1
|
Rajagopal S, Hmar RV, Mookherjee D, Ghatak A, Shanbhag AP, Katagihallimath N, Venkatraman J, Ks R, Datta S. Validated In Silico Population Model of Escherichia coli. ACS Synth Biol 2022; 11:2672-2684. [PMID: 35801944 DOI: 10.1021/acssynbio.2c00097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Flux balance analysis (FBA) and ordinary differential equation models have been instrumental in depicting the metabolic functioning of a cell. Nevertheless, they demonstrate a population's average behavior (summation of individuals), thereby portraying homogeneity. However, living organisms such as Escherichia coli contain more biochemical reactions than engaging metabolites, making them an underdetermined and degenerate system. This results in a heterogeneous population with varying metabolic patterns. We have formulated a population systems biology model that predicts this degeneracy by emulating a diverse metabolic makeup with unique biochemical signatures. The model mimics the universally accepted experimental view that a subpopulation of bacteria, even under normal growth conditions, renders a unique biochemical state, leading to the synthesis of metabolites and persister progenitors of antibiotic resistance and biofilms. We validate the platform's predictions by producing commercially important heterologous (isobutanol) and homologous (shikimate) metabolites. The predicted fluxes are tested in vitro resulting in 32- and 42-fold increased product of isobutanol and shikimate, respectively. Moreover, we authenticate the platform by mimicking a bacterial population in the presence of glyphosate, a metabolic pathway inhibitor. Here, we observe a fraction of subsisting persisters despite inhibition, thus affirming the signature of a heterogeneous populace. The platform has multiple uses based on the disposition of the user.
Collapse
Affiliation(s)
- Sreenath Rajagopal
- Bugworks Research India Private Limited, C-CAMP, National Center for Biological Sciences (TIFR), Bangalore 560065, India
| | - Rothangmawi Victoria Hmar
- Biomoneta Research Private Limited, C-CAMP, National Center for Biological Sciences (TIFR), Bangalore 560092, India
| | - Debdatto Mookherjee
- Bugworks Research India Private Limited, C-CAMP, National Center for Biological Sciences (TIFR), Bangalore 560065, India
| | - Arindam Ghatak
- Biomoneta Research Private Limited, C-CAMP, National Center for Biological Sciences (TIFR), Bangalore 560092, India.,Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata 700073, India
| | - Anirudh P Shanbhag
- Bugworks Research India Private Limited, C-CAMP, National Center for Biological Sciences (TIFR), Bangalore 560065, India.,Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata 700073, India
| | - Nainesh Katagihallimath
- Bugworks Research India Private Limited, C-CAMP, National Center for Biological Sciences (TIFR), Bangalore 560065, India
| | - Janani Venkatraman
- Biomoneta Research Private Limited, C-CAMP, National Center for Biological Sciences (TIFR), Bangalore 560092, India
| | - Ramanujan Ks
- Biomoneta Research Private Limited, C-CAMP, National Center for Biological Sciences (TIFR), Bangalore 560092, India
| | - Santanu Datta
- Bugworks Research India Private Limited, C-CAMP, National Center for Biological Sciences (TIFR), Bangalore 560065, India
| |
Collapse
|
2
|
Pan H, Wang J, Wu H, Li Z, Lian J. Synthetic biology toolkit for engineering Cupriviadus necator H16 as a platform for CO 2 valorization. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:212. [PMID: 34736496 PMCID: PMC8570001 DOI: 10.1186/s13068-021-02063-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 10/25/2021] [Indexed: 06/09/2023]
Abstract
BACKGROUND CO2 valorization is one of the effective methods to solve current environmental and energy problems, in which microbial electrosynthesis (MES) system has proved feasible and efficient. Cupriviadus necator (Ralstonia eutropha) H16, a model chemolithoautotroph, is a microbe of choice for CO2 conversion, especially with the ability to be employed in MES due to the presence of genes encoding [NiFe]-hydrogenases and all the Calvin-Benson-Basham cycle enzymes. The CO2 valorization strategy will make sense because the required hydrogen can be produced from renewable electricity independently of fossil fuels. MAIN BODY In this review, synthetic biology toolkit for C. necator H16, including genetic engineering vectors, heterologous gene expression elements, platform strain and genome engineering, and transformation strategies, is firstly summarized. Then, the review discusses how to apply these tools to make C. necator H16 an efficient cell factory for converting CO2 to value-added products, with the examples of alcohols, fatty acids, and terpenoids. The review is concluded with the limitation of current genetic tools and perspectives on the development of more efficient and convenient methods as well as the extensive applications of C. necator H16. CONCLUSIONS Great progress has been made on genetic engineering toolkit and synthetic biology applications of C. necator H16. Nevertheless, more efforts are expected in the near future to engineer C. necator H16 as efficient cell factories for the conversion of CO2 to value-added products.
