1
|
Nurwono G, O'Keeffe S, Liu N, Park JO. Sustainable metabolic engineering requires a perfect trifecta. Curr Opin Biotechnol 2023; 83:102983. [PMID: 37573625 PMCID: PMC10960266 DOI: 10.1016/j.copbio.2023.102983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 07/10/2023] [Accepted: 07/15/2023] [Indexed: 08/15/2023]
Abstract
The versatility of cellular metabolism in converting various substrates to products inspires sustainable alternatives to conventional chemical processes. Metabolism can be engineered to maximize the yield, rate, and titer of product generation. However, the numerous combinations of substrate, product, and organism make metabolic engineering projects difficult to navigate. A perfect trifecta of substrate, product, and organism is prerequisite for an environmentally and economically sustainable metabolic engineering endeavor. As a step toward this endeavor, we propose a reverse engineering strategy that starts with product selection, followed by substrate and organism pairing. While a large bioproduct space has been explored, the top-ten compounds have been synthesized mainly using glucose and model organisms. Unconventional feedstocks (e.g. hemicellulosic sugars and CO2) and non-model organisms are increasingly gaining traction for advanced bioproduct synthesis due to their specialized metabolic modes. Judicious selection of the substrate-organism-product combination will illuminate the untapped territory of sustainable metabolic engineering.
Collapse
Affiliation(s)
| | - Samantha O'Keeffe
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA
| | - Nian Liu
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA.
| | - Junyoung O Park
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA.
| |
Collapse
|
2
|
Bhalla A, Arce J, Ubanwa B, Singh G, Sani RK, Balan V. Thermophilic Geobacillus WSUCF1 Secretome for Saccharification of Ammonia Fiber Expansion and Extractive Ammonia Pretreated Corn Stover. Front Microbiol 2022; 13:844287. [PMID: 35694290 PMCID: PMC9176393 DOI: 10.3389/fmicb.2022.844287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 03/18/2022] [Indexed: 11/13/2022] Open
Abstract
A thermophilic Geobacillus bacterial strain, WSUCF1 contains different carbohydrate-active enzymes (CAZymes) capable of hydrolyzing hemicellulose in lignocellulosic biomass. We used proteomic, genomic, and bioinformatic tools, and genomic data to analyze the relative abundance of cellulolytic, hemicellulolytic, and lignin modifying enzymes present in the secretomes. Results showed that CAZyme profiles of secretomes varied based on the substrate type and complexity, composition, and pretreatment conditions. The enzyme activity of secretomes also changed depending on the substrate used. The secretomes were used in combination with commercial and purified enzymes to carry out saccharification of ammonia fiber expansion (AFEX)-pretreated corn stover and extractive ammonia (EA)-pretreated corn stover. When WSUCF1 bacterial secretome produced at different conditions was combined with a small percentage of commercial enzymes, we observed efficient saccharification of EA-CS, and the results were comparable to using a commercial enzyme cocktail (87% glucan and 70% xylan conversion). It also opens the possibility of producing CAZymes in a biorefinery using inexpensive substrates, such as AFEX-pretreated corn stover and Avicel, and eliminates expensive enzyme processing steps that are used in enzyme manufacturing. Implementing in-house enzyme production is expected to significantly reduce the cost of enzymes and biofuel processing cost.
Collapse
Affiliation(s)
- Aditya Bhalla
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, United States
- Department of Chemistry, Biology and Health Science, South Dakota School of Mines and Technology, Rapid City, SD, United States
- Great Lakes Bioenergy Center, Michigan State University, East Lansing, MI, United States
| | - Jessie Arce
- Department of Engineering Technology, College of Technology, University of Houston, Houston, TX, United States
| | - Bryan Ubanwa
- Department of Engineering Technology, College of Technology, University of Houston, Houston, TX, United States
| | - Gursharan Singh
- Department of Medical Laboratory Sciences, Lovely Professional University, Phagwara, India
| | - Rajesh K. Sani
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD, United States
- Department of Chemistry, Biology and Health Science, South Dakota School of Mines and Technology, Rapid City, SD, United States
| | - Venkatesh Balan
- Great Lakes Bioenergy Center, Michigan State University, East Lansing, MI, United States
- Department of Engineering Technology, College of Technology, University of Houston, Houston, TX, United States
- *Correspondence: Venkatesh Balan,
| |
Collapse
|
3
|
Yu L, Wu F, Chen G. Next‐Generation Industrial Biotechnology‐Transforming the Current Industrial Biotechnology into Competitive Processes. Biotechnol J 2019; 14:e1800437. [DOI: 10.1002/biot.201800437] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Revised: 02/01/2019] [Indexed: 01/16/2023]
Affiliation(s)
- Lin‐Ping Yu
- Ministry of Education Key Laboratory for Bioinformatics, School of Life SciencesTsinghua University New Biology Building 100084 Beijing China
- Center for Synthetic and Systems BiologyTsinghua University New Biology Building 100084 Beijing China
- Tsinghua‐Peking Center for Life SciencesTsinghua University New Biology Building 100084 Beijing China
| | - Fu‐Qing Wu
- Ministry of Education Key Laboratory for Bioinformatics, School of Life SciencesTsinghua University New Biology Building 100084 Beijing China
- Center for Synthetic and Systems BiologyTsinghua University New Biology Building 100084 Beijing China
- Tsinghua‐Peking Center for Life SciencesTsinghua University New Biology Building 100084 Beijing China
| | - Guo‐Qiang Chen
- Ministry of Education Key Laboratory for Bioinformatics, School of Life SciencesTsinghua University New Biology Building 100084 Beijing China
- Center for Synthetic and Systems BiologyTsinghua University New Biology Building 100084 Beijing China
- Tsinghua‐Peking Center for Life SciencesTsinghua University New Biology Building 100084 Beijing China
- Manchester Institute of Biotechnology, Centre for Synthetic BiologyThe University of Manchester 131 Princess Street Manchester M1 7DN UK
| |
Collapse
|
4
|
Homoethanol Production from Glycerol and Gluconate Using Recombinant Klebsiella oxytoca Strains. Appl Environ Microbiol 2019; 85:AEM.02122-18. [PMID: 30578264 DOI: 10.1128/aem.02122-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 11/30/2018] [Indexed: 11/20/2022] Open
Abstract
Gluconic acid, an oxidized cellulose degradation product, could be produced from cellulosic biomass. Glycerol is an inexpensive and renewable resource for fuels and chemicals production and is available as a byproduct of biodiesel production. Gluconate is a more oxidized substrate than glucose, whereas glycerol is a more reduced substrate than glucose. Although the production of homoethanol from glucose can be achieved, the conversion of gluconate to ethanol is accompanied by the production of oxidized byproduct such as acetate, and reduced byproducts such as 1,3-propanediol are produced, along with ethanol, when glycerol is used as the carbon source. When gluconate and glycerol are used as the sole carbon source by Klebsiella oxytoca BW21, the ethanol yield is about 62 to 64%. Coutilization of both gluconate and glycerol in batch fermentation increased the yield of ethanol to about 78.7% and decreased by-product accumulation (such as acetate and 1,3-propanediol) substantially. Decreasing by-product formation by deleting the pta, frd, ldh, pflA, and pduC genes in strain BW21 increased the ethanol yield to 89.3% in the batch fermentation of a glycerol-gluconate mixture. These deletions produced the strain K. oxytoca WT26. However, the utilization rate of glycerol was significantly slower than that of gluconate in batch fermentation. In addition, substantial amounts of glycerol remain unutilized after gluconate was depleted in batch fermentation. Continuous fed-batch fermentation was used to solve the utilization rate mismatch problem for gluconate and glycerol. An ethanol yield of 97.2% was achieved in continuous fed-batch fermentation of these two substrates, and glycerol was completely used at the end of the fermentation.IMPORTANCE Gluconate is a biomass-derived degradation product, and glycerol can be obtained as a biodiesel byproduct. Compared to glucose, using them as the sole substrate is accompanied by the production of by-products. Our study shows that through pathway engineering and adoption of a fed-batch culture system, high-yield homoethanol production that usually can be achieved by using glucose as the substrate is achievable using gluconate and glycerol as cosubstrates. The same strategy is expected to be able to achieve homofermentative production of other products, such as lactate and 2,3-butanediol, which can be typically achieved using glucose as the substrate and inexpensive biodiesel-derived glycerol and biomass-derived gluconate as the cosubstrates.
