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Gao S, Liao Y, He H, Yang H, Yang X, Xu S, Wang X, Chen K, Ouyang P. Advance of tolerance engineering on microbes for industrial production. Synth Syst Biotechnol 2023; 8:697-707. [PMID: 38025766 PMCID: PMC10656194 DOI: 10.1016/j.synbio.2023.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 10/19/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Industrial microbes have become the core of biological manufacturing, which utilized as the cell factory for production of plenty of chemicals, fuels and medicine. However, the challenge that the extreme stress conditions exist in production is unavoidable for cell factory. Consequently, to enhance robustness of the chassis cell lays the foundation for development of bio-manufacturing. Currently, the researches on cell tolerance covered various aspects, involving reshaping regulatory network, cell membrane modification and other stress response. In fact, the strategies employed to improve cell robustness could be summarized into two directions, irrational engineering and rational engineering. In this review, the metabolic engineering technologies on enhancement of microbe tolerance to industrial conditions are summarized. Meanwhile, the novel thoughts emerged with the development of biological instruments and synthetic biology are discussed.
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Affiliation(s)
- Siyuan Gao
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Yang Liao
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Hao He
- Petrochemical Research Institute of PetroChina Co. Ltd., Beijing, 102206, China
| | - Huiling Yang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Xuewei Yang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Sheng Xu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Xin Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Kequan Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
| | - Pingkai Ouyang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211816, Jiangsu, China
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Singh B, Kumar A, Saini AK, Saini RV, Thakur R, Mohammed SA, Tuli HS, Gupta VK, Areeshi MY, Faidah H, Jalal NA, Haque S. Strengthening microbial cell factories for efficient production of bioactive molecules. Biotechnol Genet Eng Rev 2023:1-34. [PMID: 36809927 DOI: 10.1080/02648725.2023.2177039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 01/21/2023] [Indexed: 02/24/2023]
Abstract
High demand of bioactive molecules (food additives, antibiotics, plant growth enhancers, cosmetics, pigments and other commercial products) is the prime need for the betterment of human life where the applicability of the synthetic chemical product is on the saturation due to associated toxicity and ornamentations. It has been noticed that the discovery and productivity of such molecules in natural scenarios are limited due to low cellular yields as well as less optimized conventional methods. In this respect, microbial cell factories timely fulfilling the requirement of synthesizing bioactive molecules by improving production yield and screening more promising structural homologues of the native molecule. Where the robustness of the microbial host can be potentially achieved by taking advantage of cell engineering approaches such as tuning functional and adjustable factors, metabolic balancing, adapting cellular transcription machinery, applying high throughput OMICs tools, stability of genotype/phenotype, organelle optimizations, genome editing (CRISPER/Cas mediated system) and also by developing accurate model systems via machine-learning tools. In this article, we provide an overview from traditional to recent trends and the application of newly developed technologies, for strengthening the systemic approaches and providing future directions for enhancing the robustness of microbial cell factories to speed up the production of biomolecules for commercial purposes.
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Affiliation(s)
- Bharat Singh
- Department of Biotechnology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, India
| | - Ankit Kumar
- TERI-Deakin Nanobiotechnology Centre, TERI Gram, The Energy and Resources Institute, Gurugram, India
| | - Adesh Kumar Saini
- Department of Biotechnology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, India
| | - Reena Vohra Saini
- Department of Biotechnology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, India
| | - Rahul Thakur
- Department of Biotechnology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, India
| | - Shakeel A Mohammed
- Department of Biotechnology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, India
| | - Hardeep Singh Tuli
- Department of Biotechnology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, India
| | - Vijai Kumar Gupta
- Biorefining and Advanced Materials Research Centre, Scotland's Rural College (SRUC), Edinburgh, UK
| | - Mohammed Y Areeshi
- Medical Laboratory Technology Department, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Hani Faidah
- Department of Microbiology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Naif A Jalal
- Department of Microbiology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates
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3
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Re A, Mazzoli R. Current progress on engineering microbial strains and consortia for production of cellulosic butanol through consolidated bioprocessing. Microb Biotechnol 2022; 16:238-261. [PMID: 36168663 PMCID: PMC9871528 DOI: 10.1111/1751-7915.14148] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/01/2022] [Accepted: 09/07/2022] [Indexed: 01/27/2023] Open
Abstract
In the last decades, fermentative production of n-butanol has regained substantial interest mainly owing to its use as drop-in-fuel. The use of lignocellulose as an alternative to traditional acetone-butanol-ethanol fermentation feedstocks (starchy biomass and molasses) can significantly increase the economic competitiveness of biobutanol over production from non-renewable sources (petroleum). However, the low cost of lignocellulose is offset by its high recalcitrance to biodegradation which generally requires chemical-physical pre-treatment and multiple bioreactor-based processes. The development of consolidated processing (i.e., single-pot fermentation) can dramatically reduce lignocellulose fermentation costs and promote its industrial application. Here, strategies for developing microbial strains and consortia that feature both efficient (hemi)cellulose depolymerization and butanol production will be depicted, that is, rational metabolic engineering of native (hemi)cellulolytic or native butanol-producing or other suitable microorganisms; protoplast fusion of (hemi)cellulolytic and butanol-producing strains; and co-culture of (hemi)cellulolytic and butanol-producing microbes. Irrespective of the fermentation feedstock, biobutanol production is inherently limited by the severe toxicity of this solvent that challenges process economic viability. Hence, an overview of strategies for developing butanol hypertolerant strains will be provided.
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Affiliation(s)
- Angela Re
- Centre for Sustainable Future TechnologiesFondazione Istituto Italiano di TecnologiaTorinoItaly,Department of Applied Science and TechnologyPolitecnico di TorinoTurinItaly
| | - Roberto Mazzoli
- Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes, Department of Life Sciences and Systems BiologyUniversity of TorinoTorinoItaly
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4
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Engineering E. coli to synthesize butanol. Biochem Soc Trans 2022; 50:867-876. [PMID: 35356968 DOI: 10.1042/bst20211009] [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: 11/04/2021] [Revised: 02/22/2022] [Accepted: 03/15/2022] [Indexed: 11/17/2022]
Abstract
Biobutanol is gaining much attention as a potential biofuel due to its superior properties over ethanol. Butanol has been naturally produced via acetone-butanol-ethanol (ABE) fermentation by many Clostridium species, which are not very user-friendly bacteria. Therefore, to improve butanol titers and yield, various butanol synthesis pathways have been engineered in Escherichia coli, a much more robust and convenient host than Clostridium species. This review mainly focuses on the biosynthesis of n-butanol in engineered E. coli with an emphasis on efficient enzymes for butanol production in E. coli, butanol competing pathways, and genome engineering of E. coli for butanol production. In addition, the use of alternate strategies for butanol biosynthesis/enhancement, alternate substrates for the low cost of butanol production, and genetic improvement for butanol tolerance in E. coli have also been discussed.
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5
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Jayakody LN, Chinmoy B, Turner TL. Trends in valorization of highly-toxic lignocellulosic biomass derived-compounds via engineered microbes. BIORESOURCE TECHNOLOGY 2022; 346:126614. [PMID: 34954359 DOI: 10.1016/j.biortech.2021.126614] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 12/18/2021] [Accepted: 12/19/2021] [Indexed: 05/26/2023]
Abstract
Lignocellulosic biomass-derived fuels, chemicals, and materials are promising sustainable solutions to replace the current petroleum-based production. The direct microbial conversion of thermos-chemically pretreated lignocellulosic biomass is hampered by the presence of highly toxic chemical compounds. Also, thermo-catalytic upgrading of lignocellulosic biomass generates wastewater that contains heterogeneous toxic chemicals, a mixture of unutilized carbon. Metabolic engineering efforts have primarily focused on the conversion of carbohydrates in lignocellulose biomass; substantial opportunities exist to harness value from toxic lignocellulose-derived toxic compounds. This article presents the comprehensive metabolic routes and tolerance mechanisms to develop robust synthetic microbial cell factories to valorize the highly toxic compounds to advanced-platform chemicals. The obtained platform chemicals can be used to manufacture high-value biopolymers and biomaterials via a hybrid biochemical approach for replacing petroleum-based incumbents. The proposed strategy enables a sustainable bio-based materials economy by microbial biofunneling of lignocellulosic biomass-derived toxic molecules, an untapped biogenic carbon.
