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Rychel K, Tan J, Patel A, Lamoureux C, Hefner Y, Szubin R, Johnsen J, Mohamed ETT, Phaneuf PV, Anand A, Olson CA, Park JH, Sastry AV, Yang L, Feist AM, Palsson BO. Laboratory evolution, transcriptomics, and modeling reveal mechanisms of paraquat tolerance. Cell Rep 2023; 42:113105. [PMID: 37713311 PMCID: PMC10591938 DOI: 10.1016/j.celrep.2023.113105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 07/09/2023] [Accepted: 08/23/2023] [Indexed: 09/17/2023] Open
Abstract
Relationships between the genome, transcriptome, and metabolome underlie all evolved phenotypes. However, it has proved difficult to elucidate these relationships because of the high number of variables measured. A recently developed data analytic method for characterizing the transcriptome can simplify interpretation by grouping genes into independently modulated sets (iModulons). Here, we demonstrate how iModulons reveal deep understanding of the effects of causal mutations and metabolic rewiring. We use adaptive laboratory evolution to generate E. coli strains that tolerate high levels of the redox cycling compound paraquat, which produces reactive oxygen species (ROS). We combine resequencing, iModulons, and metabolic models to elucidate six interacting stress-tolerance mechanisms: (1) modification of transport, (2) activation of ROS stress responses, (3) use of ROS-sensitive iron regulation, (4) motility, (5) broad transcriptional reallocation toward growth, and (6) metabolic rewiring to decrease NADH production. This work thus demonstrates the power of iModulon knowledge mapping for evolution analysis.
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Affiliation(s)
- Kevin Rychel
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Justin Tan
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Arjun Patel
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Cameron Lamoureux
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ying Hefner
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Richard Szubin
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Josefin Johnsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Elsayed Tharwat Tolba Mohamed
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Patrick V Phaneuf
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Amitesh Anand
- Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai, Maharashtra, India
| | - Connor A Olson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Joon Ho Park
- Department of Chemical Engineering, Massachusetts Institute of Technology, 500 Main Street, Building 76, Cambridge, MA 02139, USA
| | - Anand V Sastry
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Laurence Yang
- Department of Chemical Engineering, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Adam M Feist
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs. Lyngby, Denmark.
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2
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Li N, Zong MH. (Chemo)biocatalytic Upgrading of Biobased Furanic Platforms to Chemicals, Fuels, and Materials: A Comprehensive Review. ACS Catal 2022. [DOI: 10.1021/acscatal.2c02912] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Ning Li
- School of Food Science and Engineering, South China University of Technology, 381 Wushan Road, Guangzhou 510640, China
| | - Min-Hua Zong
- School of Food Science and Engineering, South China University of Technology, 381 Wushan Road, Guangzhou 510640, China
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3
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Narisetty V, Cox R, Bommareddy R, Agrawal D, Ahmad E, Pant KK, Chandel AK, Bhatia SK, Kumar D, Binod P, Gupta VK, Kumar V. Valorisation of xylose to renewable fuels and chemicals, an essential step in augmenting the commercial viability of lignocellulosic biorefineries. SUSTAINABLE ENERGY & FUELS 2021; 6:29-65. [PMID: 35028420 PMCID: PMC8691124 DOI: 10.1039/d1se00927c] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 10/25/2021] [Indexed: 05/30/2023]
Abstract
Biologists and engineers are making tremendous efforts in contributing to a sustainable and green society. To that end, there is growing interest in waste management and valorisation. Lignocellulosic biomass (LCB) is the most abundant material on the earth and an inevitable waste predominantly originating from agricultural residues, forest biomass and municipal solid waste streams. LCB serves as the renewable feedstock for clean and sustainable processes and products with low carbon emission. Cellulose and hemicellulose constitute the polymeric structure of LCB, which on depolymerisation liberates oligomeric or monomeric glucose and xylose, respectively. The preferential utilization of glucose and/or absence of the xylose metabolic pathway in microbial systems cause xylose valorization to be alienated and abandoned, a major bottleneck in the commercial viability of LCB-based biorefineries. Xylose is the second most abundant sugar in LCB, but a non-conventional industrial substrate unlike glucose. The current review seeks to summarize the recent developments in the biological conversion of xylose into a myriad of sustainable products and associated challenges. The review discusses the microbiology, genetics, and biochemistry of xylose metabolism with hurdles requiring debottlenecking for efficient xylose assimilation. It further describes the product formation by microbial cell factories which can assimilate xylose naturally and rewiring of metabolic networks to ameliorate xylose-based bioproduction in native as well as non-native strains. The review also includes a case study that provides an argument on a suitable pathway for optimal cell growth and succinic acid (SA) production from xylose through elementary flux mode analysis. Finally, a product portfolio from xylose bioconversion has been evaluated along with significant developments made through enzyme, metabolic and process engineering approaches, to maximize the product titers and yield, eventually empowering LCB-based biorefineries. Towards the end, the review is wrapped up with current challenges, concluding remarks, and prospects with an argument for intense future research into xylose-based biorefineries.
