1
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Li W, Guo Q, Zhao Y, Yue T, Yuan Y. Untargeted metabolomics combined with chemometrics reveals distinct metabolic profiles across two sparkling cider fermentation stages. Food Res Int 2024; 195:114946. [PMID: 39277224 DOI: 10.1016/j.foodres.2024.114946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 08/13/2024] [Accepted: 08/20/2024] [Indexed: 09/17/2024]
Abstract
This study aimed to examine the metabolic profiles of Saccharomyces cerevisiae yeasts (WLS21 and Y41) in two phases of sparkling cider making (normal and pressure fermentation) by combining untargeted metabolomic with chemometrics. The results showed that of the 634 nonvolatile metabolites identified using LC-MS and 83 volatile metabolites identified by GC-MS, the differential metabolites were 226 and 54, respectively. Metabolic pathway and correlation analyses showed that aspartic acid, phenylalanine and tyrosine, glutamic acid and purine metabolism were associated with flavor formation. The pressure fermentation process increased apigenin, naringenin, toxifolin, pyridoxine and thiamine contents in the final cider. These findings provide useful information and new research ideas for the formation of flavor in sparkling cider and the regulation of phenolic and vitamin production by microbial stress fermentation.
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Affiliation(s)
- Wenting Li
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qi Guo
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, Henan, 450002, China
| | - Yuning Zhao
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Tianli Yue
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China; College of Food Science and Technology, Northwest University, Xian, Shaanxi 710069, China.
| | - Yahong Yuan
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China; College of Food Science and Technology, Northwest University, Xian, Shaanxi 710069, China.
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2
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Wang G, Kong J, Leng T, Zhang W, Chen T, Xu X, Huang Z, Xie J. Metabolomics analysis based on UHPLC-QTOF-MS/MS to explore the synthesis mechanism and culture conditions optimization of Penicillium EF-2 exopolysaccharide. Int J Food Microbiol 2024; 423:110841. [PMID: 39059140 DOI: 10.1016/j.ijfoodmicro.2024.110841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 06/25/2024] [Accepted: 07/23/2024] [Indexed: 07/28/2024]
Abstract
Penicillium exopolysaccharide (EPS) inhibits galactose lectins and enhances immunity. However, EPS production is low and its synthesis mechanism remains unclear. Penicillium EF-2 strains with high EPS production were selected for this study, and Penicillium fermentation conditions were subsequently improved. The optimal culture conditions were 30 g/L lactose, 6 g/L yeast extract powder, 4 d seed age, 10 % inoculation amount, 3 d of secondary fermentation time, and the final EPS yield was 3.97 g/L. UHPLC-Q-TOF-MS/MS was used to explore the mechanism of EPS synthesis at the metabolic level. Optimal carbon source: lactose and optimal nitrogen source: yeast extract can provide precursors for EPS synthesis through related metabolic pathways. Moreover, regulating the energy, vitamin, and lipid metabolic pathways created favourable conditions for EPS synthesis and secretion. These findings explain the mechanism of EPS synthesis at the metabolic level and provide a theoretical basis for optimising and industrialising EPS production.
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Affiliation(s)
- Gang Wang
- State Key Laboratory of Food Science and Resources, Nanchang University, No. 235 Nanjing East Road, Nanchang 330047, China
| | - Jia Kong
- State Key Laboratory of Food Science and Resources, Nanchang University, No. 235 Nanjing East Road, Nanchang 330047, China
| | - Tuo Leng
- State Key Laboratory of Food Science and Resources, Nanchang University, No. 235 Nanjing East Road, Nanchang 330047, China
| | - Weidong Zhang
- State Key Laboratory of Food Science and Resources, Nanchang University, No. 235 Nanjing East Road, Nanchang 330047, China
| | - Ting Chen
- State Key Laboratory of Food Science and Resources, Nanchang University, No. 235 Nanjing East Road, Nanchang 330047, China
| | - Xizhe Xu
- State Key Laboratory of Food Science and Resources, Nanchang University, No. 235 Nanjing East Road, Nanchang 330047, China
| | - Zhibing Huang
- State Key Laboratory of Food Science and Resources, Nanchang University, No. 235 Nanjing East Road, Nanchang 330047, China; Sino-German Joint Research Institute, Nanchang University, No. 235 Nanjing East Road, Nanchang 330047, China.
| | - Jianhua Xie
- State Key Laboratory of Food Science and Resources, Nanchang University, No. 235 Nanjing East Road, Nanchang 330047, China.
