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Fei S, Fu M, Kang J, Luo J, Wang Y, Jia J, Liu S, Li C. Enhancing bacterial cellulose production of Komagataeibacter nataicola through fermented coconut water by Saccharomyces cerevisiae: A metabonomics approach. Curr Res Food Sci 2024; 8:100761. [PMID: 38774267 PMCID: PMC11107218 DOI: 10.1016/j.crfs.2024.100761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/18/2024] [Accepted: 05/03/2024] [Indexed: 05/24/2024] Open
Abstract
Nata de coco, an edible bacterial cellulose (BC) product, is a traditional dessert fermented in coconut water. Production of Nata de coco by Komagataeibacter nataicola is enhanced by pre-fermented coconut water, but its instability is a challenge. Here, BC production by K. nataicola Y19 was significantly improved by Saccharomyces cerevisiae 84-3 through shaping the metabolite profile of the coconut water. Different fermentation time with S. cerevisiae 84-3 resulted in distinct metabolite profiles and different promoting effect on BC yield. Compared to unfermented coconut water, coconut water fermented by S. cerevisiae 84-3 for 1d and 7d enhanced BC yield by 14.1-fold and 5.63-fold, respectively. Analysis between unfermented coconut water and 1d-fermented coconut water showed 129 significantly different metabolites, including organic acids, amino acids, nucleotides, and their derivatives. Prolonged fermentation for 7d changed levels of 155 metabolites belongs to organic acids, amino acids, nucleotides and their derivatives. Spearman correlation analysis further revealed that 17 metabolites were positively correlated with BC yield and 21 metabolites were negatively correlated with BC yield. These metabolites may affect energy metabolism, cell signaling, membrane integrity, and BC production by K. nataicola Y19. The further verification experiment gave the view that BC yield was not only closely related to the types of metabolites but also the concentration of metabolites. This study provides a novel theoretical framework for a highly efficient BC fermentation system utilizing stable fermented coconut water mediums.
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Affiliation(s)
- Shuangwen Fei
- School of Food Science and Engineering, Hainan University, Haikou, 570228, China
| | - Meijuan Fu
- School of Food Science and Engineering, Hainan University, Haikou, 570228, China
| | - Jiamu Kang
- School of Food Science and Engineering, Hainan University, Haikou, 570228, China
| | - Jiaxi Luo
- School of Food Science and Engineering, Hainan University, Haikou, 570228, China
| | - Yanmei Wang
- School of Food Science and Engineering, Hainan University, Haikou, 570228, China
| | - Jia Jia
- School of Food Science and Engineering, Hainan University, Haikou, 570228, China
| | - Sixin Liu
- School of Food Science and Engineering, Hainan University, Haikou, 570228, China
- Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Haikou, 570228, China
- Key Laboratory of Tropical Agricultural Products Processing Technology of Haikou, Haikou, 570228, China
| | - Congfa Li
- School of Food Science and Engineering, Hainan University, Haikou, 570228, China
- Key Laboratory of Food Nutrition and Functional Food of Hainan Province, Haikou, 570228, China
- Key Laboratory of Tropical Agricultural Products Processing Technology of Haikou, Haikou, 570228, China
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Xu Z, Li F, Liu Q, Ma T, Feng X, Zhao G, Zeng D, Li D, Jie H. Chemical composition and microbiota changes across musk secretion stages of forest musk deer. Front Microbiol 2024; 15:1322316. [PMID: 38505545 PMCID: PMC10948612 DOI: 10.3389/fmicb.2024.1322316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 02/16/2024] [Indexed: 03/21/2024] Open
Abstract
Forest musk deer is the most important animal for natural musk production, and the musk composition changes periodically during musk secretion, accompanied by variation in the com-position of deer-symbiotic bacteria. GC-MS and 16S rRNA sequencing were conducted in this study, the dynamic changes to correlated chemical composition and the microbiota across musk secretion periods (prime musk secretion period, vigorous musk secretion period and late musk secretion period) were investigated by integrating its serum testosterone level in different mating states. Results showed that the testosterone level, musk composition and microbiota changed with annual cycle of musk secretion and affected by its mating state. Muscone and the testosterone level peaked at vigorous musk secretion period, and the microbiota of this stage was distinct from the other 2 periods. Actinobacteria, Firmicutes and Proteobacteria were dominant bacteria across musk secretion period. PICRUSt analysis demonstrated that bacteria were ubiquitous in musk pod and involved in the metabolism of antibiotics and terpenoids in musk. "Carbohydrates and amino acids," "fatty acids and CoA" and "secretion of metabolites" were enriched at 3 periods, respectively. Pseudomonas, Corynebacterium, Clostridium, Sulfuricurvum were potential biomarkers across musk secretion. This study provides a more comprehensive understanding of genetic mechanism during musk secretion, emphasizing the importance of Actinobacteria and Corynebacterium in the synthesis of muscone and etiocholanone during musk secretion, which required further validation.
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Affiliation(s)
- Zhongxian Xu
- Sichuan Wildlife Rehabilitation and Breeding Research Center, Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Feng Li
- Sichuan Wildlife Rehabilitation and Breeding Research Center, Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Qian Liu
- Sichuan Wildlife Rehabilitation and Breeding Research Center, Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, China
| | - Tianyuan Ma
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xiaolan Feng
- Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Chongqing Institute of Medicinal Plant Cultivation, Chongqing College of Traditional Chinese Medicine, Chongqing, China
| | - Guijun Zhao
- Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Chongqing Institute of Medicinal Plant Cultivation, Chongqing College of Traditional Chinese Medicine, Chongqing, China
| | - Dejun Zeng
- Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Chongqing Institute of Medicinal Plant Cultivation, Chongqing College of Traditional Chinese Medicine, Chongqing, China
| | - Diyan Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Hang Jie
- Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Chongqing Institute of Medicinal Plant Cultivation, Chongqing College of Traditional Chinese Medicine, Chongqing, China
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Liao H, Li Q, Chen Y, Tang J, Mou B, Lu F, Feng P, Li W, Li J, Fu C, Long W, Xiao X, Han X, Xin W, Yang F, Ma M, Liu B, Yang Y, Wang H. Genome-wide identification of resistance genes and response mechanism analysis of key gene knockout strain to catechol in Saccharomyces cerevisiae. Front Microbiol 2024; 15:1364425. [PMID: 38450166 PMCID: PMC10915035 DOI: 10.3389/fmicb.2024.1364425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 02/13/2024] [Indexed: 03/08/2024] Open
Abstract
Engineering Saccharomyces cerevisiae for biodegradation and transformation of industrial toxic substances such as catechol (CA) has received widespread attention, but the low tolerance of S. cerevisiae to CA has limited its development. The exploration and modification of genes or pathways related to CA tolerance in S. cerevisiae is an effective way to further improve the utilization efficiency of CA. This study identified 36 genes associated with CA tolerance in S. cerevisiae through genome-wide identification and bioinformatics analysis and the ERG6 knockout strain (ERG6Δ) is the most sensitive to CA. Based on the omics analysis of ERG6Δ under CA stress, it was found that ERG6 knockout affects pathways such as intrinsic component of membrane and pentose phosphate pathway. In addition, the study revealed that 29 genes related to the cell wall-membrane system were up-regulated by more than twice, NADPH and NADP+ were increased by 2.48 and 4.41 times respectively, and spermidine and spermine were increased by 2.85 and 2.14 times, respectively, in ERG6Δ. Overall, the response of cell wall-membrane system, the accumulation of spermidine and NADPH, as well as the increased levels of metabolites in pentose phosphate pathway are important findings in improving the CA resistance. This study provides a theoretical basis for improving the tolerance of strains to CA and reducing the damage caused by CA to the ecological environment and human health.
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Affiliation(s)
- Hong Liao
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, College of Life Science, Leshan Normal University, Leshan, Sichuan, China
| | - Qian Li
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, College of Life Science, Leshan Normal University, Leshan, Sichuan, China
- College of Resources, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yulei Chen
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, College of Life Science, Leshan Normal University, Leshan, Sichuan, China
- College of Resources, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jiaye Tang
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, College of Life Science, Leshan Normal University, Leshan, Sichuan, China
- College of Resources, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Borui Mou
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, College of Life Science, Leshan Normal University, Leshan, Sichuan, China
| | - Fujia Lu
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, College of Life Science, Leshan Normal University, Leshan, Sichuan, China
| | - Peng Feng
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, College of Life Science, Leshan Normal University, Leshan, Sichuan, China
| | - Wei Li
- Aba Prefecture Ecological Protection and Development Research Institute, Wenchuan, Sichuan, China
| | - Jialian Li
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, College of Life Science, Leshan Normal University, Leshan, Sichuan, China
| | - Chun Fu
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, College of Life Science, Leshan Normal University, Leshan, Sichuan, China
| | - Wencong Long
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, College of Life Science, Leshan Normal University, Leshan, Sichuan, China
| | - Ximeng Xiao
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, College of Life Science, Leshan Normal University, Leshan, Sichuan, China
| | - Xuebing Han
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
| | - Wenli Xin
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, College of Life Science, Leshan Normal University, Leshan, Sichuan, China
| | - Fengxuan Yang
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, College of Life Science, Leshan Normal University, Leshan, Sichuan, China
| | - Menggen Ma
- College of Resources, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Beidong Liu
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, Zhejiang, China
- Department of Chemistry and Molecular Biology, University of Gothenburg Medicinaregatan, Gothenburg, Sweden
| | - Yaojun Yang
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, College of Life Science, Leshan Normal University, Leshan, Sichuan, China
| | - Hanyu Wang
- Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, College of Life Science, Leshan Normal University, Leshan, Sichuan, China
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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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5
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Schwob M, Kugler V, Wagner R. Cloning and Overexpressing Membrane Proteins Using Pichia pastoris (Komagataella phaffii). Curr Protoc 2023; 3:e936. [PMID: 37933574 DOI: 10.1002/cpz1.936] [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] [Indexed: 11/08/2023]
Abstract
Understanding the structure and function of key proteins located within biological membranes is essential for fundamental knowledge and therapeutic applications. Robust cell systems allowing their actual overexpression are required, among which stands the methylotrophic yeast Pichia pastoris. This system proves highly efficient in producing many eukaryotic membrane proteins of various functions and structures at levels and quality compatible with their subsequent isolation and molecular investigation. This article describes a set of basic guidelines and directions to clone and select recombinant P. pastoris clones overexpressing eukaryotic membrane proteins. Illustrative results obtained for a panel of mammalian membrane proteins are presented, and hints are given on a series of experimental parameters that may substantially improve the amount and/or the functionality of the expressed proteins. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Designing and cloning a P. pastoris expression vector Basic Protocol 2: Integrative transformation of P. pastoris and selection of recombinant clones Basic Protocol 3: Culturing transformed P. pastoris for membrane protein expression Basic Protocol 4: Yeast cell lysis and membrane preparation Basic Protocol 5: Immunodetection of expressed membrane proteins: western blot Alternate Protocol 1: Immunodetection of expressed membrane proteins: dot blot Alternate Protocol 2: Immunodetection of expressed membrane proteins: yeastern blot Basic Protocol 6: Activity assay: ligand-binding analysis of an expressed GPCR.