Collapse
Affiliation(s)
- Haojie Pan
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Jia Wang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Haoliang Wu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Zhongjian Li
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China.
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 310027, China.
| |
Collapse
|
3
|
Chen C, Yuan J, Yu H, Wang B, Huang J, Yuan H, Xu Z, Zhao S, Tian H. Characterization of metabolic pathways for biosynthesis of the flavor compound 3-methylbutanal by Lactococcus lactis. J Dairy Sci 2021; 105:97-108. [PMID: 34756442 DOI: 10.3168/jds.2021-20779] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 09/06/2021] [Indexed: 11/19/2022]
Abstract
3-Methylbutanal is a key volatile compound that imparts a nutty flavor to Cheddar cheese. Lactococcus lactis has been successfully applied as a starter to increase the level of 3-methylbutanal produced during the ripening of cheese. However, the mechanism of action and genetic diversity of this bacterium for 3-methylbutanal biosynthesis remains unclear. In this study, we investigated the association between the L. lactis genotype and phenotype in the biosynthesis of 3-methylbutanal via both direct and indirect pathways. Fourteen strains of L. lactis were screened for the capacity to produce 3-methylbutanal, and strain 408 (>140 μM) produced the highest among all tested strains, which exhibited both α-keto acid decarboxylase and α-ketoacid dehydrogenase activities. Furthermore, the results of a sodium meta-arsenite inhibition experiment showed that the 3-methylbutanal-producing capacities of each strain declined to various degrees. The kdcA gene, which encodes the direct pathway component α-ketoacid decarboxylase, was detected in 4 of the 14 strains, of which only strain 408 contained the full-length gene. We then characterized the genes associated with the indirect pathway by detecting the expression levels of the pdh gene cluster, ack, and pta, which were expressed at relatively higher levels in a high-yield strain than in a low-yield strain. As a result, these L. lactis strains were divided into 3 categories according to gene diversity, gene expression, and 3-methylbutanal production. The results of this study refine our knowledge of the genetic determinants of 3-methylbutanal biosynthesis in L. lactis and explain the effect of both synthesis pathways on 3-methylbutanal production.
Collapse
Affiliation(s)
- Chen Chen
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai 201418, P.R. China
| | - Jiajie Yuan
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai 201418, P.R. China
| | - Haiyan Yu
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai 201418, P.R. China
| | - Bei Wang
- School of Food and Health, Beijing Technology and Business University, Beijing 100048, P.R. China
| | - Juan Huang
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai 201418, P.R. China
| | - Haibin Yuan
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai 201418, P.R. China
| | - Zhiyuan Xu
- State Key Laboratory of Dairy Biotechnology, Shanghai Engineering Research Center of Dairy Biotechnology, Dairy Research Institute, Bright Dairy & Food Co., Ltd., Shanghai 201418, P.R. China
| | - Shanshan Zhao
- College of Agriculture, Hebei University of Engineering, Handan 056038, P.R. China.
| | - Huaixiang Tian
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai 201418, P.R. China.