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3
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Long Y, Han X, Meng X, Xu P, Tao F. A robust yeast chassis: comprehensive characterization of a fast-growing Saccharomyces cerevisiae. mBio 2024; 15:e0319623. [PMID: 38214535 PMCID: PMC10865977 DOI: 10.1128/mbio.03196-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 12/07/2023] [Indexed: 01/13/2024] Open
Abstract
Robust chassis are critical to facilitate advances in synthetic biology. This study describes a comprehensive characterization of a new yeast isolate Saccharomyces cerevisiae XP that grows faster than commonly used research and industrial S. cerevisiae strains. The genomic, transcriptomic, and metabolomic analyses suggest that the fast growth rate is, in part, due to the efficient electron transport chain and key growth factor synthesis. A toolbox for genetic manipulation of the yeast was developed; we used it to construct l-lactic acid producers for high lactate production. The development of genetically malleable yeast strains that grow faster than currently used strains may significantly enhance the uses of S. cerevisiae in biotechnology.IMPORTANCEYeast is known as an outstanding starting strain for constructing microbial cell factories. However, its growth rate restricts its application. A yeast strain XP, which grows fast in high concentrations of sugar and acidic environments, is revealed to demonstrate the potential in industrial applications. A toolbox was also built for its genetic manipulation including gene insertion, deletion, and ploidy transformation. The knowledge of its metabolism, which could guide the designing of genetic experiments, was generated with multi-omics analyses. This novel strain along with its toolbox was then tested by constructing an l-lactic acid efficient producer, which is conducive to the development of degradable plastics. This study highlights the remarkable competence of nonconventional yeast for applications in biotechnology.
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Affiliation(s)
- Yangdanyu Long
- State Key Laboratory of Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiao Han
- State Key Laboratory of Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xuanlin Meng
- State Key Laboratory of Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Fei Tao
- State Key Laboratory of Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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4
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Walker C, Mortensen M, Poudel B, Cotter C, Myers R, Okekeogbu IO, Ryu S, Khomami B, Giannone RJ, Laursen S, Trinh CT. Proteomes reveal metabolic capabilities of Yarrowia lipolytica for biological upcycling of polyethylene into high-value chemicals. mSystems 2023; 8:e0074123. [PMID: 37882587 PMCID: PMC10734471 DOI: 10.1128/msystems.00741-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 09/18/2023] [Indexed: 10/27/2023] Open
Abstract
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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Affiliation(s)
- Caleb Walker
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Max Mortensen
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Bindica Poudel
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Christopher Cotter
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Ryan Myers
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Ikenna O. Okekeogbu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Seunghyun Ryu
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Bamin Khomami
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Richard J. Giannone
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Siris Laursen
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Cong T. Trinh
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee, USA
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5
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Sailwal M, Mishra P, Bhaskar T, Pandey R, Ghosh D. Time-resolved transcriptomic profile of oleaginous yeast Rhodotorula mucilaginosa during lipid and carotenoids accumulation on glycerol. BIORESOURCE TECHNOLOGY 2023; 384:129379. [PMID: 37352986 DOI: 10.1016/j.biortech.2023.129379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 06/25/2023]
Abstract
The study reports the exploration of the transcriptome landscape of the red oleaginous yeast Rhodotorula mucilaginosa IIPL32 coinciding with the fermentation kinetics of the yeast cultivated in a two-stage fermentation process to exploit the time-series approach to get the complete transcripts picture and reveal the persuasive genes for fatty acid and terpenoid synthesis. The finding displayed the molecular drivers with more than 2-fold upregulation in the nitrogen-limited stage than in the nitrogen-excess stage. The rate-limiting diphosphomevalonate decarboxylase, acetylCoA-citrate lyase, and acetyl-CoA C-acetyltransferase were significant in controlling the metabolic flux in the synthesis of reduced compounds, and acetoacetyl-CoA synthase, 3-ketoacyl-acyl carrier-protein reductase, and β-subunit enoyl reductase catalyze the key starting steps of lipids or terpenoid synthesis. The last two catalyze essential reduction steps in fatty acid synthesis. These enzymes would be the prime targets for the metabolic engineering of the oleaginous yeast for enhanced fatty acids and terpenoid production.
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Affiliation(s)
- Megha Sailwal
- Material Resource Efficiency Division, CSIR-Indian Institute of Petroleum, Mohkampur, Dehradun, Uttarakhand 248005, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Pallavi Mishra
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110017, India
| | - Thallada Bhaskar
- Material Resource Efficiency Division, CSIR-Indian Institute of Petroleum, Mohkampur, Dehradun, Uttarakhand 248005, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Rajesh Pandey
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Mall Road, Delhi 110017, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Debashish Ghosh
- Material Resource Efficiency Division, CSIR-Indian Institute of Petroleum, Mohkampur, Dehradun, Uttarakhand 248005, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India.