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Affiliation(s)
- Magali Schwob
- IMPReSs Facility, Biotechnology and Cell Signaling, University of Strasbourg-CNRS, Illkirch, France
- Department of Structural Biology, NovAliX, Strasbourg, France
| | - Valérie Kugler
- IMPReSs Facility, Biotechnology and Cell Signaling, University of Strasbourg-CNRS, Illkirch, France
| | - Renaud Wagner
- IMPReSs Facility, Biotechnology and Cell Signaling, University of Strasbourg-CNRS, Illkirch, France
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Liu R, Pan Y, Wang N, Tang D, Urlacher VB, Li S. Comparative biochemical characterization of mammalian-derived CYP11A1s with cholesterol side-chain cleavage activities. J Steroid Biochem Mol Biol 2023; 229:106268. [PMID: 36764495 DOI: 10.1016/j.jsbmb.2023.106268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023]
Abstract
Steroid drugs, the second largest class of pharmaceuticals after antibiotics, have shown significant anti-inflammatory, anti-allergic, and endocrine-regulating effects. A group of cytochrome P450 enzymes, namely, CYP11A1 isoenzymes from different organisms are capable of converting cholesterol into pregnenolone, which is a pivotal reaction in both steroid metabolism and (bio)synthetic network of steroid products. However, the low activity of CYP11A1s greatly restricts the industrial application of these cholesterol side-chain cleavage enzymes. Herein, we investigate ten CYP11A1 enzymes of different origins and in vitro characterize two CYP11A1s with a relatively higher expression level from Capra hircus and Sus scrofa, together with the CYP11A1s from Homo sapiens and Bos taurus as references. Towards five selected sterol substrates with different side chain structures, S. scrofa CYP11A1 displays relatively higher activities. Through redox partners combination screening, we reveal the optimal redox partner pair of S. scrofa adrenodoxin and C. hircus adrenodoxin reductase. Moreover, the semi-rational mutagenesis for the active sites and substrate entrance channels of human and bovine CYP11A1s is performed based on comparative analysis of their crystal structures. The mutant mBtCYP11A1-Q377A derived from mature B. taurus CYP11A1 shows a 1.46 times higher activity than the wild type enzyme. These results not only demonstrate the tunability of the highly conserved CYP11A1 isoenzymes, but also lay a foundation for the following engineering efforts on these industrially relevant P450 enzymes.
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Affiliation(s)
- Ruxin Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China
| | - Yunjun Pan
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Ning Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China; College of Life Sciences, Shandong Normal University, Jinan, Shandong 250014, China
| | - Dandan Tang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Vlada B Urlacher
- Institute of Biochemistry, Heinrich-Heine-University Düsseldorf, Universitätsstraße 1, Düsseldorf 40225, Germany
| | - Shengying Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266237, China.
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Guo S, Sun X, Li R, Zhang T, Hu F, Liu F, Hua Q. Two strategies to improve the supply of PKS extender units for ansamitocin P-3 biosynthesis by CRISPR-Cas9. BIORESOUR BIOPROCESS 2022; 9:90. [PMID: 38647752 PMCID: PMC10991131 DOI: 10.1186/s40643-022-00583-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/15/2022] [Indexed: 11/10/2022] Open
Abstract
Ansamitocin P-3 (AP-3) produced by Actinosynnema pretiosum is a potent antitumor agent. However, lack of efficient genome editing tools greatly hinders the AP-3 overproduction in A. pretiosum. To solve this problem, a tailor-made pCRISPR-Cas9apre system was developed from pCRISPR-Cas9 for increasing the accessibility of A. pretiosum to genetic engineering, by optimizing cas9 for the host codon preference and replacing pSG5 with pIJ101 replicon. Using pCRISPR-Cas9apre, five large-size gene clusters for putative competition pathway were individually deleted with homology-directed repair (HDR) and their effects on AP-3 yield were investigated. Especially, inactivation of T1PKS-15 increased AP-3 production by 27%, which was most likely due to the improved intracellular triacylglycerol (TAG) pool for essential precursor supply of AP-3 biosynthesis. To enhance a "glycolate" extender unit, two combined bidirectional promoters (BDPs) ermEp-kasOp and j23119p-kasOp were knocked into asm12-asm13 spacer in the center region of gene cluster, respectively, by pCRISPR-Cas9apre. It is shown that in the two engineered strains BDP-ek and BDP-jk, the gene transcription levels of asm13-17 were significantly upregulated to improve the methoxymalonyl-acyl carrier protein (MM-ACP) biosynthetic pathway and part of the post-PKS pathway. The AP-3 yields of BDP-ek and BDP-jk were finally increased by 30% and 50% compared to the parent strain L40. Both CRISPR-Cas9-mediated engineering strategies employed in this study contributed to the availability of AP-3 PKS extender units and paved the way for further metabolic engineering of ansamitocin overproduction.
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Affiliation(s)
- Siyu Guo
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Xueyuan Sun
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Ruihua Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Tianyao Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Fengxian Hu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Feng Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China.
| | - Qiang Hua
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China.
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology, 130 Meilong Road, Shanghai, 200237, China.
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Kessi-Pérez EI, González A, Palacios JL, Martínez C. Yeast as a biological platform for vitamin D production: A promising alternative to help reduce vitamin D deficiency in humans. Yeast 2022; 39:482-492. [PMID: 35581681 DOI: 10.1002/yea.3708] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/10/2022] [Accepted: 05/12/2022] [Indexed: 11/08/2022] Open
Abstract
Vitamin D is an important human hormone, known primarily to be involved in the intestinal absorption of calcium and phosphate, but it is also involved in various non-skeletal processes (molecular, cellular, immune, and neuronal). One of the main health problems nowadays is the vitamin D deficiency of the human population due to lack of sun exposure, with estimates of one billion people worldwide with vitamin D deficiency, and the consequent need for clinical intervention (i.e., prescription of pharmacological vitamin D supplements). An alternative to reduce vitamin D deficiency is to produce good dietary sources of it, a scenario in which the yeast Saccharomyces cerevisiae seems to be a promising alternative. This review focuses on the potential use of yeast as a biological platform to produce vitamin D, summarizing both the biology aspects of vitamin D (synthesis, ecology and evolution, metabolism, and bioequivalence) and the work done to produce it in yeast (both for vitamin D2 and for vitamin D3 ), highlighting existing challenges and potential solutions. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Eduardo I Kessi-Pérez
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile.,Departamento de Ciencia y Tecnología de los Alimentos, Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Adens González
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - José Luis Palacios
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile
| | - Claudio Martínez
- Centro de Estudios en Ciencia y Tecnología de Alimentos (CECTA), Universidad de Santiago de Chile (USACH), Santiago, Chile.,Departamento de Ciencia y Tecnología de los Alimentos, Universidad de Santiago de Chile (USACH), Santiago, Chile
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9
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Jiang YQ, Lin JP. Recent progress in strategies for steroid production in yeasts. World J Microbiol Biotechnol 2022; 38:93. [PMID: 35441962 DOI: 10.1007/s11274-022-03276-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/24/2022] [Indexed: 10/18/2022]
Abstract
As essential structural molecules of fungal cell membrane, ergosterol is not only an important component of fungal growth and stress-resistance but also a key precursor for manufacturing steroid drugs of pharmaceutical or agricultural significance. So far, ergosterol biosynthesis in yeast has been elucidated elaborately, and efforts have been made to increase ergosterol production through regulation of ergosterol metabolism and storage. Furthermore, the same intermediates shared by yeasts and animals or plants make the construction of heterologous sterol pathways in yeast a promising approach to synthesize valuable steroids, such as phytosteroids and animal steroid hormones. During these challenging processes, several obstacles have arisen and been combated with great endeavors. This paper reviews recent research progress of yeast metabolic engineering for improving the production of ergosterol and heterologous steroids. The remaining tactics are also discussed.
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Affiliation(s)
- Yi-Qi Jiang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Jian-Ping Lin
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China.
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Impairment of carotenoid biosynthesis through CAR1 gene mutation results in CoQ 10, sterols, and phytoene accumulation in Rhodotorula mucilaginosa. Appl Microbiol Biotechnol 2021; 106:317-327. [PMID: 34910239 DOI: 10.1007/s00253-021-11673-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 10/26/2021] [Accepted: 10/28/2021] [Indexed: 10/19/2022]
Abstract
Red yeasts, mainly included in the genera Rhodotorula, Rhodosporidiobolus, and Sporobolomyces, are renowned biocatalysts for the production of a wide range of secondary metabolites of commercial interest, among which lipids, carotenoids, and other isoprenoids. The production of all these compounds is tightly interrelated as they share acetyl-CoA and the mevalonate pathway as common intermediates. Here, T-DNA insertional mutagenesis was applied to the wild type strain C2.5t1 of Rhodotorula mucilaginosa for the isolation of albino mutants with impaired carotenoids biosynthesis. The rationale behind this approach was that a blockage in carotenoid biosynthetic pathway could divert carbon flux toward the production of lipids and/or other molecules deriving from terpenoid precursors. One characterized albino mutant, namely, strain W4, carries a T-DNA insertion in the CAR1 gene coding for phytoene desaturase. When cultured in glycerol-containing medium, W4 strain showed significant decreases in cell density and fatty acids content in respect to the wild type strain. Conversely, it reached significantly higher productions of phytoene, CoQ10, and sterols. These were supported by an increased expression of CAR2 gene that codes for phytoene synthase/lycopene cyclase. Thus, in accordance with the starting hypothesis, the impairment of carotenoids biosynthesis can be explored to pursue the biotechnological exploitation of red yeasts for enhanced production of secondary metabolites with several commercial applications. KEY POINTS: • The production of lipids, carotenoids, and other isoprenoids is tightly interrelated. • CAR1 gene mutation results in the overproduction of phytoene, CoQ10, and sterols. • Albino mutants are promising tools for the production of secondary metabolites.
