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Ran Y, Yang Q, Zeng J, Li F, Cao Y, Xu Q, Qiao D, Xu H, Cao Y. Potential xylose transporters regulated by CreA improved lipid yield and furfural tolerance in oleaginous yeast Saitozyma podzolica zwy-2-3. BIORESOURCE TECHNOLOGY 2023; 386:129413. [PMID: 37390935 DOI: 10.1016/j.biortech.2023.129413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/02/2023]
Abstract
Lignocellulose's hydrolysate, a significant renewable source, contains xylose and furfural, making it challenging for industrial production of oleaginous yeast. On xylose fermentation with furfural treatment, OE::DN7263 and OE::DN7661 increased lipid yield and furfural tolerance versus WT, while, which of OE::CreA were decreased owing to CreA regulating DN7263 and DN7661 negatively. OE::CreA generated reactive oxygen species (ROS) causing oxidative damage. OE::DN7263, OE::DN7661, and ΔCreA reduced furfural via NADH; while ΔCreA produced less ROS and OE::DN7263, and OE::DN7661 scavenged ROS quickly, minimizing oxidative damage. Overall, CreA knockout increased DN7263 and DN7661 expression to facilitate xylose assimilation, enhancing NADH generation and ROS clearance. Finally, with mixed sugar fermentation, ΔCreA and OE::DN7263's biomass and lipid yield rose without furfural addition, while that of ΔCreA remained higher than WT after furfural treatment. These findings revealed how oleaginous yeast zwy-2-3 resisted furfural stress and indicated ΔCreA and OE::DN7263 might develop into robust industrial chassis strains.
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Affiliation(s)
- Yulu Ran
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, Sichuan Province 610065, PR China
| | - Qingzhuoma Yang
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, Sichuan Province 610065, PR China
| | - Jie Zeng
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, Sichuan Province 610065, PR China
| | - Fazhi Li
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, Sichuan Province 610065, PR China
| | - Yu Cao
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, Sichuan Province 610065, PR China
| | - Qingrui Xu
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, Sichuan Province 610065, PR China
| | - Dairong Qiao
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, Sichuan Province 610065, PR China
| | - Hui Xu
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, Sichuan Province 610065, PR China.
| | - Yi Cao
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, Sichuan Province 610065, PR China.
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Bilbao A, Munoz N, Kim J, Orton DJ, Gao Y, Poorey K, Pomraning KR, Weitz K, Burnet M, Nicora CD, Wilton R, Deng S, Dai Z, Oksen E, Gee A, Fasani RA, Tsalenko A, Tanjore D, Gardner J, Smith RD, Michener JK, Gladden JM, Baker ES, Petzold CJ, Kim YM, Apffel A, Magnuson JK, Burnum-Johnson KE. PeakDecoder enables machine learning-based metabolite annotation and accurate profiling in multidimensional mass spectrometry measurements. Nat Commun 2023; 14:2461. [PMID: 37117207 PMCID: PMC10147702 DOI: 10.1038/s41467-023-37031-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 02/24/2023] [Indexed: 04/30/2023] Open
Abstract
Multidimensional measurements using state-of-the-art separations and mass spectrometry provide advantages in untargeted metabolomics analyses for studying biological and environmental bio-chemical processes. However, the lack of rapid analytical methods and robust algorithms for these heterogeneous data has limited its application. Here, we develop and evaluate a sensitive and high-throughput analytical and computational workflow to enable accurate metabolite profiling. Our workflow combines liquid chromatography, ion mobility spectrometry and data-independent acquisition mass spectrometry with PeakDecoder, a machine learning-based algorithm that learns to distinguish true co-elution and co-mobility from raw data and calculates metabolite identification error rates. We apply PeakDecoder for metabolite profiling of various engineered strains of Aspergillus pseudoterreus, Aspergillus niger, Pseudomonas putida and Rhodosporidium toruloides. Results, validated manually and against selected reaction monitoring and gas-chromatography platforms, show that 2683 features could be confidently annotated and quantified across 116 microbial sample runs using a library built from 64 standards.
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Affiliation(s)
- Aivett Bilbao
- Pacific Northwest National Laboratory, Richland, WA, USA.
