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Chen YC, Destouches L, Cook A, Fedorec AJH. Synthetic microbial ecology: engineering habitats for modular consortia. J Appl Microbiol 2024; 135:lxae158. [PMID: 38936824 DOI: 10.1093/jambio/lxae158] [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: 04/27/2024] [Revised: 06/13/2024] [Accepted: 06/26/2024] [Indexed: 06/29/2024]
Abstract
Microbiomes, the complex networks of micro-organisms and the molecules through which they interact, play a crucial role in health and ecology. Over at least the past two decades, engineering biology has made significant progress, impacting the bio-based industry, health, and environmental sectors; but has only recently begun to explore the engineering of microbial ecosystems. The creation of synthetic microbial communities presents opportunities to help us understand the dynamics of wild ecosystems, learn how to manipulate and interact with existing microbiomes for therapeutic and other purposes, and to create entirely new microbial communities capable of undertaking tasks for industrial biology. Here, we describe how synthetic ecosystems can be constructed and controlled, focusing on how the available methods and interaction mechanisms facilitate the regulation of community composition and output. While experimental decisions are dictated by intended applications, the vast number of tools available suggests great opportunity for researchers to develop a diverse array of novel microbial ecosystems.
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Affiliation(s)
- Yue Casey Chen
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Louie Destouches
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Alice Cook
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
| | - Alex J H Fedorec
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK
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2
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Willers VP, Beer B, Sieber V. Integrating Carbohydrate and C1 Utilization for Chemicals Production. CHEMSUSCHEM 2023; 16:e202202122. [PMID: 36520644 DOI: 10.1002/cssc.202202122] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/14/2022] [Indexed: 06/17/2023]
Abstract
In the face of increasing mobility and energy demand, as well as the mitigation of climate change, the development of sustainable and environmentally friendly alternatives to fossil fuels will be one of the most important tasks facing humankind in the coming years. In order to initiate the transition from a petroleum-based economy to a new, greener future, biofuels and synthetic fuels have great potential as they can be adapted to already common processes. Thereby, especially synthetic fuels from CO2 and renewable energies are seen as the next big step for a sustainable and ecological life. In our study, we directly address the sustainable production of the most common biofuel, ethanol, and the highly interesting next-generation biofuel, isobutanol, from methanol and xylose, which are directly derivable from CO2 and lignocellulosic waste streams, respectively, such integrating synthetic fuel and biofuel production. After enzyme and reaction optimization, we succeeded in producing either 3 g L-1 ethanol or 2 g L-1 isobutanol from 7.5 g L-1 xylose and 1.6 g L-1 methanol. In our cell-free enzyme system, C1-compounds are efficiently combined and fixed by the key enzyme transketolase and converted to the intermediate pyruvate. This opens the way for a hybrid production of biofuels, platform chemicals and fine chemicals from CO2 and lignocellulosic waste streams as alternative to conventional routes depending solely either on CO2 or sugars.
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Affiliation(s)
- Vivian Pascal Willers
- Chair of Chemistry of Biogenic Resources, Technical University of Munich Campus Straubing, 94315, Straubing, Germany
| | - Barbara Beer
- Chair of Chemistry of Biogenic Resources, Technical University of Munich Campus Straubing, 94315, Straubing, Germany
- Current address: CASCAT GmbH, 94315, Straubing, Germany
| | - Volker Sieber
- Chair of Chemistry of Biogenic Resources, Technical University of Munich Campus Straubing, 94315, Straubing, Germany
- Technical University of Munich, 94315, Straubing, Germany
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, 4072, Australia
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3
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Sanchez A, Bajic D, Diaz-Colunga J, Skwara A, Vila JCC, Kuehn S. The community-function landscape of microbial consortia. Cell Syst 2023; 14:122-134. [PMID: 36796331 DOI: 10.1016/j.cels.2022.12.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 10/17/2022] [Accepted: 12/21/2022] [Indexed: 02/17/2023]
Abstract
Quantitatively linking the composition and function of microbial communities is a major aspiration of microbial ecology. Microbial community functions emerge from a complex web of molecular interactions between cells, which give rise to population-level interactions among strains and species. Incorporating this complexity into predictive models is highly challenging. Inspired by a similar problem in genetics of predicting quantitative phenotypes from genotypes, an ecological community-function (or structure-function) landscape could be defined that maps community composition and function. In this piece, we present an overview of our current understanding of these community landscapes, their uses, limitations, and open questions. We argue that exploiting the parallels between both landscapes could bring powerful predictive methodologies from evolution and genetics into ecology, providing a boost to our ability to engineer and optimize microbial consortia.
