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Duperray M, Delvenne M, François JM, Delvigne F, Capp JP. Genomic and metabolic instability during long-term fermentation of an industrial Saccharomyces cerevisiae strain engineered for C5 sugar utilization. Front Bioeng Biotechnol 2024; 12:1357671. [PMID: 38595997 PMCID: PMC11002265 DOI: 10.3389/fbioe.2024.1357671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 03/07/2024] [Indexed: 04/11/2024] Open
Abstract
The genetic stability and metabolic robustness of production strains is one of the key criteria for the production of bio-based products by microbial fermentation on an industrial scale. These criteria were here explored in an industrial ethanol-producer strain of Saccharomyces cerevisiae able to co-ferment D-xylose and L-arabinose with glucose through the chromosomal integration of several copies of pivotal genes for the use of these pentose (C5) sugars. Using batch sequential cultures in a controlled bioreactor that mimics long-term fermentation in an industrial setting, this strain was found to exhibit significant fluctuations in D-xylose and L-arabinose consumption as early as the 50th generation and beyond. These fluctuations seem not related to the few low-consumption C5 sugar clones that appeared throughout the sequential batch cultures at a frequency lower than 1.5% and that were due to the reduction in the number of copies of transgenes coding for C5 sugar assimilation enzymes. Also, subpopulations enriched with low or high RAD52 expression, whose expression level was reported to be proportional to homologous recombination rate did not exhibit defect in C5-sugar assimilation, arguing that other mechanisms may be responsible for copy number variation of transgenes. Overall, this work highlighted the existence of genetic and metabolic instabilities in an industrial yeast which, although modest in our conditions, could be more deleterious in harsher industrial conditions, leading to reduced production performance.
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Affiliation(s)
- Maëlle Duperray
- Toulouse Biotechnology Institute, INSA/University of Toulouse, CNRS, INRAE, Toulouse, France
| | - Mathéo Delvenne
- TERRA Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Jean Marie François
- Toulouse Biotechnology Institute, INSA/University of Toulouse, CNRS, INRAE, Toulouse, France
- Toulouse White Biotechnology, INSA, INRAE, CNRS, Toulouse, France
| | - Frank Delvigne
- TERRA Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Jean-Pascal Capp
- Toulouse Biotechnology Institute, INSA/University of Toulouse, CNRS, INRAE, Toulouse, France
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2
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Trivedi VD, Sullivan SF, Choudhury D, Endalur Gopinarayanan V, Hart T, Nair NU. Integration of metabolism and regulation reveals rapid adaptability to growth on non-native substrates. Cell Chem Biol 2023; 30:1135-1143.e5. [PMID: 37421944 PMCID: PMC10529486 DOI: 10.1016/j.chembiol.2023.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 05/18/2023] [Accepted: 06/08/2023] [Indexed: 07/10/2023]
Abstract
Engineering synthetic heterotrophy is a key to the efficient bio-based valorization of renewable and waste substrates. Among these, engineering hemicellulosic pentose utilization has been well-explored in Saccharomyces cerevisiae (yeast) over several decades-yet the answer to what makes their utilization inherently recalcitrant remains elusive. Through implementation of a semi-synthetic regulon, we find that harmonizing cellular and engineering objectives are a key to obtaining highest growth rates and yields with minimal metabolic engineering effort. Concurrently, results indicate that "extrinsic" factors-specifically, upstream genes that direct flux of pentoses into central carbon metabolism-are rate-limiting. We also reveal that yeast metabolism is innately highly adaptable to rapid growth on non-native substrates and that systems metabolic engineering (i.e., functional genomics, network modeling, etc.) is largely unnecessary. Overall, this work provides an alternate, novel, holistic (and yet minimalistic) approach based on integrating non-native metabolic genes with a native regulon system.
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Affiliation(s)
- Vikas D Trivedi
- Department of Chemical & Biological Engineering, Tufts University, Medford, MA, USA
| | - Sean F Sullivan
- Department of Chemical & Biological Engineering, Tufts University, Medford, MA, USA
| | - Debika Choudhury
- Department of Chemical & Biological Engineering, Tufts University, Medford, MA, USA
| | | | - Taylor Hart
- Department of Chemical & Biological Engineering, Tufts University, Medford, MA, USA
| | - Nikhil U Nair
- Department of Chemical & Biological Engineering, Tufts University, Medford, MA, USA.
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3
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Identification of traits to improve co-assimilation of glucose and xylose by adaptive evolution of Spathaspora passalidarum and Scheffersomyces stipitis yeasts. Appl Microbiol Biotechnol 2023; 107:1143-1157. [PMID: 36625916 DOI: 10.1007/s00253-023-12362-1] [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: 08/26/2022] [Revised: 11/21/2022] [Accepted: 12/31/2022] [Indexed: 01/11/2023]
Abstract
Lignocellulosic biomass is a renewable raw material for producing several high-value-added chemicals and fuels. In general, xylose and glucose are the major sugars in biomass hydrolysates, and their efficient utilization by microorganisms is critical for an economical production process. Yeasts capable of co-consuming mixed sugars might lead to higher yields and productivities in industrial fermentation processes. Herein, we performed adaptive evolution assays with two xylose-fermenting yeasts, Spathaspora passalidarum and Scheffersomyces stipitis, to obtain derived clones with improved capabilities of glucose and xylose co-consumption. Adapted strains were obtained after successive growth selection using xylose and the non-metabolized glucose analog 2-deoxy-D-glucose as a selective pressure. The co-fermentation capacity of evolved and parental strains was evaluated on xylose-glucose mixtures. Our results revealed an improved co-assimilation capability by the evolved strains; however, xylose and glucose consumption were observed at slower rates than the parental yeasts. Genome resequencing of the evolved strains revealed genes affected by non-synonymous variants that might be involved with the co-consumption phenotype, including the HXT2.4 gene that encodes a putative glucose transporter in Sp. passalidarum. Expression of this mutant HXT2.4 in Saccharomyces cerevisiae improved the cells' co-assimilation of glucose and xylose. Therefore, our results demonstrated the successful improvement of co-fermentation through evolutionary engineering and the identification of potential targets for further genetic engineering of different yeast strains. KEY POINTS: • Laboratory evolution assay was used to obtain improved sugar co-consumption of non-Saccharomyces strains. • Evolved Sp. passalidarum and Sc. stipitis were able to more efficiently co-ferment glucose and xylose. • A mutant Hxt2.4 permease, which co-transports xylose and glucose, was identified.
