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Chen X, Song C, Zhao J, Xiong Z, Peng L, Zou L, Liu B, Li Q. Effect of a New Fermentation Strain Combination on the Fermentation Process and Quality of Highland Barley Yellow Wine. Foods 2024; 13:2193. [PMID: 39063277 PMCID: PMC11276116 DOI: 10.3390/foods13142193] [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: 06/13/2024] [Revised: 07/06/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
Yellow wine fermented from highland barley is an alcoholic beverage with high nutritional value. However, the industrialization of barley yellow wine has been constrained to a certain extent due to the lack of a systematic starter culture. Therefore, the present study aims to simulate barley yellow wine fermentation using a starter culture consisting of Rhizopus arrhizus, Saccharomyces cerevisiae, Pichia kudriavzevii, and Lacticaseibacillus rhamnosus. In this study, changes in enzyme activity, fermentation characteristics, volatile substance production, and amino acid content during the fermentation of highland barley yellow wine brewed with different starter cultures were evaluated. The results of this study show that regulating the proportion of mixed starter bacteria can effectively control the various stages of the fermentation process and improve the organoleptic characteristics and quality of yellow wine to varying degrees. Additionally, we found that the addition of probiotics could effectively improve the palatability of yellow wine. To the best of our knowledge, we have validated for the first time the use of the above multispecies starter culture, consisting of R. arrhizus, S. cerevisiae, P. kudriavzevii, and L. rhamnosus, in the production of highland barley yellow wine. The obtained findings provided reference data for optimizing highland barley yellow wine fermentation.
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Affiliation(s)
- Xiaodie Chen
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China; (X.C.); (Z.X.); (L.P.); (L.Z.)
| | - Chuan Song
- Luzhou Laojiao Co., Ltd., Luzhou 646000, China;
- National Engineering Research Center of Solid-State Brewing, Luzhou 646000, China
- Postdoctoral Research Station of Luzhou Laojiao Company, Luzhou 646000, China
| | - Jian Zhao
- School of Life Sciences, Sichuan University, Chengdu 610041, China;
| | - Zhuang Xiong
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China; (X.C.); (Z.X.); (L.P.); (L.Z.)
| | - Lianxin Peng
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China; (X.C.); (Z.X.); (L.P.); (L.Z.)
| | - Liang Zou
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China; (X.C.); (Z.X.); (L.P.); (L.Z.)
| | - Bingliang Liu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China; (X.C.); (Z.X.); (L.P.); (L.Z.)
| | - Qiang Li
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Sichuan Engineering & Technology Research Center of Coarse Cereal Industrialization, School of Food and Biological Engineering, Chengdu University, Chengdu 610106, China; (X.C.); (Z.X.); (L.P.); (L.Z.)
- Postdoctoral Research Station of Luzhou Laojiao Company, Luzhou 646000, China
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Gorczyca M, Białas W, Nicaud JM, Celińska E. 'Mother(Nature) knows best' - hijacking nature-designed transcriptional programs for enhancing stress resistance and protein production in Yarrowia lipolytica; presentation of YaliFunTome database. Microb Cell Fact 2024; 23:26. [PMID: 38238843 PMCID: PMC10797999 DOI: 10.1186/s12934-023-02285-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 12/21/2023] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND In the era of rationally designed synthetic biology, heterologous metabolites production, and other counter-nature engineering of cellular metabolism, we took a step back and recalled that 'Mother(-Nature) knows best'. While still aiming at synthetic, non-natural outcomes of generating an 'over-production phenotype' we dug into the pre-designed transcriptional programs evolved in our host organism-Yarrowia lipolytica, hoping that some of these fine-tuned orchestrated programs could be hijacked and used. Having an interest in the practical outcomes of the research, we targeted industrially-relevant functionalities-stress resistance and enhanced synthesis of proteins, and gauged them over extensive experimental design's completion. RESULTS Technically, the problem was addressed by screening a broad library of over 120 Y. lipolytica strains under 72 combinations of variables through a carefully pre-optimized high-throughput cultivation protocol, which enabled actual phenotype development. The abundance of the transcription program elicitors-transcription factors (TFs), was secured by their overexpression, while challenging the strains with the multitude of conditions was inflicted to impact their activation stratus. The data were subjected to mathematical modeling to increase their informativeness. The amount of the gathered data prompted us to present them in the form of a searchable catalog - the YaliFunTome database ( https://sparrow.up.poznan.pl/tsdatabase/ )-to facilitate the withdrawal of biological sense from numerical data. We succeeded in the identification of TFs that act as omni-boosters of protein synthesis, enhance resistance to limited oxygen availability, and improve protein synthesis capacity under inorganic nitrogen provision. CONCLUSIONS All potential users are invited to browse YaliFunTome in the search for homologous TFs and the TF-driven phenotypes of interest.
