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Sun X, Chen M, Li Y, Wang J, Zhang M, Li N, Dai R, Wang Z, Wang X. A novel Anaerobic Cathodic Dynamic Membrane Bioreactor (AnCDMBR) for efficient mitigating fouling and recovering bioenergy from municipal wastewater. WATER RESEARCH 2024; 265:122225. [PMID: 39142072 DOI: 10.1016/j.watres.2024.122225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 07/25/2024] [Accepted: 08/05/2024] [Indexed: 08/16/2024]
Abstract
Concerns regarding membrane fouling and suboptimal bioenergy recovery have constrained the implementation of anaerobic membrane bioreactor (AnMBR) for treating low-strength municipal wastewater. This study presents a novel anaerobic cathodic dynamic membrane bioreactor (AnCDMBR) designed to address these challenges. A self-formed cathodic dynamic membrane (CDM) on inexpensive carbon cloth was developed to function as both a membrane and biocathode to achieve dual-function effects of mitigating membrane fouling and accelerating organics conversion. Compared with common dynamic membrane (1.52 kPa/d) and commercial membranes (7.52 kPa/d), the developed CDM presented a significantly reduced fouling rate (1.02 kPa/d), exhibiting the potential as a substitute for high-cost conductive membranes. Furthermore, efficient and stable biomethanation occurred in AnCDMBR with a superior methane yield rate of 0.26 L-CH4/g-COD (CH4 content > 95 %), which was 1.42 times higher than the control, linked to the higher activities of microbial metabolism and methanogenic-related key enzymes. Further analysis revealed that electrostimulation-induced niche differentiation of microbiota regulated interspecies interactions between electroactive microorganisms and complex anaerobic digestion microbiomes, facilitating organic matter conversion to methane and leading to superior bioenergy recovery. This study offered a new strategy for effectively mitigating fouling and recovering bioenergy from low-strength wastewater, potentially expanding the application of AnMBRs.
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Affiliation(s)
- Xinyi Sun
- MOE Key Laboratory of Pollution Processes and Environmental Criteria / Tianjin Engineering Center of Environmental Diagnosis and Contamination Remediation, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
| | - Mei Chen
- MOE Key Laboratory of Pollution Processes and Environmental Criteria / Tianjin Engineering Center of Environmental Diagnosis and Contamination Remediation, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China.
| | - Yanli Li
- MOE Key Laboratory of Pollution Processes and Environmental Criteria / Tianjin Engineering Center of Environmental Diagnosis and Contamination Remediation, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China; Department of Civil, Construction, and Environmental Engineering, The university of Alabama, Tuscaloosa, AL 35487, USA
| | - Jinning Wang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria / Tianjin Engineering Center of Environmental Diagnosis and Contamination Remediation, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
| | - Minliang Zhang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria / Tianjin Engineering Center of Environmental Diagnosis and Contamination Remediation, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
| | - Nan Li
- School of Environmental Science and Engineering, Tianjin University, No. 92 Weijin Road, Nankai District, Tianjin 300072, China
| | - Ruobin Dai
- State Key Laboratory of Pollution Control and Resource Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji Advanced Membrane Technology Center, School of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Zhiwei Wang
- State Key Laboratory of Pollution Control and Resource Reuse, Shanghai Institute of Pollution Control and Ecological Security, Tongji Advanced Membrane Technology Center, School of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Xin Wang
- MOE Key Laboratory of Pollution Processes and Environmental Criteria / Tianjin Engineering Center of Environmental Diagnosis and Contamination Remediation, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China
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Zhuang XM, Guo ZY, Zhang M, Chen YH, Qi FN, Wang RQ, Zhang L, Zhao PJ, Lu CJ, Zou CG, Ma YC, Xu J, Zhang KQ, Cao YR, Liang LM. Ethanol mediates the interaction between Caenorhabditis elegans and the nematophagous fungus Purpureocillium lavendulum. Microbiol Spectr 2023; 11:e0127023. [PMID: 37560934 PMCID: PMC10580998 DOI: 10.1128/spectrum.01270-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 06/26/2023] [Indexed: 08/11/2023] Open
Abstract
Accurately recognizing pathogens by the host is vital for initiating appropriate immune response against infecting microorganisms. Caenorhabditis elegans has no known receptor to recognize pathogen-associated molecular pattern. However, recent studies showed that nematodes have a strong specificity for transcriptomes infected by different pathogens, indicating that they can identify different pathogenic microorganisms. However, the mechanism(s) for such specificity remains largely unknown. In this study, we showed that the nematophagous fungus Purpureocillium lavendulum can infect the intestinal tract of the nematode C. elegans and the infection led to the accumulation of reactive oxygen species (ROS) in the infected intestinal tract, which suppressed fungal growth. Co-transcriptional analysis revealed that fungal genes related to anaerobic respiration and ethanol production were up-regulated during infection. Meanwhile, the ethanol dehydrogenase Sodh-1 in C. elegans was also up-regulated. Together, these results suggested that the infecting fungi encounter hypoxia stress in the nematode gut and that ethanol may play a role in the host-pathogen interaction. Ethanol production in vitro during fungal cultivation in hypoxia conditions was confirmed by gas chromatography-mass spectrometry. Direct treatment of C. elegans with ethanol elevated the sodh-1 expression and ROS accumulation while repressing a series of immunity genes that were also repressed during fungal infection. Mutation of sodh-1 in C. elegans blocked ROS accumulation and increased the nematode's susceptibility to fungal infection. Our study revealed a new recognition and antifungal mechanism in C. elegans. The novel mechanism of ethanol-mediated interaction between the fungus and nematode provides new insights into fungal pathogenesis and for developing alternative biocontrol of pathogenic nematodes by nematophagous fungi. IMPORTANCE Nematodes are among the most abundant animals on our planet. Many of them are parasites in animals and plants and cause human and animal health problems as well as agricultural losses. Studying the interaction of nematodes and their microbial pathogens is of great importance for the biocontrol of animal and plant parasitic nematodes. In this study, we found that the model nematode Caenorhabditis elegans can recognize its fungal pathogen, the nematophagous fungus Purpureocillium lavendulum, through fungal-produced ethanol. Then the nematode elevated the reactive oxygen species production in the gut to inhibit fungal growth in an ethanol dehydrogenase-dependent manner. With this mechanism, novel biocontrol strategies may be developed targeting the ethanol receptor or metabolic pathway of nematodes. Meanwhile, as a volatile organic compound, ethanol should be taken seriously as a vector molecule in the microbial-host interaction in nature.
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Affiliation(s)
- Xue-Mei Zhuang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan and The Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
| | - Zhi-Yi Guo
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan and The Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
| | - Meng Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan and The Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
| | - Yong-Hong Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan and The Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
| | - Feng-Na Qi
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan and The Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
| | - Ren-Qiao Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan and The Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
| | - Ling Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan and The Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
| | - Pei-Ji Zhao
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan and The Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
| | - Chao-Jun Lu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan and The Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
| | - Cheng-Gang Zou
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan and The Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
| | - Yi-Cheng Ma
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan and The Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
| | - Jianping Xu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan and The Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Ke-Qin Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan and The Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
| | - Yan-Ru Cao
- College of Agriculture and Life Sciences, Kunming University, Kunming, China
| | - Lian-Ming Liang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan and The Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, Yunnan University, Kunming, China
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Qiu Y, Qiu Z, Xia J, Liu X, Zhang H, Yang Y, Hou W, Li X, He J. Co-expression of Xylose Transporter and Fructose-Bisphosphate Aldolase Enhances the Utilization of Xylose by Lactococcus lactis IO-1. Appl Biochem Biotechnol 2023; 195:816-831. [PMID: 36205844 DOI: 10.1007/s12010-022-04168-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/28/2022] [Indexed: 01/24/2023]
Abstract
The raw material cost of lactic acid fermentation accounts for the main part of the production cost, and this necessitates the exploration of the efficient use of cheap raw materials in lactic acid production. We compared the outcomes of the homologous expressions of xylose transporters (xylFGH, xylE, araE, and xylT), 6-phosphofructokinase (pfkA), fructose-bisphosphate aldolase (fbaA), and their co-expression in Lactococcus lactis IO-1 on lactic acid production using xylose as the raw material. We found that the production rate of lactic acid on xylose fermentation by L. lactis IO-1 overexpressing fbaA was the highest (14.42%). Among the xylose transporters investigated, XylT had the strongest xylose transport capacity in L. lactis IO-1, with an increase in the lactic acid production rate by 10.38%. The genes near the overexpression of fbaA or xylT in the metabolic pathway were more upregulated than the distant genes. The co-expression of fbaA and xylT increased the production rate of lactic acid by 27.84% on xylose fermentation by L. lactis IO-1. This work presents a novel strategy for the simultaneous enhancement of the expression of important genes at the beginning and midway of the xylose metabolic pathway of L. lactis IO-1, which could greatly improve the target production.
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Affiliation(s)
- Yejuan Qiu
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, 1 Meicheng Road, Huaian, 223003, Jiangsu Province, China
| | - Zhongyang Qiu
- Jiangsu Key Laboratory for Biomass-Based Energy and Enzyme Technology, Huaiyin Normal University, 111 Changjiang West Road, Huaian, 223300, Jiangsu Province, China
| | - Jun Xia
- Jiangsu Key Laboratory for Biomass-Based Energy and Enzyme Technology, Huaiyin Normal University, 111 Changjiang West Road, Huaian, 223300, Jiangsu Province, China
| | - Xiaoyan Liu
- Jiangsu Key Laboratory for Biomass-Based Energy and Enzyme Technology, Huaiyin Normal University, 111 Changjiang West Road, Huaian, 223300, Jiangsu Province, China
| | - Hanwen Zhang
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, 1 Meicheng Road, Huaian, 223003, Jiangsu Province, China
| | - Yuxiang Yang
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, 1 Meicheng Road, Huaian, 223003, Jiangsu Province, China
| | - Wenyi Hou
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, 1 Meicheng Road, Huaian, 223003, Jiangsu Province, China
| | - Xiangqian Li
- Jiangsu Provincial Key Construction Laboratory of Probiotics Preparation, Huaiyin Institute of Technology, 1 Meicheng Road, Huaian, 223003, Jiangsu Province, China.
| | - Jianlong He
- Jiangsu Key Laboratory for Biomass-Based Energy and Enzyme Technology, Huaiyin Normal University, 111 Changjiang West Road, Huaian, 223300, Jiangsu Province, China.
