251
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Jönsson LJ, Alriksson B, Nilvebrant NO. Bioconversion of lignocellulose: inhibitors and detoxification. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:16. [PMID: 23356676 PMCID: PMC3574029 DOI: 10.1186/1754-6834-6-16] [Citation(s) in RCA: 611] [Impact Index Per Article: 55.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Accepted: 01/16/2013] [Indexed: 05/17/2023]
Abstract
Bioconversion of lignocellulose by microbial fermentation is typically preceded by an acidic thermochemical pretreatment step designed to facilitate enzymatic hydrolysis of cellulose. Substances formed during the pretreatment of the lignocellulosic feedstock inhibit enzymatic hydrolysis as well as microbial fermentation steps. This review focuses on inhibitors from lignocellulosic feedstocks and how conditioning of slurries and hydrolysates can be used to alleviate inhibition problems. Novel developments in the area include chemical in-situ detoxification by using reducing agents, and methods that improve the performance of both enzymatic and microbial biocatalysts.
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Affiliation(s)
- Leif J Jönsson
- Department of Chemistry, Umeå University, Umeå SE-901 87, Sweden
| | - Björn Alriksson
- Processum Biorefinery Initiative AB, Örnsköldsvik, SE-891 22, Sweden
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252
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Kondo A, Ishii J, Hara KY, Hasunuma T, Matsuda F. Development of microbial cell factories for bio-refinery through synthetic bioengineering. J Biotechnol 2013; 163:204-16. [DOI: 10.1016/j.jbiotec.2012.05.021] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Revised: 05/10/2012] [Accepted: 05/18/2012] [Indexed: 12/24/2022]
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253
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Özaydın B, Burd H, Lee TS, Keasling JD. Carotenoid-based phenotypic screen of the yeast deletion collection reveals new genes with roles in isoprenoid production. Metab Eng 2013; 15:174-83. [DOI: 10.1016/j.ymben.2012.07.010] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Revised: 07/17/2012] [Accepted: 07/23/2012] [Indexed: 10/28/2022]
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254
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den Haan R, Kroukamp H, van Zyl JHD, van Zyl WH. Cellobiohydrolase secretion by yeast: Current state and prospects for improvement. Process Biochem 2013. [DOI: 10.1016/j.procbio.2012.11.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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255
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Xu G, Zou W, Chen X, Xu N, Liu L, Chen J. Fumaric acid production in Saccharomyces cerevisiae by in silico aided metabolic engineering. PLoS One 2012; 7:e52086. [PMID: 23300594 PMCID: PMC3530589 DOI: 10.1371/journal.pone.0052086] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Accepted: 11/15/2012] [Indexed: 01/12/2023] Open
Abstract
Fumaric acid (FA) is a promising biomass-derived building-block chemical. Bio-based FA production from renewable feedstock is a promising and sustainable alternative to petroleum-based chemical synthesis. Here we report on FA production by direct fermentation using metabolically engineered Saccharomyces cerevisiae with the aid of in silico analysis of a genome-scale metabolic model. First, FUM1 was selected as the target gene on the basis of extensive literature mining. Flux balance analysis (FBA) revealed that FUM1 deletion can lead to FA production and slightly lower growth of S. cerevisiae. The engineered S. cerevisiae strain obtained by deleting FUM1 can produce FA up to a concentration of 610±31 mg L–1 without any apparent change in growth in fed-batch culture. FT-IR and 1H and 13C NMR spectra confirmed that FA was synthesized by the engineered S. cerevisiae strain. FBA identified pyruvate carboxylase as one of the factors limiting higher FA production. When the RoPYC gene was introduced, S. cerevisiae produced 1134±48 mg L–1 FA. Furthermore, the final engineered S. cerevisiae strain was able to produce 1675±52 mg L–1 FA in batch culture when the SFC1 gene encoding a succinate–fumarate transporter was introduced. These results demonstrate that the model shows great predictive capability for metabolic engineering. Moreover, FA production in S. cerevisiae can be efficiently developed with the aid of in silico metabolic engineering.
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Affiliation(s)
- Guoqiang Xu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Wei Zou
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Nan Xu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- * E-mail: (LML); (JC)
| | - Jian Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
- * E-mail: (LML); (JC)
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256
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Du X, He W, Zhang X, Ma J, Wang C, Li C, Yue Y. Low temperature biosynthesis of Li2O-MgO-P2O5-TiO2 nanocrystalline glass with mesoporous structure exhibiting fast lithium ion conduction. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2012; 33:1592-600. [PMID: 23827612 DOI: 10.1016/j.msec.2012.12.065] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 11/13/2012] [Accepted: 12/17/2012] [Indexed: 11/26/2022]
Abstract
We demonstrate a biomimetic synthesis methodology that allows us to create Li2O-MgO-P2O5-TiO2 nanocrystalline glass with mesoporous structure at lower temperature. We design a 'nanocrystal-glass' configuration to build a nanoarchitecture by means of yeast cell templates self-assembly followed by the controlled in-situ biomineralization of materials on the cell wall. Electrochemically active nanocrystals are used as the lamellar building blocks of mesopores, and the semiconductive glass phase can act both as the 'glue' between nanocrystals and functionalized component. The Li2O-MgO-P2O5-TiO2 nanocrystalline glass exhibits outstanding thermal stability, high conductivity and wide potential window. This approach could be applied to many other multicomponent glass-ceramics to fabricate mesoporous conducting materials for solid-state lithium batteries.
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Affiliation(s)
- Xiaoyong Du
- Shandong Provincial Key Laboratory of Processing and Testing Technology of Glass and Functional Ceramics, Shandong Polytechnic University, Jinan, 250353, China
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257
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Liang J, Ning JC, Zhao H. Coordinated induction of multi-gene pathways in Saccharomyces cerevisiae. Nucleic Acids Res 2012; 41:e54. [PMID: 23262224 PMCID: PMC3581276 DOI: 10.1093/nar/gks1293] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Bacterial operons are nature’s tool for regulating and coordinating multi-gene expression in prokaryotes. They are also a gene architecture commonly used in the biosynthesis of many pharmaceutically important compounds and industrially useful chemicals. Despite being an important eukaryotic production host, Saccharomyces cerevisiae has never had such gene architecture. Here, we report the development of a system to assemble and regulate a multi-gene pathway in S. cerevisiae. Full pathways can be constructed using pre-made parts from a plasmid toolbox. Subsequently, through the use of a yeast strain containing a stably integrated gene switch, the assembled pathway can be regulated using a readily available and inexpensive compound—estradiol—with extremely high sensitivity (10 nM). To demonstrate the use of the system, we assembled the five-gene zeaxanthin biosynthetic pathway in a single step and showed the ligand-dependent coordinated expression of all five genes as well as the tightly regulated production of zeaxanthin. Compared with a previously reported constitutive zeaxanthin pathway, our inducible pathway was shown to have 50-fold higher production level.
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Affiliation(s)
- Jing Liang
- Department of Chemical and Biomolecular Engineering and Departments of Chemistry, Biochemistry, and Bioengineering, Center for Biophysics and Computational Biology, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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258
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Ha SJ, Galazka JM, Joong Oh E, Kordić V, Kim H, Jin YS, Cate JHD. Energetic benefits and rapid cellobiose fermentation by Saccharomyces cerevisiae expressing cellobiose phosphorylase and mutant cellodextrin transporters. Metab Eng 2012. [PMID: 23178501 DOI: 10.1016/j.ymben.2012.11.005] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Anaerobic bacteria assimilate cellodextrins from plant biomass by using a phosphorolytic pathway to generate glucose intermediates for growth. The yeast Saccharomyces cerevisiae can also be engineered to ferment cellobiose to ethanol using a cellodextrin transporter and a phosphorolytic pathway. However, strains with an intracellular cellobiose phosphorylase initially fermented cellobiose slowly relative to a strain employing an intracellular β-glucosidase. Fermentations by the phosphorolytic strains were greatly improved by using cellodextrin transporters with elevated rates of cellobiose transport. Furthermore under stress conditions, these phosphorolytic strains had higher biomass and ethanol yields compared to hydrolytic strains. These observations suggest that, although cellobiose phosphorolysis has energetic advantages, phosphorolytic strains are limited by the thermodynamics of cellobiose phosphorolysis (ΔG°=+3.6kJmol(-1)). A thermodynamic "push" from the reaction immediately upstream (transport) is therefore likely to be necessary to achieve high fermentation rates and energetic benefits of phosphorolysis pathways in engineered S. cerevisiae.