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Affiliation(s)
- Maria Gorczyca
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, 60-637, Poznań, Poland
| | - Wojciech Białas
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, 60-637, Poznań, Poland
| | - Jean-Marc Nicaud
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Ewelina Celińska
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, 60-637, Poznań, Poland.
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Liao H, Asif H, Huang X, Luo Y, Xia X. Mitigation of microbial nitrogen-derived metabolic hazards as a driver for safer alcoholic beverage choices: An evidence-based review and future perspectives. Compr Rev Food Sci Food Saf 2023; 22:5020-5062. [PMID: 37823801 DOI: 10.1111/1541-4337.13253] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 10/13/2023]
Abstract
Alcoholic beverages have been enjoyed worldwide as hedonistic commodities for thousands of years. The unique quality and flavor are attributed to the rich microbiota and nutritional materials involved in fermentation. However, the metabolism of these microbiota can also introduce toxic compounds into foods. Nitrogen-derived metabolic hazards (NMH) are toxic metabolic hazards produced by microorganisms metabolizing nitrogen sources that can contaminate alcoholic beverages during fermentation and processing. NMH contamination poses a risk to dietary safety and human health without effective preventive strategies. Existing literature has primarily focused on investigating the causes of NMH formation, detection methods, and abatement techniques for NMH in fermentation end-products. Devising effective process regulation strategies represents a major challenge for the alcoholic beverage industry considering our current lack of understanding regarding the processes whereby NMH are generated, real-time and online detection, and the high degradation rate after NMH formation. This review summarizes the types and mechanisms of nitrogenous hazard contamination, the potential risk points, and the analytical techniques to detect NMH contamination. We discussed the changing patterns of NMH contamination and effective strategies to prevent contamination at different stages in the production of alcoholic beverages. Moreover, we also discussed the advanced technologies and methods to control NMH contamination in alcoholic beverages based on intelligent monitoring, synthetic ecology, and computational assistance. Overall, this review highlights the risks of NMH contamination during alcoholic beverage production and proposes promising strategies that could be adopted to eliminate the risk of NMH contamination.
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Affiliation(s)
- Hui Liao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, P. R. China
| | - Hussain Asif
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, P. R. China
| | - Xinlei Huang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, P. R. China
| | - Yi Luo
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, P. R. China
| | - Xiaole Xia
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, P. R. China
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Abstract
Our current food system relies on unsustainable practices, which often fail to provide healthy diets to a growing population. Therefore, there is an urgent demand for new sustainable nutrition sources and processes. Microorganisms have gained attention as a new food source solution, due to their low carbon footprint, low reliance on land, water and seasonal variations coupled with a favourable nutritional profile. Furthermore, with the emergence and use of new tools, specifically in synthetic biology, the uses of microorganisms have expanded showing great potential to fulfil many of our dietary needs. In this review, we look at the different applications of microorganisms in food, and examine the history, state-of-the-art and potential to disrupt current foods systems. We cover both the use of microbes to produce whole foods out of their biomass and as cell factories to make highly functional and nutritional ingredients. The technical, economical, and societal limitations are also discussed together with the current and future perspectives.
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Affiliation(s)
- Alicia E Graham
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK.