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6
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Suo H, Shishir MRI, Wang Q, Wang M, Chen F, Cheng KW. Red Wine High-Molecular-Weight Polyphenolic Complex Ameliorates High-Fat Diet-Induced Metabolic Dysregulation and Perturbation in Gut Microbiota in Mice. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:6882-6893. [PMID: 37126594 DOI: 10.1021/acs.jafc.2c06459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Red wine polyphenolic complexes have attracted increasing attention as potential modulators of human metabolic disease risk. Our previous study discovered that red wine high-molecular-weight polymeric polyphenolic complexes (HPPCs) could inhibit key metabolic syndrome-associated enzymes and favorably modulate human gut microbiota (GM) in simulated colonic fermentation assay in vitro. In this work, the efficacy of HPPC supplementation (150 and 300 mg/kg/day, respectively) against high-fat diet (HFD)-induced metabolic disturbance in mice was investigated. HPPCs effectively attenuated HFD-induced obesity, insulin resistance, and lipid and glucose metabolic dysregulation and ameliorated inflammatory response and hepatic and colonic damage. It also improved the relative abundance of Bacteroidetes and Firmicutes, consistent with an anti-obesity phenotype. The favorable modulation of GM was further supported by improvement in the profile of fecal short-chain fatty acids. The higher dosage generally had a better performance in these effects than the low dosage. Moreover, serum metabolite profiling and pathway enrichment analysis revealed that HPPCs significantly modulated vitamin B metabolism-associated pathways and identified N-acetylneuraminic acid and 2-methylbutyroylcarnitine as potential biomarkers of the favorable effect on HFD-induced metabolic dysregulation. These findings highlight that dietary supplementation with red wine HPPCs is a promising strategy for the management of weight gain and metabolic dysregulation associated with HFD.
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Affiliation(s)
- Hao Suo
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
- Institute for Innovative Development of Food Industry, Shenzhen University, Shenzhen 518060, China
| | - Mohammad Rezaul Islam Shishir
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
- Institute for Innovative Development of Food Industry, Shenzhen University, Shenzhen 518060, China
| | - Qi Wang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Mingfu Wang
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
- Institute for Innovative Development of Food Industry, Shenzhen University, Shenzhen 518060, China
| | - Feng Chen
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
- Institute for Innovative Development of Food Industry, Shenzhen University, Shenzhen 518060, China
| | - Ka Wing Cheng
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
- Institute for Innovative Development of Food Industry, Shenzhen University, Shenzhen 518060, China
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7
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Rasor BJ, Chirania P, Rybnicky GA, Giannone RJ, Engle NL, Tschaplinski TJ, Karim AS, Hettich RL, Jewett MC. Mechanistic Insights into Cell-Free Gene Expression through an Integrated -Omics Analysis of Extract Processing Methods. ACS Synth Biol 2023; 12:405-418. [PMID: 36700560 DOI: 10.1021/acssynbio.2c00339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Cell-free systems derived from crude cell extracts have developed into tools for gene expression, with applications in prototyping, biosensing, and protein production. Key to the development of these systems is optimization of cell extract preparation methods. However, the applied nature of these optimizations often limits investigation into the complex nature of the extracts themselves, which contain thousands of proteins and reaction networks with hundreds of metabolites. Here, we sought to uncover the black box of proteins and metabolites in Escherichia coli cell-free reactions based on different extract preparation methods. We assess changes in transcription and translation activity from σ70 promoters in extracts prepared with acetate or glutamate buffer and the common post-lysis processing steps of a runoff incubation and dialysis. We then utilize proteomic and metabolomic analyses to uncover potential mechanisms behind these changes in gene expression, highlighting the impact of cold shock-like proteins and the role of buffer composition.