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Lee HJ, Kim B, Kim S, Cho DH, Jung H, Bhatia SK, Gurav R, Ahn J, Park JH, Choi KY, Yang YH. Controlling catabolite repression for isobutanol production using glucose and xylose by overexpressing the xylose regulator. J Biotechnol 2022; 359:21-28. [PMID: 36152769 DOI: 10.1016/j.jbiotec.2022.09.012] [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: 07/06/2022] [Revised: 09/14/2022] [Accepted: 09/19/2022] [Indexed: 10/31/2022]
Abstract
Using lignocellulosic biomass is immensely beneficial for the economical production of biochemicals. However, utilizing mixed sugars from lignocellulosic biomass is challenging because of bacterial preference for specific sugar such as glucose. Although previous studies have attempted to overcome this challenge, no studies have been reported on isobutanol production from mixed sugars in the Escherichia coli strain. To overcome catabolite repression of xylose and produce isobutanol using mixed sugars, we applied the combination of three strategies: (1) deletion of the gene for the glucose-specific transporter of the phosphotransferase system (ptsG); (2) overexpression of glucose kinase (glk) and glucose facilitator protein (glf); and (3) overexpression of the xylose regulator (xylR). xylR gene overexpression resulted in 100% of glucose and 82.5% of xylose consumption in the glucose-xylose mixture (1:1). Moreover, isobutanol production increased by 192% in the 1:1 medium, equivalent to the amount of isobutanol produced using only glucose. These results indicate the effectiveness of xylR overexpression in isobutanol production. Our findings demonstrated various strategies to overcome catabolite repression for a specific product, isobutanol. The present study suggests that the selected strategy in E. coli could overcome the major challenge using lignocellulosic biomass to produce isobutanol.
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Affiliation(s)
- Hong-Ju Lee
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, South Korea
| | - Byungchan Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, South Korea
| | - Suhyun Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, South Korea
| | - Do-Hyun Cho
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, South Korea
| | - Heeju Jung
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, South Korea
| | - Shashi Kant Bhatia
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, South Korea; Institute for Ubiquitous Information Technology and Applications, Konkuk University, Seoul 05029, South Korea
| | - Ranjit Gurav
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, South Korea
| | - Jungoh Ahn
- Biotechnology Process Engineering Center, Korea Research Institute Bioscience Biotechnology (KRIBB), South Korea
| | - Jung-Ho Park
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, South Korea
| | - Kwon-Young Choi
- Department of Environmental and Safety Engineering, College of Engineering, Ajou University, South Korea
| | - Yung-Hun Yang
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, South Korea; Institute for Ubiquitous Information Technology and Applications, Konkuk University, Seoul 05029, South Korea.
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Shanmugam KT, Ingram LO. Principles and practice of designing microbial biocatalysts for fuel and chemical production. J Ind Microbiol Biotechnol 2021; 49:6158391. [PMID: 33686428 PMCID: PMC9118985 DOI: 10.1093/jimb/kuab016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 03/03/2021] [Indexed: 11/14/2022]
Abstract
The finite nature of fossil fuels and the environmental impact of its use have raised interest in alternate renewable energy sources. Specifically, non-food carbohydrates, such as lignocellulosic biomass, can be used to produce next generation biofuels, including cellulosic ethanol and other non-ethanol fuels like butanol. However, currently there is no native microorganism that can ferment all lignocellulosic sugars to fuel molecules. Thus, research is focused on engineering improved microbial biocatalysts for production of liquid fuels at high productivity, titer and yield. A clear understanding and application of the basic principles of microbial physiology and biochemistry are crucial to achieve this goal. In this review, we present and discuss the construction of microbial biocatalysts that integrate these principles with ethanol-producing Escherichia coli as an example of metabolic engineering. These principles also apply to fermentation of lignocellulosic sugars to other chemicals that are currently produced from petroleum.
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Affiliation(s)
- K T Shanmugam
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Lonnie O Ingram
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
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Abdelaal AS, Jawed K, Yazdani SS. CRISPR/Cas9-mediated engineering of Escherichia coli for n-butanol production from xylose in defined medium. J Ind Microbiol Biotechnol 2019; 46:965-975. [PMID: 30982114 DOI: 10.1007/s10295-019-02180-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 04/09/2019] [Indexed: 01/14/2023]
Abstract
Butanol production from agricultural residues is the most promising alternative for fossil fuels. To reach the economic viability of biobutanol production, both glucose and xylose should be utilized and converted into butanol. Here, we engineered a dual-operon-based synthetic pathway in the genome of E. coli MG1655 to produce n-butanol using CRISPR/Cas9 technology. Further deletion of competing pathway followed by fed-batch cultivation of the engineered strain in a bioreactor with glucose-containing complex medium yielded 5.4 g/L n-butanol along with pyruvate as major co-product, indicating a redox imbalance. To ferment xylose into butanol in redox-balanced manner, we selected SSK42, an ethanologenic E. coli strain engineered and evolved in our laboratory to produce ethanol from xylose, for integrating synthetic butanol cassette in its genome via CRISPR/Cas9 after deleting the gene responsible for endogenous ethanol production. The engineered plasmid- and marker-free strain, ASA02, produced 4.32 g/L butanol in fed-batch fermentation in completely defined AM1-xylose medium.
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Affiliation(s)
- Ali Samy Abdelaal
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
- Department of Genetics, Faculty of Agriculture, Damietta University, Damietta, Egypt
| | - Kamran Jawed
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Syed Shams Yazdani
- Microbial Engineering Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.
- DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.
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Kawaguchi H, Yoshihara K, Hara KY, Hasunuma T, Ogino C, Kondo A. Metabolome analysis-based design and engineering of a metabolic pathway in Corynebacterium glutamicum to match rates of simultaneous utilization of D-glucose and L-arabinose. Microb Cell Fact 2018; 17:76. [PMID: 29773073 PMCID: PMC5956887 DOI: 10.1186/s12934-018-0927-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 05/11/2018] [Indexed: 11/24/2022] Open
Abstract
Background l-Arabinose is the second most abundant component of hemicellulose in lignocellulosic biomass, next to d-xylose. However, few microorganisms are capable of utilizing pentoses, and catabolic genes and operons enabling bacterial utilization of pentoses are typically subject to carbon catabolite repression by more-preferred carbon sources, such as d-glucose, leading to a preferential utilization of d-glucose over pentoses. In order to simultaneously utilize both d-glucose and l-arabinose at the same rate, a modified metabolic pathway was rationally designed based on metabolome analysis. Results Corynebacterium glutamicum ATCC 31831 utilized d-glucose and l-arabinose simultaneously at a low concentration (3.6 g/L each) but preferentially utilized d-glucose over l-arabinose at a high concentration (15 g/L each), although l-arabinose and d-glucose were consumed at comparable rates in the absence of the second carbon source. Metabolome analysis revealed that phosphofructokinase and pyruvate kinase were major bottlenecks for d-glucose and l-arabinose metabolism, respectively. Based on the results of metabolome analysis, a metabolic pathway was engineered by overexpressing pyruvate kinase in combination with deletion of araR, which encodes a repressor of l-arabinose uptake and catabolism. The recombinant strain utilized high concentrations of d-glucose and l-arabinose (15 g/L each) at the same consumption rate. During simultaneous utilization of both carbon sources at high concentrations, intracellular levels of phosphoenolpyruvate declined and acetyl-CoA levels increased significantly as compared with the wild-type strain that preferentially utilized d-glucose. These results suggest that overexpression of pyruvate kinase in the araR deletion strain increased the specific consumption rate of l-arabinose and that citrate synthase activity becomes a new bottleneck in the engineered pathway during the simultaneous utilization of d-glucose and l-arabinose. Conclusions Metabolome analysis identified potential bottlenecks in d-glucose and l-arabinose metabolism and was then applied to the following rational metabolic engineering. Manipulation of only two genes enabled simultaneous utilization of d-glucose and l-arabinose at the same rate in metabolically engineered C. glutamicum. This is the first report of rational metabolic design and engineering for simultaneous hexose and pentose utilization without inactivating the phosphotransferase system. Electronic supplementary material The online version of this article (10.1186/s12934-018-0927-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hideo Kawaguchi
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Kumiko Yoshihara
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Kiyotaka Y Hara
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.,Department of Environmental and Life Sciences, School of Food and Nutritional Sciences, University of Shizuoka, 52-1 Yada, Suruga, Shizuoka, 422-8526, Japan
| | - Tomohisa Hasunuma
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Chiaki Ogino
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan. .,Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan. .,Biomass Engineering Research Division, RIKEN, 1-7-22 Suehiro, Turumi, Yokohama, Kanagawa, 230-0045, Japan.
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xylA and xylB overexpression as a successful strategy for improving xylose utilization and poly-3-hydroxybutyrate production in Burkholderia sacchari. ACTA ACUST UNITED AC 2018; 45:165-173. [DOI: 10.1007/s10295-018-2007-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 01/08/2018] [Indexed: 12/31/2022]
Abstract
Abstract
Despite the versatility and many advantages of polyhydroxyalkanoates as petroleum-based plastic substitutes, their higher production cost compared to petroleum-based polymers has historically limited their large-scale production. One appealing approach to reducing production costs is to employ less expensive, renewable feedstocks. Xylose, for example is an abundant and inexpensive carbon source derived from hemicellulosic residues abundant in agro-industrial waste (sugarcane bagasse hemicellulosic hydrolysates). In this work, the production of poly-3-hydroxybutyrate P(3HB) from xylose was studied to develop technologies for conversion of agro-industrial waste into high-value chemicals and biopolymers. Specifically, this work elucidates the organization of the xylose assimilation operon of Burkholderia sacchari, a non-model bacterium with high capacity for P(3HB) accumulation. Overexpression of endogenous xylose isomerase and xylulokinase genes was successfully assessed, improving both specific growth rate and P(3HB) production. Compared to control strain (harboring pBBR1MCS-2), xylose utilization in the engineered strain was substantially improved with 25% increase in specific growth rate, 34% increase in P(3HB) production, and the highest P(3HB) yield from xylose reported to date for B. sacchari (Y P3HB/Xil = 0.35 g/g). This study highlights that xylA and xylB overexpression is an effective strategy to improve xylose utilization and P(3HB) production in B. sacchari.