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Affiliation(s)
- Lahiru N Jayakody
- School of Biological Science, Southern Illinois University Carbondale, Carbondale, IL, USA; Fermentation Science Institute, Southern Illinois University Carbondale, Carbondale, IL, USA.
| | - Baroi Chinmoy
- Illinois Sustainable Technology Center, University of Illinois Urbana Champaign, IL, USA
| | - Timothy L Turner
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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6
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Costa P, Usai G, Re A, Manfredi M, Mannino G, Bertea CM, Pessione E, Mazzoli R. Clostridium cellulovorans Proteomic Responses to Butanol Stress. Front Microbiol 2021; 12:674639. [PMID: 34367082 PMCID: PMC8336468 DOI: 10.3389/fmicb.2021.674639] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 06/14/2021] [Indexed: 12/16/2022] Open
Abstract
Combination of butanol-hyperproducing and hypertolerant phenotypes is essential for developing microbial strains suitable for industrial production of bio-butanol, one of the most promising liquid biofuels. Clostridium cellulovorans is among the microbial strains with the highest potential for direct production of n-butanol from lignocellulosic wastes, a process that would significantly reduce the cost of bio-butanol. However, butanol exhibits higher toxicity compared to ethanol and C. cellulovorans tolerance to this solvent is low. In the present investigation, comparative gel-free proteomics was used to study the response of C. cellulovorans to butanol challenge and understand the tolerance mechanisms activated in this condition. Sequential Window Acquisition of all Theoretical fragment ion spectra Mass Spectrometry (SWATH-MS) analysis allowed identification and quantification of differentially expressed soluble proteins. The study data are available via ProteomeXchange with the identifier PXD024183. The most important response concerned modulation of protein biosynthesis, folding and degradation. Coherent with previous studies on other bacteria, several heat shock proteins (HSPs), involved in protein quality control, were up-regulated such as the chaperones GroES (Cpn10), Hsp90, and DnaJ. Globally, our data indicate that protein biosynthesis is reduced, likely not to overload HSPs. Several additional metabolic adaptations were triggered by butanol exposure such as the up-regulation of V- and F-type ATPases (involved in ATP synthesis/generation of proton motive force), enzymes involved in amino acid (e.g., arginine, lysine, methionine, and branched chain amino acids) biosynthesis and proteins involved in cell envelope re-arrangement (e.g., the products of Clocel_4136, Clocel_4137, Clocel_4144, Clocel_4162 and Clocel_4352, involved in the biosynthesis of saturated fatty acids) and a redistribution of carbon flux through fermentative pathways (acetate and formate yields were increased and decreased, respectively). Based on these experimental findings, several potential gene targets for metabolic engineering strategies aimed at improving butanol tolerance in C. cellulovorans are suggested. This includes overexpression of HSPs (e.g., GroES, Hsp90, DnaJ, ClpC), RNA chaperone Hfq, V- and F-type ATPases and a number of genes whose function in C. cellulovorans is currently unknown.
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Affiliation(s)
- Paolo Costa
- Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes, Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Giulia Usai
- Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes, Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy.,Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy.,Department of Applied Science and Technology, Politecnico di Torino, Turin, Italy
| | - Angela Re
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy
| | - Marcello Manfredi
- Center for Translational Research on Autoimmune and Allergic Diseases, Università del Piemonte Orientale, Novara, Italy.,Department of Translational Medicine, Università del Piemonte Orientale, Novara, Italy
| | - Giuseppe Mannino
- Plant Physiology Unit, Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Cinzia Margherita Bertea
- Plant Physiology Unit, Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Enrica Pessione
- Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes, Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Roberto Mazzoli
- Structural and Functional Biochemistry, Laboratory of Proteomics and Metabolic Engineering of Prokaryotes, Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
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Schalck T, den Bergh BV, Michiels J. Increasing Solvent Tolerance to Improve Microbial Production of Alcohols, Terpenoids and Aromatics. Microorganisms 2021; 9:249. [PMID: 33530454 PMCID: PMC7912173 DOI: 10.3390/microorganisms9020249] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/14/2021] [Accepted: 01/20/2021] [Indexed: 12/16/2022] Open
Abstract
Fuels and polymer precursors are widely used in daily life and in many industrial processes. Although these compounds are mainly derived from petrol, bacteria and yeast can produce them in an environment-friendly way. However, these molecules exhibit toxic solvent properties and reduce cell viability of the microbial producer which inevitably impedes high product titers. Hence, studying how product accumulation affects microbes and understanding how microbial adaptive responses counteract these harmful defects helps to maximize yields. Here, we specifically focus on the mode of toxicity of industry-relevant alcohols, terpenoids and aromatics and the associated stress-response mechanisms, encountered in several relevant bacterial and yeast producers. In practice, integrating heterologous defense mechanisms, overexpressing native stress responses or triggering multiple protection pathways by modifying the transcription machinery or small RNAs (sRNAs) are suitable strategies to improve solvent tolerance. Therefore, tolerance engineering, in combination with metabolic pathway optimization, shows high potential in developing superior microbial producers.
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Affiliation(s)
- Thomas Schalck
- VIB Center for Microbiology, Flanders Institute for Biotechnology, B-3001 Leuven, Belgium; (T.S.); (B.V.d.B.)
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
| | - Bram Van den Bergh
- VIB Center for Microbiology, Flanders Institute for Biotechnology, B-3001 Leuven, Belgium; (T.S.); (B.V.d.B.)
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
| | - Jan Michiels
- VIB Center for Microbiology, Flanders Institute for Biotechnology, B-3001 Leuven, Belgium; (T.S.); (B.V.d.B.)
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
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Xu G, Xiao L, Wu A, Han R, Ni Y. Enhancing n-Butanol Tolerance of Escherichia coli by Overexpressing of Stress-Responsive Molecular Chaperones. Appl Biochem Biotechnol 2020; 193:257-270. [PMID: 32929579 DOI: 10.1007/s12010-020-03417-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 06/23/2020] [Indexed: 12/14/2022]
Abstract
Microbial tolerance to organic solvents is critical for efficient production of biofuels. In this study, n-butanol tolerance of Escherichia coli JM109 was improved by overexpressing of genes encoding stress-responsive small RNA-regulator, RNA chaperone, and molecular chaperone. Gene rpoS, coding for sigma S subunit of RNA polymerase, was the most efficient in improving n-butanol tolerance of E. coli. The highest OD600 and the specific growth rate of JM109/pQE80L-rpoS reached 1.692 and 0.144 h-1 respectively at 1.0% (v/v) n-butanol. Double and triple expression of molecular chaperones rpoS, secB, and groS were conducted and optimized. Recombinant strains JM109/pQE80L-secB-rpoS and JM109/pQE80L-groS-secB-rpoS exhibited the highest n-butanol tolerance, with specific growth rates of 0.164 and 0.165 h-1, respectively. Membrane integrity, potentials, and cell morphology analyses demonstrated the high viability of JM109/pQE80L-groS-secB-rpoS. This study provides guidance on employing various molecular chaperones for enhancing the tolerance of E. coli against n-butanol.
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Affiliation(s)
- Guochao Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Lin Xiao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Anning Wu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Ruizhi Han
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Ye Ni
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China.
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9
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Recent advances in improving metabolic robustness of microbial cell factories. Curr Opin Biotechnol 2020; 66:69-77. [PMID: 32683192 DOI: 10.1016/j.copbio.2020.06.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 06/12/2020] [Accepted: 06/17/2020] [Indexed: 12/20/2022]
Abstract
Engineering microbial cell factories has been widely applied to produce compounds spanning from intricate natural products to bulk commodities. In each case, host robustness is essential to ensure the reliable and sustainable production of targeted metabolites. However, it can be negatively affected by metabolic burden, pathway toxicity, and harsh environment, resulting in a decreased titer and productivity. Enhanced robustness enables host to have better production performance under complicated growth circumstances. Here, we review current strategies for boosting host robustness, including metabolic balancing, genetic and phenotype stability enhancement, and tolerance engineering. In addition, we discuss the challenges and future perspectives on microbial host engineering for increased robustness.
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Luo H, Zheng P, Bilal M, Xie F, Zeng Q, Zhu C, Yang R, Wang Z. Efficient bio-butanol production from lignocellulosic waste by elucidating the mechanisms of Clostridium acetobutylicum response to phenolic inhibitors. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 710:136399. [PMID: 31923698 DOI: 10.1016/j.scitotenv.2019.136399] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 12/24/2019] [Accepted: 12/27/2019] [Indexed: 05/12/2023]
Abstract
Lignocellulosic biomass is considered abundant renewable feedstock to constitute a green and environmentally friendly approach for biofuels (bio-butanol) production as an effective substitute for fossil resources. However, a variety of fermentable inhibitors can be generated in hydrolysates during the biomass pretreatment process. Among them, phenolics including phenolic acids and phenolic aldehydes are the most toxic inhibitors to solventogenic clostridia for bio-butanol production. This study elucidates the physiological mechanism of Clostridium acetobutylicum ATCC 824 response to phenolic inhibitors by the integration of kinetics and transcriptional analysis. Butanol fermentations were stressed by 0.4 g/L phenolic acids or 0.4 g/L phenolic aldehydes at 12 h at the beginning of solventogenesis. With post-stress for 12 h, butanol titer was 7.01 g/L in fermentation with phenolic acid stress, while only 5.82 g/L butanol was produced in the case of phenolic aldehydes stress. Reductions in the two fermentations were 27.6% and 40.0% in comparison with the control (without stress), indicated that phenolic aldehydes had a stronger inhibitory effect on solvents synthesis in C. acetobutylicum than phenolic acids. Additionally, the transcriptional analysis revealed that phenolics altered the gene expression profiles related to membrane transporters such as ATP-binding cassette (ABC)-transporter and phosphotransferase system (PTS), glycolysis, and heat shock proteins. The lower expression levels of PTS-related genes might result in reduced glucose consumption and finally inhibited solvents synthesis under phenolic aldehydes stress. Some genes encoding histidine kinase (CA_C0323, CA_C0903, and CA_C3319) were also affected by phenolics, which might inhibit sporulation. In conclusion, our results provide valuable guidance for the construction of robust strain to efficiently produce bio-butanol from lignocellulosic biomass.