- US Department of Energy, Agile BioFoundry, Emeryville, CA, USA.
| | - Nathalie Munoz
- Pacific Northwest National Laboratory, Richland, WA, USA
- US Department of Energy, Agile BioFoundry, Emeryville, CA, USA
| | - Joonhoon Kim
- Pacific Northwest National Laboratory, Richland, WA, USA
- US Department of Energy, Agile BioFoundry, Emeryville, CA, USA
| | - Daniel J Orton
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Yuqian Gao
- Pacific Northwest National Laboratory, Richland, WA, USA
- US Department of Energy, Agile BioFoundry, Emeryville, CA, USA
| | | | - Kyle R Pomraning
- Pacific Northwest National Laboratory, Richland, WA, USA
- US Department of Energy, Agile BioFoundry, Emeryville, CA, USA
| | - Karl Weitz
- Pacific Northwest National Laboratory, Richland, WA, USA
| | - Meagan Burnet
- Pacific Northwest National Laboratory, Richland, WA, USA
| | | | - Rosemarie Wilton
- US Department of Energy, Agile BioFoundry, Emeryville, CA, USA
- Argonne National Laboratory, Lemont, IL, USA
| | - Shuang Deng
- Pacific Northwest National Laboratory, Richland, WA, USA
- US Department of Energy, Agile BioFoundry, Emeryville, CA, USA
| | - Ziyu Dai
- Pacific Northwest National Laboratory, Richland, WA, USA
- US Department of Energy, Agile BioFoundry, Emeryville, CA, USA
| | - Ethan Oksen
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Aaron Gee
- Agilent Research Laboratories, Agilent Technologies, Santa Clara, CA, USA
| | - Rick A Fasani
- Agilent Research Laboratories, Agilent Technologies, Santa Clara, CA, USA
| | - Anya Tsalenko
- Agilent Research Laboratories, Agilent Technologies, Santa Clara, CA, USA
| | - Deepti Tanjore
- US Department of Energy, Agile BioFoundry, Emeryville, CA, USA
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - James Gardner
- US Department of Energy, Agile BioFoundry, Emeryville, CA, USA
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Joshua K Michener
- US Department of Energy, Agile BioFoundry, Emeryville, CA, USA
- Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - John M Gladden
- US Department of Energy, Agile BioFoundry, Emeryville, CA, USA
- Sandia National Laboratory, Livermore, CA, USA
| | - Erin S Baker
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA
| | - Christopher J Petzold
- US Department of Energy, Agile BioFoundry, Emeryville, CA, USA
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Young-Mo Kim
- Pacific Northwest National Laboratory, Richland, WA, USA
- US Department of Energy, Agile BioFoundry, Emeryville, CA, USA
| | - Alex Apffel
- Agilent Research Laboratories, Agilent Technologies, Santa Clara, CA, USA
| | - Jon K Magnuson
- Pacific Northwest National Laboratory, Richland, WA, USA
- US Department of Energy, Agile BioFoundry, Emeryville, CA, USA
| | - Kristin E Burnum-Johnson
- Pacific Northwest National Laboratory, Richland, WA, USA.
- US Department of Energy, Agile BioFoundry, Emeryville, CA, USA.
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Liang S, Zhang Y, Lyu L, Wang S, Zhao ZK. Secretory expression of β-1,3-glucomannanase in the oleaginous yeast Rhodosporidium toruloides for improved lipid extraction. BIORESOUR BIOPROCESS 2023; 10:16. [PMID: 38647878 PMCID: PMC10991151 DOI: 10.1186/s40643-023-00639-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 02/26/2023] [Indexed: 03/05/2023] Open
Abstract
Lipids produced by oleaginous yeasts are considered as sustainable sources for the production of biofuels and oleochemicals. The red yeast Rhodosporidium toruloides can accumulate lipids to over 70% of its dry cell mass. To facilitate lipid extraction, a recombinant β-1,3-glucomannanase, MAN5C, has been applied to partially breakdown R. toruloides cell wall. In this study, R. toruloides NP11 was engineered for secretory expression of MAN5C to simplify the lipid extraction process. Specifically, a cassette contained a codon-optimized gene MAN5C was integrated into the genome of R. toruloides by Agrobacterium-mediated transformation. The engineered strain NP11-MAN5C was found with proper expression and secretion of active MAN5C, yet no notable compromise in terms of cell growth and lipid production. When NP11-MAN5C cell cultures were extracted with ethyl acetate without any pretreatment, 20% of total lipids were recovered, 4.3-fold higher than that of the parental strain NP11. When the cells were heat-treated followed by extraction with ethyl acetate in the presence of the culture broth supernatants, up to 93% of total lipids were recovered, confirming beneficial effects of MAN5C produced in situ. This study provides a new strategy to engineer oleaginous yeasts for more viable lipid extraction and down-stream processes.