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Identification of Mutations Responsible for Improved Xylose Utilization in an Adapted Xylose Isomerase Expressing Saccharomyces cerevisiae Strain. FERMENTATION 2022. [DOI: 10.3390/fermentation8120669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Economic conversion of biomass to biofuels and chemicals requires efficient and complete utilization of xylose. Saccharomyces cerevisiae strains engineered for xylose utilization are still considerably limited in their overall ability to metabolize xylose. In this study, we identified causative mutations resulting in improved xylose fermentation of an adapted S. cerevisiae strain expressing codon-optimized xylose isomerase and xylulokinase genes from the rumen bacterium Prevotella ruminicola. Genome sequencing identified single-nucleotide polymorphisms in seven open reading frames. Tetrad analysis showed that mutations in both PBS2 and PHO13 genes were required for increased xylose utilization. Single deletion of either PBS2 or PHO13 did not improve xylose utilization in strains expressing the xylose isomerase pathway. Saccharomyces can also be engineered for xylose metabolism using the xylose reductase/xylitol dehydrogenase genes from Scheffersomyces stipitis. In strains expressing the xylose reductase pathway, single deletion of PHO13 did show a significant increase xylose utilization, and further improvement in growth and fermentation was seen when PBS2 was also deleted. These findings will extend the understanding of metabolic limitations for xylose utilization in S. cerevisiae as well as understanding of how they differ among strains engineered with two different xylose utilization pathways.
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Moreno AD, González-Fernández C, Tomás-Pejó E. Insights into cell robustness against lignocellulosic inhibitors and insoluble solids in bioethanol production processes. Sci Rep 2022; 12:557. [PMID: 35017613 PMCID: PMC8752620 DOI: 10.1038/s41598-021-04554-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 12/24/2021] [Indexed: 11/28/2022] Open
Abstract
Increasing yeast robustness against lignocellulosic-derived inhibitors and insoluble solids in bioethanol production is essential for the transition to a bio-based economy. This work evaluates the effect exerted by insoluble solids on yeast tolerance to inhibitory compounds, which is crucial in high gravity processes. Adaptive laboratory evolution (ALE) was applied on a xylose-fermenting Saccharomyces cerevisiae strain to simultaneously increase the tolerance to lignocellulosic inhibitors and insoluble solids. The evolved strain gave rise to a fivefold increase in bioethanol yield in fermentation experiments with high concentration of inhibitors and 10% (w/v) of water insoluble solids. This strain also produced 5% (P > 0.01) more ethanol than the parental in simultaneous saccharification and fermentation of steam-exploded wheat straw, mainly due to an increased xylose consumption. In response to the stress conditions (solids and inhibitors) imposed in ALE, cells induced the expression of genes related to cell wall integrity (SRL1, CWP2, WSC2 and WSC4) and general stress response (e.g., CDC5, DUN1, CTT1, GRE1), simultaneously repressing genes related to protein synthesis and iron transport and homeostasis (e.g., FTR1, ARN1, FRE1), ultimately leading to the improved phenotype. These results contribute towards understanding molecular mechanisms that cells might use to convert lignocellulosic substrates effectively.
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Affiliation(s)
- Antonio D Moreno
- Advanced Biofuels and Bioproducts Unit, CIEMAT, Avda. Complutense 40, 28040, Madrid, Spain
| | - Cristina González-Fernández
- Biotechnological Processes Unit, IMDEA Energy Institute, Avda. Ramón de la Sagra 3, 28935, Móstoles, Madrid, Spain
| | - Elia Tomás-Pejó
- Biotechnological Processes Unit, IMDEA Energy Institute, Avda. Ramón de la Sagra 3, 28935, Móstoles, Madrid, Spain.
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Godoy P, García-Franco A, Recio MI, Ramos JL, Duque E. Synthesis of aromatic amino acids from 2G lignocellulosic substrates. Microb Biotechnol 2021; 14:1931-1943. [PMID: 34403199 PMCID: PMC8449653 DOI: 10.1111/1751-7915.13844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/04/2021] [Accepted: 05/13/2021] [Indexed: 11/29/2022] Open
Abstract
Pseudomonas putida is a highly solvent‐resistant microorganism and useful chassis for the production of value‐added compounds from lignocellulosic residues, in particular aromatic compounds that are made from phenylalanine. The use of these agricultural residues requires a two‐step treatment to release the components of the polysaccharides of cellulose and hemicellulose as monomeric sugars, the most abundant monomers being glucose and xylose. Pan‐genomic studies have shown that Pseudomonas putida metabolizes glucose through three convergent pathways to yield 6‐phosphogluconate and subsequently metabolizes it through the Entner–Doudoroff pathway, but the strains do not degrade xylose. The valorization of both sugars is critical from the point of view of economic viability of the process. For this reason, a P. putida strain was endowed with the ability to metabolize xylose via the xylose isomerase pathway, by incorporating heterologous catabolic genes that convert this C5 sugar into intermediates of the pentose phosphate cycle. In addition, the open reading frame T1E_2822, encoding glucose dehydrogenase, was knocked‐out to avoid the production of the dead‐end product xylonate. We generated a set of DOT‐T1E‐derived strains that metabolized glucose and xylose simultaneously in culture medium and that reached high cell density with generation times of around 100 min with glucose and around 300 min with xylose. The strains grew in 2G hydrolysates from diluted acid and steam explosion pretreated corn stover and sugarcane straw. During growth, the strains metabolized > 98% of glucose, > 96% xylose and > 85% acetic acid. In 2G hydrolysates P. putida 5PL, a DOT‐T1E derivative strain that carries up to five independent mutations to avoid phenylalanine metabolism, accumulated this amino acid in the medium. We constructed P. putida 5PLΔgcd (xylABE) that produced up to 250 mg l−1 of phenylalanine when grown in 2G pretreated corn stover or sugarcane straw. These results support as a proof of concept the potential of P. putida as a chassis for 2G processes.