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Novel Insight into the Formation of Odour—Active Compounds in Sea Buckthorn Wine and Distilled Liquor Based on GC–MS and E–Nose Analysis. Foods 2022. [PMCID: PMC9601902 DOI: 10.3390/foods11203273] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Sea buckthorn wine (SW) and distilled liquor (DL) are fruit wines with beneficial health effects. However, their unpleasant flavour limits their development and widespread acceptance. Therefore, it is necessary to analyse their flavour composition and changes. In this study, differential metabolites of sea buckthorn DL during processing were analysed, and the relationships between E–nose sensor values and key volatile organic compounds (VOCs) were established. The results show that 133 VOCs were identified, with 22 aroma–contributing components. Fermentation significantly increased the content of VOCs, especially esters. A total of seven and 51 VOCs were significantly upregulated after fermentation and distillation, respectively. Meanwhile, seven sensors were positively correlated with the increased level of alcohols and esters, and reflected the increasing trends of 10 key VOCs.
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Larroude M, Nicaud J, Rossignol T. Yarrowia lipolytica chassis strains engineered to produce aromatic amino acids via the shikimate pathway. Microb Biotechnol 2021; 14:2420-2434. [PMID: 33438818 PMCID: PMC8601196 DOI: 10.1111/1751-7915.13745] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 12/20/2020] [Indexed: 12/16/2022] Open
Abstract
Yarrowia lipolytica is widely used as a microbial producer of lipids and lipid derivatives. Here, we exploited this yeast's potential to generate aromatic amino acids by developing chassis strains optimized for the production of phenylalanine, tyrosine and tryptophan. We engineered the shikimate pathway to overexpress a combination of Y. lipolytica and heterologous feedback-insensitive enzyme variants. Our best chassis strain displayed high levels of de novo Ehrlich metabolite production (up to 0.14 g l-1 in minimal growth medium), which represented a 93-fold increase compared to the wild-type strain (0.0015 g l-1 ). Production was further boosted to 0.48 g l-1 when glycerol, a low-cost carbon source, was used, concomitantly to high secretion of phenylalanine precursor (1 g l-1 ). Among these metabolites, 2-phenylethanol is of particular interest due to its rose-like flavour. We also established a production pathway for generating protodeoxyviolaceinic acid, a dye derived from tryptophan, in a chassis strain optimized for chorismate, the precursor of tryptophan. We have thus demonstrated that Y. lipolytica can serve as a platform for the sustainable de novo bio-production of high-value aromatic compounds, and we have greatly improved our understanding of the potential feedback-based regulation of the shikimate pathway in this yeast.
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Affiliation(s)
- Macarena Larroude
- Université Paris‐Saclay, INRAE, AgroParisTech, Micalis Institute78350Jouy‐en‐JosasFrance
| | - Jean‐Marc Nicaud
- Université Paris‐Saclay, INRAE, AgroParisTech, Micalis Institute78350Jouy‐en‐JosasFrance
| | - Tristan Rossignol
- Université Paris‐Saclay, INRAE, AgroParisTech, Micalis Institute78350Jouy‐en‐JosasFrance
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Zhao Y, Liu S, Lu Z, Zhao B, Wang S, Zhang C, Xiao D, Foo JL, Yu A. Hybrid promoter engineering strategies in Yarrowia lipolytica: isoamyl alcohol production as a test study. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:149. [PMID: 34215293 PMCID: PMC8252286 DOI: 10.1186/s13068-021-02002-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 06/22/2021] [Indexed: 05/11/2023]
Abstract
BACKGROUND In biological cells, promoters drive gene expression by specific binding of RNA polymerase. They determine the starting position, timing and level of gene expression. Therefore, rational fine-tuning of promoters to regulate the expression levels of target genes for optimizing biosynthetic pathways in metabolic engineering has recently become an active area of research. RESULTS In this study, we systematically detected and characterized the common promoter elements in the unconventional yeast Yarrowia lipolytica, and constructed an artificial hybrid promoter library that covers a wide range of promoter strength. The results indicate that the hybrid promoter strength can be fine-tuned by promoter elements, namely, upstream activation sequences (UAS), TATA box and core promoter. Notably, the UASs of Saccharomyces cerevisiae promoters were reported for the first time to be functionally transferred to Y. lipolytica. Subsequently, using the production of a versatile platform chemical isoamyl alcohol as a test study, the hybrid promoter library was applied to optimize the biosynthesis pathway expression in Y. lipolytica. By expressing the key pathway gene, ScARO10, with the promoter library, 1.1-30.3 folds increase in the isoamyl alcohol titer over that of the control strain Y. lipolytica Po1g KU70∆ was achieved. Interestingly, the highest titer increase was attained with a weak promoter PUAS1B4-EXPm to express ScARO10. These results suggest that our hybrid promoter library can be a powerful toolkit for identifying optimum promoters for expressing metabolic pathways in Y. lipolytica. CONCLUSION We envision that this promoter engineering strategy and the rationally engineered promoters constructed in this study could also be extended to other non-model fungi for strain improvement.