Collapse
|
5
|
Koppolu V, Vasigala VK. Role of Escherichia coli in Biofuel Production. Microbiol Insights 2016; 9:29-35. [PMID: 27441002 PMCID: PMC4946582 DOI: 10.4137/mbi.s10878] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 06/26/2016] [Accepted: 06/28/2016] [Indexed: 12/19/2022] Open
Abstract
Increased energy consumption coupled with depleting petroleum reserves and increased greenhouse gas emissions have renewed our interest in generating fuels from renewable energy sources via microbial fermentation. Central to this problem is the choice of microorganism that catalyzes the production of fuels at high volumetric productivity and yield from cheap and abundantly available renewable energy sources. Microorganisms that are metabolically engineered to redirect renewable carbon sources into desired fuel products are contemplated as best choices to obtain high volumetric productivity and yield. Considering the availability of vast knowledge in genomic and metabolic fronts, Escherichia coli is regarded as a primary choice for the production of biofuels. Here, we reviewed the microbial production of liquid biofuels that have the potential to be used either alone or in combination with the present-day fuels. We specifically highlighted the metabolic engineering and synthetic biology approaches used to improve the production of biofuels from E. coli over the past few years. We also discussed the challenges that still exist for the biofuel production from E. coli and their possible solutions.
Collapse
Affiliation(s)
- Veerendra Koppolu
- Scientist, Department of Analytical Biotechnology, MedImmune/AstraZeneca, Gaithersburg, MD, USA.; Former affiliation: Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA
| | - Veneela Kr Vasigala
- Rangaraya Medical College, NTR University of Health Sciences, Kakinada, AP, India
| |
Collapse
|
6
|
Munir R, Levin DB. Enzyme Systems of Anaerobes for Biomass Conversion. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2016; 156:113-138. [PMID: 26907548 DOI: 10.1007/10_2015_5002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Biofuels from abundantly available cellulosic biomass are an attractive alternative to current petroleum-based fuels (fossil fuels). Although several strategies exist for commercial production of biofuels, conversion of biomass to biofuels via consolidated bioprocessing offers the potential to reduce production costs and increase processing efficiencies. In consolidated bioprocessing (CBP), enzyme production, cellulose hydrolysis, and fermentation are all carried out in a single-step by microorganisms that efficiently employ a multitude of intricate enzymes which act synergistically to breakdown cellulose and its associated cell wall components. Various strategies employed by anaerobic cellulolytic bacteria for biomass hydrolysis are described in this chapter. In addition, the regulation of CAZymes, the role of "omics" technologies in assessing lignocellulolytic ability, and current strategies for improving biomass hydrolysis for optimum biofuel production are highlighted.
Collapse
Affiliation(s)
- Riffat Munir
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB, Canada, R3T 5V6
| | - David B Levin
- Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB, Canada, R3T 5V6.
| |
Collapse
|
7
|
Akinosho H, Rydzak T, Borole A, Ragauskas A, Close D. Toxicological challenges to microbial bioethanol production and strategies for improved tolerance. ECOTOXICOLOGY (LONDON, ENGLAND) 2015; 24:2156-2174. [PMID: 26423392 DOI: 10.1007/s10646-015-1543-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/16/2015] [Indexed: 06/05/2023]
Abstract
Bioethanol production output has increased steadily over the last two decades and is now beginning to become competitive with traditional liquid transportation fuels due to advances in engineering, the identification of new production host organisms, and the development of novel biodesign strategies. A significant portion of these efforts has been dedicated to mitigating the toxicological challenges encountered across the bioethanol production process. From the release of potentially cytotoxic or inhibitory compounds from input feedstocks, through the metabolic co-synthesis of ethanol and potentially detrimental byproducts, and to the potential cytotoxicity of ethanol itself, each stage of bioethanol production requires the application of genetic or engineering controls that ensure the host organisms remain healthy and productive to meet the necessary economies required for large scale production. In addition, as production levels continue to increase, there is an escalating focus on the detoxification of the resulting waste streams to minimize their environmental impact. This review will present the major toxicological challenges encountered throughout each stage of the bioethanol production process and the commonly employed strategies for reducing or eliminating potential toxic effects.
Collapse
Affiliation(s)
- Hannah Akinosho
- Renewable BioProducts Institute, Georgia Institute of Technology, Atlanta, GA, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831, USA
| | - Thomas Rydzak
- BioEnergy Science Center, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831, USA
- Biosciences Division, Oak Ridge National Laboratory, P.O. Box 2008, MS6342, Oak Ridge, TN, 37831-6342, USA
| | - Abhijeet Borole
- Biosciences Division, Oak Ridge National Laboratory, P.O. Box 2008, MS6342, Oak Ridge, TN, 37831-6342, USA
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN, USA
- Bredesen Center for Interdisciplinary Research and Education, University of Tennessee, Knoxville, TN, USA
| | - Arthur Ragauskas
- Renewable BioProducts Institute, Georgia Institute of Technology, Atlanta, GA, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831, USA
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN, USA
| | - Dan Close
- Biosciences Division, Oak Ridge National Laboratory, P.O. Box 2008, MS6342, Oak Ridge, TN, 37831-6342, USA.
| |
Collapse
|
8
|
Metabolic potential of Bacillus subtilis 168 for the direct conversion of xylans to fermentation products. Appl Microbiol Biotechnol 2015; 100:1501-1510. [PMID: 26559526 DOI: 10.1007/s00253-015-7124-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 09/30/2015] [Accepted: 10/20/2015] [Indexed: 10/22/2022]
Abstract
Methylglucuronoxylans (MeGXn) and methylglucuronoarabinoxylans (MeGAXn) respectively comprise most of the hemicellulose fractions in dicots and monocots and, next to cellulose, are the major resources for the production of fuels and chemicals from lignocellulosics. With either MeGXn or MeGAXn as a substrate, Bacillus subtilis 168 accumulates acidic methylglucuronoxylotriose as a limit product following the uptake and metabolism of neutral xylooligosaccharides. Secreted GH11 endoxylanase (Xyn11A), GH30 endoxylanase (Xyn30C), and GH43 arabinoxylan arabinofuranohydrolase (Axh43) respectively encoded by the xynA, xynC, and xynD genes collectively contribute to the depolymerization of MeGAXn. Studies here demonstrate the complementary roles of these enzymes in the digestion of MeGAXn. Coordinate expression of the xynD and xynC genes defines an operon accounting for the Axh43-catalyzed release of arabinose followed by Xyn30C and Xyn11A-catalyzed depolymerization of MeGAXn. Both sources generate acetate and lactate as the principal fermentation products, with yields of 26 % acetate and 32 % lactate from MeGXn compared to 22 % acetate and 21 % lactate from MeGAXn. These studies of the GH43/GH30/GH11 system in B. subtilis 168 provide a basis for the further development of B. subtilis and related species as biocatalysts for direct conversion of hemicellulose derived from energy crops as well as agricultural and forest residues to chemical feedstocks.