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Affiliation(s)
- Blake J Rasor
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States.,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States.,Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Payal Chirania
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States.,Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Grant A Rybnicky
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States.,Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States.,Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, Illinois 60208, United States
| | - Richard J Giannone
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Nancy L Engle
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Timothy J Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Ashty S Karim
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States.,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States.,Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Robert L Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States.,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States.,Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois 60611, United States.,Simpson Querrey Institute, Northwestern University, Chicago, Illinois 60611, United States
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8
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Lu Q, Shan X, Zeng W, Zhou J. Production of pyruvic acid with Candida glabrata using self-fermenting spent yeast cell dry powder as a seed nitrogen source. BIORESOUR BIOPROCESS 2022; 9:109. [PMID: 38647593 PMCID: PMC10991669 DOI: 10.1186/s40643-022-00593-5] [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: 07/16/2022] [Accepted: 09/10/2022] [Indexed: 11/10/2022] Open
Abstract
Pyruvic acid is an important organic acid and a key industrial raw material. It is widely used in the chemical, agricultural, and food fields. Candida glabrata is the preferred strain for pyruvic acid production. The waste yeast cell for pyruvic acid fermentation with C. glabrata are rich in protein, amino acid, nucleic acid, and vitamins, as potential and cost-effective nitrogen source raw material. In this study, the potential of C. glabrata to produce pyruvic acid using spent yeast cell dry powder was evaluated. When 30 g/L of spray-dried spent yeast cell powder was used as the seed nitrogen source, a high titer of pyruvic acid was obtained. The pyruvic acid production reached 63.4 g/L with a yield of 0.59 g/g in a 5 L bioreactor. After scale-up to a 50 L bioreactor using the fermented spent yeast cell dry powder as a seed nitrogen source, 65.1 g/L of pyruvic acid was harvested, with a yield of 0.61 g/g. This study proposes a promisingapproach for increasing the pyruvic acid titer and reducing the costs.
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Affiliation(s)
- Qiyuan Lu
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Xiaoyu Shan
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Weizhu Zeng
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
| | - Jingwen Zhou
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
- School of Biotechnology and Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
- Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
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9
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Nogle R, Nagaraju S, Utturkar SM, Giannone RJ, Reynoso V, Leang C, Hettich RL, Mitchell WP, Simpson SD, Jewett MC, Köpke M, Brown SD. Clostridium autoethanogenum isopropanol production via native plasmid pCA replicon. Front Bioeng Biotechnol 2022; 10:932363. [PMID: 36032736 PMCID: PMC9413188 DOI: 10.3389/fbioe.2022.932363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/29/2022] [Indexed: 11/17/2022] Open
Abstract
Clostridium autoethanogenum is a model gas-fermenting acetogen for commercial ethanol production. It is also a platform organism being developed for the carbon-negative production of acetone and isopropanol by gas fermentation. We have assembled a 5.5 kb pCA plasmid for type strain DSM10061 (JA1-1) using three genome sequence datasets. pCA is predicted to encode seven open-reading frames and estimated to be a low-copy number plasmid present at approximately 12 copies per chromosome. RNA-seq analyses indicate that pCA genes are transcribed at low levels and two proteins, CAETHG_05090 (putative replication protein) and CAETHG_05115 (hypothetical, a possible Mob protein), were detected at low levels during batch gas fermentations. Thiolase (thlA), CoA-transferase (ctfAB), and acetoacetate decarboxylase (adc) genes were introduced into a vector for isopropanol production in C. autoethanogenum using the native plasmid origin of replication. The availability of the pCA sequence will facilitate studies into its physiological role and could form the basis for genetic tool optimization.
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Affiliation(s)
| | | | - Sagar M. Utturkar
- Center for Cancer Research, Purdue University, West Lafayette, IN, United States
| | | | | | | | | | | | | | - Michael C. Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, United States
- Center for Synthetic Biology, Northwestern University, Evanston, IL, United States
- Simpson Querrey Institute, Northwestern University, Evanston, IL, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, United States
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL, United States
| | | | - Steven D. Brown
- LanzaTech Inc., Skokie, IL, United States
- *Correspondence: Steven D. Brown,
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10
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Metaproteomics reveals enzymatic strategies deployed by anaerobic microbiomes to maintain lignocellulose deconstruction at high solids. Nat Commun 2022; 13:3870. [PMID: 35790765 PMCID: PMC9256739 DOI: 10.1038/s41467-022-31433-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 06/16/2022] [Indexed: 11/08/2022] Open
Abstract
AbstractEconomically viable production of cellulosic biofuels requires operation at high solids loadings—on the order of 15 wt%. To this end we characterize Nature’s ability to deconstruct and utilize mid-season switchgrass at increasing solid loadings using an anaerobic methanogenic microbiome. This community exhibits undiminished fractional carbohydrate solubilization at loadings ranging from 30 g/L to 150 g/L. Metaproteomic interrogation reveals marked increases in the abundance of specific carbohydrate-active enzyme classes. Significant enrichment of auxiliary activity family 6 enzymes at higher solids suggests a role for Fenton chemistry. Stress-response proteins accompanying these reactions are similarly upregulated at higher solids, as are β-glucosidases, xylosidases, carbohydrate-debranching, and pectin-acting enzymes—all of which indicate that removal of deconstruction inhibitors is important for observed undiminished solubilization. Our work provides insights into the mechanisms by which natural microbiomes effectively deconstruct and utilize lignocellulose at high solids loadings, informing the future development of defined cultures for efficient bioconversion.