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Affiliation(s)
- Alvaro Sanchez
- Department of Ecology & Evolutionary Biology & Microbial Sciences Institute, Yale University, New Haven, CT, USA; Department of Microbial Biotechnology, CNB-CSIC, Campus de Cantoblanco, Madrid, Spain.
| | - Djordje Bajic
- Department of Ecology & Evolutionary Biology & Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Juan Diaz-Colunga
- Department of Ecology & Evolutionary Biology & Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Abigail Skwara
- Department of Ecology & Evolutionary Biology & Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Jean C C Vila
- Department of Ecology & Evolutionary Biology & Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Seppe Kuehn
- Center for the Physics of Evolving Systems, The Unviersity of Chicago, Chicago, IL, USA; Department of Ecology and Evolution, The University of Chicago, Chicago, IL, USA
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4
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Metabolic Engineering of Microorganisms to Produce Pyruvate and Derived Compounds. Molecules 2023; 28:molecules28031418. [PMID: 36771084 PMCID: PMC9919917 DOI: 10.3390/molecules28031418] [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: 01/09/2023] [Revised: 01/27/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023] Open
Abstract
Pyruvate is a hub of various endogenous metabolic pathways, including glycolysis, TCA cycle, amino acid, and fatty acid biosynthesis. It has also been used as a precursor for pyruvate-derived compounds such as acetoin, 2,3-butanediol (2,3-BD), butanol, butyrate, and L-alanine biosynthesis. Pyruvate and derivatives are widely utilized in food, pharmaceuticals, pesticides, feed additives, and bioenergy industries. However, compounds such as pyruvate, acetoin, and butanol are often chemically synthesized from fossil feedstocks, resulting in declining fossil fuels and increasing environmental pollution. Metabolic engineering is a powerful tool for producing eco-friendly chemicals from renewable biomass resources through microbial fermentation. Here, we review and systematically summarize recent advances in the biosynthesis pathways, regulatory mechanisms, and metabolic engineering strategies for pyruvate and derivatives. Furthermore, the establishment of sustainable industrial synthesis platforms based on alternative substrates and new tools to produce these compounds is elaborated. Finally, we discuss the potential difficulties in the current metabolic engineering of pyruvate and derivatives and promising strategies for constructing efficient producers.
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Kant Bhatia S, Ahuja V, Chandel N, Gurav R, Kant Bhatia R, Govarthanan M, Kumar Tyagi V, Kumar V, Pugazendhi A, Rajesh Banu J, Yang YH. Advances in algal biomass pretreatment and its valorisation into biochemical and bioenergy by the microbial processes. BIORESOURCE TECHNOLOGY 2022; 358:127437. [PMID: 35680087 DOI: 10.1016/j.biortech.2022.127437] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/03/2022] [Accepted: 06/04/2022] [Indexed: 06/15/2023]
Abstract
Urbanization and pollution are the major issues of the current time own to the exhaustive consumption of fossil fuels which have a detrimental effect on the nation's economies and air quality due to greenhouse gas (GHG) emissions and shortage of energy reserves. Algae, an autotrophic organism provides a green substitute for energy as well as commercial products. Algal extracts become an efficient source for bioactive compounds having anti-microbial, anti-oxidative, anti-inflammatory, and anti-cancerous potential. Besides the conventional approach, residual biomass from any algal-based process might act as a renewable substrate for fermentation. Likewise, lignocellulosic biomass, algal biomass can also be processed for sugar recovery by different pre-treatment strategies like acid and alkali hydrolysis, microwave, ionic liquid, and ammonia fiber explosion, etc. Residual algal biomass hydrolysate can be used as a feedstock to produce bioenergy (biohydrogen, biogas, methane) and biochemicals (organic acids, polyhydroxyalkanoates) via microbial fermentation.