Collapse
|
9
|
Yeasmin S, Kim CH, Islam SMA, Lee JY. Population dynamics of cellulolytic bacteria depend on the richness of cellulosic materials in the habitat. Microbiology (Reading) 2015. [DOI: 10.1134/s0026261715020186] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
|
10
|
Li YH, Ou-Yang FY, Yang CH, Li SY. The coupling of glycolysis and the Rubisco-based pathway through the non-oxidative pentose phosphate pathway to achieve low carbon dioxide emission fermentation. BIORESOURCE TECHNOLOGY 2015; 187:189-197. [PMID: 25846189 DOI: 10.1016/j.biortech.2015.03.090] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 03/19/2015] [Accepted: 03/20/2015] [Indexed: 06/04/2023]
Abstract
In this study, Rubisco-based engineered Escherichia coli, containing two heterologous enzymes of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) and phosphoribulokinase (PrkA), has been shown to be capable of the in situ recycling of carbon dioxide (CO2) during glycolysis. Two alternative approaches have been proposed to further enhance the carbon flow from glycolysis to a Rubisco-based pathway through the non-oxidative pentose phosphate pathway (NOPPP). The first is achieved by elevating the expression of transketolase I (TktA) and the second by blocking the native oxidation-decarboxylation reaction of E. coli by deleting the zwf gene from the chromosome (designated as JB/pTA and MZB, respectively). Decreases in the CO2 yield and the CO2 evolution per unit mole of ethanol production by at least 81% and 40% are observed. It is demonstrated in this study that the production of one mole of ethanol using E. coli strain MZB, the upper limit of CO2 emission is 0.052mol.
Collapse
Affiliation(s)
- Ya-Han Li
- Department of Chemical Engineering, National Chung Hsing University, Taichung 402, Taiwan
| | - Fan-Yu Ou-Yang
- Department of Chemical Engineering, National Chung Hsing University, Taichung 402, Taiwan
| | - Cheng-Han Yang
- Department of Chemical Engineering, National Chung Hsing University, Taichung 402, Taiwan
| | - Si-Yu Li
- Department of Chemical Engineering, National Chung Hsing University, Taichung 402, Taiwan.
| |
Collapse
|
11
|
Multigene editing in the Escherichia coli genome via the CRISPR-Cas9 system. Appl Environ Microbiol 2015; 81:2506-14. [PMID: 25636838 DOI: 10.1128/aem.04023-14] [Citation(s) in RCA: 749] [Impact Index Per Article: 83.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
An efficient genome-scale editing tool is required for construction of industrially useful microbes. We describe a targeted, continual multigene editing strategy that was applied to the Escherichia coli genome by using the Streptococcus pyogenes type II CRISPR-Cas9 system to realize a variety of precise genome modifications, including gene deletion and insertion, with a highest efficiency of 100%, which was able to achieve simultaneous multigene editing of up to three targets. The system also demonstrated successful targeted chromosomal deletions in Tatumella citrea, another species of the Enterobacteriaceae, with highest efficiency of 100%.
Collapse
|
12
|
|
13
|
Wu H, Lee J, Karanjikar M, San KY. Efficient free fatty acid production from woody biomass hydrolysate using metabolically engineered Escherichia coli. BIORESOURCE TECHNOLOGY 2014; 169:119-125. [PMID: 25043344 DOI: 10.1016/j.biortech.2014.06.092] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 06/24/2014] [Accepted: 06/25/2014] [Indexed: 06/03/2023]
Abstract
Four engineered Escherichia coli strains, ML103(pXZ18), ML103(pXZ18Z), ML190(pXZ18) and ML190(pXZ18Z), were constructed to investigate free fatty acid production using hydrolysate as carbon source. These strains exhibited efficient fatty acid production when xylose was used as the sole carbon source. For mixed sugars, ML103 based strains utilized glucose and xylose sequentially under the carbon catabolite repression (CCR) regulation, while ML190 based strains, with ptsG mutation, used glucose and xylose simultaneously. The total free fatty acid concentration and yield of the strain ML190(pXZ18Z) based on the mixed sugar reached 3.64 g/L and 24.88%, respectively. Furthermore, when hydrolysate from a commercial plant was used as the carbon source, the strain ML190(pXZ18Z) can produce 3.79 g/L FFAs with a high yield of 21.42%.
Collapse
Affiliation(s)
- Hui Wu
- Department of Bioengineering, Rice University, Houston, TX, United States
| | - Jane Lee
- Department of Bioengineering, Rice University, Houston, TX, United States
| | | | - Ka-Yiu San
- Department of Bioengineering, Rice University, Houston, TX, United States; Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, United States.
| |
Collapse
|
14
|
Toward aldehyde and alkane production by removing aldehyde reductase activity in Escherichia coli. Metab Eng 2014; 25:227-37. [PMID: 25108218 DOI: 10.1016/j.ymben.2014.07.012] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 06/30/2014] [Accepted: 07/30/2014] [Indexed: 01/15/2023]
Abstract
Advances in synthetic biology and metabolic engineering have enabled the construction of novel biological routes to valuable chemicals using suitable microbial hosts. Aldehydes serve as chemical feedstocks in the synthesis of rubbers, plastics, and other larger molecules. Microbial production of alkanes is dependent on the formation of a fatty aldehyde intermediate which is converted to an alkane by an aldehyde deformylating oxygenase (ADO). However, microbial hosts such as Escherichia coli are plagued by many highly active endogenous aldehyde reductases (ALRs) that convert aldehydes to alcohols, which greatly complicates strain engineering for aldehyde and alkane production. It has been shown that the endogenous ALR activity outcompetes the ADO enzyme for fatty aldehyde substrate. The large degree of ALR redundancy coupled with an incomplete database of ALRs represents a significant obstacle in engineering E. coli for either aldehyde or alkane production. In this study, we identified 44 ALR candidates encoded in the E. coli genome using bioinformatics tools, and undertook a comprehensive screening by measuring the ability of these enzymes to produce isobutanol. From the pool of 44 candidates, we found five new ALRs using this screening method (YahK, DkgA, GldA, YbbO, and YghA). Combined deletions of all 13 known ALRs resulted in a 90-99% reduction in endogenous ALR activity for a wide range of aldehyde substrates (C2-C12). Elucidation of the ALRs found in E. coli could guide one in reducing competing alcohol formation during alkane or aldehyde production.
