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Belcour A, Got J, Aite M, Delage L, Collén J, Frioux C, Leblanc C, Dittami SM, Blanquart S, Markov GV, Siegel A. Inferring and comparing metabolism across heterogeneous sets of annotated genomes using AuCoMe. Genome Res 2023; 33:972-987. [PMID: 37468308 PMCID: PMC10629481 DOI: 10.1101/gr.277056.122] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 05/23/2023] [Indexed: 07/21/2023]
Abstract
Comparative analysis of genome-scale metabolic networks (GSMNs) may yield important information on the biology, evolution, and adaptation of species. However, it is impeded by the high heterogeneity of the quality and completeness of structural and functional genome annotations, which may bias the results of such comparisons. To address this issue, we developed AuCoMe, a pipeline to automatically reconstruct homogeneous GSMNs from a heterogeneous set of annotated genomes without discarding available manual annotations. We tested AuCoMe with three data sets, one bacterial, one fungal, and one algal, and showed that it successfully reduces technical biases while capturing the metabolic specificities of each organism. Our results also point out shared and divergent metabolic traits among evolutionarily distant algae, underlining the potential of AuCoMe to accelerate the broad exploration of metabolic evolution across the tree of life.
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Affiliation(s)
- Arnaud Belcour
- Univ Rennes, Inria, CNRS, IRISA, F-35000 Rennes, France;
| | - Jeanne Got
- Univ Rennes, Inria, CNRS, IRISA, F-35000 Rennes, France
| | - Méziane Aite
- Univ Rennes, Inria, CNRS, IRISA, F-35000 Rennes, France
| | - Ludovic Delage
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Jonas Collén
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | | | - Catherine Leblanc
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Simon M Dittami
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | | | - Gabriel V Markov
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Anne Siegel
- Univ Rennes, Inria, CNRS, IRISA, F-35000 Rennes, France;
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2
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Li YW, Guo Q, Peng QQ, Shen Q, Nie ZK, Ye C, Shi TQ. Recent Development of Advanced Biotechnology in the Oleaginous Fungi for Arachidonic Acid Production. ACS Synth Biol 2022; 11:3163-3173. [PMID: 36221956 DOI: 10.1021/acssynbio.2c00483] [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] [Indexed: 01/24/2023]
Abstract
Arachidonic acid is an essential ω-6 polyunsaturated fatty acid, which plays a significant role in cardiovascular health and neurological development, leading to its wide use in the food and pharmaceutical industries. Traditionally, ARA is obtained from deep-sea fish oil. However, this source is limited by season and is depleting the already threatened global fish stocks. With the rapid development of synthetic biology in recent years, oleaginous fungi have gradually attracted increasing attention as promising microbial sources for large-scale ARA production. Numerous advanced technologies including metabolic engineering, dynamic regulation of fermentation conditions, and multiomics analysis were successfully adapted to increase ARA synthesis. This review summarizes recent advances in the bioengineering of oleaginous fungi for ARA production. Finally, perspectives for future engineering approaches are proposed to further improve the titer yield and productivity of ARA.