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Affiliation(s)
- Shashi Kant Bhatia
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea; Institute for Ubiquitous Information Technology and Applications, Seoul 05029, Republic of Korea
| | - Vishal Ahuja
- Department of Biotechnology, Himachal Pradesh University, Shimla 171005, India
| | - Neha Chandel
- School of Medical and Allied Sciences, GD Goenka University, Gurugram 122103, Haryana, India
| | - Ranjit Gurav
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Ravi Kant Bhatia
- Department of Biotechnology, Himachal Pradesh University, Shimla 171005, India
| | - Muthusamy Govarthanan
- Department of Environmental Engineering, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Vinay Kumar Tyagi
- Environmental Hydrology Division National Institute of Hydrology (NIH), Roorkee 247667, Uttarakhand, India
| | - Vinod Kumar
- Centre for Climate and Environmental Protection, School of Water, Energy and Environment, Cranfield University, Cranfield MK43 0AL, UK
| | - Arivalagan Pugazendhi
- Emerging Materials for Energy and Environmental Applications Research Group, School of Engineering and Technology, Van Lang University, Ho Chi Minh City, Vietnam
| | - J Rajesh Banu
- Department of Life Sciences, Central University of Tamil Nadu, Neelakudi, Thiruvarur 610005, India
| | - Yung-Hun Yang
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea; Institute for Ubiquitous Information Technology and Applications, Seoul 05029, Republic of Korea.
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Akdemir H, Liu Y, Zhuang L, Zhang H, Koffas MAG. Utilization of microbial cocultures for converting mixed substrates to valuable bioproducts. Curr Opin Microbiol 2022; 68:102157. [DOI: 10.1016/j.mib.2022.102157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/26/2022] [Accepted: 04/21/2022] [Indexed: 11/03/2022]
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Gao H, Tuyishime P, Zhang X, Yang T, Xu M, Rao Z. Engineering of microbial cells for L-valine production: challenges and opportunities. Microb Cell Fact 2021; 20:172. [PMID: 34461907 PMCID: PMC8406616 DOI: 10.1186/s12934-021-01665-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 08/24/2021] [Indexed: 11/10/2022] Open
Abstract
L-valine is an essential amino acid that has wide and expanding applications with a suspected growing market demand. Its applicability ranges from animal feed additive, ingredient in cosmetic and special nutrients in pharmaceutical and agriculture fields. Currently, fermentation with the aid of model organisms, is a major method for the production of L-valine. However, achieving the optimal production has often been limited because of the metabolic imbalance in recombinant strains. In this review, the constrains in L-valine biosynthesis are discussed first. Then, we summarize the current advances in engineering of microbial cell factories that have been developed to address and overcome major challenges in the L-valine production process. Future prospects for enhancing the current L-valine production strategies are also discussed.
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Affiliation(s)
- Hui Gao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Philibert Tuyishime
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Xian Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Taowei Yang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Meijuan Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China.
| | - Zhiming Rao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China.