| |
Collapse
|
4
|
Fu C, Li Z, Zhang Y, Yi C, Xie S. Assessment of extraction options for a next-generation biofuel: Recovery of bio-isobutanol from aqueous solutions. Eng Life Sci 2021; 21:653-665. [PMID: 34690636 PMCID: PMC8518583 DOI: 10.1002/elsc.202000090] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 05/02/2021] [Accepted: 05/31/2021] [Indexed: 11/15/2022] Open
Abstract
Isobutanol is a widely used platform compound and a raw material for synthesizing many high value-added compounds. It also has excellent fuel properties and is an ideal gasoline additive or substitute with a very broad development space. Isobutanol production by biological fermentation has the advantages of a comprehensive source of raw materials, low cost, environmental protection, and sustainability. However, it also has disadvantages such as many impurities, low isobutanol concentration, and difficulty separating the water + isobutanol azeotrope. Thus, it is necessary to explore an appropriate downstream separation process for the water + isobutanol azeotrope. K2CO3 with a strong salting-out effect was used as the salting-out agent, and the salting-out of isobutanol from aqueous solutions was investigated at 298.15 K. The effect of the initial salt concentration in the aqueous solution, the recovery of isobutanol, and the effect of dehydration were investigated in detail. The e-NRTL-RK model was employed to generate the binary parameters for isobutanol and water, and electrolyte pair parameters for water/isobutanol and ions to reproduce the phase diagram with high accuracy. The processes of solvent extractive distillation, and salting-out + distillation were simulated by Aspen Plus. The energy consumptions for the solvent-based and salting-out-based processes were compared. The salting-out + distillation process turned out to be more energy-saving than the solvent extraction process.
Collapse
Affiliation(s)
- Chuhan Fu
- The Gene and Linda Voiland School of Chemical Engineering and BioengineeringWashington State UniversityPullmanWAUSA
| | - Zhuoxi Li
- School of PharmacyGuangzhou Xinhua UniversityGuangzhouP. R. China
| | - Yulei Zhang
- School of Chemistry & Chemical EngineeringSouth China University of TechnologyGuangzhouP. R. China
| | - Conghua Yi
- School of Chemistry & Chemical EngineeringSouth China University of TechnologyGuangzhouP. R. China
| | - Shaoqu Xie
- The Gene and Linda Voiland School of Chemical Engineering and BioengineeringWashington State UniversityPullmanWAUSA
| |
Collapse
|
5
|
Metabolic engineering of Escherichia coli for the production of isobutanol: a review. World J Microbiol Biotechnol 2021; 37:168. [PMID: 34487256 DOI: 10.1007/s11274-021-03140-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 08/30/2021] [Indexed: 10/20/2022]
Abstract
With the ongoing depletion of fossil fuel resources and emerging environmental issues, increasing research effort is being dedicated to producing biofuels from renewable substrates. With its advantages over ethanol in terms of energy density, octane number, and hygroscopicity, isobutanol is considered a potential alternative to traditional gasoline. However, as wild-type microorganisms cannot achieve the production of isobutanol with high titers and yields, rational genetic engineering has been employed to enhance its production. Herein, we review the latest developments in the metabolic engineering of Escherichia coli for the production of isobutanol, including those related to the utilization of diverse carbon sources, balancing the redox state, improving isobutanol tolerance, and application of synthetic biology circuits and tools.
Collapse
|
6
|
Shehu IA, Auwal NM, Musa MK, Mukhtar A, Yusuf MS, Yau AA, Muhammad M, Baba Dala Y, Sani SA, Ahmad MS, Islam M. Innovative Nanotechnology a Boon for Fight Against Pandemic COVID–19. FRONTIERS IN NANOTECHNOLOGY 2021. [DOI: 10.3389/fnano.2021.651308] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
COVID – 19 is a contagious disease caused by severe acute respiratory syndrome (SARS-CoV2). The rate at which COVID – 19-virus spread from epidemic to pandemic within a short period is quite alarming. As of July 2020, the Dashboard of the World Health Organization (WHO) recorded over 15 million COVID – 19 cases across 213 countries, with mortality of over 620,000. The governments and healthcare agencies responsible for mitigating the virus's spread have adopted several strategies to end the pandemic. However, all hands were on deck to establish the standard treatment modalities of SARS-CoV-2 through inventing new drugs, vaccine candidates, or repurposing the existing medicines and robust diagnostic tools, in addition to other technological innovations. Therefore, nanotechnology’s employment would play a vital role in bringing multidisciplinary ways of developing affordable, reliable, and powerful tools for diagnosis, in addition to personal protection and effective medicines. Additionally, nanosensors' application would significantly aid the diagnoses of the COVID–19 even on asymptomatic patients, and thus would be an essential means for determining its prevalence. Likewise, nanoscale fibers can optimize personal equipment protection and allow their reusability for medical and economic benefits. Accordingly, the literature was intensively reviewed by searching for the combinations of the research keywords in the official scientific databases such as Science Direct, PubMed, and Google Scholar. Hence, this research highlighted the perspective contributions of nanotechnology in the war against the COVID-19 pandemic.