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Affiliation(s)
- Patricia Godoy
- Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, c/Profesor Albareda 1, Granada, 18008, Spain
| | - Ana García-Franco
- Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, c/Profesor Albareda 1, Granada, 18008, Spain
| | - María-Isabel Recio
- Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, c/Profesor Albareda 1, Granada, 18008, Spain.,BioEnterprise Master Program, School of Pharmacy, University of Granada, Granada, Spain
| | - Juan-Luis Ramos
- Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, c/Profesor Albareda 1, Granada, 18008, Spain
| | - Estrella Duque
- Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, c/Profesor Albareda 1, Granada, 18008, Spain
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7
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Ruchala J, Sibirny AA. Pentose metabolism and conversion to biofuels and high-value chemicals in yeasts. FEMS Microbiol Rev 2020; 45:6034013. [PMID: 33316044 DOI: 10.1093/femsre/fuaa069] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 12/09/2020] [Indexed: 12/15/2022] Open
Abstract
Pentose sugars are widespread in nature and two of them, D-xylose and L-arabinose belong to the most abundant sugars being the second and third by abundance sugars in dry plant biomass (lignocellulose) and in general on planet. Therefore, it is not surprising that metabolism and bioconversion of these pentoses attract much attention. Several different pathways of D-xylose and L-arabinose catabolism in bacteria and yeasts are known. There are even more common and really ubiquitous though not so abundant pentoses, D-ribose and 2-deoxy-D-ribose, the constituents of all living cells. Thus, ribose metabolism is example of endogenous metabolism whereas metabolism of other pentoses, including xylose and L-arabinose, represents examples of the metabolism of foreign exogenous compounds which normally are not constituents of yeast cells. As a rule, pentose degradation by the wild-type strains of microorganisms does not lead to accumulation of high amounts of valuable substances; however, productive strains have been obtained by random selection and metabolic engineering. There are numerous reviews on xylose and (less) L-arabinose metabolism and conversion to high value substances; however, they mostly are devoted to bacteria or the yeast Saccharomyces cerevisiae. This review is devoted to reviewing pentose metabolism and bioconversion mostly in non-conventional yeasts, which naturally metabolize xylose. Pentose metabolism in the recombinant strains of S. cerevisiae is also considered for comparison. The available data on ribose, xylose, L-arabinose transport, metabolism, regulation of these processes, interaction with glucose catabolism and construction of the productive strains of high-value chemicals or pentose (ribose) itself are described. In addition, genome studies of the natural xylose metabolizing yeasts and available tools for their molecular research are reviewed. Metabolism of other pentoses (2-deoxyribose, D-arabinose, lyxose) is briefly reviewed.
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Affiliation(s)
- Justyna Ruchala
- Department of Microbiology and Molecular Genetics, University of Rzeszow, Zelwerowicza 4, Rzeszow 35-601, Poland.,Department of Molecular Genetics and Biotechnology, Institute of Cell Biology NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine
| | - Andriy A Sibirny
- Department of Microbiology and Molecular Genetics, University of Rzeszow, Zelwerowicza 4, Rzeszow 35-601, Poland.,Department of Molecular Genetics and Biotechnology, Institute of Cell Biology NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine
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8
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Sun L, Jin YS. Xylose Assimilation for the Efficient Production of Biofuels and Chemicals by Engineered Saccharomyces cerevisiae. Biotechnol J 2020; 16:e2000142. [PMID: 33135317 DOI: 10.1002/biot.202000142] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 10/15/2020] [Indexed: 11/09/2022]
Abstract
Microbial conversion of plant biomass into fuels and chemicals offers a practical solution to global concerns over limited natural resources, environmental pollution, and climate change. Pursuant to these goals, researchers have put tremendous efforts and resources toward engineering the yeast Saccharomyces cerevisiae to efficiently convert xylose, the second most abundant sugar in lignocellulosic biomass, into various fuels and chemicals. Here, recent advances in metabolic engineering of yeast is summarized to address bottlenecks on xylose assimilation and to enable simultaneous co-utilization of xylose and other substrates in lignocellulosic hydrolysates. Distinct characteristics of xylose metabolism that can be harnessed to produce advanced biofuels and chemicals are also highlighted. Although many challenges remain, recent research investments have facilitated the efficient fermentation of xylose and simultaneous co-consumption of xylose and glucose. In particular, understanding xylose-induced metabolic rewiring in engineered yeast has encouraged the use of xylose as a carbon source for producing various non-ethanol bioproducts. To boost the lignocellulosic biomass-based bioeconomy, much attention is expected to promote xylose-utilizing efficiency via reprogramming cellular regulatory networks, to attain robust co-fermentation of xylose and other cellulosic carbon sources under industrial conditions, and to exploit the advantageous traits of yeast xylose metabolism for producing diverse fuels and chemicals.
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Affiliation(s)
- Liang Sun
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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9
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Godara A, Kao KC. Adaptive laboratory evolution for growth coupled microbial production. World J Microbiol Biotechnol 2020; 36:175. [DOI: 10.1007/s11274-020-02946-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 10/08/2020] [Indexed: 12/18/2022]
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10
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Improving Xylose Fermentation in Saccharomyces cerevisiae by Expressing Nuclear-Localized Hexokinase 2. Microorganisms 2020; 8:microorganisms8060856. [PMID: 32517148 PMCID: PMC7356972 DOI: 10.3390/microorganisms8060856] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/03/2020] [Accepted: 06/04/2020] [Indexed: 12/20/2022] Open
Abstract
Understanding the relationship between xylose and the metabolic regulatory systems is a prerequisite to enhance xylose utilization in recombinant S. cerevisiae strains. Hexokinase 2 (Hxk2p) is an intracellular glucose sensor that localizes to the cytoplasm or the nucleus depending on the carbon source. Hxk2p interacts with Mig1p to regulate gene transcription in the nucleus. Here, we investigated the effect of nucleus-localized Hxk2p and Mig1p on xylose fermentation. The results show that the expression of HXK2S14A, which encodes a constitutively nucleus-localized Hxk2p, increased the xylose consumption rate, the ethanol production rate, and the ethanol yield of the engineered yeast strain by 23.5%, 78.6% and 42.6%, respectively. The deletion of MIG1 decreased xylose utilization and eliminated the positive effect of Hxk2p. We then performed RNA-seq and found that the targets of Hxk2pS14A on xylose were mainly genes that encode RNA-binding proteins. This is very different from the known targets of Mig1p and supports the notion that the Hxk2p-Mig1p interaction is abolished in the presence of xylose. These results will improve our understanding of the interrelation between the Snf1p-Mig1p-Hxk2p glucose signaling pathway and xylose utilization in S. cerevisiae and suggests that the expression of HXK2S14A could be a viable strategy to improve xylose utilization.
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11
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Extended fed-batch fermentation of a C5/C6 optimised yeast strain on wheat straw hydrolysate using an online refractive index sensor to measure the relative fermentation rate. Sci Rep 2020; 10:6705. [PMID: 32317712 PMCID: PMC7174321 DOI: 10.1038/s41598-020-63626-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 02/18/2020] [Indexed: 02/06/2023] Open
Abstract
In the production of 2nd generation ethanol, using Saccharomyces cerevisiae, the highest productivity obtained using C5/C6 fermenting yeast is in the co-fermentation phase, in which xylose and glucose are fermented simultaneously. Extending this phase in a fed-batch process increases the yield, rate and additionally reduces needed yeast amount for pitching. Extending this phase, as long as possible, would further enhance yield and economy of the process. To realise the concept a fermentation monitoring technique was developed and applied. Based on online measured refractive index an optimal residual sugar concentration could be maintained in the primary fermentor during the feed phase, requiring little knowledge of the nature of the substrate. The system was able to run stably for at least five fermentor volumes giving an ethanol yield >90% throughout the run. This was achieved with addition of only urea to the wheat straw hydrolysate and with an initial yeast pitch of 0.2 g/L total of finished broth. It has the potential to improve the fermentation technology used in fuel ethanol plants, which could help to meet the growing demand for more sustainable fuels.