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Affiliation(s)
- Ya-Wen Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210046, People's Republic of China
| | - Qi Guo
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210046, People's Republic of China.,College of Pharmaceutical Sciences, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Qian-Qian Peng
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210046, People's Republic of China
| | - Qi Shen
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210046, People's Republic of China
| | - Zhi-Kui Nie
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210046, People's Republic of China.,Jiangxi New Reyphon Biochemical Co., Ltd, Salt & Chemical Industry, Xingan, Jiangxi 331399, People's Republic of China
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210046, People's Republic of China
| | - Tian-Qiong Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing 210046, People's Republic of China.,College of Food Science and Technology, Nanchang University, No. 999 Xuefu Road, Nanchang 330031, People's Republic of China
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3
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Fazili ABA, Shah AM, Zan X, Naz T, Nosheen S, Nazir Y, Ullah S, Zhang H, Song Y. Mucor circinelloides: a model organism for oleaginous fungi and its potential applications in bioactive lipid production. Microb Cell Fact 2022; 21:29. [PMID: 35227264 PMCID: PMC8883733 DOI: 10.1186/s12934-022-01758-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 02/10/2022] [Indexed: 11/10/2022] Open
Abstract
Microbial oils have gained massive attention because of their significant role in industrial applications. Currently plants and animals are the chief sources of medically and nutritionally important fatty acids. However, the ever-increasing global demand for polyunsaturated fatty acids (PUFAs) cannot be met by the existing sources. Therefore microbes, especially fungi, represent an important alternative source of microbial oils being investigated. Mucor circinelloides—an oleaginous filamentous fungus, came to the forefront because of its high efficiency in synthesizing and accumulating lipids, like γ-linolenic acid (GLA) in high quantity. Recently, mycelium of M. circinelloides has acquired substantial attraction towards it as it has been suggested as a convenient raw material source for the generation of biodiesel via lipid transformation. Although M. circinelloides accumulates lipids naturally, metabolic engineering is found to be important for substantial increase in their yields. Both modifications of existing pathways and re-formation of biosynthetic pathways in M. circinelloides have shown the potential to improve lipid levels. In this review, recent advances in various important metabolic aspects of M. circinelloides have been discussed. Furthermore, the potential applications of M. circinelloides in the fields of antioxidants, nutraceuticals, bioremediation, ethanol production, and carotenoids like beta carotene and astaxanthin having significant nutritional value are also deliberated.
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4
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Cerone M, Smith TK. A Brief Journey into the History of and Future Sources and Uses of Fatty Acids. Front Nutr 2021; 8:570401. [PMID: 34355007 PMCID: PMC8329090 DOI: 10.3389/fnut.2021.570401] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 06/21/2021] [Indexed: 01/04/2023] Open
Abstract
Fats and lipids have always had a primary role in the history of humankind, from ancient civilisations to the modern and contemporary time, going from domestic and cosmetic uses, to the first medical applications and later to the large-scale industrial uses for food, pharmaceutical, cosmetics, and biofuel production. Sources and uses of those have changed during time following the development of chemical sciences and industrial technological advances. Plants, fish, and animal fats have represented the primary source of lipids and fats for century. Nowadays, the use of fatty acid sources has taken a turn: industries are mainly interested in polyunsaturated fatty acids (PUFAs), which have beneficial properties in human health; and also, for high-value fatty acids product for innovative and green production of biofuel and feedstocks. Thus, the constant increase in demand of fatty acids, the fact that marine and vegetable sources are not adequate to meet the high level of fatty acids required worldwide and climate change, have determined the necessity of the search for renewable and sustainable sources for fatty acids. Biotechnological advances and bioengineering have started looking at the genetic modification of algae, bacteria, yeasts, seeds, and plants to develop cell factory able to produce high value fatty acid products in a renewable and sustainable manner. This innovative approach applied to FA industry is a peculiar example of how biotechnology can serve as a powerful mean to drive the production of high value fatty acid derivatives on the concept of circular bioeconomy, based on the reutilisation of organic resources for alternative and sustainable productive patterns that are environmentally friendly.
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Affiliation(s)
- Michela Cerone
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, United Kingdom
| | - Terry K Smith
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, United Kingdom
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5
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Zan X, Sun J, Chu L, Cui F, Huo S, Song Y, Koffas MAG. Improved glucose and xylose co-utilization by overexpression of xylose isomerase and/or xylulokinase genes in oleaginous fungus Mucor circinelloides. Appl Microbiol Biotechnol 2021; 105:5565-5575. [PMID: 34215904 DOI: 10.1007/s00253-021-11392-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 04/28/2021] [Accepted: 06/07/2021] [Indexed: 12/17/2022]
Abstract
Most of the oleaginous microorganisms cannot assimilate xylose in the presence of glucose, which is the major bottleneck in the bioconversion of lignocellulose to biodiesel. Our present study revealed that overexpression of xylose isomerase (XI) gene xylA or xylulokinase (XK) gene xks1 increased the xylose consumption by 25 to 37% and enhanced the lipid content by 8 to 28% during co-fermentation of glucose and xylose. In xylA overexpressing strain Mc-XI, the activity of XI was 1.8-fold higher and the mRNA level of xylA at 24 h and 48 h was 11- and 13-fold higher than that of the control, respectively. In xks1 overexpressing strain Mc-XK, the mRNA level of xks1 was 4- to 11-fold of that of the control strain and the highest XK activity of 950 nmol min-1 mg-1 at 72 h which was 2-fold higher than that of the control. Additionally, expression of a translational fusion of xylA and xks1 further enhanced the xylose utilization rate by 45%. Our results indicated that overexpression of xylA and/or xks1 is a promising strategy to improve the xylose and glucose co-utilization, alleviate the glucose repression, and produce lipid from lignocellulosic biomass in the oleaginous fungus M. circinelloides. KEY POINTS: • Overexpressing xylA or xks1 increased the xylose consumption and the lipid content. • The xylose isomerase activity and the xylA mRNA level were enhanced in strain Mc-XI. • Co-expression of xylA and xks1 further enhanced the xylose utilization rate by 45%.