Collapse
|
7
|
Deb SS, Reshamwala SMS, Lali AM. Activation of alternative metabolic pathways diverts carbon flux away from isobutanol formation in an engineered Escherichia coli strain. Biotechnol Lett 2019; 41:823-836. [PMID: 31093837 DOI: 10.1007/s10529-019-02683-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Accepted: 05/02/2019] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Metabolic engineering efforts are guided by identifying gene targets for overexpression and/or deletion. Isobutanol, a biofuel candidate, is biosynthesized using the valine biosynthesis pathway and enzymes of the Ehrlich pathway. Most reported studies for isobutanol production in Escherichia coli employ multicopy plasmids, an approach that suffers from disadvantages such as plasmid instability, increased metabolic burden, and use of antibiotics to maintain selection pressure. Cofactor imbalance is another issue that may limit production of isobutanol, as two enzymes of the pathway utilize NADPH as a cofactor. RESULTS To address these issues, we constructed E. coli strains with chromosomally-integrated, codon-optimized isobutanol pathway genes (ilvGM, ilvC, kivd, adh) selected on the basis of their cofactor preferences. Genes involved in diverting pyruvate flux toward fermentation byproducts were deleted. Metabolite analyses of the constructed strains revealed extracellular accumulation of significant amounts of isobutyraldehyde, a pathway intermediate, and the overflow metabolites 2,3-butanediol and acetol. CONCLUSIONS These results demonstrate that the genetic modifications carried out led to activation of alternative pathways that diverted carbon flux toward formation of unwanted metabolites. The present study highlights how precursor metabolites can be metabolized through enzymatic routes that have not been considered important in previous studies due to the different strategies employed therein. The insights gained from the present study will allow rational genetic modification of host cells for production of metabolites of interest.
Collapse
Affiliation(s)
- Shalini S Deb
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology, Nathatlal Parekh Marg, Matunga (East), Mumbai, Maharashtra, 400019, India
| | - Shamlan M S Reshamwala
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology, Nathatlal Parekh Marg, Matunga (East), Mumbai, Maharashtra, 400019, India.
| | - Arvind M Lali
- DBT-ICT Centre for Energy Biosciences, Institute of Chemical Technology, Nathatlal Parekh Marg, Matunga (East), Mumbai, Maharashtra, 400019, India
- Department of Chemical Engineering, Institute of Chemical Technology, Nathatlal Parekh Marg, Matunga (East), Mumbai, Maharashtra, 400019, India
| |
Collapse
|
8
|
Savrasova EA, Stoynova NV. Application of leucine dehydrogenase Bcd from Bacillus subtilis for l-valine synthesis in Escherichia coli under microaerobic conditions. Heliyon 2019; 5:e01406. [PMID: 30993221 PMCID: PMC6449708 DOI: 10.1016/j.heliyon.2019.e01406] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 03/05/2019] [Accepted: 03/20/2019] [Indexed: 12/02/2022] Open
Abstract
Microaerobic cultivation conditions have been shown experimentally and theoretically to improve the performance of a number of bioproduction systems. However, under these conditions, the production of l-valine by Escherichia coli is decreased mainly because of a redox cofactor imbalance and a decreased l-glutamate supply. The synthesis of one mole of l-valine from one mole of glucose generates two moles of NADH via glycolysis but consumes a total of two moles of NADPH, one in the ketol-acid reductoisomerase (KARI) reaction and the other in the regeneration of l-glutamate as an amino group donor for the branched-chain amino acid aminotransferase (BCAT) reaction. The improvement of l-valine synthesis under oxygen deprivation may be due to solving these problems. Increased l-valine synthesis under oxygen deprivation conditions was previously shown in Corynebacterium glutamicum (Hasegawa et al., 2012). In this study, we have proposed the use of NADH-dependent leucine dehydrogenase (LeuDH; EC 1.4.1.9) Bcd from B. subtilis instead of the native NADPH-dependent pathway including aminotransferase encoded by ilvE to improve l-valine production in E. coli under microaerobic conditions. We have created l-valine-producing strains on the base of the aminotransferase B-deficient strain V1 (B-7 ΔilvBN ΔilvIH ΔilvGME::PL-ilvBNN17KDA) by introducing one chromosomal copy of the bcd gene or the ilvE gene. Evaluation of the l-valine production by the obtained strains under microaerobic and aerobic conditions revealed that leucine dehydrogenase Bcd had a higher potential for l-valine production under microaerobic conditions. The Bcd-possessing strain exhibited 2.2-fold higher l-valine accumulation (up to 9.1 g/L) and 2.0-fold higher yield (up to 35.3%) under microaerobic conditions than the IlvE-possessing strain. The obtained results could be interpreted as follows: an altering of redox cofactor balance in the l-valine biosynthesis pathway increased the production and yield by E. coli cells under microaerobic conditions. Thus, the effective synthesis of l-valine by means of “valine fermentation” was shown in E. coli. This methodology has the advantages of being an economical and environmentally friendly process.