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12
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Aßkamp MR, Klein M, Nevoigt E. Saccharomyces cerevisiae exhibiting a modified route for uptake and catabolism of glycerol forms significant amounts of ethanol from this carbon source considered as 'non-fermentable'. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:257. [PMID: 31695748 PMCID: PMC6822349 DOI: 10.1186/s13068-019-1597-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 10/22/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Due to its inevitable formation during biodiesel production and its relatively high degree of reduction, glycerol is an attractive carbon source for microbial fermentation processes. However, glycerol is catabolized in a fully respiratory manner by the eukaryotic platform organism Saccharomyces cerevisiae. We previously engineered S. cerevisiae strains to favor fermentative metabolism of glycerol by replacing the native FAD-dependent glycerol catabolic pathway with the NAD-dependent 'DHA pathway'. In addition, a heterologous aquaglyceroporin (Fps1 homolog) was expressed to facilitate glycerol uptake. The current study was launched to scrutinize the formation of S. cerevisiae's natural fermentation product ethanol from glycerol caused by the conducted genetic modifications. This understanding is supposed to facilitate future engineering of this yeast for fermenting glycerol into valuable products more reduced than ethanol. RESULTS A strain solely exhibiting the glycerol catabolic pathway replacement produced ethanol at concentrations close to the detection limit. The expression of the heterologous aquaglyceroporin caused significant ethanol production (8.5 g L-1 from 51.5 g L-1 glycerol consumed) in a strain catabolizing glycerol via the DHA pathway but not in the wild-type background. A reduction of oxygen availability in the shake flask cultures further increased the ethanol titer up to 15.7 g L-1 (from 45 g L-1 glycerol consumed). CONCLUSION The increased yield of cytosolic NADH caused by the glycerol catabolic pathway replacement seems to be a minimal requirement for the occurrence of alcoholic fermentation in S. cerevisiae growing in synthetic glycerol medium. The remarkable metabolic switch to ethanol formation in the DHA pathway strain with the heterologous aquaglyceroporin supports the assumption of a much stronger influx of glycerol accompanied by an increased rate of cytosolic NADH production via the DHA pathway. The fact that a reduction of oxygen supply increases ethanol production in DHA pathway strains is in line with the hypothesis that a major part of glycerol in normal shake flask cultures still enters the catabolism in a respiratory manner.
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Affiliation(s)
- Maximilian R. Aßkamp
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany
| | - Mathias Klein
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany
| | - Elke Nevoigt
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany
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13
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Patiño MA, Ortiz JP, Velásquez M, Stambuk BU. d-Xylose consumption by nonrecombinant Saccharomyces cerevisiae: A review. Yeast 2019; 36:541-556. [PMID: 31254359 DOI: 10.1002/yea.3429] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 06/02/2019] [Accepted: 06/21/2019] [Indexed: 01/24/2023] Open
Abstract
Xylose is the second most abundant sugar in nature. Its efficient fermentation has been considered as a critical factor for a feasible conversion of renewable biomass resources into biofuels and other chemicals. The yeast Saccharomyces cerevisiae is of exceptional industrial importance due to its excellent capability to ferment sugars. However, although S. cerevisiae is able to ferment xylulose, it is considered unable to metabolize xylose, and thus, a lot of research has been directed to engineer this yeast with heterologous genes to allow xylose consumption and fermentation. The analysis of the natural genetic diversity of this yeast has also revealed some nonrecombinant S. cerevisiae strains that consume or even grow (modestly) on xylose. The genome of this yeast has all the genes required for xylose transport and metabolism through the xylose reductase, xylitol dehydrogenase, and xylulokinase pathway, but there seems to be problems in their kinetic properties and/or required expression. Self-cloning industrial S. cerevisiae strains overexpressing some of the endogenous genes have shown interesting results, and new strategies and approaches designed to improve these S. cerevisiae strains for ethanol production from xylose will also be presented in this review.
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Affiliation(s)
- Margareth Andrea Patiño
- Instituto de Biotecnología.,Departamento de Ingeniería Química y Ambiental, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Juan Pablo Ortiz
- Facultad de Ciencias e Ingeniería, Universidad de Boyacá, Tunja, Colombia
| | - Mario Velásquez
- Departamento de Ingeniería Química y Ambiental, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Boris U Stambuk
- Departamento de Bioquímica, Universidad Federal de Santa Catarina, Florianópolis, Brazil
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14
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Sandberg TE, Salazar MJ, Weng LL, Palsson BO, Feist AM. The emergence of adaptive laboratory evolution as an efficient tool for biological discovery and industrial biotechnology. Metab Eng 2019; 56:1-16. [PMID: 31401242 DOI: 10.1016/j.ymben.2019.08.004] [Citation(s) in RCA: 262] [Impact Index Per Article: 52.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 08/01/2019] [Accepted: 08/05/2019] [Indexed: 12/21/2022]
Abstract
Harnessing the process of natural selection to obtain and understand new microbial phenotypes has become increasingly possible due to advances in culturing techniques, DNA sequencing, bioinformatics, and genetic engineering. Accordingly, Adaptive Laboratory Evolution (ALE) experiments represent a powerful approach both to investigate the evolutionary forces influencing strain phenotypes, performance, and stability, and to acquire production strains that contain beneficial mutations. In this review, we summarize and categorize the applications of ALE to various aspects of microbial physiology pertinent to industrial bioproduction by collecting case studies that highlight the multitude of ways in which evolution can facilitate the strain construction process. Further, we discuss principles that inform experimental design, complementary approaches such as computational modeling that help maximize utility, and the future of ALE as an efficient strain design and build tool driven by growing adoption and improvements in automation.
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Affiliation(s)
- Troy E Sandberg
- Department of Bioengineering, University of California, San Diego, CA, 92093, USA
| | - Michael J Salazar
- Department of Bioengineering, University of California, San Diego, CA, 92093, USA
| | - Liam L Weng
- Department of Bioengineering, University of California, San Diego, CA, 92093, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, CA, 92093, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Adam M Feist
- Department of Bioengineering, University of California, San Diego, CA, 92093, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark.