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Affiliation(s)
- Yu Zhao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 the 13th Street TEDA, Tianjin, 300457 People’s Republic of China
| | - Shiqi Liu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 the 13th Street TEDA, Tianjin, 300457 People’s Republic of China
| | - Zhihui Lu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 the 13th Street TEDA, Tianjin, 300457 People’s Republic of China
| | - Baixiang Zhao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 the 13th Street TEDA, Tianjin, 300457 People’s Republic of China
| | - Shuhui Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 the 13th Street TEDA, Tianjin, 300457 People’s Republic of China
| | - Cuiying Zhang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 the 13th Street TEDA, Tianjin, 300457 People’s Republic of China
| | - Dongguang Xiao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 the 13th Street TEDA, Tianjin, 300457 People’s Republic of China
| | - Jee Loon Foo
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228 Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore, 117456 Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597 Singapore
| | - Aiqun Yu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, No. 29 the 13th Street TEDA, Tianjin, 300457 People’s Republic of China
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Korpys-Woźniak P, Celińska E. Global transcriptome profiling reveals genes responding to overproduction of a small secretory, a high cysteine- and a high glycosylation-bearing protein in Yarrowia lipolytica. ACTA ACUST UNITED AC 2021; 31:e00646. [PMID: 34189064 PMCID: PMC8220174 DOI: 10.1016/j.btre.2021.e00646] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/08/2021] [Accepted: 06/09/2021] [Indexed: 11/16/2022]
Abstract
Secretion of a protein results in > 10-fold higher titer compared to its retention. Overproduction of rs-Prots induces oxidative stress and detoxification response. Excessive vacuolar protein degradation limits rs-Prot production in Y. lipolytica. Non-classical export protein NCE102 is upregulated upon rs-Prot overloading. Downregulation of cyclin CLN1 marks growth arrest in G1 under rs-Prot synthesis.
Investigation of the yeast cell’s response to recombinant secretory protein (rs-Prot) overproduction is relevant for both basic and applied research. Imbalance, overloading or stress within this process impacts the whole cell. In the present study, by using steady-state cultures and transcriptomics, we investigated the cellular response of Yarrowia lipolytica challenged with high-level expression of genes encoding proteins with significantly different biochemical characteristics: a small protein retained within the cell i) or secreted ii), a medium size secretory protein with a high number of disulfide bonds iii), or glycosylation sites iv). Extensive analysis of omics data, supported by careful manual curation, led to some anticipated observations on oxidative and unfolded protein stress (CTT1, PXMP2/4, HAC1), glycosylation (ALGs, KTRs, MNTs, MNNs), folding and translocation (SSAs, SSEs) but also generated new exciting knowledge on non-conventional protein secretion (NCE102), transcriptional regulators (FLO11, MHY1, D01353 g, RSFA, E23925g or MAF1), vacuolar proteolysis targets in Y. lipolytica (ATGs, VPSs, HSE1, PRB1, PRC1, PEP4) or growth arrest (CLN1) upon rs-Prots overproduction.