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Affiliation(s)
- Vivek Narisetty
- School of Water, Energy and Environment, Cranfield University Cranfield MK43 0AL UK +44 (0)1234754786
| | - Rylan Cox
- School of Water, Energy and Environment, Cranfield University Cranfield MK43 0AL UK +44 (0)1234754786
- School of Aerospace, Transport and Manufacturing, Cranfield University Cranfield MK43 0AL UK
| | - Rajesh Bommareddy
- Department of Applied Sciences, Northumbria University Newcastle upon Tyne NE1 8ST UK
| | - Deepti Agrawal
- Biochemistry and Biotechnology Area, Material Resource Efficiency Division, CSIR- Indian Institute of Petroleum Mohkampur Dehradun 248005 India
| | - Ejaz Ahmad
- Department of Chemical Engineering, Indian Institute of Technology (ISM) Dhanbad 826004 India
| | - Kamal Kumar Pant
- Department of Chemical Engineering, Indian Institute of Technology Delhi New Delhi 110016 India
| | - Anuj Kumar Chandel
- Department of Biotechnology, Engineering School of Lorena (EEL), University of São Paulo Lorena 12.602.810 Brazil
| | - Shashi Kant Bhatia
- Department of Biological Engineering, College of Engineering, Konkuk University Seoul 05029 Republic of Korea
| | - Dinesh Kumar
- School of Bioengineering & Food Technology, Shoolini University of Biotechnology and Management Sciences Solan 173229 Himachal Pradesh India
| | - Parmeswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST) Thiruvananthapuram 695 019 Kerala India
| | | | - Vinod Kumar
- School of Water, Energy and Environment, Cranfield University Cranfield MK43 0AL UK +44 (0)1234754786
- Department of Chemical Engineering, Indian Institute of Technology Delhi New Delhi 110016 India
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4
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The challenges and prospects of Escherichia coli as an organic acid production host under acid stress. Appl Microbiol Biotechnol 2021; 105:8091-8107. [PMID: 34617140 DOI: 10.1007/s00253-021-11577-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 12/17/2022]
Abstract
OBJECTIVE Organic acids have a wide range of applications and have attracted the attention of many industries, and their large-scale applications have led fermentation production to low-cost development. Among them, the microbial fermentation method, especially using Escherichia coli as the production host, has the advantages of fast growth and low energy consumption, and has gradually shown better advantages and prospects in organic acid fermentation production. IMPORTANCE However, when the opportunity comes, the acidified environment caused by the acid products accumulated during the fermentation process also challenges E. coli. The acid sensitivity of E. coli is a core problem that needs to be solved urgently. The addition of neutralizers in traditional operations led to the emergence of osmotic stress inadvertently, the addition of strong acid substances to recover products in the salt state not only increases production costs, but the discharged sewage is also harmful to the environment. ELABORATION This article summarizes the current status of the application of E. coli in the production of organic acids, and based on the impact of acid stress on the physiological state of cells and the impact of industrial production profits, put forward some new conjectures that can make up for the deficiencies in existing research and application. IMPLICATION At this point, the diversified transformation of E. coli has become a chassis microbe that is more suitable for industrial fermentation, enhancing industrial application value. KEY POINTS • E. coli is a potential host for high value-added organic acids production. • Classify the damage mechanism and coping strategies of E. coli when stimulated by acid molecules. • Multi-dimensional expansion tools are needed to create acid-resistant E. coli chassis.