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15
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Passoth V, Sandgren M. Biofuel production from straw hydrolysates: current achievements and perspectives. Appl Microbiol Biotechnol 2019; 103:5105-5116. [PMID: 31081521 PMCID: PMC6570699 DOI: 10.1007/s00253-019-09863-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 04/18/2019] [Accepted: 04/19/2019] [Indexed: 12/15/2022]
Abstract
Straw is an agricultural residue of the production of e.g. cereals, rapeseed or sunflowers. It includes dried stalks, leaves, and empty ears and corncobs, which are separated from the grains during harvest. Straw is a promising lignocellulosic feedstock with a beneficial greenhouse gas balance for the production of biofuels and chemicals. Like all lignocellulosic materials, straw is recalcitrant and requires thermochemical and enzymatic pretreatment to enable access to the three major biopolymers of straw-the polysaccharides cellulose and hemicellulose and the polyaromatic compound lignin. Straw is used for commercial ethanol and biogas production. Considerable research has also been conducted to produce biobutanol, biodiesel and biochemicals from this raw material, but more research is required to establish them on a commercial scale. The major hindrance for launching industrial biofuel and chemicals' production from straw is the high cost necessitated by pretreatment of the material. Improvements of microbial strains, production and extraction technologies, as well as co-production of high-value compounds represent ways of establishing straw as feedstock for the production of biofuels, chemicals and food.
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Affiliation(s)
- Volkmar Passoth
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, SE-75007, Uppsala, Sweden.
| | - Mats Sandgren
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Box 7015, SE-75007, Uppsala, Sweden
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16
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Park JO, Liu N, Holinski KM, Emerson DF, Qiao K, Woolston BM, Xu J, Lazar Z, Islam MA, Vidoudez C, Girguis PR, Stephanopoulos G. Synergistic substrate cofeeding stimulates reductive metabolism. Nat Metab 2019; 1:643-651. [PMID: 32694804 DOI: 10.1038/s42255-019-0077-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 05/13/2019] [Indexed: 11/09/2022]
Abstract
Advanced bioproduct synthesis via reductive metabolism requires coordinating carbons, ATP and reducing agents, which are generated with varying efficiencies depending on metabolic pathways. Substrate mixtures with direct access to multiple pathways may optimally satisfy these biosynthetic requirements. However, native regulation favouring preferential use precludes cells from co-metabolizing multiple substrates. Here we explore mixed substrate metabolism and tailor pathway usage to synergistically stimulate carbon reduction. By controlled cofeeding of superior ATP and NADPH generators as 'dopant' substrates to cells primarily using inferior substrates, we circumvent catabolite repression and drive synergy in two divergent organisms. Glucose doping in Moorella thermoacetica stimulates CO2 reduction (2.3 g gCDW-1 h-1) into acetate by augmenting ATP synthesis via pyruvate kinase. Gluconate doping in Yarrowia lipolytica accelerates acetate-driven lipogenesis (0.046 g gCDW-1 h-1) by obligatory NADPH synthesis through the pentose cycle. Together, synergistic cofeeding produces CO2-derived lipids with 38% energy yield and demonstrates the potential to convert CO2 into advanced bioproducts. This work advances the systems-level control of metabolic networks and CO2 use, the most pressing and difficult reduction challenge.
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Affiliation(s)
- Junyoung O Park
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA
| | - Nian Liu
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kara M Holinski
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - David F Emerson
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kangjian Qiao
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Benjamin M Woolston
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jingyang Xu
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Key Laboratory of Drug Prevention and Control Technology of Zhejiang Province, Zhejiang Police College, Hangzhou, China
| | - Zbigniew Lazar
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biotechnology and Food Microbiology, Wroclaw University of Environmental and Life Sciences, Monskiego, Wroclaw, Poland
| | - M Ahsanul Islam
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Chemical Engineering, Loughborough University, Loughborough, UK
| | - Charles Vidoudez
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Peter R Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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17
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Nguyen-Vo TP, Liang Y, Sankaranarayanan M, Seol E, Chun AY, Ashok S, Chauhan AS, Kim JR, Park S. Development of 3-hydroxypropionic-acid-tolerant strain of Escherichia coli W and role of minor global regulator yieP. Metab Eng 2019; 53:48-58. [DOI: 10.1016/j.ymben.2019.02.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 01/18/2019] [Accepted: 02/06/2019] [Indexed: 10/27/2022]
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18
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Enhanced ethanol production from industrial lignocellulose hydrolysates by a hydrolysate-cofermenting Saccharomyces cerevisiae strain. Bioprocess Biosyst Eng 2019; 42:883-896. [PMID: 30820665 DOI: 10.1007/s00449-019-02090-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 02/11/2019] [Indexed: 10/27/2022]
Abstract
Industrial production of lignocellulosic ethanol requires a microorganism utilizing both hexose and pentose, and tolerating inhibitors. In this study, a hydrolysate-cofermenting Saccharomyces cerevisiae strain was obtained through one step in vivo DNA assembly of pentose-metabolizing pathway genes, followed by consecutive adaptive evolution in pentose media containing acetic acid, and direct screening in biomass hydrolysate media. The strain was able to coferment glucose and xylose in synthetic media with the respective maximal specific rates of glucose and xylose consumption, and ethanol production of 3.47, 0.38 and 1.62 g/g DW/h, with an ethanol titre of 41.07 g/L and yield of 0.42 g/g. Industrial wheat straw hydrolysate fermentation resulted in maximal specific rates of glucose and xylose consumption, and ethanol production of 2.61, 0.54 and 1.38 g/g DW/h, respectively, with an ethanol titre of 54.11 g/L and yield of 0.44 g/g. These are among the best for wheat straw hydrolysate fermentation through separate hydrolysis and cofermentation.
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19
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Li X, Chen Y, Nielsen J. Harnessing xylose pathways for biofuels production. Curr Opin Biotechnol 2019; 57:56-65. [PMID: 30785001 DOI: 10.1016/j.copbio.2019.01.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 01/04/2019] [Accepted: 01/15/2019] [Indexed: 01/02/2023]
Abstract
Energy security, environmental pollution, and economic development drive the development of alternatives to fossil fuels as an urgent global priority. Lignocellulosic biomass has the potential to contribute to meeting the demand for biofuel production via hydrolysis and fermentation of released sugars, such as glucose, xylose, and arabinose. Construction of robust cell factories requires introducing and rewiring of their metabolism to efficiently use all these sugars. Here, we review recent advances in re-constructing pathways for metabolism of pentoses, with special focus on xylose metabolism in the most widely used cell factories Saccharomyces cerevisiae and Escherichia coli. We also highlight engineering advanced biofuels-synthesis pathways and describes progress toward overcoming the challenges facing adoption of large-scale biofuel production.
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Affiliation(s)
- Xiaowei Li
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
| | - Yun Chen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark; Wallenberg Center for Protein Research, Chalmers University of Technology, Gothenburg, Sweden.