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11
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Gu Y, Jiao X, Ye L, Yu H. Metabolic engineering strategies for de novo biosynthesis of sterols and steroids in yeast. BIORESOUR BIOPROCESS 2021; 8:110. [PMID: 38650187 PMCID: PMC10992410 DOI: 10.1186/s40643-021-00460-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 10/16/2021] [Indexed: 12/17/2022] Open
Abstract
Steroidal compounds are of great interest in the pharmaceutical field, with steroidal drugs as the second largest category of medicine in the world. Advances in synthetic biology and metabolic engineering have enabled de novo biosynthesis of sterols and steroids in yeast, which is a green and safe production route for these valuable steroidal compounds. In this review, we summarize the metabolic engineering strategies developed and employed for improving the de novo biosynthesis of sterols and steroids in yeast based on the regulation mechanisms, and introduce the recent progresses in de novo synthesis of some typical sterols and steroids in yeast. The remaining challenges and future perspectives are also discussed.
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Affiliation(s)
- Yuehao Gu
- Key Laboratory of Biomass Chemical Engineering (Education Ministry), College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Xue Jiao
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Lidan Ye
- Key Laboratory of Biomass Chemical Engineering (Education Ministry), College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China.
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China.
| | - Hongwei Yu
- Key Laboratory of Biomass Chemical Engineering (Education Ministry), College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China.
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China.
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12
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Chen Y, Wu J, Yu D, Du X. Advances in steroidal saponins biosynthesis. PLANTA 2021; 254:91. [PMID: 34617240 DOI: 10.1007/s00425-021-03732-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 09/11/2021] [Indexed: 06/13/2023]
Abstract
This work reviews recent advances in the pathways and key enzymes of steroidal saponins biosynthesis and sets the foundation for the biotechnological production of these useful compounds through transformation of microorganisms. Steroidal saponins, due to their specific chemical structures and active effects, have long been important natural products and that are irreplaceable in hormone production and other pharmaceutical industries. This article comprehensively reviewed the previous and current research progress and summarized the biosynthesis pathways and key biosynthetic enzymes of steroidal saponins that have been discovered in plants and microoganisms. On the basis of the general biosynthetic pathway in plants, it was found that the starting components, intermediates and catalysing enzymes were diverse between plants and microorganisms; however, the functions of their related enzymes tended to be similar. The biosynthesis pathways of steroidal saponins in microorganisms and marine organisms have not been revealed as clearly as those in plants and need further investigation. The elucidation of biosynthetic pathways and key enzymes is essential for understanding the synthetic mechanisms of these compounds and provides researchers with important information to further develop and implement the massive production of steroidal saponins by biotechnological approaches and methodologies.
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Affiliation(s)
- Yiyang Chen
- Key Laboratory of Chinese Materia Medica, Ministry of Education, Pharmaceutical College, Heilongjiang University of Chinese Medicine, 24 Heping Road, Harbin, 150040, China
| | - Junkai Wu
- Key Laboratory of Chinese Materia Medica, Ministry of Education, Pharmaceutical College, Heilongjiang University of Chinese Medicine, 24 Heping Road, Harbin, 150040, China
| | - Dan Yu
- Key Laboratory of Chinese Materia Medica, Ministry of Education, Pharmaceutical College, Heilongjiang University of Chinese Medicine, 24 Heping Road, Harbin, 150040, China
| | - Xiaowei Du
- Key Laboratory of Chinese Materia Medica, Ministry of Education, Pharmaceutical College, Heilongjiang University of Chinese Medicine, 24 Heping Road, Harbin, 150040, China.
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13
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Li M, Zhao M, Wei P, Zhang C, Lu W. Biosynthesis of Soyasapogenol B by Engineered Saccharomyces cerevisiae. Appl Biochem Biotechnol 2021; 193:3202-3213. [PMID: 34097255 DOI: 10.1007/s12010-021-03599-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 05/28/2021] [Indexed: 11/28/2022]
Abstract
Soyasapogenol B is an oleanane-type pentacyclic triterpene that has various applications in food and healthcare and has a higher biological activity than soyasaponin. Saccharomyces cerevisiae is a potential platform for terpenoid production with mature genetic tools for metabolic pathway manipulation. In this study, we developed a biosynthesis method to produce soyasapogenol B. First, we expressed β-amyrin synthase derived from Glycyrrhiza glabra in S. cerevisiae to generate β-amyrin, as the precursor of soyasapogenol B. Several different types of promoters were then used to regulate the expression of key genes in the mevalonate pathway (MVA), and this subsequently increased the yield of β-amyrin to 17.6 mg/L, 25-fold more than that produced in the original strain L01 (0.68 mg/L). Then, using the β-amyrin-producing strain, we expressed soyasapogenol B synthases from Medicago truncatula (CYP93E2 and CYP72A61V2) and from G. glabra (CYP93E3 and CYP72A566). Soyasapogenol B yields were then optimized by using soyasapogenol B synthases and cytochrome P450 reductase from G. glabra. The most effective soyasapogenol B production strain was used for fermentation, and the yield of soyasapogenol B reached 2.9 mg/L in flask and 8.36 mg/L in a 5-L bioreactor with fed glucose and ethanol. This study demonstrated the heterologous synthesis of soyasapogenol B in S. cerevisiae using the combined expression of CYP93E3 and CYP72A566 in the synthesis pathway, which significantly increased the production of soyasapogenol B and provides a reference method for the biosynthesis of other triterpenes.
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Affiliation(s)
- Man Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Mengya Zhao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Panpan Wei
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Chuanbo Zhang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
- Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education, Tianjin, People's Republic of China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, People's Republic of China
| | - Wenyu Lu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.
- Key Laboratory of System Bioengineering (Tianjin University), Ministry of Education, Tianjin, People's Republic of China.
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, People's Republic of China.
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14
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Wang H, Chen B, Tian J, Kong Z. Verticillium dahliae VdBre1 is required for cotton infection by modulating lipid metabolism and secondary metabolites. Environ Microbiol 2020; 23:1991-2003. [PMID: 33185953 DOI: 10.1111/1462-2920.15319] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/19/2020] [Accepted: 11/09/2020] [Indexed: 01/01/2023]
Abstract
The soil-borne ascomycete Verticillium dahliae causes wilt disease in more than two hundred dicotyledonous plants including the economically important crop cotton, and results in a severe reduction in cotton fiber yield and quality. During infection, V. dahliae secretes numerous secondary metabolites, which act as toxic factors to promote the infection process. However, the mechanism underlying how V. dahliae secondary metabolites regulate cotton infection remains largely unexplored. In this study, we report that VdBre1, an ubiquitin ligase (E3) enzyme to modify H2B, regulates radial growth and conidia production of V. dahliae. The VdBre1 deletion strains show nonpathogenic symptoms on cotton, and microscopic inspection and penetration assay indicated that penetration ability of the ∆VdBre1 strain was dramatically reduced. RNA-seq revealed that a total of 1643 differentially expressed genes between the ∆VdBre1 strain and the wild type strain V592, among which genes related to lipid metabolism were significantly overrepresented. Remarkably, the volume of lipid droplets in the ∆VdBre1 conidia was shown to be smaller than that of wild-type strains. Further metabolomics analysis revealed that the pathways of lipid metabolism and secondary metabolites, such as steroid biosynthesis and metabolism of terpenoids and polyketides, have dramatically changed in the ∆VdBre1 metabolome. Taken together, these results indicate that VdBre1 plays crucial roles in cotton infection and pathogenecity, by globally regulating lipid metabolism and secondary metabolism of V. dahliae.
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Affiliation(s)
- Huan Wang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.,State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bin Chen
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Juan Tian
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhaosheng Kong
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.,State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
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15
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Yeast as a promising heterologous host for steroid bioproduction. J Ind Microbiol Biotechnol 2020; 47:829-843. [PMID: 32661815 PMCID: PMC7358296 DOI: 10.1007/s10295-020-02291-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/06/2020] [Indexed: 12/18/2022]
Abstract
With the rapid development of synthetic biology and metabolic engineering technologies, yeast has been generally considered as promising hosts for the bioproduction of secondary metabolites. Sterols are essential components of cell membrane, and are the precursors for the biosynthesis of steroid hormones, signaling molecules, and defense molecules in the higher eukaryotes, which are of pharmaceutical and agricultural significance. In this mini-review, we summarize the recent engineering efforts of using yeast to synthesize various steroids, and discuss the structural diversity that the current steroid-producing yeast can achieve, the challenge and the potential of using yeast as the bioproduction platform of various steroids from higher eukaryotes.
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16
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Wiltschi B, Cernava T, Dennig A, Galindo Casas M, Geier M, Gruber S, Haberbauer M, Heidinger P, Herrero Acero E, Kratzer R, Luley-Goedl C, Müller CA, Pitzer J, Ribitsch D, Sauer M, Schmölzer K, Schnitzhofer W, Sensen CW, Soh J, Steiner K, Winkler CK, Winkler M, Wriessnegger T. Enzymes revolutionize the bioproduction of value-added compounds: From enzyme discovery to special applications. Biotechnol Adv 2020; 40:107520. [DOI: 10.1016/j.biotechadv.2020.107520] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 10/18/2019] [Accepted: 01/13/2020] [Indexed: 12/11/2022]
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17
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Li WN, Fan DD. Biocatalytic strategies for the production of ginsenosides using glycosidase: current state and perspectives. Appl Microbiol Biotechnol 2020; 104:3807-3823. [DOI: 10.1007/s00253-020-10455-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 01/31/2020] [Accepted: 02/07/2020] [Indexed: 12/22/2022]
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18
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19
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Sui Y, Wisniewski M, Droby S, Piombo E, Wu X, Yue J. Genome Sequence, Assembly, and Characterization of the Antagonistic Yeast Candida oleophila Used as a Biocontrol Agent Against Post-harvest Diseases. Front Microbiol 2020; 11:295. [PMID: 32158440 PMCID: PMC7052047 DOI: 10.3389/fmicb.2020.00295] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 02/10/2020] [Indexed: 11/29/2022] Open
Abstract
Candida oleophila is an effective biocontrol agent used to control post-harvest diseases of fruits and vegetables. C. oleophila I-182 was the active agent used in the first-generation yeast-based commercial product, Aspire®, for post-harvest disease management. Several action modes, like competition for nutrients and space, induction of pathogenesis-related genes in host tissues, and production of extracellular lytic enzymes, have been demonstrated for the biological control activity exhibited by C. oleophila through which it inhibits post-harvest pathogens. In the present study, the whole genome of C. oleophila I-182 was sequenced using PacBio and Illumina shotgun sequencing technologies, yielding an estimated genome size of 14.73 Mb. The genome size is similar in length to that of the model yeast strain Saccharomyces cerevisiae S288c. Based on the assembled genome, protein-coding sequences were identified and annotated. The predicted genes were further assigned with gene ontology terms and clustered in special functional groups. A comparative analysis of C. oleophila proteome with the proteomes of 11 representative yeasts revealed 2 unique and 124 expanded families of proteins in C. oleophila. Availability of the genome sequence will facilitate a better understanding the properties of biocontrol yeasts at the molecular level.