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Affiliation(s)
- Suk-Jin Ha
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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259
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Bioprospecting of thermo- and osmo-tolerant fungi from mango pulp-peel compost for bioethanol production. Antonie van Leeuwenhoek 2012. [PMID: 23180376 DOI: 10.1007/s10482-012-9854-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The persistent edaphic stress on microbial succession due to dynamic changes during composting was explored for selection of multi-stress tolerant microbe(s) desirable for ethanol production. A total of 23 strains were isolated from mango compost using four successive enrichments in YP broth (g l(-1)): glucose, 100; 150; 250 with ethanol (40) and cycloheximide (0.4) at 40 °C, pH 6.0. Based on multi-gene ribotyping, 14 yeasts (61 %) of Saccharomycetaceae, 2 filamentous fungi (8.6 %) and 7 bacteria (30.4 %) were obtained. Phenetic and phylogenetic analysis of the 14 yeasts revealed 64.3 % tolerant to 500 g l(-1) glucose, growth at 45 °C and resemblance to Candida sp. (14.3 %), Kluyveromyces marxianus (35.7 %), Pichia kudriavzevii (21.4 %) and Saccharomyces cerevisiae (28.6 %). Assessment of the 14 yeasts in glucose fermentation medium (pH 4.5 at 40 °C) showed ethanol productivity of ≥92 % by 12 yeasts with theoretical yields of 90-97 %. Fermentation of molasses (150 g l(-1) glucose equivalent) by P. kudriavzevii D1C at 40 °C resulted in 73.70 ± 0.02 g l(-1) ethanol and productivity of 4.91 ± 0.01 g l(-1) h(-1). Assessment of P. kudriavzevii D1C revealed multi-stress tolerance towards 5-hydroxymethyl furfural, ethanol (20 %, v/v), high gravity and H2O2 (0.3 M) indicating suitability for ethanol production using high gravity molasses and pre-treated lignocellulosic biomass fermentation.
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260
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Karim AS, Curran KA, Alper HS. Characterization of plasmid burden and copy number in Saccharomyces cerevisiae for optimization of metabolic engineering applications. FEMS Yeast Res 2012; 13:107-16. [PMID: 23107142 DOI: 10.1111/1567-1364.12016] [Citation(s) in RCA: 140] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Revised: 10/22/2012] [Accepted: 10/23/2012] [Indexed: 11/28/2022] Open
Abstract
Many metabolic engineering and genetic engineering applications in yeast rely on the use of plasmids. Despite their pervasive use and the diverse collections available, there is a fundamental lack of understanding of how commonly used DNA plasmids affect the cell's ability to grow and how the choice of plasmid components can influence plasmid load and burden. In this study, we characterized the major attributes of the 2 micron and centromeric plasmids typically used in yeast by examining the impact of choice of selection marker, promoter, origin of replication, and strain ploidy on conferred growth rates and plasmid copy number. We conclude that the 'plasmid burden', as demonstrated by a reduced growth rate, is primarily due to the choice of selection marker, especially when auxotrophic markers are utilized. The plasmid burden traditionally attributed to replication and maintenance of plasmid DNA plays only a minor role in haploid yeast yet is much more significant in diploid strains. The selection marker can also significantly change plasmid copy number. In fact, plasmid copy number can be influenced to some extent by all of the parameters tested. The information presented in this study will allow for more rational design and selection of plasmids for engineering applications.
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Affiliation(s)
- Ashty S Karim
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
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261
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Chen Y, Daviet L, Schalk M, Siewers V, Nielsen J. Establishing a platform cell factory through engineering of yeast acetyl-CoA metabolism. Metab Eng 2012; 15:48-54. [PMID: 23164578 DOI: 10.1016/j.ymben.2012.11.002] [Citation(s) in RCA: 228] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 10/01/2012] [Accepted: 11/05/2012] [Indexed: 11/29/2022]
Abstract
Production of fuels and chemicals by industrial biotechnology requires efficient, safe and flexible cell factory platforms that can be used for production of a wide range of compounds. Here we developed a platform yeast cell factory for efficient provision of acetyl-CoA that serves as precursor metabolite for a wide range of industrially interesting products. We demonstrate that the platform cell factory can be used to improve the production of α-santalene, a plant sesquiterpene that can be used as a perfume by four-fold. This strain would be a useful tool to produce a wide range of acetyl-CoA-derived products.
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Affiliation(s)
- Yun Chen
- Department of Chemical and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
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262
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Aragon AD, Torrez-Martinez N, Edwards JS. Genomic analysis of Saccharomyces cerevisiae isolates that grow optimally with glucose as the sole carbon source. Electrophoresis 2012; 33:3514-20. [PMID: 23135695 DOI: 10.1002/elps.201200172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Revised: 07/07/2012] [Accepted: 07/09/2012] [Indexed: 11/07/2022]
Abstract
A population of Saccharomyces cerevisiae was cultured for approximately 450 generations in the presence of high glucose to select for genetic variants that grew optimally under these conditions. Using the parental strain BY4741 as the starting population, an evolved culture was obtained after aerobic growth in a high glucose medium for approximately 450 generations. After the evolution period, three single colony isolates were selected for analysis. Next-generation Ion Torrent sequencing was used to evaluate genetic changes. Greater than 100 deletion/insertion changes were found with approximately half of these effecting genes. Additionally, over 180 SNPs were identified with more than one-quarter of these resulting in a nonsynonymous mutation. Affymetrix DNA microarrays and RNseq analysis were used to determine differences in gene expression in the evolved strains compared to the parental strain. It was established that approximately 900 genes demonstrated significantly altered expression in the evolved strains relative to the parental strain. Many of these genes showed similar alterations in their expression in all three evolved strains. Interestingly, genes with altered expression in the three evolved strains included genes with a role in oxidative metabolism. Overall these results are consistent with the physiological observations of optimal growth with glucose as the carbon source. Namely, the decreased ethanol production suggest that the underlying metabolism switched from fermentation to respiration during the selection for optimal growth on glucose.
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Affiliation(s)
- Anthony D Aragon
- UNM Department of Molecular Genetics and Microbiology, University of New Mexico, Albuquerque, NM 87131, USA
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263
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Kampranis SC, Makris AM. Developing a yeast cell factory for the production of terpenoids. Comput Struct Biotechnol J 2012; 3:e201210006. [PMID: 24688666 PMCID: PMC3962098 DOI: 10.5936/csbj.201210006] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 10/25/2012] [Accepted: 10/25/2012] [Indexed: 12/21/2022] Open
Abstract
Technological developments over the past century have made microbes the work-horses of large scale industrial production processes. Current efforts focus on the metabolic engineering of microbial strains to produce high levels of desirable end-products. The arsenal of the contemporary metabolic engineer contains tools that allow either targeted rational interventions or global screens that combine classical approaches with –omics technologies. Production of terpenoids in S. cerevisiae presents a characteristic example of contemporary biotechnology that integrates all the variety of novel approaches used in metabolic engineering. Terpenoids have attracted significant interest as pharmaceuticals, flavour and fragrance additives, and, more recently, biofuels. The ongoing metabolic engineering efforts, combined with the continuously increasing number of terpene biosynthetic enzymes discovered will enable the economical and environmentally friendly production of a wide range of compounds.