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20
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Gao M, Ploessl D, Shao Z. Enhancing the Co-utilization of Biomass-Derived Mixed Sugars by Yeasts. Front Microbiol 2019; 9:3264. [PMID: 30723464 PMCID: PMC6349770 DOI: 10.3389/fmicb.2018.03264] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 12/14/2018] [Indexed: 12/11/2022] Open
Abstract
Plant biomass is a promising carbon source for producing value-added chemicals, including transportation biofuels, polymer precursors, and various additives. Most engineered microbial hosts and a select group of wild-type species can metabolize mixed sugars including oligosaccharides, hexoses, and pentoses that are hydrolyzed from plant biomass. However, most of these microorganisms consume glucose preferentially to non-glucose sugars through mechanisms generally defined as carbon catabolite repression. The current lack of simultaneous mixed-sugar utilization limits achievable titers, yields, and productivities. Therefore, the development of microbial platforms capable of fermenting mixed sugars simultaneously from biomass hydrolysates is essential for economical industry-scale production, particularly for compounds with marginal profits. This review aims to summarize recent discoveries and breakthroughs in the engineering of yeast cell factories for improved mixed-sugar co-utilization based on various metabolic engineering approaches. Emphasis is placed on enhanced non-glucose utilization, discovery of novel sugar transporters free from glucose repression, native xylose-utilizing microbes, consolidated bioprocessing (CBP), improved cellulase secretion, and creation of microbial consortia for improving mixed-sugar utilization. Perspectives on the future development of biorenewables industry are provided in the end.
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Affiliation(s)
- Meirong Gao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, United States.,NSF Engineering Research Center for Biorenewable Chemicals (CBiRC), Iowa State University, Ames, IA, United States
| | - Deon Ploessl
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, United States.,NSF Engineering Research Center for Biorenewable Chemicals (CBiRC), Iowa State University, Ames, IA, United States
| | - Zengyi Shao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, United States.,NSF Engineering Research Center for Biorenewable Chemicals (CBiRC), Iowa State University, Ames, IA, United States.,The Ames Laboratory, Iowa State University, Ames, IA, United States.,The Interdisciplinary Microbiology Program, Biorenewables Research Laboratory, Iowa State University, Ames, IA, United States
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21
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Pothakos V, Debeer N, Debonne I, Rodriguez A, Starr JN, Anderson T. Fermentation Titer Optimization and Impact on Energy and Water Consumption during Downstream Processing. Chem Eng Technol 2018; 41:2358-2365. [PMID: 31007402 PMCID: PMC6472596 DOI: 10.1002/ceat.201800279] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 08/30/2018] [Accepted: 09/07/2018] [Indexed: 01/02/2023]
Abstract
A common focus of fermentation process optimization is the product titer. Different strategies to boost fermentation titer target whole-cell biocatalyst selection, process control, and medium composition. Working at higher product concentrations reduces the water that needs to be removed in the case of aqueous systems and, therefore, lowers the cost of downstream separation and purification. Different approaches to achieve higher titer in fermentation are examined. Energy and water consumption data collected from different Cargill fermentation plants, i.e., ethanol, lactic acid, and 2-keto-L-gulonic acid, confirm that improvements in fermentation titer play a decisive role in downstream economics and environmental footprint.
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Affiliation(s)
| | - Nadine Debeer
- Cargill R&D Centre Europe BVBAHavenstraat 841800VilvoordeBelgium
| | - Ignace Debonne
- Cargill R&D Centre Europe BVBAHavenstraat 841800VilvoordeBelgium
| | - Asier Rodriguez
- Cargill R&D Centre Europe BVBAHavenstraat 841800VilvoordeBelgium
| | - John N. Starr
- Engineering R&D, Cargill, IncP.O. Box 9300MN 55440MinneapolisUSA
| | - Todd Anderson
- Cargill R&D Centre Europe BVBAHavenstraat 841800VilvoordeBelgium
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22
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Son HF, Lee SM, Kim KJ. Structural insight into D-xylose utilization by xylose reductase from Scheffersomyces stipitis. Sci Rep 2018; 8:17442. [PMID: 30487522 PMCID: PMC6261992 DOI: 10.1038/s41598-018-35703-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 11/09/2018] [Indexed: 11/09/2022] Open
Abstract
Lignocellulosic biomass, of which D-xylose accounts for approximately 35% of the total sugar, has attracted attention as a future energy source for biofuel. To elucidate molecular mechanism of D-xylose utilization, we determined the crystal structure of D-xylose reductase from Schefferzomyces stipitis (SsXR) at a 1.95 Å resolution. We also determined the SsXR structure in complex with the NADPH cofactor and revealed that the protein undergoes an open/closed conformation change upon NADPH binding. The substrate binding pocket of SsXR is somewhat hydrophobic, which seems to result in low binding affinity to the substrate. Phylogenetic tree analysis showed that AKR enzymes annotated with bacterial/archaeal XRs belonged to uncharacterized AKR families and might have no XR function, and yeast/fungi derived enzymes, which belong to the same group with SsXR, can be candidates for XR to increase xylose consumption.
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Affiliation(s)
- Hyeoncheol Francis Son
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu, 41566, Republic of Korea
- KNU Institute for Microorganisms, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Sun-Mi Lee
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792, Republic of Korea.
| | - Kyung-Jin Kim
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu, 41566, Republic of Korea.
- KNU Institute for Microorganisms, Kyungpook National University, Daegu, 41566, Republic of Korea.
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23
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Papapetridis I, Verhoeven MD, Wiersma SJ, Goudriaan M, van Maris AJA, Pronk JT. Laboratory evolution for forced glucose-xylose co-consumption enables identification of mutations that improve mixed-sugar fermentation by xylose-fermenting Saccharomyces cerevisiae. FEMS Yeast Res 2018; 18:4996351. [PMID: 29771304 PMCID: PMC6001886 DOI: 10.1093/femsyr/foy056] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 05/14/2018] [Indexed: 01/18/2023] Open
Abstract
Simultaneous fermentation of glucose and xylose can contribute to improved productivity and robustness of yeast-based processes for bioethanol production from lignocellulosic hydrolysates. This study explores a novel laboratory evolution strategy for identifying mutations that contribute to simultaneous utilisation of these sugars in batch cultures of Saccharomyces cerevisiae. To force simultaneous utilisation of xylose and glucose, the genes encoding glucose-6-phosphate isomerase (PGI1) and ribulose-5-phosphate epimerase (RPE1) were deleted in a xylose-isomerase-based xylose-fermenting strain with a modified oxidative pentose-phosphate pathway. Laboratory evolution of this strain in serial batch cultures on glucose-xylose mixtures yielded mutants that rapidly co-consumed the two sugars. Whole-genome sequencing of evolved strains identified mutations in HXK2, RSP5 and GAL83, whose introduction into a non-evolved xylose-fermenting S. cerevisiae strain improved co-consumption of xylose and glucose under aerobic and anaerobic conditions. Combined deletion of HXK2 and introduction of a GAL83G673T allele yielded a strain with a 2.5-fold higher xylose and glucose co-consumption ratio than its xylose-fermenting parental strain. These two modifications decreased the time required for full sugar conversion in anaerobic bioreactor batch cultures, grown on 20 g L-1 glucose and 10 g L-1 xylose, by over 24 h. This study demonstrates that laboratory evolution and genome resequencing of microbial strains engineered for forced co-consumption is a powerful approach for studying and improving simultaneous conversion of mixed substrates.