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Zhu X, Zhao D, Qiu H, Fan F, Man S, Bi C, Zhang X. The CRISPR/Cas9-facilitated multiplex pathway optimization (CFPO) technique and its application to improve the Escherichia coli xylose utilization pathway. Metab Eng 2017; 43:37-45. [PMID: 28800965 DOI: 10.1016/j.ymben.2017.08.003] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 07/04/2017] [Accepted: 08/03/2017] [Indexed: 01/09/2023]
Abstract
One of the most important research subjects of metabolic engineering is the pursuit of balanced metabolic pathways, which requires the modulation of expression of many genes. However, simultaneously modulating multiple genes on the chromosome remains challenging in prokaryotic organisms, including the industrial workhorse - Escherichia coli. In this work, the CRISPR/Cas9-facilitated multiplex pathway optimization (CFPO) technique was developed to simultaneously modulate the expression of multiple genes on the chromosome. To implement it, two plasmids were employed to target Cas9 to regulatory sequences of pathway genes, and a donor DNA plasmid library was constructed containing a regulator pool to modulate the expression of these genes. A modularized plasmid construction strategy was used to enable the assembly of a complex donor DNA plasmid library. After genome editing using this technique, a combinatorial library was obtained with variably expressed pathway genes. As a demonstration, the CFPO technique was applied to the xylose metabolic pathway genes in E. coli to improve xylose utilization. Three transcriptional units containing a total of four genes were modulated simultaneously with 70% efficiency, and improved strains were selected from the resulting combinatorial library by growth enrichment. The best strain, HQ304, displayed a 3-fold increase of the xylose-utilization rate. Finally, the xylose-utilization pathway of HQ304 was analyzed enzymologically to determine the optimal combination of enzyme activities.
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Affiliation(s)
- Xinna Zhu
- Tianjin Institute of Industrial Biotechnology, Chinese of Academy of Sciences, Tianjin 300308, China; Key Laboratory of Systems Microbial Biotechnology, Tianjin 300308, China
| | - Dongdong Zhao
- Tianjin Institute of Industrial Biotechnology, Chinese of Academy of Sciences, Tianjin 300308, China; Key Laboratory of Systems Microbial Biotechnology, Tianjin 300308, China
| | - Huanna Qiu
- Tianjin Institute of Industrial Biotechnology, Chinese of Academy of Sciences, Tianjin 300308, China; Key Laboratory of Systems Microbial Biotechnology, Tianjin 300308, China; College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Feiyu Fan
- Tianjin Institute of Industrial Biotechnology, Chinese of Academy of Sciences, Tianjin 300308, China; Key Laboratory of Systems Microbial Biotechnology, Tianjin 300308, China
| | - Shuli Man
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Changhao Bi
- Tianjin Institute of Industrial Biotechnology, Chinese of Academy of Sciences, Tianjin 300308, China; Key Laboratory of Systems Microbial Biotechnology, Tianjin 300308, China.
| | - Xueli Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese of Academy of Sciences, Tianjin 300308, China; Key Laboratory of Systems Microbial Biotechnology, Tianjin 300308, China.
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Gonzalez JE, Long CP, Antoniewicz MR. Comprehensive analysis of glucose and xylose metabolism in Escherichia coli under aerobic and anaerobic conditions by 13C metabolic flux analysis. Metab Eng 2016; 39:9-18. [PMID: 27840237 DOI: 10.1016/j.ymben.2016.11.003] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Revised: 10/09/2016] [Accepted: 11/07/2016] [Indexed: 12/13/2022]
Abstract
Glucose and xylose are the two most abundant sugars derived from the breakdown of lignocellulosic biomass. While aerobic glucose metabolism is relatively well understood in E. coli, until now there have been only a handful of studies focused on anaerobic glucose metabolism and no 13C-flux studies on xylose metabolism. In the absence of experimentally validated flux maps, constraint-based approaches such as MOMA and RELATCH cannot be used to guide new metabolic engineering designs. In this work, we have addressed this critical gap in current understanding by performing comprehensive characterizations of glucose and xylose metabolism under aerobic and anaerobic conditions, using recent state-of-the-art techniques in 13C metabolic flux analysis (13C-MFA). Specifically, we quantified precise metabolic fluxes for each condition by performing parallel labeling experiments and analyzing the data through integrated 13C-MFA using the optimal tracers [1,2-13C]glucose, [1,6-13C]glucose, [1,2-13C]xylose and [5-13C]xylose. We also quantified changes in biomass composition and confirmed turnover of macromolecules by applying [U-13C]glucose and [U-13C]xylose tracers. We demonstrated that under anaerobic growth conditions there is significant turnover of lipids and that a significant portion of CO2 originates from biomass turnover. Using knockout strains, we also demonstrated that β-oxidation is critical for anaerobic growth on xylose. Quantitative analysis of co-factor balances (NADH/FADH2, NADPH, and ATP) for different growth conditions provided new insights regarding the interplay of energy and redox metabolism and the impact on E. coli cell physiology.
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Affiliation(s)
- Jacqueline E Gonzalez
- Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, Newark, DE 19716, USA
| | - Christopher P Long
- Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, Newark, DE 19716, USA
| | - Maciek R Antoniewicz
- Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, Newark, DE 19716, USA.
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11
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Modulating the direction of carbon flow in Escherichia coli to improve l-tryptophan production by inactivating the global regulator FruR. J Biotechnol 2016; 231:141-148. [PMID: 27297546 DOI: 10.1016/j.jbiotec.2016.06.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 05/30/2016] [Accepted: 06/09/2016] [Indexed: 11/22/2022]
Abstract
The fructose repressor (FruR) affects carbon flux through the central metabolic pathways of Escherichia coli. In this study, l-tryptophan production in Escherichia coli FB-04 was improved by knocking out the fruR gene, thereby inactivating FruR. This fruR knockout strain, E. coli FB-04(ΔfruR), not only exhibited higher growth efficiency, it also showed substantially improved l-tryptophan production. l-tryptophan production by E. coli FB-04(ΔfruR) and l-tryptophan yield per glucose were increased by 62.5% and 52.4%, respectively, compared with the parent E. coli FB-04. Metabolomics analysis showed that the fruR knockout significantly enhances metabolic flow through glycolysis, the pentose phosphate pathway and the TCA cycle, increasing levels of critical precursors and substrates for l-tryptophan biosynthesis. These results indicate that fruR deletion should enhance l-tryptophan production and improve the efficiency of carbon source utilization independent of genetic background.
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12
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Ali SS, Nugent B, Mullins E, Doohan FM. Fungal-mediated consolidated bioprocessing: the potential of Fusarium oxysporum for the lignocellulosic ethanol industry. AMB Express 2016; 6:13. [PMID: 26888202 PMCID: PMC4757592 DOI: 10.1186/s13568-016-0185-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Accepted: 02/09/2016] [Indexed: 12/21/2022] Open
Abstract
Microbial bioprocessing of lignocellulose to bioethanol still poses challenges in terms of substrate catabolism. The most important challenge is to overcome substrate recalcitrance and to thus reduce the number of steps needed to biorefine lignocellulose. Conventionally, conversion involves chemical pretreatment of lignocellulose, followed by hydrolysis of biomass to monomer sugars that are subsequently fermented into bioethanol. Consolidated bioprocessing (CBP) has been suggested as an efficient and economical method of manufacturing bioethanol from lignocellulose. CBP integrates the hydrolysis and fermentation steps into a single process, thereby significantly reducing the amount of steps in the biorefining process. Filamentous fungi are remarkable organisms that are naturally specialised in deconstructing plant biomass and thus they have tremendous potential as components of CBP. The fungus Fusarium oxysporum has potential for CBP of lignocellulose to bioethanol. Here we discuss the complexity and potential of CBP, the bottlenecks in the process, and the potential influence of fungal genetic diversity, substrate complexity and new technologies on the efficacy of CPB of lignocellulose, with a focus on F. oxysporum.
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Tomás-Pejó E, Olsson L. Influence of the propagation strategy for obtaining robust Saccharomyces cerevisiae cells that efficiently co-ferment xylose and glucose in lignocellulosic hydrolysates. Microb Biotechnol 2015; 8:999-1005. [PMID: 25989314 PMCID: PMC4621452 DOI: 10.1111/1751-7915.12280] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 02/06/2015] [Accepted: 02/22/2015] [Indexed: 12/31/2022] Open
Abstract
Development of xylose-fermenting yeast strains that are tolerant to the inhibitors present in lignocellulosic hydrolysates is crucial to achieve efficient bioethanol production processes. In this study, the importance of the propagation strategy for obtaining robust cells was studied. Addition of hydrolysate during propagation of the cells adapted them to the inhibitors, resulting in more tolerant cells with shorter lag phases and higher specific growth rates in minimal medium containing acetic acid and vanillin than unadapted cells. Addition of hydrolysate during propagation also resulted in cells with better fermentation capabilities. Cells propagated without hydrolysate were unable to consume xylose in wheat straw hydrolysate fermentations, whereas 40.3% and 97.7% of the xylose was consumed when 12% and 23% (v/v) hydrolysate, respectively, was added during propagation. Quantitative polymerase chain reaction revealed changes in gene expression, depending on the concentration of hydrolysate added during propagation. This study highlights the importance of using an appropriate propagation strategy for the optimum performance of yeast in fermentation of lignocellulosic hydrolysates.