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Affiliation(s)
| | - Antonios M Makris
- Institute of Applied Biosciences/ CERTH, P.O. Box 60361, Thermi 57001, Thessaloniki, Greece
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264
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Enhancement of stress tolerance and ethanol production in Saccharomyces cerevisiae by heterologous expression of a trehalose biosynthetic gene from Streptomyces albus. BIOTECHNOL BIOPROC E 2012. [DOI: 10.1007/s12257-012-0148-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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265
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Huisjes EH, Luttik MAH, Almering MJH, Bisschops MMM, Dang DHN, Kleerebezem M, Siezen R, van Maris AJA, Pronk JT. Toward pectin fermentation by Saccharomyces cerevisiae: expression of the first two steps of a bacterial pathway for D-galacturonate metabolism. J Biotechnol 2012; 162:303-10. [PMID: 23079077 DOI: 10.1016/j.jbiotec.2012.10.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 10/04/2012] [Accepted: 10/08/2012] [Indexed: 10/27/2022]
Abstract
Saccharomyces cerevisiae cannot metabolize D-galacturonate, an important monomer of pectin. Use of S. cerevisiae for production of ethanol or other compounds of interest from pectin-rich feedstocks therefore requires introduction of a heterologous pathway for D-galacturonate metabolism. Bacterial D-galacturonate pathways involve D-galacturonate isomerase, D-tagaturonate reductase and three additional enzymes. This study focuses on functional expression of bacterial D-galacturonate isomerases in S. cerevisiae. After demonstrating high-level functional expression of a D-tagaturonate reductase gene (uxaB from Lactococcus lactis), the resulting yeast strain was used to screen for functional expression of six codon-optimized bacterial D-galacturonate isomerase (uxaC) genes. The L. lactis uxaC gene stood out, yielding a tenfold higher enzyme activity than the other uxaC genes. Efficient expression of D-galacturonate isomerase and D-tagaturonate reductase represents an important step toward metabolic engineering of S. cerevisiae for bioethanol production from D-galacturonate. To investigate in vivo activity of the first steps of the D-galacturonate pathway, the L. lactis uxaB and uxaC genes were expressed in a gpd1Δ gpd2Δ S. cerevisiae strain. Although D-tagaturonate reductase could, in principle, provide an alternative means for re-oxidizing cytosolic NADH, addition of D-galacturonate did not restore anaerobic growth, possibly due to absence of a functional D-altronate exporter in S. cerevisiae.
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Affiliation(s)
- Eline H Huisjes
- Department of Biotechnology, Delft University of Technology and Kluyver Centre for Genomics of Industrial Fermentation, Julianalaan 67, 2628 BC Delft, The Netherlands
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266
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Oud B, Flores CL, Gancedo C, Zhang X, Trueheart J, Daran JM, Pronk JT, van Maris AJA. An internal deletion in MTH1 enables growth on glucose of pyruvate-decarboxylase negative, non-fermentative Saccharomyces cerevisiae. Microb Cell Fact 2012; 11:131. [PMID: 22978798 PMCID: PMC3503853 DOI: 10.1186/1475-2859-11-131] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 09/11/2012] [Indexed: 12/02/2022] Open
Abstract
Background Pyruvate-decarboxylase negative (Pdc-) strains of Saccharomyces cerevisiae combine the robustness and high glycolytic capacity of this yeast with the absence of alcoholic fermentation. This makes Pdc-S. cerevisiae an interesting platform for efficient conversion of glucose towards pyruvate-derived products without formation of ethanol as a by-product. However, Pdc- strains cannot grow on high glucose concentrations and require C2-compounds (ethanol or acetate) for growth under conditions with low glucose concentrations, which hitherto has limited application in industry. Results Genetic analysis of a Pdc- strain previously evolved to overcome these deficiencies revealed a 225bp in-frame internal deletion in MTH1, encoding a transcriptional regulator involved in glucose sensing. This internal deletion contains a phosphorylation site required for degradation, thereby hypothetically resulting in increased stability of the protein. Reverse engineering of this alternative MTH1 allele into a non-evolved Pdc- strain enabled growth on 20 g l-1 glucose and 0.3% (v/v) ethanol at a maximum specific growth rate (0.24 h-1) similar to that of the evolved Pdc- strain (0.23 h-1). Furthermore, the reverse engineered Pdc- strain grew on glucose as sole carbon source, albeit at a lower specific growth rate (0.10 h-1) than the evolved strain (0.20 h-1). The observation that overexpression of the wild-type MTH1 allele also restored growth of Pdc-S. cerevisiae on glucose is consistent with the hypothesis that the internal deletion results in decreased degradation of Mth1. Reduced degradation of Mth1 has been shown to result in deregulation of hexose transport. In Pdc- strains, reduced glucose uptake may prevent intracellular accumulation of pyruvate and/or redox problems, while release of glucose repression due to the MTH1 internal deletion may contribute to alleviation of the C2-compound auxotrophy. Conclusions In this study we have discovered and characterised a mutation in MTH1 enabling Pdc- strains to grow on glucose as the sole carbon source. This successful example of reverse engineering not only increases the understanding of the glucose tolerance of evolved Pdc-S. cerevisiae, but also allows introduction of this portable genetic element into various industrial yeast strains, thereby simplifying metabolic engineering strategies.
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Affiliation(s)
- Bart Oud
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
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267
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Liang YL, Zhao SJ, Xu LX, Zhang XY. Heterologous expression of dammarenediol synthase gene in an engineered Saccharomyces cerevisiae. Lett Appl Microbiol 2012; 55:323-9. [PMID: 22897704 DOI: 10.1111/j.1472-765x.2012.03295.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS Dammarenediol production by an engineered yeast Saccharomyces cerevisiae was investigated. METHODS AND RESULTS A dammarenediol-producing engineered yeast was constructed by heterologous expression of the dammarenediol synthase gene from Panax ginseng hairy roots through RT-PCR. Fermentation was carried out in a 5-L GRJY-bioreactor with an inoculum size of 1% v/v at 30°C. Dammarenediol detection was performed with silica gel chromatography and HPLC. Determination of dammarenediol synthase activity subcellular distribution was carried out by surveying the enzyme activity in microsomes, lipid particles and total yeast homogenate. When cultured under aerobic conditions, the engineered yeast could produce dammarenediol up to 250μgl(-1). However, when an anaerobic shift strategy was employed, dammarenediol accumulated at a level as twice as that under aerobic condition. The dammarenediol synthase and dammarenediol were mainly localized in lipid particles. CONCLUSIONS Dammarenediol could be heterologously produced in engineered yeast. The heterologously expressed dammarenediol synthase is mainly localized in lipid particles. Anaerobic shift strategy could enhance the dammarenediol level in the engineered yeast. SIGNIFICANCE AND IMPACT OF THE STUDY This study showed that the high-value plant product dammarenediol could be produced by heterologous expression of the according gene in yeast. Furthermore, the anaerobic shift strategy could be potentially applied in oxidosqualene-derived compounds production in yeast. Here, the information about subcellular distribution of heterologously expressed dammarenediol synthase in the engineered yeast was also provided.
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Affiliation(s)
- Y-L Liang
- Department of Bioengineering, College of Biological and Agricultural Engineering, Jilin University, ChangChun, China
| | - S-J Zhao
- Department of Bioengineering, College of Biological and Agricultural Engineering, Jilin University, ChangChun, China
| | - L-X Xu
- Department of Bioengineering, College of Biological and Agricultural Engineering, Jilin University, ChangChun, China
| | - X-Y Zhang
- Department of Bioengineering, College of Biological and Agricultural Engineering, Jilin University, ChangChun, China
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268
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Cao Y, Cao Y, Zhao M. Biotechnological production of eicosapentaenoic acid: From a metabolic engineering point of view. Process Biochem 2012. [DOI: 10.1016/j.procbio.2012.05.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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269
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Goel A, Wortel MT, Molenaar D, Teusink B. Metabolic shifts: a fitness perspective for microbial cell factories. Biotechnol Lett 2012; 34:2147-60. [PMID: 22936303 PMCID: PMC3487007 DOI: 10.1007/s10529-012-1038-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 08/16/2012] [Indexed: 04/28/2023]
Abstract
Performance of industrial microorganisms as cell factories is limited by the capacity to channel nutrients to desired products, of which optimal production usually requires careful manipulation of process conditions, or strain improvement. The focus in process improvement is often on understanding and manipulating the regulation of metabolism. Nonetheless, one encounters situations where organisms are remarkably resilient to further optimization or their properties become unstable. Therefore it is important to understand the origin of these apparent limitations to find whether and how they can be improved. We argue that by considering fitness effects of regulation, a more generic explanation for certain behaviour can be obtained. In this view, apparent process limitations arise from trade-offs that cells faced as they evolved to improve fitness. A deeper understanding of such trade-offs using a systems biology approach can ultimately enhance performance of cell factories.