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Affiliation(s)
- Yuan Sui
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, College of Forestry and Life Science, Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, China
| | - Michael Wisniewski
- U.S. Department of Agriculture-Agricultural Research Service, Kearneysville, WV, United States
| | - Samir Droby
- Department of Postharvest Science, Agricultural Research Organization, Volcani Center, Bet Dagan, Israel
| | - Edoardo Piombo
- Department of Agricultural, Forestry and Food Sciences, University of Turin, Turin, Italy
| | - Xuehong Wu
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Junyang Yue
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
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20
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Yeast Engineering for New Antifungal Compounds: A Contextualized Overview. Fungal Biol 2020. [DOI: 10.1007/978-3-030-41870-0_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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21
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Zhang R, Zhang Y, Wang Y, Yao M, Zhang J, Liu H, Zhou X, Xiao W, Yuan Y. Pregnenolone Overproduction in Yarrowia lipolytica by Integrative Components Pairing of the Cytochrome P450scc System. ACS Synth Biol 2019; 8:2666-2678. [PMID: 31621297 DOI: 10.1021/acssynbio.9b00018] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Microbial production of steroid drugs exhibits great potentials in much greener and more sustainable manners, in which engineering multiple cytochrome P450s is the prerequisite requirement. The pairing of multicomponents of P450 systems is a tremendous challenge. Herein, biosynthesis of pregnenolone (a common precursor of steroid drugs) in Yarrowia lipolytica was taken as a typical instance to explore the engineering strategy of the cytochrome P450 side-chain cleavage enzyme (P450scc) system. The mature forms of the components belonging to P450scc system, CYP11A1, adrenodoxin (Adx), and adrenodoxin reductase (AdR), were coexpressed in a former constructed campesterol producing strain. To maximize pregnenolone production, an integrative components pairing strategy was proposed for pairing the component sources and balancing the expression levels of CYP11A1, Adx, and AdR. Led by the above approaches, a 2344-fold improvement of pregnenolone titer was achieved at the shake flask level. Consequently, a highest reported pregnenolone titer of 78.0 mg/L in microbes was obtained in a 5 L bioreactor. Our study not only highlights the integrative components pairing of cytochrome P450scc as a general strategy for engineering other cytochrome P450s, but also provides a feasible and efficient platform of Y. lipolytica for other steroids production.
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Affiliation(s)
- Ruosi Zhang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Yu Zhang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Ying Wang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Mingdong Yao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Jinlai Zhang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Hong Liu
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Xiao Zhou
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Wenhai Xiao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
| | - Yingjin Yuan
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China
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22
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Wang R, Ma P, Li C, Xiao L, Liang Z, Dong J. Combining transcriptomics and metabolomics to reveal the underlying molecular mechanism of ergosterol biosynthesis during the fruiting process of Flammulina velutipes. BMC Genomics 2019; 20:999. [PMID: 31856715 PMCID: PMC6924009 DOI: 10.1186/s12864-019-6370-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 12/05/2019] [Indexed: 01/01/2023] Open
Abstract
Background Flammulina velutipes has been recognized as a useful basidiomycete with nutritional and medicinal values. Ergosterol, one of the main sterols of F. velutipes is an important precursor of novel anticancer and anti-HIV drugs. Therefore, many studies have focused on the biosynthesis of ergosterol and have attempted to upregulate its content in multiple organisms. Great progress has been made in understanding the regulation of ergosterol biosynthesis in Saccharomyces cerevisiae. However, this molecular mechanism in F. velutipes remains largely uncharacterized. Results In this study, nine cDNA libraries, prepared from mycelia, young fruiting bodies and mature fruiting bodies of F. velutipes (three replicate sets for each stage), were sequenced using the Illumina HiSeq™ 4000 platform, resulting in at least 6.63 Gb of clean reads from each library. We studied the changes in genes and metabolites in the ergosterol biosynthesis pathway of F. velutipes during the development of fruiting bodies. A total of 13 genes (6 upregulated and 7 downregulated) were differentially expressed during the development from mycelia to young fruiting bodies (T1), while only 1 gene (1 downregulated) was differentially expressed during the development from young fruiting bodies to mature fruiting bodies (T2). A total of 7 metabolites (3 increased and 4 reduced) were found to have changed in content during T1, and 4 metabolites (4 increased) were found to be different during T2. A conjoint analysis of the genome-wide connection network revealed that the metabolites that were more likely to be regulated were primarily in the post-squalene pathway. Conclusions This study provides useful information for understanding the regulation of ergosterol biosynthesis and the regulatory relationship between metabolites and genes in the ergosterol biosynthesis pathway during the development of fruiting bodies in F. velutipes.
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Affiliation(s)
- Ruihong Wang
- College of Life Sciences, Northwest A&F University, Yangling, 712100, China
| | - Pengda Ma
- College of Life Sciences, Northwest A&F University, Yangling, 712100, China
| | - Chen Li
- College of Life Sciences, Northwest A&F University, Yangling, 712100, China
| | - Lingang Xiao
- Shaanxi Zhongxing Gaoke Biological Technology Co., Ltd, Yangling, 712100, China
| | - Zongsuo Liang
- College of Life Sciences, Northwest A&F University, Yangling, 712100, China.,College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, China
| | - Juane Dong
- College of Life Sciences, Northwest A&F University, Yangling, 712100, China.
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Vilela A, Bacelar E, Pinto T, Anjos R, Correia E, Gonçalves B, Cosme F. Beverage and Food Fragrance Biotechnology, Novel Applications, Sensory and Sensor Techniques: An Overview. Foods 2019; 8:E643. [PMID: 31817355 PMCID: PMC6963671 DOI: 10.3390/foods8120643] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 11/29/2019] [Accepted: 12/03/2019] [Indexed: 12/19/2022] Open
Abstract
Flavours and fragrances are especially important for the beverage and food industries. Biosynthesis or extraction are the two main ways to obtain these important compounds that have many different chemical structures. Consequently, the search for new compounds is challenging for academic and industrial investigation. This overview aims to present the current state of art of beverage fragrance biotechnology, including recent advances in sensory and sensor methodologies and statistical techniques for data analysis. An overview of all the recent findings in beverage and food fragrance biotechnology, including those obtained from natural sources by extraction processes (natural plants as an important source of flavours) or using enzymatic precursor (hydrolytic enzymes), and those obtained by de novo synthesis (microorganisms' respiration/fermentation of simple substrates such as glucose and sucrose), are reviewed. Recent advances have been made in what concerns "beverage fragrances construction" as also in their application products. Moreover, novel sensory and sensor methodologies, primarily used for fragrances quality evaluation, have been developed, as have statistical techniques for sensory and sensors data treatments, allowing a rapid and objective analysis.
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Affiliation(s)
- Alice Vilela
- CQ-VR, Chemistry Research Centre, Department of Biology and Environment, School of Life Sciences and Environment, University of Trás-os-Montes and Alto Douro, P-5000-801 Vila Real, Portugal;
| | - Eunice Bacelar
- CITAB, Centre for the Research and Technology of Agro-Environmental and Biological Sciences, Department of Biology and Environment, School of Life Sciences and Environment, University of Trás-os-Montes and Alto Douro, P-5000-801 Vila Real, Portugal; (E.B.); (T.P.); (R.A.); (B.G.)
| | - Teresa Pinto
- CITAB, Centre for the Research and Technology of Agro-Environmental and Biological Sciences, Department of Biology and Environment, School of Life Sciences and Environment, University of Trás-os-Montes and Alto Douro, P-5000-801 Vila Real, Portugal; (E.B.); (T.P.); (R.A.); (B.G.)
| | - Rosário Anjos
- CITAB, Centre for the Research and Technology of Agro-Environmental and Biological Sciences, Department of Biology and Environment, School of Life Sciences and Environment, University of Trás-os-Montes and Alto Douro, P-5000-801 Vila Real, Portugal; (E.B.); (T.P.); (R.A.); (B.G.)
| | - Elisete Correia
- CQ-VR, Chemistry Research Centre, Department of Mathematics, School of Life Sciences and Environment, University of Trás-os-Montes and Alto Douro, P-5000-801 Vila Real, Portugal;
- Center for Computational and Stochastic Mathematics (CEMAT), Department of Mathematics, IST-UL, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal
| | - Berta Gonçalves
- CITAB, Centre for the Research and Technology of Agro-Environmental and Biological Sciences, Department of Biology and Environment, School of Life Sciences and Environment, University of Trás-os-Montes and Alto Douro, P-5000-801 Vila Real, Portugal; (E.B.); (T.P.); (R.A.); (B.G.)
| | - Fernanda Cosme
- CQ-VR, Chemistry Research Centre, Department of Biology and Environment, School of Life Sciences and Environment, University of Trás-os-Montes and Alto Douro, P-5000-801 Vila Real, Portugal;
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24
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Madhavan A, Arun KB, Sindhu R, Binod P, Kim SH, Pandey A. Tailoring of microbes for the production of high value plant-derived compounds: From pathway engineering to fermentative production. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:140262. [PMID: 31404685 DOI: 10.1016/j.bbapap.2019.140262] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 08/03/2019] [Accepted: 08/05/2019] [Indexed: 12/20/2022]
Abstract
Plant natural products have been an attracting platform for the isolation of various active drugs and other bioactives. However large-scale extraction of these compounds is affected by the difficulty in mass cultivation of these plants and absence of strategies for successful extraction. Even though, synthesis by chemical method is an alternative method; it is less efficient as their chemical structure is highly complex which involve enantio-selectivity. Thus an alternate bio-system for heterologous production of plant natural products using microbes has emerged. Advent of various omics, synthetic and metabolic engineering strategies revolutionised the field of heterologous plant metabolite production. In this context, various engineering methods taken to synthesise plant natural products are described with an additional focus to fermentation strategies.