Collapse
|
9
|
Acedos MG, Ramon A, de la Morena S, Santos VE, Garcia-Ochoa F. Isobutanol production by a recombinant biocatalyst Shimwellia blattae (p424IbPSO): Study of the operational conditions. Biochem Eng J 2018. [DOI: 10.1016/j.bej.2018.02.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
10
|
Bernardi AC, Gai CS, Lu J, Sinskey AJ, Brigham CJ. Experimental evolution and gene knockout studies reveal AcrA-mediated isobutanol tolerance in Ralstonia eutropha. J Biosci Bioeng 2016; 122:64-9. [DOI: 10.1016/j.jbiosc.2015.12.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 12/02/2015] [Accepted: 12/18/2015] [Indexed: 12/12/2022]
|
11
|
Milne N, van Maris AJA, Pronk JT, Daran JM. Comparative assessment of native and heterologous 2-oxo acid decarboxylases for application in isobutanol production by Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS 2015; 8:204. [PMID: 26628917 PMCID: PMC4665922 DOI: 10.1186/s13068-015-0374-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 11/09/2015] [Indexed: 06/05/2023]
Abstract
BACKGROUND Decarboxylation of α-ketoisovalerate to isobutyraldehyde is a key reaction in metabolic engineering of Saccharomyces cerevisiae for isobutanol production with published studies relying on overexpression of either the native ARO10 gene or of the Lactococcus lactis kivD decarboxylase gene resulting in low enzymatic activities. Here, we compare relevant properties for isobutanol production of Aro10, KivD and an additional, less studied, L. lactis decarboxylase KdcA. RESULTS To eliminate interference by native decarboxylases, each 2-oxo acid decarboxylase was overexpressed in a 'decarboxylase-negative' (pdc1Δ pdc5Δ pdc6Δ aro10Δ) S. cerevisiae background. Kinetic analyses in cell extracts revealed a superior V max/K m ratio of KdcA for α-ketoisovalerate and a wide range of linear and branched-chain 2-oxo acids. However, KdcA also showed the highest activity with pyruvate which, in engineered strains, can contribute to formation of ethanol as a by-product. Removal of native decarboxylase genes eliminated growth on valine as sole nitrogen source and subsequent complementation of this growth impairment by expression of each decarboxylase indicated that based on the increased growth rate, the in vivo activity of KdcA with α-ketoisovalerate was higher than that of KivD and Aro10. Moreover, during oxygen-limited incubation in the presence of glucose, strains expressing kdcA or kivD showed a ca. twofold higher in vivo rate of conversion of α-ketoisovalerate into isobutanol than an ARO10-expressing strain. Finally, cell extracts from cultures grown on different nitrogen sources revealed increased activity of constitutively expressed KdcA after growth on both valine and phenylalanine, while KivD and Aro10 activity was only increased after growth on phenylalanine suggesting a difference in the regulation of these enzymes. CONCLUSIONS This study illustrates important differences in substrate specificity, enzyme kinetics and functional expression between different decarboxylases in the context of isobutanol production and identifies KdcA as a promising alternative decarboxylase not only for isobutanol production but also for other branched-chain and linear alcohols.