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Affiliation(s)
- Anisha Goel
- Systems Bioinformatics IBIVU, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
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270
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Yang J, Dang H, Lu JR. Improving genetic immobilization of a cellulase on yeast cell surface for bioethanol production using cellulose. J Basic Microbiol 2012; 53:381-9. [DOI: 10.1002/jobm.201100602] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2011] [Accepted: 03/03/2012] [Indexed: 11/08/2022]
Affiliation(s)
- Jinying Yang
- State Key Laboratory of Heavy Oil Processing & Centre for Bioengineering and Biotechnology; China University of Petroleum (East China); Qingdao; China
| | - Hongyue Dang
- State Key Laboratory of Heavy Oil Processing & Centre for Bioengineering and Biotechnology; China University of Petroleum (East China); Qingdao; China
| | - Jian Ren Lu
- Biological Physics Laboratory; School of Physics and Astronomy, University of Manchester; Manchester; UK
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271
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Zhou H, Cheng JS, Wang BL, Fink GR, Stephanopoulos G. Xylose isomerase overexpression along with engineering of the pentose phosphate pathway and evolutionary engineering enable rapid xylose utilization and ethanol production by Saccharomyces cerevisiae. Metab Eng 2012; 14:611-22. [PMID: 22921355 DOI: 10.1016/j.ymben.2012.07.011] [Citation(s) in RCA: 183] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Revised: 07/10/2012] [Accepted: 07/21/2012] [Indexed: 11/28/2022]
Abstract
Xylose is the main pentose and second most abundant sugar in lignocellulosic feedstocks. To improve xylose utilization, necessary for the cost-effective bioconversion of lignocellulose, several metabolic engineering approaches have been employed in the yeast Saccharomyces cerevisiae. In this study, we describe the rational metabolic engineering of a S. cerevisiae strain, including overexpression of the Piromyces xylose isomerase gene (XYLA), Pichia stipitis xylulose kinase (XYL3) and genes of the non-oxidative pentose phosphate pathway (PPP). This engineered strain (H131-A3) was used to initialize a three-stage process of evolutionary engineering, through first aerobic and anaerobic sequential batch cultivation followed by growth in a xylose-limited chemostat. The evolved strain H131-A3-AL(CS) displayed significantly increased anaerobic growth rate (0.203±0.006 h⁻¹) and xylose consumption rate (1.866 g g⁻¹ h⁻¹) along with high ethanol conversion yield (0.41 g/g). These figures exceed by a significant margin any other performance metrics on xylose utilization and ethanol production by S. cerevisiae reported to-date. Further inverse metabolic engineering based on functional complementation suggested that efficient xylose assimilation is attributed, in part, to the elevated expression level of xylose isomerase, which was accomplished through the multiple-copy integration of XYLA in the chromosome of the evolved strain.
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Affiliation(s)
- Hang Zhou
- Department of Chemical Engineering, Massachusetts Institute of Technology, Room 56-469, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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272
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Blazeck J, Alper HS. Promoter engineering: Recent advances in controlling transcription at the most fundamental level. Biotechnol J 2012; 8:46-58. [DOI: 10.1002/biot.201200120] [Citation(s) in RCA: 237] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Revised: 06/25/2012] [Accepted: 07/17/2012] [Indexed: 12/25/2022]
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273
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Zikmanis P, Kampenusa I. Relationships between kinetic constants and the amino acid composition of enzymes from the yeast Saccharomyces cerevisiae glycolysis pathway. EURASIP JOURNAL ON BIOINFORMATICS & SYSTEMS BIOLOGY 2012; 2012:11. [PMID: 22867018 PMCID: PMC3494524 DOI: 10.1186/1687-4153-2012-11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Accepted: 07/21/2012] [Indexed: 01/23/2023]
Abstract
The kinetic models of metabolic pathways represent a system of biochemical reactions in terms of metabolic fluxes and enzyme kinetics. Therefore, the apparent differences of metabolic fluxes might reflect distinctive kinetic characteristics, as well as sequence-dependent properties of the employed enzymes. This study aims to examine possible linkages between kinetic constants and the amino acid (AA) composition (AAC) for enzymes from the yeast Saccharomyces cerevisiae glycolytic pathway. The values of Michaelis-Menten constant (KM), turnover number (kcat), and specificity constant (ksp = kcat/KM) were taken from BRENDA (15, 17, and 16 values, respectively) and protein sequences of nine enzymes (HXK, GADH, PGK, PGM, ENO, PK, PDC, TIM, and PYC) from UniProtKB. The AAC and sequence properties were computed by ExPASy/ProtParam tool and data processed by conventional methods of multivariate statistics. Multiple linear regressions were found between the log-values of kcat (3 models, 85.74% < Radj.2 <94.11%, p < 0.00001), KM (1 model, Radj.2 = 96.70%, p < 0.00001), ksp (3 models, 96.15% < Radj.2 < 96.50%, p < 0.00001), and the sets of AA frequencies (four to six for each model) selected from enzyme sequences while assessing the potential multicollinearity between variables. It was also found that the selection of independent variables in multiple regression models may reflect certain advantages for definite AA physicochemical and structural propensities, which could affect the properties of sequences. The results support the view on the actual interdependence of catalytic, binding, and structural residues to ensure the efficiency of biocatalysts, since the kinetic constants of the yeast enzymes appear as closely related to the overall AAC of sequences.
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Affiliation(s)
- Peteris Zikmanis
- Institute of Microbiology and Biotechnology, University of Latvia, Kronvalda Boulevard 4, Riga, LV-1010, Latvia
| | - Inara Kampenusa
- Institute of Microbiology and Biotechnology, University of Latvia, Kronvalda Boulevard 4, Riga, LV-1010, Latvia
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274
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Self-surface assembly of cellulosomes with two miniscaffoldins on Saccharomyces cerevisiae for cellulosic ethanol production. Proc Natl Acad Sci U S A 2012; 109:13260-5. [PMID: 22853950 DOI: 10.1073/pnas.1209856109] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Yeast to directly convert cellulose and, especially, the microcrystalline cellulose into bioethanol, was engineered through display of minicellulosomes on the cell surface of Saccharomyces cerevisiae. The construction and cell surface attachment of cellulosomes were accomplished with two individual miniscaffoldins to increase the display level. All of the cellulases including a celCCA (endoglucanase), a celCCE (cellobiohydrolase), and a Ccel_2454 (β-glucosidase) were cloned from Clostridium cellulolyticum, ensuring the thermal compatibility between cellulose hydrolysis and yeast fermentation. Cellulases and one of miniscaffoldins were secreted by α-factor; thus, the assembly and attachment to anchoring miniscaffoldin were accomplished extracellularly. Immunofluorescence microscopy, flow cytometric analysis (FACS), and cellulosic ethanol fermentation confirmed the successful display of such complex on the yeast surface. Enzyme-enzyme synergy, enzyme-proximity synergy, and cellulose-enzyme-cell synergy were analyzed, and the length of anchoring miniscaffoldin was optimized. The engineered S. cerevisiae was applied in fermentation of carboxymethyl cellulose (CMC), phosphoric acid-swollen cellulose (PASC), or Avicel. It showed a significant hydrolytic activity toward microcrystalline cellulose, with an ethanol titer of 1,412 mg/L. This indicates that simultaneous saccharification and fermentation of crystalline cellulose to ethanol can be accomplished by the yeast, engineered with minicellulosome.
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275
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Hong KK, Nielsen J. Metabolic engineering of Saccharomyces cerevisiae: a key cell factory platform for future biorefineries. Cell Mol Life Sci 2012; 69:2671-90. [PMID: 22388689 PMCID: PMC11115109 DOI: 10.1007/s00018-012-0945-1] [Citation(s) in RCA: 318] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Revised: 02/07/2012] [Accepted: 02/15/2012] [Indexed: 11/25/2022]
Abstract
Metabolic engineering is the enabling science of development of efficient cell factories for the production of fuels, chemicals, pharmaceuticals, and food ingredients through microbial fermentations. The yeast Saccharomyces cerevisiae is a key cell factory already used for the production of a wide range of industrial products, and here we review ongoing work, particularly in industry, on using this organism for the production of butanol, which can be used as biofuel, and isoprenoids, which can find a wide range of applications including as pharmaceuticals and as biodiesel. We also look into how engineering of yeast can lead to improved uptake of sugars that are present in biomass hydrolyzates, and hereby allow for utilization of biomass as feedstock in the production of fuels and chemicals employing S. cerevisiae. Finally, we discuss the perspectives of how technologies from systems biology and synthetic biology can be used to advance metabolic engineering of yeast.