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Affiliation(s)
- Aravind Madhavan
- Rajiv Gandhi Centre for Biotechnology, Trivandrum 695 014, India
| | | | - Raveendran Sindhu
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR- NIIST), Trivandrum 695 019, India
| | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR- NIIST), Trivandrum 695 019, India
| | - Sang Hyoun Kim
- Department of Civil and Environmental Engineering, Yonsei University, Seoul, South Korea
| | - Ashok Pandey
- Department of Civil and Environmental Engineering, Yonsei University, Seoul, South Korea; Center for Innovation and Translational Research, CSIR- Indian Institute of Toxicology Research (CSIR-IITR), Lucknow 226 001, India.
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25
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Nazhand A, Durazzo A, Lucarini M, Mobilia MA, Omri B, Santini A. Rewiring cellular metabolism for heterologous biosynthesis of Taxol. Nat Prod Res 2019; 34:110-121. [DOI: 10.1080/14786419.2019.1630122] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Amirhossein Nazhand
- Biotechnology Department, Sari University of Agricultural Sciences and Natural Resources, Mazandaran, Sari, Iran
| | | | | | | | - Besma Omri
- Laboratory of Improvement & Integrated Development of Animal Productivity & Food Resources, Higher School of Agriculture of Mateur, University of Carthage, Bizerte, Tunisia
| | - Antonello Santini
- Department of Pharmacy, University of Napoli Federico II, Napoli, Italy
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26
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Moser S, Pichler H. Identifying and engineering the ideal microbial terpenoid production host. Appl Microbiol Biotechnol 2019; 103:5501-5516. [PMID: 31129740 PMCID: PMC6597603 DOI: 10.1007/s00253-019-09892-y] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 05/03/2019] [Accepted: 05/06/2019] [Indexed: 12/11/2022]
Abstract
More than 70,000 different terpenoid structures are known so far; many of them offer highly interesting applications as pharmaceuticals, flavors and fragrances, or biofuels. Extraction of these compounds from their natural sources or chemical synthesis is-in many cases-technically challenging with low or moderate yields while wasting valuable resources. Microbial production of terpenoids offers a sustainable and environment-friendly alternative starting from simple carbon sources and, frequently, safeguards high product specificity. Here, we provide an overview on employing recombinant bacteria and yeasts for heterologous de novo production of terpenoids. Currently, Escherichia coli and Saccharomyces cerevisiae are the two best-established production hosts for terpenoids. An increasing number of studies have been successful in engineering alternative microorganisms for terpenoid biosynthesis, which we intend to highlight in this review. Moreover, we discuss the specific engineering challenges as well as recent advances for microbial production of different classes of terpenoids. Rationalizing the current stages of development for different terpenoid production hosts as well as future prospects shall provide a valuable decision basis for the selection and engineering of the cell factory(ies) for industrial production of terpenoid target molecules.
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Affiliation(s)
- Sandra Moser
- Austrian Centre of Industrial Biotechnology (acib GmbH), Petersgasse 14, 8010, Graz, Austria
- Institute of Molecular Biotechnology, NAWI Graz, BioTechMed Graz, Graz University of Technology, Petersgasse 14/2, 8010, Graz, Austria
| | - Harald Pichler
- Austrian Centre of Industrial Biotechnology (acib GmbH), Petersgasse 14, 8010, Graz, Austria.
- Institute of Molecular Biotechnology, NAWI Graz, BioTechMed Graz, Graz University of Technology, Petersgasse 14/2, 8010, Graz, Austria.
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27
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Primary and Secondary Metabolic Effects of a Key Gene Deletion (Δ YPL062W) in Metabolically Engineered Terpenoid-Producing Saccharomyces cerevisiae. Appl Environ Microbiol 2019; 85:AEM.01990-18. [PMID: 30683746 DOI: 10.1128/aem.01990-18] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 01/16/2019] [Indexed: 01/06/2023] Open
Abstract
Saccharomyces cerevisiae is an established cell factory for production of terpenoid pharmaceuticals and chemicals. Numerous studies have demonstrated that deletion or overexpression of off-pathway genes in yeast can improve terpenoid production. The deletion of YPL062W in S. cerevisiae, in particular, has benefitted carotenoid production by channeling carbon toward carotenoid precursors acetyl coenzyme A (acetyl-CoA) and mevalonate. The genetic function of YPL062W and the molecular mechanisms for these benefits are unknown. In this study, we systematically examined this gene deletion to uncover the gene function and its molecular mechanism. RNA sequencing (RNA-seq) analysis uncovered that YPL062W deletion upregulated the pyruvate dehydrogenase bypass, the mevalonate pathway, heterologous expression of galactose (GAL) promoter-regulated genes, energy metabolism, and membrane composition synthesis. Bioinformatics analysis and serial promoter deletion assay revealed that YPL062W functions as a core promoter for ALD6 and that the expression level of ALD6 is negatively correlated to terpenoid productivity. We demonstrate that ΔYPL062W increases the production of all major terpenoid classes (C10, C15, C20, C30, and C40). Our study not only elucidated the biological function of YPL062W but also provided a detailed methodology for understanding the mechanistic aspects of strain improvement.IMPORTANCE Although computational and reverse metabolic engineering approaches often lead to improved gene deletion mutants for cell factory engineering, the systems level effects of such gene deletions on the production phenotypes have not been extensively studied. Understanding the genetic and molecular function of such gene alterations on production strains will minimize the risk inherent in the development of large-scale fermentation processes, which is a daunting challenge in the field of industrial biotechnology. Therefore, we established a detailed experimental and systems biology approach to uncover the molecular mechanisms of YPL062W deletion in S. cerevisiae, which is shown to improve the production of all terpenoid classes. This study redefines the genetic function of YPL062W, demonstrates a strong correlation between YPL062W and terpenoid production, and provides a useful modification for the creation of terpenoid production platform strains. Further, this study underscores the benefits of detailed and systematic characterization of the metabolic effects of genetic alterations on engineered biosynthetic factories.
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28
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Hu Z, Li G, Sun Y, Niu Y, Ma L, He B, Ai M, Han J, Zeng B. Gene transcription profiling of Aspergillus oryzae 3.042 treated with ergosterol biosynthesis inhibitors. Braz J Microbiol 2019; 50:43-52. [PMID: 30637636 PMCID: PMC6863321 DOI: 10.1007/s42770-018-0026-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 10/04/2018] [Indexed: 01/05/2023] Open
Abstract
Ergosterol, a unique component of fungal cells, is not only important for fungal growth and stress responses but also holds great economic value. Limited studies have been performed on ergosterol biosynthesis in Aspergillus oryzae, a safe filamentous fungus that has been used for the manufacture of oriental fermented foods. This study revealed that the ergosterol biosynthesis pathway is conserved between Saccharomyces cerevisiae and A. oryzae 3.042 by treatment with ergosterol biosynthesis inhibitors and bioinformatics analysis. However, the ergosterol biosynthesis pathway in A. oryzae 3.042 is more complicated than that in S. cerevisiae as there are multiple paralogs encoding the same biosynthetic enzymes. Using RNA-seq, this study identified 138 and 104 differentially expressed genes (DEG) in response to the ergosterol biosynthesis inhibitors tebuconazole and terbinafine, respectively. The results showed that the most common DEGs were transport- and metabolism-related genes. There were only 17 DEGs regulated by both tebuconazole and terbinafine treatments and there were 256 DEGs between tebuconazole and terbinafine treatments. These results provide new information on A. oryzae ergosterol biosynthesis and regulation mechanisms, which may lay the foundation for genetic modification of the ergosterol biosynthesis pathway in A. oryzae.
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Affiliation(s)
- Zhihong Hu
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-vitro Diagnostic Reagents and Devices of Jiangxi Province, college of life sciences, Jiangxi Science & Technology Normal University, Nanchang, 330013, China
| | - Ganghua Li
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, Hubei Normal University, Huangshi, 435002, China
| | - Yunlong Sun
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-vitro Diagnostic Reagents and Devices of Jiangxi Province, college of life sciences, Jiangxi Science & Technology Normal University, Nanchang, 330013, China
| | - Yali Niu
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-vitro Diagnostic Reagents and Devices of Jiangxi Province, college of life sciences, Jiangxi Science & Technology Normal University, Nanchang, 330013, China
| | - Long Ma
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-vitro Diagnostic Reagents and Devices of Jiangxi Province, college of life sciences, Jiangxi Science & Technology Normal University, Nanchang, 330013, China
| | - Bin He
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-vitro Diagnostic Reagents and Devices of Jiangxi Province, college of life sciences, Jiangxi Science & Technology Normal University, Nanchang, 330013, China
| | - Mingqiang Ai
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-vitro Diagnostic Reagents and Devices of Jiangxi Province, college of life sciences, Jiangxi Science & Technology Normal University, Nanchang, 330013, China
| | - Jizhong Han
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-vitro Diagnostic Reagents and Devices of Jiangxi Province, college of life sciences, Jiangxi Science & Technology Normal University, Nanchang, 330013, China
| | - Bin Zeng
- Jiangxi Key Laboratory of Bioprocess Engineering and Co-Innovation Center for In-vitro Diagnostic Reagents and Devices of Jiangxi Province, college of life sciences, Jiangxi Science & Technology Normal University, Nanchang, 330013, China.