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Affiliation(s)
- Elia Tomás-Pejó
- Department of Biology and Biological Engineering, Industrial Biotechnology, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden.,Unit of Biotechnological Processes for Energy Production, Instituto Madrileño De Estudios Avanzados (IMDEA) Energy, 28935, Móstoles (Madrid), Spain
| | - Lisbeth Olsson
- Department of Biology and Biological Engineering, Industrial Biotechnology, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
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Manzano-Robleda MDC, Barranco-Fragoso B, Uribe M, Méndez-Sánchez N. Portal vein thrombosis: what is new? Ann Hepatol 2014; 71:2-7. [PMID: 25536638 DOI: 10.1016/j.ijbiomac.2014.06.065] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 05/28/2014] [Accepted: 06/11/2014] [Indexed: 02/06/2023]
Abstract
Portal vein thrombosis (PVT) is one of the most common vascular disorders of the liver with significant morbidity and mortality. Large cohort studies have reported a global prevalence of 1%, but in some risk groups it can be up to 26%. Causes of PVT are cirrhosis, hepatobiliary malignancy, abdominal infectious or inflammatory diseases, and myeloproliferative disorders. Most patients with PVT have a general risk factor. The natural history of PVT results in portal hypertension leading to splenomegaly and the formation of portosystemic collateral blood vessels and esophageal, gastric, duodenal, and jejunal varices. Diagnosis of PVT is made by imaging, mainly Doppler ultrasonography. According to its time of development, localization, pathophysiology, and evolution, PVT should be classified in every patient. Some clinical features such as cirrhosis, hepatocellular carcinoma, and hepatic transplantation are areas of special interest and are discussed in this review. The goal of treatment of acute PVT is to reconstruct the blocked veins. Endoscopic variceal ligation is safe and highly effective in patients with variceal bleeding caused by chronic PVT. In conclusion, PVT is the most common cause of vascular disease of the liver and its prevalence has being increasing, especially among patients with an underlying liver disease. All patients should be investigated for thrombophilic conditions, and in those with cirrhosis, anticoagulation prophylaxis should be considered.
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Affiliation(s)
| | | | - Misael Uribe
- Liver Research Unit. Medica Sur Clinic & Foundation. Mexico City, Mexico
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15
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The transport and mediation mechanisms of the common sugars in Escherichia coli. Biotechnol Adv 2014; 32:905-19. [DOI: 10.1016/j.biotechadv.2014.04.009] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 03/23/2014] [Accepted: 04/18/2014] [Indexed: 11/17/2022]
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16
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Wang C, Cai H, Zhou Z, Zhang K, Chen Z, Chen Y, Wan H, Ouyang P. Investigation of ptsG gene in response to xylose utilization in Corynebacterium glutamicum. J Ind Microbiol Biotechnol 2014; 41:1249-58. [PMID: 24859809 DOI: 10.1007/s10295-014-1455-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 04/28/2014] [Indexed: 11/26/2022]
Abstract
Corynebacterium glutamicum strains NC-2 were able to grow on xylose as sole carbon sources in our previous work. Nevertheless, it exhibited the major shortcoming that the xylose consumption was repressed in the presence of glucose. So far, regarding C. glutamicum, there are a number of reports on ptsG gene, the glucose-specific transporter, involved in glucose metabolism. Recently, we found ptsG had influence on xylose utilization and investigated the ptsG gene in response to xylose utilization in C. glutamicum with the aim to improve xylose consumption and simultaneously utilized glucose and xylose. The ptsG-deficient mutant could grow on xylose, while exhibiting noticeably reduced growth on xylose as sole carbon source. A mutant deficient in ptsH, a general PTS gene, exhibited a similar phenomenon. When complementing ptsG gene, the mutant ΔptsG-ptsG restored the ability to grow on xylose similarly to NC-2. These indicate that ptsG gene is not only essential for metabolism on glucose but also important in xylose utilization. A ptsG-overexpressing recombinant strain could not accelerate glucose or xylose metabolism. When strains were aerobically cultured in a sugar mixture of glucose and xylose, glucose and xylose could not be utilized simultaneously. Interestingly, the ΔptsG strain could co-utilize glucose and xylose under oxygen-deprived conditions, though the consumption rate of glucose and xylose dramatically declined. It was the first report of ptsG gene in response to xylose utilization in C. glutamicum.
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Affiliation(s)
- Chen Wang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, Nanjing, 211816, China
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17
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Förster AH, Gescher J. Metabolic Engineering of Escherichia coli for Production of Mixed-Acid Fermentation End Products. Front Bioeng Biotechnol 2014; 2:16. [PMID: 25152889 PMCID: PMC4126452 DOI: 10.3389/fbioe.2014.00016] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 05/09/2014] [Indexed: 01/25/2023] Open
Abstract
Mixed-acid fermentation end products have numerous applications in biotechnology. This is probably the main driving force for the development of multiple strains that are supposed to produce individual end products with high yields. The process of engineering Escherichia coli strains for applied production of ethanol, lactate, succinate, or acetate was initiated several decades ago and is still ongoing. This review follows the path of strain development from the general characteristics of aerobic versus anaerobic metabolism over the regulatory machinery that enables the different metabolic routes. Thereafter, major improvements for broadening the substrate spectrum of E. coli toward cheap carbon sources like molasses or lignocellulose are highlighted before major routes of strain development for the production of ethanol, acetate, lactate, and succinate are presented.
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Affiliation(s)
- Andreas H Förster
- Institute of Applied Biosciences, Karlsruhe Institute of Technology , Karlsruhe , Germany
| | - Johannes Gescher
- Institute of Applied Biosciences, Karlsruhe Institute of Technology , Karlsruhe , Germany
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18
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Optimization of Two-Step Acid-Catalyzed Hydrolysis of Oil Palm Empty Fruit Bunch for High Sugar Concentration in Hydrolysate. INTERNATIONAL JOURNAL OF CHEMICAL ENGINEERING 2014. [DOI: 10.1155/2014/954632] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Getting high sugar concentrations in lignocellulosic biomass hydrolysate with reasonable yields of sugars is commercially attractive but very challenging. Two-step acid-catalyzed hydrolysis of oil palm empty fruit bunch (EFB) was conducted to get high sugar concentrations in the hydrolysate. The biphasic kinetic model was used to guide the optimization of the first step dilute acid-catalyzed hydrolysis of EFB. A total sugar concentration of 83.0 g/L with a xylose concentration of 69.5 g/L and a xylose yield of 84.0% was experimentally achieved, which is in well agreement with the model predictions under optimal conditions (3% H2SO4and 1.2% H3PO4, w/v, liquid to solid ratio 3 mL/g, 130°C, and 36 min). To further increase total sugar and xylose concentrations in hydrolysate, a second step hydrolysis was performed by adding fresh EFB to the hydrolysate at 130°C for 30 min, giving a total sugar concentration of 114.4 g/L with a xylose concentration of 93.5 g/L and a xylose yield of 56.5%. To the best of our knowledge, the total sugar and xylose concentrations are the highest among those ever reported for acid-catalyzed hydrolysis of lignocellulose.
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Zhuang ZY, Li SY. Rubisco-based engineered Escherichia coli for in situ carbon dioxide recycling. BIORESOURCE TECHNOLOGY 2013; 150:79-88. [PMID: 24152790 DOI: 10.1016/j.biortech.2013.09.116] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 09/21/2013] [Accepted: 09/25/2013] [Indexed: 05/16/2023]
Abstract
In this study, ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) and phosphoribulokinase (PrkA) were overexpressed individually and in combination in Escherichia coli under different fermentation conditions. While wild-type E. coli produced 0.731 mol of CO2 per consumption of one mole of arabinose, engineered E. coli JB, containing both heterologous Rubisco and PrkA, produced only 0.621 mol of CO2 per consumption of one mole of arabinose. This represents a 15% reduction in CO2 emission and achieves 38% of theoretical CO2 reduction. The CO2 fixation rate of Rubisco-based engineered E. coli JB is 67 mg-CO2·mole-arabinose(-1) L(-1) h(-1), which is comparable to the performance of microalgae and cyanobacteria. It has been found that overexpressing Rubisco dramatically elevates the bacteria growth and sugar consumptions in the presence of oxygen and L-arabinose. It has been also found that overexpressing PrkA could demolish the balance of ATP regeneration, yet can be recovered simply by controlling the pH at 7.0±0.1.
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Affiliation(s)
- Zong-Yu Zhuang
- Department of Chemical Engineering, National Chung Hsing University, Taichung 402, Taiwan
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20
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Wang C, Zhang H, Cai H, Zhou Z, Chen Y, Chen Y, Ouyang P. Succinic Acid Production from Corn Cob Hydrolysates by Genetically Engineered Corynebacterium glutamicum. Appl Biochem Biotechnol 2013; 172:340-50. [DOI: 10.1007/s12010-013-0539-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 09/15/2013] [Indexed: 11/25/2022]
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21
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Synthetic non-oxidative glycolysis enables complete carbon conservation. Nature 2013; 502:693-7. [PMID: 24077099 DOI: 10.1038/nature12575] [Citation(s) in RCA: 260] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 08/15/2013] [Indexed: 01/19/2023]
Abstract
Glycolysis, or its variations, is a fundamental metabolic pathway in life that functions in almost all organisms to decompose external or intracellular sugars. The pathway involves the partial oxidation and splitting of sugars to pyruvate, which in turn is decarboxylated to produce acetyl-coenzyme A (CoA) for various biosynthetic purposes. The decarboxylation of pyruvate loses a carbon equivalent, and limits the theoretical carbon yield to only two moles of two-carbon (C2) metabolites per mole of hexose. This native route is a major source of carbon loss in biorefining and microbial carbon metabolism. Here we design and construct a non-oxidative, cyclic pathway that allows the production of stoichiometric amounts of C2 metabolites from hexose, pentose and triose phosphates without carbon loss. We tested this pathway, termed non-oxidative glycolysis (NOG), in vitro and in vivo in Escherichia coli. NOG enables complete carbon conservation in sugar catabolism to acetyl-CoA, and can be used in conjunction with CO2 fixation and other one-carbon (C1) assimilation pathways to achieve a 100% carbon yield to desirable fuels and chemicals.