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Affiliation(s)
- Xinyi Zan
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, People's Republic of China
| | - Jianing Sun
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, People's Republic of China
| | - Linfang Chu
- School of Food Science and Technology, Jiang University, Wuxi, 214000, People's Republic of China
| | - Fengjie Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, People's Republic of China
| | - Shuhao Huo
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, 212013, People's Republic of China
| | - Yuanda Song
- Colin Ratledge Center for Microbial Lipids, School of Agriculture Engineering and Food Science, Shandong University of Technology, Zibo, 255049, People's Republic of China.
| | - Mattheos A G Koffas
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
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6
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Tomás-Pejó E, Morales-Palomo S, González-Fernández C. Microbial lipids from organic wastes: Outlook and challenges. BIORESOURCE TECHNOLOGY 2021; 323:124612. [PMID: 33418352 DOI: 10.1016/j.biortech.2020.124612] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 12/18/2020] [Accepted: 12/20/2020] [Indexed: 06/12/2023]
Abstract
Microbial lipids have recently drawn a lot of attention as renewable sources for biochemicals production. Strong research efforts have been addressed to efficiently use organic wastes as carbon source for microbial lipids, which would definitively increase the profitability of the production process and boost a bio-based economy. This review compiles interesting traits of oleaginous microorganisms and highlights current trends on microbial- and process-oriented approaches to maximize microbial oil production from inexpensive substrates like lignocellulosic sugars, volatile fatty acids and glycerol. Furthermore, downstream processes such as cell harvesting or lipid extraction, that are decisive for the cost-effectiveness of the process, are discussed. To underpin microbial oils within the so demanded circular economy, associated challenges, recent advances and possible industrial applications that are also identified in this review.
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Affiliation(s)
- E Tomás-Pejó
- IMDEA Energy, Biotechnological Processes Unit, Av. Ramón de la Sagra, 29835 Móstoles, Madrid, Spain.
| | - S Morales-Palomo
- IMDEA Energy, Biotechnological Processes Unit, Av. Ramón de la Sagra, 29835 Móstoles, Madrid, Spain
| | - C González-Fernández
- IMDEA Energy, Biotechnological Processes Unit, Av. Ramón de la Sagra, 29835 Móstoles, Madrid, Spain
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7
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Systematic genome analysis of a novel arachidonic acid-producing strain uncovered unique metabolic traits in the production of acetyl-CoA-derived products in Mortierellale fungi. Gene 2020; 741:144559. [PMID: 32169630 DOI: 10.1016/j.gene.2020.144559] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Accepted: 03/08/2020] [Indexed: 11/27/2022]
Abstract
The fungi in order Mortierellales are attractive producers for long-chain polyunsaturated fatty acids (PUFAs). Here, the genome sequencing and assembly of a novel strain of Mortierella sp. BCC40632 were done, yielding 65 contigs spanning of 49,964,116 total bases with predicted 12,149 protein-coding genes. We focused on the acetyl-CoA in relevant to its derived metabolic pathways for biosynthesis of macromolecules with biological functions, including PUFAs, eicosanoids and carotenoids. By comparative genome analysis between Mortierellales and Mucorales, the signature genetic characteristics of the arachidonic acid-producing strains, including Δ5-desaturase and GLELO-like elongase, were also identified in the strain BCC40632. Remarkably, this fungal strain contained only n-6 pathway of PUFA biosynthesis due to the absence of Δ15-desaturase or ω3-desaturase gene in contrast to other Mortierella species. Four putative enzyme sequences in the eicosanoid biosynthetic pathways were identified in the strain BCC40632 and others Mortierellale fungi, but were not detected in the Mucorales. Another unique metabolic trait of the Mortierellales was the inability in carotenoid synthesis as a result of the lack of phytoene synthase and phytoene desaturase genes. The findings provide a perspective in strain optimization for production of tailored-made products with industrial applications.