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29
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Evaluation of lipid profile in different tissues of Japanese abalone Haliotis discus hannai Ino with UPLC-ESI-Q-TOF-MS-based lipidomic study. Food Chem 2018; 265:49-56. [DOI: 10.1016/j.foodchem.2018.05.077] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 05/13/2018] [Accepted: 05/16/2018] [Indexed: 01/05/2023]
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30
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Farbo MG, Urgeghe PP, Fiori S, Marcello A, Oggiano S, Balmas V, Hassan ZU, Jaoua S, Migheli Q. Effect of yeast volatile organic compounds on ochratoxin A-producing Aspergillus carbonarius and A. ochraceus. Int J Food Microbiol 2018; 284:1-10. [DOI: 10.1016/j.ijfoodmicro.2018.06.023] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Revised: 06/25/2018] [Accepted: 06/29/2018] [Indexed: 01/17/2023]
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31
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Spady ES, Wyche TP, Rollins NJ, Clardy J, Way JC, Silver PA. Mammalian Cells Engineered To Produce New Steroids. Chembiochem 2018; 19:1827-1833. [PMID: 29931794 PMCID: PMC6156985 DOI: 10.1002/cbic.201800214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Indexed: 11/12/2022]
Abstract
Steroids can be difficult to modify through traditional organic synthesis methods, but many enzymes regio- and stereoselectively process a wide variety of steroid substrates. We tested whether steroid-modifying enzymes could make novel steroids from non-native substrates. Numerous genes encoding steroid-modifying enzymes, including some bacterial enzymes, were expressed in mammalian cells by transient transfection and found to be active. We made three unusual steroids by stable expression, in HEK293 cells, of the 7α-hydroxylase CYP7B1, which was selected because of its high native product yield. These cells made 7α,17α-dihydroxypregnenolone and 7β,17α-dihydroxypregnenolone from 17α-hydroxypregnenolone and produced 11α,16α-dihydroxyprogesterone from 16α-hydroxyprogesterone. The last two products were the result of CYP7B1-catalyzed hydroxylation at previously unobserved sites. A Rosetta docking model of CYP7B1 suggested that these substrates' D-ring hydroxy groups might prevent them from binding in the same way as the native substrates, bringing different carbon atoms close to the active ferryl oxygen atom. This new approach could potentially use other enzymes and substrates to produce many novel steroids for drug candidate testing.
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Affiliation(s)
- Emma S. Spady
- Department of Systems Biology, Harvard Medical School – Boston, MA 02115, United States
- Laboratory of Systems Pharmacology, Harvard University – Boston, MA 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Harvard University – Boston, MA 02115, United States
| | - Thomas P. Wyche
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School – Boston, MA 02115, United States
| | - Nathanael J. Rollins
- Department of Systems Biology, Harvard Medical School – Boston, MA 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Harvard University – Boston, MA 02115, United States
| | - Jon Clardy
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School – Boston, MA 02115, United States
| | - Jeffrey C. Way
- Department of Systems Biology, Harvard Medical School – Boston, MA 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Harvard University – Boston, MA 02115, United States
| | - Pamela A. Silver
- Department of Systems Biology, Harvard Medical School – Boston, MA 02115, United States
- Wyss Institute for Biologically Inspired Engineering, Harvard University – Boston, MA 02115, United States
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32
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Moser S, Strohmeier GA, Leitner E, Plocek TJ, Vanhessche K, Pichler H. Whole-cell (+)-ambrein production in the yeast Pichia pastoris. Metab Eng Commun 2018; 7:e00077. [PMID: 30197866 PMCID: PMC6127371 DOI: 10.1016/j.mec.2018.e00077] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 08/13/2018] [Accepted: 08/14/2018] [Indexed: 11/30/2022] Open
Abstract
The triterpenoid (+)-ambrein is a natural precursor for (-)-ambrox, which constitutes one of the most sought-after fragrances and fixatives for the perfume industry. (+)-Ambrein is a major component of ambergris, an intestinal excretion of sperm whales that is found only serendipitously. Thus, the demand for (-)-ambrox is currently mainly met by chemical synthesis. A recent study described for the first time the applicability of an enzyme cascade consisting of two terpene cyclases, namely squalene-hopene cyclase from Alicyclobacillus acidocaldarius (AaSHC D377C) and tetraprenyl-β-curcumene cyclase from Bacillus megaterium (BmeTC) for in vitro (+)-ambrein production starting from squalene. Yeasts, such as Pichia pastoris, are natural producers of squalene and have already been shown in the past to be excellent hosts for the biosynthesis of hydrophobic compounds such as terpenoids. By targeting a central enzyme in the sterol biosynthesis pathway, squalene epoxidase Erg1, intracellular squalene levels in P. pastoris could be strongly enhanced. Heterologous expression of AaSHC D377C and BmeTC and, particularly, development of suitable methods to analyze all products of the engineered strain provided conclusive evidence of whole-cell (+)-ambrein production. Engineering of BmeTC led to a remarkable one-enzyme system that was by far superior to the cascade, thereby increasing (+)-ambrein levels approximately 7-fold in shake flask cultivation. Finally, upscaling to 5 L bioreactor yielded more than 100 mg L-1 of (+)-ambrein, demonstrating that metabolically engineered yeast P. pastoris represents a valuable, whole-cell system for high-level production of (+)-ambrein.
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Key Words
- (+)-ambrein
- AOX1, alcohol oxidase
- AaSHC, Alicyclobacillus acidocaldarius squalene-hopene cyclase
- BSM, basal salt medium
- BmeTC, Bacillus megaterium terpene cyclase
- CDW, cell dry weight
- FLD1, formaldehyde dehydrogenase 1
- HRP, horse radish peroxidase
- Metabolic engineering
- PTM1, Pichia trace metals
- Pichia pastoris
- Squalene
- Terpene cyclase
- Triterpenoid
- YNB, yeast nitrogen base
- YPD, yeast extract peptone dextrose medium
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Affiliation(s)
- Sandra Moser
- Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria
| | - Gernot A Strohmeier
- Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria.,Institute of Organic Chemistry, NAWI Graz, Stremayrgasse 9, 8010 Graz, Austria
| | - Erich Leitner
- Institute of Analytical Chemistry and Food Chemistry, Graz University of Technology, NAWI Graz, Stremayrgasse 9, 8010 Graz, Austria
| | - Thomas J Plocek
- ACS International S.A., 184 Route de St-Julien, CH-1228 Plan-les-Ouates, Switzerland
| | - Koenraad Vanhessche
- ACS International S.A., 184 Route de St-Julien, CH-1228 Plan-les-Ouates, Switzerland
| | - Harald Pichler
- Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria.,Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, BioTechMed Graz, Petersgasse 14/2, 8010 Graz, Austria
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33
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The Smell of Synthetic Biology: Engineering Strategies for Aroma Compound Production in Yeast. FERMENTATION-BASEL 2018. [DOI: 10.3390/fermentation4030054] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Yeast—especially Saccharomyces cerevisiae—have long been a preferred workhorse for the production of numerous recombinant proteins and other metabolites. S. cerevisiae is a noteworthy aroma compound producer and has also been exploited to produce foreign bioflavour compounds. In the past few years, important strides have been made in unlocking the key elements in the biochemical pathways involved in the production of many aroma compounds. The expression of these biochemical pathways in yeast often involves the manipulation of the host strain to direct the flux towards certain precursors needed for the production of the given aroma compound. This review highlights recent advances in the bioengineering of yeast—including S. cerevisiae—to produce aroma compounds and bioflavours. To capitalise on recent advances in synthetic yeast genomics, this review presents yeast as a significant producer of bioflavours in a fresh context and proposes new directions for combining engineering and biology principles to improve the yield of targeted aroma compounds.
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34
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Liu Y, Wei WP, Ye BC. High GC Content Cas9-Mediated Genome-Editing and Biosynthetic Gene Cluster Activation in Saccharopolyspora erythraea. ACS Synth Biol 2018; 7:1338-1348. [PMID: 29634237 DOI: 10.1021/acssynbio.7b00448] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The overexpression of bacterial secondary metabolite biosynthetic enzymes is the basis for industrial overproducing strains. Genome editing tools can be used to further improve gene expression and yield. Saccharopolyspora erythraea produces erythromycin, which has extensive clinical applications. In this study, the CRISPR-Cas9 system was used to edit genes in the S. erythraea genome. A temperature-sensitive plasmid containing the PermE promoter, to drive Cas9 expression, and the Pj23119 and PkasO promoters, to drive sgRNAs, was designed. Erythromycin esterase, encoded by S. erythraea SACE_1765, inactivates erythromycin by hydrolyzing the macrolactone ring. Sequencing and qRT-PCR confirmed that reporter genes were successfully inserted into the SACE_1765 gene. Deletion of SACE_1765 in a high-producing strain resulted in a 12.7% increase in erythromycin levels. Subsequent PermE- egfp knock-in at the SACE_0712 locus resulted in an 80.3% increase in erythromycin production compared with that of wild type. Further investigation showed that PermE promoter knock-in activated the erythromycin biosynthetic gene clusters at the SACE_0712 locus. Additionally, deletion of indA (SACE_1229) using dual sgRNA targeting without markers increased the editing efficiency to 65%. In summary, we have successfully applied Cas9-based genome editing to a bacterial strain, S. erythraea, with a high GC content. This system has potential application for both genome-editing and biosynthetic gene cluster activation in Actinobacteria.
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Affiliation(s)
- Yong Liu
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering , East China University of Science and Technology , Shanghai 200237 , China
| | - Wen-Ping Wei
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering , East China University of Science and Technology , Shanghai 200237 , China
| | - Bang-Ce Ye
- Laboratory of Biosystems and Microanalysis, State Key Laboratory of Bioreactor Engineering , East China University of Science and Technology , Shanghai 200237 , China
- Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences , Zhejiang University of Technology , Hangzhou 310014 , Zhejiang , China
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35
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Rampler E, Criscuolo A, Zeller M, El Abiead Y, Schoeny H, Hermann G, Sokol E, Cook K, Peake DA, Delanghe B, Koellensperger G. A Novel Lipidomics Workflow for Improved Human Plasma Identification and Quantification Using RPLC-MSn Methods and Isotope Dilution Strategies. Anal Chem 2018; 90:6494-6501. [PMID: 29708737 DOI: 10.1021/acs.analchem.7b05382] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Lipid identification and quantification are essential objectives in comprehensive lipidomics studies challenged by the high number of lipids, their chemical diversity, and their dynamic range. In this work, we developed a tailored method for profiling and quantification combining (1) isotope dilution, (2) enhanced isomer separation by C30 fused-core reversed-phase material, and (3) parallel Orbitrap and ion trap detection by the Orbitrap Fusion Lumos Tribid mass spectrometer. The combination of parallelizable ion analysis without time loss together with different fragmentation techniques (HCD/CID) and an inclusion list led to higher quality in lipid identifications exemplified in human plasma and yeast samples. Moreover, we used lipidome isotope-labeling of yeast (LILY)-a fast and efficient in vivo labeling strategy in Pichia pastoris-to produce (nonradioactive) isotopically labeled eukaryotic lipid standards in yeast. We integrated the 13C lipids in the LC-MS workflow to enable relative and absolute compound-specific quantification in yeast and human plasma samples by isotope dilution. Label-free and compound-specific quantification was validated by comparison against a recent international interlaboratory study on human plasma SRM 1950. In this way, we were able to prove that LILY enabled quantification leads to accurate results, even in complex matrices. Excellent analytical figures of merit with enhanced trueness, precision and linearity over 4-5 orders of magnitude were observed applying compound-specific quantification with 13C-labeled lipids. We strongly believe that lipidomics studies will benefit from incorporating isotope dilution and LC-MSn strategies.