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Affiliation(s)
- Kuk-Ki Hong
- Novo Nordisk Centre for Biosustainability, Department of Chemical and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
- Research Institute of Biotechnology, CJ CheilJedang, Seoul, 157-724 Korea
| | - Jens Nielsen
- Novo Nordisk Centre for Biosustainability, Department of Chemical and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
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276
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Implementation of a transhydrogenase-like shunt to counter redox imbalance during xylose fermentation in Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2012; 97:1669-78. [PMID: 22851014 DOI: 10.1007/s00253-012-4298-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Revised: 07/10/2012] [Accepted: 07/11/2012] [Indexed: 01/10/2023]
Abstract
Three enzymes responsible for the transhydrogenase-like shunt, including malic enzyme (encoded by MAE1), malate dehydrogenase (MDH2), and pyruvate carboxylase (PYC2), were overexpressed to regulate the redox state in xylose-fermenting recombinant Saccharomyces cerevisiae. The YPH499XU/MAE1 strain was constructed by overexpressing native Mae1p in the YPH499XU strain expressing xylose reductase and xylitol dehydrogenase from Scheffersomyces stipitis, and native xylulokinase. Analysis of the xylose fermentation profile under semi-anaerobic conditions revealed that the ethanol yield in the YPH499XU/MAE1 strain (0.38 ± 0.01 g g⁻¹ xylose consumed) was improved from that of the control strain (0.31 ± 0.01 g g⁻¹ xylose consumed). Reduced xylitol production was also observed in YPH499XU/MAE1, suggesting that the redox balance was altered by Mae1p overexpression. Analysis of intracellular metabolites showed that the redox imbalance during xylose fermentation was partly relieved in the transformant. The specific ethanol production rate in the YPH499XU/MAE1-MDH2 strain was 1.25-fold higher than that of YPH499XU/MAE1 due to the additional overexpression of Mdh2p, whereas the ethanol yield was identical to that of YPH499XU/MAE1. The specific xylose consumption rate was drastically increased in the YPH499XU/MAE1-MDH2-PYC2 strain. However, poor ethanol yield as well as increased production of xylitol was observed. These results demonstrate that the transhydrogenase function implemented in S. cerevisiae can regulate the redox state of yeast cells.
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277
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Wang Z, Gao C, Wang Q, Liang Q, Qi Q. Production of pyruvate in Saccharomyces cerevisiae through adaptive evolution and rational cofactor metabolic engineering. Biochem Eng J 2012. [DOI: 10.1016/j.bej.2012.06.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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278
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Steensels J, Snoek T, Meersman E, Picca Nicolino M, Aslankoohi E, Christiaens JF, Gemayel R, Meert W, New AM, Pougach K, Saels V, van der Zande E, Voordeckers K, Verstrepen KJ. Selecting and generating superior yeasts for the brewing industry. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.cervis.2012.08.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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279
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Abstract
A metabolism is a complex network of chemical reactions that converts sources of energy and chemical elements into biomass and other molecules. To design a metabolism from scratch and to implement it in a synthetic genome is almost within technological reach. Ideally, a synthetic metabolism should be able to synthesize a desired spectrum of molecules at a high rate, from multiple different nutrients, while using few chemical reactions, and producing little or no waste. Not all of these properties are achievable simultaneously. We here use a recently developed technique to create random metabolic networks with pre-specified properties to quantify trade-offs between these and other properties. We find that for every additional molecule to be synthesized a network needs on average three additional reactions. For every additional carbon source to be utilized, it needs on average two additional reactions. Networks able to synthesize 20 biomass molecules from each of 20 alternative sole carbon sources need to have at least 260 reactions. This number increases to 518 reactions for networks that can synthesize more than 60 molecules from each of 80 carbon sources. The maximally achievable rate of biosynthesis decreases by approximately 5 percent for every additional molecule to be synthesized. Biochemically related molecules can be synthesized at higher rates, because their synthesis produces less waste. Overall, the variables we study can explain 87 percent of variation in network size and 84 percent of the variation in synthesis rate. The constraints we identify prescribe broad boundary conditions that can help to guide synthetic metabolism design.
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Affiliation(s)
- Tugce Bilgin
- Institute of Evolutionary Biology and Environmental Sciences, University of Zurich, Zürich, Switzerland.
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280
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Edwards MC, Doran-Peterson J. Pectin-rich biomass as feedstock for fuel ethanol production. Appl Microbiol Biotechnol 2012; 95:565-75. [PMID: 22695801 PMCID: PMC3396330 DOI: 10.1007/s00253-012-4173-2] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Revised: 05/11/2012] [Accepted: 05/13/2012] [Indexed: 01/17/2023]
Abstract
The USA has proposed that 30 % of liquid transportation fuel be produced from renewable resources by 2030 (Perlack and Stokes 2011). It will be impossible to reach this goal using corn kernel-based ethanol alone. Pectin-rich biomass, an under-utilized waste product of the sugar and juice industry, can augment US ethanol supplies by capitalizing on this already established feedstock. Currently, pectin-rich biomass is sold (at low value) as animal feed. This review focuses on the three most studied types of pectin-rich biomass: sugar beet pulp, citrus waste and apple pomace. Fermentations of these materials have been conducted with a variety of ethanologens, including yeasts and bacteria. Escherichia coli can ferment a wide range of sugars including galacturonic acid, the primary component of pectin. However, the mixed acid metabolism of E. coli can produce unwanted side products. Saccharomyces cerevisiae cannot naturally ferment galacturonic acid nor pentose sugars but has a homoethanol pathway. Erwinia chrysanthemi is capable of degrading many of the cell wall components of pectin-rich materials, including pectin. Klebsiella oxytoca can metabolize a diverse array of sugars including cellobiose, one degradation product of cellulose. However, both E. chrysanthemi and K. oxytoca produce side products during fermentation, similar to E. coli. Using pectin-rich residues from industrial processes is beneficial because the material is already collected and partially pretreated to facilitate enzymatic deconstruction of the plant cell walls. Using biomass already produced for other purposes is an attractive practice because fewer greenhouse gases (GHG) will be anticipated from land-use changes.
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Affiliation(s)
- Meredith C Edwards
- Department of Microbiology, University of Georgia, 1000 Cedar Street, 550, Biological Sciences, Athens, GA 30602, USA
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281
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Directed evolution of xylose isomerase for improved xylose catabolism and fermentation in the yeast Saccharomyces cerevisiae. Appl Environ Microbiol 2012; 78:5708-16. [PMID: 22685138 DOI: 10.1128/aem.01419-12] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The heterologous expression of a highly functional xylose isomerase pathway in Saccharomyces cerevisiae would have significant advantages for ethanol yield, since the pathway bypasses cofactor requirements found in the traditionally used oxidoreductase pathways. However, nearly all reported xylose isomerase-based pathways in S. cerevisiae suffer from poor ethanol productivity, low xylose consumption rates, and poor cell growth compared with an oxidoreductase pathway and, additionally, often require adaptive strain evolution. Here, we report on the directed evolution of the Piromyces sp. xylose isomerase (encoded by xylA) for use in yeast. After three rounds of mutagenesis and growth-based screening, we isolated a variant containing six mutations (E15D, E114G, E129D, T142S, A177T, and V433I) that exhibited a 77% increase in enzymatic activity. When expressed in a minimally engineered yeast host containing a gre3 knockout and tal1 and XKS1 overexpression, the strain expressing this mutant enzyme improved its aerobic growth rate by 61-fold and both ethanol production and xylose consumption rates by nearly 8-fold. Moreover, the mutant enzyme enabled ethanol production by these yeasts under oxygen-limited fermentation conditions, unlike the wild-type enzyme. Under microaerobic conditions, the ethanol production rates of the strain expressing the mutant xylose isomerase were considerably higher than previously reported values for yeast harboring a xylose isomerase pathway and were also comparable to those of the strains harboring an oxidoreductase pathway. Consequently, this study shows the potential to evolve a xylose isomerase pathway for more efficient xylose utilization.