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Affiliation(s)
- Shiyu Liang
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Road, Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yue Zhang
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Road, Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liting Lyu
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Road, Dalian, 116023, China
| | - Shuang Wang
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Road, Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zongbao K Zhao
- Laboratory of Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Road, Dalian, 116023, China.
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, CAS, Dalian, 116023, China.
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4
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Liu GL, Bu XY, Chen C, Fu C, Chi Z, Kosugi A, Cui Q, Chi ZM, Liu YJ. Bioconversion of non-food corn biomass to polyol esters of fatty acid and single-cell oils. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:9. [PMID: 36650607 PMCID: PMC9844004 DOI: 10.1186/s13068-023-02260-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 01/05/2023] [Indexed: 01/18/2023]
Abstract
BACKGROUND Lignocellulose is a valuable carbon source for the production of biofuels and biochemicals, thus having the potential to substitute fossil resources. Consolidated bio-saccharification (CBS) is a whole-cell-based catalytic technology previously developed to produce fermentable sugars from lignocellulosic agricultural wastes. The deep-sea yeast strain Rhodotorula paludigena P4R5 can produce extracellular polyol esters of fatty acids (PEFA) and intracellular single-cell oils (SCO) simultaneously. Therefore, the integration of CBS and P4R5 fermentation processes would achieve high-value-added conversion of lignocellulosic biomass. RESULTS The strain P4R5 could co-utilize glucose and xylose, the main monosaccharides from lignocellulose, and also use fructose and arabinose for PEFA and SCO production at high levels. By regulating the sugar metabolism pathways for different monosaccharides, the strain could produce PEFA with a single type of polyol head. The potential use of PEFA as functional micelles was also determined. Most importantly, when sugar-rich CBS hydrolysates derived from corn stover or corncob residues were used to replace grain-derived pure sugars for P4R5 fermentation, similar PEFA and SCO productions were obtained, indicating the robust conversion of non-food corn plant wastes to high-value-added glycolipids and lipids. Since the produced PEFA could be easily collected from the culture via short-time standing, we further developed a semi-continuous process for PEFA production from corncob residue-derived CBS hydrolysate, and the PEFA titer and productivity were enhanced up to 41.1 g/L and 8.22 g/L/day, respectively. CONCLUSIONS Here, we integrated the CBS process and the P4R5 fermentation for the robust production of high-value-added PEFA and SCO from non-food corn plant wastes. Therefore, this study suggests a feasible way for lignocellulosic agro-waste utilization and the potential application of P4R5 in industrial PEFA production.