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Affiliation(s)
- Hongzhen Luo
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China.
| | - Panli Zheng
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Fang Xie
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Qingwei Zeng
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Chun Zhu
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Rongling Yang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Zhaoyu Wang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
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Westbrook AW, Miscevic D, Kilpatrick S, Bruder MR, Moo-Young M, Chou CP. Strain engineering for microbial production of value-added chemicals and fuels from glycerol. Biotechnol Adv 2019; 37:538-568. [DOI: 10.1016/j.biotechadv.2018.10.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Revised: 10/03/2018] [Accepted: 10/10/2018] [Indexed: 12/22/2022]
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12
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Xu G, Wu A, Xiao L, Han R, Ni Y. Enhancing butanol tolerance of Escherichia coli reveals hydrophobic interaction of multi-tasking chaperone SecB. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:164. [PMID: 31297152 PMCID: PMC6598250 DOI: 10.1186/s13068-019-1507-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 06/19/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Escherichia coli has been proved to be one promising platform chassis for the production of various natural products, such as biofuels. Product toxicity is one of the main bottlenecks for achieving maximum production of biofuels. Host strain engineering is an effective approach to alleviate solvent toxicity issue in fermentation. RESULTS Thirty chaperones were overexpressed in E. coli JM109, and SecB recombinant strain was identified with the highest n-butanol tolerance. The tolerance (T) of E. coli overexpressing SecB, calculated by growth difference in the presence and absence of solvents, was determined to be 9.13% at 1.2% (v/v) butanol, which was 3.2-fold of the control strain. Random mutagenesis of SecB was implemented and homologously overexpressed in E. coli, and mutant SecBT10A was identified from 2800 variants rendering E. coli the highest butanol tolerance. Saturation mutagenesis on T10 site revealed that hydrophobic residues were required for high butanol tolerance of E. coli. Compared with wild-type (WT) SecB, the T of SecBT10A strain was further increased from 9.14 to 14.4% at 1.2% butanol, which was 5.3-fold of control strain. Remarkably, E. coli engineered with SecBT10A could tolerate as high as 1.8% butanol (~ 14.58 g/L). The binding affinity of SecBT10A toward model substrate unfolded maltose binding protein (preMBP) was 11.9-fold of that of WT SecB as determined by isothermal titration calorimetry. Residue T10 locates at the entrance of hydrophobic substrate binding groove of SecB, and might play an important role in recognition and binding of cargo proteins. CONCLUSIONS SecB chaperone was identified by chaperone mining to be effective in enhancing butanol tolerance of E. coli. Maximum butanol tolerance of E. coli could reach 1.6% and 1.8% butanol by engineering single gene of SecB or SecBT10A. Hydrophobic interaction is vital for enhanced binding affinity between SecB and cargo proteins, and therefore improved butanol tolerance.
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Affiliation(s)
- Guochao Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 Jiangsu China
| | - Anning Wu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 Jiangsu China
| | - Lin Xiao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 Jiangsu China
| | - Ruizhi Han
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 Jiangsu China
| | - Ye Ni
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 Jiangsu China
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Improvement of stress tolerance and riboflavin production of Bacillus subtilis by introduction of heat shock proteins from thermophilic bacillus strains. Appl Microbiol Biotechnol 2019; 103:4455-4465. [PMID: 30968162 DOI: 10.1007/s00253-019-09788-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 03/12/2019] [Accepted: 03/19/2019] [Indexed: 10/27/2022]
Abstract
In this study, stress tolerance devices consisting of heat shock protein (HSP) genes from thermophiles Geobacillus and Parageobacillus were introduced into riboflavin-producing strain Bacillus subtilis 446 to improve its stress tolerance and riboflavin production. The 12 HSP homologs were selected from 28 Geobacillus and Parageobacillus genomes according to their sequence clustering and phylogenetically analysis which represents the diversity of HSPs from thermophilic bacillus. The 12 HSP genes and 2 combinations of them (PtdnaK-PtdnaJ-PtgrpE and PtgroeL-PtgroeS) were heterologously expressed in B. subtilis 446 under the control of a strong constitutive promoter P43. Most of the 14 engineered strains showed increased cell density at 44 to 48 °C and less cell death at 50 °C compared with the control strains. Among them, strains B.s446-HSP20-3, B.s446-HSP20-2, and B.s446-PtDnaK-PtDnaJ-PtGrpE increased their cell densities over 25% at 44 to 48 °C. They also showed 5-, 4-, and 4-fold improved cell survivals after the 10-h heat shock treatment at 50 °C, respectively. These three strains also showed reduced cell death rates under osmotic stress of 10% NaCl, indicating that the introduction of HSPs improved not only the heat tolerance of B. subtilis 446 but also its osmotic tolerance. Fermentation of these three strains at higher temperatures of 39 and 43 °C showed 23-66% improved riboflavin titers, as well as 24-h shortened fermentation period. These results indicated that implanting HSPs from thermophiles to B. subtilis 446 would be an efficient approach to improve its stress tolerance and riboflavin production.
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14
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A mutation in the AdhE alcohol dehydrogenase of Clostridium thermocellum increases tolerance to several primary alcohols, including isobutanol, n-butanol and ethanol. Sci Rep 2019; 9:1736. [PMID: 30741948 PMCID: PMC6370804 DOI: 10.1038/s41598-018-37979-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 12/17/2018] [Indexed: 01/17/2023] Open
Abstract
Clostridium thermocellum is a good candidate organism for producing cellulosic biofuels due to its native ability to ferment cellulose, however its maximum biofuel titer is limited by tolerance. Wild type C. thermocellum is inhibited by 5 g/L n-butanol. Using growth adaptation in a chemostat, we increased n-butanol tolerance to 15 g/L. We discovered that several tolerant strains had acquired a D494G mutation in the adhE gene. Re-introducing this mutation recapitulated the n-butanol tolerance phenotype. In addition, it increased tolerance to several other primary alcohols including isobutanol and ethanol. To confirm that adhE is the cause of inhibition by primary alcohols, we showed that deleting adhE also increases tolerance to several primary alcohols.
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Solvent Tolerance in Bacteria: Fulfilling the Promise of the Biotech Era? Trends Biotechnol 2018; 36:1025-1039. [DOI: 10.1016/j.tibtech.2018.04.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 04/17/2018] [Accepted: 04/19/2018] [Indexed: 01/01/2023]
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Vinayavekhin N, Vangnai AS. The effects of disruption in membrane lipid biosynthetic genes on 1-butanol tolerance of Bacillus subtilis. Appl Microbiol Biotechnol 2018; 102:9279-9289. [DOI: 10.1007/s00253-018-9298-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 07/23/2018] [Accepted: 08/02/2018] [Indexed: 01/24/2023]
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17
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Identification and manipulation of a novel locus to improve cell tolerance to short-chain alcohols in Escherichia coli. ACTA ACUST UNITED AC 2018; 45:589-598. [DOI: 10.1007/s10295-017-1996-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 12/09/2017] [Indexed: 12/30/2022]
Abstract
Abstract
Escherichia coli KO11 is a popular ethanologenic strain, but is more sensitive to ethanol than other producers. Here, an ethanol-tolerant mutant EM was isolated from ultraviolet mutagenesis library of KO11. Comparative genomic analysis added by piecewise knockout strategy and complementation assay revealed EKO11_3023 (espA) within the 36.6-kb deletion from KO11 was the only locus responsible for ethanol sensitivity. Interestingly, when espA was deleted in strain W (the parent strain of KO11), ethanol tolerance was dramatically elevated to the level of espA-free hosts [e.g., MG1655 and BL21(DE3)]. And overexpression of espA in strains MG1655 and BL21(DE3) led to significantly enhanced ethanol sensitivity. In addition to ethanol, deletion of espA also improved cell tolerance to other short-chain (C2–C4) alcohols, including methanol, isopropanol, n-butanol, isobutanol and 2-butanol. Therefore, espA was responsible for short-chain alcohol sensitivity of W-strains compared to other cells, which provides a potential engineering target for alcohols production.
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Run S, Tian P. Improved Tolerance of Escherichia coli to Propionic Acid by Overexpression of Sigma Factor RpoS. APPL BIOCHEM MICRO+ 2018. [DOI: 10.1134/s0003683818030122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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19
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Patakova P, Kolek J, Sedlar K, Koscova P, Branska B, Kupkova K, Paulova L, Provaznik I. Comparative analysis of high butanol tolerance and production in clostridia. Biotechnol Adv 2018; 36:721-738. [DOI: 10.1016/j.biotechadv.2017.12.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 12/05/2017] [Accepted: 12/12/2017] [Indexed: 12/24/2022]
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20
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Branska B, Pechacova Z, Kolek J, Vasylkivska M, Patakova P. Flow cytometry analysis of Clostridium beijerinckii NRRL B-598 populations exhibiting different phenotypes induced by changes in cultivation conditions. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:99. [PMID: 29632557 PMCID: PMC5887253 DOI: 10.1186/s13068-018-1096-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 03/26/2018] [Indexed: 05/08/2023]
Abstract
BACKGROUND Biobutanol production by clostridia via the acetone-butanol-ethanol (ABE) pathway is a promising future technology in bioenergetics , but identifying key regulatory mechanisms for this pathway is essential in order to construct industrially relevant strains with high tolerance and productivity. We have applied flow cytometric analysis to C. beijerinckii NRRL B-598 and carried out comparative screening of physiological changes in terms of viability under different cultivation conditions to determine its dependence on particular stages of the life cycle and the concentration of butanol. RESULTS Dual staining by propidium iodide (PI) and carboxyfluorescein diacetate (CFDA) provided separation of cells into four subpopulations with different abilities to take up PI and cleave CFDA, reflecting different physiological states. The development of a staining pattern during ABE fermentation showed an apparent decline in viability, starting at the pH shift and onset of solventogenesis, although an appreciable proportion of cells continued to proliferate. This was observed for sporulating as well as non-sporulating phenotypes at low solvent concentrations, suggesting that the increase in percentage of inactive cells was not a result of solvent toxicity or a transition from vegetative to sporulating stages. Additionally, the sporulating phenotype was challenged with butanol and cultivation with a lower starting pH was performed; in both these experiments similar trends were obtained-viability declined after the pH breakpoint, independent of the actual butanol concentration in the medium. Production characteristics of both sporulating and non-sporulating phenotypes were comparable, showing that in C. beijerinckii NRRL B-598, solventogenesis was not conditional on sporulation. CONCLUSION We have shown that the decline in C. beijerinckii NRRL B-598 culture viability during ABE fermentation was not only the result of accumulated toxic metabolites, but might also be associated with a special survival strategy triggered by pH change.