Collapse
|
15
|
Zabed H, Faruq G, Sahu JN, Azirun MS, Hashim R, Nasrulhaq Boyce A. Bioethanol production from fermentable sugar juice. ScientificWorldJournal 2014; 2014:957102. [PMID: 24715820 PMCID: PMC3970039 DOI: 10.1155/2014/957102] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 12/31/2013] [Indexed: 11/25/2022] Open
Abstract
Bioethanol production from renewable sources to be used in transportation is now an increasing demand worldwide due to continuous depletion of fossil fuels, economic and political crises, and growing concern on environmental safety. Mainly, three types of raw materials, that is, sugar juice, starchy crops, and lignocellulosic materials, are being used for this purpose. This paper will investigate ethanol production from free sugar containing juices obtained from some energy crops such as sugarcane, sugar beet, and sweet sorghum that are the most attractive choice because of their cost-effectiveness and feasibility to use. Three types of fermentation process (batch, fed-batch, and continuous) are employed in ethanol production from these sugar juices. The most common microorganism used in fermentation from its history is the yeast, especially, Saccharomyces cerevisiae, though the bacterial species Zymomonas mobilis is also potentially used nowadays for this purpose. A number of factors related to the fermentation greatly influences the process and their optimization is the key point for efficient ethanol production from these feedstocks.
Collapse
Affiliation(s)
- Hossain Zabed
- Institute of Biological Sciences, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Golam Faruq
- Institute of Biological Sciences, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Jaya Narayan Sahu
- Department of Petroleum and Chemical Engineering, Faculty of Engineering, Institut Teknologi Brunei, Tungku Gadong, P.O. Box 2909, Brunei Darussalam
| | - Mohd Sofian Azirun
- Institute of Biological Sciences, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Rosli Hashim
- Institute of Biological Sciences, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Amru Nasrulhaq Boyce
- Institute of Biological Sciences, University of Malaya, 50603 Kuala Lumpur, Malaysia
| |
Collapse
|
16
|
Maki M, Iskhakova S, Zhang T, Qin W. Bacterial consortia constructed for the decomposition of Agave biomass. Bioengineered 2014; 5:165-72. [PMID: 24637707 DOI: 10.4161/bioe.28431] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Research has shown that a greater variety of enzymes, as well as variety of microorganisms producing enzymes, can have an overall synergistic effect on the decomposition of lignocellulosic biomass for the production of value-added bio-products. Here, 8 cellulase-degrading bacterial isolates were selected to develop co-, tri-, and tetra-cultures for the decomposition of lignocellulosic biomass. Glucose and xylose equivalents released from imitation biomass media containing 0.5% (w/v) beechwood xylan and 0.5% (w/v) Avicel was measured using di-nitrosalicylic acid for all consortia, along with cell growth and survival. Thereafter, 6 co- and 2 tri-cultures with greatest decomposition were examined for ability to degrade Agave americana fiber. Interestingly, when strains were paired up in co-culture, four pairs: G+5, G+A, C+A1, and G+A1 produced high reducing sugars in 24 h: 6 µM, 8 µM, 8 µM, and finally, 6 µM, respectively. From 4 co-cultures with highest reducing sugar equivalents, tri- and tetra-cultures were produced. The bacterial consortia which had the highest reducing sugars detected were 2 tri-cultures: G + A1 + A4 and G + A1 + 5, displaying levels as high as 9 µM and 5 µM in day 1, respectively. All co- and tri-cultures maintained high cell survival for 14 days with 0.5 g ground Agave. Upon evaluating Agave dry weight after treatment, it was evident that almost half the biomass could be decomposed in 14 days. Scanning electron microscopy of treated Agave supported decomposition when compared with the control. These bacterial consortia have potential for further study of value-added by-product production during metabolism of lignocellulosic biomasses.
Collapse
Affiliation(s)
- Miranda Maki
- Department of Biology; Lakehead University; Thunder Bay, ON Canada
| | | | - Tingzhou Zhang
- Department of Environmental Engineering; Zhejiang Gongshang University; Hangzhou, China
| | - Wensheng Qin
- Department of Biology; Lakehead University; Thunder Bay, ON Canada
| |
Collapse
|
17
|
Singh LK, Majumder CB, Ghosh S. Development of sequential-co-culture system (Pichia stipitis and Zymomonas mobilis) for bioethanol production from Kans grass biomass. Biochem Eng J 2014. [DOI: 10.1016/j.bej.2013.10.023] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
18
|
Genome-scale engineering for systems and synthetic biology. Mol Syst Biol 2013; 9:641. [PMID: 23340847 PMCID: PMC3564264 DOI: 10.1038/msb.2012.66] [Citation(s) in RCA: 205] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Accepted: 12/16/2012] [Indexed: 12/15/2022] Open
Abstract
This review provides an overview of methodologies and technologies enabling genome-scale engineering, focusing on the design, construction, and testing of modified genomes in a variety of organisms. Future applications for systems and synthetic biology are discussed. Genome-modification technologies enable the rational engineering and perturbation of biological systems. Historically, these methods have been limited to gene insertions or mutations at random or at a few pre-defined locations across the genome. The handful of methods capable of targetedgene editing suffered from low efficiencies, significant labor costs, or both. Recent advances have dramatically expanded our ability to engineer cells in a directed and combinatorial manner. Here, we review current technologies and methodologies for genome-scale engineering, discuss the prospects for extending efficient genome modification to new hosts, and explore the implications of continued advances toward the development of flexibly programmable chasses, novel biochemistries, and safer organismal and ecological engineering.
Collapse
|
19
|
Ibraheem O, Ndimba BK. Molecular adaptation mechanisms employed by ethanologenic bacteria in response to lignocellulose-derived inhibitory compounds. Int J Biol Sci 2013; 9:598-612. [PMID: 23847442 PMCID: PMC3708040 DOI: 10.7150/ijbs.6091] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 04/26/2013] [Indexed: 11/12/2022] Open
Abstract
Current international interest in finding alternative sources of energy to the diminishing supplies of fossil fuels has encouraged research efforts in improving biofuel production technologies. In countries which lack sufficient food, the use of sustainable lignocellulosic feedstocks, for the production of bioethanol, is an attractive option. In the pre-treatment of lignocellulosic feedstocks for ethanol production, various chemicals and/or enzymatic processes are employed. These methods generally result in a range of fermentable sugars, which are subjected to microbial fermentation and distillation to produce bioethanol. However, these methods also produce compounds that are inhibitory to the microbial fermentation process. These compounds include products of sugar dehydration and lignin depolymerisation, such as organic acids, derivatised furaldehydes and phenolic acids. These compounds are known to have a severe negative impact on the ethanologenic microorganisms involved in the fermentation process by compromising the integrity of their cell membranes, inhibiting essential enzymes and negatively interact with their DNA/RNA. It is therefore important to understand the molecular mechanisms of these inhibitions, and the mechanisms by which these microorganisms show increased adaptation to such inhibitors. Presented here is a concise overview of the molecular adaptation mechanisms of ethanologenic bacteria in response to lignocellulose-derived inhibitory compounds. These include general stress response and tolerance mechanisms, which are typically those that maintain intracellular pH homeostasis and cell membrane integrity, activation/regulation of global stress responses and inhibitor substrate-specific degradation pathways. We anticipate that understanding these adaptation responses will be essential in the design of 'intelligent' metabolic engineering strategies for the generation of hyper-tolerant fermentation bacteria strains.
