1
|
Qiao J, Chen M, Zhong S, Tong H, Li F. Soil Humic Acid Stimulates Potentially Active Dissimilatory Arsenate-Reducing Bacteria in Flooded Paddy Soil as Revealed by Metagenomic Stable Isotope Probing. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:2303-2312. [PMID: 38263620 DOI: 10.1021/acs.est.3c07753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
Dissimilatory arsenate reduction contributes a large proportion of arsenic flux from flooded paddy soil, which is closely linked to soil organic carbon input and efflux. Humic acid (HA) represents a natural ingredient in soil and is shown to enhance microbial arsenate respiration to promote arsenic mobility. However, the community and function profiles of metabolically active arsenate-respiring bacteria and their interactions with HA in paddy soil remain unclear. To probe this linkage, we performed a genome-centric comparison of potentially active arsenate-respiring bacteria in anaerobic microcosms amended with 13C-lactate and HA by combining stable-isotope probing with genome-resolved metagenomics. Indeed, HA greatly accelerated the microbial reduction of arsenate to arsenite. Enrichment of bacteria that harbor arsenate-respiring reductase genes (arrA) in HA-enriched 13C-DNA was confirmed by metagenomic binning, which are affiliated with Firmicutes (mainly Desulfitobacterium, Bacillus, Brevibacillus, and Clostridia) and Acidobacteria. Characterization of reference extracellular electron transfer (EET)-related genes in these arrA-harboring bacteria supports the presence of EET-like genes, with partial electron-transport chain genes identified. This suggests that Gram-positive Firmicutes- and Acidobacteria-related members may harbor unspecified EET-associated genes involved in metal reduction. Our findings highlight the link between soil HA and potentially active arsenate-respiring bacteria, which can be considered when using HA for arsenic removal.
Collapse
Affiliation(s)
- Jiangtao Qiao
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou 510650, China
| | - Manjia Chen
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou 510650, China
| | - Songxiong Zhong
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou 510650, China
| | - Hui Tong
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou 510650, China
| | - Fangbai Li
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management, Institute of Eco-environmental and Soil Sciences, Guangdong Academy of Sciences, Guangzhou 510650, China
- National-Regional Joint Engineering Research Center for Soil Pollution Control and Remediation in South China, Guangzhou 510650, China
| |
Collapse
|
2
|
Sierra-Ibarra E, Vargas-Tah A, Moss-Acosta CL, Trujillo-Martínez B, Molina-Vázquez ER, Rosas-Aburto A, Valdivia-López Á, Hernández-Luna MG, Vivaldo-Lima E, Martínez A. Co-Fermentation of Glucose-Xylose Mixtures from Agroindustrial Residues by Ethanologenic Escherichia coli: A Study on the Lack of Carbon Catabolite Repression in Strain MS04. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27248941. [PMID: 36558077 PMCID: PMC9785048 DOI: 10.3390/molecules27248941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022]
Abstract
The production of biofuels, such as bioethanol from lignocellulosic biomass, is an important task within the sustainable energy concept. Understanding the metabolism of ethanologenic microorganisms for the consumption of sugar mixtures contained in lignocellulosic hydrolysates could allow the improvement of the fermentation process. In this study, the ethanologenic strain Escherichia coli MS04 was used to ferment hydrolysates from five different lignocellulosic agroindustrial wastes, which contained different glucose and xylose concentrations. The volumetric rates of glucose and xylose consumption and ethanol production depend on the initial concentration of glucose and xylose, concentrations of inhibitors, and the positive effect of acetate in the fermentation to ethanol. Ethanol yields above 80% and productivities up to 1.85 gEtOH/Lh were obtained. Furthermore, in all evaluations, a simultaneous co-consumption of glucose and xylose was observed. The effect of deleting the xyIR regulator was studied, concluding that it plays an important role in the metabolism of monosaccharides and in xylose consumption. Moreover, the importance of acetate was confirmed for the ethanologenic strain, showing the positive effect of acetate on the co-consumption rates of glucose and xylose in cultivation media and hydrolysates containing sugar mixtures.
Collapse
Affiliation(s)
- Estefanía Sierra-Ibarra
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de Mexico. Av. Universidad 2001, Col. Chamilpa, Cuernavaca 62210, Mexico
| | - Alejandra Vargas-Tah
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de Mexico. Av. Universidad 2001, Col. Chamilpa, Cuernavaca 62210, Mexico
| | - Cessna L. Moss-Acosta
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de Mexico. Av. Universidad 2001, Col. Chamilpa, Cuernavaca 62210, Mexico
| | - Berenice Trujillo-Martínez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de Mexico. Av. Universidad 2001, Col. Chamilpa, Cuernavaca 62210, Mexico
| | - Eliseo R. Molina-Vázquez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de Mexico. Av. Universidad 2001, Col. Chamilpa, Cuernavaca 62210, Mexico
| | - Alberto Rosas-Aburto
- Departamento de Ingeniería Química, Facultad de Química, Universidad Nacional Autónoma de Mexico, Ciudad de Mexico 04510, Mexico
| | - Ángeles Valdivia-López
- Departamento de Ingeniería Química, Facultad de Química, Universidad Nacional Autónoma de Mexico, Ciudad de Mexico 04510, Mexico
| | - Martín G. Hernández-Luna
- Departamento de Ingeniería Química, Facultad de Química, Universidad Nacional Autónoma de Mexico, Ciudad de Mexico 04510, Mexico
| | - Eduardo Vivaldo-Lima
- Departamento de Ingeniería Química, Facultad de Química, Universidad Nacional Autónoma de Mexico, Ciudad de Mexico 04510, Mexico
| | - Alfredo Martínez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de Mexico. Av. Universidad 2001, Col. Chamilpa, Cuernavaca 62210, Mexico
- Correspondence: ; Tel.: +52-7773291601
| |
Collapse
|
3
|
Galactitol Transport Factor GatA Relieves ATP Supply Restriction to Enhance Acid Tolerance of Escherichia coli in the Two-Stage Fermentation Production of D-Lactate. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8120665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Escherichia coli is a major contributor to the industrial production of organic acids, but its production capacity and cost are limited by its acid sensitivity. Enhancing acid resistance in E. coli is essential for improving cell performance and production value. Here, we propose a feasible strategy for improving cellular acid tolerance by reducing ATP supply restriction. Transcriptome assays of acid-tolerant evolved strains revealed that the galactitol phosphotransferase system transporter protein GatA is an acid-tolerance factor that assists E. coli in improving its resistance to a variety of organic acids. Enhanced GatA expression increased cell survival under conditions of lethal stress due to D-lactic acid, itaconic acid and succinic acid by 101.8-fold, 29.4-fold and 41.6-fold, respectively. In addition, fermentation patterns for aerobic growth and oxygen-limited production of D-lactic acid were identified, and suitable transition and induction stages were evaluated. GatA effectively compensated for the lack of cellular energy during oxygen limitation and enabled the D-lactic acid producing strain to exhibit more sustainable productivity in acidic fermentation environments with a 55.7% increase in D-lactic acid titer from 9.5 g·L−1 to 14.8 g·L−1 and reduced generation of by-product. Thus, this study developed a method to improve the acid resistance of E. coli cells by compensating for the energy gap without affecting normal cell metabolism while reducing the cost of organic acid production.
Collapse
|
4
|
Tan B, Zheng Y, Yan H, Liu Y, Li ZJ. Metabolic engineering of Halomonas bluephagenesis to metabolize xylose for poly-3-hydroxybutyrate production. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2022.108623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
5
|
Zhu X, Fan F, Qiu H, Shao M, Li D, Yu Y, Bi C, Zhang X. New xylose transporters support the simultaneous consumption of glucose and xylose in Escherichia coli. MLIFE 2022; 1:156-170. [PMID: 38817680 PMCID: PMC10989795 DOI: 10.1002/mlf2.12021] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 03/11/2022] [Accepted: 04/14/2022] [Indexed: 06/01/2024]
Abstract
Glucose and xylose are two major components of lignocellulose. Simultaneous consumption of glucose and xylose is critical for engineered microorganisms to produce fuels and chemicals from lignocellulosic biomass. Although many production limitations have been resolved, glucose-induced inhibition of xylose transport remains a challenge. In this study, a cell growth-based screening strategy was designed to identify xylose transporters uninhibited by glucose. The glucose pathway was genetically blocked in Escherichia coli so that glucose functions only as an inhibitor and cells need xylose as the carbon source for survival. Through adaptive evolution, omics analysis and reverse metabolic engineering, a new phosphoenolpyruvate: carbohydrate phosphotransferase system (PTS) galactitol transporter (GalABC, encoded by EcolC_1640, EcolC_1641, and EcolC_1642 genes) that is not inhibited by glucose was identified. Inactivation of adenylate cyclase led to increased expression of the EcolC_1642 gene, and a point mutation in gene EcolC_1642 (N13S) further enhanced xylose transport. During the second round of gene mining, AraE and a new ABC transporter (AraFGH) of xylose were identified. A point mutation in the transcription regulator araC (L156I) caused increased expression of araE and araFGH genes without arabinose induction, and a point mutation in araE (D223Y) further enhanced xylose transport. These newly identified xylose transporters can support the simultaneous consumption of glucose and xylose and have potential use in producing chemicals from lignocellulose.