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Affiliation(s)
- Guang-Lei Liu
- grid.4422.00000 0001 2152 3263College of Marine Life Sciences, Ocean University of China, Qingdao, 266101 People’s Republic of China ,grid.484590.40000 0004 5998 3072Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266101 China
| | - Xian-Ying Bu
- grid.4422.00000 0001 2152 3263College of Marine Life Sciences, Ocean University of China, Qingdao, 266101 People’s Republic of China
| | - Chaoyang Chen
- grid.9227.e0000000119573309CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China ,Shandong Energy Institute, Qingdao, China ,Qingdao New Energy Shandong Laboratory, Qingdao, China ,grid.410752.5Dalian National Laboratory for Clean Energy, Qingdao, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Chunxiang Fu
- grid.9227.e0000000119573309CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China ,Shandong Energy Institute, Qingdao, China ,Qingdao New Energy Shandong Laboratory, Qingdao, China ,grid.410752.5Dalian National Laboratory for Clean Energy, Qingdao, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Zhe Chi
- grid.4422.00000 0001 2152 3263College of Marine Life Sciences, Ocean University of China, Qingdao, 266101 People’s Republic of China ,grid.484590.40000 0004 5998 3072Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266101 China
| | - Akihiko Kosugi
- grid.452611.50000 0001 2107 8171Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki Japan
| | - Qiu Cui
- grid.9227.e0000000119573309CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China ,Shandong Energy Institute, Qingdao, China ,Qingdao New Energy Shandong Laboratory, Qingdao, China ,grid.410752.5Dalian National Laboratory for Clean Energy, Qingdao, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Zhen-Ming Chi
- grid.4422.00000 0001 2152 3263College of Marine Life Sciences, Ocean University of China, Qingdao, 266101 People’s Republic of China ,grid.484590.40000 0004 5998 3072Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, 266101 China
| | - Ya-Jun Liu
- grid.9227.e0000000119573309CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China ,Shandong Energy Institute, Qingdao, China ,Qingdao New Energy Shandong Laboratory, Qingdao, China ,grid.410752.5Dalian National Laboratory for Clean Energy, Qingdao, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
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Cao M, Tran VG, Qin J, Olson A, Mishra S, Schultz JC, Huang C, Xie D, Zhao H. Metabolic engineering of oleaginous yeast Rhodotorula toruloides for overproduction of triacetic acid lactone. Biotechnol Bioeng 2022; 119:2529-2540. [PMID: 35701887 PMCID: PMC9540541 DOI: 10.1002/bit.28159] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/16/2022] [Accepted: 06/12/2022] [Indexed: 12/19/2022]
Abstract
The plant‐sourced polyketide triacetic acid lactone (TAL) has been recognized as a promising platform chemical for the biorefinery industry. However, its practical application was rather limited due to low natural abundance and inefficient cell factories for biosynthesis. Here, we report the metabolic engineering of oleaginous yeast Rhodotorula toruloides for TAL overproduction. We first introduced a 2‐pyrone synthase gene from Gerbera hybrida (GhPS) into R. toruloides and investigated the effects of different carbon sources on TAL production. We then systematically employed a variety of metabolic engineering strategies to increase the flux of acetyl‐CoA by enhancing its biosynthetic pathways and disrupting its competing pathways. We found that overexpression of ATP‐citrate lyase (ACL1) improved TAL production by 45% compared to the GhPS overexpressing strain, and additional overexpression of acetyl‐CoA carboxylase (ACC1) further increased TAL production by 29%. Finally, we characterized the resulting strain I12‐ACL1‐ACC1 using fed‐batch bioreactor fermentation in glucose or oilcane juice medium with acetate supplementation and achieved a titer of 28 or 23 g/L TAL, respectively. This study demonstrates that R. toruloides is a promising host for the production of TAL and other acetyl‐CoA‐derived polyketides from low‐cost carbon sources.
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Affiliation(s)
- Mingfeng Cao
- Department of Chemical and Biomolecular Engineering, US Department of Energy Center for Bioenergy and Bioproducts Innovation (CABBI), Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Vinh G Tran
- Department of Chemical and Biomolecular Engineering, US Department of Energy Center for Bioenergy and Bioproducts Innovation (CABBI), Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jiansong Qin
- Department of Chemical Engineering, University of Massachusetts-Lowell, Lowell, Massachusetts, USA
| | - Andrew Olson
- Department of Chemical Engineering, University of Massachusetts-Lowell, Lowell, Massachusetts, USA
| | - Shekhar Mishra
- Department of Chemical and Biomolecular Engineering, US Department of Energy Center for Bioenergy and Bioproducts Innovation (CABBI), Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - John C Schultz
- Department of Chemical and Biomolecular Engineering, US Department of Energy Center for Bioenergy and Bioproducts Innovation (CABBI), Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Chunshuai Huang
- Department of Chemical and Biomolecular Engineering, US Department of Energy Center for Bioenergy and Bioproducts Innovation (CABBI), Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Dongming Xie
- Department of Chemical Engineering, University of Massachusetts-Lowell, Lowell, Massachusetts, USA
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, US Department of Energy Center for Bioenergy and Bioproducts Innovation (CABBI), Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Departments of Chemistry, Biochemistry, and Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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