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Affiliation(s)
- Barbora Branska
- Department of Biotechnology, University of Chemistry and Technology Prague, Technicka 5, 166 28 Prague, Czech Republic
| | - Zora Pechacova
- Department of Biotechnology, University of Chemistry and Technology Prague, Technicka 5, 166 28 Prague, Czech Republic
| | - Jan Kolek
- Department of Biotechnology, University of Chemistry and Technology Prague, Technicka 5, 166 28 Prague, Czech Republic
| | - Maryna Vasylkivska
- Department of Biotechnology, University of Chemistry and Technology Prague, Technicka 5, 166 28 Prague, Czech Republic
| | - Petra Patakova
- Department of Biotechnology, University of Chemistry and Technology Prague, Technicka 5, 166 28 Prague, Czech Republic
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Luo H, Yang R, Zhao Y, Wang Z, Liu Z, Huang M, Zeng Q. Recent advances and strategies in process and strain engineering for the production of butyric acid by microbial fermentation. BIORESOURCE TECHNOLOGY 2018; 253:343-354. [PMID: 29329775 DOI: 10.1016/j.biortech.2018.01.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 12/28/2017] [Accepted: 01/01/2018] [Indexed: 06/07/2023]
Abstract
Butyric acid is an important platform chemical, which is widely used in the fields of food, pharmaceutical, energy, etc. Microbial fermentation as an alternative approach for butyric acid production is attracting great attention as it is an environmentally friendly bioprocessing. However, traditional fermentative butyric acid production is still not economically competitive compared to chemical synthesis route, due to the low titer, low productivity, and high production cost. Therefore, reduction of butyric acid production cost by utilization of alternative inexpensive feedstock, and improvement of butyric acid production and productivity has become an important target. Recently, several advanced strategies have been developed for enhanced butyric acid production, including bioprocess techniques and metabolic engineering methods. This review provides an overview of advances and strategies in process and strain engineering for butyric acid production by microbial fermentation. Additionally, future perspectives on improvement of butyric acid production are also proposed.
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Affiliation(s)
- Hongzhen Luo
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China.
| | - Rongling Yang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Yuping Zhao
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Zhaoyu Wang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Zheng Liu
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Mengyu Huang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Qingwei Zeng
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
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22
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Tailoring cyanobacterial cell factory for improved industrial properties. Biotechnol Adv 2018; 36:430-442. [DOI: 10.1016/j.biotechadv.2018.01.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 01/07/2018] [Accepted: 01/08/2018] [Indexed: 11/20/2022]
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23
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Potential Applications of the Escherichia coli Heat Shock Response in Synthetic Biology. Trends Biotechnol 2018; 36:186-198. [DOI: 10.1016/j.tibtech.2017.10.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 10/20/2017] [Accepted: 10/20/2017] [Indexed: 01/06/2023]
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24
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Zhang R, Cao Y, Liu W, Xian M, Liu H. Improving phloroglucinol tolerance and production in Escherichia coli by GroESL overexpression. Microb Cell Fact 2017; 16:227. [PMID: 29258595 PMCID: PMC5735909 DOI: 10.1186/s12934-017-0839-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 12/05/2017] [Indexed: 11/21/2022] Open
Abstract
Background Phloroglucinol is an important chemical which has been successfully produced by engineered Escherichia coli. However, the toxicity of phloroglucinol can enormously inhibit E. coli cell growth and viability, and the productivity is still too low and not economically feasible for industrial applications. Therefore, strain tolerance to toxic metabolites remains a key issue during the production of chemicals using biological processes. Results In the present work, we examined the impact of the native GroESL chaperone system with different overexpression levels on phloroglucinol tolerance and production in E. coli. The groESL gene was cloned into an expression vector, of which expression level was regulated by three different promoters (natural, tac and T7 promoter). Strain tolerance was evaluated employing viable cell counts and phloroglucinol production. In comparison with the control strain, all GroESL overexpressing strains showed good characteristics in cell viability and phloroglucinol synthesis. Strain which overexpressed GroESL under tac promoter was found to show the best tolerance in all of those tested, resulting in a 3.19-fold increase in viable cell numbers compared with control strain of agar-plate culture under the condition of 0.7 g/L phloroglucinol, and a 39.5% increase in phloroglucinol production under fed-batch fermentation. This engineered strain finally accumulated phloroglucinol up to 5.3 g/L in the fed-batch cultivation 10 h after induction, and the productivity was 0.53 g/L/h. To date, the highest phloroglucinol production was achieved in this work compared with the previous reports, which is promising to make the bioprocess feasible from the economical point. Conclusions The data show that appropriate expression level of GroESL plays a critical role in improving phloroglucinol tolerance and production in E. coli, and maybe involve in controlling some aspects of the stress response system through upregulation of GroESL. GroESL overexpression is therefore a feasible and efficient approach for improvement of E. coli tolerance. Electronic supplementary material The online version of this article (10.1186/s12934-017-0839-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rubing Zhang
- CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yujin Cao
- CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Wei Liu
- CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China
| | - Mo Xian
- CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
| | - Huizhou Liu
- CAS Key Laboratory of Bio-Based Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.
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25
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Over expression of GroESL in Cupriavidus necator for heterotrophic and autotrophic isopropanol production. Metab Eng 2017; 42:74-84. [DOI: 10.1016/j.ymben.2017.05.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 03/30/2017] [Accepted: 05/31/2017] [Indexed: 01/09/2023]
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26
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A New Player in the Biorefineries Field: Phasin PhaP Enhances Tolerance to Solvents and Boosts Ethanol and 1,3-Propanediol Synthesis in Escherichia coli. Appl Environ Microbiol 2017; 83:AEM.00662-17. [PMID: 28476770 DOI: 10.1128/aem.00662-17] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 05/02/2017] [Indexed: 11/20/2022] Open
Abstract
The microbial production of biofuels and other added-value chemicals is often limited by the intrinsic toxicity of these compounds. The phasin PhaP from the soil bacterium Azotobacter sp. strain FA8 is a polyhydroxyalkanoate granule-associated protein that protects recombinant Escherichia coli against several kinds of stress. PhaP enhances growth and poly(3-hydroxybutyrate) synthesis in polymer-producing recombinant strains and reduces the formation of inclusion bodies during overproduction of heterologous proteins. In this work, the heterologous expression of this phasin in E. coli was used as a strategy to increase tolerance to several biotechnologically relevant chemicals. PhaP was observed to enhance bacterial fitness in the presence of biofuels, such as ethanol and butanol, and other chemicals, such as 1,3-propanediol. The effect of PhaP was also studied in a groELS mutant strain, in which both GroELS and PhaP were observed to exert a beneficial effect that varied depending on the chemical tested. Lastly, the potential of PhaP and GroEL to enhance the accumulation of ethanol or 1,3-propanediol was analyzed in recombinant E. coli Strains that overexpressed either groEL or phaP had increased growth, reflected in a higher final biomass and product titer than the control strain. Taken together, these results add a novel application to the already multifaceted phasin protein group, suggesting that expression of these proteins or other chaperones can be used to improve the production of biofuels and other chemicals.IMPORTANCE This work has both basic and applied aspects. Our results demonstrate that a phasin with chaperone-like properties can increase bacterial tolerance to several biochemicals, providing further evidence of the diverse properties of these proteins. Additionally, both the PhaP phasin and the well-known chaperone GroEL were used to increase the biosynthesis of the biotechnologically relevant compounds ethanol and 1,3-propanediol in recombinant E. coli These findings open the road for the use of these proteins for the manipulation of bacterial strains to optimize the synthesis of diverse bioproducts from renewable carbon sources.
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Yang X, Teng K, Zhang J, Wang F, Zhang T, Ai G, Han P, Bai F, Zhong J. Transcriptome responses of Lactobacillus acetotolerans F28 to a short and long term ethanol stress. Sci Rep 2017; 7:2650. [PMID: 28572611 PMCID: PMC5453994 DOI: 10.1038/s41598-017-02975-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 04/20/2017] [Indexed: 01/21/2023] Open
Abstract
Lactobacillus acetotolerans is a major microbe contributing to the Chinese liquor fermentation with unknown function. It can be grown well in a high concentration of ethanol. RNA sequencing (RNA-seq) was performed on L. acetotolerans F28 growing in 12% ethanol to determine important genetic mechanisms for both a short and long term adaption to this environment. A genome-wide transcriptional analysis revealed that the most important genetic elements for L. acetotolerans F28 grown in ethanol are related to high levels of stress response and fatty acid biosynthesis, and a reduction of amino acid transport and metabolism after both a short and long time stress. The fatty acid methyl ester analyses showed that most fatty acids were increased in L. acetotolerans F28 after exposure to ethanol while the unsaturated fatty acid octadecenoic acid (C18:1) was significantly increased. The increasing unsaturated fatty acid biosynthesis in L. acetotolerans F28 might enhance cell membrane fluidity and protect the cells against high concentration of ethanol. Overall, the transcriptome and functional analysis indicated that the elevated stress response and fatty acid biosynthesis, and the decrease of amino acid transport and metabolism might play important roles for L. acetotolerans F28 to adapt to environmental ethanol.