Collapse
Affiliation(s)
- Xinna Zhu
- Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjinChina
- Key Laboratory of Systems Microbial BiotechnologyChinese Academy of SciencesTianjinChina
| | - Feiyu Fan
- Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjinChina
- Key Laboratory of Systems Microbial BiotechnologyChinese Academy of SciencesTianjinChina
| | - Huanna Qiu
- Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjinChina
- Key Laboratory of Systems Microbial BiotechnologyChinese Academy of SciencesTianjinChina
- College of BiotechnologyTianjin University of Sciences and TechnologyTianjinChina
| | - Mengyao Shao
- Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjinChina
- Key Laboratory of Systems Microbial BiotechnologyChinese Academy of SciencesTianjinChina
- College of BiotechnologyTianjin University of Sciences and TechnologyTianjinChina
| | - Di Li
- Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjinChina
- Key Laboratory of Systems Microbial BiotechnologyChinese Academy of SciencesTianjinChina
- College of BiotechnologyTianjin University of Sciences and TechnologyTianjinChina
| | - Yong Yu
- Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjinChina
- Key Laboratory of Systems Microbial BiotechnologyChinese Academy of SciencesTianjinChina
- University of Chinese Academy of SciencesBeijingChina
| | - Changhao Bi
- Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjinChina
- Key Laboratory of Systems Microbial BiotechnologyChinese Academy of SciencesTianjinChina
| | - Xueli Zhang
- Tianjin Institute of Industrial BiotechnologyChinese Academy of SciencesTianjinChina
- Key Laboratory of Systems Microbial BiotechnologyChinese Academy of SciencesTianjinChina
| |
Collapse
|
6
|
Heo JM, Kim HJ, Lee SJ. Efficient anaerobic consumption of D-xylose by E. coli BL21(DE3) via xylR adaptive mutation. BMC Microbiol 2021; 21:332. [PMID: 34872501 PMCID: PMC8647362 DOI: 10.1186/s12866-021-02395-9] [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: 03/30/2021] [Accepted: 11/22/2021] [Indexed: 11/20/2022] Open
Abstract
Background Microorganisms can prioritize the uptake of different sugars depending on their metabolic needs and preferences. When both D-glucose and D-xylose are present in growth media, E. coli cells typically consume D-glucose first and then D-xylose. Similarly, when E. coli BL21(DE3) is provided with both D-glucose and D-xylose under anaerobic conditions, glucose is consumed first, whereas D-xylose is consumed very slowly. Results When BL21(DE3) was adaptively evolved via subculture, the consumption rate of D-xylose increased gradually. Strains JH001 and JH019, whose D-xylose consumption rate was faster, were isolated after subculture. Genome analysis of the JH001 and JH019 strains revealed that C91A (Q31K) and C740T (A247V) missense mutations in the xylR gene (which encodes the XylR transcriptional activator), respectively, controlled the expression of the xyl operon. RT-qPCR analyses demonstrated that the XylR mutation caused a 10.9-fold and 3.5-fold increase in the expression of the xylA (xylose isomerase) and xylF (xylose transporter) genes, respectively, in the adaptively evolved JH001 and JH019 strains. A C91A adaptive mutation was introduced into a new BL21(DE3) background via single-base genome editing, resulting in immediate and efficient D-xylose consumption. Conclusions Anaerobically-adapted BL21(DE3) cells were obtained through short-term adaptive evolution and xylR mutations responsible for faster D-xylose consumption were identified, which may aid in the improvement of microbial fermentation technology. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02395-9.
Collapse
Affiliation(s)
- Jung Min Heo
- Department of Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Hyun Ju Kim
- Department of Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Sang Jun Lee
- Department of Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea.
| |
Collapse
|
7
|
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.
Collapse
|
8
|
Kim J, Hwang S, Lee SM. Metabolic engineering for the utilization of carbohydrate portions of lignocellulosic biomass. Metab Eng 2021; 71:2-12. [PMID: 34626808 DOI: 10.1016/j.ymben.2021.10.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/16/2021] [Accepted: 10/03/2021] [Indexed: 01/01/2023]
Abstract
The petrochemical industry has grown to meet the need for massive production of energy and commodities along with an explosive population growth; however, serious side effects such as greenhouse gas emissions and global warming have negatively impacted the environment. Lignocellulosic biomass with myriad quantities on Earth is an attractive resource for the production of carbon-neutral fuels and chemicals through environmentally friendly processes of microbial fermentation. This review discusses metabolic engineering efforts to achieve economically feasible industrial production of fuels and chemicals from microbial cell factories using the carbohydrate portion of lignocellulosic biomass as substrates. The combined knowledge of systems biology and metabolic engineering has been applied to construct robust platform microorganisms with maximum conversion of monomeric sugars, such as glucose and xylose, derived from lignocellulosic biomass. By comprehensively revisiting carbon conversion pathways, we provide a rationale for engineering strategies, as well as their features, feasibility, and recent representative studies. In addition, we briefly discuss how tools in systems biology can be applied in the field of metabolic engineering to accelerate the development of microbial cell factories that convert lignocellulosic biomass into carbon-neutral fuels and chemicals with economic feasibility.
Collapse
Affiliation(s)
- Jiwon Kim
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea; Department of Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Sungmin Hwang
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea
| | - Sun-Mi Lee
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea; Clean Energy and Chemical Engineering, University of Science and Technology, Daejeon, 34113, Republic of Korea; Green School (Graduate School of Energy and Environment), Korea University, Seoul, 02841, Republic of Korea.
| |
Collapse
|
9
|
Kurgan G, Onyeabor M, Holland SC, Taylor E, Schneider A, Kurgan L, Billings T, Wang X. Directed evolution of Zymomonas mobilis sugar facilitator Glf to overcome glucose inhibition. J Ind Microbiol Biotechnol 2021; 49:6371102. [PMID: 34529081 PMCID: PMC9118996 DOI: 10.1093/jimb/kuab066] [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: 06/22/2021] [Accepted: 09/04/2021] [Indexed: 12/01/2022]
Abstract
Cellular import of D-xylose, the second most abundant sugar in typical lignocellulosic biomass, has been evidenced to be an energy-depriving process in bacterial biocatalysts. The sugar facilitator of Zymomonas mobilis, Glf, is capable of importing xylose at high rates without extra energy input, but is inhibited by D-glucose (the primary biomass sugar), potentially limiting the utility of this transporter for fermentation of sugar mixtures derived from lignocellulose. In this work we developed an Escherichia coli platform strain deficient in glucose and xylose transport to facilitate directed evolution of Glf to overcome glucose inhibition. Using this platform, we isolated nine Glf variants created by both random and site-saturation mutagenesis with increased xylose utilization rates ranging from 4.8-fold to 13-fold relative to wild-type Glf when fermenting 100 g l–1 glucose–xylose mixtures. Diverse point mutations such as A165M and L445I were discovered leading to released glucose inhibition. Most of these mutations likely alter sugar coordinating pocket for the 6-hydroxymethyl group of D-glucose. These discovered glucose-resistant Glf variants can be potentially used as energy-conservative alternatives to the native sugar transport systems of bacterial biocatalysts for fermentation of lignocellulose-derived sugars.
Collapse
Affiliation(s)
- Gavin Kurgan
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Moses Onyeabor
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Steven C Holland
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Eric Taylor
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Aidan Schneider
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Logan Kurgan
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Tommy Billings
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Xuan Wang
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| |
Collapse
|
10
|
Bañares AB, Nisola GM, Valdehuesa KNG, Lee WK, Chung WJ. Engineering of xylose metabolism in Escherichia coli for the production of valuable compounds. Crit Rev Biotechnol 2021; 41:649-668. [PMID: 33563072 DOI: 10.1080/07388551.2021.1873243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The lignocellulosic sugar d-xylose has recently gained prominence as an inexpensive alternative substrate for the production of value-added compounds using genetically modified organisms. Among the prokaryotes, Escherichia coli has become the de facto host for the development of engineered microbial cell factories. The favored status of E. coli resulted from a century of scientific explorations leading to a deep understanding of its systems. However, there are limited literature reviews that discuss engineered E. coli as a platform for the conversion of d-xylose to any target compounds. Additionally, available critical review articles tend to focus on products rather than the host itself. This review aims to provide relevant and current information about significant advances in the metabolic engineering of d-xylose metabolism in E. coli. This focusses on unconventional and synthetic d-xylose metabolic pathways as several review articles have already discussed the engineering of native d-xylose metabolism. This paper, in particular, is essential to those who are working on engineering of d-xylose metabolism using E. coli as the host.