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Affiliation(s)
- Evelyn Rampler
- Department of Analytical Chemistry, Faculty of Chemistry , University of Vienna , Währingerstrasse 38 , 1090 Vienna , Austria.,Vienna Metabolomics Center (VIME) , University of Vienna , Althanstraße 14 , 1090 Vienna , Austria.,Chemistry Meets Microbiology , Althanstraße 14 , 1090 Vienna , Austria
| | - Angela Criscuolo
- Thermo Fisher Scientific (Bremen GmbH) , Hanna-Kunath-Str. 11 , 28199 Bremen , Germany.,Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy , Universität Leipzig , Leipzig , Germany
| | - Martin Zeller
- Thermo Fisher Scientific (Bremen GmbH) , Hanna-Kunath-Str. 11 , 28199 Bremen , Germany
| | - Yasin El Abiead
- Department of Analytical Chemistry, Faculty of Chemistry , University of Vienna , Währingerstrasse 38 , 1090 Vienna , Austria
| | - Harald Schoeny
- Department of Analytical Chemistry, Faculty of Chemistry , University of Vienna , Währingerstrasse 38 , 1090 Vienna , Austria
| | - Gerrit Hermann
- Department of Analytical Chemistry, Faculty of Chemistry , University of Vienna , Währingerstrasse 38 , 1090 Vienna , Austria.,ISOtopic solutions , Währingerstrasse 38 , 1090 Vienna , Austria
| | - Elena Sokol
- Thermo Fisher Scientific , 1 Boundary Park , Hemel Hempstead HP2 7GE , United Kingdom
| | - Ken Cook
- Thermo Fisher Scientific , 1 Boundary Park , Hemel Hempstead HP2 7GE , United Kingdom
| | - David A Peake
- Thermo Fisher Scientific , 355 River Oaks Parkway , 95134 San Jose , California United States
| | - Bernard Delanghe
- Thermo Fisher Scientific (Bremen GmbH) , Hanna-Kunath-Str. 11 , 28199 Bremen , Germany
| | - Gunda Koellensperger
- Department of Analytical Chemistry, Faculty of Chemistry , University of Vienna , Währingerstrasse 38 , 1090 Vienna , Austria.,Vienna Metabolomics Center (VIME) , University of Vienna , Althanstraße 14 , 1090 Vienna , Austria.,Chemistry Meets Microbiology , Althanstraße 14 , 1090 Vienna , Austria
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36
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Czarnotta E, Dianat M, Korf M, Granica F, Merz J, Maury J, Baallal Jacobsen SA, Förster J, Ebert BE, Blank LM. Fermentation and purification strategies for the production of betulinic acid and its lupane-type precursors in Saccharomyces cerevisiae. Biotechnol Bioeng 2017; 114:2528-2538. [DOI: 10.1002/bit.26377] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 07/02/2017] [Indexed: 12/25/2022]
Affiliation(s)
- Eik Czarnotta
- iAMB-Institute of Applied Microbiology; ABBt-Aachen Biology and Biotechnology; RWTH Aachen University; Aachen Germany
| | - Mariam Dianat
- iAMB-Institute of Applied Microbiology; ABBt-Aachen Biology and Biotechnology; RWTH Aachen University; Aachen Germany
| | - Marcel Korf
- APT-Laboratory of Plant and Process Design; Department of Biochemical and Chemical Engineering; TU Dortmund University; Dortmund Germany
| | - Fabian Granica
- APT-Laboratory of Plant and Process Design; Department of Biochemical and Chemical Engineering; TU Dortmund University; Dortmund Germany
| | - Juliane Merz
- APT-Laboratory of Plant and Process Design; Department of Biochemical and Chemical Engineering; TU Dortmund University; Dortmund Germany
| | - Jérôme Maury
- Technical University of Denmark; Novo Nordisk Foundation Center for Biosustainability; Kgs. Lyngby Denmark
| | - Simo A. Baallal Jacobsen
- Technical University of Denmark; Novo Nordisk Foundation Center for Biosustainability; Kgs. Lyngby Denmark
| | - Jochen Förster
- Technical University of Denmark; Novo Nordisk Foundation Center for Biosustainability; Kgs. Lyngby Denmark
| | - Birgitta E. Ebert
- iAMB-Institute of Applied Microbiology; ABBt-Aachen Biology and Biotechnology; RWTH Aachen University; Aachen Germany
| | - Lars M. Blank
- iAMB-Institute of Applied Microbiology; ABBt-Aachen Biology and Biotechnology; RWTH Aachen University; Aachen Germany
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37
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Recent Advances in Ergosterol Biosynthesis and Regulation Mechanisms in Saccharomyces cerevisiae. Indian J Microbiol 2017; 57:270-277. [PMID: 28904410 DOI: 10.1007/s12088-017-0657-1] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 06/27/2017] [Indexed: 01/04/2023] Open
Abstract
Ergosterol, an important component of the fungal cell membrane, is not only essential for fungal growth and development but also very important for adaptation to stress in fungi. Ergosterol is also a direct precursor for steroid drugs. The biosynthesis of ergosterol can be divided into three modules: mevalonate, farnesyl pyrophosphate (farnesyl-PP) and ergosterol biosynthesis. The regulation of ergosterol content is mainly achieved by feedback regulation of ergosterol synthase activity through transcription, translation and posttranslational modification. The synthesis of HMG-CoA, catalyzed by HMGR, is a major metabolic check point in ergosterol biosynthesis. Excessive sterols can be subsequently stored in lipid droplets or secreted into the extracellular milieu by esterification or acetylation to avoid toxic effects. As sterols are insoluble, the intracellular transport of ergosterol in cells requires transporters. In recent years, great progress has been made in understanding ergosterol biosynthesis and its regulation in Saccharomyces cerevisiae. However, few reviews have focused on these studies, especially the regulation of biosynthesis and intracellular transport. Therefore, this review summarizes recent research progress on the physiological functions, biosynthesis, regulation of biosynthesis and intracellular transportation of ergosterol in S. cerevisiae.
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Metabolomic changes and metabolic responses to expression of heterologous biosynthetic genes for lycopene production in Yarrowia lipolytica. J Biotechnol 2017; 251:174-185. [DOI: 10.1016/j.jbiotec.2017.04.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 03/27/2017] [Accepted: 04/16/2017] [Indexed: 11/19/2022]
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Genome editing approaches: manipulating of lovastatin and taxol synthesis of filamentous fungi by CRISPR/Cas9 system. Appl Microbiol Biotechnol 2017; 101:3953-3976. [PMID: 28389711 DOI: 10.1007/s00253-017-8263-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 03/23/2017] [Accepted: 03/27/2017] [Indexed: 12/28/2022]
Abstract
Filamentous fungi are prolific repertoire of structurally diverse secondary metabolites of remarkable biological activities such as lovastatin and paclitaxel that have been approved by FDA as drugs for hypercholesterolemia and cancer treatment. The clusters of genes encoding lovastatin and paclitaxel are cryptic at standard laboratory cultural conditions (Kennedy et al. Science 284:1368-1372, 1999; Bergmann et al. Nature Chem Biol 3:213-217, 2007). The expression of these genes might be triggered in response to nutritional and physical conditions; nevertheless, the overall yield of these metabolites does not match the global need. Consequently, overexpression of the downstream limiting enzymes and/or blocking the competing metabolic pathways of these metabolites could be the most successful technologies to enhance their yield. This is the first review summarizing the different strategies implemented for fungal genome editing, molecular regulatory mechanisms, and prospective of clustered regulatory interspaced short palindromic repeat/Cas9 system in metabolic engineering of fungi to improve their yield of lovastatin and taxol to industrial scale. Thus, elucidating the putative metabolic pathways in fungi for overproduction of lovastatin and taxol was the ultimate objective of this review.