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Study on microbial communities and higher alcohol formations in the fermentation of Chinese Xiaoqu Baijiu produced by traditional and new mechanical technologies. Food Res Int 2021; 140:109876. [DOI: 10.1016/j.foodres.2020.109876] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 10/22/2020] [Accepted: 11/03/2020] [Indexed: 01/13/2023]
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10
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Celińska E, Nicaud JM, Białas W. Hydrolytic secretome engineering in Yarrowia lipolytica for consolidated bioprocessing on polysaccharide resources: review on starch, cellulose, xylan, and inulin. Appl Microbiol Biotechnol 2021; 105:975-989. [PMID: 33447867 PMCID: PMC7843476 DOI: 10.1007/s00253-021-11097-1] [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] [Received: 12/09/2020] [Revised: 12/22/2020] [Accepted: 01/03/2021] [Indexed: 10/25/2022]
Abstract
Consolidated bioprocessing (CBP) featuring concomitant hydrolysis of renewable substrates and microbial conversion into value-added biomolecules is considered to bring substantial benefits to the overall process efficiency. The biggest challenge in developing an economically feasible CBP process is identification of bifunctional biocatalyst merging the ability to utilize the substrate and convert it to value-added product with high efficiency. Yarrowia lipolytica is known for its exceptional performance in hydrophobic substrates assimilation and storage. On the other hand, its capacity to grow on plant-derived biomass is strongly limited. Still, its high potential to simultaneously overproduce several secretory proteins makes Y. lipolytica a platform of choice for expanding its substrate range to complex polysaccharides by engineering its hydrolytic secretome. This review provides an overview of different genetic engineering strategies advancing development of Y. lipolytica strains able to grow on the following four complex polysaccharides: starch, cellulose, xylan, and inulin. Much attention has been paid to genome mining studies uncovering native potential of this species to assimilate untypical sugars, as in many cases it turns out that dormant pathways are present in Y. lipolytica's genome. In addition, the magnitude of the economic gain by CBP processing is here discussed and supported with adequate calculations based on simulated process models. KEY POINTS: • The mini-review updates the knowledge on polysaccharide-utilizing Yarrowia lipolytica. • Insight into molecular bases founding new biochemical qualities is provided. • Model industrial processes were simulated and the associated costs were calculated.
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Affiliation(s)
- Ewelina Celińska
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, ul. Wojska Polskiego 48, 60-627, Poznań, Poland.
| | - Jean-Marc Nicaud
- Micalis Institute, INRAE-AgroParisTech, UMR1319, Team BIMLip: Integrative Metabolism of Microbial Lipids, Domaine de Vilvert, 78352, Jouy-en-Josas, France
| | - Wojciech Białas
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, ul. Wojska Polskiego 48, 60-627, Poznań, Poland
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Xia Y, Liu Y, Zhao Y, Wang J, Shuang Q. Nitrogen metabolism of branched‐chain alcohols acetates in jujube wine assessed by
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C‐labeling. J FOOD PROCESS PRES 2020. [DOI: 10.1111/jfpp.14741] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Yanan Xia
- College of Food Science and Engineering Inner Mongolia Agricultural University Hohhot China
| | - Yaqiong Liu
- College of Food Science and Technology Agricultural University of Hebei Baoding China
| | - Yun Zhao
- Department of Food and Bioengineering Handan Polytechnic College Handan China
| | - Jie Wang
- College of Food Science and Technology Agricultural University of Hebei Baoding China
| | - Quan Shuang
- College of Food Science and Engineering Inner Mongolia Agricultural University Hohhot China
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Celińska E, Borkowska M, Korpys-Woźniak P, Kubiak M, Nicaud JM, Kubiak P, Gorczyca M, Białas W. Optimization of Yarrowia lipolytica-based consolidated biocatalyst through synthetic biology approach: transcription units and signal peptides shuffling. Appl Microbiol Biotechnol 2020; 104:5845-5859. [PMID: 32358762 PMCID: PMC7306051 DOI: 10.1007/s00253-020-10644-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/16/2020] [Accepted: 04/22/2020] [Indexed: 11/28/2022]
Abstract