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11
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Carbon-negative production of acetone and isopropanol by gas fermentation at industrial pilot scale. Nat Biotechnol 2022; 40:335-344. [DOI: 10.1038/s41587-021-01195-w] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 12/09/2021] [Indexed: 12/21/2022]
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12
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Debottlenecking 4-hydroxybenzoate hydroxylation in Pseudomonas putida KT2440 improves muconate productivity from p-coumarate. Metab Eng 2022; 70:31-42. [PMID: 34982998 DOI: 10.1016/j.ymben.2021.12.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 12/15/2021] [Accepted: 12/29/2021] [Indexed: 12/31/2022]
Abstract
The transformation of 4-hydroxybenzoate (4-HBA) to protocatechuate (PCA) is catalyzed by flavoprotein oxygenases known as para-hydroxybenzoate-3-hydroxylases (PHBHs). In Pseudomonas putida KT2440 (P. putida) strains engineered to convert lignin-related aromatic compounds to muconic acid (MA), PHBH activity is rate-limiting, as indicated by the accumulation of 4-HBA, which ultimately limits MA productivity. Here, we hypothesized that replacement of PobA, the native P. putida PHBH, with PraI, a PHBH from Paenibacillus sp. JJ-1b with a broader nicotinamide cofactor preference, could alleviate this bottleneck. Biochemical assays confirmed the strict preference of NADPH for PobA, while PraI can utilize either NADH or NADPH. Kinetic assays demonstrated that both PobA and PraI can utilize NADPH with comparable catalytic efficiency and that PraI also efficiently utilizes NADH at roughly half the catalytic efficiency. The X-ray crystal structure of PraI was solved and revealed absolute conservation of the active site architecture to other PHBH structures despite their differing cofactor preferences. To understand the effect in vivo, we compared three P. putida strains engineered to produce MA from p-coumarate (pCA), showing that expression of praI leads to lower 4-HBA accumulation and decreased NADP+/NADPH ratios relative to strains harboring pobA, indicative of a relieved 4-HBA bottleneck due to increased NADPH availability. In bioreactor cultivations, a strain exclusively expressing praI achieved a titer of 40 g/L MA at 100% molar yield and a productivity of 0.5 g/L/h. Overall, this study demonstrates the benefit of sampling readily available natural enzyme diversity for debottlenecking metabolic flux in an engineered strain for microbial conversion of lignin-derived compounds to value-added products.
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Exploring Proteomes of Robust Yarrowia lipolytica Isolates Cultivated in Biomass Hydrolysate Reveals Key Processes Impacting Mixed Sugar Utilization, Lipid Accumulation, and Degradation. mSystems 2021; 6:e0044321. [PMID: 34342539 PMCID: PMC8407480 DOI: 10.1128/msystems.00443-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Yarrowia lipolytica is an oleaginous yeast exhibiting robust phenotypes beneficial for industrial biotechnology. The phenotypic diversity found within the undomesticated Y. lipolytica clade from various origins illuminates desirable phenotypic traits not found in the conventional laboratory strain CBS7504 (or W29), which include xylose utilization, lipid accumulation, and growth on undetoxified biomass hydrolysates. Currently, the related phenotypes of lipid accumulation and degradation when metabolizing nonpreferred sugars (e.g., xylose) associated with biomass hydrolysates are poorly understood, making it difficult to control and engineer in Y. lipolytica. To fill this knowledge gap, we analyzed the genetic diversity of five undomesticated Y. lipolytica strains and identified singleton genes and genes exclusively shared by strains exhibiting desirable phenotypes. Strain characterizations from controlled bioreactor cultures revealed that the undomesticated strain YB420 used xylose to support cell growth and maintained high lipid levels, while the conventional strain CBS7504 degraded cell biomass and lipids when xylose was the sole remaining carbon source. From proteomic analysis, we identified carbohydrate transporters, xylose metabolic enzymes, and pentose phosphate pathway proteins stimulated during the xylose uptake stage for both strains. Furthermore, we distinguished proteins involved in lipid metabolism (e.g., lipase, NADPH generation, lipid regulators, and β-oxidation) activated by YB420 (lipid maintenance phenotype) or CBS7504 (lipid degradation phenotype) when xylose was the sole remaining carbon source. Overall, the results relate genetic diversity of undomesticated Y. lipolytica strains to complex phenotypes of superior growth, sugar utilization, lipid accumulation, and degradation in biomass hydrolysates. IMPORTANCE Yarrowia lipolytica is an important industrial oleaginous yeast due to its robust phenotypes for effective conversion of inhibitory lignocellulosic biomass hydrolysates into neutral lipids. While lipid accumulation has been well characterized in this organism, its interconnected lipid degradation phenotype is poorly understood during fermentation of biomass hydrolysates. Our investigation into the genetic diversity of undomesticated Y. lipolytica strains, coupled with detailed strain characterization and proteomic analysis, revealed metabolic processes and regulatory elements conferring desirable phenotypes for growth, sugar utilization, and lipid accumulation in undetoxified biomass hydrolysates by these natural variants. This study provides a better understanding of the robust metabolism of Y. lipolytica and suggests potential metabolic engineering strategies to enhance its performance.