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5
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Soffer G, Perry JM, Shih SCC. Real-Time Optogenetics System for Controlling Gene Expression Using a Model-Based Design. Anal Chem 2021; 93:3181-3188. [PMID: 33543619 DOI: 10.1021/acs.analchem.0c04594] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Optimization of engineered biological systems requires precise control over the rates and timing of gene expression. Optogenetics is used to dynamically control gene expression as an alternative to conventional chemical-based methods since it provides a more convenient interface between digital control software and microbial culture. Here, we describe the construction of a real-time optogenetics platform, which performs closed-loop control over the CcaR-CcaS two-plasmid system in Escherichia coli. We showed the first model-based design approach by constructing a nonlinear representation of the CcaR-CcaS system, tuned the model through open-loop experimentation to capture the experimental behavior, and applied the model in silico to inform the necessary changes to build a closed-loop optogenetic control system. Our system periodically induces and represses the CcaR-CcaS system while recording optical density and fluorescence using image processing techniques. We highlight the facile nature of constructing our system and how our model-based design approach will potentially be used to model other systems requiring closed-loop optogenetic control.
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Affiliation(s)
- Guy Soffer
- Department of Electrical and Computer Engineering, Concordia University, 1455 de Maisonneuve Blvd West, Montréal, Québec H3G1M8, Canada.,Centre for Applied Synthetic Biology, Concordia University, 7141 Sherbrooke St. West, Montréal, Québec H4B1R6, Canada
| | - James M Perry
- Centre for Applied Synthetic Biology, Concordia University, 7141 Sherbrooke St. West, Montréal, Québec H4B1R6, Canada.,Department of Biology, Concordia University, 7141 Sherbrooke St. West, Montréal, Québec H4B1R6, Canada
| | - Steve C C Shih
- Department of Electrical and Computer Engineering, Concordia University, 1455 de Maisonneuve Blvd West, Montréal, Québec H3G1M8, Canada.,Centre for Applied Synthetic Biology, Concordia University, 7141 Sherbrooke St. West, Montréal, Québec H4B1R6, Canada.,Department of Biology, Concordia University, 7141 Sherbrooke St. West, Montréal, Québec H4B1R6, Canada
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6
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Caicedo-Burbano P, Smit T, Pineda Hernández H, Du W, Branco dos Santos F. Construction of Fully Segregated Genomic Libraries in Polyploid Organisms Such as Synechocystis sp. PCC 6803. ACS Synth Biol 2020; 9:2632-2638. [PMID: 33017143 PMCID: PMC7573980 DOI: 10.1021/acssynbio.0c00353] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Indexed: 12/11/2022]
Abstract
Several microbes are polyploid, meaning they contain several copies of their chromosome. Cyanobacteria, while holding great potential as photosynthetic cell factories of various products, are found among them. In these clades the diversity of genetic elements that serve within the basic molecular toolbox is often limiting. To assist mining for the latter, we present here a method for the generation of fully segregated genomic libraries, specifically designed for polyploids. We provide proof-of-principle for this method by generating a fully segregated genomic promoter library in the cyanobacterium Synechocystis sp. PCC 6803. This new tool was first analyzed through fluorescence activated cell sorting (FACS) and then a fraction was further characterized regarding promoter sequence. The location of libraries on the chromosome provides a better reflection of the behavior of its elements. Our work presents the first method for constructing fully segregated genomic libraries in polyploids, which may facilitate their usage in synthetic biology applications.