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22
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Yanagisawa M, Kawai S, Murata K. Strategies for the production of high concentrations of bioethanol from seaweeds: production of high concentrations of bioethanol from seaweeds. Bioengineered 2013; 4:224-35. [PMID: 23314751 DOI: 10.4161/bioe.23396] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Bioethanol has attracted attention as an alternative to petroleum-derived fuel. Seaweeds have been proposed as some of the most promising raw materials for bioethanol production because they have several advantages over lignocellulosic biomass. However, because seaweeds contain low contents of glucans, i.e., polysaccharides composed of glucose, the conversion of only the glucans from seaweed is not sufficient to produce high concentrations of ethanol. Therefore, it is also necessary to produce ethanol from other specific carbohydrate components of seaweeds, including sulfated polysaccharides, mannitol, alginate, agar and carrageenan. This review summarizes the current state of research on the production of ethanol from seaweed carbohydrates for which the conversion of carbohydrates to sugars is a key step and makes comparisons with the production of ethanol from lignocellulosic biomass. This review provides valuable information necessary for the production of high concentrations of ethanol from seaweeds.
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Affiliation(s)
- Mitsunori Yanagisawa
- Laboratory of Basic and Applied Molecular Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
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23
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Utrilla J, Licona-Cassani C, Marcellin E, Gosset G, Nielsen LK, Martinez A. Engineering and adaptive evolution of Escherichia coli for d-lactate fermentation reveals GatC as a xylose transporter. Metab Eng 2012; 14:469-76. [DOI: 10.1016/j.ymben.2012.07.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2012] [Revised: 06/28/2012] [Accepted: 07/25/2012] [Indexed: 10/28/2022]
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Liu R, Liang L, Chen K, Ma J, Jiang M, Wei P, Ouyang P. Fermentation of xylose to succinate by enhancement of ATP supply in metabolically engineered Escherichia coli. Appl Microbiol Biotechnol 2012; 94:959-68. [PMID: 22294432 DOI: 10.1007/s00253-012-3896-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Revised: 01/07/2012] [Accepted: 01/09/2012] [Indexed: 11/25/2022]
Abstract
In Escherichia coli K12, succinate was not the dominant fermentation product from xylose. To reduce byproduct formation and increase succinate accumulation,pyruvate formate lyase and lactate dehydrogenase, encoded by pflB and ldhA genes, were inactivated. However, these mutations eliminated cell growth and xylose utilization. During anaerobic growth of bacteria, organic intermediates,such as pyruvate, serve as electron acceptors to maintain the overall redox balance. Under these conditions, the ATP needed for cell growth is derived from substrate level phosphorylation. In E. coli K12, conversion of xylose to pyruvate only yielded 0.67 net ATP per xylose during anaerobic fermentation. However, E. coli produces equimolar amounts of acetate and ethanol from two pyruvates, and these reactions generate one additional ATP. Conversion of xylose to acetate and ethanol increases the net ATP yield from 0.67 to 1.5 per xylose, which could meet the ATP needed for xylose metabolism. A pflB deletion strain cannot convert pyruvate to acetyl coenzyme A, the precursor for acetate and ethanol production, and could not produce the additional ATP. Thus,the double mutations eliminated cell growth and xylose utilization. To supply the sufficient ATPs, overexpression of ATP-forming phosphoenolpyruvate-carboxykinase from Bacillus subtilis 168 in an ldhA, pflB, and ppc deletion strain resulted in a significant increase in cell mass and succinate production. In addition, fermentation of corn stalk hydrolysate containing a high percentage of xylose and glucose produced a final succinate concentration of 11.13 g l−1 with a yield of1.02 g g−1 total sugars during anaerobic fermentation.
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Affiliation(s)
- Rongming Liu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, Nanjing, China
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Su Y, Rhee MS, Ingram LO, Shanmugam KT. Physiological and fermentation properties of Bacillus coagulans and a mutant lacking fermentative lactate dehydrogenase activity. J Ind Microbiol Biotechnol 2010; 38:441-50. [PMID: 20677017 DOI: 10.1007/s10295-010-0788-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Accepted: 07/12/2010] [Indexed: 11/29/2022]
Abstract
Bacillus coagulans, a sporogenic lactic acid bacterium, grows optimally at 50-55 °C and produces lactic acid as the primary fermentation product from both hexoses and pentoses. The amount of fungal cellulases required for simultaneous saccharification and fermentation (SSF) at 55 °C was previously reported to be three to four times lower than for SSF at the optimum growth temperature for Saccharomyces cerevisiae of 35 °C. An ethanologenic B. coagulans is expected to lower the cellulase loading and production cost of cellulosic ethanol due to SSF at 55 °C. As a first step towards developing B. coagulans as an ethanologenic microbial biocatalyst, activity of the primary fermentation enzyme L-lactate dehydrogenase was removed by mutation (strain Suy27). Strain Suy27 produced ethanol as the main fermentation product from glucose during growth at pH 7.0 (0.33 g ethanol per g glucose fermented). Pyruvate dehydrogenase (PDH) and alcohol dehydrogenase (ADH) acting in series contributed to about 55% of the ethanol produced by this mutant while pyruvate formate lyase and ADH were responsible for the remainder. Due to the absence of PDH activity in B. coagulans during fermentative growth at pH 5.0, the l-ldh mutant failed to grow anaerobically at pH 5.0. Strain Suy27-13, a derivative of the l-ldh mutant strain Suy27, that produced PDH activity during anaerobic growth at pH 5.0 grew at this pH and also produced ethanol as the fermentation product (0.39 g per g glucose). These results show that construction of an ethanologenic B. coagulans requires optimal expression of PDH activity in addition to the removal of the LDH activity to support growth and ethanol production.
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Affiliation(s)
- Yue Su
- Department of Microbiology and Cell Science, University of Florida, Box 110700, Gainesville, FL 32611, USA
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27
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Murarka A, Clomburg JM, Gonzalez R. Metabolic flux analysis of wild-type Escherichia coli and mutants deficient in pyruvate-dissimilating enzymes during the fermentative metabolism of glucuronate. MICROBIOLOGY-SGM 2010; 156:1860-1872. [PMID: 20167619 DOI: 10.1099/mic.0.036251-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The fermentative metabolism of d-glucuronic acid (glucuronate) in Escherichia coli was investigated with emphasis on the dissimilation of pyruvate via pyruvate formate-lyase (PFL) and pyruvate dehydrogenase (PDH). In silico and in vivo metabolic flux analysis (MFA) revealed that PFL and PDH share the dissimilation of pyruvate in wild-type MG1655. Surprisingly, it was found that PDH supports fermentative growth on glucuronate in the absence of PFL. The PDH-deficient strain (Pdh-) exhibited a slower transition into the exponential phase and a decrease in specific rates of growth and glucuronate utilization. Moreover, a significant redistribution of metabolic fluxes was found in PDH- and PFL-deficient strains. Since no role had been proposed for PDH in the fermentative metabolism of E. coli, the metabolic differences between MG1655 and Pdh- were further investigated. An increase in the oxidative pentose phosphate pathway (ox-PPP) flux was observed in response to PDH deficiency. A comparison of the ox-PPP and PDH pathways led to the hypothesis that the role of PDH is the supply of reducing equivalents. The finding that a PDH deficiency lowers the NADH : NAD(+) ratio supported the proposed role of PDH. Moreover, the NADH : NAD(+) ratio in a strain deficient in both PDH and the ox-PPP (Pdh-Zwf-) was even lower than that observed for Pdh-. Strain Pdh-Zwf- also exhibited a slower transition into the exponential phase and a lower growth rate than Pdh-. Finally, a transhydrogenase-deficient strain grew more slowly than wild-type but did not show the slower transition into the exponential phase characteristic of Pdh- mutants. It is proposed that PDH fulfils two metabolic functions. First, by creating the appropriate internal redox state (i.e. appropriate NADH : NAD(+) ratio), PDH ensures the functioning of the glucuronate utilization pathway. Secondly, the NADH generated by PDH can be converted to NADPH by the action of transhydrogenases, thus serving as biosynthetic reducing power in the synthesis of building blocks and macromolecules.
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Affiliation(s)
- Abhishek Murarka
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - James M Clomburg
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - Ramon Gonzalez
- Department of Bioengineering, Rice University, Houston, TX, USA.,Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
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Biofuel production in Escherichia coli: the role of metabolic engineering and synthetic biology. Appl Microbiol Biotechnol 2010; 86:419-34. [DOI: 10.1007/s00253-010-2446-1] [Citation(s) in RCA: 141] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2009] [Revised: 01/07/2010] [Accepted: 01/09/2010] [Indexed: 01/06/2023]
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Dellomonaco C, Fava F, Gonzalez R. The path to next generation biofuels: successes and challenges in the era of synthetic biology. Microb Cell Fact 2010; 9:3. [PMID: 20089184 PMCID: PMC2817670 DOI: 10.1186/1475-2859-9-3] [Citation(s) in RCA: 133] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2009] [Accepted: 01/20/2010] [Indexed: 01/11/2023] Open
Abstract
Volatility of oil prices along with major concerns about climate change, oil supply security and depleting reserves have sparked renewed interest in the production of fuels from renewable resources. Recent advances in synthetic biology provide new tools for metabolic engineers to direct their strategies and construct optimal biocatalysts for the sustainable production of biofuels. Metabolic engineering and synthetic biology efforts entailing the engineering of native and de novo pathways for conversion of biomass constituents to short-chain alcohols and advanced biofuels are herewith reviewed. In the foreseeable future, formal integration of functional genomics and systems biology with synthetic biology and metabolic engineering will undoubtedly support the discovery, characterization, and engineering of new metabolic routes and more efficient microbial systems for the production of biofuels.