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Dorfer V, Strobl M, Winkler S, Mechtler K. MS Amanda 2.0: Advancements in the standalone implementation. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2021; 35:e9088. [PMID: 33759252 PMCID: PMC8244010 DOI: 10.1002/rcm.9088] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/27/2021] [Accepted: 03/18/2021] [Indexed: 06/12/2023]
Abstract
RATIONALE Database search engines are the preferred method to identify peptides in mass spectrometry data. However, valuable software is in this context not only defined by a powerful algorithm to separate correct from false identifications, but also by constant maintenance and continuous improvements. METHODS In 2014, we presented our peptide identification algorithm MS Amanda, showing its suitability for identifying peptides in high-resolution tandem mass spectrometry data and its ability to outperform widely used tools to identify peptides. Since then, we have continuously worked on improvements to enhance its usability and to support new trends and developments in this fast-growing field, while keeping the original scoring algorithm to assess the quality of a peptide spectrum match unchanged. RESULTS We present the outcome of these efforts, MS Amanda 2.0, a faster and more flexible standalone version with the original scoring algorithm. The new implementation has led to a 3-5× speedup, is able to handle new ion types and supports standard data formats. We also show that MS Amanda 2.0 works best when using only the most common ion types in a particular search instead of all possible ion types. CONCLUSIONS MS Amanda is available free of charge from https://ms.imp.ac.at/index.php?action=msamanda.
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Affiliation(s)
- Viktoria Dorfer
- Bioinformatics Research GroupUniversity of Applied Sciences Upper AustriaSoftwarepark 11, 4232 HagenbergAustria
| | - Marina Strobl
- Bioinformatics Research GroupUniversity of Applied Sciences Upper AustriaSoftwarepark 11, 4232 HagenbergAustria
| | - Stephan Winkler
- Bioinformatics Research GroupUniversity of Applied Sciences Upper AustriaSoftwarepark 11, 4232 HagenbergAustria
| | - Karl Mechtler
- Institute of Molecular Pathology (IMP)Vienna BioCenter (VBC)Campus‐Vienna‐Biocenter 1Vienna1030Austria
- Institute of Molecular Biotechnology (IMBA)Austrian Academy of Sciences, Vienna BioCenter (VBC)Dr. Bohr‐Gasse 3Vienna1030Austria
- Gregor Mendel Institute (GMI)Austrian Academy of Sciences, Vienna BioCenter (VBC)Dr. Bohr‐ Gasse 3Vienna1030Austria
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Poorinmohammad N, Kerkhoven EJ. Systems-level approaches for understanding and engineering of the oleaginous cell factory Yarrowia lipolytica. Biotechnol Bioeng 2021; 118:3640-3654. [PMID: 34129240 DOI: 10.1002/bit.27859] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 03/07/2021] [Accepted: 06/10/2021] [Indexed: 12/12/2022]
Abstract
Concerns about climate change and the search for renewable energy sources together with the goal of attaining sustainable product manufacturing have boosted the use of microbial platforms to produce fuels and high-value chemicals. In this regard, Yarrowia lipolytica has been known as a promising yeast with potentials in diverse array of biotechnological applications such as being a host for different oleochemicals, organic acid, and recombinant protein production. Having a rapidly increasing number of molecular and genetic tools available, Y. lipolytica has been well studied amongst oleaginous yeasts and metabolic engineering has been used to explore its potentials. More recently, with the advancement in systems biotechnology and the implementation of mathematical modeling and high throughput omics data-driven approaches, in-depth understanding of cellular mechanisms of cell factories have been made possible resulting in enhanced rational strain design. In case of Y. lipolytica, these systems-level studies and the related cutting-edge technologies have recently been initiated which is expected to result in enabling the biotechnology sector to rationally engineer Y. lipolytica-based cell factories with favorable production metrics. In this regard, here, we highlight the current status of systems metabolic engineering research and assess the potential of this yeast for future cell factory design development.