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Affiliation(s)
- Patricia Caicedo-Burbano
- Molecular
Microbial Physiology Group, Swammerdam Institute for Life Sciences,
Faculty of Science, University of Amsterdam, Science Park 904, Amsterdam 1098 XH,The Netherlands
| | - Tycho Smit
- Molecular
Microbial Physiology Group, Swammerdam Institute for Life Sciences,
Faculty of Science, University of Amsterdam, Science Park 904, Amsterdam 1098 XH,The Netherlands
| | - Hugo Pineda Hernández
- Molecular
Microbial Physiology Group, Swammerdam Institute for Life Sciences,
Faculty of Science, University of Amsterdam, Science Park 904, Amsterdam 1098 XH,The Netherlands
| | - Wei Du
- Molecular
Microbial Physiology Group, Swammerdam Institute for Life Sciences,
Faculty of Science, University of Amsterdam, Science Park 904, Amsterdam 1098 XH,The Netherlands
| | - Filipe Branco dos Santos
- Molecular
Microbial Physiology Group, Swammerdam Institute for Life Sciences,
Faculty of Science, University of Amsterdam, Science Park 904, Amsterdam 1098 XH,The Netherlands
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7
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Yang J, Kim HE, Jung YH, Kim J, Kim DH, Walmsley AR, Kim KH. Zmo0994, a novel LEA-like protein from Zymomonas mobilis, increases multi-abiotic stress tolerance in Escherichia coli. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:151. [PMID: 32863881 PMCID: PMC7448490 DOI: 10.1186/s13068-020-01790-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 08/16/2020] [Indexed: 05/25/2023]
Abstract
BACKGROUND Pretreatment processes and subsequent enzymatic hydrolysis are prerequisites to utilize lignocellulosic sugar for fermentation. However, the resulting hydrolysate frequently hinders fermentation processes due to the presence of inhibitors and toxic products (e.g., ethanol). Thus, it is crucial to develop robust microbes conferring multi-stress tolerance. RESULTS Zmo0994, a functionally uncharacterized protein from Zymomonas mobilis, was identified and characterized for the first time. A major effect of Zmo0994 was a significant enhancement in the tolerance to abiotic stresses such as ethanol, furfural, 5'-hydroxymethylfurfural and high temperature, when expressed in Escherichia coli. Through transcriptome analysis and in vivo experiments, the cellular mechanism of this protein was revealed as due to its ability to trigger genes, involved in aerobic respiration for ATP synthesis. CONCLUSIONS These findings have significant implications that might lead to the development of robust microbes for the highly efficient industrial fermentation processes.
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Affiliation(s)
- Jungwoo Yang
- Department of Biotechnology, Graduate School, Korea University, Seoul, 02841 Republic of Korea
| | - Ha Eun Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul, 02841 Republic of Korea
| | - Young Hoon Jung
- School of Food Science and Biotechnology, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu, 41566 Republic of Korea
| | - Jungyeon Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul, 02841 Republic of Korea
| | - Do Hyoung Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul, 02841 Republic of Korea
| | - Adrian R. Walmsley
- Department of Biosciences, Durham University, South Road, Durham, DH1 3LE UK
| | - Kyoung Heon Kim
- Department of Biotechnology, Graduate School, Korea University, Seoul, 02841 Republic of Korea
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8
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Building cell factories for the production of advanced fuels. Biochem Soc Trans 2020; 47:1701-1714. [PMID: 31803925 DOI: 10.1042/bst20190168] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 11/13/2019] [Accepted: 11/15/2019] [Indexed: 12/31/2022]
Abstract
Synthetic biology-based engineering strategies are being extensively employed for microbial production of advanced fuels. Advanced fuels, being comparable in energy efficiency and properties to conventional fuels, have been increasingly explored as they can be directly incorporated into the current fuel infrastructure without the need for reconstructing the pre-existing set-up rendering them economically viable. Multiple metabolic engineering approaches have been used for rewiring microbes to improve existing or develop newly programmed cells capable of efficient fuel production. The primary challenge in using these approaches is improving the product yield for the feasibility of the commercial processes. Some of the common roadblocks towards enhanced fuel production include - limited availability of flux towards precursors and desired pathways due to presence of competing pathways, limited cofactor and energy supply in cells, the low catalytic activity of pathway enzymes, obstructed product transport, and poor tolerance of host cells for end products. Consequently, despite extensive studies on the engineering of microbial hosts, the costs of industrial-scale production of most of these heterologously produced fuel compounds are still too high. Though considerable progress has been made towards successfully producing some of these biofuels, a substantial amount of work needs to be done for improving the titers of others. In this review, we have summarized the different engineering strategies that have been successfully used for engineering pathways into commercial hosts for the production of advanced fuels and different approaches implemented for tuning host strains and pathway enzymes for scaling up production levels.