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Zhang K, Zhang F, Wu YR. Emerging technologies for conversion of sustainable algal biomass into value-added products: A state-of-the-art review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 784:147024. [PMID: 33895504 DOI: 10.1016/j.scitotenv.2021.147024] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 03/28/2021] [Accepted: 04/05/2021] [Indexed: 06/12/2023]
Abstract
Concerns regarding high energy demand and gradual depletion of fossil fuels have attracted the desire of seeking renewable and sustainable alternatives. Similar to but better than the first- and second-generation biomass, algae derived third-generation biorefinery aims to generate value-added products by microbial cell factories and has a great potential due to its abundant, carbohydrate-rich and lignin-lacking properties. However, it is crucial to establish an efficient process with higher competitiveness over the current petroleum industry to effectively utilize algal resources. In this review, we summarize the recent technological advances in maximizing the bioavailability of different algal resources. Following an overview of approaches to enhancing the hydrolytic efficiency, we review prominent opportunities involved in microbial conversion into various value-added products including alcohols, organic acids, biogas and other potential industrial products, and also provide key challenges and trends for future insights into developing biorefineries of marine biomass.
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Affiliation(s)
- Kan Zhang
- Department of Biology, Shantou University, Shantou 515063, Guangdong, China
| | - Feifei Zhang
- Department of Biology, Shantou University, Shantou 515063, Guangdong, China
| | - Yi-Rui Wu
- Department of Biology, Shantou University, Shantou 515063, Guangdong, China; Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou 515063, Guangdong, China; Institute of Marine Sciences, Shantou University, Shantou, Guangdong 515063, China.
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9
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Luo Z, Yu S, Zeng W, Zhou J. Comparative analysis of the chemical and biochemical synthesis of keto acids. Biotechnol Adv 2021; 47:107706. [PMID: 33548455 DOI: 10.1016/j.biotechadv.2021.107706] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 12/28/2022]
Abstract
Keto acids are essential organic acids that are widely applied in pharmaceuticals, cosmetics, food, beverages, and feed additives as well as chemical synthesis. Currently, most keto acids on the market are prepared via chemical synthesis. The biochemical synthesis of keto acids has been discovered with the development of metabolic engineering and applied toward the production of specific keto acids from renewable carbohydrates using different metabolic engineering strategies in microbes. In this review, we provide a systematic summary of the types and applications of keto acids, and then summarize and compare the chemical and biochemical synthesis routes used for the production of typical keto acids, including pyruvic acid, oxaloacetic acid, α-oxobutanoic acid, acetoacetic acid, ketoglutaric acid, levulinic acid, 5-aminolevulinic acid, α-ketoisovaleric acid, α-keto-γ-methylthiobutyric acid, α-ketoisocaproic acid, 2-keto-L-gulonic acid, 2-keto-D-gluconic acid, 5-keto-D-gluconic acid, and phenylpyruvic acid. We also describe the current challenges for the industrial-scale production of keto acids and further strategies used to accelerate the green production of keto acids via biochemical routes.
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Affiliation(s)
- Zhengshan Luo
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; State Key Laboratory of Materials-Oriented Chemical Engineering, College of Food Science and Light Industry, Nanjing Tech University, Nanjing 211816, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Shiqin Yu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Weizhu Zeng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
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10
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Cao M, Jiang T, Li P, Zhang Y, Guo S, Meng W, Lü C, Zhang W, Xu P, Gao C, Ma C. Pyruvate Production from Whey Powder by Metabolic Engineered Klebsiella oxytoca. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:15275-15283. [PMID: 33300786 DOI: 10.1021/acs.jafc.0c06724] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Pyruvate is an important platform material widely used in food, pharmaceutical, and chemical industries. Pyruvate-tolerant Klebsiella oxytoca PDL-0 was chosen as a chassis for pyruvate production via metabolic engineering. Genes related to by-product generation were knocked out to decrease the production of 2,3-butantediol, acetate, ethanol, and succinate. The NADH oxidase encoding gene nox was inserted into the locus of the lactate dehydrogenase encoding gene ldhD in the genome of K. oxytoca to simultaneously block lactate production and regenerate NAD+. The pyruvate importers CstA and YjiY were identified, and their encoding genes were deleted to increase pyruvate accumulation. The engineered strain K. oxytoca PDL-YC produced 71.0 g/L pyruvate from glucose. Furthermore, K. oxytoca PDL-YC can use whey powder, an abundant by-product of the cheese making process, as substrate for pyruvate production. Pyruvate production with a concentration of 62.3 g/L and a productivity of 1.60 g/[L·h] was realized using whey powder as substrate.