Collapse
Affiliation(s)
- N. Milne
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - A. J. A. van Maris
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - J. T. Pronk
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - J. M. Daran
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| |
Collapse
|
12
|
Sommer B, von Moeller H, Haack M, Qoura F, Langner C, Bourenkov G, Garbe D, Loll B, Brück T. Detailed structure-function correlations of Bacillus subtilis acetolactate synthase. Chembiochem 2014; 16:110-8. [PMID: 25393087 DOI: 10.1002/cbic.201402541] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Indexed: 02/04/2023]
Abstract
Isobutanol is deemed to be a next-generation biofuel and a renewable platform chemical.1 Non-natural biosynthetic pathways for isobutanol production have been implemented in cell-based and in vitro systems with Bacillus subtilis acetolactate synthase (AlsS) as key biocatalyst.2-6 AlsS catalyzes the condensation of two pyruvate molecules to acetolactate with thiamine diphosphate and Mg(2+) as cofactors. AlsS also catalyzes the conversion of 2-ketoisovalerate into isobutyraldehyde, the immediate precursor of isobutanol. Our phylogenetic analysis suggests that the ALS enzyme family forms a distinct subgroup of ThDP-dependent enzymes. To unravel catalytically relevant structure-function relationships, we solved the AlsS crystal structure at 2.3 Å in the presence of ThDP, Mg(2+) and in a transition state with a 2-lactyl moiety bound to ThDP. We supplemented our structural data by point mutations in the active site to identify catalytically important residues.
Collapse
Affiliation(s)
- Bettina Sommer
- Fachgebiet Industrielle Biokatalyse, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching (Germany)
| | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Wu D, Yue D, You F, Broadbelt LJ. Computational evaluation of factors governing catalytic 2-keto acid decarboxylation. J Mol Model 2014; 20:2310. [PMID: 24912593 DOI: 10.1007/s00894-014-2310-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 05/19/2014] [Indexed: 11/25/2022]
Abstract
Recent advances in computational approaches for creating pathways for novel biochemical reactions has motivated the development of approaches for identifying enzyme-substrate pairs that are attractive candidates for effecting catalysis. We present an improved structural-based strategy to probe and study enzyme-substrate binding based on binding geometry, energy, and molecule characteristics, which allows for in silico screening of structural features that imbue higher catalytic potential with specific substrates. The strategy is demonstrated using 2-keto acid decarboxylation with various pairs of 2-keto acids and enzymes. We show that this approach fitted experimental values for a wide range of 2-keto acid decarboxylases for different 2-keto acid substrates. In addition, we show that the structure-based methods can be used to select specific enzymes that may be promising candidates to catalyze decarboxylation of certain 2-keto acids. The key features and principles of the candidate enzymes evaluated by the strategy can be used to design novel biosynthesis pathways, to guide enzymatic mutation or to guide biomimetic catalyst design.
Collapse
Affiliation(s)
- Di Wu
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
| | | | | | | |
Collapse
|
14
|
Gak E, Tyurin M, Kiriukhin M. Genome tailoring powered production of isobutanol in continuous CO2/H2 blend fermentation using engineered acetogen biocatalyst. J Ind Microbiol Biotechnol 2014; 41:763-81. [PMID: 24659176 DOI: 10.1007/s10295-014-1416-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 02/06/2014] [Indexed: 11/24/2022]
Abstract
The cell energy fraction that powered maintenance and expression of genes encoding pro-phage elements, pta-ack cluster, early sporulation, sugar ABC transporter periplasmic proteins, 6-phosphofructokinase, pyruvate kinase, and fructose-1,6-disphosphatase in acetogen Clostridium sp. MT871 was re-directed to power synthetic operon encoding isobutanol biosynthesis at the expense of these genes achieved via their elimination. Genome tailoring decreased cell duplication time by 7.0 ± 0.1 min (p < 0.05) compared to the parental strain, with intact genome and cell duplication time of 68 ± 1 min (p < 0.05). Clostridium sp. MT871 with tailored genome was UVC-mutated to withstand 6.1 % isobutanol in fermentation broth to prevent product inhibition in an engineered commercial biocatalyst producing 5 % (674.5 mM) isobutanol during two-step continuous fermentation of CO2/H2 gas blend. Biocatalyst Clostridium sp. MT871RG- 11IBR6 was engineered to express six copies of synthetic operon comprising optimized synthetic format dehydrogenase, pyruvate formate lyase, acetolactate synthase, acetohydroxyacid reductoisomerase, 2,3-dihydroxy-isovalerate dehydratase, branched-chain alpha-ketoacid decarboxylase gene, aldehyde dehydrogenase, and alcohol dehydrogenase, regaining cell duplication time of 68 ± 1 min (p < 0.05) for the parental strain. This is the first report on isobutanol production by an engineered acetogen biocatalyst suitable for commercial manufacturing of this chemical/fuel using continuous fermentation of CO2/H2 blend thus contributing to the reversal of global warming.