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9
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Sandberg TE, Salazar MJ, Weng LL, Palsson BO, Feist AM. The emergence of adaptive laboratory evolution as an efficient tool for biological discovery and industrial biotechnology. Metab Eng 2019; 56:1-16. [PMID: 31401242 DOI: 10.1016/j.ymben.2019.08.004] [Citation(s) in RCA: 254] [Impact Index Per Article: 50.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 08/01/2019] [Accepted: 08/05/2019] [Indexed: 12/21/2022]
Abstract
Harnessing the process of natural selection to obtain and understand new microbial phenotypes has become increasingly possible due to advances in culturing techniques, DNA sequencing, bioinformatics, and genetic engineering. Accordingly, Adaptive Laboratory Evolution (ALE) experiments represent a powerful approach both to investigate the evolutionary forces influencing strain phenotypes, performance, and stability, and to acquire production strains that contain beneficial mutations. In this review, we summarize and categorize the applications of ALE to various aspects of microbial physiology pertinent to industrial bioproduction by collecting case studies that highlight the multitude of ways in which evolution can facilitate the strain construction process. Further, we discuss principles that inform experimental design, complementary approaches such as computational modeling that help maximize utility, and the future of ALE as an efficient strain design and build tool driven by growing adoption and improvements in automation.
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Affiliation(s)
- Troy E Sandberg
- Department of Bioengineering, University of California, San Diego, CA, 92093, USA
| | - Michael J Salazar
- Department of Bioengineering, University of California, San Diego, CA, 92093, USA
| | - Liam L Weng
- Department of Bioengineering, University of California, San Diego, CA, 92093, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, CA, 92093, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Adam M Feist
- Department of Bioengineering, University of California, San Diego, CA, 92093, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark.
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10
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Evolutionary engineering of industrial microorganisms-strategies and applications. Appl Microbiol Biotechnol 2018; 102:4615-4627. [DOI: 10.1007/s00253-018-8937-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 03/13/2018] [Accepted: 03/13/2018] [Indexed: 10/17/2022]
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11
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Chouhan S, Sharma K, Zha J, Guleria S, Koffas MAG. Recent Advances in the Recombinant Biosynthesis of Polyphenols. Front Microbiol 2017; 8:2259. [PMID: 29201020 PMCID: PMC5696593 DOI: 10.3389/fmicb.2017.02259] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 11/01/2017] [Indexed: 01/29/2023] Open
Abstract
Plants are the source of various natural compounds with pharmaceutical and nutraceutical importance which have shown numerous health benefits with relatively fewer side effects. However, extraction of these compounds from native producers cannot meet the ever-increasing demands of the growing population due to, among other things, the limited production of the active compound(s). Their production depends upon the metabolic demands of the plant and is also subjected to environmental conditions, abundance of crop species and seasonal variations. Moreover, their extraction from plants requires complex downstream processing and can also lead to the extinction of many useful plant varieties. Microbial engineering is one of the alternative approaches which can meet the global demand for natural products in an eco-friendly manner. Metabolic engineering of microbes or pathway reconstruction using synthetic biology tools and novel enzymes lead to the generation of a diversity of compounds (like flavonoids, stilbenes, anthocyanins etc.) and their natural and non-natural derivatives. Strain and pathway optimization, pathway regulation and tolerance engineering have produced microbial cell factories into which the metabolic pathway of plants can be introduced for the production of compounds of interest on an industrial scale in an economical and eco-friendly way. While microbial production of phytochemicals needs to further increase product titer if it is ever to become a commercial success. The present review covers the advancements made for the improvement of microbial cell factories in order to increase the product titer of recombinant polyphenolic compounds.