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282
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Yamanishi M, Matsuyama T. A modified Cre-lox genetic switch to dynamically control metabolic flow in Saccharomyces cerevisiae. ACS Synth Biol 2012; 1:172-80. [PMID: 23651155 DOI: 10.1021/sb200017p] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The control of metabolic flow is a prerequisite for efficient chemical production in transgenic microorganisms. Exogenous genes required for the biosynthesis of target chemicals are expressed under strong promoters, while the endogenous genes of the original metabolic pathway are repressed by disruption or mutation. These genetic manipulations occasionally cause harmful effects to the host. In the lactate-producing yeast Saccharomyces cerevisiae, where endogenous pyruvate decarboxylase (PDC) is disrupted and exogenous lactate dehydrogenase (LDH) is introduced, PDC deletion is extremely detrimental to cell growth but is required for efficient production of lactate. A suitable means to dynamically control the metabolic flow from ethanol fermentation during the growth phase to lactate fermentation during the production phase is needed. Here, we demonstrated that this flow can be controlled by the exclusive expression of PDC and LDH with a Cre-lox genetic switch. This switch was evaluated with a gene cassette that encoded two different fluorescence proteins and enabled changes in genotype and phenotype within 2 and 10 h, respectively. Transgenic yeast harboring this switch and the PDC-LDH cassette showed a specific growth rate (0.45 h (-1)) that was almost the same as that of wild-type (0.47 h (-1)). Upon induction of the genetic switch, the transgenic yeast produced lactate from up to 85.4% of the glucose substrate, while 91.7% of glucose went to ethanol before induction. We thus propose a "metabolic shift" concept that can serve as an alternative means to obtain gene products that are currently difficult to obtain by using conventional methodologies.
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Affiliation(s)
- Mamoru Yamanishi
- Toyota Central Research and Development
Laboratories,
Inc., 41-1 Nagakute Yokomichi, Nagakute, Aichi 480-1192, Japan
| | - Takashi Matsuyama
- Toyota Central Research and Development
Laboratories,
Inc., 41-1 Nagakute Yokomichi, Nagakute, Aichi 480-1192, Japan
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283
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Walker GM. 125th Anniversary Review: Fuel Alcohol: Current Production and Future Challenges. JOURNAL OF THE INSTITUTE OF BREWING 2012. [DOI: 10.1002/j.2050-0416.2011.tb00438.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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284
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Bergdahl B, Heer D, Sauer U, Hahn-Hägerdal B, van Niel EWJ. Dynamic metabolomics differentiates between carbon and energy starvation in recombinant Saccharomyces cerevisiae fermenting xylose. BIOTECHNOLOGY FOR BIOFUELS 2012; 5:34. [PMID: 22587303 PMCID: PMC3462113 DOI: 10.1186/1754-6834-5-34] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Accepted: 04/23/2012] [Indexed: 05/15/2023]
Abstract
BACKGROUND The concerted effects of changes in gene expression due to changes in the environment are ultimately reflected in the metabolome. Dynamics of metabolite concentrations under a certain condition can therefore give a description of the cellular state with a high degree of functional information. We used this potential to evaluate the metabolic status of two recombinant strains of Saccharomyces cerevisiae during anaerobic batch fermentation of a glucose/xylose mixture. Two isogenic strains were studied, differing only in the pathways used for xylose assimilation: the oxidoreductive pathway with xylose reductase (XR) and xylitol dehydrogenase (XDH) or the isomerization pathway with xylose isomerase (XI). The isogenic relationship between the two strains ascertains that the observed responses are a result of the particular xylose pathway and not due to unknown changes in regulatory systems. An increased understanding of the physiological state of these strains is important for further development of efficient pentose-utilizing strains for bioethanol production. RESULTS Using LC-MS/MS we determined the dynamics in the concentrations of intracellular metabolites in central carbon metabolism, nine amino acids, the purine nucleotides and redox cofactors. The general response to the transition from glucose to xylose was increased concentrations of amino acids and TCA-cycle intermediates, and decreased concentrations of sugar phosphates and redox cofactors. The two strains investigated had significantly different uptake rates of xylose which led to an enhanced response in the XI-strain. Despite the difference in xylose uptake rate, the adenylate energy charge remained high and stable around 0.8 in both strains. In contrast to the adenylate pool, large changes were observed in the guanylate pool. CONCLUSIONS The low uptake of xylose by the XI-strain led to several distinguished responses: depletion of key metabolites in glycolysis and NADPH, a reduced GTP/GDP ratio and accumulation of PEP and aromatic amino acids. These changes are strong indicators of carbon starvation. The XR/XDH-strain displayed few such traits. The coexistence of these traits and a stable adenylate charge indicates that xylose supplies energy to the cells but does not suppress a response similar to carbon starvation. Particular signals may play a role in the latter, of which the GTP/GMP ratio could be a candidate as it decreased significantly in both strains.
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Affiliation(s)
- Basti Bergdahl
- Applied Microbiology, Lund University, PO Box 124, SE-221 00, Lund, Sweden
| | | | - Uwe Sauer
- ETH Zurich, Zurich, 8093, Switzerland
| | | | - Ed WJ van Niel
- Applied Microbiology, Lund University, PO Box 124, SE-221 00, Lund, Sweden
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285
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Kato H, Izumi Y, Hasunuma T, Matsuda F, Kondo A. Widely targeted metabolic profiling analysis of yeast central metabolites. J Biosci Bioeng 2012; 113:665-73. [DOI: 10.1016/j.jbiosc.2011.12.013] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Revised: 12/09/2011] [Accepted: 12/25/2011] [Indexed: 11/26/2022]
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286
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Dymond J, Boeke J. The Saccharomyces cerevisiae SCRaMbLE system and genome minimization. Bioeng Bugs 2012; 3:168-71. [PMID: 22572789 DOI: 10.4161/bbug.19543] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We have recently reported the first partially synthetic eukaryotic genome. Saccharomyces cerevisiae chromosomes synIXR and semi-synVIL are fully synthetic versions of the right arm of chromosome IX and the telomeric segment of the left arm of chromosome VI, respectively, and represent the beginning of the synthetic yeast genome project, Sc2.0, that progressively replaces native yeast DNA with synthetic sequences. We have designed synthetic chromosome sequences according to principles specifying a wild-type phenotype, highly stable genome, and maintenance of genetic flexibility. Although other synthetic genome projects exist, the Sc2.0 approach is unique in that we have implemented design specifications predicted to generate a wild-type phenotype until induction of "SCRaMbLE," an inducible evolution system that generates significant genetic diversity. Here we further explore the significance of Sc2.0 and show how SCRaMbLE can serve as a genome minimization tool.
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Affiliation(s)
- Jessica Dymond
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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287
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Celton M, Goelzer A, Camarasa C, Fromion V, Dequin S. A constraint-based model analysis of the metabolic consequences of increased NADPH oxidation in Saccharomyces cerevisiae. Metab Eng 2012; 14:366-79. [PMID: 22709677 DOI: 10.1016/j.ymben.2012.03.008] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Revised: 01/22/2012] [Accepted: 03/16/2012] [Indexed: 11/28/2022]
Abstract
Controlling the amounts of redox cofactors to manipulate metabolic fluxes is emerging as a useful approach to optimizing byproduct yields in yeast biotechnological processes. Redox cofactors are extensively interconnected metabolites, so predicting metabolite patterns is challenging and requires in-depth knowledge of how the metabolic network responds to a redox perturbation. Our aim was to analyze comprehensively the metabolic consequences of increased cytosolic NADPH oxidation during yeast fermentation. Using a genetic device based on the overexpression of a modified 2,3-butanediol dehydrogenase catalyzing the NADPH-dependent reduction of acetoin into 2,3-butanediol, we increased the NADPH demand to between 8 and 40-fold the anabolic demand. We developed (i) a dedicated constraint-based model of yeast fermentation and (ii) a constraint-based modeling method based on the dynamical analysis of mass distribution to quantify the in vivo contribution of pathways producing NADPH to the maintenance of redox homeostasis. We report that yeast responds to NADPH oxidation through a gradual increase in the flux through the PP and acetate pathways, providing 80% and 20% of the NADPH demand, respectively. However, for the highest NADPH demand, the model reveals a saturation of the PP pathway and predicts an exchange between NADH and NADPH in the cytosol that may be mediated by the glycerol-DHA futile cycle. We also reveal the contribution of mitochondrial shuttles, resulting in a net production of NADH in the cytosol, to fine-tune the NADH/NAD(+) balance. This systems level study helps elucidate the physiological adaptation of yeast to NADPH perturbation. Our findings emphasize the robustness of yeast to alterations in NADPH metabolism and highlight the role of the glycerol-DHA cycle as a redox valve, providing additional NADPH from NADH under conditions of very high demand.