Collapse
Affiliation(s)
- Angelo B Bañares
- Environmental Waste Recycle Institute (EWRI), Department of Energy Science and Technology (DEST), Myongji University, Yongin, Gyeonggi, South Korea
| | - Grace M Nisola
- Environmental Waste Recycle Institute (EWRI), Department of Energy Science and Technology (DEST), Myongji University, Yongin, Gyeonggi, South Korea
| | - Kris N G Valdehuesa
- Environmental Waste Recycle Institute (EWRI), Department of Energy Science and Technology (DEST), Myongji University, Yongin, Gyeonggi, South Korea
| | - Won-Keun Lee
- Division of Bioscience and Bioinformatics, Myongji University, Yongin, Gyeonggi, South Korea
| | - Wook-Jin Chung
- Environmental Waste Recycle Institute (EWRI), Department of Energy Science and Technology (DEST), Myongji University, Yongin, Gyeonggi, South Korea
| |
Collapse
|
11
|
Nduko JM, Taguchi S. Microbial Production of Biodegradable Lactate-Based Polymers and Oligomeric Building Blocks From Renewable and Waste Resources. Front Bioeng Biotechnol 2021; 8:618077. [PMID: 33614605 PMCID: PMC7889595 DOI: 10.3389/fbioe.2020.618077] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/17/2020] [Indexed: 12/20/2022] Open
Abstract
Polyhydroxyalkanoates (PHAs) are naturally occurring biopolymers produced by microorganisms. PHAs have become attractive research biomaterials in the past few decades owing to their extensive potential industrial applications, especially as sustainable alternatives to the fossil fuel feedstock-derived products such as plastics. Among the biopolymers are the bioplastics and oligomers produced from the fermentation of renewable plant biomass. Bioplastics are intracellularly accumulated by microorganisms as carbon and energy reserves. The bioplastics, however, can also be produced through a biochemistry process that combines fermentative secretory production of monomers and/or oligomers and chemical synthesis to generate a repertoire of biopolymers. PHAs are particularly biodegradable and biocompatible, making them a part of today's commercial polymer industry. Their physicochemical properties that are similar to those of petrochemical-based plastics render them potential renewable plastic replacements. The design of efficient tractable processes using renewable biomass holds key to enhance their usage and adoption. In 2008, a lactate-polymerizing enzyme was developed to create new category of polyester, lactic acid (LA)-based polymer and related polymers. This review aims to introduce different strategies including metabolic and enzyme engineering to produce LA-based biopolymers and related oligomers that can act as precursors for catalytic synthesis of polylactic acid. As the cost of PHA production is prohibitive, the review emphasizes attempts to use the inexpensive plant biomass as substrates for LA-based polymer and oligomer production. Future prospects and challenges in LA-based polymer and oligomer production are also highlighted.
Collapse
Affiliation(s)
- John Masani Nduko
- Department of Dairy and Food Science and Technology, Faculty of Agriculture, Egerton University, Egerton, Kenya
| | - Seiichi Taguchi
- Department of Chemistry for Life Sciences and Agriculture, Faculty of Life Sciences and Agriculture, Tokyo University of Agriculture, Tokyo, Japan
| |
Collapse
|
12
|
Connolly JPR, Roe AJ, O'Boyle N. Prokaryotic life finds a way: insights from evolutionary experimentation in bacteria. Crit Rev Microbiol 2020; 47:126-140. [PMID: 33332206 DOI: 10.1080/1040841x.2020.1854172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
While evolution proceeds through the generation of random variant alleles, the application of selective pressures can select for subsets of mutations that confer fitness-improving physiological benefits. This, in essence, defines the process of adaptive evolution. The rapid replication rate of bacteria has allowed for the design of experiments to study these processes over a reasonable timeframe within a laboratory setting. This has been greatly assisted by advances in tractability of diverse microorganisms, next generation sequencing technologies and bioinformatic analysis pipelines. Examining the processes by which organisms adapt their genetic code to cope with sub-optimal growth conditions has yielded a wealth of molecular insight into diverse biological processes. Here we discuss how the study of adaptive evolutionary trajectories in bacteria has allowed for improved understanding of stress responses, revealed important insight into microbial physiology, allowed for the production of highly optimised strains for use in biotechnology and increased our knowledge of the role of genomic plasticity in chronic infections.
Collapse
Affiliation(s)
- James P R Connolly
- Newcastle University Biosciences Institute, Newcastle University, Newcastle-upon-Tyne, United Kingdom
| | - Andrew J Roe
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Nicky O'Boyle
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| |
Collapse
|
13
|
Sierra-Ibarra E, Leal-Reyes LJ, Huerta-Beristain G, Hernández-Orihuela AL, Gosset G, Martínez-Antonio A, Martinez A. Limited oxygen conditions as an approach to scale-up and improve D and L-lactic acid production in mineral media and avocado seed hydrolysates with metabolically engineered Escherichia coli. Bioprocess Biosyst Eng 2020; 44:379-389. [PMID: 33029675 DOI: 10.1007/s00449-020-02450-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 09/14/2020] [Indexed: 10/23/2022]
Abstract
The effectiveness of micro-aeration on lactate (LA) production by metabolically engineered Escherichia coli was evaluated in 1 L bioreactors containing mineral media and glucose (70 g/L). Volumetric oxygen transfer coefficients (kLa) between 12.6 and 28.7 h-1 increased the specific growth rate (µ) and volumetric productivity (QLA) by 300 and 400%, respectively, without a significant decrease in lactate yield (YLA), when compared with non-aerated fermentations. A kLa of 12.6 h-1 was successfully used as a criterion to scale-up the production of L and D-lactate from 1 to 11 and 130 L. Approximately constant QLA and YLA values were obtained throughout the fermentation scale-up process. Furthermore, a D-lactogenic fermentation was carried out in 1 L bioreactors using avocado seed hydrolysate as a culture medium under the same kLa value, displaying high QLA and YLA.
Collapse
Affiliation(s)
- Estefanía Sierra-Ibarra
- Departamento de Ingeniería Celular Y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México. Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos, 62210, México
| | - Laura J Leal-Reyes
- Departamento de Ingeniería Celular Y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México. Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos, 62210, México
| | - Gerardo Huerta-Beristain
- Departamento de Ingeniería Celular Y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México. Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos, 62210, México.,Facultad de Ciencias Quıímico Biológicas, Universidad Autónoma de Guerrero, Av. Lazaro Cardenas S/N. Cd. Universitaria, 39070, Chilpancingo, Guerrero, Mexico
| | - Ana L Hernández-Orihuela
- Departamento de Ingeniería Genética. Centro de Investigación Y de Estudios Avanzados del, Instituto Politécnico Nacional. Unidad Irapuato. Km. 9.6 Libramiento Norte Carretera Irapuato-León, Irapuato, C.P. 36821, Guanajuato, México
| | - Guillermo Gosset
- Departamento de Ingeniería Celular Y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México. Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos, 62210, México
| | - Agustino Martínez-Antonio
- Departamento de Ingeniería Genética. Centro de Investigación Y de Estudios Avanzados del, Instituto Politécnico Nacional. Unidad Irapuato. Km. 9.6 Libramiento Norte Carretera Irapuato-León, Irapuato, C.P. 36821, Guanajuato, México
| | - Alfredo Martinez
- Departamento de Ingeniería Celular Y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México. Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos, 62210, México.
| |
Collapse
|
14
|
Zhao Z, Xian M, Liu M, Zhao G. Biochemical routes for uptake and conversion of xylose by microorganisms. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:21. [PMID: 32021652 PMCID: PMC6995148 DOI: 10.1186/s13068-020-1662-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 01/21/2020] [Indexed: 05/23/2023]
Abstract
Xylose is a major component of lignocellulose and the second most abundant sugar present in nature. Efficient utilization of xylose is required for the development of economically viable processes to produce biofuels and chemicals from biomass. However, there are still some bottlenecks in the bioconversion of xylose, including the fact that some microorganisms cannot assimilate xylose naturally and that the uptake and metabolism of xylose are inhibited by glucose, which is usually present with xylose in lignocellulose hydrolysate. To overcome these issues, numerous efforts have been made to discover, characterize, and engineer the transporters and enzymes involved in xylose utilization to relieve glucose inhibition and to develop recombinant microorganisms to produce fuels and chemicals from xylose. Here we describe a recent advancement focusing on xylose-utilizing pathways, biosynthesis of chemicals from xylose, and engineering strategies used to improve the conversion efficiency of xylose.
Collapse
Affiliation(s)
- Zhe Zhao
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Mo Xian
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
| | - Min Liu
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
| | - Guang Zhao
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
| |
Collapse
|
15
|
Alva A, Sabido-Ramos A, Escalante A, Bolívar F. New insights into transport capability of sugars and its impact on growth from novel mutants of Escherichia coli. Appl Microbiol Biotechnol 2020; 104:1463-1479. [PMID: 31900563 DOI: 10.1007/s00253-019-10335-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 12/12/2019] [Accepted: 12/27/2019] [Indexed: 12/27/2022]
Abstract
The fast-growing capability of Escherichia coli strains used to produce industrially relevant metabolites relies on their capability to transport efficiently glucose or potential industrial feedstocks such as sucrose or xylose as carbon sources. E. coli imports extracellular glucose into the periplasmic space across the outer membrane porins: OmpC, OmpF, and LamB. As the internal membrane is an impermeable barrier for sugars, the cell employs several primary and secondary active transport systems, and the phosphoenolpyruvate (PEP)-sugar phosphotransferase (PTS) system for glucose transport. PTS:glucose is the preferred system by E. coli to transport and phosphorylate the periplasmic glucose; nevertheless, PTS imposes a strict metabolic control mechanism on the preferential consumption of glucose over other carbon sources in sugar mixtures such as glucose and xylose resulting from the hydrolysis of lignocellulosic biomass, by the carbon catabolite repression. In this contribution, we summarize the major sugar transport systems for glucose and disaccharide transport, the exhibited substrate plasticity, and their impact on the growth of E. coli, highlighting the relevance of PTS in the control of the expression of genes for the transport and catabolism of other sugars as xylose. We discuss the strategies developed by evolved mutants of E. coli during adaptive laboratory evolution experiments to overcome the nutritional stress condition imposed by inactivation of PTS as a strategy for the selection of fast-growing derivatives in glucose, xylose, or mixtures of glucose:xylose. This approach results in the recruitment of other primary and secondary active transporters, demonstrating relevant sugar plasticity in derivative-evolved mutants. Elucidation of the molecular and biochemical basis of sugar-transport substrate plasticity represents a consistent approach for sugar-transport system engineering for the design of efficient E. coli derivative strains with improved substrate assimilation for biotechnological purposes.