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8
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Chen M, Gao X, Yang W, Sun C, Yang J, Zhang H, Song Y. Discovery and characterization of a stable lipase with preference toward long-chain fatty acids. Biotechnol Lett 2019; 42:171-180. [DOI: 10.1007/s10529-019-02765-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 11/14/2019] [Indexed: 11/30/2022]
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9
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Tiukova IA, Prigent S, Nielsen J, Sandgren M, Kerkhoven EJ. Genome‐scale model of
Rhodotorula toruloides
metabolism. Biotechnol Bioeng 2019; 116:3396-3408. [DOI: 10.1002/bit.27162] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 08/08/2019] [Accepted: 09/05/2019] [Indexed: 12/31/2022]
Affiliation(s)
- Ievgeniia A. Tiukova
- Systems and Synthetic Biology, Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburg Sweden
- Department of Molecular SciencesSwedish University of Agricultural SciencesUppsala Sweden
| | | | - Jens Nielsen
- Systems and Synthetic Biology, Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburg Sweden
| | - Mats Sandgren
- Department of Molecular SciencesSwedish University of Agricultural SciencesUppsala Sweden
| | - Eduard J. Kerkhoven
- Systems and Synthetic Biology, Department of Biology and Biological EngineeringChalmers University of TechnologyGothenburg Sweden
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10
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Isarankura Na Ayudhya N, Laoteng K, Song Y, Meechai A, Vongsangnak W. Metabolic traits specific for lipid-overproducing strain of Mucor circinelloides WJ11 identified by genome-scale modeling approach. PeerJ 2019; 7:e7015. [PMID: 31316868 PMCID: PMC6613434 DOI: 10.7717/peerj.7015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 04/20/2019] [Indexed: 01/02/2023] Open
Abstract
The genome-scale metabolic model of a lipid-overproducing strain of Mucor circinelloides WJ11 was developed. The model (iNI1159) contained 1,159 genes, 648 EC numbers, 1,537 metabolites, and 1,355 metabolic reactions, which were localized in different compartments of the cell. Using flux balance analysis (FBA), the iNI1159 model was validated by predicting the specific growth rate. The metabolic traits investigated by phenotypic phase plane analysis (PhPP) showed a relationship between the nutrient uptake rate, cell growth, and the triacylglycerol production rate, demonstrating the strength of the model. A putative set of metabolic reactions affecting the lipid-accumulation process was identified when the metabolic flux distributions under nitrogen-limited conditions were altered by performing fast flux variability analysis (fastFVA) and relative flux change. Comparative analysis of the metabolic models of the lipid-overproducing strain WJ11 (iNI1159) and the reference strain CBS277.49 (iWV1213) using both fastFVA and coordinate hit-and-run with rounding (CHRR) showed that the flux distributions between these two models were significantly different. Notably, a higher flux distribution through lipid metabolisms such as lanosterol, zymosterol, glycerolipid and fatty acids biosynthesis in iNI1159 was observed, leading to an increased lipid production when compared to iWV1213. In contrast, iWV1213 exhibited a higher flux distribution across carbohydrate and amino acid metabolisms and thus generated a high flux for biomass production. This study demonstrated that iNI1159 is an effective predictive tool for the pathway engineering of oleaginous strains for the production of diversified oleochemicals with industrial relevance.