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Lopes MSG, Gomez JGC, Silva LF. Cloning and overexpression of the xylose isomerase gene from Burkholderia sacchari and production of polyhydroxybutyrate from xylose. Can J Microbiol 2009; 55:1012-5. [DOI: 10.1139/w09-055] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A different organization for the xyl operon was found in different genomes of Burkholderia and Pseudomomas species. Degenerated primers were designed based on Burkholderia genomes and used to amplify the xylose isomerase gene (xylA) from Burkholderia sacchari IPT101. The gene encoded a protein of 329 amino acids, which showed the highest similarity (90%) to the homologous gene of Burkholderia dolosa . It was cloned in the broad host range plasmid pBBR1MCS-2, which partially restored growth and polyhydroxybutyrate production capability in xylose to a B. sacchari xyl– mutant. When xylA was overexpressed in the wild-type strain, it was not able to increase growth and polyhydroxybutyrate production, suggesting that XylA activity is not limiting for xylose utilization in B. sacchari.
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Affiliation(s)
- Mateus Schreiner Garcez Lopes
- Department of Microbiology, University of São Paulo, Av. Prof. Lineus Prestes, 1374, Cidade Universitária, CEP 05508-000 - São Paulo, SP, Brazil
| | - José Gregório Cabrera Gomez
- Department of Microbiology, University of São Paulo, Av. Prof. Lineus Prestes, 1374, Cidade Universitária, CEP 05508-000 - São Paulo, SP, Brazil
| | - Luiziana Ferreira Silva
- Department of Microbiology, University of São Paulo, Av. Prof. Lineus Prestes, 1374, Cidade Universitária, CEP 05508-000 - São Paulo, SP, Brazil
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Xu Q, Singh A, Himmel ME. Perspectives and new directions for the production of bioethanol using consolidated bioprocessing of lignocellulose. Curr Opin Biotechnol 2009; 20:364-71. [PMID: 19520566 DOI: 10.1016/j.copbio.2009.05.006] [Citation(s) in RCA: 231] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2009] [Revised: 05/13/2009] [Accepted: 05/14/2009] [Indexed: 11/24/2022]
Abstract
The U.S. DOE Energy Independence and Security Act (EISA) mandated attainment of a national production level of 36 billion gallons of biofuels (to be added to gasoline) by 2022, of which 21 billion gallons must be derived from renewable/sustainable feedstocks (e.g. lignocellulose). In order to attain these goals, the development of cost effective process technologies that can convert plant biomass to fermentable sugars must occur. An alternative route to production of bioethanol is the utilization of microorganisms that can both convert biomass to fermentable sugars and ferment the resultant sugars to ethanol in a process known as consolidated bioprocessing (CBP). Although various economic benefits and technology hurdles must be weighed in the course of choosing the CBP strategy to be pursued, we present arguments for developing the powerfully cellulolytic fungus, Trichoderma reesei, as an effective CBP microorganism.
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Affiliation(s)
- Qi Xu
- Chemical and Biosciences Center, National Renewable Energy Laboratory, Golden CO 80401, USA
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Durnin G, Clomburg J, Yeates Z, Alvarez PJ, Zygourakis K, Campbell P, Gonzalez R. Understanding and harnessing the microaerobic metabolism of glycerol inEscherichia coli. Biotechnol Bioeng 2009; 103:148-61. [DOI: 10.1002/bit.22246] [Citation(s) in RCA: 148] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Shams Yazdani S, Gonzalez R. Engineering Escherichia coli for the efficient conversion of glycerol to ethanol and co-products. Metab Eng 2008; 10:340-51. [DOI: 10.1016/j.ymben.2008.08.005] [Citation(s) in RCA: 177] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2008] [Accepted: 08/13/2008] [Indexed: 10/21/2022]
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Shaw AJ, Podkaminer KK, Desai SG, Bardsley JS, Rogers SR, Thorne PG, Hogsett DA, Lynd LR. Metabolic engineering of a thermophilic bacterium to produce ethanol at high yield. Proc Natl Acad Sci U S A 2008; 105:13769-74. [PMID: 18779592 PMCID: PMC2544529 DOI: 10.1073/pnas.0801266105] [Citation(s) in RCA: 195] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2008] [Indexed: 12/23/2022] Open
Abstract
We report engineering Thermoanaerobacterium saccharolyticum, a thermophilic anaerobic bacterium that ferments xylan and biomass-derived sugars, to produce ethanol at high yield. Knockout of genes involved in organic acid formation (acetate kinase, phosphate acetyltransferase, and L-lactate dehydrogenase) resulted in a strain able to produce ethanol as the only detectable organic product and substantial changes in electron flow relative to the wild type. Ethanol formation in the engineered strain (ALK2) utilizes pyruvate:ferredoxin oxidoreductase with electrons transferred from ferredoxin to NAD(P), a pathway different from that in previously described microbes with a homoethanol fermentation. The homoethanologenic phenotype was stable for >150 generations in continuous culture. The growth rate of strain ALK2 was similar to the wild-type strain, with a reduction in cell yield proportional to the decreased ATP availability resulting from acetate kinase inactivation. Glucose and xylose are co-utilized and utilization of mannose and arabinose commences before glucose and xylose are exhausted. Using strain ALK2 in simultaneous hydrolysis and fermentation experiments at 50 degrees C allows a 2.5-fold reduction in cellulase loading compared with using Saccharomyces cerevisiae at 37 degrees C. The maximum ethanol titer produced by strain ALK2, 37 g/liter, is the highest reported thus far for a thermophilic anaerobe, although further improvements are desired and likely possible. Our results extend the frontier of metabolic engineering in thermophilic hosts, have the potential to significantly lower the cost of cellulosic ethanol production, and support the feasibility of further cost reductions through engineering a diversity of host organisms.
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Affiliation(s)
- A. Joe Shaw
- *Thayer School of Engineering, and
- Mascoma Corporation, 16 Cavendish Court, Lebanon, NH 03766
| | | | | | | | | | | | - David A. Hogsett
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755; and
| | - Lee R. Lynd
- *Thayer School of Engineering, and
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755; and
- Mascoma Corporation, 16 Cavendish Court, Lebanon, NH 03766
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Peterson JD, Ingram LO. Anaerobic respiration in engineered Escherichia coli with an internal electron acceptor to produce fuel ethanol. Ann N Y Acad Sci 2008; 1125:363-72. [PMID: 18378606 DOI: 10.1196/annals.1419.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Environmental concerns and unease with U.S. dependence on foreign oil have renewed interest in converting biomass into fuel ethanol. The volume of plant matter available makes lignocellulose conversion to ethanol desirable, although no one isolated organism has been shown to break bonds in lignocellulose and efficiently metabolize resulting sugars into one product. This work reviews directed engineering coupled with metabolic evolution resulting in microbial biocatalysts that produce up to 45 g L(-1) ethanol in 48 hours in a simple mineral salts medium and that convert various compounds of lignocellulosic materials to ethanol. Mutations contributing to ethanologenesis are discussed along with adding enzymatic capabilities to existing biocatalysts in order to decrease the commercial enzymes required to reduce plant matter into fermentable sugars.
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A new model for the anaerobic fermentation of glycerol in enteric bacteria: trunk and auxiliary pathways in Escherichia coli. Metab Eng 2008; 10:234-45. [PMID: 18632294 DOI: 10.1016/j.ymben.2008.05.001] [Citation(s) in RCA: 124] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2007] [Revised: 05/03/2008] [Accepted: 05/13/2008] [Indexed: 11/22/2022]
Abstract
Anaerobic fermentation of glycerol in the Enterobacteriaceae family has long been considered a unique property of species that synthesize 1,3-propanediol (1,3-PDO). However, we have discovered that Escherichia coli can ferment glycerol in a 1,3-PDO-independent manner. We identified 1,2-propanediol (1,2-PDO) as a fermentation product and established the pathway that mediates its synthesis as well as its role in the metabolism of glycerol. We also showed that the trunk pathway responsible for the conversion of glycerol into glycolytic intermediates is composed of two enzymes: a type II glycerol dehydrogenase (glyDH-II) and a dihydroxyacetone kinase (DHAK), the former of previously unknown physiological role. Based on our findings, we propose a new model for glycerol fermentation in enteric bacteria in which: (i) the production of 1,2-PDO provides a means to consume reducing equivalents generated in the synthesis of cell mass, thus facilitating redox balance, and (ii) the conversion of glycerol to ethanol, through a redox-balanced pathway, fulfills energy requirements by generating ATP via substrate-level phosphorylation. The activity of the formate hydrogen-lyase and F(0)F(1)-ATPase systems were also found to facilitate the fermentative metabolism of glycerol, and along with the ethanol and 1,2-PDO pathways, were considered auxiliary or enabling. We demonstrated that glycerol fermentation in E. coli was not previously observed due to the use of medium formulations and culture conditions that impair the aforementioned pathways. These include high concentrations of potassium and phosphate, low concentrations of glycerol, alkaline pH, and closed cultivation systems that promote the accumulation of hydrogen gas.
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Orencio-Trejo M, Flores N, Escalante A, Hernández-Chávez G, Bolívar F, Gosset G, Martinez A. Metabolic regulation analysis of an ethanologenic Escherichia coli strain based on RT-PCR and enzymatic activities. BIOTECHNOLOGY FOR BIOFUELS 2008; 1:8. [PMID: 18471274 PMCID: PMC2396614 DOI: 10.1186/1754-6834-1-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2008] [Accepted: 05/01/2008] [Indexed: 05/07/2023]
Abstract
BACKGROUND A metabolic regulation study was performed, based upon measurements of enzymatic activities, fermentation performance, and RT-PCR analysis of pathways related to central carbon metabolism, in an ethanologenic Escherichia coli strain (CCE14) derived from lineage C. In comparison with previous engineered strains, this E coli derivative has a higher ethanol production rate in mineral medium, as a result of the elevated heterologous expression of the chromosomally integrated genes encoding PDCZm and ADHZm (pyruvate decarboxylase and alcohol dehydrogenase from Zymomonas mobilis). It is suggested that this behavior might be due to lineage differences between E. coli W and C. RESULTS This study demonstrated that the glycolytic flux is controlled, in this case, by reactions outside glycolysis, i.e., the fermentative pathways. Changes in ethanol production rate in this ethanologenic strain result in low organic acid production rates, and high glycolytic and ethanologenic fluxes, that correlate with enhanced transcription and enzymatic activity levels of PDCZm and ADHZm. Furthermore, a higher ethanol yield (90% of the theoretical) in glucose-mineral media was obtained with CCE14 in comparison with previous engineered E. coli strains, such as KO11, that produces a 70% yield under the same conditions. CONCLUSION Results suggest that a higher ethanol formation rate, caused by ahigher PDCZm and ADHZm activities induces a metabolic state that cells compensate through enhanced glucose transport, ATP synthesis, and NAD-NADH+H turnover rates. These results show that glycolytic enzymatic activities, present in E. coli W and C under fermentative conditions, are sufficient to contend with increases in glucose consumption and product formation rates.