Collapse
Affiliation(s)
- Omodele Ibraheem
- Research and Services Unit, Agricultural Research Council/Infruitech & The University of Western Cape, Biotechnology Department, Private Bag X17, Bellville, Cape Town, South Africa
| | | |
Collapse
|
20
|
Jäger G, Büchs J. Biocatalytic conversion of lignocellulose to platform chemicals. Biotechnol J 2012; 7:1122-36. [DOI: 10.1002/biot.201200033] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2012] [Revised: 05/17/2012] [Accepted: 06/08/2012] [Indexed: 01/12/2023]
|
21
|
Taylor M, Ramond JB, Tuffin M, Burton S, Eley K, Cowan D. Mechanisms and Applications of Microbial Solvent Tolerance. MICROBIOLOGY MONOGRAPHS 2012. [DOI: 10.1007/978-3-642-21467-7_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
|
22
|
Enhanced microbial utilization of recalcitrant cellulose by an ex vivo cellulosome-microbe complex. Appl Environ Microbiol 2011; 78:1437-44. [PMID: 22210210 DOI: 10.1128/aem.07138-11] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A cellulosome-microbe complex was assembled ex vivo on the surface of Bacillus subtilis displaying a miniscaffoldin that can bind with three dockerin-containing cellulase components: the endoglucanase Cel5, the processive endoglucanase Cel9, and the cellobiohydrolase Cel48. The hydrolysis performances of the synthetic cellulosome bound to living cells, the synthetic cellulosome, a noncomplexed cellulase mixture with the same catalytic components, and a commercial fungal enzyme mixture were investigated on low-accessibility recalcitrant Avicel and high-accessibility regenerated amorphous cellulose (RAC). The cell-bound cellulosome exhibited 4.5- and 2.3-fold-higher hydrolysis ability than cell-free cellulosome on Avicel and RAC, respectively. The cellulosome-microbe synergy was not completely explained by the removal of hydrolysis products from the bulk fermentation broth by free-living cells and appeared to be due to substrate channeling of long-chain hydrolysis products assimilated by the adjacent cells located in the boundary layer. Our results implied that long-chain hydrolysis products in the boundary layer may inhibit cellulosome activity to a greater extent than the short-chain products in bulk phase. The findings that cell-bound cellulosome expedited the microbial cellulose utilization rate by 2.3- to 4.5-fold would help in the development of better consolidated bioprocessing microorganisms (e.g., B. subtilis) that can hydrolyze recalcitrant cellulose rapidly at low secretory cellulase levels.
Collapse
|
23
|
Correlation of genomic and physiological traits of thermoanaerobacter species with biofuel yields. Appl Environ Microbiol 2011; 77:7998-8008. [PMID: 21948836 DOI: 10.1128/aem.05677-11] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Thermophilic anaerobic noncellulolytic Thermoanaerobacter species are of great biotechnological importance in cellulosic ethanol production due to their ability to produce high ethanol yields by simultaneous fermentation of hexose and pentose. Understanding the genome structure of these species is critical to improving and implementing these bacteria for possible biotechnological use in consolidated bioprocessing schemes (CBP) for cellulosic ethanol production. Here we describe a comparative genome analysis of two ethanologenic bacteria, Thermoanaerobacter sp. X514 and Thermoanaerobacter pseudethanolicus 39E. Compared to 39E, X514 has several unique key characteristics important to cellulosic biotechnology, including additional alcohol dehydrogenases and xylose transporters, modifications to pentose metabolism, and a complete vitamin B₁₂ biosynthesis pathway. Experimental results from growth, metabolic flux, and microarray gene expression analyses support genome sequencing-based predictions which help to explain the distinct differences in ethanol production between these strains. The availability of whole-genome sequence and comparative genomic analyses will aid in engineering and optimizing Thermoanaerobacter strains for viable CBP strategies.
Collapse
|
24
|
Thermophilic, lignocellulolytic bacteria for ethanol production: current state and perspectives. Appl Microbiol Biotechnol 2011; 92:13-27. [DOI: 10.1007/s00253-011-3456-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Revised: 06/15/2011] [Accepted: 06/15/2011] [Indexed: 10/17/2022]
|
25
|
Production of recombinant proteins and metabolites in yeasts. Appl Microbiol Biotechnol 2010; 89:939-48. [DOI: 10.1007/s00253-010-3019-z] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2010] [Revised: 11/12/2010] [Accepted: 11/15/2010] [Indexed: 12/27/2022]
|
26
|
Chen Y. Development and application of co-culture for ethanol production by co-fermentation of glucose and xylose: a systematic review. J Ind Microbiol Biotechnol 2010; 38:581-97. [PMID: 21104106 DOI: 10.1007/s10295-010-0894-3] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2010] [Accepted: 10/21/2010] [Indexed: 01/29/2023]
Abstract
This article reviews current co-culture systems for fermenting mixtures of glucose and xylose to ethanol. Thirty-five co-culture systems that ferment either synthetic glucose and xylose mixture or various biomass hydrolysates are examined. Strain combinations, fermentation modes and conditions, and fermentation performance for these co-culture systems are compared and discussed. It is noted that the combination of Pichia stipitis with Saccharomyces cerevisiae or its respiratory-deficient mutant is most commonly used. One of the best results for fermentation of glucose and xylose mixture is achieved by using co-culture of immobilized Zymomonas mobilis and free cells of P. stipitis, giving volumetric ethanol production of 1.277 g/l/h and ethanol yield of 0.49-0.50 g/g. The review discloses that, as a strategy for efficient conversion of glucose and xylose, co-culture fermentation for ethanol production from lignocellulosic biomass can increase ethanol yield and production rate, shorten fermentation time, and reduce process costs, and it is a promising technology although immature.
Collapse
Affiliation(s)
- Yanli Chen
- Department of Chemical Engineering, Auburn University, Auburn, AL 36849, USA.
| |
Collapse
|
27
|
Isolation and characterization of Shigella flexneri G3, capable of effective cellulosic saccharification under mesophilic conditions. Appl Environ Microbiol 2010; 77:517-23. [PMID: 21097577 DOI: 10.1128/aem.01230-10] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A novel Shigella strain (Shigella flexneri G3) showing high cellulolytic activity under mesophilic, anaerobic conditions was isolated and characterized. The bacterium is Gram negative, short rod shaped, and nonmotile and displays effective production of glucose, cellobiose, and other oligosaccharides from cellulose (Avicel PH-101) under optimal conditions (40°C and pH 6.5). Approximately 75% of the cellulose was hydrolyzed in modified ATCC 1191 medium containing 0.3% cellulose, and the oligosaccharide production yield and specific production rate reached 375 mg g Avicel(-1) and 6.25 mg g Avicel(-1) h(-1), respectively, after a 60-hour incubation. To our knowledge, this represents the highest oligosaccharide yield and specific rate from cellulose for mesophilic bacterial monocultures reported so far. The results demonstrate that S. flexneri G3 is capable of rapid conversion of cellulose to oligosaccharides, with potential biofuel applications under mesophilic conditions.