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Affiliation(s)
- Xiaopan Yang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Kunling Teng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Jie Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Fangfang Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Tong Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Guomin Ai
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Peijie Han
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Fengyan Bai
- University of Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.,State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China
| | - Jin Zhong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China. .,University of Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.
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28
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Rau MH, Calero P, Lennen RM, Long KS, Nielsen AT. Genome-wide Escherichia coli stress response and improved tolerance towards industrially relevant chemicals. Microb Cell Fact 2016; 15:176. [PMID: 27737709 PMCID: PMC5064937 DOI: 10.1186/s12934-016-0577-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 10/03/2016] [Indexed: 01/17/2023] Open
Abstract
Background Economically viable biobased production of bulk chemicals and biofuels typically requires high product titers. During microbial bioconversion this often leads to product toxicity, and tolerance is therefore a critical element in the engineering of production strains. Results Here, a systems biology approach was employed to understand the chemical stress response of Escherichia coli, including a genome-wide screen for mutants with increased fitness during chemical stress. Twelve chemicals with significant production potential were selected, consisting of organic solvent-like chemicals (butanol, hydroxy-γ-butyrolactone, 1,4-butanediol, furfural), organic acids (acetate, itaconic acid, levulinic acid, succinic acid), amino acids (serine, threonine) and membrane-intercalating chemicals (decanoic acid, geraniol). The transcriptional response towards these chemicals revealed large overlaps of transcription changes within and between chemical groups, with functions such as energy metabolism, stress response, membrane modification, transporters and iron metabolism being affected. Regulon enrichment analysis identified key regulators likely mediating the transcriptional response, including CRP, RpoS, OmpR, ArcA, Fur and GadX. These regulators, the genes within their regulons and the above mentioned cellular functions therefore constitute potential targets for increasing E. coli chemical tolerance. Fitness determination of genome-wide transposon mutants (Tn-seq) subjected to the same chemical stress identified 294 enriched and 336 depleted mutants and experimental validation revealed up to 60 % increase in mutant growth rates. Mutants enriched in several conditions contained, among others, insertions in genes of the Mar-Sox-Rob regulon as well as transcription and translation related gene functions. Conclusions The combination of the transcriptional response and mutant screening provides general targets that can increase tolerance towards not only single, but multiple chemicals. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0577-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Martin Holm Rau
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Patricia Calero
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Rebecca M Lennen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Katherine S Long
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Alex T Nielsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark.
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Mi J, Schewe H, Buchhaupt M, Holtmann D, Schrader J. Efficient hydroxylation of 1,8-cineole with monoterpenoid-resistant recombinant Pseudomonas putida GS1. World J Microbiol Biotechnol 2016; 32:112. [PMID: 27263007 DOI: 10.1007/s11274-016-2071-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 04/23/2016] [Indexed: 10/21/2022]
Abstract
In this work, monoterpenoid hydroxylation with Pseudomonas putida GS1 and KT2440 were investigated as host strains, and the cytochrome P450 monooxygenase CYP176A1 (P450cin) and its native redox partner cindoxin (CinC) from Citrobacter braakii were introduced in P. putida to catalyze the stereoselective hydroxylation of 1,8-cineole to (1R)-6β-hydroxy-1,8-cineole. Growth experiments in the presence of 1,8-cineole confirmed pseudomonads' superior resilience compared to E. coli. Whole-cell P. putida harboring P450cin with and without CinC were capable of hydroxylating 1,8-cineole, whereas coexpression of CinC has been shown to accelerate this bioconversion. Under the same conditions, P. putida GS1 produced more than twice the amount of heterologous P450cin and bioconversion product than P. putida KT2440. A concentration of 1.1 ± 0.1 g/L (1R)-6β-hydroxy-1,8-cineole was obtained within 55 h in shake flasks and 13.3 ± 1.9 g/L in 89 h in a bioreactor, the latter of which corresponds to a yield YP/S of 79 %. To the authors' knowledge, this is the highest product titer for a P450 based whole-cell monoterpene oxyfunctionalization reported so far. These results show that solvent-tolerant P. putida GS1 can be used as a highly efficient recombinant whole-cell biocatalyst for a P450 monooxygenase-based valorization of monoterpenoids.
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Affiliation(s)
- Jia Mi
- Biochemical Engineering, DECHEMA-Forschungsinstitut, Theodor-Heuss-Allee 25, 60486, Frankfurt, Germany
| | - Hendrik Schewe
- Biochemical Engineering, DECHEMA-Forschungsinstitut, Theodor-Heuss-Allee 25, 60486, Frankfurt, Germany
| | - Markus Buchhaupt
- Biochemical Engineering, DECHEMA-Forschungsinstitut, Theodor-Heuss-Allee 25, 60486, Frankfurt, Germany
| | - Dirk Holtmann
- Biochemical Engineering, DECHEMA-Forschungsinstitut, Theodor-Heuss-Allee 25, 60486, Frankfurt, Germany
| | - Jens Schrader
- Biochemical Engineering, DECHEMA-Forschungsinstitut, Theodor-Heuss-Allee 25, 60486, Frankfurt, Germany.
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Chubukov V, Mukhopadhyay A, Petzold CJ, Keasling JD, Martín HG. Synthetic and systems biology for microbial production of commodity chemicals. NPJ Syst Biol Appl 2016; 2:16009. [PMID: 28725470 PMCID: PMC5516863 DOI: 10.1038/npjsba.2016.9] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 02/01/2016] [Accepted: 02/05/2016] [Indexed: 01/08/2023] Open
Abstract
The combination of synthetic and systems biology is a powerful framework to study fundamental questions in biology and produce chemicals of immediate practical application such as biofuels, polymers, or therapeutics. However, we cannot yet engineer biological systems as easily and precisely as we engineer physical systems. In this review, we describe the path from the choice of target molecule to scaling production up to commercial volumes. We present and explain some of the current challenges and gaps in our knowledge that must be overcome in order to bring our bioengineering capabilities to the level of other engineering disciplines. Challenges start at molecule selection, where a difficult balance between economic potential and biological feasibility must be struck. Pathway design and construction have recently been revolutionized by next-generation sequencing and exponentially improving DNA synthesis capabilities. Although pathway optimization can be significantly aided by enzyme expression characterization through proteomics, choosing optimal relative protein expression levels for maximum production is still the subject of heuristic, non-systematic approaches. Toxic metabolic intermediates and proteins can significantly affect production, and dynamic pathway regulation emerges as a powerful but yet immature tool to prevent it. Host engineering arises as a much needed complement to pathway engineering for high bioproduct yields; and systems biology approaches such as stoichiometric modeling or growth coupling strategies are required. A final, and often underestimated, challenge is the successful scale up of processes to commercial volumes. Sustained efforts in improving reproducibility and predictability are needed for further development of bioengineering.
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Affiliation(s)
- Victor Chubukov
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Christopher J Petzold
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jay D Keasling
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Héctor García Martín
- Joint BioEnergy Institute, Emeryville, CA, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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Lin H, Travisano M, Kazlauskas RJ. Experimental Evolution of Trichoderma citrinoviride for Faster Deconstruction of Cellulose. PLoS One 2016; 11:e0147024. [PMID: 26820897 PMCID: PMC4731210 DOI: 10.1371/journal.pone.0147024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 12/28/2015] [Indexed: 01/16/2023] Open
Abstract
Engineering faster cellulose deconstruction is difficult because it is a complex, cooperative, multi-enzyme process. Here we use experimental evolution to select for populations of Trichoderma citrinoviride that deconstruct up to five-fold more cellulose. Ten replicate populations of T. citrinoviride were selected for growth on filter paper by serial culture. After 125 periods of growth and transfer to fresh media, the filter paper deconstruction increased an average of 2.5 fold. Two populations were examined in more detail. The activity of the secreted cellulase mixtures increased more than two-fold relative to the ancestor and the largest increase was in the extracellular β-glucosidase activity. qPCR showed at least 16-fold more transcribed RNA for egl4 (endoglucanase IV gene), cbh1 (cellobiohydrolase I gene) and bgl1 (extracellular β-glucosidase I gene) in selected populations as compared to the ancestor, and earlier peak expressions of these genes. Deep sequencing shows that the regulatory strategies used to alter cellulase secretion differ in the two strains. The improvements in cellulose deconstruction come from earlier expression of all cellulases and increased relative amount of β-glucosidase, but with small increases in the total secreted protein and therefore little increase in metabolic cost.