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Affiliation(s)
- Menghao Cao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, People's Republic of China
| | - Tongtong Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, People's Republic of China
- Tumen Inspection and Testing Center, Tumen, Jilin 133100, People's Republic of China
| | - Ping Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, People's Republic of China
| | - Yipeng Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, People's Republic of China
| | - Shiting Guo
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, People's Republic of China
| | - Wensi Meng
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, People's Republic of China
| | - Chuanjuan Lü
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, People's Republic of China
| | - Wen Zhang
- Center for Gene and Immunotherapy, The Second Hospital of Shandong University, Jinan 250033, People's Republic of China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
| | - Chao Gao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, People's Republic of China
| | - Cuiqing Ma
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, People's Republic of China
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11
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Pretreatment and Detoxification of Acid-Treated Wood Hydrolysates for Pyruvate Production by an Engineered Consortium of Escherichia coli. Appl Biochem Biotechnol 2020; 192:243-256. [PMID: 32372381 DOI: 10.1007/s12010-020-03320-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 04/23/2020] [Indexed: 10/24/2022]
Abstract
The biorefinery concept makes use of renewable lignocellulosic biomass to produce commodities sustainably. A synthetic microbial consortium can enable the simultaneous utilization of sugars such as glucose and xylose to produce biochemicals, where each consortium member converts one sugar into the target product. In this study, woody biomass was used to generate glucose and xylose after pretreatment with 20% (w/v) sulfuric acid and 60-min reaction time. We compared several strategies for detoxification with charcoal and sodium borohydride treatments to improve the fermentability of this hydrolysate in a defined medium for the production of the growth-associated product pyruvate. In shake flask culture, the highest pyruvate yield on xylose of 0.8 g/g was found using pH 6 charcoal-treated hydrolysate. In bioreactor studies, a consortium of two engineered E. coli strains converted the mixture of glucose and xylose in batch studies to 12.8 ± 2.7 g/L pyruvate in 13 h. These results demonstrate that lignocellulosic biomass as the sole carbon source can be used to produce growth-related products after employing suitable detoxification strategies.
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Flores AD, Choi HG, Martinez R, Onyeabor M, Ayla EZ, Godar A, Machas M, Nielsen DR, Wang X. Catabolic Division of Labor Enhances Production of D-Lactate and Succinate From Glucose-Xylose Mixtures in Engineered Escherichia coli Co-culture Systems. Front Bioeng Biotechnol 2020; 8:329. [PMID: 32432089 PMCID: PMC7214542 DOI: 10.3389/fbioe.2020.00329] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 03/25/2020] [Indexed: 01/01/2023] Open
Abstract
Although biological upgrading of lignocellulosic sugars represents a promising and sustainable route to bioplastics, diverse and variable feedstock compositions (e.g., glucose from the cellulose fraction and xylose from the hemicellulose fraction) present several complex challenges. Specifically, sugar mixtures are often incompletely metabolized due to carbon catabolite repression while composition variability further complicates the optimization of co-utilization rates. Benefiting from several unique features including division of labor, increased metabolic diversity, and modularity, synthetic microbial communities represent a promising platform with the potential to address persistent bioconversion challenges. In this work, two unique and catabolically orthogonal Escherichia coli co-cultures systems were developed and used to enhance the production of D-lactate and succinate (two bioplastic monomers) from glucose-xylose mixtures (100 g L-1 total sugars, 2:1 by mass). In both cases, glucose specialist strains were engineered by deleting xylR (encoding the xylose-specific transcriptional activator, XylR) to disable xylose catabolism, whereas xylose specialist strains were engineered by deleting several key components involved with glucose transport and phosphorylation systems (i.e., ptsI, ptsG, galP, glk) while also increasing xylose utilization by introducing specific xylR mutations. Optimization of initial population ratios between complementary sugar specialists proved a key design variable for each pair of strains. In both cases, ∼91% utilization of total sugars was achieved in mineral salt media by simple batch fermentation. High product titer (88 g L-1 D-lactate, 84 g L-1 succinate) and maximum productivity (2.5 g L-1 h-1 D-lactate, 1.3 g L-1 h-1 succinate) and product yield (0.97 g g-total sugar-1 for D-lactate, 0.95 g g-total sugar-1 for succinate) were also achieved.