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Affiliation(s)
- Montserrat Orencio-Trejo
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México. Cuernavaca, Mor., México
| | - Noemí Flores
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México. Cuernavaca, Mor., México
| | - Adelfo Escalante
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México. Cuernavaca, Mor., México
| | - Georgina Hernández-Chávez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México. Cuernavaca, Mor., México
| | - Francisco Bolívar
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México. Cuernavaca, Mor., México
| | - Guillermo Gosset
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México. Cuernavaca, Mor., México
| | - Alfredo Martinez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México. Cuernavaca, Mor., México
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Dihydrolipoamide dehydrogenase mutation alters the NADH sensitivity of pyruvate dehydrogenase complex of Escherichia coli K-12. J Bacteriol 2008; 190:3851-8. [PMID: 18375566 DOI: 10.1128/jb.00104-08] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Under anaerobic growth conditions, an active pyruvate dehydrogenase (PDH) is expected to create a redox imbalance in wild-type Escherichia coli due to increased production of NADH (>2 NADH molecules/glucose molecule) that could lead to growth inhibition. However, the additional NADH produced by PDH can be used for conversion of acetyl coenzyme A into reduced fermentation products, like alcohols, during metabolic engineering of the bacterium. E. coli mutants that produced ethanol as the main fermentation product were recently isolated as derivatives of an ldhA pflB double mutant. In all six mutants tested, the mutation was in the lpd gene encoding dihydrolipoamide dehydrogenase (LPD), a component of PDH. Three of the LPD mutants carried an H322Y mutation (lpd102), while the other mutants carried an E354K mutation (lpd101). Genetic and physiological analysis revealed that the mutation in either allele supported anaerobic growth and homoethanol fermentation in an ldhA pflB double mutant. Enzyme kinetic studies revealed that the LPD(E354K) enzyme was significantly less sensitive to NADH inhibition than the native LPD. This reduced NADH sensitivity of the mutated LPD was translated into lower sensitivity of the appropriate PDH complex to NADH inhibition. The mutated forms of the PDH had a 10-fold-higher K(i) for NADH than the native PDH. The lower sensitivity of PDH to NADH inhibition apparently increased PDH activity in anaerobic E. coli cultures and created the new ethanologenic fermentation pathway in this bacterium. Analogous mutations in the LPD of other bacteria may also significantly influence the growth and physiology of the organisms in a similar fashion.
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Huerta-Beristain G, Utrilla J, Hernández-Chávez G, Bolívar F, Gosset G, Martinez A. Specific ethanol production rate in ethanologenic Escherichia coli strain KO11 Is limited by pyruvate decarboxylase. J Mol Microbiol Biotechnol 2008; 15:55-64. [PMID: 18349551 DOI: 10.1159/000111993] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Modification of ethanol productivity and yield, using mineral medium supplemented with glucose or xylose as carbon sources, was studied in ethanologenic Escherichia coli KO11 by increasing the activity of five key carbon metabolism enzymes. KO11 efficiently converted glucose or xylose to ethanol with a yield close to 100% of the theoretical maximum when growing in rich medium. However, when KO11 ferments glucose or xylose in mineral medium, the ethanol yields decreased to only 70 and 60%, respectively. An increase in GALP(Ec) (permease of galactose-glucose-xylose) or PGK(Ec) (phosphoglycerate kinase) activities did not change xylose or glucose and ethanol flux. However, when PDC(Zm) (pyruvate decarboxylase from Zymomonas mobilis) activity was increased 7-fold, the yields of ethanol from glucose or xylose were increased to 85 and 75%, respectively, and organic acid formation rates were reduced. Furthermore, as a response to a reduction in acetate and ATP yield, and a limited PDC(Zm) activity, an increase in PFK(Ec) (phosphofructokinase) or PYK(Bs) (pyruvate kinase from Bacillus stearothermophilus) activity drastically reduced glucose or xylose consumption and ethanol formation flux. This experimental metabolic control analysis showed that ethanol flux in KO11 is negatively controlled by phosphofructokinase and pyruvate kinase, and positively influenced by the PDC(Zm) activity level.
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Affiliation(s)
- Gerardo Huerta-Beristain
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, México
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Murarka A, Dharmadi Y, Yazdani SS, Gonzalez R. Fermentative utilization of glycerol by Escherichia coli and its implications for the production of fuels and chemicals. Appl Environ Microbiol 2008; 74:1124-35. [PMID: 18156341 PMCID: PMC2258577 DOI: 10.1128/aem.02192-07] [Citation(s) in RCA: 247] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2007] [Accepted: 12/10/2007] [Indexed: 11/20/2022] Open
Abstract
Availability, low prices, and a high degree of reduction make glycerol an ideal feedstock to produce reduced chemicals and fuels via anaerobic fermentation. Although glycerol metabolism in Escherichia coli had been thought to be restricted to respiratory conditions, we report here the utilization of this carbon source in the absence of electron acceptors. Cells grew fermentatively on glycerol and exhibited exponential growth at a maximum specific growth rate of 0.040 +/- 0.003 h(-1). The fermentative nature of glycerol metabolism was demonstrated through studies in which cell growth and glycerol utilization were observed despite blocking several respiratory processes. The incorporation of glycerol in cellular biomass was also investigated via nuclear magnetic resonance analysis of cultures in which either 50% U-13C-labeled or 100% unlabeled glycerol was used. These studies demonstrated that about 20% of the carbon incorporated into the protein fraction of biomass originated from glycerol. The use of U-13C-labeled glycerol also allowed the unambiguous identification of ethanol and succinic, acetic, and formic acids as the products of glycerol fermentation. The synthesis of ethanol was identified as a metabolic determinant of glycerol fermentation; this pathway fulfills energy requirements by generating, in a redox-balanced manner, 1 mol of ATP per mol of glycerol converted to ethanol. A fermentation balance analysis revealed an excellent closure of both carbon (approximately 95%) and redox (approximately 96%) balances. On the other hand, cultivation conditions that prevent H2 accumulation were shown to be an environmental determinant of glycerol fermentation. The negative effect of H2 is related to its metabolic recycling, which in turn generates an unfavorable internal redox state. The implications of our findings for the production of reduced chemicals and fuels were illustrated by coproducing ethanol plus formic acid and ethanol plus hydrogen from glycerol at yields approaching their theoretical maximum.
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Affiliation(s)
- Abhishek Murarka
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX 77251-1892, USA
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Romero S, Merino E, Bolívar F, Gosset G, Martinez A. Metabolic engineering of Bacillus subtilis for ethanol production: lactate dehydrogenase plays a key role in fermentative metabolism. Appl Environ Microbiol 2007; 73:5190-8. [PMID: 17586670 PMCID: PMC1950962 DOI: 10.1128/aem.00625-07] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Wild-type Bacillus subtilis ferments 20 g/liter glucose in 48 h, producing lactate and butanediol, but not ethanol or acetate. To construct an ethanologenic B. subtilis strain, homologous recombination was used to disrupt the native lactate dehydrogenase (LDH) gene (ldh) by chromosomal insertion of the Zymomonas mobilis pyruvate decarboxylase gene (pdc) and alcohol dehydrogenase II gene (adhB) under the control of the ldh native promoter. The values of the intracellular PDC and ADHII enzymatic activities of the engineered B. subtilis BS35 strain were similar to those found in an ethanologenic Escherichia coli strain. BS35 produced ethanol and butanediol; however, the cell growth and glucose consumption rates were reduced by 70 and 65%, respectively, in comparison to those in the progenitor strain. To eliminate butanediol production, the acetolactate synthase gene (alsS) was inactivated. In the BS36 strain (BS35 delta alsS), ethanol production was enhanced, with a high yield (89% of the theoretical); however, the cell growth and glucose consumption rates remained low. Interestingly, kinetic characterization of LDH from B. subtilis showed that it is able to oxidize NADH and NADPH. The expression of the transhydrogenase encoded by udhA from E. coli allowed a partial recovery of the cell growth rate and an early onset of ethanol production. Beyond pyruvate-to-lactate conversion and NADH oxidation, an additional key physiological role of LDH for glucose consumption under fermentative conditions is suggested. Long-term cultivation showed that 8.9 g/liter of ethanol can be obtained using strain BS37 (BS35 delta alsS udhA+). As far as we know, this is the highest ethanol titer and yield reported with a B. subtilis strain.
