Erratum for Ryu et al., Activating and Elucidating Metabolism of Complex Sugars in Yarrowia lipolytica

Ryu, Seunghyun; Hipp, Julie; Trinh, Cong T.

doi:10.1128/aem.00457-16

Cited by 3 publications

(4 citation statements)

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“…Short-term adaptation improved cell growth on both DP oil and n-hexadecane (a model hydrocarbon substrate) ( Fig. 2C and D ), suggesting hydrocarbon metabolism was cryptic and required activation as previously observed in both hydrophobic ( 75 ) and hydrophilic ( 76 ) substrate metabolism. Y. lipolytica grew more robustly on n-hexadecane than DP oil because utilizing DP oil required expression of more specialized enzymes to assimilate the mixture of complex hydrocarbons.…”

Section: Discussionsupporting

confidence: 74%

Proteomes reveal metabolic capabilities of Yarrowia lipolytica for biological upcycling of polyethylene into high-value chemicals

Walker,

Mortensen,

Poudel

et al. 2023

mSystems

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Polyolefins derived from plastic wastes are recalcitrant for biological upcycling. However, chemical depolymerization of polyolefins can generate depolymerized plastic (DP) oil, comprising of a complex mixture of saturated, unsaturated, even, and odd hydrocarbons suitable for biological conversion. While DP oil contains a rich carbon and energy source, it is inhibitory to cells. Understanding and harnessing robust metabolic capabilities of microorganisms to upcycle the hydrocarbons in DP oil, both naturally and unnaturally occurring, into high-value chemicals are limited. Here, we discovered that an oleaginous yeast, Yarrowia lipolytica, undergoing short-term adaptation to DP oil robustly utilized a wide range of hydrocarbons for cell growth and production of citric acid and neutral lipids. When growing on hydrocarbons, Y. lipolytica partitioned into planktonic and oil-bound cells with each exhibiting distinct proteomes and amino acid distributions invested in establishing these proteomes. Significant proteome reallocation toward energy and lipid metabolism, belonging to 2 of the 23 Eukaryotic Orthologous Groups classes C and I, enabled robust growth of Y. lipolytica on hydrocarbons, with n-hexadecane as the preferential substrate. This investment was even higher for growth on DP oil where classes C and I were ranked one and two, respectively, and many associated proteins and pathways were expressed and upregulated including the hydrocarbon degradation pathway, Krebs cycle, glyoxylate shunt and, unexpectedly, propionate metabolism. However, a reduction in proteome allocation for protein biosynthesis, at the expense of the observed increase toward energy and lipid metabolisms, might have caused the inhibitory effect of DP oil on cell growth. IMPORTANCE Sustainable processes for biological upcycling of plastic wastes in a circular bioeconomy are needed to promote decarbonization and reduce environmental pollution due to increased plastic consumption, incineration, and landfill storage. Strain characterization and proteomic analysis revealed the robust metabolic capabilities of Yarrowia lipolytica to upcycle polyethylene into high-value chemicals. Significant proteome reallocation toward energy and lipid metabolisms was required for robust growth on hydrocarbons with n-hexadecane as the preferential substrate. However, an apparent over-investment in these same categories to utilize complex depolymerized plastic (DP) oil came at the expense of protein biosynthesis, limiting cell growth. Taken together, this study elucidates how Y. lipolytica activates its metabolism to utilize DP oil and establishes Y. lipolytica as a promising host for the upcycling of plastic wastes.

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Section: Discussionsupporting

confidence: 74%

Proteomes reveal metabolic capabilities of Yarrowia lipolytica for biological upcycling of polyethylene into high-value chemicals

Walker,

Mortensen,

Poudel

et al. 2023

mSystems

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“…Genome mining suggested that a complete xylose pathway was present in Y. lipolytica ; however, growth on xylose was not observed in three studies ( Ledesma-Amaro and Nicaud, 2016b ; Rodriguez et al, 2016 ), and extremely weak growth was observed in a fourth study after a long period of adaptation ( Ryu et al, 2016b ). In these weakly growing strains, mRNA expression levels measured with quantitative polymerase chain reaction (qPCR) indicated inducibility of ylXDH gene ( YALI0E12463 ), but overall weak expression ( Ryu et al, 2016b ). This observation led to their hypothesis that the ylXDH expression was limiting.…”

Section: Pentose Substratesmentioning

confidence: 98%

“…This observation led to their hypothesis that the ylXDH expression was limiting. Overexpression of ylXDH resulted in a significant improvement in growth on xylose after adaptation ( Ryu et al, 2016b ).…”

Section: Pentose Substratesmentioning

confidence: 99%

“…Co-utilization studies with glucose and xylose suggest that glucose transporters may be non-specifically transporting xylose across the yeast cell membrane ( Sedlak and Ho, 2004 ). Using known xylose transporters as queries, 22 endogenous genes have been linked to xylose transport in Y. lipolytica through a BLAST analysis ( Ryu et al, 2016b ). Analysis of the mRNA expression showed that two of these genes, YALI0D01111 and YALI0C04730, were upregulated nearly 10-fold in xylose media ( Ryu et al, 2016a ).…”

Section: Pentose Substratesmentioning

confidence: 99%

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Alternative Substrate Metabolism in Yarrowia lipolytica

et al. 2018

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Recent advances in genetic engineering capabilities have enabled the development of oleochemical producing strains of Yarrowia lipolytica. Much of the metabolic engineering effort has focused on pathway engineering of the product using glucose as the feedstock; however, alternative substrates, including various other hexose and pentose sugars, glycerol, lipids, acetate, and less-refined carbon feedstocks, have not received the same attention. In this review, we discuss recent work leading to better utilization of alternative substrates. This review aims to provide a comprehensive understanding of the current state of knowledge for alternative substrate utilization, suggest potential pathways identified through homology in the absence of prior characterization, discuss recent work that either identifies, endogenous or cryptic metabolism, and describe metabolic engineering to improve alternative substrate utilization. Finally, we describe the critical questions and challenges that remain for engineering Y. lipolytica for better alternative substrate utilization.

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Application of adaptive laboratory evolution for Yarrowia lipolytica: A comprehensive review

Chen,

Li,

Chen

et al. 2024

Bioresource Technology

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Erratum for Ryu et al., Activating and Elucidating Metabolism of Complex Sugars in Yarrowia lipolytica

Cited by 3 publications

References 0 publications

Proteomes reveal metabolic capabilities of Yarrowia lipolytica for biological upcycling of polyethylene into high-value chemicals

Proteomes reveal metabolic capabilities of Yarrowia lipolytica for biological upcycling of polyethylene into high-value chemicals

Alternative Substrate Metabolism in Yarrowia lipolytica

Application of adaptive laboratory evolution for Yarrowia lipolytica: A comprehensive review

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