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Náhlík J, Hrnčiřík P, Mareš J, Rychtera M, Kent CA. Towards the design of an optimal strategy for the production of ergosterol from
Saccharomyces cerevisiae
yeasts. Biotechnol Prog 2017; 33:838-848. [DOI: 10.1002/btpr.2436] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 08/31/2016] [Indexed: 11/07/2022]
Affiliation(s)
- Jan Náhlík
- Dept. of Computing and Control EngineeringUniversity of Chemistry and TechnologyPrague Czech Republic
| | - Pavel Hrnčiřík
- Dept. of Computing and Control EngineeringUniversity of Chemistry and TechnologyPrague Czech Republic
| | - Jan Mareš
- Dept. of Computing and Control EngineeringUniversity of Chemistry and TechnologyPrague Czech Republic
| | - Mojmír Rychtera
- Dept. of BiotechnologyUniversity of Chemistry and TechnologyPrague Czech Republic
| | - Christopher A. Kent
- School of Chemical Engineering, College of Engineering and Physical SciencesUniversity of BirminghamEdgbaston Birmingham, U.K
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Reyes I, Cruz-Sosa F, Roman-Guerrero A, Vernon-Carter EJ, Alvarez-Ramirez J. Structural changes of corn starch duringSaccharomyces cerevisiaefermentation. STARCH-STARKE 2016. [DOI: 10.1002/star.201600088] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Isabel Reyes
- Departamento de Biotecnologia; Universidad Autonoma Metropolitana-Iztapalapa; Iztapalapa Mexico
| | - Francisco Cruz-Sosa
- Departamento de Biotecnologia; Universidad Autonoma Metropolitana-Iztapalapa; Iztapalapa Mexico
| | - Angelica Roman-Guerrero
- Departamento de Biotecnologia; Universidad Autonoma Metropolitana-Iztapalapa; Iztapalapa Mexico
| | - E. Jaime Vernon-Carter
- Departamento de Ingenieria de Procesos e Hidraulica; Universidad Autonoma Metropolitana-Iztapalapa; Iztapalapa Mexico
| | - Jose Alvarez-Ramirez
- Departamento de Ingenieria de Procesos e Hidraulica; Universidad Autonoma Metropolitana-Iztapalapa; Iztapalapa Mexico
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Wriessnegger T, Moser S, Emmerstorfer-Augustin A, Leitner E, Müller M, Kaluzna I, Schürmann M, Mink D, Pichler H. Enhancing cytochrome P450-mediated conversions in P. pastoris through RAD52 over-expression and optimizing the cultivation conditions. Fungal Genet Biol 2016; 89:114-125. [DOI: 10.1016/j.fgb.2016.02.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 02/12/2016] [Accepted: 02/15/2016] [Indexed: 11/15/2022]
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43
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Screening for new brewing yeasts in the non-Saccharomycessector withTorulaspora delbrueckiias model. Yeast 2016; 33:129-44. [DOI: 10.1002/yea.3146] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 11/16/2015] [Accepted: 11/30/2015] [Indexed: 11/07/2022] Open
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44
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Zhang G, Cao Q, Liu J, Liu B, Li J, Li C. Refactoring β-amyrin synthesis inSaccharomyces cerevisiae. AIChE J 2015. [DOI: 10.1002/aic.14950] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Genlin Zhang
- School of Life Science; Beijing Institute of Technology; Beijing 100081 China
- Key Laboratory for Green Processing of Chemical Engineering of Xinjiang Bingtuan, School of Chemistry and Chemical Engineering; Shihezi University; Shihezi 832000 China
| | - Qian Cao
- School of Life Science; Beijing Institute of Technology; Beijing 100081 China
| | - Jingzhu Liu
- School of Life Science; Beijing Institute of Technology; Beijing 100081 China
| | - Baiyang Liu
- School of Life Science; Beijing Institute of Technology; Beijing 100081 China
| | - Jun Li
- School of Life Science; Beijing Institute of Technology; Beijing 100081 China
| | - Chun Li
- School of Life Science; Beijing Institute of Technology; Beijing 100081 China
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Cuperus JT, Lo RS, Shumaker L, Proctor J, Fields S. A tetO Toolkit To Alter Expression of Genes in Saccharomyces cerevisiae. ACS Synth Biol 2015; 4:842-52. [PMID: 25742460 PMCID: PMC4506738 DOI: 10.1021/sb500363y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Strategies to optimize a metabolic pathway often involve building a large collection of strains, each containing different versions of sequences that regulate the expression of pathway genes. Here, we develop reagents and methods to carry out this process at high efficiency in the yeast Saccharomyces cerevisiae. We identify variants of the Escherichia coli tet operator (tetO) sequence that bind a TetR-VP16 activator with differential affinity and therefore result in different TetR-VP16 activator-driven expression. By recombining these variants upstream of the genes of a pathway, we generate unique combinations of expression levels. Here, we built a tetO toolkit, which includes the I-OnuI homing endonuclease to create double-strand breaks, which increases homologous recombination by 10(5); a plasmid carrying six variant tetO sequences flanked by I-OnuI sites, uncoupling transformation and recombination steps; an S. cerevisiae-optimized TetR-VP16 activator; and a vector to integrate constructs into the yeast genome. We introduce into the S. cerevisiae genome the three crt genes from Erwinia herbicola required for yeast to synthesize lycopene and carry out the recombination process to produce a population of cells with permutations of tetO variants regulating the three genes. We identify 0.7% of this population as making detectable lycopene, of which the vast majority have undergone recombination at all three crt genes. We estimate a rate of ∼20% recombination per targeted site, much higher than that obtained in other studies. Application of this toolkit to medically or industrially important end products could reduce the time and labor required to optimize the expression of a set of metabolic genes.
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Affiliation(s)
- Josh T. Cuperus
- Howard Hughes Medical
Institute, ‡Department of Genome Sciences, §Department of Medicine, University of Washington, Seattle, Washington 98195, United States
| | - Russell S. Lo
- Howard Hughes Medical
Institute, ‡Department of Genome Sciences, §Department of Medicine, University of Washington, Seattle, Washington 98195, United States
| | - Lucia Shumaker
- Howard Hughes Medical
Institute, ‡Department of Genome Sciences, §Department of Medicine, University of Washington, Seattle, Washington 98195, United States
| | - Julia Proctor
- Howard Hughes Medical
Institute, ‡Department of Genome Sciences, §Department of Medicine, University of Washington, Seattle, Washington 98195, United States
| | - Stanley Fields
- Howard Hughes Medical
Institute, ‡Department of Genome Sciences, §Department of Medicine, University of Washington, Seattle, Washington 98195, United States
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Alleviating Redox Imbalance Enhances 7-Dehydrocholesterol Production in Engineered Saccharomyces cerevisiae. PLoS One 2015; 10:e0130840. [PMID: 26098102 PMCID: PMC4476719 DOI: 10.1371/journal.pone.0130840] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 05/25/2015] [Indexed: 11/19/2022] Open
Abstract
Maintaining redox balance is critical for the production of heterologous secondary metabolites, whereas on various occasions the native cofactor balance does not match the needs in engineered microorganisms. In this study, 7-dehydrocholesterol (7-DHC, a crucial precursor of vitamin D3) biosynthesis pathway was constructed in Saccharomyces cerevisiae BY4742 with endogenous ergosterol synthesis pathway blocked by knocking out the erg5 gene (encoding C-22 desaturase). The deletion of erg5 led to redox imbalance with higher ratio of cytosolic free NADH/NAD+ and more glycerol and ethanol accumulation. To alleviate the redox imbalance, a water-forming NADH oxidase (NOX) and an alternative oxidase (AOX1) were employed in our system based on cofactor regeneration strategy. Consequently, the production of 7-dehydrocholesterol was increased by 74.4% in shake flask culture. In the meanwhile, the ratio of free NADH/NAD+ and the concentration of glycerol and ethanol were reduced by 78.0%, 50.7% and 7.9% respectively. In a 5-L bioreactor, the optimal production of 7-DHC reached 44.49(±9.63) mg/L. This study provides a reference to increase the production of some desired compounds that are restricted by redox imbalance.
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Suppression of cell division-associated genes by Helicobacter pylori attenuates proliferation of RAW264.7 monocytic macrophage cells. Sci Rep 2015; 5:11046. [PMID: 26078204 PMCID: PMC4468580 DOI: 10.1038/srep11046] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 05/07/2015] [Indexed: 02/06/2023] Open
Abstract
Helicobacter pylori at multiplicity of infection (MOI ≥ 50) have been shown to cause apoptosis in RAW264.7 monocytic macrophage cells. Because chronic gastric infection by H. pylori results in the persistence of macrophages in the host's gut, it is likely that H. pylori is present at low to moderate, rather than high numbers in the infected host. At present, the effect of low-MOI H. pylori infection on macrophage has not been fully elucidated. In this study, we investigated the genome-wide transcriptional regulation of H. pylori-infected RAW264.7 cells at MOI 1, 5 and 10 in the absence of cellular apoptosis. Microarray data revealed up- and down-regulation of 1341 and 1591 genes, respectively. The expression of genes encoding for DNA replication and cell cycle-associated molecules, including Aurora-B kinase (AurkB) were down-regulated. Immunoblot analysis verified the decreased expression of AurkB and downstream phosphorylation of Cdk1 caused by H. pylori infection. Consistently, we observed that H. pylori infection inhibited cell proliferation and progression through the G1/S and G2/M checkpoints. In summary, we suggest that H. pylori disrupts expression of cell cycle-associated genes, thereby impeding proliferation of RAW264.7 cells, and such disruption may be an immunoevasive strategy utilized by H. pylori.
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Synthetic biology advances for pharmaceutical production. Curr Opin Biotechnol 2015; 35:46-51. [PMID: 25744872 PMCID: PMC4617476 DOI: 10.1016/j.copbio.2015.02.004] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 02/11/2015] [Accepted: 02/12/2015] [Indexed: 01/12/2023]
Abstract
Synthetic biology is quickly moving from proof of concept to industrial application. Pharmaceuticals are a promising target for advanced genetic engineering. Genome sequence data indicate vast underexploited biosynthetic capacity. Synthetic biology can create libraries of novel chemicals enriched for bioactivity. Synthetic biology expands the range of available chassis organisms for industry.
Synthetic biology enables a new generation of microbial engineering for the biotechnological production of pharmaceuticals and other high-value chemicals. This review presents an overview of recent advances in the field, describing new computational and experimental tools for the discovery, optimization and production of bioactive molecules, and outlining progress towards the application of these tools to pharmaceutical production systems.
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49
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Huang Y, Wu X, Jian D, Zhan Y, Fan G. De novo transcriptome analysis of a medicinal fungi Phellinus linteus and identification of SSR markers. BIOTECHNOL BIOTEC EQ 2015; 29:395-403. [PMID: 26019658 PMCID: PMC4434122 DOI: 10.1080/13102818.2015.1008228] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 10/18/2014] [Indexed: 10/27/2022] Open
Abstract
The aim of this study was to facilitate gene discovery for functional genome studies and to identify simple sequence repeat (SSR) markers for molecular-assisted selection in Phellinus linteus. The transcriptome of Phellinus linteus was sequenced using а high-throughput RNA sequencing system - the Illumina Hiseq 2000. A total of 16,383,818 clean sequencing reads, 35,532 contigs and 25,811 unigenes were postulated. Based on similarity searches with known proteins, 19,350 genes (74.97% of the unigenes) were annotated. In the present research, 19,266, 10,978 and 7831 unigenes were mapped in Nr, Swiss-Prot and clusters of orthologous groups (COG) classifications, respectively. Of all unigenes, 6845 were categorized into three functional groups, namely biological process, cellular components and molecular function and 11,088 were annotated to 108 pathways by searching the Kyoto Encyclopedia of Genes and Genomes pathway database. A total of 1129 SSRs were identified in these unigenes. In addition, 23 candidate genes, potentially involved in sterol biosynthesis, were identified and were worthy of further investigation.
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Affiliation(s)
- Yating Huang
- Department of Forest Bioengineering, College of Life Science, Northeast Forestry University , Harbin , P.R. China
| | - Xiaoqiu Wu
- Department of Forest Bioengineering, College of Life Science, Northeast Forestry University , Harbin , P.R. China
| | - Duan Jian
- Department of Forest Bioengineering, College of Life Science, Northeast Forestry University , Harbin , P.R. China
| | - Yaguang Zhan
- Department of Forest Bioengineering, College of Life Science, Northeast Forestry University , Harbin , P.R. China
| | - Guizhi Fan
- Department of Forest Bioengineering, College of Life Science, Northeast Forestry University , Harbin , P.R. China
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50
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Production of squalene by squalene synthases and their truncated mutants in Escherichia coli. J Biosci Bioeng 2015; 119:165-71. [DOI: 10.1016/j.jbiosc.2014.07.013] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 07/31/2014] [Accepted: 07/31/2014] [Indexed: 02/08/2023]
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