Collapse
|
15
|
Latendresse M, Krummenacker M, Karp PD. Optimal metabolic route search based on atom mappings. Bioinformatics 2014; 30:2043-50. [DOI: 10.1093/bioinformatics/btu150] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
16
|
Chen X, Zhou L, Tian K, Kumar A, Singh S, Prior BA, Wang Z. Metabolic engineering of Escherichia coli: A sustainable industrial platform for bio-based chemical production. Biotechnol Adv 2013; 31:1200-23. [DOI: 10.1016/j.biotechadv.2013.02.009] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 02/04/2013] [Accepted: 02/25/2013] [Indexed: 12/20/2022]
|
17
|
The Biotechnological Potential of Corynebacterium glutamicum, from Umami to Chemurgy. CORYNEBACTERIUM GLUTAMICUM 2013. [DOI: 10.1007/978-3-642-29857-8_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
18
|
Liu X, Bastian S, Snow CD, Brustad EM, Saleski TE, Xu JH, Meinhold P, Arnold FH. Structure-guided engineering of Lactococcus lactis alcohol dehydrogenase LlAdhA for improved conversion of isobutyraldehyde to isobutanol. J Biotechnol 2012; 164:188-95. [PMID: 22974724 PMCID: PMC3542407 DOI: 10.1016/j.jbiotec.2012.08.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Revised: 08/14/2012] [Accepted: 08/20/2012] [Indexed: 11/17/2022]
Abstract
We have determined the X-ray crystal structures of the NADH-dependent alcohol dehydrogenase LlAdhA from Lactococcus lactis and its laboratory-evolved variant LlAdhA(RE1) at 1.9Å and 2.5Å resolution, respectively. LlAdhA(RE1), which contains three amino acid mutations (Y50F, I212T, and L264V), was engineered to increase the microbial production of isobutanol (2-methylpropan-1-ol) from isobutyraldehyde (2-methylpropanal). Structural comparison of LlAdhA and LlAdhA(RE1) indicates that the enhanced activity on isobutyraldehyde stems from increases in the protein's active site size, hydrophobicity, and substrate access. Further structure-guided mutagenesis generated a quadruple mutant (Y50F/N110S/I212T/L264V), whose KM for isobutyraldehyde is ∼17-fold lower and catalytic efficiency (kcat/KM) is ∼160-fold higher than wild-type LlAdhA. Combining detailed structural information and directed evolution, we have achieved significant improvements in non-native alcohol dehydrogenase activity that will facilitate the production of next-generation fuels such as isobutanol from renewable resources.
