity and genetic engineering for advanced lipid producing cell factory.

Keywords: Atg9; Rhodotorula toruloides; autophagy; lipid accumulation; phosphate limitation.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Overview of the experimental and analytical strategy.
Figure 2
Figure 2
Phosphorylation-specific motifs using the Motif-X algorithm (Schwartz and Gygi, 2005). The complete set of motifs is shown in Supplementary Table S5. (A) In total, 5,659 phosphosites (4,499 pSer, 978 pThr, and 182 pTyr) were identified. (B,C) Sequence logos for some examples of single-phosphorylation motifs where the phosphorylated residue (S or T) is centered. (B) Pro-directed motifs. (C) Acidic motifs. (D) Basic motif.
Figure 3
Figure 3
Schematic overview of the key components in autophagy regulation and the regulation of proteins in proteome. Up-regulated proteins were in red; not changed proteins were in black; not detected proteins were in blue.
Figure 4
Figure 4
RT-PCR detection of the first (1) and second (2) exon in ATG9 gene and the first exon with intron (3) to detect the gDNA. (A–C) Three ATG9 RNAi strains. (D) The wild type strain NP11. (E) There is an endogenous gene GAPDH as a reference.
Figure 5
Figure 5
The R. toruloides WT and RNAi strains cultured in the PL medium with the fluorescence microscope after LysoTracker® Green DND-26 staining.
Figure 6
Figure 6
Lipid content of R. toruloides WT and ATG9 RNAi silencing cells under phosphorus limitation conditions.
Figure 7
Figure 7
Schematic overview of the regulation of autophagy and lipid accumulation under phosphate limitation in R. toruloides. Up-regulated proteins were in red; not changed proteins were in black; not detected proteins were in blue.
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References

    1. Ballif B. A., Roux P. P., Gerber S. A., Mac Keigan J. P., Blenis J., Gygi S. P. (2005). Quantitative phosphorylation profiling of the ERK/p 90 ribosomal S6 kinase-signaling cassette and its targets, the tuberous sclerosis tumor suppressors. Proc. Natl. Acad. Sci. U. S. A. 102, 667–672. doi: 10.1073/pnas.0409143102, PMID: - DOI - PMC - PubMed
    1. Beausoleil S. A., Jedrychowski M., Schwartz D., Elias J. E., Villen J., Li J., et al. . (2004). Large-scale characterization of HeLa cell nuclear phosphoproteins. Proc. Natl. Acad. Sci. U. S. A. 101, 12130–12135. doi: 10.1073/pnas.0404720101, PMID: - DOI - PMC - PubMed
    1. Budovskaya Y. V., Stephan J. S., Reggiori F., Klionsky D. J., Herman P. K. (2004). The Ras/cAMP-dependent protein kinase signaling pathway regulates an early step of the autophagy process in Saccharomyces cerevisiae. J. Biol. Chem. 279, 20663–20671. doi: 10.1074/jbc.M400272200, PMID: - DOI - PMC - PubMed
    1. Carroll A. S., O’Shea E. K. (2002). Pho85 and signaling environmental conditions. Trends Biochem. Sci. 27, 87–93. doi: 10.1016/s0968-0004(01)02040-0, PMID: - DOI - PubMed
    1. Chang Y. Y., Neufeld T. P. (2009). An Atg1/Atg13 complex with multiple roles in TOR-mediated autophagy regulation. Mol. Biol. Cell 20, 2004–2014. doi: 10.1091/mbc.E08-12-1250, PMID: - DOI - PMC - PubMed