Nowadays considerable effort is being pursued towards development of consolidated microbial biocatalysts that will be able to utilize complex, non-pretreated substrates and produce valuable compounds. In such engineered microbes, synthesis of extracellular hydrolases may be fine-tuned by different approaches, like strength of promoter, type of secretory tag, and gene copy number. In this study, we investigated if organization of a multi-element expression cassette impacts the resultant Yarrowia lipolytica transformants' phenotype, presuming that different variants of the cassette are composed of the same regulatory elements and encode the same mature proteins. To this end, Y. lipolytica cells were transformed with expression cassettes bearing a pair of genes encoding exactly the same mature amylases, but fused to four different signal peptides (SP), and located interchangeably in either first or second position of a synthetic DNA construction. The resultant strains were tested for growth on raw and pretreated complex substrates of different plant origin for comprehensive examination of the strains' acquired characteristics. Optimized strain was tested in batch bioreactor cultivations for growth and lipids accumulation. Based on the conducted research, we concluded that the positional order of transcription units (TU) and the type of exploited SP affect final characteristics of the resultant consolidated biocatalyst strains, and thus could be considered as additional factors to be evaluated upon consolidated biocatalysts optimization. KEY POINTS: • Y. lipolytica growing on raw starch was constructed and tested on different substrates. • Impact of expression cassette design and SP on biocatalysts' phenotype was evidenced. • Consolidated biocatalyst process for lipids production from starch was conducted.
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Affiliation(s)
- Ewelina Celińska
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, ul. Wojska Polskiego 48, 60-627, Poznań, Poland.
| | - Monika Borkowska
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, ul. Wojska Polskiego 48, 60-627, Poznań, Poland
| | - Paulina Korpys-Woźniak
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, ul. Wojska Polskiego 48, 60-627, Poznań, Poland
| | - Monika Kubiak
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, ul. Wojska Polskiego 48, 60-627, Poznań, Poland
| | - Jean-Marc Nicaud
- INRA-AgroParisTech, UMR1319, Team BIMLip: Integrative Metabolism of Microbial Lipids, Micalis Institute, Domaine de Vilvert, 78352, Jouy-en-Josas, France
| | - Piotr Kubiak
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, ul. Wojska Polskiego 48, 60-627, Poznań, Poland
| | - Maria Gorczyca
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, ul. Wojska Polskiego 48, 60-627, Poznań, Poland
| | - Wojciech Białas
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, ul. Wojska Polskiego 48, 60-627, Poznań, Poland
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Orive-Milla N, Delmulle T, de Mey M, Faijes M, Planas A. Metabolic engineering for glycoglycerolipids production in E. coli: Tuning phosphatidic acid and UDP-glucose pathways. Metab Eng 2020; 61:106-119. [PMID: 32492511 DOI: 10.1016/j.ymben.2020.05.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 05/04/2020] [Accepted: 05/25/2020] [Indexed: 12/12/2022]
Abstract
Glycolipids are target molecules in biotechnology and biomedicine as biosurfactants, biomaterials and bioactive molecules. An engineered E. coli strain for the production of glycoglycerolipids (GGL) used the MG517 glycolipid synthase from M. genitalium for glucosyl transfer from UDPGlc to diacylglycerol acceptor (Mora-Buyé et al., 2012). The intracellular diacylglycerol pool proved to be the limiting factor for GGL production. Here we designed different metabolic engineering strategies to enhance the availability of precursor substrates for the glycolipid synthase by modulating fatty acids, acyl donor and phosphatidic acid biosynthesis. Knockouts of tesA, fadE and fabR genes involved in fatty acids degradation, overexpression of the transcriptional regulator FadR, the acyltransferases PlsB and C, and the pyrophosphatase Cdh for phosphatidic acid biosynthesis, as well as the phosphatase PgpB for conversion to diacylglycerol were explored with the aim of improving GGL titers. Among the different engineered strains, the ΔtesA strain co-expressing MG517 and a fusion PlsCxPgpB protein was the best producer, with a 350% increase of GGL titer compared to the parental strain expressing MG517 alone. Attempts to boost UDPGlc availability by overexpressing the uridyltransferase GalU or knocking out the UDP-sugar diphosphatase encoding gene ushA did not further improve GGL titers. Most of the strains produced GGL containing a variable number of glucosyl units from mono-to tetra-saccharides. Interestingly, the strains co-expressing Cdh showed a shift in the GGL profile towards the diglucosylated lipid (up to 80% of total GGLs) whereas the strains with a fadR knockout presented a higher amount of unsaturated acyl chains. In all cases, GGL production altered the lipidic composition of the E. coli membrane, observing that GGL replace phosphatidylethanolamine to maintain the overall membrane charge balance.