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Affiliation(s)
- Hui Lin
- The Biotechnology Institute, University of Minnesota, Twin Cities, Minnesota, United States of America
| | - Michael Travisano
- The Biotechnology Institute, University of Minnesota, Twin Cities, Minnesota, United States of America
- Department of Ecology Evolution and Behavior, University of Minnesota, Twin Cities, Minnesota, United States of America
- * E-mail: (MT); (RJK)
| | - Romas J. Kazlauskas
- The Biotechnology Institute, University of Minnesota, Twin Cities, Minnesota, United States of America
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Twin Cities, Minnesota, United States of America
- * E-mail: (MT); (RJK)
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Yung PY, Grasso LL, Mohidin AF, Acerbi E, Hinks J, Seviour T, Marsili E, Lauro FM. Global transcriptomic responses of Escherichia coli K-12 to volatile organic compounds. Sci Rep 2016; 6:19899. [PMID: 26818886 PMCID: PMC4730218 DOI: 10.1038/srep19899] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 12/21/2015] [Indexed: 12/16/2022] Open
Abstract
Volatile organic compounds (VOCs) are commonly used as solvents in various industrial settings. Many of them present a challenge to receiving environments, due to their toxicity and low bioavailability for degradation. Microorganisms are capable of sensing and responding to their surroundings and this makes them ideal detectors for toxic compounds. This study investigates the global transcriptomic responses of Escherichia coli K-12 to selected VOCs at sub-toxic levels. Cells grown in the presence of VOCs were harvested during exponential growth, followed by whole transcriptome shotgun sequencing (RNAseq). The analysis of the data revealed both shared and unique genetic responses compared to cells without exposure to VOCs. Results suggest that various functional gene categories, for example, those relating to Fe/S cluster biogenesis, oxidative stress responses and transport proteins, are responsive to selected VOCs in E. coli. The differential expression (DE) of genes was validated using GFP-promoter fusion assays. A variety of genes were differentially expressed even at non-inhibitory concentrations and when the cells are at their balanced-growth. Some of these genes belong to generic stress response and others could be specific to VOCs. Such candidate genes and their regulatory elements could be used as the basis for designing biosensors for selected VOCs.
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Affiliation(s)
- Pui Yi Yung
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE). 60 Nanyang Drive, SBS-01N-27, Singapore 637551
| | - Letizia Lo Grasso
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE). 60 Nanyang Drive, SBS-01N-27, Singapore 637551
| | - Abeed Fatima Mohidin
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE). 60 Nanyang Drive, SBS-01N-27, Singapore 637551
| | - Enzo Acerbi
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE). 60 Nanyang Drive, SBS-01N-27, Singapore 637551
| | - Jamie Hinks
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE). 60 Nanyang Drive, SBS-01N-27, Singapore 637551
| | - Thomas Seviour
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE). 60 Nanyang Drive, SBS-01N-27, Singapore 637551
| | - Enrico Marsili
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE). 60 Nanyang Drive, SBS-01N-27, Singapore 637551.,School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore 637459.,School of Biotechnology, Dublin City University, Collins Avenue, Dublin 9, Ireland
| | - Federico M Lauro
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE). 60 Nanyang Drive, SBS-01N-27, Singapore 637551.,Asian School of the Environment, Nanyang Technological University, 50 Nanyang Avenue, N2-01C-45, Singapore 639798
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Klanchui A, Raethong N, Prommeenate P, Vongsangnak W, Meechai A. Cyanobacterial Biofuels: Strategies and Developments on Network and Modeling. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 160:75-102. [PMID: 27783135 DOI: 10.1007/10_2016_42] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cyanobacteria, the phototrophic microorganisms, have attracted much attention recently as a promising source for environmentally sustainable biofuels production. However, barriers for commercial markets of cyanobacteria-based biofuels concern the economic feasibility. Miscellaneous strategies for improving the production performance of cyanobacteria have thus been developed. Among these, the simple ad hoc strategies resulting in failure to optimize fully cell growth coupled with desired product yield are explored. With the advancement of genomics and systems biology, a new paradigm toward systems metabolic engineering has been recognized. In particular, a genome-scale metabolic network reconstruction and modeling is a crucial systems-based tool for whole-cell-wide investigation and prediction. In this review, the cyanobacterial genome-scale metabolic models, which offer a system-level understanding of cyanobacterial metabolism, are described. The main process of metabolic network reconstruction and modeling of cyanobacteria are summarized. Strategies and developments on genome-scale network and modeling through the systems metabolic engineering approach are advanced and employed for efficient cyanobacterial-based biofuels production.
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Affiliation(s)
- Amornpan Klanchui
- Biological Engineering Program, Faculty of Engineering, King Mongkut's University of Technology Thonburi, Bangkok, 10140, Thailand
| | - Nachon Raethong
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Peerada Prommeenate
- Biochemical Engineering and Pilot Plant Research and Development (BEC) Unit, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Wanwipa Vongsangnak
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand.,Computational Biomodelling Laboratory for Agricultural Science and Technology (CBLAST), Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Asawin Meechai
- Department of Chemical Engineering, Faculty of Engineering, King Mongkut's University of Technology Thonburi, Bangkok, 10140, Thailand.
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Building cellular pathways and programs enabled by the genetic diversity of allo-genomes and meta-genomes. Curr Opin Biotechnol 2015; 36:16-31. [DOI: 10.1016/j.copbio.2015.08.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 08/06/2015] [Accepted: 08/09/2015] [Indexed: 12/21/2022]
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Mukhopadhyay A. Tolerance engineering in bacteria for the production of advanced biofuels and chemicals. Trends Microbiol 2015; 23:498-508. [DOI: 10.1016/j.tim.2015.04.008] [Citation(s) in RCA: 163] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 04/17/2015] [Accepted: 04/23/2015] [Indexed: 02/06/2023]
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36
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Abdelaal AS, Ageez AM, Abd El-Hadi AEHA, Abdallah NA. Genetic improvement of n-butanol tolerance in Escherichia coli by heterologous overexpression of groESL operon from Clostridium acetobutylicum. 3 Biotech 2015; 5:401-410. [PMID: 28324542 PMCID: PMC4522734 DOI: 10.1007/s13205-014-0235-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 06/05/2014] [Indexed: 11/29/2022] Open
Abstract
Strain tolerance to toxic metabolites remains an important issue in the
production of biofuels. Here we examined the impact of overexpressing the
heterologous groESL chaperone from Clostridium acetobutylicum to enhance the tolerance of
Escherichia coli against several stressors.
Strain tolerance was identified using strain maximum specific growth rate (μ) and strain growth after a period of solvent exposure.
In comparison with control strain, the groESL
overexpressing strain yielded a 27 % increase in growth under 0.8 % (v/v) butanol, a
9 % increase under 1 % (v/v) butanol, and a 64 % increase under 1.75 (g/l) acetate.
Moreover, after 10 h, groESL overexpression
resulted in increase in relative tolerance of 58 % compared with control strain
under 0.8 % (v/v) butanol, 56 % increase under 1 % (v/v) butanol, 42 % increase
under 1 % (v/v) isobutanol, 36 % increase under 4 % (v/v) ethanol, 58 % increase
under 1.75 (g/l) acetate. These data demonstrate that overexpression of the
groESL from C.
acetobutylicum in E. coli increased
tolerance to several stressors. Solvent tolerant strain of E. coli was developed to be used as a basic strain for biofuel
production.
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Affiliation(s)
- Ali S Abdelaal
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt.
| | - Amr M Ageez
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
| | | | - Naglaa A Abdallah
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
- Genetics Department, Faculty of Agriculture, Cairo University, Giza, Egypt
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Papoutsakis ET. Reassessing the Progress in the Production of Advanced Biofuels in the Current Competitive Environment and Beyond: What Are the Successes and Where Progress Eludes Us and Why. Ind Eng Chem Res 2015. [DOI: 10.1021/acs.iecr.5b01695] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Eleftherios T. Papoutsakis
- Molecular Biotechnology Laboratory, Department of Chemical & Biomolecular Engineering, Department of Biological Sciences & the Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, United States
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38
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Metaproteomic analysis of bacterial communities in marine mudflat aquaculture sediment. World J Microbiol Biotechnol 2015; 31:1397-408. [DOI: 10.1007/s11274-015-1891-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 06/12/2015] [Indexed: 10/23/2022]
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39
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Cray JA, Stevenson A, Ball P, Bankar SB, Eleutherio ECA, Ezeji TC, Singhal RS, Thevelein JM, Timson DJ, Hallsworth JE. Chaotropicity: a key factor in product tolerance of biofuel-producing microorganisms. Curr Opin Biotechnol 2015; 33:228-59. [PMID: 25841213 DOI: 10.1016/j.copbio.2015.02.010] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 02/13/2015] [Accepted: 02/18/2015] [Indexed: 10/23/2022]
Abstract
Fermentation products can chaotropically disorder macromolecular systems and induce oxidative stress, thus inhibiting biofuel production. Recently, the chaotropic activities of ethanol, butanol and vanillin have been quantified (5.93, 37.4, 174kJ kg(-1)m(-1) respectively). Use of low temperatures and/or stabilizing (kosmotropic) substances, and other approaches, can reduce, neutralize or circumvent product-chaotropicity. However, there may be limits to the alcohol concentrations that cells can tolerate; e.g. for ethanol tolerance in the most robust Saccharomyces cerevisiae strains, these are close to both the solubility limit (<25%, w/v ethanol) and the water-activity limit of the most xerotolerant strains (0.880). Nevertheless, knowledge-based strategies to mitigate or neutralize chaotropicity could lead to major improvements in rates of product formation and yields, and also therefore in the economics of biofuel production.