Collapse
Affiliation(s)
- Alma Alva
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Andrea Sabido-Ramos
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana-Unidad Cuajimalpa, Ciudad de México, México
| | - Adelfo Escalante
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México.
| | - Francisco Bolívar
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| |
Collapse
|
16
|
Cubas-Cano E, González-Fernández C, Tomás-Pejó E. Evolutionary engineering of Lactobacillus pentosus improves lactic acid productivity from xylose-rich media at low pH. BIORESOURCE TECHNOLOGY 2019; 288:121540. [PMID: 31174085 DOI: 10.1016/j.biortech.2019.121540] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/20/2019] [Accepted: 05/21/2019] [Indexed: 06/09/2023]
Abstract
Since xylose is the second most abundant sugar in lignocellulose, using microorganisms able to metabolize it into bio-based chemicals like lactic acid is an attractive approach. In this study, Lactobacillus pentosus CECT4023T was evolved to improve its xylose fermentation capacity even at acid pH by adaptive laboratory evolution in repeated anaerobic batch cultures at increasing xylose concentration. The resulting strain (named MAX2) presented between 1.5 and 2-fold more xylose consumption and lactic acid production than the parental strain in 20 g L-1 xylose defined media independently of the initial pH value. When the pH was controlled in bioreactor, lactic acid productivity at 16 h increased 1.4-fold when MAX2 was grown both in xylose defined media and in wheat straw hydrolysate. These results demonstrated the potential of this new strain to produce lactic acid from hemicellulosic substrates at low pH, reducing the need of using neutralizing agents in the process.
Collapse
Affiliation(s)
- Enrique Cubas-Cano
- IMDEA Energy Institute, Biotechnological Processes for Energy Production Unit, 28935 Móstoles, Spain.
| | | | - Elia Tomás-Pejó
- IMDEA Energy Institute, Biotechnological Processes for Energy Production Unit, 28935 Móstoles, Spain
| |
Collapse
|
17
|
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: 244] [Impact Index Per Article: 48.8] [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.
Collapse
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.
| |
Collapse
|
18
|
Production of d-Lactate from Avocado Seed Hydrolysates by Metabolically Engineered Escherichia coli JU15. FERMENTATION-BASEL 2019. [DOI: 10.3390/fermentation5010026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Agroindustry residues can be used to produce valuable chemicals such as lactic acid, which is a primary chemical platform with many industrial applications. Biotechnological processes are the main approach of lactic acid production; however, culture media has an important impact on their costs. As a result, researchers are exploring various methods of production that use residual or waste biomass as raw materials, most of which are rich in lignocellulose. Nevertheless, starch and micronutrients such as those contained in avocado seeds stand out as promising feedstock for the bioprocess as well. In this study, the lactogenic Escherichia coli strain JU15 was evaluated for producing d-lactate using an avocado seed hydrolysate medium in a controlled stirred-tank bioreactor. The highest lactic acid concentration achieved was 37.8 g L−1 using 120 g L−1 as the content of initial reducing sugars. The results showed that d-lactate can be produced from avocado seed, which hydrolysates to 0.52 g L−1 h−1 using the engineered E. coli JU15. This study may serve as a starting point to further develop bioprocesses for producing metabolites using avocado seed hydrolysates.
Collapse
|
19
|
Parra-Ramírez D, Martinez A, Cardona CA. Lactic acid production from glucose and xylose using the lactogenic Escherichia coli strain JU15: Experiments and techno-economic results. BIORESOURCE TECHNOLOGY 2019; 273:86-92. [PMID: 30415073 DOI: 10.1016/j.biortech.2018.10.061] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 10/20/2018] [Accepted: 10/23/2018] [Indexed: 06/09/2023]
Abstract
In this work, d-lactic acid production was evaluated from a simulated hydrolysate of corn stover (32 g/L xylose, 42 g/L glucose) with the metabolically engineered Escherichia coli strain JU15. Based on the experimental results, a technical and economic analysis of the entire process was performed using the Aspen Plus software. As a result, it was possible to show that the strain can efficiently produce lactic acid from both sugars, reaching a final concentration of 40 g/L and a yield of 0.6 g lactic acid/g sugars. The process is economically viable at higher scales of 1000 tons/day. The cost distribution is influenced by the scale of the process; on a larger scale, the cost of raw materials represents a higher percentage of total cost than it does on smaller scales. The use of a metabolically engineered strain allows a better use of the sugars obtained from agroindustrial residues.
Collapse
Affiliation(s)
- Daniela Parra-Ramírez
- Instituto de Biotecnología y Agroindustria, Departamento de Ingeniería Química, Universidad Nacional de Colombia, Km 07 vía al Magdalena, Manizales, Colombia
| | - Alfredo Martinez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Morelos 62210, Mexico
| | - Carlos Ariel Cardona
- Instituto de Biotecnología y Agroindustria, Departamento de Ingeniería Química, Universidad Nacional de Colombia, Km 07 vía al Magdalena, Manizales, Colombia.
| |
Collapse
|
20
|
Luna-Flores CH, Stowers CC, Cox BM, Nielsen LK, Marcellin E. Linking genotype and phenotype in an economically viable propionic acid biosynthesis process. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:224. [PMID: 30123322 PMCID: PMC6090647 DOI: 10.1186/s13068-018-1222-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 08/03/2018] [Indexed: 05/03/2023]
Abstract
BACKGROUND Propionic acid (PA) is used as a food preservative and increasingly, as a precursor for the synthesis of monomers. PA is produced mainly through hydrocarboxylation of ethylene, also known as the 'oxo-process'; however, Propionibacterium species are promising biological PA producers natively producing PA as their main fermentation product. However, for fermentation to be competitive, a PA yield of at least 0.6 g/g is required. RESULTS A new strain able to reach the required yield was obtained using genome shuffling. To gain insight into the changes leading to the improved phenotype, the genome of the new strain was sequenced, and metabolomics and transcriptomics data were obtained. In combination, the data revealed three key mutations: (i) a mutation in the promoter region of a sugar transporter which enables an increase in the uptake rate of sucrose; (ii) a mutation in a polar amino acid transporter which improves consumption of amino acids and acid tolerance; and (iii) a mutation in a gene annotated as a cytochrome C biogenesis gene, which is likely responsible for the coupling of the Wood-Werkman cycle to ATP production were responsible for the phenotype. The bioprocess was further enhanced with a feeding strategy that achieved 70 g/L of product. The proposed bioprocess is expected to outperform the economics of the current 'oxo-process' by 2020. CONCLUSIONS In this study, using genome shuffling, we obtained a strain capable of producing PA exceeding the commercial needs. The multiomics comparison between the novel strain and the wild type revealed overexpression of amino acid pathways, changes in sucrose transporters and an increased activity in the methylglyoxal and the glucuronate interconversion pathways. The analysis also suggests that a mutation in the cytochrome C biogenesis gene, coupled with ATP production through the Wood-Werkman cycle, may be responsible for the increased PA production.
Collapse
Affiliation(s)
- Carlos H. Luna-Flores
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072 Australia
| | - Chris C. Stowers
- BioEngineering and Bioprocessing R&D, Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN 46268 USA
| | - Brad M. Cox
- BioEngineering and Bioprocessing R&D, Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN 46268 USA
| | - Lars K. Nielsen
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072 Australia
- Queensland Node of Metabolomics Australia, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072 Australia
- Queensland Node of Metabolomics Australia, The University of Queensland, Brisbane, QLD 4072 Australia
| |
Collapse
|
21
|
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]
|
22
|
Lee SJ, Lee HS, Kim SY, Shin KS. Immunostimulatory and anti-metastatic activity of polysaccharides isolated from byproducts of the corn starch industry. Carbohydr Polym 2017; 181:911-917. [PMID: 29254053 PMCID: PMC7112432 DOI: 10.1016/j.carbpol.2017.11.060] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Revised: 11/15/2017] [Accepted: 11/16/2017] [Indexed: 10/25/2022]
Abstract
Corn steep liquor (CSL) is a major by-product of the corn steeping process that is utilized in the wet milling industry. To develop new physiologically active polysaccharides from CSL, polysaccharides were isolated and their innate immunostimulatory and anti-metastatic activities were investigated. Corn byproduct polysaccharides (CBP) were preferentially isolated from CSL and further separated into supernatant (CBP1S) and precipitate (CBP1P) fractions. The anti-complementary activity of CBP1S was more potent than CBP1P and CBP. In addition, CBP1S enhanced production of macrophage-stimulating cytokines (e.g., IL-6 and IL-12) and natural killer (NK) cell-activating substances (e.g., granzyme and interferon-γ). Further, CBP1S significantly inhibited lung metastasis at a dose of 1000μg per mouse in an experimental lung metastasis model. These results suggest that CBP1S seems to promote the inhibition of lung metastasis through a mechanism leading to stimulation of the innate immune system, and CBP1S could be used as immunostimulating agents and for industrial applications.