Collapse
|
28
|
Sriyudthsak K, Shiraishi F. Investigation of the performance of fermentation processes using a mathematical model including effects of metabolic bottleneck and toxic product on cells. Math Biosci 2010; 228:1-9. [DOI: 10.1016/j.mbs.2010.08.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2010] [Revised: 07/26/2010] [Accepted: 08/04/2010] [Indexed: 10/19/2022]
|
29
|
Lau MW, Dale BE. Effect of primary degradation-reaction products from Ammonia Fiber Expansion (AFEX)-treated corn stover on the growth and fermentation of Escherichia coli KO11. BIORESOURCE TECHNOLOGY 2010; 101:7849-55. [PMID: 20627718 DOI: 10.1016/j.biortech.2010.04.076] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2010] [Revised: 04/09/2010] [Accepted: 04/22/2010] [Indexed: 05/05/2023]
Abstract
The primary degradation-reaction products (DRP) identified in Ammonia Fiber Expansion (AFEX)-pretreated corn stover are acetate, lactate, 4-hydroxybenzaldehyde (4HBD) and acetamide. The effects of these products at a broad concentration range were tested on Escherichia coli KO11, a strain engineered for cellulosic ethanol production. Fermentations using glucose or xylose as the sole carbohydrate source and a sugar mixture of glucose and xylose were conducted to determine how these products and sugar selection affected fermentation performance. Co-fermentation of the sugar mixture exhibited the lowest overall ethanol productivity compared to single-sugar fermentations and was more susceptible to inhibition. Metabolic ethanol yield increased with the increasing initial concentration of acetate. Although these degradation-reaction products (with exception of acetamide) are generally perceived to be inhibitory, organic acids and 4-hydroxybenzaldehyde at low levels stimulated fermentation. Adaptation of cells to these products prior to fermentation increased overall fermentation rate.
Collapse
Affiliation(s)
- Ming W Lau
- Department of Chemical Engineering and Materials Science, DOE Great Lakes Bioenergy Research Center, Michigan State University, 3900 Collins Rd., Lansing, MI 48910, USA
| | | |
Collapse
|
30
|
Abstract
Industrial production of solvents such as EtOH and BuOH from cellulosic biomass has the potential to provide a sustainable energy source that is relatively cheap, abundant, and environmentally sound, but currently production costs are driven up by expensive enzymes, which are necessary to degrade cellulose into fermentable sugars. These costs could be significantly reduced if a microorganism could be engineered to efficiently and quickly convert cellulosic biomass directly to product in a one-step process. There is a large amount of biodiversity in the number of existing microorganisms that naturally possess the enzymes necessary to convert cellulose to usable sugars, and many of these microorganisms can directly ferment sugars to EtOH or other solvents. Currently, the vast majority of cellulolytic organisms are poorly understood and have complex metabolic networks. In this review, we survey the current state of knowledge on different cellulases and metabolic capabilities found in various cellulolytic microorganisms. We also propose that the use of large-scale metabolic models (and associated analyses) is potentially an ideal means for improving our understanding of basic metabolic network function and directing metabolic engineering efforts for cellulolytic microorganisms.
Collapse
Affiliation(s)
- Christopher M Gowen
- Department of Chemical and Life Science Engineering, Virginia Commonwealth University, Richmond, VA 23284-3028, USA
| | | |
Collapse
|
31
|
Barnard D, Casanueva A, Tuffin M, Cowan D. Extremophiles in biofuel synthesis. ENVIRONMENTAL TECHNOLOGY 2010; 31:871-888. [PMID: 20662378 DOI: 10.1080/09593331003710236] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The current global energy situation has demonstrated an urgent need for the development of alternative fuel sources to the continually diminishing fossil fuel reserves. Much research to address this issue focuses on the development of financially viable technologies for the production of biofuels. The current market for biofuels, defined as fuel products obtained from organic substrates, is dominated by bioethanol, biodiesel, biobutanol and biogas, relying on the use of substrates such as sugars, starch and oil crops, agricultural and animal wastes, and lignocellulosic biomass. This conversion from biomass to biofuel through microbial catalysis has gained much momentum as biotechnology has evolved to its current status. Extremophiles are a robust group of organisms producing stable enzymes, which are often capable of tolerating changes in environmental conditions such as pH and temperature. The potential application of such organisms and their enzymes in biotechnology is enormous, and a particular application is in biofuel production. In this review an overview of the different biofuels is given, covering those already produced commercially as well as those under development. The past and present trends in biofuel production are discussed, and future prospects for the industry are highlighted. The focus is on the current and future application of extremophilic organisms and enzymes in technologies to develop and improve the biotechnological production of biofuels.
Collapse
Affiliation(s)
- Desire Barnard
- Institute for Microbial Biotechnology and Metagenomics, Department of Biotechnology, University of the Western Cape, Private Bag X17, Bellville 7535, Cape Town, South Africa
| | | | | | | |
Collapse
|
32
|
Redirecting reductant flux into hydrogen production via metabolic engineering of fermentative carbon metabolism in a cyanobacterium. Appl Environ Microbiol 2010; 76:5032-8. [PMID: 20543051 DOI: 10.1128/aem.00862-10] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Some aquatic microbial oxygenic photoautotrophs (AMOPs) make hydrogen (H(2)), a carbon-neutral, renewable product derived from water, in low yields during autofermentation (anaerobic metabolism) of intracellular carbohydrates previously stored during aerobic photosynthesis. We have constructed a mutant (the ldhA mutant) of the cyanobacterium Synechococcus sp. strain PCC 7002 lacking the enzyme for the NADH-dependent reduction of pyruvate to D-lactate, the major fermentative reductant sink in this AMOP. Both nuclear magnetic resonance (NMR) spectroscopy and liquid chromatography-mass spectrometry (LC-MS) metabolomic methods have shown that autofermentation by the ldhA mutant resulted in no D-lactate production and higher concentrations of excreted acetate, alanine, succinate, and hydrogen (up to 5-fold) compared to that by the wild type. The measured intracellular NAD(P)(H) concentrations demonstrated that the NAD(P)H/NAD(P)(+) ratio increased appreciably during autofermentation in the ldhA strain; we propose this to be the principal source of the observed increase in H(2) production via an NADH-dependent, bidirectional [NiFe] hydrogenase. Despite the elevated NAD(P)H/NAD(P)(+) ratio, no decrease was found in the rate of anaerobic conversion of stored carbohydrates. The measured energy conversion efficiency (ECE) from biomass (as glucose equivalents) converted to hydrogen in the ldhA mutant is 12%. Together with the unimpaired photoautotrophic growth of the ldhA mutant, these attributes reveal that metabolic engineering is an effective strategy to enhance H(2) production in AMOPs without compromising viability.