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Affiliation(s)
- Jonathan A Cray
- Institute for Global Food Security, School of Biological Sciences, MBC, Queen's University Belfast, Belfast BT9 7BL, Northern Ireland, UK
| | - Andrew Stevenson
- Institute for Global Food Security, School of Biological Sciences, MBC, Queen's University Belfast, Belfast BT9 7BL, Northern Ireland, UK
| | - Philip Ball
- 18 Hillcourt Road, East Dulwich, London SE22 0PE, UK
| | - Sandip B Bankar
- Department of Chemical Engineering, College of Engineering, Bharati Vidyapeeth University, Pune-Satara Road, Pune 411043, India
| | - Elis C A Eleutherio
- Universidade Federal do Rio de Janeiro, Instituto de Quimica, Programa de Pós-graduação Bioquimica, Rio de Janeiro, RJ, Brazil
| | - Thaddeus C Ezeji
- Department of Animal Sciences and Ohio Agricultural Research and Development Center (OARDC), The Ohio State University, 305 Gerlaugh Hall, 1680 Madison Avenue, Wooster, OH 44691, USA
| | - Rekha S Singhal
- Department of Food Engineering and Technology, Institute of Chemical Technology, N.P. Marg, Matunga, Mumbai, Maharashtra 400019, India
| | - Johan M Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven and Department of Molecular Microbiology, VIB, Kasteelpark Arenberg 31, Flanders, Leuven-Heverlee B-3001, Belgium
| | - David J Timson
- Institute for Global Food Security, School of Biological Sciences, MBC, Queen's University Belfast, Belfast BT9 7BL, Northern Ireland, UK
| | - John E Hallsworth
- Institute for Global Food Security, School of Biological Sciences, MBC, Queen's University Belfast, Belfast BT9 7BL, Northern Ireland, UK.
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40
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Vinayavekhin N, Mahipant G, Vangnai AS, Sangvanich P. Untargeted metabolomics analysis revealed changes in the composition of glycerolipids and phospholipids in Bacillus subtilis under 1-butanol stress. Appl Microbiol Biotechnol 2015; 99:5971-83. [PMID: 26025016 DOI: 10.1007/s00253-015-6692-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 04/18/2015] [Accepted: 05/15/2015] [Indexed: 01/21/2023]
Abstract
1-Butanol has been utilized widely in industry and can be produced or transformed by microbes. However, current knowledge about the mechanisms of 1-butanol tolerance in bacteria remains quite limited. Here, we applied untargeted metabolomics to study Bacillus subtilis cells under 1-butanol stress and identified 55 and 37 ions with significantly increased and decreased levels, respectively. Using accurate mass determination, tandem mass spectra, and synthetic standards, 86 % of these ions were characterized. The levels of phosphatidylethanolamine, diglucosyldiacylglycerol, and phosphatidylserine were found to be upregulated upon 1-butanol treatment, whereas those of diacylglycerol and lysyl phosphatidylglycerol were downregulated. Most lipids contained 15:0/15:0, 16:0/15:0, and 17:0/15:0 acyl chains, and all were mapped to membrane lipid biosynthetic pathways. Subsequent two-stage quantitative real-time reverse transcriptase PCR analyses of genes in the two principal membrane lipid biosynthesis pathways revealed elevated levels of ywiE transcripts in the presence of 1-butanol and reduced expression levels of cdsA, pgsA, mprF, clsA, and yfnI transcripts. Thus, the gene transcript levels showed agreement with the metabolomics data. Lastly, the cell morphology was investigated by scanning electron microscopy, which indicated that cells became almost twofold longer after 1.4 % (v/v) 1-butanol stress for 12 h. Overall, the studies uncovered changes in the composition of glycerolipids and phospholipids in B. subtilis under 1-butanol stress, emphasizing the power of untargeted metabolomics in the discovery of new biological insights.
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Affiliation(s)
- Nawaporn Vinayavekhin
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand,
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41
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Expression of heterologous sigma factors enables functional screening of metagenomic and heterologous genomic libraries. Nat Commun 2015; 6:7045. [PMID: 25944046 PMCID: PMC4432631 DOI: 10.1038/ncomms8045] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 03/26/2015] [Indexed: 11/20/2022] Open
Abstract
A key limitation in using heterologous genomic or metagenomic libraries in functional genomics and genome engineering is the low expression of heterologous genes in screening hosts, such as Escherichia coli. To overcome this limitation, here we generate E. coli strains capable of recognizing heterologous promoters by expressing heterologous sigma factors. Among seven sigma factors tested, RpoD from Lactobacillus plantarum (Lpl) appears to be able of initiating transcription from all sources of DNA. Using the promoter GFP-trap concept, we successfully screen several heterologous and metagenomic DNA libraries, thus enlarging the genomic space that can be functionally sampled in E. coli. For an application, we show that screening fosmid-based Lpl genomic libraries in an E. coli strain with a chromosomally integrated Lpl rpoD enables the identification of Lpl genetic determinants imparting strong ethanol tolerance in E. coli. Transcriptome analysis confirms increased expression of heterologous genes in the engineered strain. Screening genomic or metagenomic libraries for interesting products or activities is often hampered by poor gene expression in a heterologous host. Here the authors show that the expression of a Lactobacillus sigma factor greatly enhances transcription of heterologous and environmental DNA in E. coli.
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Venkataramanan KP, Min L, Hou S, Jones SW, Ralston MT, Lee KH, Papoutsakis ET. Complex and extensive post-transcriptional regulation revealed by integrative proteomic and transcriptomic analysis of metabolite stress response in Clostridium acetobutylicum. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:81. [PMID: 26269711 PMCID: PMC4533764 DOI: 10.1186/s13068-015-0260-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2015] [Accepted: 04/30/2015] [Indexed: 05/16/2023]
Abstract
BACKGROUND Clostridium acetobutylicum is a model organism for both clostridial biology and solvent production. The organism is exposed to its own toxic metabolites butyrate and butanol, which trigger an adaptive stress response. Integrative analysis of proteomic and RNAseq data may provide novel insights into post-transcriptional regulation. RESULTS The identified iTRAQ-based quantitative stress proteome is made up of 616 proteins with a 15 % genome coverage. The differentially expressed proteome correlated poorly with the corresponding differential RNAseq transcriptome. Up to 31 % of the differentially expressed proteins under stress displayed patterns opposite to those of the transcriptome, thus suggesting significant post-transcriptional regulation. The differential proteome of the translation machinery suggests that cells employ a different subset of ribosomal proteins under stress. Several highly upregulated proteins but with low mRNA levels possessed mRNAs with long 5'UTRs and strong RBS scores, thus supporting the argument that regulatory elements on the long 5'UTRs control their translation. For example, the oxidative stress response rubrerythrin was upregulated only at the protein level up to 40-fold without significant mRNA changes. We also identified many leaderless transcripts, several displaying different transcriptional start sites, thus suggesting mRNA-trimming mechanisms under stress. Downregulation of Rho and partner proteins pointed to changes in transcriptional elongation and termination under stress. CONCLUSIONS The integrative proteomic-transcriptomic analysis demonstrated complex expression patterns of a large fraction of the proteome. Such patterns could not have been detected with one or the other omic analyses. Our analysis proposes the involvement of specific molecular mechanisms of post-transcriptional regulation to explain the observed complex stress response.
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Affiliation(s)
- Keerthi P. Venkataramanan
- />15 Innovation Way, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711 USA
- />150 Academy Street, Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711 USA
| | - Lie Min
- />15 Innovation Way, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711 USA
- />150 Academy Street, Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711 USA
| | - Shuyu Hou
- />15 Innovation Way, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711 USA
- />150 Academy Street, Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711 USA
| | - Shawn W. Jones
- />15 Innovation Way, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711 USA
- />150 Academy Street, Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711 USA
| | - Matthew T. Ralston
- />15 Innovation Way, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711 USA
- />15 Innovation Way, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711 USA
| | - Kelvin H. Lee
- />15 Innovation Way, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711 USA
- />150 Academy Street, Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711 USA
| | - E. Terry Papoutsakis
- />15 Innovation Way, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711 USA
- />150 Academy Street, Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19711 USA
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Pei G, Chen L, Wang J, Qiao J, Zhang W. Protein Network Signatures Associated with Exogenous Biofuels Treatments in Cyanobacterium Synechocystis sp. PCC 6803. Front Bioeng Biotechnol 2014; 2:48. [PMID: 25405149 PMCID: PMC4217553 DOI: 10.3389/fbioe.2014.00048] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 10/17/2014] [Indexed: 12/04/2022] Open
Abstract
Although recognized as a promising microbial cell factory for producing biofuels, current productivity in cyanobacterial systems is low. To make the processes economically feasible, one of the hurdles, which need to be overcome is the low tolerance of hosts to toxic biofuels. Meanwhile, little information is available regarding the cellular responses to biofuels stress in cyanobacteria, which makes it challenging for tolerance engineering. Using large proteomic datasets of Synechocystis under various biofuels stress and environmental perturbation, a protein co-expression network was first constructed and then combined with the experimentally determined protein–protein interaction network. Proteins with statistically higher topological overlap in the integrated network were identified as common responsive proteins to both biofuels stress and environmental perturbations. In addition, a weighted gene co-expression network analysis was performed to distinguish unique responses to biofuels from those to environmental perturbations and to uncover metabolic modules and proteins uniquely associated with biofuels stress. The results showed that biofuel-specific proteins and modules were enriched in several functional categories, including photosynthesis, carbon fixation, and amino acid metabolism, which may represent potential key signatures for biofuels stress responses in Synechocystis. Network-based analysis allowed determination of the responses specifically related to biofuels stress, and the results constituted an important knowledge foundation for tolerance engineering against biofuels in Synechocystis.