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Affiliation(s)
- Sonam Chouhan
- Natural Product Laboratory, Division of Biochemistry, Faculty of Basic Sciences, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, India
| | - Kanika Sharma
- Natural Product Laboratory, Division of Biochemistry, Faculty of Basic Sciences, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, India
| | - Jian Zha
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - Sanjay Guleria
- Natural Product Laboratory, Division of Biochemistry, Faculty of Basic Sciences, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, India
| | - Mattheos A G Koffas
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States.,Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, United States
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12
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Winkler JD, Halweg-Edwards AL, Erickson KE, Choudhury A, Pines G, Gill RT. The Resistome: A Comprehensive Database of Escherichia coli Resistance Phenotypes. ACS Synth Biol 2016; 5:1566-1577. [PMID: 27438180 DOI: 10.1021/acssynbio.6b00150] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The microbial ability to resist stressful environmental conditions and chemical inhibitors is of great industrial and medical interest. Much of the data related to mutation-based stress resistance, however, is scattered through the academic literature, making it difficult to apply systematic analyses to this wealth of information. To address this issue, we introduce the Resistome database: a literature-curated collection of Escherichia coli genotypes-phenotypes containing over 5,000 mutants that resist hundreds of compounds and environmental conditions. We use the Resistome to understand our current state of knowledge regarding resistance and to detect potential synergy or antagonism between resistance phenotypes. Our data set represents one of the most comprehensive collections of genomic data related to resistance currently available. Future development will focus on the construction of a combined genomic-transcriptomic-proteomic framework for understanding E. coli's resistance biology. The Resistome can be downloaded at https://bitbucket.org/jdwinkler/resistome_release/overview .
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Affiliation(s)
- James D. Winkler
- Department
of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Andrea L. Halweg-Edwards
- Department
of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Keesha E. Erickson
- Department
of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Alaksh Choudhury
- Department
of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Gur Pines
- Department
of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80303, United States
| | - Ryan T. Gill
- Department
of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80303, United States
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13
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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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Sandoval NR, Papoutsakis ET. Engineering membrane and cell-wall programs for tolerance to toxic chemicals: Beyond solo genes. Curr Opin Microbiol 2016; 33:56-66. [PMID: 27376665 DOI: 10.1016/j.mib.2016.06.005] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 06/09/2016] [Accepted: 06/16/2016] [Indexed: 10/21/2022]
Abstract
Metabolite toxicity in microbes, particularly at the membrane, remains a bottleneck in the production of fuels and chemicals. Under chemical stress, native adaptation mechanisms combat hyper-fluidization by modifying the phospholipids in the membrane. Recent work in fluxomics reveals the mechanism of how membrane damage negatively affects energy metabolism while lipidomic and transcriptomic analyses show that strains evolved to be tolerant maintain membrane fluidity under stress through a variety of mechanisms such as incorporation of cyclopropanated fatty acids, trans-unsaturated fatty acids, and upregulation of cell wall biosynthesis genes. Engineered strains with modifications made in the biosynthesis of fatty acids, peptidoglycan, and lipopolysaccharide have shown increased tolerance to exogenous stress as well as increased production of desired metabolites of industrial importance. We review recent advances in elucidation of mechanisms or toxicity and tolerance as well as efforts to engineer the bacterial membrane and cell wall.