Collapse
Affiliation(s)
- Xiang Liu
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Mail code 210-41, Pasadena, CA 91125, USA
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Sabine Bastian
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Mail code 210-41, Pasadena, CA 91125, USA
| | - Christopher D. Snow
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Mail code 210-41, Pasadena, CA 91125, USA
| | - Eric M. Brustad
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Mail code 210-41, Pasadena, CA 91125, USA
| | - Tatyana E. Saleski
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Mail code 210-41, Pasadena, CA 91125, USA
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Peter Meinhold
- Gevo, Inc., 345 Inverness Drive S., Buiding C, Suite 310, Englewood, CO 80112, USA
| | - Frances H. Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Mail code 210-41, Pasadena, CA 91125, USA
| |
Collapse
|
19
|
El-Nahas AM, Mangood AH, El-Meleigy AB. A computational study on the structures and energetics of isobutanol pyrolysis. COMPUT THEOR CHEM 2012. [DOI: 10.1016/j.comptc.2012.08.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
|
20
|
Huffer S, Roche CM, Blanch HW, Clark DS. Escherichia coli for biofuel production: bridging the gap from promise to practice. Trends Biotechnol 2012; 30:538-45. [DOI: 10.1016/j.tibtech.2012.07.002] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Revised: 07/09/2012] [Accepted: 07/10/2012] [Indexed: 02/04/2023]
|
21
|
Lu J, Brigham CJ, Gai CS, Sinskey AJ. Studies on the production of branched-chain alcohols in engineered Ralstonia eutropha. Appl Microbiol Biotechnol 2012; 96:283-97. [DOI: 10.1007/s00253-012-4320-9] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Revised: 07/16/2012] [Accepted: 07/17/2012] [Indexed: 11/25/2022]
|
22
|
Lee WH, Seo SO, Bae YH, Nan H, Jin YS, Seo JH. Isobutanol production in engineered Saccharomyces cerevisiae by overexpression of 2-ketoisovalerate decarboxylase and valine biosynthetic enzymes. Bioprocess Biosyst Eng 2012; 35:1467-75. [DOI: 10.1007/s00449-012-0736-y] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Accepted: 04/08/2012] [Indexed: 11/30/2022]
|
23
|
Jurgens G, Survase S, Berezina O, Sklavounos E, Linnekoski J, Kurkijärvi A, Väkevä M, van Heiningen A, Granström T. Butanol production from lignocellulosics. Biotechnol Lett 2012; 34:1415-34. [PMID: 22526420 DOI: 10.1007/s10529-012-0926-3] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Accepted: 03/27/2012] [Indexed: 12/20/2022]
Abstract
Clostridium spp. produce n-butanol in the acetone/butanol/ethanol process. For sustainable industrial scale butanol production, a number of obstacles need to be addressed including choice of feedstock, the low product yield, toxicity to production strain, multiple-end products and downstream processing of alcohol mixtures. This review describes the use of lignocellulosic feedstocks, bioprocess and metabolic engineering, downstream processing and catalytic refining of n-butanol.
Collapse
Affiliation(s)
- German Jurgens
- Department of Biotechnology and Chemical Technology, Aalto University, 00076, Espoo, Finland.
| | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Application of the bacteriophage Mu-driven system for the integration/amplification of target genes in the chromosomes of engineered Gram-negative bacteria--mini review. Appl Microbiol Biotechnol 2011; 91:857-71. [PMID: 21698377 PMCID: PMC3145075 DOI: 10.1007/s00253-011-3416-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Revised: 05/24/2011] [Accepted: 05/24/2011] [Indexed: 11/04/2022]
Abstract
The advantages of phage Mu transposition-based systems for the chromosomal editing of plasmid-less strains are reviewed. The cis and trans requirements for Mu phage-mediated transposition, which include the L/R ends of the Mu DNA, the transposition factors MuA and MuB, and the cis/trans functioning of the E element as an enhancer, are presented. Mini-Mu(LR)/(LER) units are Mu derivatives that lack most of the Mu genes but contain the L/R ends or a properly arranged E element in cis to the L/R ends. The dual-component system, which consists of an integrative plasmid with a mini-Mu and an easily eliminated helper plasmid encoding inducible transposition factors, is described in detail as a tool for the integration/amplification of recombinant DNAs. This chromosomal editing method is based on replicative transposition through the formation of a cointegrate that can be resolved in a recombination-dependent manner. (E-plus)- or (E-minus)-helpers that differ in the presence of the trans-acting E element are used to achieve the proper mini-Mu transposition intensity. The systems that have been developed for the construction of stably maintained mini-Mu multi-integrant strains of Escherichia coli and Methylophilus methylotrophus are described. A novel integration/amplification/fixation strategy is proposed for consecutive independent replicative transpositions of different mini-Mu(LER) units with “excisable” E elements in methylotrophic cells.
Collapse
|