Collapse
Affiliation(s)
- Sue Jung Lee
- Department of Food Science and Biotechnology, Kyonggi University, San 94-6, Ieudong, Youngtong-gu, Suwon, Gyeonggi-do 443-760, Republic of Korea
| | - Ho Sung Lee
- Sandolfood, 1009-9, Seorak-ro, Sang-oan-ri, Hongcheon-eup, Hongcheon-gun, Gangwon-do, 25117, Republic of Korea
| | - Sun Young Kim
- Hongcheon Institute of Medicinal Herb, 84, Saengmyeonggwahakgwan-gil, Yeonbongri, Hongcheon-eup, Hongcheon-gun, Gangwon-do, 25142, Republic of Korea
| | - Kwang-Soon Shin
- Department of Food Science and Biotechnology, Kyonggi University, San 94-6, Ieudong, Youngtong-gu, Suwon, Gyeonggi-do 443-760, Republic of Korea.
| |
Collapse
|
23
|
Khunnonkwao P, Jantama SS, Kanchanatawee S, Jantama K. Re-engineering Escherichia coli KJ122 to enhance the utilization of xylose and xylose/glucose mixture for efficient succinate production in mineral salt medium. Appl Microbiol Biotechnol 2017; 102:127-141. [PMID: 29079860 DOI: 10.1007/s00253-017-8580-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 10/05/2017] [Accepted: 10/09/2017] [Indexed: 11/30/2022]
Abstract
Escherichia coli KJ122 was previously engineered to produce high concentration and yield of succinate in mineral salt medium containing glucose and sucrose under anaerobic conditions. However, this strain does not efficiently utilize xylose. To improve the xylose uptake and utilization in the strain KJ122, xylFGH and xylE genes were individually and simultaneously deleted. E. coli KJ12201 (KJ122::ΔxylFGH) exhibited superior abilities in growth, xylose consumption, and succinate production compared to those of the parental strain KJ122. However, E. coli KJ12202 (KJ122::ΔxylE) lessened xylose consumption due to an ATP deficit for metabolizing xylose thus making succinate production from xylose not preferable. Moreover, E. coli KJ12203 (KJ122::ΔxylFGHΔxylE) exhibited an impaired growth on xylose due to lacking of xylose transporters. After performing metabolic evolution, the evolved KJ12201-14T strain exhibited a great improvement in succinate production from pure xylose with higher concentration and productivity about 18 and 21%, respectively, compared to KJ12201 strain. During fed-batch fermentation, KJ12201-14T also produced succinate from xylose at a concentration, yield, and overall productivity of 84.6 ± 0.7 g/L, 0.86 ± 0.01 g/g and 1.01 ± 0.01 g/L/h, respectively. KJ12201 and KJ12201-14T strains co-utilized glucose/xylose mixture without catabolite repression. Both strains produced succinate from glucose/xylose mixture at concentration, yield, and overall and specific productivities of about 85 g/L, 0.85 g/g, 0.70 g/L/h, and 0.44 g/gCDW/h, respectively. Based on our results, KJ12201 and KJ12201-14T strains exhibited a greater performance in succinate production from xylose containing medium than those of other published works. They would be potential strains for the economic bio-based succinate production from xylose.
Collapse
Affiliation(s)
- Panwana Khunnonkwao
- Metabolic Engineering Research Unit, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, 111 University Avenue, Suranaree Sub-District, Muang District, Nakhon Ratchasima, 30000, Thailand
| | - Sirima Suvarnakuta Jantama
- Division of Biopharmacy, Faculty of Pharmaceutical Sciences, Ubon Ratchathani University, Warinchamrap, Ubon Ratchathani, 34190, Thailand
| | - Sunthorn Kanchanatawee
- Metabolic Engineering Research Unit, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, 111 University Avenue, Suranaree Sub-District, Muang District, Nakhon Ratchasima, 30000, Thailand
| | - Kaemwich Jantama
- Metabolic Engineering Research Unit, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, 111 University Avenue, Suranaree Sub-District, Muang District, Nakhon Ratchasima, 30000, Thailand.
| |
Collapse
|
24
|
Zhu M, Fan W, Cha Y, Yang X, Lai Z, Li S, Wang X. Dynamic cell responses in Thermoanaerobacterium sp. under hyperosmotic stress. Sci Rep 2017; 7:10088. [PMID: 28855699 PMCID: PMC5577258 DOI: 10.1038/s41598-017-10514-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 08/09/2017] [Indexed: 12/17/2022] Open
Abstract
As a nongenetic engineering technique, adaptive evolution is an effective and easy-to-operate approach to strain improvement. In this work, a commercial Thermoanaerobacterium aotearoense SCUT27/Δldh-G58 was successfully isolated via sequential batch fermentation with step-increased carbon concentrations. Mutants were isolated under selective high osmotic pressures for 58 passages. The evolved isolate rapidly catabolized sugars at high concentrations and subsequently produced ethanol with good yield. A 1.6-fold improvement of ethanol production was achieved in a medium containing 120 g/L of carbon substrate using the evolved strain, compared to the start strain. The analysis of transcriptome and intracellular solute pools suggested that the adaptive evolution altered the synthesis of some compatible solutes and activated the DNA repair system in the two Thermoanaerobacterium sp. evolved strains. Overall, the results indicated the potential of adaptive evolution as a simple and effective tool for the modification and optimization of industrial microorganisms.
Collapse
Affiliation(s)
- Muzi Zhu
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Wudi Fan
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Yaping Cha
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Xiaofeng Yang
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Zhicheng Lai
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Shuang Li
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China.
| | - Xiaoning Wang
- State Key Laboratory of Kidney, the Institute of Life Sciences, Chinese PLA General Hospital, Beijing, China
| |
Collapse
|
25
|
Experimental evolution reveals an effective avenue to release catabolite repression via mutations in XylR. Proc Natl Acad Sci U S A 2017; 114:7349-7354. [PMID: 28655843 DOI: 10.1073/pnas.1700345114] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Microbial production of fuels and chemicals from lignocellulosic biomass provides promising biorenewable alternatives to the conventional petroleum-based products. However, heterogeneous sugar composition of lignocellulosic biomass hinders efficient microbial conversion due to carbon catabolite repression. The most abundant sugar monomers in lignocellulosic biomass materials are glucose and xylose. Although industrial Escherichia coli strains efficiently use glucose, their ability to use xylose is often repressed in the presence of glucose. Here we independently evolved three E. coli strains from the same ancestor to achieve high efficiency for xylose fermentation. Each evolved strain has a point mutation in a transcriptional activator for xylose catabolic operons, either CRP or XylR, and these mutations are demonstrated to enhance xylose fermentation by allelic replacements. Identified XylR variants (R121C and P363S) have a higher affinity to their DNA binding sites, leading to a xylose catabolic activation independent of catabolite repression control. Upon introducing these amino acid substitutions into the E. coli D-lactate producer TG114, 94% of a glucose-xylose mixture (50 g⋅L-1 each) was used in mineral salt media that led to a 50% increase in product titer after 96 h of fermentation. The two amino acid substitutions in XylR enhance xylose utilization and release glucose-induced repression in different E. coli hosts, including wild type, suggesting its potential wide application in industrial E. coli biocatalysts.
Collapse
|
26
|
Li F, Li Y, Sun L, Li X, Yin C, An X, Chen X, Tian Y, Song H. Engineering Shewanella oneidensis enables xylose-fed microbial fuel cell. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:196. [PMID: 28804512 PMCID: PMC5549365 DOI: 10.1186/s13068-017-0881-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 08/01/2017] [Indexed: 05/22/2023]
Abstract
BACKGROUND The microbial fuel cell (MFC) is a green and sustainable technology for electricity energy harvest from biomass, in which exoelectrogens use metabolism and extracellular electron transfer pathways for the conversion of chemical energy into electricity. However, Shewanella oneidensis MR-1, one of the most well-known exoelectrogens, could not use xylose (a key pentose derived from hydrolysis of lignocellulosic biomass) for cell growth and power generation, which limited greatly its practical applications. RESULTS Herein, to enable S. oneidensis to directly utilize xylose as the sole carbon source for bioelectricity production in MFCs, we used synthetic biology strategies to successfully construct four genetically engineered S. oneidensis (namely XE, GE, XS, and GS) by assembling one of the xylose transporters (from Candida intermedia and Clostridium acetobutylicum) with one of intracellular xylose metabolic pathways (the isomerase pathway from Escherichia coli and the oxidoreductase pathway from Scheffersomyces stipites), respectively. We found that among these engineered S. oneidensis strains, the strain GS (i.e. harbouring Gxf1 gene encoding the xylose facilitator from C. intermedi, and XYL1, XYL2, and XKS1 genes encoding the xylose oxidoreductase pathway from S. stipites) was able to generate the highest power density, enabling a maximum electricity power density of 2.1 ± 0.1 mW/m2. CONCLUSION To the best of our knowledge, this was the first report on the rationally designed Shewanella that could use xylose as the sole carbon source and electron donor to produce electricity. The synthetic biology strategies developed in this study could be further extended to rationally engineer other exoelectrogens for lignocellulosic biomass utilization to generate electricity power.