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Affiliation(s)
- Naghmeh Poorinmohammad
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Eduard J Kerkhoven
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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Qiu X, Gu Y, Du G, Zhang J, Xu P, Li J. Conferring thermotolerant phenotype to wild-type Yarrowia lipolytica improves cell growth and erythritol production. Biotechnol Bioeng 2021; 118:3117-3127. [PMID: 34009652 DOI: 10.1002/bit.27835] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 04/22/2021] [Accepted: 05/09/2021] [Indexed: 12/19/2022]
Abstract
In microbial engineering, heat stress is an important environmental factor modulating cell growth, metabolic flux distribution and the synthesis of target products. Yarrowia lipolytica, as a GARS (generally recognized as safe) nonconventional yeast, has been widely used in the food industry, especially as the host of erythritol production. Biomanufacturing economics is limited by the high operational cost of cooling energy in large-scale fermentation. It is of great significance to select thermotolerant Y. lipolytica to reduce the cooling cost and elucidate the heat-resistant mechanism at molecular level. For this purpose, we performed adaptive evolution and obtained a thermotolerant strain named Y. lipolytica BBE-18. Transcriptome analysis allows us to identify four genes in thiamine metabolism pathway that are responsible for the complicated thermotolerant phenotype. The heat-resistant phenotype was validated with the model strain Y. lipolytica Po1f by overexpression of single and combined genes. Then, conferring the thermotolerant phenotype to the wild-type Y. lipolytica BBE-17 enable the strain to produce three-times more erythritol of the control strain with 3°C higher than optimal cultivation temperature. To our knowledge, this is the first report on engineering heat-resistant phenotype to improve the erythritol production in Y. lipolytica. However, due to the increase of culture temperature, a large amount of adenosine triphosphate is consumed to ensure the life activities of Y. lipolytica which limits the potential of cell synthetic products to a certain extent. Even so, this study provides a reference for Y. lipolytica to produce other products under high temperature.
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Affiliation(s)
- Xueliang Qiu
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yang Gu
- Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland Baltimore County, Baltimore, Maryland, USA.,School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Guocheng Du
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China
| | - Juan Zhang
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, Jiangsu, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Peng Xu
- Department of Chemical, Biochemical, and Environmental Engineering, University of Maryland Baltimore County, Baltimore, Maryland, USA
| | - Jianghua Li
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China.,National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, Jiangsu, China
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17
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Pathway discovery and engineering for cleavage of a β-1 lignin-derived biaryl compound. Metab Eng 2021; 65:1-10. [PMID: 33636323 DOI: 10.1016/j.ymben.2021.02.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 01/11/2021] [Accepted: 02/09/2021] [Indexed: 11/22/2022]
Abstract
Lignin biosynthesis typically results in a polymer with several inter-monomer bond linkages, and the heterogeneity of linkages presents a challenge for depolymerization processes. While several enzyme classes have been shown to cleave common dimer linkages in lignin, the pathway of bacterial β-1 spirodienone linkage cleavage has not been elucidated. Here, we identified a pathway for cleavage of 1,2-diguaiacylpropane-1,3-diol (DGPD), a β-1 linked biaryl representative of a ring-opened spirodienone linkage, in Novosphingobium aromaticivorans DSM12444. In vitro assays using cell lysates demonstrated that RS14230 (LsdE) converts DGPD to a lignostilbene intermediate, which the carotenoid oxygenase, LsdA, then converts to vanillin. A Pseudomonas putida KT2440 strain engineered with lsdEA expression catabolizes erythro-DGPD, but not threo-DGPD. We further engineered P. putida to convert DGPD to a product, cis,cis-muconic acid. Overall, this work demonstrates the potential to identify new enzymatic reactions in N. aromaticivorans and expands the biological funnel of P. putida for microbial lignin valorization.