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Affiliation(s)
- Nicholas R Sandoval
- Department of Chemical and Biomolecular Engineering, Molecular Biotechnology Laboratory, Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA
| | - Eleftherios T Papoutsakis
- Department of Chemical and Biomolecular Engineering, Molecular Biotechnology Laboratory, Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA.
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15
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Wallace S, Balskus EP. Designer Micelles Accelerate Flux Through Engineered Metabolism in E. coli and Support Biocompatible Chemistry. Angew Chem Int Ed Engl 2016; 55:6023-7. [PMID: 27061024 PMCID: PMC4973394 DOI: 10.1002/anie.201600966] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 03/17/2016] [Indexed: 01/04/2023]
Abstract
Synthetic biology has enabled the production of many value-added chemicals via microbial fermentation. However, the problem of low product titers from recombinant pathways has limited the utility of this approach. Methods to increase metabolic flux are therefore critical to the success of metabolic engineering. Here we demonstrate that vitamin E-derived designer micelles, originally developed for use in synthetic chemistry, are biocompatible and accelerate flux through a styrene production pathway in Escherichia coli. We show that these micelles associate non-covalently with the bacterial outer-membrane and that this interaction increases membrane permeability. In addition, these micelles also accommodate both heterogeneous and organic-soluble transition metal catalysts and accelerate biocompatible cyclopropanation in vivo. Overall, this work demonstrates that these surfactants hold great promise for further application in the field of synthetic biotechnology, and for expanding the types of molecules that can be readily accessed from renewable resources via the combination of microbial fermentation and biocompatible chemistry.
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Affiliation(s)
- Stephen Wallace
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA.
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16
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Wallace S, Balskus EP. Designer Micelles Accelerate Flux Through Engineered Metabolism in
E. coli
and Support Biocompatible Chemistry. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201600966] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Stephen Wallace
- Department of Chemistry and Chemical Biology Harvard University 12 Oxford Street Cambridge MA 02138 USA
| | - Emily P. Balskus
- Department of Chemistry and Chemical Biology Harvard University 12 Oxford Street Cambridge MA 02138 USA
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17
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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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18
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Tomko TA, Dunlop MJ. Engineering improved bio-jet fuel tolerance in Escherichia coli using a transgenic library from the hydrocarbon-degrader Marinobacter aquaeolei. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:165. [PMID: 26448785 PMCID: PMC4596283 DOI: 10.1186/s13068-015-0347-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 09/22/2015] [Indexed: 06/05/2023]
Abstract
BACKGROUND Recent metabolic engineering efforts have generated microorganisms that can produce biofuels, including bio-jet fuels, however these fuels are often toxic to cells, limiting production yields. There are natural examples of microorganisms that have evolved mechanisms for tolerating hydrocarbon-rich environments, such as those that thrive near natural oil seeps and in oil-polluted waters. RESULTS Using genomic DNA from the hydrocarbon-degrading microbe Marinobacter aquaeolei, we constructed a transgenic library that we expressed in Escherichia coli. We exposed cells to inhibitory levels of pinene, a monoterpene that can serve as a jet fuel precursor with chemical properties similar to existing tactical fuels. Using a sequential strategy with a fosmid library followed by a plasmid library, we were able to isolate a region of DNA from the M. aquaeolei genome that conferred pinene tolerance when expressed in E. coli. We determined that a single gene, yceI, was responsible for the tolerance improvements. Overexpression of this gene placed no additional burden on the host. We also tested tolerance to other monoterpenes and showed that yceI selectively improves tolerance. CONCLUSIONS The genomes of hydrocarbon-tolerant microbes represent a rich resource for tolerance engineering. Using a transgenic library, we were able to identify a single gene that improves E. coli's tolerance to the bio-jet fuel precursor pinene.
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Affiliation(s)
- Timothy A. Tomko
- School of Engineering, University of Vermont, 33 Colchester Ave, Burlington, VT 05405 USA
| | - Mary J. Dunlop
- School of Engineering, University of Vermont, 33 Colchester Ave, Burlington, VT 05405 USA
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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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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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