Collapse
Affiliation(s)
- Feng Li
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering, Tianjin University, Tianjin, 300072 China
| | - Yuanxiu Li
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering, Tianjin University, Tianjin, 300072 China
| | - Liming Sun
- Petrochemical Research Institute, PetroChina Company Limited, Beijing, 102206 People’s Republic of China
| | - Xiaofei Li
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering, Tianjin University, Tianjin, 300072 China
| | - Changji Yin
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering, Tianjin University, Tianjin, 300072 China
| | - Xingjuan An
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering, Tianjin University, Tianjin, 300072 China
| | - Xiaoli Chen
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering, Tianjin University, Tianjin, 300072 China
| | - Yao Tian
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering, Tianjin University, Tianjin, 300072 China
| | - Hao Song
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering, Tianjin University, Tianjin, 300072 China
| |
Collapse
|
27
|
Morales-Sánchez D, Kyndt J, Ogden K, Martinez A. Toward an understanding of lipid and starch accumulation in microalgae: A proteomic study of Neochloris oleoabundans cultivated under N-limited heterotrophic conditions. ALGAL RES 2016. [DOI: 10.1016/j.algal.2016.09.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
28
|
Winkler JD, Halweg-Edwards AL, Gill RT. Quantifying complexity in metabolic engineering using the LASER database. Metab Eng Commun 2016; 3:227-233. [PMID: 29468127 PMCID: PMC5779719 DOI: 10.1016/j.meteno.2016.07.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 07/04/2016] [Indexed: 11/26/2022] Open
Abstract
We previously introduced the LASER database (Learning Assisted Strain EngineeRing, https://bitbucket.org/jdwinkler/laser_release) (Winkler et al. 2015) to serve as a platform for understanding past and present metabolic engineering practices. Over the past year, LASER has been expanded by 50% to include over 600 engineered strains from 450 papers, including their growth conditions, genetic modifications, and other information in an easily searchable format. Here, we present the results of our efforts to use LASER as a means for defining the complexity of a metabolic engineering "design". We evaluate two complexity metrics based on the concepts of construction difficulty and novelty. No correlation is observed between expected product yield and complexity, allowing minimization of complexity without a performance trade-off. We envision the use of such complexity metrics to filter and prioritize designs prior to implementation of metabolic engineering efforts, thereby potentially reducing the time, labor, and expenses of large-scale projects. Possible future developments based on an expanding LASER database are then discussed.
Collapse
Affiliation(s)
| | | | - Ryan T. Gill
- Department of Chemical and Biological Engineering, University of Colorado-Boulder, Jennie Smoly Caruthers Biotechnology Building, Research Park, Boulder, CO 80303, USA
| |
Collapse
|
29
|
Utrilla J, Vargas-Tah A, Trujillo-Martínez B, Gosset G, Martinez A. Production of d-lactate from sugarcane bagasse and corn stover hydrolysates using metabolic engineered Escherichia coli strains. BIORESOURCE TECHNOLOGY 2016; 220:208-214. [PMID: 27573474 DOI: 10.1016/j.biortech.2016.08.067] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 08/15/2016] [Accepted: 08/17/2016] [Indexed: 06/06/2023]
Abstract
In this study, the lactogenic Escherichia coli strain JU15 was used and modified to produce d-lactate (d-LA) from plant hydrolysates with a minimal nutrient addition in pH controlled fermenters. Results showed that strain JU15 produces d-LA with high yield and productivity in laboratory simulated hydrolysate media and actual sugar cane bagasse hemicellulosic hydrolysate. Strain JU15 showed sequential carbon source utilization and acetic acid production. The l-lactic and acetic acid production pathways were deleted in JU15, resulting strain AV03 (JU15 ΔpoxB, ΔackA-pta, ΔmgsA), which showed simultaneous consumption of glucose and xylose and no acetic acid production in the simulated hydrolysate. The d-LA yield from hydrolysate sugars was close to 0.95gD-LA/gsugars in all cases. Our results show that d-LA can be produced from plant hydrolysates in simple batch fermentation processes with a high productivity using engineered E. coli strains at fermenter scales from 0.2 up to 10L.
Collapse
Affiliation(s)
- José Utrilla
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apdo. Postal 510-3, Cuernavaca, Mor. 62250, Mexico
| | - Alejandra Vargas-Tah
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apdo. Postal 510-3, Cuernavaca, Mor. 62250, Mexico
| | - Berenice Trujillo-Martínez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apdo. Postal 510-3, Cuernavaca, Mor. 62250, Mexico
| | - Guillermo Gosset
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apdo. Postal 510-3, Cuernavaca, Mor. 62250, Mexico
| | - Alfredo Martinez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apdo. Postal 510-3, Cuernavaca, Mor. 62250, Mexico.
| |
Collapse
|
30
|
Gustavsson M, Lee SY. Prospects of microbial cell factories developed through systems metabolic engineering. Microb Biotechnol 2016; 9:610-7. [PMID: 27435545 PMCID: PMC4993179 DOI: 10.1111/1751-7915.12385] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Accepted: 06/21/2016] [Indexed: 11/27/2022] Open
Abstract
While academic‐level studies on metabolic engineering of microorganisms for production of chemicals and fuels are ever growing, a significantly lower number of such production processes have reached commercial‐scale. In this work, we review the challenges associated with moving from laboratory‐scale demonstration of microbial chemical or fuel production to actual commercialization, focusing on key requirements on the production organism that need to be considered during the metabolic engineering process. Metabolic engineering strategies should take into account techno‐economic factors such as the choice of feedstock, the product yield, productivity and titre, and the cost effectiveness of midstream and downstream processes. Also, it is important to develop an industrial strain through metabolic engineering for pathway construction and flux optimization together with increasing tolerance to products and inhibitors present in the feedstock, and ensuring genetic stability and strain robustness under actual fermentation conditions.
Collapse
Affiliation(s)
- Martin Gustavsson
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), BioProcess Engineering Research Center, Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Korea.,KTH Royal Institute of Technology, School of Biotechnology, Division of Industrial Biotechnology, AlbaNova University Center, 106 91, Stockholm, Sweden
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), BioProcess Engineering Research Center, Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Korea
| |
Collapse
|
31
|
Bioconversion of methane to lactate by an obligate methanotrophic bacterium. Sci Rep 2016; 6:21585. [PMID: 26902345 PMCID: PMC4763203 DOI: 10.1038/srep21585] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 01/25/2016] [Indexed: 01/21/2023] Open
Abstract
Methane is the second most abundant greenhouse gas (GHG), with nearly 60% of emissions derived from anthropogenic sources. Microbial conversion of methane to fuels and value-added chemicals offers a means to reduce GHG emissions, while also valorizing this otherwise squandered high-volume, high-energy gas. However, to date, advances in methane biocatalysis have been constrained by the low-productivity and limited genetic tractability of natural methane-consuming microbes. Here, leveraging recent identification of a novel, tractable methanotrophic bacterium, Methylomicrobium buryatense, we demonstrate microbial biocatalysis of methane to lactate, an industrial platform chemical. Heterologous overexpression of a Lactobacillus helveticus L-lactate dehydrogenase in M. buryatense resulted in an initial titer of 0.06 g lactate/L from methane. Cultivation in a 5 L continuously stirred tank bioreactor enabled production of 0.8 g lactate/L, representing a 13-fold improvement compared to the initial titer. The yields (0.05 g lactate/g methane) and productivity (0.008 g lactate/L/h) indicate the need and opportunity for future strain improvement. Additionally, real-time analysis of methane utilization implicated gas-to-liquid transfer and/or microbial methane consumption as process limitations. This work opens the door to develop an array of methanotrophic bacterial strain-engineering strategies currently employed for biocatalytic sugar upgrading to "green" chemicals and fuels.