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Affiliation(s)
| | | | - Sanne J Wiersma
- Delft University of Technology, Department of Biotechnology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Maaike Goudriaan
- Delft University of Technology, Department of Biotechnology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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24
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Verhoeven MD, de Valk SC, Daran JMG, van Maris AJA, Pronk JT. Fermentation of glucose-xylose-arabinose mixtures by a synthetic consortium of single-sugar-fermenting Saccharomyces cerevisiae strains. FEMS Yeast Res 2018; 18:5054444. [DOI: 10.1093/femsyr/foy075] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 07/13/2018] [Indexed: 11/15/2022] Open
Affiliation(s)
- Maarten D Verhoeven
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Sophie C de Valk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Jean-Marc G Daran
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Antonius J A van Maris
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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25
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Lane S, Dong J, Jin YS. Value-added biotransformation of cellulosic sugars by engineered Saccharomyces cerevisiae. BIORESOURCE TECHNOLOGY 2018; 260:380-394. [PMID: 29655899 DOI: 10.1016/j.biortech.2018.04.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Revised: 03/31/2018] [Accepted: 04/02/2018] [Indexed: 05/26/2023]
Abstract
The substantial research efforts into lignocellulosic biofuels have generated an abundance of valuable knowledge and technologies for metabolic engineering. In particular, these investments have led to a vast growth in proficiency of engineering the yeast Saccharomyces cerevisiae for consuming lignocellulosic sugars, enabling the simultaneous assimilation of multiple carbon sources, and producing a large variety of value-added products by introduction of heterologous metabolic pathways. While microbial conversion of cellulosic sugars into large-volume low-value biofuels is not currently economically feasible, there may still be opportunities to produce other value-added chemicals as regulation of cellulosic sugar metabolism is quite different from glucose metabolism. This review summarizes these recent advances with an emphasis on employing engineered yeast for the bioconversion of lignocellulosic sugars into a variety of non-ethanol value-added products.
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Affiliation(s)
- Stephan Lane
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jia Dong
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yong-Su Jin
- Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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26
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Sun J, Tian K, Wang J, Dong Z, Liu X, Permaul K, Singh S, Prior BA, Wang Z. Improved ethanol productivity from lignocellulosic hydrolysates by Escherichia coli with regulated glucose utilization. Microb Cell Fact 2018; 17:66. [PMID: 29720171 PMCID: PMC5930954 DOI: 10.1186/s12934-018-0915-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 04/24/2018] [Indexed: 12/03/2022] Open
Abstract
Background Lignocellulosic ethanol could offer a sustainable source to meet the increasing worldwide demand for fuel. However, efficient and simultaneous metabolism of all types of sugars in lignocellulosic hydrolysates by ethanol-producing strains is still a challenge. Results An engineered strain Escherichia coli B0013-2021HPA with regulated glucose utilization, which could use all monosaccharides in lignocellulosic hydrolysates except glucose for cell growth and glucose for ethanol production, was constructed. In E. coli B0013-2021HPA, pta-ackA, ldhA and pflB were deleted to block the formation of acetate, lactate and formate and additional three mutations at glk, ptsG and manZ generated to block the glucose uptake and catabolism, followed by the replacement of the wild-type frdA locus with the ptsG expression cassette under the control of the temperature-inducible λ pR and pL promoters, and the final introduction of pEtac-PA carrying Zymomonas mobilis pdc and adhB for the ethanol pathway. B0013-2021HPA was able to utilize almost all xylose, galactose and arabinose but not glucose for cell propagation at 34 °C and converted all sugars to ethanol at 42 °C under oxygen-limited fermentation conditions. Conclusions Engineered E. coli strain with regulated glucose utilization showed efficient metabolism of mixed sugars in lignocellulosic hydrolysates and thus higher productivity of ethanol production. Electronic supplementary material The online version of this article (10.1186/s12934-018-0915-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jinfeng Sun
- Center for Bioresource and Bioenergy, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.,School of Life Science and Food Engineering, Huaiyin Institute of Technology, 1st East Meicheng Road, Huaian, 223003, China
| | - Kangming Tian
- Department of Biological Chemical Engineering, College of Chemical Engineering and Materials Science, Tianjin University of Science and Technology, TEDA, Tianjin, 300457, China
| | - Jie Wang
- Department of Biological Chemical Engineering, College of Chemical Engineering and Materials Science, Tianjin University of Science and Technology, TEDA, Tianjin, 300457, China
| | - Zixing Dong
- Department of Biological Chemical Engineering, College of Chemical Engineering and Materials Science, Tianjin University of Science and Technology, TEDA, Tianjin, 300457, China
| | - Xiaoguang Liu
- Department of Biological Chemical Engineering, College of Chemical Engineering and Materials Science, Tianjin University of Science and Technology, TEDA, Tianjin, 300457, China
| | - Kugenthiren Permaul
- Department of Biotechnology and Food Technology, Durban University of Technology, Durban, 4002, South Africa
| | - Suren Singh
- Department of Biotechnology and Food Technology, Durban University of Technology, Durban, 4002, South Africa
| | - Bernard A Prior
- Department of Microbiology, University of Stellenbosch, Matieland, 7602, South Africa
| | - Zhengxiang Wang
- Center for Bioresource and Bioenergy, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China. .,Department of Biological Chemical Engineering, College of Chemical Engineering and Materials Science, Tianjin University of Science and Technology, TEDA, Tianjin, 300457, China.
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27
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Sardi M, Gasch AP. Incorporating comparative genomics into the design-test-learn cycle of microbial strain engineering. FEMS Yeast Res 2018. [PMID: 28637316 DOI: 10.1093/femsyr/fox042] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Engineering microbes with new properties is an important goal in industrial engineering, to establish biological factories for production of biofuels, commodity chemicals and pharmaceutics. But engineering microbes to produce new compounds with high yield remains a major challenge toward economically viable production. Incorporating several modern approaches, including synthetic and systems biology, metabolic modeling and regulatory rewiring, has proven to significantly advance industrial strain engineering. This review highlights how comparative genomics can also facilitate strain engineering, by identifying novel genes and pathways, regulatory mechanisms and genetic background effects for engineering. We discuss how incorporating comparative genomics into the design-test-learn cycle of strain engineering can provide novel information that complements other engineering strategies.