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Affiliation(s)
- Nattapat Isarankura Na Ayudhya
- Department of Chemical Engineering, Faculty of Engineering, King Mongkut's Institute of Technology Thonburi, Bangkok, Thailand
| | - Kobkul Laoteng
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Sciences and Technology Development Agency (NSTDA), Khong Luang, Pathum Thani, Thailand
| | - Yuanda Song
- Colin Ratledge Center for Microbial Lipids, School of Agriculture Engineering and Food Sciences, Shandong University of Technology, Shandong, China
| | - Asawin Meechai
- Department of Chemical Engineering, Faculty of Engineering, King Mongkut's Institute of Technology Thonburi, Bangkok, Thailand
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Omics Center for Agriculture, Bioresources, Food, and Health, Faculty of Science, Kasetsart University (OmiKU), Bangkok, Thailand
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11
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Wilken SE, Swift CL, Podolsky IA, Lankiewicz TS, Seppälä S, O'Malley MA. Linking ‘omics’ to function unlocks the biotech potential of non-model fungi. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.coisb.2019.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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12
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Yang J, Li S, Kabir Khan MA, Garre V, Vongsangnak W, Song Y. Increased Lipid Accumulation in Mucor circinelloides by Overexpression of Mitochondrial Citrate Transporter Genes. Ind Eng Chem Res 2019. [DOI: 10.1021/acs.iecr.8b05564] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Junhuan Yang
- Colin Ratledge Center for Microbial Lipids, School of Agriculture Engineering and Food Sciences, Shandong University of Technology, Shandong zibo 255049, P. R. China
| | - Shaoqi Li
- Colin Ratledge Center for Microbial Lipids, School of Agriculture Engineering and Food Sciences, Shandong University of Technology, Shandong zibo 255049, P. R. China
| | - Md. Ahsanul Kabir Khan
- Colin Ratledge Center for Microbial Lipids, School of Agriculture Engineering and Food Sciences, Shandong University of Technology, Shandong zibo 255049, P. R. China
| | - Victoriano Garre
- Departmento de Genética y Microbiología (Unidad Asociada al Instituto de Química Física Rocasolano, Consejo Superior de Investigaciones Científicas), Facultad de Biología, Universidad de Murcia, Murcia 30100, Spain
| | - Wanwipa Vongsangnak
- Omics Center for Agriculture, Bioresources, Food and Health, Faculty of Science, Kasetsart University (OmiKU), Bangkok 10900, Thailand
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Yuanda Song
- Colin Ratledge Center for Microbial Lipids, School of Agriculture Engineering and Food Sciences, Shandong University of Technology, Shandong zibo 255049, P. R. China
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Dissecting metabolic behavior of lipid over-producing strain of Mucor circinelloides through genome-scale metabolic network and multi-level data integration. Gene 2018; 670:87-97. [PMID: 29800733 DOI: 10.1016/j.gene.2018.05.085] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 05/14/2018] [Accepted: 05/21/2018] [Indexed: 12/19/2022]
Abstract
Lipid accumulation is an important cellular process of oleaginous microorganisms. To dissect metabolic behavior of oleaginous Zygomycetes, the lipid over-producing strain, Mucor circinelloides WJ11, was subjected for omics-scale analysis. The genome annotation was improved and used for construction of genome-scale metabolic network of WJ11 strain. Then, the quality of the metabolic network was enhanced by incorporating gene and protein expression data. In addition to the known oleaginous genes, our results showed a number of newly identified unique genes of WJ11 strain, which involved in central carbon metabolism, lipid, amino acid and nitrogen metabolisms. The systematic compilations indicated the additional metabolic routes with the involvement in supplying precursors (acetyl-CoA, NADPH and fatty acyl substrate) for fatty acid and lipid biosynthesis. Interestingly, amino acid metabolism played a substantial role in responsive mechanism of the fungal cells to nutrient imbalance circumstance through lipogenesis as the finding of reporter metabolites (l-methionine, l-glutamate, l-aspartate, l-asparagine and l-glutamine) at lipid-accumulating stage. The cooperative function of certain lipid-degrading enzymes at the particular growth stage was elucidated by integrating the metabolic networks with gene expression data. The unique feature of carotenoid biosynthetic route in WJ11 strain was also identified by protein domain analysis. Taken together, there were cross-functional metabolisms in regulating lipid biosynthesis and retaining high level of cellular lipids in the representative of lipid over-producing strains.