Collapse
|
32
|
Systems strategies for developing industrial microbial strains. Nat Biotechnol 2015; 33:1061-72. [DOI: 10.1038/nbt.3365] [Citation(s) in RCA: 357] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 08/23/2015] [Indexed: 12/11/2022]
|
33
|
Sawisit A, Jantama K, Zheng H, Yomano LP, York SW, Shanmugam KT, Ingram LO. Mutation in galP improved fermentation of mixed sugars to succinate using engineered Escherichia coli AS1600a and AM1 mineral salts medium. BIORESOURCE TECHNOLOGY 2015; 193:433-441. [PMID: 26159300 DOI: 10.1016/j.biortech.2015.06.108] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Revised: 06/18/2015] [Accepted: 06/19/2015] [Indexed: 06/04/2023]
Abstract
Escherichia coli KJ122 was engineered to produce succinate from glucose using the wild type GalP for glucose uptake instead of the native phosphotransferase system (ptsI mutation). This strain now ferments 10% xylose poorly. Mutants were selected by serial transfers in AM1 mineral salts medium with 10% xylose. Clones from this population all exhibited a similar improvement, co-fermentation of an equal mixture of xylose and glucose. One of these, AS1600a, produced 84.26 ± 1.37 g/L succinate, equivalent to that produced by the parent (KJ122) from 10% glucose (85.46 ± 1.78 g/L). AS1600a was sequenced and found to contain a mutation in galactose permease (GalP, G236D). This mutation was shown to be responsible for the improvement in fermentation using KJΔgalP as the host and expression vectors with native galP and with mutant galP(∗). Strain AS1600a and KJΔgalP(pLOI5746; galP(∗)) also co-fermented a mixture of glucose, xylose, arabinose, and galactose in sugarcane bagasse hydrolysate using mineral salts medium.
Collapse
Affiliation(s)
- Apichai Sawisit
- Metabolic Engineering Research Unit, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Kaemwich Jantama
- Metabolic Engineering Research Unit, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Huabao Zheng
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Lorraine P Yomano
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Sean W York
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Keelnatham T Shanmugam
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Lonnie O Ingram
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA.
| |
Collapse
|
34
|
Kim SM, Choi BY, Ryu YS, Jung SH, Park JM, Kim GH, Lee SK. Simultaneous utilization of glucose and xylose via novel mechanisms in engineered Escherichia coli. Metab Eng 2015; 30:141-148. [DOI: 10.1016/j.ymben.2015.05.002] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 05/20/2015] [Accepted: 05/21/2015] [Indexed: 11/29/2022]
|
35
|
Liu P, Zhu X, Tan Z, Zhang X, Ma Y. Construction of Escherichia Coli Cell Factories for Production of Organic Acids and Alcohols. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2015; 155:107-40. [PMID: 25577396 DOI: 10.1007/10_2014_294] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Production of bulk chemicals from renewable biomass has been proved to be sustainable and environmentally friendly. Escherichia coli is the most commonly used host strain for constructing cell factories for production of bulk chemicals since it has clear physiological and genetic characteristics, grows fast in minimal salts medium, uses a wide range of substrates, and can be genetically modified easily. With the development of metabolic engineering, systems biology, and synthetic biology, a technology platform has been established to construct E. coli cell factories for bulk chemicals production. In this chapter, we will introduce this technology platform, as well as E. coli cell factories successfully constructed for production of organic acids and alcohols.
Collapse
Affiliation(s)
- Pingping Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Xinna Zhu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Zaigao Tan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Area, Tianjin, 300308, China.,University of Chinese Academy of Sciences, Tianjin, China
| | - Xueli Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China. .,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Area, Tianjin, 300308, China.
| | - Yanhe Ma
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| |
Collapse
|
36
|
Inverse metabolic engineering of Bacillus subtilis for xylose utilization based on adaptive evolution and whole-genome sequencing. Appl Microbiol Biotechnol 2014; 99:885-96. [DOI: 10.1007/s00253-014-6131-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 08/23/2014] [Accepted: 09/29/2014] [Indexed: 10/24/2022]
|
37
|
Arifin Y, Archer C, Lim S, Quek LE, Sugiarto H, Marcellin E, Vickers CE, Krömer JO, Nielsen LK. Escherichia coli W shows fast, highly oxidative sucrose metabolism and low acetate formation. Appl Microbiol Biotechnol 2014; 98:9033-44. [DOI: 10.1007/s00253-014-5956-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2014] [Revised: 07/07/2014] [Accepted: 07/08/2014] [Indexed: 10/24/2022]
|
38
|
Muñoz-Gutiérrez I, Moss-Acosta C, Trujillo-Martinez B, Gosset G, Martinez A. Ag43-mediated display of a thermostable β-glucosidase in Escherichia coli and its use for simultaneous saccharification and fermentation at high temperatures. Microb Cell Fact 2014; 13:106. [PMID: 25078445 PMCID: PMC4347601 DOI: 10.1186/s12934-014-0106-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 07/14/2014] [Indexed: 11/26/2022] Open
Abstract
Background The autotransporter (AT) system can potentially be used in the secretion of saccharolytic enzymes for the production of lignocellulosic biofuels and chemicals using Escherichia coli. Although ATs share similar structural characteristics, their capacity for secreting heterologous proteins widely varies. Additionally, the saccharolytic enzyme selected to be secreted should match the cell growth or cell fermentation conditions of E. coli. Results In the search for an AT that suits the physiological performance of the homo-ethanologenic E. coli strain MS04, an expression plasmid based on the AT antigen 43 (Ag43) from E. coli was developed. The β-glucosidase BglC from the thermophile bacterium Thermobifida fusca was displayed on the outer membrane of the E. coli strain MS04 using the Ag43 system (MS04/pAg43BglC). This strain was used to hydrolyze and ferment 40 g/L of cellobiose in mineral media to produce 16.65 g/L of ethanol in 48 h at a yield of 81% of the theoretical maximum. Knowing that BglC shows its highest activity at 50°C and retains more than 70% of its activity at pH 6, therefore E. coli MS04/pAg43BglC was used to ferment crystalline cellulose (Avicel) in a simultaneous saccharification and fermentation (SSF) process using a commercial cocktail of cellulases (endo and exo) at pH 6 and at a relatively high temperature for E. coli (45°C). As much as 22 g/L of ethanol was produced in 48 h. Conclusions The Ag43-BglC system can be used in E. coli strains without commercial β-glucosidases, reducing the quantities of commercial enzymes needed for the SSF process. Furthermore, the present work shows that E. coli cells are able to ferment sugars at 45°C during the SSF process using 40 g/L of Avicel, reducing the gap between the working conditions of the commercial saccharolytic enzymes and ethanologenic E. coli.
Collapse
Affiliation(s)
- Iván Muñoz-Gutiérrez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, A. P. 510-3, 62250, Cuernavaca, Mor, México. .,Present address: Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
| | - Cessna Moss-Acosta
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, A. P. 510-3, 62250, Cuernavaca, Mor, México.
| | - Berenice Trujillo-Martinez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, A. P. 510-3, 62250, Cuernavaca, Mor, México.
| | - Guillermo Gosset
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, A. P. 510-3, 62250, Cuernavaca, Mor, México.
| | - Alfredo Martinez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, A. P. 510-3, 62250, Cuernavaca, Mor, México.
| |
Collapse
|
39
|
Nduko JM, Matsumoto K, Ooi T, Taguchi S. Enhanced production of poly(lactate-co-3-hydroxybutyrate) from xylose in engineered Escherichia coli overexpressing a galactitol transporter. Appl Microbiol Biotechnol 2013; 98:2453-60. [PMID: 24337250 DOI: 10.1007/s00253-013-5401-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Revised: 11/11/2013] [Accepted: 11/11/2013] [Indexed: 10/25/2022]
Abstract
Poly(lactate-co-3-hydroxybutyrate) (P(LA-co-3HB)) was previously produced from xylose in engineered Escherichia coli. The aim of this study was to increase the polymer productivity and LA fraction in P(LA-co-3HB) using two metabolic engineering approaches: (1) deletions of competing pathways to lactate production and (2) overexpression of a galactitol transporter (GatC), which contributes to the ATP-independent xylose uptake. Engineered E. coli mutants (ΔpflA, Δpta, ΔackA, ΔpoxB, Δdld, and a dual mutant; ΔpflA + Δdld) and their parent strain, BW25113, were grown on 20 g l(-1) xylose for P(LA-co-3HB) production. The single deletions of ΔpflA, Δpta, and Δdld increased the LA fraction (58-66 mol%) compared to BW25113 (56 mol%). In particular, the ΔpflA + Δdld strain produced P(LA-co-3HB) containing 73 mol% LA. Furthermore, GatC overexpression increased both polymer yields and LA fractions in ΔpflA, Δpta, and Δdld mutants, and BW25113. The ΔpflA + gatC strain achieved a productivity of 8.3 g l(-1), which was 72 % of the theoretical maximum yield. Thus, to eliminate limitation of the carbon source, higher concentration of xylose was fed. As a result, BW25113 harboring gatC grown on 40 g l(-1) xylose reached the highest P(LA-co-3HB) productivity of 14.4 g l(-1). On the other hand, the ΔpflA + Δdld strain grown on 30 g l(-1) xylose synthesized 6.4 g l(-1) P(LA-co-3HB) while maintaining the highest LA fraction (73 mol%). The results indicated the usefulness of GatC for enhanced production of P(LA-co-3HB) from xylose, and the gene deletions to upregulate the LA fraction in P(LA-co-3HB). The polymers obtained had weight-averaged molecular weights in the range of 34,000-114,000.