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Affiliation(s)
- Nuria Orive-Milla
- Laboratory of Biochemistry, Institut Químic de Sarrià, University Ramon Llull, Via Augusta 350, E-08017, Barcelona, Spain
| | - Tom Delmulle
- Centre for Synthetic Biology (CSB), Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Marjan de Mey
- Centre for Synthetic Biology (CSB), Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Magda Faijes
- Laboratory of Biochemistry, Institut Químic de Sarrià, University Ramon Llull, Via Augusta 350, E-08017, Barcelona, Spain.
| | - Antoni Planas
- Laboratory of Biochemistry, Institut Químic de Sarrià, University Ramon Llull, Via Augusta 350, E-08017, Barcelona, Spain.
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Colomer MS, Chailyan A, Fennessy RT, Olsson KF, Johnsen L, Solodovnikova N, Forster J. Assessing Population Diversity of Brettanomyces Yeast Species and Identification of Strains for Brewing Applications. Front Microbiol 2020; 11:637. [PMID: 32373090 PMCID: PMC7177047 DOI: 10.3389/fmicb.2020.00637] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 03/20/2020] [Indexed: 01/09/2023] Open
Abstract
Brettanomyces yeasts have gained popularity in many sectors of the biotechnological industry, specifically in the field of beer production, but also in wine and ethanol production. Their unique properties enable Brettanomyces to outcompete conventional brewer’s yeast in industrially relevant traits such as production of ethanol and pleasant flavors. Recent advances in next-generation sequencing (NGS) and high-throughput screening techniques have facilitated large population studies allowing the selection of appropriate yeast strains with improved traits. In order to get a better understanding of Brettanomyces species and its potential for beer production, we sequenced the whole genome of 84 strains, which we make available to the scientific community and carried out several in vitro assays for brewing-relevant properties. The collection includes isolates from different substrates and geographical origin. Additionally, we have included two of the oldest Carlsberg Research Laboratory isolates. In this study, we reveal the phylogenetic pattern of Brettanomyces species by comparing the predicted proteomes of each strain. Furthermore, we show that the Brettanomyces collection is well described using similarity in genomic organization, and that there is a direct correlation between genomic background and phenotypic characteristics. Particularly, genomic patterns affecting flavor production, maltose assimilation, beta-glucosidase activity, and phenolic off-flavor (POF) production are reported. This knowledge yields new insights into Brettanomyces population survival strategies, artificial selection pressure, and loss of carbon assimilation traits. On a species-specific level, we have identified for the first time a POF negative Brettanomyces anomalus strain, without the main spoilage character of Brettanomyces species. This strain (CRL-90) has lost DaPAD1, making it incapable of converting ferulic acid to 4-ethylguaiacol (4-EG) and 4-ethylphenol (4-EP). This loss of function makes CRL-90 a good candidate for the production of characteristic Brettanomyces flavors in beverages, without the contaminant increase in POF. Overall, this study displays the potential of exploring Brettanomyces yeast species biodiversity to find strains with relevant properties applicable to the brewing industry.
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Affiliation(s)
- Marc Serra Colomer
- Carlsberg Research Laboratory, Group Research, Copenhagen, Denmark.,National Institute for Food, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Anna Chailyan
- Carlsberg Research Laboratory, Group Research, Copenhagen, Denmark
| | - Ross T Fennessy
- Carlsberg Research Laboratory, Group Research, Copenhagen, Denmark
| | - Kim Friis Olsson
- Carlsberg Research Laboratory, Group Research, Copenhagen, Denmark
| | | | | | - Jochen Forster
- Carlsberg Research Laboratory, Group Research, Copenhagen, Denmark
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