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Affiliation(s)
- Susana Romero
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, A.P. 510-3 Cuernavaca, Mor. 62250, México
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Okuda N, Ninomiya K, Takao M, Katakura Y, Shioya S. Microaeration enhances productivity of bioethanol from hydrolysate of waste house wood using ethanologenic Escherichia coli KO11. J Biosci Bioeng 2007; 103:350-7. [PMID: 17502277 DOI: 10.1263/jbb.103.350] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2006] [Accepted: 01/17/2007] [Indexed: 11/17/2022]
Abstract
This is the first study showing the successful application of waste house wood (WHW) to the pilot-scale production of bioethanol by hydrolysis using diluted acid and fermentation using the ethanologenic recombinant Escherichia coli KO11. The major sugars in the WHW hydrolysate were glucose, mannose and xylose; the percentages were approximately 35%, 35% and 20% (w/w), respectively. In anaerobic fermentation using a 5-l reactor in which the oxygen transfer rate (OTR) was 0 mmol/(l x h), KO11 consumed only 25% of the xylose in the WHW hydrolysate over the examined fermentation time of 100 h; however, hexoses such as glucose and mannose were consumed completely. Microaeration at an OTR of 4 mmol/(l x h) enhanced the xylose utilization ratio of KO11 to 100%, at which the ethanol concentration was 35.4 g/l and the ethanol yield was 0.42, although the maximum ethanol concentrations were 28.8 and 26.6 g/l at OTRs of 0 mmol/(l x h) and 15 mmol/(l x h), respectively. Moreover, this microaerobic fermentation at OTR of 4 mmol/(l x h) was applied to 1000-l scale bioethanol production using the WHW hydrolysate. The xylose utilization ratio reached 100% and the ethanol yield was determined to be 0.45 for a 63-h fermentation, which were comparable to those obtained from the laboratory-scale fermentation.
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Affiliation(s)
- Naoyuki Okuda
- Bio Business Development Group, Tsukishima Kikai Co., Ltd., 17-15 Tsukuda 2-Chome, Chuo-ku, Tokyo 104-0051, Japan
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Turner P, Mamo G, Karlsson EN. Potential and utilization of thermophiles and thermostable enzymes in biorefining. Microb Cell Fact 2007; 6:9. [PMID: 17359551 PMCID: PMC1851020 DOI: 10.1186/1475-2859-6-9] [Citation(s) in RCA: 317] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2007] [Accepted: 03/15/2007] [Indexed: 11/10/2022] Open
Abstract
In today's world, there is an increasing trend towards the use of renewable, cheap and readily available biomass in the production of a wide variety of fine and bulk chemicals in different biorefineries. Biorefineries utilize the activities of microbial cells and their enzymes to convert biomass into target products. Many of these processes require enzymes which are operationally stable at high temperature thus allowing e.g. easy mixing, better substrate solubility, high mass transfer rate, and lowered risk of contamination. Thermophiles have often been proposed as sources of industrially relevant thermostable enzymes. Here we discuss existing and potential applications of thermophiles and thermostable enzymes with focus on conversion of carbohydrate containing raw materials. Their importance in biorefineries is explained using examples of lignocellulose and starch conversions to desired products. Strategies that enhance thermostablity of enzymes both in vivo and in vitro are also assessed. Moreover, this review deals with efforts made on developing vectors for expressing recombinant enzymes in thermophilic hosts.
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Affiliation(s)
- Pernilla Turner
- Dept Biotechnology, Center for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Gashaw Mamo
- Dept Biotechnology, Center for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Eva Nordberg Karlsson
- Dept Biotechnology, Center for Chemistry and Chemical Engineering, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden
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van Zyl WH, Lynd LR, den Haan R, McBride JE. Consolidated bioprocessing for bioethanol production using Saccharomyces cerevisiae. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2007; 108:205-35. [PMID: 17846725 DOI: 10.1007/10_2007_061] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Consolidated bioprocessing (CBP) of lignocellulose to bioethanol refers to the combining of the four biological events required for this conversion process (production of saccharolytic enzymes, hydrolysis of the polysaccharides present in pretreated biomass, fermentation of hexose sugars, and fermentation of pentose sugars) in one reactor. CBP is gaining increasing recognition as a potential breakthrough for low-cost biomass processing. Although no natural microorganism exhibits all the features desired for CBP, a number of microorganisms, both bacteria and fungi, possess some of the desirable properties. This review focuses on progress made toward the development of baker's yeast (Saccharomyces cerevisiae) for CBP. The current status of saccharolytic enzyme (cellulases and hemicellulases) expression in S. cerevisiae to complement its natural fermentative ability is highlighted. Attention is also devoted to the challenges ahead to integrate all required enzymatic activities in an industrial S. cerevisiae strain(s) and the need for molecular and selection strategies pursuant to developing a yeast capable of CBP.
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Affiliation(s)
- Willem H van Zyl
- Department of Microbiology, Stellenbosch University, Private Bag X1, 7602, Matieland, South Africa.
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Jarboe LR, Grabar TB, Yomano LP, Shanmugan KT, Ingram LO. Development of ethanologenic bacteria. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2007; 108:237-61. [PMID: 17665158 DOI: 10.1007/10_2007_068] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The utilization of lignocellulosic biomass as a petroleum alternative faces many challenges. This work reviews recent progress in the engineering of Escherichia coli and Klebsiella oxytoca to produce ethanol from biomass with minimal nutritional supplementation. A combination of directed engineering and metabolic evolution has resulted in microbial biocatalysts that produce up to 45 g L(-1) ethanol in 48 h in a simple mineral salts medium, and convert various lignocellulosic materials to ethanol. Mutations contributing to ethanologenesis are discussed. The ethanologenic biocatalyst design approach was applied to other commodity chemicals, including optically pure D: (-)- and L: (+)-lactic acid, succinate and L: -alanine with similar success. This review also describes recent progress in growth medium development, the reduction of hemicellulose hydrolysate toxicity and reduction of the demand for fungal cellulases.
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Affiliation(s)
- L R Jarboe
- Department of Microbiology and Cell Science, University of Florida, 32611, Gainesville, FL 32611, USA.
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47
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Abstract
The ethanol-producing bacterium Zymomonas mobilis can serve as a model organism for the study of rapid catabolism and inefficient energy conversion in bacteria. Some basic aspects of its physiology still remain poorly understood. Here, the energy-spilling pathways during uncoupled growth, the structure and function of electron transport chain, and the possible reasons for the inefficient oxidative phosphorylation are analysed. Also, the interaction between ethanol synthesis and respiration is considered. The search for mechanisms of futile transmembrane proton cycling, as well as identification of respiratory electron transport complexes, like the energy-coupling NAD(P)H:quinone oxidoreductase and the cyanide-sensitive terminal oxidase(s), are outlined as the key problems for further research of Z. mobilis energy metabolism.
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Affiliation(s)
- Uldis Kalnenieks
- Institute of Microbiology and Biotechnology, Chair of Microbiology and Biotechnology, University of Latvia, Kronvalda boulv. 4, Riga, LV-1586, Latvia
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48
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Ehrenreich A. DNA microarray technology for the microbiologist: an overview. Appl Microbiol Biotechnol 2006; 73:255-73. [PMID: 17043830 DOI: 10.1007/s00253-006-0584-2] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2006] [Revised: 07/11/2006] [Accepted: 07/11/2006] [Indexed: 10/24/2022]
Abstract
DNA microarrays have found widespread use as a flexible tool to investigate bacterial metabolism. Their main advantage is the comprehensive data they produce on the transcriptional response of the whole genome to an environmental or genetic stimulus. This allows the microbiologist to monitor metabolism and to define stimulons and regulons. Other fields of application are the identification of microorganisms or the comparison of genomes. The importance of this technology increases with the number of sequenced genomes and the falling prices for equipment and oligonucleotides. Knowledge of DNA microarrays is of rising relevance for many areas in microbiological research. Much literature has been published on various specific aspects of this technique that can be daunting to the casual user and beginner. This article offers a comprehensive outline of microarray technology for transcription analysis in microbiology. It shortly discusses the types of DNA microarrays available, the printing of custom arrays, common labeling strategies for targets, hybridization, scanning, normalization, and clustering of expression data.
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Affiliation(s)
- Armin Ehrenreich
- Institute of Microbiology and Genetics, Georg August University, 37077 Göttingen, Germany.
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Effect of poxB gene knockout on metabolism in Escherichia coli based on growth characteristics and enzyme activities. World J Microbiol Biotechnol 2006. [DOI: 10.1007/s11274-006-9267-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Kawaguchi H, Vertès AA, Okino S, Inui M, Yukawa H. Engineering of a xylose metabolic pathway in Corynebacterium glutamicum. Appl Environ Microbiol 2006; 72:3418-28. [PMID: 16672486 PMCID: PMC1472363 DOI: 10.1128/aem.72.5.3418-3428.2006] [Citation(s) in RCA: 184] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2005] [Accepted: 03/08/2006] [Indexed: 11/20/2022] Open
Abstract
The aerobic microorganism Corynebacterium glutamicum was metabolically engineered to broaden its substrate utilization range to include the pentose sugar xylose, which is commonly found in agricultural residues and other lignocellulosic biomass. We demonstrated the functionality of the corynebacterial xylB gene encoding xylulokinase and constructed two recombinant C. glutamicum strains capable of utilizing xylose by cloning the Escherichia coli gene xylA encoding xylose isomerase, either alone (strain CRX1) or in combination with the E. coli gene xylB (strain CRX2). These genes were provided on a high-copy-number plasmid and were under the control of the constitutive promoter trc derived from plasmid pTrc99A. Both recombinant strains were able to grow in mineral medium containing xylose as the sole carbon source, but strain CRX2 grew faster on xylose than strain CRX1. We previously reported the use of oxygen deprivation conditions to arrest cell replication in C. glutamicum and divert carbon source utilization towards product production rather than towards vegetative functions (M. Inui, S. Murakami, S. Okino, H. Kawaguchi, A. A. Vertès, and H. Yukawa, J. Mol. Microbiol. Biotechnol. 7:182-196, 2004). Under these conditions, strain CRX2 efficiently consumed xylose and produced predominantly lactic and succinic acids without growth. Moreover, in mineral medium containing a sugar mixture of 5% glucose and 2.5% xylose, oxygen-deprived strain CRX2 cells simultaneously consumed both sugars, demonstrating the absence of diauxic phenomena relative to the new xylA-xylB construct, albeit glucose-mediated regulation still exerted a measurable influence on xylose consumption kinetics.
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Affiliation(s)
- Hideo Kawaguchi
- Research Institute of Innovative Technology for the Earth, 9-2 Kizugawadai, Kizu-cho, Soraku-gun, Kyoto 619-0292, Japan
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