Collapse
Affiliation(s)
- John Masani Nduko
- Division of Biotechnology and Macromolecular Chemistry, Graduate School of Engineering, Hokkaido University, N13-W8, Kita-ku, Sapporo, 060-8628, Japan
| | | | | | | |
Collapse
|
40
|
Hwang KS, Kim HU, Charusanti P, Palsson BØ, Lee SY. Systems biology and biotechnology of Streptomyces species for the production of secondary metabolites. Biotechnol Adv 2013; 32:255-68. [PMID: 24189093 DOI: 10.1016/j.biotechadv.2013.10.008] [Citation(s) in RCA: 138] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 10/20/2013] [Accepted: 10/25/2013] [Indexed: 11/29/2022]
Abstract
Streptomyces species continue to attract attention as a source of novel medicinal compounds. Despite a long history of studies on these microorganisms, they still have many biochemical mysteries to be elucidated. Investigations of novel secondary metabolites and their biosynthetic gene clusters have been more systematized with high-throughput techniques through inspections of correlations among components of the primary and secondary metabolisms at the genome scale. Moreover, up-to-date information on the genome of Streptomyces species with emphasis on their secondary metabolism has been collected in the form of databases and knowledgebases, providing predictive information and enabling one to explore experimentally unrecognized biological spaces of secondary metabolism. Herein, we review recent trends in the systems biology and biotechnology of Streptomyces species.
Collapse
Affiliation(s)
- Kyu-Sang Hwang
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 program), and Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea
| | - Hyun Uk Kim
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark; Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 program), and Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea
| | - Pep Charusanti
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Bernhard Ø Palsson
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Sang Yup Lee
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark; Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 program), and Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 305-701, Republic of Korea.
| |
Collapse
|
41
|
Wang Y, Li K, Huang F, Wang J, Zhao J, Zhao X, Garza E, Manow R, Grayburn S, Zhou S. Engineering and adaptive evolution of Escherichia coli W for L-lactic acid fermentation from molasses and corn steep liquor without additional nutrients. BIORESOURCE TECHNOLOGY 2013; 148:394-400. [PMID: 24063823 DOI: 10.1016/j.biortech.2013.08.114] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 08/16/2013] [Accepted: 08/19/2013] [Indexed: 06/02/2023]
Abstract
The D-lactic acid producing strain, Escherichia coli HBUT-D, was reengineered for L(+)-lactic acid fermentation by replacing the D-lactate dehydrogenase gene (ldhA) with an L(+)-lactate dehydrogenase gene (ldhL) from Pedicoccus acidilactici, followed by adaptive evolution in sucrose. The resulting strain, WYZ-L, has enhanced expression of the sucrose operon (cscA and cscKB). In 100 g L(-1) of sucrose fermentation using mineral salt medium, WYZ-L produced 97 g L(-1) of l(+)-lactic acid, with a yield of 90%, a maximum productivity of 3.17 g L(-1)h(-1) and an optical purity of greater than 99%. In fermentations using sugarcane molasses and corn steep liquor without additional nutrients, WYZ-L produced 75 g L(-1) of l(+)-lactic acid, with a yield of 85%, a maximum productivity of 1.18 g L(-1)h(-1), and greater than 99% optical purity. These results demonstrated that WYZ-L has the potential to use waste molasses and corn steep liquor as a resource for L(+)-lactic acid fermentation.
Collapse
Affiliation(s)
- Yongze Wang
- Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Key Laboratory of Fermentation Engineering, Ministry of Education, College of Bioengineering, Hubei University of Technology, Wuhan 430068, PR China
| | | | | | | | | | | | | | | | | | | |
Collapse
|
42
|
Polysaccharide hydrolysis with engineered Escherichia coli for the production of biocommodities. ACTA ACUST UNITED AC 2013; 40:401-10. [DOI: 10.1007/s10295-013-1245-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2012] [Accepted: 02/13/2013] [Indexed: 02/06/2023]
Abstract
Abstract
Escherichia coli can ferment a broad range of sugars, including pentoses, hexoses, uronic acids, and polyols. These features make E. coli a suitable microorganism for the development of biocatalysts to be used in the production of biocommodities and biofuels by metabolic engineering. E. coli cannot directly ferment polysaccharides because it does not produce and secrete the necessary saccharolytic enzymes; however, there are many genetic tools that can be used to confer this ability on this prokaryote. The construction of saccharolytic E. coli strains will reduce costs and simplify the production process because the saccharification and fermentation can be conducted in a single reactor with a reduced concentration or absence of additional external saccharolytic enzymes. Recent advances in metabolic engineering, surface display, and excretion of hydrolytic enzymes provide a framework for developing E. coli strains for the so-called consolidated bioprocessing. This review presents the different strategies toward the development of E. coli strains that have the ability to display and secrete saccharolytic enzymes to hydrolyze different sugar-polymeric substrates and reduce the loading of saccharolytic enzymes.
Collapse
|
43
|
Genome-wide analysis of redox reactions reveals metabolic engineering targets for D-lactate overproduction in Escherichia coli. Metab Eng 2013; 18:44-52. [PMID: 23563322 DOI: 10.1016/j.ymben.2013.03.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Revised: 02/11/2013] [Accepted: 03/12/2013] [Indexed: 11/21/2022]
Abstract
Most current metabolic engineering applications rely on the inactivation of unwanted reactions and the amplification of product-oriented reactions. All of the biochemical reactions involved with cellular metabolism are tightly coordinated with the electron flow, which depends on the cellular energy status. Thus, the cellular metabolic flux can be controlled either by modulation of the electron flow or the regulation of redox reactions. This study analyzed the genome-wide anaerobic fermentation products of 472 Escherichia coli single gene knockouts, which comprised mainly of dehydrogenases, oxidoreductases, and redox-related proteins. Many metabolic pathways that were located far from anaerobic mixed-acid fermentation significantly affected the profiles of lactic acid, succinic acid, acetic acid, formic acid, and ethanol. Unexpectedly, D-lactate overproduction was determined by a single gene deletion in dehydrogenases (e.g., guaB, pyrD, and serA) involved with nucleotide and amino acid metabolism. Furthermore, the combined knockouts of guaB, pyrD, serA, fnr, arcA, or arcB genes, which are involved with anaerobic transcription regulation, enhanced D-lactate overproduction. These results suggest that the anaerobic fermentation profiles of E. coli can be tuned via the disruption of peripheral dehydrogenases in anaerobic conditions.
Collapse
|
44
|
Skretas G, Kolisis FN. Combinatorial approaches for inverse metabolic engineering applications. Comput Struct Biotechnol J 2013; 3:e201210021. [PMID: 24688681 PMCID: PMC3962077 DOI: 10.5936/csbj.201210021] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Revised: 02/11/2013] [Accepted: 02/17/2013] [Indexed: 11/22/2022] Open
Abstract
Traditional metabolic engineering analyzes biosynthetic and physiological pathways, identifies bottlenecks, and makes targeted genetic modifications with the ultimate goal of increasing the production of high-value products in living cells. Such efforts have led to the development of a variety of organisms with industrially relevant properties. However, there are a number of cellular phenotypes important for research and the industry for which the rational selection of cellular targets for modification is not easy or possible. In these cases, strain engineering can be alternatively carried out using “inverse metabolic engineering”, an approach that first generates genetic diversity by subjecting a population of cells to a particular mutagenic process, and then utilizes genetic screens or selections to identify the clones exhibiting the desired phenotype. Given the availability of an appropriate screen for a particular property, the success of inverse metabolic engineering efforts usually depends on the level and quality of genetic diversity which can be generated. Here, we review classic and recently developed combinatorial approaches for creating such genetic diversity and discuss the use of these methodologies in inverse metabolic engineering applications.
Collapse
Affiliation(s)
- Georgios Skretas
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Fragiskos N Kolisis
- Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens - Zografou Campus, Athens, Greece
| |
Collapse
|
45
|
Liu P, Jarboe LR. Metabolic engineering of biocatalysts for carboxylic acids production. Comput Struct Biotechnol J 2012; 3:e201210011. [PMID: 24688671 PMCID: PMC3962109 DOI: 10.5936/csbj.201210011] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 10/24/2012] [Accepted: 10/29/2012] [Indexed: 11/22/2022] Open
Abstract
Fermentation of renewable feedstocks by microbes to produce sustainable fuels and chemicals has the potential to replace petrochemical-based production. For example, carboxylic acids produced by microbial fermentation can be used to generate primary building blocks of industrial chemicals by either enzymatic or chemical catalysis. In order to achieve the titer, yield and productivity values required for economically viable processes, the carboxylic acid-producing microbes need to be robust and well-performing. Traditional strain development methods based on mutagenesis have proven useful in the selection of desirable microbial behavior, such as robustness and carboxylic acid production. On the other hand, rationally-based metabolic engineering, like genetic manipulation for pathway design, has becoming increasingly important to this field and has been used for the production of several organic acids, such as succinic acid, malic acid and lactic acid. This review investigates recent works on Saccharomyces cerevisiae and Escherichia coli, as well as the strategies to improve tolerance towards these chemicals.
Collapse
Affiliation(s)
- Ping Liu
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, USA
| | - Laura R. Jarboe
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, USA
| |
Collapse
|