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Affiliation(s)
- Andrew D. Flores
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ, United States
| | - Hyun G. Choi
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Rodrigo Martinez
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Moses Onyeabor
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - E. Zeynep Ayla
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ, United States
| | - Amanda Godar
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Michael Machas
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ, United States
| | - David R. Nielsen
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ, United States
| | - Xuan Wang
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
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Zhao C, Sinumvayo JP, Zhang Y, Li Y. Design and development of a “Y-shaped” microbial consortium capable of simultaneously utilizing biomass sugars for efficient production of butanol. Metab Eng 2019; 55:111-119. [DOI: 10.1016/j.ymben.2019.06.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 06/18/2019] [Accepted: 06/22/2019] [Indexed: 10/26/2022]
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14
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Zhang W, Oulego P, Slot TK, Rothenberg G, Shiju NR. Selective Aerobic Oxidation of Lactate to Pyruvate Catalyzed by Vanadium‐Nitrogen‐Doped Carbon Nanosheets. ChemCatChem 2019. [DOI: 10.1002/cctc.201900819] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Wei Zhang
- Van't Hoff Institute for Molecular SciencesUniversity of Amsterdam Science Park 904 1098 XH Amsterdam The Netherlands
| | - Paula Oulego
- Department of Chemical and Environmental EngineeringUniversity of Oviedo C/ Julián Clavería, s/n. 33071 Oviedo Spain
| | - Thierry K. Slot
- Van't Hoff Institute for Molecular SciencesUniversity of Amsterdam Science Park 904 1098 XH Amsterdam The Netherlands
| | - Gadi Rothenberg
- Van't Hoff Institute for Molecular SciencesUniversity of Amsterdam Science Park 904 1098 XH Amsterdam The Netherlands
| | - N. Raveendran Shiju
- Van't Hoff Institute for Molecular SciencesUniversity of Amsterdam Science Park 904 1098 XH Amsterdam The Netherlands
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15
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Flores AD, Ayla EZ, Nielsen DR, Wang X. Engineering a Synthetic, Catabolically Orthogonal Coculture System for Enhanced Conversion of Lignocellulose-Derived Sugars to Ethanol. ACS Synth Biol 2019; 8:1089-1099. [PMID: 30979337 DOI: 10.1021/acssynbio.9b00007] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Fermentation of lignocellulosic sugar mixtures is often suboptimal due to inefficient xylose catabolism and sequential sugar utilization caused by carbon catabolite repression. Unlike in conventional applications employing a single engineered strain, the alternative development of synthetic microbial communities facilitates the execution of complex metabolic tasks by exploiting the unique community features, including modularity, division of labor, and facile tunability. A series of synthetic, catabolically orthogonal coculture systems were systematically engineered, as derived from either wild-type Escherichia coli W or ethanologenic LY180. Net catabolic activities were effectively balanced by simple tuning of the inoculum ratio between specialist strains, which enabled coutilization (98% of 100 g L-1 total sugars) of glucose-xylose mixtures (2:1 by mass) for both culture systems in simple batch fermentations. The engineered ethanologenic cocultures achieved ethanol titer (46 g L-1), productivity (488 mg L-1 h-1), and yield (∼90% of theoretical maximum), which were all significantly increased compared to LY180 monocultures.