Collapse
|
33
|
Trends and challenges in the microbial production of lignocellulosic bioalcohol fuels. Appl Microbiol Biotechnol 2010; 87:1303-15. [DOI: 10.1007/s00253-010-2707-z] [Citation(s) in RCA: 256] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2010] [Revised: 05/27/2010] [Accepted: 05/27/2010] [Indexed: 12/30/2022]
|
34
|
la Grange DC, den Haan R, van Zyl WH. Engineering cellulolytic ability into bioprocessing organisms. Appl Microbiol Biotechnol 2010; 87:1195-208. [DOI: 10.1007/s00253-010-2660-x] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Revised: 05/02/2010] [Accepted: 05/02/2010] [Indexed: 10/19/2022]
|
35
|
Lau MW, Gunawan C, Balan V, Dale BE. Comparing the fermentation performance of Escherichia coli KO11, Saccharomyces cerevisiae 424A(LNH-ST) and Zymomonas mobilis AX101 for cellulosic ethanol production. BIOTECHNOLOGY FOR BIOFUELS 2010; 3:11. [PMID: 20507563 PMCID: PMC2898752 DOI: 10.1186/1754-6834-3-11] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2009] [Accepted: 05/27/2010] [Indexed: 05/04/2023]
Abstract
BACKGROUND Fermentations using Escherichia coli KO11, Saccharomyces cerevisiae 424A(LNH-ST), and Zymomonas mobilis AX101 are compared side-by-side on corn steep liquor (CSL) media and the water extract and enzymatic hydrolysate from ammonia fiber expansion (AFEX)-pretreated corn stover. RESULTS The three ethanologens are able produce ethanol from a CSL-supplemented co-fermentation at a metabolic yield, final concentration and rate greater than 0.42 g/g consumed sugars, 40 g/L and 0.7 g/L/h (0-48 h), respectively. Xylose-only fermentation of the tested ethanologenic bacteria are five to eight times faster than 424A(LNH-ST) in the CSL fermentation.All tested strains grow and co-ferment sugars at 15% w/v solids loading equivalent of ammonia fiber explosion (AFEX)-pretreated corn stover water extract. However, both KO11 and 424A(LNH-ST) exhibit higher growth robustness than AX101. In 18% w/w solids loading lignocellulosic hydrolysate from AFEX pretreatment, complete glucose fermentations can be achieved at a rate greater than 0.77 g/L/h. In contrast to results from fermentation in CSL, S. cerevisiae 424A(LNH-ST) consumed xylose at the greatest extent and rate in the hydrolysate compared to the bacteria tested. CONCLUSIONS Our results confirm that glucose fermentations among the tested strains are effective even at high solids loading (18% by weight). However, xylose consumption in the lignocellulosic hydrolysate is the major bottleneck affecting overall yield, titer or rate of the process. In comparison, Saccharomyces cerevisiae 424A(LNH-ST) is the most relevant strains for industrial production for its ability to ferment both glucose and xylose from undetoxified and unsupplemented hydrolysate from AFEX-pretreated corn stover at high yield.
Collapse
Affiliation(s)
- Ming W Lau
- Department of Chemical Engineering and Materials Science, DOE Great Lakes Bioenergy Research Center, Michigan State University, 3900 Collins Rd, Lansing, MI 48910, USA
| | - Christa Gunawan
- Department of Chemical Engineering and Materials Science, DOE Great Lakes Bioenergy Research Center, Michigan State University, 3900 Collins Rd, Lansing, MI 48910, USA
| | - Venkatesh Balan
- Department of Chemical Engineering and Materials Science, DOE Great Lakes Bioenergy Research Center, Michigan State University, 3900 Collins Rd, Lansing, MI 48910, USA
| | - Bruce E Dale
- Department of Chemical Engineering and Materials Science, DOE Great Lakes Bioenergy Research Center, Michigan State University, 3900 Collins Rd, Lansing, MI 48910, USA
| |
Collapse
|
36
|
Key drivers influencing the commercialization of ethanol-based biorefineries. ACTA ACUST UNITED AC 2010. [DOI: 10.1057/jcb.2010.5] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
37
|
Chen ML, Wang FS. Optimization of a Fed-Batch Simultaneous Saccharification and Cofermentation Process from Lignocellulose to Ethanol. Ind Eng Chem Res 2010. [DOI: 10.1021/ie1001982] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ming-Liang Chen
- Department of Chemical Engineering, National Chung Cheng University, Chia-yi 62102, Taiwan
| | - Feng-Sheng Wang
- Department of Chemical Engineering, National Chung Cheng University, Chia-yi 62102, Taiwan
| |
Collapse
|
38
|
Metabolic engineering for production of biorenewable fuels and chemicals: contributions of synthetic biology. J Biomed Biotechnol 2010; 2010:761042. [PMID: 20414363 PMCID: PMC2857869 DOI: 10.1155/2010/761042] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2009] [Revised: 12/18/2009] [Accepted: 01/13/2010] [Indexed: 12/18/2022] Open
Abstract
Production of fuels and chemicals through microbial fermentation of plant material is a desirable alternative to petrochemical-based production. Fermentative production of biorenewable fuels and chemicals requires the engineering of biocatalysts that can quickly and efficiently convert sugars to target products at a cost that is competitive with existing petrochemical-based processes. It is also important that biocatalysts be robust to extreme fermentation conditions, biomass-derived inhibitors, and their target products. Traditional metabolic engineering has made great advances in this area, but synthetic biology has contributed and will continue to contribute to this field, particularly with next-generation biofuels. This work reviews the use of metabolic engineering and synthetic biology in biocatalyst engineering for biorenewable fuels and chemicals production, such as ethanol, butanol, acetate, lactate, succinate, alanine, and xylitol. We also examine the existing challenges in this area and discuss strategies for improving biocatalyst tolerance to chemical inhibitors.
Collapse
|
39
|
Dellomonaco C, Fava F, Gonzalez R. The path to next generation biofuels: successes and challenges in the era of synthetic biology. Microb Cell Fact 2010; 9:3. [PMID: 20089184 PMCID: PMC2817670 DOI: 10.1186/1475-2859-9-3] [Citation(s) in RCA: 133] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2009] [Accepted: 01/20/2010] [Indexed: 01/11/2023] Open
Abstract
Volatility of oil prices along with major concerns about climate change, oil supply security and depleting reserves have sparked renewed interest in the production of fuels from renewable resources. Recent advances in synthetic biology provide new tools for metabolic engineers to direct their strategies and construct optimal biocatalysts for the sustainable production of biofuels. Metabolic engineering and synthetic biology efforts entailing the engineering of native and de novo pathways for conversion of biomass constituents to short-chain alcohols and advanced biofuels are herewith reviewed. In the foreseeable future, formal integration of functional genomics and systems biology with synthetic biology and metabolic engineering will undoubtedly support the discovery, characterization, and engineering of new metabolic routes and more efficient microbial systems for the production of biofuels.
Collapse
|
40
|
Nikel PI, Ramirez MC, Pettinari MJ, Méndez BS, Galvagno MA. Ethanol synthesis from glycerol by Escherichia coli redox mutants expressing adhE from Leuconostoc mesenteroides. J Appl Microbiol 2010; 109:492-504. [PMID: 20149000 DOI: 10.1111/j.1365-2672.2010.04668.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AIMS Analysis of the physiology and metabolism of Escherichia coli arcA and creC mutants expressing a bifunctional alcohol-acetaldehyde dehydrogenase from Leuconostoc mesenteroides growing on glycerol under oxygen-restricted conditions. The effect of an ldhA mutation and different growth medium modifications was also assessed. METHODS AND RESULTS Expression of adhE in E. coli CT1061 [arcA creC(Con)] resulted in a 1.4-fold enhancement in ethanol synthesis. Significant amounts of lactate were produced during micro-oxic cultures and strain CT1061LE, in which fermentative lactate dehydrogenase was deleted, produced up to 6.5 +/- 0.3 g l(-1) ethanol in 48 h. Escherichia coli CT1061LE derivatives resistant to >25 g l(-1) ethanol were obtained by metabolic evolution. Pyruvate and acetaldehyde addition significantly increased both biomass and ethanol concentrations, probably by overcoming acetyl-coenzyme A (CoA) shortage. Yeast extract also promoted growth and ethanol synthesis, and this positive effect was mainly attributable to its vitamin content. Two-stage bioreactor cultures were conducted in a minimal medium containing 100 microg l(-1) calcium d-pantothenate to evaluate oxic acetyl-CoA synthesis followed by a switch into fermentative conditions. Ethanol reached 15.4 +/- 0.9 g l(-1) with a volumetric productivity of 0.34 +/- 0.02 g l(-1) h(-1). CONCLUSIONS Escherichia coli responded to adhE over-expression by funnelling carbon and reducing equivalents into a highly reduced metabolite, ethanol. Acetyl-CoA played a key role in micro-oxic ethanol synthesis and growth. SIGNIFICANCE AND IMPACT OF THE STUDY Insight into the micro-oxic metabolism of E. coli growing on glycerol is essential for the development of efficient industrial processes for reduced biochemicals production from this substrate, with special relevance to biofuels synthesis.