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Beri D, Herring CD, Blahova S, Poudel S, Giannone RJ, Hettich RL, Lynd LR. Coculture with hemicellulose-fermenting microbes reverses inhibition of corn fiber solubilization by Clostridium thermocellum at elevated solids loadings. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:24. [PMID: 33461608 PMCID: PMC7814735 DOI: 10.1186/s13068-020-01867-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 12/24/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND The cellulolytic thermophile Clostridium thermocellum is an important biocatalyst due to its ability to solubilize lignocellulosic feedstocks without the need for pretreatment or exogenous enzyme addition. At low concentrations of substrate, C. thermocellum can solubilize corn fiber > 95% in 5 days, but solubilization declines markedly at substrate concentrations higher than 20 g/L. This differs for model cellulose like Avicel, on which the maximum solubilization rate increases in proportion to substrate concentration. The goal of this study was to examine fermentation at increasing corn fiber concentrations and investigate possible reasons for declining performance. RESULTS The rate of growth of C. thermocellum on corn fiber, inferred from CipA scaffoldin levels measured by LC-MS/MS, showed very little increase with increasing solids loading. To test for inhibition, we evaluated the effects of spent broth on growth and cellulase activity. The liquids remaining after corn fiber fermentation were found to be strongly inhibitory to growth on cellobiose, a substrate that does not require cellulose hydrolysis. Additionally, the hydrolytic activity of C. thermocellum cellulase was also reduced to less-than half by adding spent broth. Noting that > 15 g/L hemicellulose oligosaccharides accumulated in the spent broth of a 40 g/L corn fiber fermentation, we tested the effect of various model carbohydrates on growth on cellobiose and Avicel. Some compounds like xylooligosaccharides caused a decline in cellulolytic activity and a reduction in the maximum solubilization rate on Avicel. However, there were no relevant model compounds that could replicate the strong inhibition by spent broth on C. thermocellum growth on cellobiose. Cocultures of C. thermocellum with hemicellulose-consuming partners-Herbinix spp. strain LL1355 and Thermoanaerobacterium thermosaccharolyticum-exhibited lower levels of unfermented hemicellulose hydrolysis products, a doubling of the maximum solubilization rate, and final solubilization increased from 67 to 93%. CONCLUSIONS This study documents inhibition of C. thermocellum with increasing corn fiber concentration and demonstrates inhibition of cellulase activity by xylooligosaccharides, but further work is needed to understand why growth on cellobiose was inhibited by corn fiber fermentation broth. Our results support the importance of hemicellulose-utilizing coculture partners to augment C. thermocellum in the fermentation of lignocellulosic feedstocks at high solids loading.
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Affiliation(s)
- Dhananjay Beri
- Thayer School of Engineering, Dartmouth College, Hanover, NH, 03755, USA
- Centre for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Christopher D Herring
- Thayer School of Engineering, Dartmouth College, Hanover, NH, 03755, USA.
- Centre for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA.
- Enchi Corporation, Lebanon, NH, 03766, USA.
| | - Sofie Blahova
- Thayer School of Engineering, Dartmouth College, Hanover, NH, 03755, USA
| | - Suresh Poudel
- Centre for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Richard J Giannone
- Centre for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Robert L Hettich
- Centre for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Lee R Lynd
- Thayer School of Engineering, Dartmouth College, Hanover, NH, 03755, USA
- Centre for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
- Enchi Corporation, Lebanon, NH, 03766, USA
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Wang J, Ledesma-Amaro R, Wei Y, Ji B, Ji XJ. Metabolic engineering for increased lipid accumulation in Yarrowia lipolytica - A Review. BIORESOURCE TECHNOLOGY 2020; 313:123707. [PMID: 32595069 DOI: 10.1016/j.biortech.2020.123707] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/15/2020] [Accepted: 06/16/2020] [Indexed: 06/11/2023]
Abstract
Current energy security and climate change policies encourage the development and utilization of bioenergy. Oleaginous yeasts provide a particularly attractive platform for the sustainable production of biofuels and industrial chemicals due to their ability to accumulate high amounts of lipids. In particular, microbial lipids in the form of triacylglycerides (TAGs) produced from renewable feedstocks have attracted considerable attention because they can be directly used in the production of biodiesel and oleochemicals analogous to petrochemicals. As an oleaginous yeast that is generally regarded as safe, Yarrowia lipolytica has been extensively studied, with large amounts of data on its lipid metabolism, genetic tools, and genome sequencing and annotation. In this review, we highlight the newest strategies for increasing lipid accumulation using metabolic engineering and summarize the research advances on the overaccumulation of lipids in Y. lipolytica. Finally, perspectives for future engineering approaches are proposed.
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Affiliation(s)
- Jinpeng Wang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
| | - Yongjun Wei
- School of Pharmaceutical Sciences, Key Laboratory of State Ministry of Education, Key Laboratory of Henan Province for Drug Quality Control and Evaluation, Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou University, 100 Kexue Avenue, Zhengzhou 450001, People's Republic of China
| | - Boyang Ji
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Xiao-Jun Ji
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China.
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