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Affiliation(s)
- Andrew D. Flores
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, ECG 301, 501 E. Tyler Mall, Tempe, Arizona 85287, United States
| | - E. Zeynep Ayla
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, ECG 301, 501 E. Tyler Mall, Tempe, Arizona 85287, United States
| | - David R. Nielsen
- Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, ECG 301, 501 E. Tyler Mall, Tempe, Arizona 85287, United States
| | - Xuan Wang
- School of Life Sciences, Arizona State University, 427 E. Tyler Mall, Tempe, Arizona 85287, United States
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Singh A, Bedore SR, Sharma NK, Lee SA, Eiteman MA, Neidle EL. Removal of aromatic inhibitors produced from lignocellulosic hydrolysates by Acinetobacter baylyi ADP1 with formation of ethanol by Kluyveromyces marxianus. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:91. [PMID: 31044004 PMCID: PMC6477725 DOI: 10.1186/s13068-019-1434-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 04/12/2019] [Indexed: 05/15/2023]
Abstract
BACKGROUND Lignocellulosic biomass is an attractive, inexpensive source of potentially fermentable sugars. However, hydrolysis of lignocellulose results in a complex mixture containing microbial inhibitors at variable composition. A single microbial species is unable to detoxify or even tolerate these non-sugar components while converting the sugar mixtures effectively to a product of interest. Often multiple substrates are metabolized sequentially because of microbial regulatory mechanisms. To overcome these problems, we engineered strains of Acinetobacter baylyi ADP1 to comprise a consortium able to degrade benzoate and 4-hydroxybenzoate simultaneously under batch and continuous conditions in the presence of sugars. We furthermore used a thermotolerant yeast, Kluyveromyces marxianus, to convert the glucose remaining after detoxification to ethanol. RESULTS The two engineered strains, one unable to metabolize benzoate and another unable to metabolize 4-hydroxybenzoate, when grown together removed these two inhibitors simultaneously under batch conditions. Under continuous conditions, a single strain with a deletion in the gcd gene metabolized both inhibitors in the presence of sugars. After this batch detoxification using ADP1-derived mutants, K. marxianus generated 36.6 g/L ethanol. CONCLUSIONS We demonstrated approaches for the simultaneous removal of two aromatic inhibitors from a simulated lignocellulosic hydrolysate. A two-stage batch process converted the residual sugar into a non-growth-associated product, ethanol. Such a two-stage process with bacteria (A. baylyi) and yeast (K. marxianus) is advantageous, because the yeast fermentation occurs at a higher temperature which prevents growth and ethanol consumption of A. baylyi. Conceptually, the process can be extended to other inhibitors or sugars found in real hydrolysates. That is, additional strains which degrade components of lignocellulosic hydrolysates could be made substrate-selective and targeted for use with specific complex mixtures found in a hydrolysate.
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Affiliation(s)
- Anita Singh
- Department of Environmental Sciences, Central University of Jammu, Rahya-Suchani, Bagla, India
- School of Chemical, Materials and Biomedical Engineering, University of Georgia, Athens, GA 30602 USA
| | - Stacy R. Bedore
- Department of Microbiology, University of Georgia, Athens, GA 30602 USA
| | - Nilesh K. Sharma
- School of Chemical, Materials and Biomedical Engineering, University of Georgia, Athens, GA 30602 USA
| | - Sarah A. Lee
- School of Chemical, Materials and Biomedical Engineering, University of Georgia, Athens, GA 30602 USA
| | - Mark A. Eiteman
- Department of Environmental Sciences, Central University of Jammu, Rahya-Suchani, Bagla, India
- School of Chemical, Materials and Biomedical Engineering, University of Georgia, Athens, GA 30602 USA
| | - Ellen L. Neidle
- Department of Microbiology, University of Georgia, Athens, GA 30602 USA
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