Collapse
Affiliation(s)
- P I Nikel
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina., Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autonoma de Buenos Aires, Argentina
| | - M C Ramirez
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - M J Pettinari
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autonoma de Buenos Aires, Argentina
| | - B S Méndez
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autonoma de Buenos Aires, Argentina
| | - M A Galvagno
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina., Departamento de Ingeniería Química, Facultad de Ingeniería, Universidad de Buenos Aires, Ciudad Autonoma de Buenos Aires, Argentina
| |
Collapse
|
41
|
Banerjee S, Mudliar S, Sen R, Giri B, Satpute D, Chakrabarti T, Pandey R. Commercializing lignocellulosic bioethanol: technology bottlenecks and possible remedies. BIOFUELS, BIOPRODUCTS AND BIOREFINING 2010; 4:77-93. [PMID: 0 DOI: 10.1002/bbb.188] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
|
42
|
Engineering for biofuels: exploiting innate microbial capacity or importing biosynthetic potential? Nat Rev Microbiol 2009; 7:715-23. [DOI: 10.1038/nrmicro2186] [Citation(s) in RCA: 304] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
43
|
Fermentation of Sugarcane Bagasse and Chicken Manure to Calcium Carboxylates under Thermophilic Conditions. Appl Biochem Biotechnol 2009; 162:561-78. [DOI: 10.1007/s12010-009-8748-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2009] [Accepted: 08/10/2009] [Indexed: 11/26/2022]
|
44
|
Yomano LP, York SW, Shanmugam KT, Ingram LO. Deletion of methylglyoxal synthase gene (mgsA) increased sugar co-metabolism in ethanol-producing Escherichia coli. Biotechnol Lett 2009; 31:1389-98. [PMID: 19458924 PMCID: PMC2721133 DOI: 10.1007/s10529-009-0011-8] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2009] [Revised: 04/27/2009] [Accepted: 04/30/2009] [Indexed: 11/28/2022]
Abstract
The use of lignocellulose as a source of sugars for bioproducts requires the development of biocatalysts that maximize product yields by fermenting mixtures of hexose and pentose sugars to completion. In this study, we implicate mgsA encoding methylglyoxal synthase (and methylglyoxal) in the modulation of sugar metabolism. Deletion of this gene (strain LY168) resulted in the co-metabolism of glucose and xylose, and accelerated the metabolism of a 5-sugar mixture (mannose, glucose, arabinose, xylose and galactose) to ethanol.
Collapse
Affiliation(s)
- L P Yomano
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | | | | | | |
Collapse
|
45
|
Sellick CA, Hansen R, Maqsood AR, Dunn WB, Stephens GM, Goodacre R, Dickson AJ. Effective quenching processes for physiologically valid metabolite profiling of suspension cultured Mammalian cells. Anal Chem 2009; 81:174-83. [PMID: 19061395 DOI: 10.1021/ac8016899] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Global metabolite analysis approaches, coupled with sophisticated data analysis and modeling procedures (metabolomics), permit a dynamic read-out of how cellular proteins interact with cellular and environmental conditions to determine cell status. This type of approach has profound potential for understanding, and subsequently manipulating, the regulation of cell function. As part of our study to define the regulatory events that may be used to maximize production of commercially valuable recombinant proteins from cultured mammalian cells, we have optimized the quenching process to allow retention of physiologically relevant intracellular metabolite profiles in samples from recombinant Chinese hamster ovary (CHO) cells. In a comparison of a series of candidate quenching procedures, we have shown that quenching in 60% methanol supplemented with 0.85% ammonium bicarbonate (AMBIC) at -40 degrees C generates a profile of metabolites that is representative of a physiological status based upon examination of key labile cellular metabolites. This represents a key feature for any metabolomic study with suspension cultured mammalian cells and provides confidence in the validity of subsequent data analysis and modeling procedures.
Collapse
Affiliation(s)
- Christopher A Sellick
- Faculty of Life Sciences, The University of Manchester, Michael Smith Building, Oxford Road, Manchester M139PT, UK.
| | | | | | | | | | | | | |
Collapse
|
46
|
Yan Y, Liao JC. Engineering metabolic systems for production of advanced fuels. J Ind Microbiol Biotechnol 2009; 36:471-9. [PMID: 19198907 DOI: 10.1007/s10295-009-0532-0] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2008] [Accepted: 01/14/2009] [Indexed: 11/26/2022]
Abstract
The depleting petroleum storage and increasing environmental deterioration are threatening the sustainable development of human societies. As such, biofuels and chemical feedstocks generated from renewable sources are becoming increasingly important. Although previous efforts led to great success in bio-ethanol production, higher alcohols, fatty acid derivatives including biodiesels, alkanes, and alkenes offer additional advantages because of their compatibility with existing infrastructure. In addition, some of these compounds are useful chemical feedstocks. Since native organisms do not naturally produce these compounds in high quantities, metabolic engineering becomes essential in constructing producing organisms. In this article, we briefly review the four major metabolic systems, the coenzyme-A mediated pathways, the keto acid pathways, the fatty acid pathway, and the isoprenoid pathways, that allow production of these fuel-grade chemicals.
Collapse
Affiliation(s)
- Yajun Yan
- Department of Chemical and Biomolecular Engineering, University of California at Los Angeles, 5531 Boelter Hall, 420 Westwood Plaza, Los Angeles, CA 90095, USA
| | | |
Collapse
|
47
|
|
48
|
Lu Y, Mosier NS. Kinetic modeling analysis of maleic acid-catalyzed hemicellulose hydrolysis in corn stover. Biotechnol Bioeng 2008; 101:1170-81. [DOI: 10.1002/bit.22008] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
49
|
Yomano LP, York SW, Zhou S, Shanmugam KT, Ingram LO. Re-engineering Escherichia coli for ethanol production. Biotechnol Lett 2008; 30:2097-103. [DOI: 10.1007/s10529-008-9821-3] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2008] [Revised: 07/23/2008] [Accepted: 08/11/2008] [Indexed: 11/29/2022]
|
50
|
Peterson JD, Ingram LO. Anaerobic respiration in engineered Escherichia coli with an internal electron acceptor to produce fuel ethanol. Ann N Y Acad Sci 2008; 1125:363-72. [PMID: 18378606 DOI: 10.1196/annals.1419.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Environmental concerns and unease with U.S. dependence on foreign oil have renewed interest in converting biomass into fuel ethanol. The volume of plant matter available makes lignocellulose conversion to ethanol desirable, although no one isolated organism has been shown to break bonds in lignocellulose and efficiently metabolize resulting sugars into one product. This work reviews directed engineering coupled with metabolic evolution resulting in microbial biocatalysts that produce up to 45 g L(-1) ethanol in 48 hours in a simple mineral salts medium and that convert various compounds of lignocellulosic materials to ethanol. Mutations contributing to ethanologenesis are discussed along with adding enzymatic capabilities to existing biocatalysts in order to decrease the commercial enzymes required to reduce plant matter into fermentable sugars.
Collapse
|