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Affiliation(s)
- Magalie Celton
- INRA, UMR1083, Sciences Pour l'Oenologie, 2 Place Viala, F-34060 Montpellier, France.
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288
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Kato H, Suyama H, Yamada R, Hasunuma T, Kondo A. Improvements in ethanol production from xylose by mating recombinant xylose-fermenting Saccharomyces cerevisiae strains. Appl Microbiol Biotechnol 2012; 94:1585-92. [PMID: 22406859 DOI: 10.1007/s00253-012-3914-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Revised: 01/13/2012] [Accepted: 01/19/2012] [Indexed: 11/30/2022]
Abstract
To improve the ability of recombinant Saccharomyces cerevisiae strains to utilize the hemicellulose components of lignocellulosic feedstocks, the efficiency of xylose conversion to ethanol needs to be increased. In the present study, xylose-fermenting, haploid, yeast cells of the opposite mating type were hybridized to produce a diploid strain harboring two sets of xylose-assimilating genes encoding xylose reductase, xylitol dehydrogenase, and xylulokinase. The hybrid strain MN8140XX showed a 1.3- and 1.9-fold improvement in ethanol production compared to its parent strains MT8-1X405 and NBRC1440X, respectively. The rate of xylose consumption and ethanol production was also improved by the hybridization. This study revealed that the resulting improvements in fermentation ability arose due to chromosome doubling as well as the increase in the copy number of xylose assimilation genes. Moreover, compared to the parent strain, the MN8140XX strain exhibited higher ethanol production under elevated temperatures (38 °C) and acidic conditions (pH 3.8). Thus, the simple hybridization technique facilitated an increase in the xylose fermentation activity.
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Affiliation(s)
- Hiroko Kato
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodaicho, Nada, Kobe 657-8501, Japan
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289
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Laluce C, Schenberg ACG, Gallardo JCM, Coradello LFC, Pombeiro-Sponchiado SR. Advances and Developments in Strategies to Improve Strains of Saccharomyces cerevisiae and Processes to Obtain the Lignocellulosic Ethanol−A Review. Appl Biochem Biotechnol 2012; 166:1908-26. [DOI: 10.1007/s12010-012-9619-6] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Accepted: 02/16/2012] [Indexed: 10/28/2022]
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290
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Xu G, Liu L, Chen J. Reconstruction of cytosolic fumaric acid biosynthetic pathways in Saccharomyces cerevisiae. Microb Cell Fact 2012; 11:24. [PMID: 22335940 PMCID: PMC3340314 DOI: 10.1186/1475-2859-11-24] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 02/15/2012] [Indexed: 11/12/2022] Open
Abstract
Background Fumaric acid is a commercially important component of foodstuffs, pharmaceuticals and industrial materials, yet the current methods of production are unsustainable and ecologically destructive. Results In this study, the fumarate biosynthetic pathway involving reductive reactions of the tricarboxylic acid cycle was exogenously introduced in S. cerevisiae by a series of simple genetic modifications. First, the Rhizopus oryzae genes for malate dehydrogenase (RoMDH) and fumarase (RoFUM1) were heterologously expressed. Then, expression of the endogenous pyruvate carboxylase (PYC2) was up-regulated. The resultant yeast strain, FMME-001 ↑PYC2 + ↑RoMDH, was capable of producing significantly higher yields of fumarate in the glucose medium (3.18 ± 0.15 g liter-1) than the control strain FMME-001 empty vector. Conclusions The results presented here provide a novel strategy for fumarate biosynthesis, which represents an important advancement in producing high yields of fumarate in a sustainable and ecologically-friendly manner.
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Affiliation(s)
- Guoqiang Xu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
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291
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Benjaphokee S, Hasegawa D, Yokota D, Asvarak T, Auesukaree C, Sugiyama M, Kaneko Y, Boonchird C, Harashima S. Highly efficient bioethanol production by a Saccharomyces cerevisiae strain with multiple stress tolerance to high temperature, acid and ethanol. N Biotechnol 2012; 29:379-86. [DOI: 10.1016/j.nbt.2011.07.002] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2011] [Revised: 06/20/2011] [Accepted: 07/11/2011] [Indexed: 10/17/2022]
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292
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Swinnen S, Thevelein JM, Nevoigt E. Genetic mapping of quantitative phenotypic traits in Saccharomyces cerevisiae. FEMS Yeast Res 2012; 12:215-27. [PMID: 22150948 DOI: 10.1111/j.1567-1364.2011.00777.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Revised: 12/01/2011] [Accepted: 12/05/2011] [Indexed: 12/13/2022] Open
Abstract
Saccharomyces cerevisiae has become a favorite production organism in industrial biotechnology presenting new challenges to yeast engineers in terms of introducing advantageous traits such as stress tolerances. Exploring subspecies diversity of S. cerevisiae has identified strains that bear industrially relevant phenotypic traits. Provided that the genetic basis of such phenotypic traits can be identified inverse engineering allows the targeted modification of production strains. Most phenotypic traits of interest in S. cerevisiae strains are quantitative, meaning that they are controlled by multiple genetic loci referred to as quantitative trait loci (QTL). A straightforward approach to identify the genetic basis of quantitative traits is QTL mapping which aims at the allocation of the genetic determinants to regions in the genome. The application of high-density oligonucleotide arrays and whole-genome re-sequencing to detect genetic variations between strains has facilitated the detection of large numbers of molecular markers thus allowing high-resolution QTL mapping over the entire genome. This review focuses on the basic principle and state of the art of QTL mapping in S. cerevisiae. Furthermore we discuss several approaches developed during the last decade that allow down-scaling of the regions identified by QTL mapping to the gene level. We also emphasize the particular challenges of QTL mapping in nonlaboratory strains of S. cerevisiae.
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Affiliation(s)
- Steve Swinnen
- School of Engineering and Science, Jacobs University gGmbH, Bremen, Germany
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293
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Kim IK, Roldão A, Siewers V, Nielsen J. A systems-level approach for metabolic engineering of yeast cell factories. FEMS Yeast Res 2012; 12:228-48. [DOI: 10.1111/j.1567-1364.2011.00779.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Revised: 12/05/2011] [Accepted: 12/09/2011] [Indexed: 12/01/2022] Open
Affiliation(s)
- Il-Kwon Kim
- Department of Chemical and Biological Engineering; Chalmers University of Technology; Gothenburg; Sweden
| | - António Roldão
- Department of Chemical and Biological Engineering; Chalmers University of Technology; Gothenburg; Sweden
| | - Verena Siewers
- Department of Chemical and Biological Engineering; Chalmers University of Technology; Gothenburg; Sweden
| | - Jens Nielsen
- Department of Chemical and Biological Engineering; Chalmers University of Technology; Gothenburg; Sweden
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294
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Oud B, van Maris AJA, Daran JM, Pronk JT. Genome-wide analytical approaches for reverse metabolic engineering of industrially relevant phenotypes in yeast. FEMS Yeast Res 2012; 12:183-96. [PMID: 22152095 PMCID: PMC3615171 DOI: 10.1111/j.1567-1364.2011.00776.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Revised: 11/21/2011] [Accepted: 11/21/2011] [Indexed: 11/28/2022] Open
Abstract
Successful reverse engineering of mutants that have been obtained by nontargeted strain improvement has long presented a major challenge in yeast biotechnology. This paper reviews the use of genome-wide approaches for analysis of Saccharomyces cerevisiae strains originating from evolutionary engineering or random mutagenesis. On the basis of an evaluation of the strengths and weaknesses of different methods, we conclude that for the initial identification of relevant genetic changes, whole genome sequencing is superior to other analytical techniques, such as transcriptome, metabolome, proteome, or array-based genome analysis. Key advantages of this technique over gene expression analysis include the independency of genome sequences on experimental context and the possibility to directly and precisely reproduce the identified changes in naive strains. The predictive value of genome-wide analysis of strains with industrially relevant characteristics can be further improved by classical genetics or simultaneous analysis of strains derived from parallel, independent strain improvement lineages.