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14
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Satari B, Karimi K. Mucoralean fungi for sustainable production of bioethanol and biologically active molecules. Appl Microbiol Biotechnol 2017; 102:1097-1117. [DOI: 10.1007/s00253-017-8691-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 12/01/2017] [Accepted: 12/02/2017] [Indexed: 11/27/2022]
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15
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Genome-scale metabolic network of Cordyceps militaris useful for comparative analysis of entomopathogenic fungi. Gene 2017; 626:132-139. [DOI: 10.1016/j.gene.2017.05.027] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 03/12/2017] [Accepted: 05/10/2017] [Indexed: 11/21/2022]
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16
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Park BG, Kim M, Kim J, Yoo H, Kim BG. Systems biology for understanding and engineering of heterotrophic oleaginous microorganisms. Biotechnol J 2016; 12. [DOI: 10.1002/biot.201600104] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 09/21/2016] [Accepted: 09/22/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Beom Gi Park
- School of Chemical and Biological Engineering, Institute of Molecular Biology and Genetics, and Bioengineering Institute; Seoul National University; Seoul Republic of Korea
| | - Minsuk Kim
- School of Chemical and Biological Engineering, Institute of Molecular Biology and Genetics, and Bioengineering Institute; Seoul National University; Seoul Republic of Korea
| | - Joonwon Kim
- School of Chemical and Biological Engineering, Institute of Molecular Biology and Genetics, and Bioengineering Institute; Seoul National University; Seoul Republic of Korea
| | - Heewang Yoo
- Interdisciplinary Program for Biochemical Engineering and Biotechnology; Seoul National University; Seoul Republic of Korea
| | - Byung-Gee Kim
- School of Chemical and Biological Engineering, Institute of Molecular Biology and Genetics, and Bioengineering Institute; Seoul National University; Seoul Republic of Korea
- Interdisciplinary Program for Biochemical Engineering and Biotechnology; Seoul National University; Seoul Republic of Korea
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17
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Lipase genes in Mucor circinelloides: identification, sub-cellular location, phylogenetic analysis and expression profiling during growth and lipid accumulation. J Ind Microbiol Biotechnol 2016; 43:1467-80. [PMID: 27535142 DOI: 10.1007/s10295-016-1820-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 07/30/2016] [Indexed: 01/12/2023]
Abstract
Lipases or triacylglycerol hydrolases are widely spread in nature and are particularly common in the microbial world. The filamentous fungus Mucor circinelloides is a potential lipase producer, as it grows well in triacylglycerol-contained culture media. So far only one lipase from M. circinelloides has been characterized, while the majority of lipases remain unknown in this fungus. In the present study, 47 potential lipase genes in M. circinelloides WJ11 and 30 potential lipase genes in M. circinelloides CBS 277.49 were identified by extensive bioinformatics analysis. An overview of these lipases is presented, including several characteristics, sub-cellular location, phylogenetic analysis and expression profiling of the lipase genes during growth and lipid accumulation. All of these proteins contained the consensus sequence for a classical lipase (GXSXG motif) and were divided into four types including α/β-hydrolase_1, α/β-hydrolase_3, class_3 and GDSL lipase (GDSL) based on gene annotations. Phylogenetic analyses revealed that class_3 family and α/β-hydrolase_3 family were the conserved lipase family in M. circinelloides. Additionally, some lipases also contained a typical acyltransferase motif of H-(X) 4-D, and these lipases may play a dual role in lipid metabolism, catalyzing both lipid hydrolysis and transacylation reactions. The differential expression of all lipase genes were confirmed by quantitative real-time PCR, and the expression profiling were analyzed to predict the possible biological roles of these lipase genes in lipid metabolism in M. circinelloides. We preliminarily hypothesized that lipases may be involved in triacylglycerol degradation, phospholipid synthesis and beta-oxidation. Moreover, the results of sub-cellular localization, the presence of signal peptide and transcriptional analyses of lipase genes indicated that four lipase in WJ11 most likely belong to extracellular lipases with a signal peptide. These findings provide a platform for the selection of candidate lipase genes for further detailed functional study.
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