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Affiliation(s)
- Guangsheng Pei
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University , Tianjin , China ; Key Laboratory of Systems Bioengineering, Ministry of Education of China , Tianjin , China ; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering , Tianjin , China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University , Tianjin , China ; Key Laboratory of Systems Bioengineering, Ministry of Education of China , Tianjin , China ; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering , Tianjin , China
| | - Jiangxin Wang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University , Tianjin , China ; Key Laboratory of Systems Bioengineering, Ministry of Education of China , Tianjin , China ; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering , Tianjin , China
| | - Jianjun Qiao
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University , Tianjin , China ; Key Laboratory of Systems Bioengineering, Ministry of Education of China , Tianjin , China ; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering , Tianjin , China
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University , Tianjin , China ; Key Laboratory of Systems Bioengineering, Ministry of Education of China , Tianjin , China ; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering , Tianjin , China
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44
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Microbial tolerance engineering toward biochemical production: from lignocellulose to products. Curr Opin Biotechnol 2014; 29:99-106. [DOI: 10.1016/j.copbio.2014.03.005] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2013] [Revised: 03/01/2014] [Accepted: 03/18/2014] [Indexed: 11/19/2022]
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Overexpression of the Lactobacillus plantarum peptidoglycan biosynthesis murA2 gene increases the tolerance of Escherichia coli to alcohols and enhances ethanol production. Appl Microbiol Biotechnol 2014; 98:8399-411. [DOI: 10.1007/s00253-014-6004-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 07/28/2014] [Accepted: 08/03/2014] [Indexed: 10/24/2022]
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Polyamine transporters and polyamines increase furfural tolerance during xylose fermentation with ethanologenic Escherichia coli strain LY180. Appl Environ Microbiol 2014; 80:5955-64. [PMID: 25063650 DOI: 10.1128/aem.01913-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Expression of genes encoding polyamine transporters from plasmids and polyamine supplements increased furfural tolerance (growth and ethanol production) in ethanologenic Escherichia coli LY180 (in AM1 mineral salts medium containing xylose). This represents a new approach to increase furfural tolerance and may be useful for other organisms. Microarray comparisons of two furfural-resistant mutants (EMFR9 and EMFR35) provided initial evidence for the importance of polyamine transporters. Each mutant contained a single polyamine transporter gene that was upregulated over 100-fold (microarrays) compared to that in the parent LY180, as well as a mutation that silenced the expression of yqhD. Based on these genetic changes, furfural tolerance was substantially reconstructed in the parent, LY180. Deletion of potE in EMFR9 lowered furfural tolerance to that of the parent. Deletion of potE and puuP in LY180 also decreased furfural tolerance, indicating functional importance of the native genes. Of the 8 polyamine transporters (18 genes) cloned and tested, half were beneficial for furfural tolerance (PotE, PuuP, PlaP, and PotABCD). Supplementing AM1 mineral salts medium with individual polyamines (agmatine, putrescine, and cadaverine) also increased furfural tolerance but to a smaller extent. In pH-controlled fermentations, polyamine transporter plasmids were shown to promote the metabolism of furfural and substantially reduce the time required to complete xylose fermentation. This increase in furfural tolerance is proposed to result from polyamine binding to negatively charged cellular constituents such as nucleic acids and phospholipids, providing protection from damage by furfural.
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Zingaro KA, Nicolaou SA, Yuan Y, Papoutsakis ET. Exploring the heterologous genomic space for building, stepwise, complex, multicomponent tolerance to toxic chemicals. ACS Synth Biol 2014; 3:476-86. [PMID: 24933690 DOI: 10.1021/sb400156v] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Modern bioprocessing depends on superior cellular traits, many stemming from unknown genes and gene interactions. Tolerance to toxic chemicals is such an industrially important complex trait, which frequently limits the economic feasibility of producing commodity chemicals and biofuels. Chemical tolerance encompasses both improved cell viability and growth under chemical stress. Building upon the success of our recently reported semisynthetic stress response system expressed off plasmid pHSP (Heat Shock Protein), we probed the genomic space of the solvent tolerant Lactobacillus plantarum to identify genetic determinants that impart solvent tolerance in combination with pHSP. Using two targeted enrichments, one for superior viability and one for better growth under ethanol stress, we identified several beneficial heterologous DNA determinants that act synergistically with pHSP. In separate strains, a 209% improvement in survival and an 83% improvement in growth over previously engineered strains based on pHSP were thus generated. We then developed a composite phenotype of improved growth and survival by combining the identified L. plantarum genetic fragments. This demonstrates the concept for a sequential, iterative assembly strategy for building multigenic traits by exploring the synergistic effects of genetic determinants from a much broader genomic space. The best performing strain produced a 3.7-fold improved survival under 8% ethanol stress, as well as a 32% increase in growth under 4% ethanol. This strain also shows significantly improved tolerance to n-butanol. Improved solvent production is rarely examined in tolerance engineering studies. Here, we show that our system significantly improves ethanol productivity in a Melle-Boinot-like fermentation process.
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Affiliation(s)
- Kyle A. Zingaro
- Molecular Biotechnology Laboratory, Dept. of Chemical & Biomolecular Engineering, the Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, United States
| | - Sergios A. Nicolaou
- Molecular Biotechnology Laboratory, Dept. of Chemical & Biomolecular Engineering, the Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, United States
| | - Yongbo Yuan
- Molecular Biotechnology Laboratory, Dept. of Chemical & Biomolecular Engineering, the Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, United States
| | - Eleftherios Terry Papoutsakis
- Molecular Biotechnology Laboratory, Dept. of Chemical & Biomolecular Engineering, the Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, United States
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Correcting direct effects of ethanol on translation and transcription machinery confers ethanol tolerance in bacteria. Proc Natl Acad Sci U S A 2014; 111:E2576-85. [PMID: 24927582 DOI: 10.1073/pnas.1401853111] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The molecular mechanisms of ethanol toxicity and tolerance in bacteria, although important for biotechnology and bioenergy applications, remain incompletely understood. Genetic studies have identified potential cellular targets for ethanol and have revealed multiple mechanisms of tolerance, but it remains difficult to separate the direct and indirect effects of ethanol. We used adaptive evolution to generate spontaneous ethanol-tolerant strains of Escherichia coli, and then characterized mechanisms of toxicity and resistance using genome-scale DNAseq, RNAseq, and ribosome profiling coupled with specific assays of ribosome and RNA polymerase function. Evolved alleles of metJ, rho, and rpsQ recapitulated most of the observed ethanol tolerance, implicating translation and transcription as key processes affected by ethanol. Ethanol induced miscoding errors during protein synthesis, from which the evolved rpsQ allele protected cells by increasing ribosome accuracy. Ribosome profiling and RNAseq analyses established that ethanol negatively affects transcriptional and translational processivity. Ethanol-stressed cells exhibited ribosomal stalling at internal AUG codons, which may be ameliorated by the adaptive inactivation of the MetJ repressor of methionine biosynthesis genes. Ethanol also caused aberrant intragenic transcription termination for mRNAs with low ribosome density, which was reduced in a strain with the adaptive rho mutation. Furthermore, ethanol inhibited transcript elongation by RNA polymerase in vitro. We propose that ethanol-induced inhibition and uncoupling of mRNA and protein synthesis through direct effects on ribosomes and RNA polymerase conformations are major contributors to ethanol toxicity in E. coli, and that adaptive mutations in metJ, rho, and rpsQ help protect these central dogma processes in the presence of ethanol.
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Jang YS, Im JA, Choi SY, Lee JI, Lee SY. Metabolic engineering of Clostridium acetobutylicum for butyric acid production with high butyric acid selectivity. Metab Eng 2014; 23:165-74. [DOI: 10.1016/j.ymben.2014.03.004] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Revised: 03/22/2014] [Accepted: 03/25/2014] [Indexed: 12/24/2022]
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Nikel PI, de Lorenzo V. Robustness of Pseudomonas putida KT2440 as a host for ethanol biosynthesis. N Biotechnol 2014; 31:562-71. [PMID: 24572656 DOI: 10.1016/j.nbt.2014.02.006] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 02/10/2014] [Accepted: 02/15/2014] [Indexed: 12/01/2022]
Abstract
Expansion of the burgeoning biofuels agenda involves not only the design of suitable genetic and metabolic devices but also their deployment into suitable hosts that can endure the stress brought about by the products themselves. The microorganisms that are easiest to genetically manipulate for these endeavors (e.g. Escherichia coli) are often afflicted by an undesirable sensitivity to the very product that they are engineered to synthesize. In this context, we have examined the resistance to the stress arising from ethanol synthesis and/or its addition to cultures of recombinant Pseudomonas putida, using as a benchmark the same trait in an E. coli strain. To this end, ethanologenic strains of these two species were constructed by functionally expressing pdc (pyruvate decarboxylase) and adhB (alcohol dehydrogenase) from Zymomonas mobilis. Recombinants were compared under anoxic conditions as ethanol producers, and cell survival, stress resistance, and phenotypic stability were quantified in each case. P. putida consistently outperformed E. coli in every ethanol tolerance test conducted - whether the alcohol was produced endogenously or added exogenously. These results highlight the value of this bacterium as a microbial cell factory for the production of biofuels owing to its naturally pre-evolved ability to withstand different kinds of chemical stresses.
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Affiliation(s)
- Pablo I Nikel
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Madrid 28049, Spain
| | - Víctor de Lorenzo
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Madrid 28049, Spain.
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