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Affiliation(s)
- Bart Oud
- Department of Biotechnology, Delft University of Technology and Kluyver Centre for Genomics of Industrial Fermentation, Delft, The Netherlands
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295
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Li Y, Tschaplinski TJ, Engle NL, Hamilton CY, Rodriguez M, Liao JC, Schadt CW, Guss AM, Yang Y, Graham DE. Combined inactivation of the Clostridium cellulolyticum lactate and malate dehydrogenase genes substantially increases ethanol yield from cellulose and switchgrass fermentations. BIOTECHNOLOGY FOR BIOFUELS 2012; 5:2. [PMID: 22214220 PMCID: PMC3268733 DOI: 10.1186/1754-6834-5-2] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Accepted: 01/04/2012] [Indexed: 05/03/2023]
Abstract
BACKGROUND The model bacterium Clostridium cellulolyticum efficiently degrades crystalline cellulose and hemicellulose, using cellulosomes to degrade lignocellulosic biomass. Although it imports and ferments both pentose and hexose sugars to produce a mixture of ethanol, acetate, lactate, H2 and CO2, the proportion of ethanol is low, which impedes its use in consolidated bioprocessing for biofuels production. Therefore genetic engineering will likely be required to improve the ethanol yield. Plasmid transformation, random mutagenesis and heterologous expression systems have previously been developed for C. cellulolyticum, but targeted mutagenesis has not been reported for this organism, hindering genetic engineering. RESULTS The first targeted gene inactivation system was developed for C. cellulolyticum, based on a mobile group II intron originating from the Lactococcus lactis L1.LtrB intron. This markerless mutagenesis system was used to disrupt both the paralogous L-lactate dehydrogenase (Ccel_2485; ldh) and L-malate dehydrogenase (Ccel_0137; mdh) genes, distinguishing the overlapping substrate specificities of these enzymes. Both mutations were then combined in a single strain, resulting in a substantial shift in fermentation toward ethanol production. This double mutant produced 8.5-times more ethanol than wild-type cells growing on crystalline cellulose. Ethanol constituted 93% of the major fermentation products, corresponding to a molar ratio of ethanol to organic acids of 15, versus 0.18 in wild-type cells. During growth on acid-pretreated switchgrass, the double mutant also produced four times as much ethanol as wild-type cells. Detailed metabolomic analyses identified increased flux through the oxidative branch of the mutant's tricarboxylic acid pathway. CONCLUSIONS The efficient intron-based gene inactivation system produced the first non-random, targeted mutations in C. cellulolyticum. As a key component of the genetic toolbox for this bacterium, markerless targeted mutagenesis enables functional genomic research in C. cellulolyticum and rapid genetic engineering to significantly alter the mixture of fermentation products. The initial application of this system successfully engineered a strain with high ethanol productivity from cellobiose, cellulose and switchgrass.
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Affiliation(s)
- Yongchao Li
- Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, MS-6038, Oak Ridge, TN 37831-6038, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Timothy J Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, MS-6038, Oak Ridge, TN 37831-6038, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Nancy L Engle
- Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, MS-6038, Oak Ridge, TN 37831-6038, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Choo Y Hamilton
- Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, MS-6038, Oak Ridge, TN 37831-6038, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Miguel Rodriguez
- Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, MS-6038, Oak Ridge, TN 37831-6038, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - James C Liao
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Christopher W Schadt
- Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, MS-6038, Oak Ridge, TN 37831-6038, USA
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996-0845, USA
| | - Adam M Guss
- Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, MS-6038, Oak Ridge, TN 37831-6038, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Yunfeng Yang
- Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, MS-6038, Oak Ridge, TN 37831-6038, USA
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - David E Graham
- Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, MS-6038, Oak Ridge, TN 37831-6038, USA
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996-0845, USA
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296
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Abstract
Genetic engineering has been successfully applied to Saccharomyces cerevisiae laboratory strains for different purposes: extension of substrate range, improvement of productivity and yield, elimination of by-products, improvement of process performance and cellular properties, and extension of product range. The potential of genetically engineered yeasts for the massive production of biofuels as bioethanol and other nonfuel products from renewable resources as lignocellulosic biomass hydrolysates has been recognized. For such applications, robust industrial strains of S. cerevisiae have to be used. Here, some relevant genetic and genomic characteristics of industrial strains are discussed in relation to the problematic of the genetic engineering of such strains. General molecular tools applicable to the manipulation of S. cerevisiae industrial strains are presented and examples of genetically engineered industrial strains developed for the production of bioethanol from lignocellulosic biomass are given.
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Affiliation(s)
- Sylvie Le Borgne
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana-Cuajimalpa, Mexico City, Mexico.
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297
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Du X, He W, Zhang X, Yue Y, Liu H, Zhang X, Min D, Ge X, Du Y. Enhancing the electrochemical performance of lithium ion batteries using mesoporous Li3V2(PO4)3/C microspheres. ACTA ACUST UNITED AC 2012. [DOI: 10.1039/c1jm14758g] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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298
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Zhang X, Zhang X, He W, Yue Y, Liu H, Ma J. Biocarbon-coated LiFePO4 nucleus nanoparticles enhancing electrochemical performances. Chem Commun (Camb) 2012; 48:10093-5. [DOI: 10.1039/c2cc34207c] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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299
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Hasunuma T, Kondo A. Development of yeast cell factories for consolidated bioprocessing of lignocellulose to bioethanol through cell surface engineering. Biotechnol Adv 2011; 30:1207-18. [PMID: 22085593 DOI: 10.1016/j.biotechadv.2011.10.011] [Citation(s) in RCA: 132] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2011] [Revised: 10/12/2011] [Accepted: 10/30/2011] [Indexed: 10/15/2022]
Abstract
To build an energy and material secure future, a next generation of renewable fuels produced from lignocellulosic biomass is required. Although lignocellulosic biomass, which represents an abundant, inexpensive and renewable source for bioethanol production, is of great interest as a feedstock, the complicated ethanol production processes involved make the cost of producing bioethanol from it higher compared to corn starch and cane juice. Therefore, consolidated bioprocessing (CBP), which combines enzyme production, saccharification and fermentation in a single step, has gained increased recognition as a potential bioethanol production system. CBP requires a highly engineered microorganism developed for several different process-specific characteristics. The dominant strategy for engineering a CBP biocatalyst is to express multiple components of a cellulolytic system from either fungi or bacteria in the yeast Saccharomyces cerevisiae. The development of recombinant yeast strains displaying cellulases and hemicellulases on the cell surface represents significant progress toward realization of CBP. Regardless of the process used for biomass hydrolysis, CBP-enabling microorganisms encounter a variety of toxic compounds produced during biomass pretreatment that inhibit microbial growth and ethanol yield. Systems biology approaches including disruptome screening, transcriptomics, and metabolomics have been recently exploited to gain insight into the molecular and genetic traits involved in tolerance and adaptation to the fermentation inhibitors. In this review, we focus on recent advances in development of yeast strains with both the ability to directly convert lignocellulosic material to ethanol and tolerance in the harsh environments containing toxic compounds in the presence of ethanol.
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Affiliation(s)
- Tomohisa Hasunuma
- Organization of Advanced Science and Technology, Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
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300
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Duong C, Strack L, Futschik M, Katou Y, Nakao Y, Fujimura T, Shirahige K, Kodama Y, Nevoigt E. Identification of Sc-type ILV6 as a target to reduce diacetyl formation in lager brewers' yeast. Metab Eng 2011; 13:638-47. [DOI: 10.1016/j.ymben.2011.07.005] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Revised: 07/04/2011] [Accepted: 07/22/2011] [Indexed: 11/28/2022]
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