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Affiliation(s)
- Maria Sardi
- Great Lakes Bioenergy Research Center, Madison, WI 53706, USA
| | - Audrey P Gasch
- Great Lakes Bioenergy Research Center, Madison, WI 53706, USA.,Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
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28
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Gyamerah M, Ampaw-Asiedu M, Mackey J, Menezes B, Woldesenbet S. Effect of Brönsted acidic ionic liquid 1-(1-propylsulfonic)-3-methylimidazolium chloride on growth and co-fermentation of glucose, xylose and arabinose by Zymomonas mobilis AX101. Lett Appl Microbiol 2018; 66:549-557. [PMID: 29573262 DOI: 10.1111/lam.12885] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Revised: 03/11/2018] [Accepted: 03/12/2018] [Indexed: 11/28/2022]
Abstract
The potential of large-scale lignocellulosic biomass hydrolysis to fermentable sugars using ionic liquids has increased interest in this green chemistry route to fermentation for fuel-ethanol production. The ionic liquid 1-(1-propylsulfonic)-3-methylimidazolium chloride compared to other reported ionic liquids has the advantage of hydrolysing lignocellulosic biomass to reducing sugars at catalytic concentrations (≤0·032 mol l-1 ) in a single step. However, effects of this ionic liquid on co-fermentation of glucose, xylose and arabinose to ethanol by recombinant Zymomonas mobilisAX101 has not been studied. Authentic glucose, xylose and arabinose were used to formulate fermentation media at varying catalytic 1-(1-propylsulfonic)-3-methylimidazolium chloride concentrations for batch co-fermentation of the sugars using Z. mobilisAX101. The results showed that at 0·008, 0·016 and 0·032 mol l-1 ionic liquid in the culture medium, cell growth decreased by 10, 27 and 67% respectively compared to the control. Ethanol yields were 62·6, 61·8, 50·5 and 23·1% for the control, 0·008, 0·016 and 0·032 mol l-1 ionic liquid respectively. The results indicate that lignocellulosic biomass hydrolysed using 0·008 mol l-1 of 1-(1-propylsulfonic)-3-methylimidazolium chloride would eliminate an additional separation step and provide a ready to use fermentation substrate. SIGNIFICANCE AND IMPACT OF STUDY This is the first reported study of the effect of the Brönsted acidic ionic liquid 1-(1-propylsulfonic)-3-methylimidazolium chloride on growth and co-fermentation of glucose, xylose and arabinose by Zymomonas mobilisAX101 in batch culture. Growth on and co-fermentation of the sugars by Z. mobilisAX 101 with no significant inhibition by the ionic liquid at the same catalytic amounts of 0·008 mol l-1 used to hydrolyse lignocellulosic biomass to reducing sugars overcome two major hurdles that adversely affect the process economics of large-scale industrial cellulosic fuel ethanol production; the energy-intensive hydrolysis and ionic liquid separation steps.
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Affiliation(s)
- M Gyamerah
- NSF CREST Center for Energy & Environmental Sustainability, Prairie View A & M University, Prairie View, TX, USA.,Department of Chemical Engineering, Prairie View A & M University, Prairie View, TX, USA
| | - M Ampaw-Asiedu
- NSF CREST Center for Energy & Environmental Sustainability, Prairie View A & M University, Prairie View, TX, USA.,Department of Chemical Engineering, Prairie View A & M University, Prairie View, TX, USA
| | - J Mackey
- NSF CREST Center for Energy & Environmental Sustainability, Prairie View A & M University, Prairie View, TX, USA.,Department of Chemical Engineering, Prairie View A & M University, Prairie View, TX, USA
| | - B Menezes
- NSF CREST Center for Energy & Environmental Sustainability, Prairie View A & M University, Prairie View, TX, USA.,Department of Chemical Engineering, Prairie View A & M University, Prairie View, TX, USA
| | - S Woldesenbet
- Cooperative Agricultural Research Center, Prairie View A& M University, Prairie View, TX, USA
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A novel strategy for production of ethanol and recovery of xylose from simulated corncob hydrolysate. Biotechnol Lett 2018; 40:781-788. [PMID: 29564679 DOI: 10.1007/s10529-018-2537-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 03/05/2018] [Indexed: 10/17/2022]
Abstract
OBJECTIVES To develop a xylose-nonutilizing Escherichia coli strain for ethanol production and xylose recovery. RESULTS Xylose-nonutilizing E. coli CICIM B0013-2012 was successfully constructed from E. coli B0013-1030 (pta-ack, ldhA, pflB, xylH) by deletion of frdA, xylA and xylE. It exhibited robust growth on plates containing glucose, arabinose or galactose, but failed to grow on xylose. The ethanol synthesis pathway was then introduced into B0013-2012 to create an ethanologenic strain B0013-2012PA. In shaking flask fermentation, B0013-2012PA fermented glucose to ethanol with the yield of 48.4 g/100 g sugar while xylose remained in the broth. In a 7-l bioreactor, B0013-2012PA fermented glucose, galactose and arabinose in the simulated corncob hydrolysate to 53.4 g/l ethanol with the yield of 48.9 g/100 g sugars and left 69.6 g/l xylose in the broth, representing 98.6% of the total xylose in the simulated corncob hydrolysate. CONCLUSIONS By using newly constructed strain B0013-2012PA, we successfully developed an efficient bioprocess for ethanol production and xylose recovery from the simulated corncob hydrolysate.
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Comparison and Optimization of Saccharification Conditions of Alkaline Pre-Treated Triticale Straw for Acid and Enzymatic Hydrolysis Followed by Ethanol Fermentation. ENERGIES 2018. [DOI: 10.3390/en11030639] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Bilal M, Iqbal HM, Hu H, Wang W, Zhang X. Metabolic engineering and enzyme-mediated processing: A biotechnological venture towards biofuel production – A review. RENEWABLE & SUSTAINABLE ENERGY REVIEWS 2018. [DOI: 10.1016/j.rser.2017.09.070] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Jansen MLA, Bracher JM, Papapetridis I, Verhoeven MD, de Bruijn H, de Waal PP, van Maris AJA, Klaassen P, Pronk JT. Saccharomyces cerevisiae strains for second-generation ethanol production: from academic exploration to industrial implementation. FEMS Yeast Res 2017; 17:3868933. [PMID: 28899031 PMCID: PMC5812533 DOI: 10.1093/femsyr/fox044] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 06/15/2017] [Indexed: 11/18/2022] Open
Abstract
The recent start-up of several full-scale 'second generation' ethanol plants marks a major milestone in the development of Saccharomyces cerevisiae strains for fermentation of lignocellulosic hydrolysates of agricultural residues and energy crops. After a discussion of the challenges that these novel industrial contexts impose on yeast strains, this minireview describes key metabolic engineering strategies that have been developed to address these challenges. Additionally, it outlines how proof-of-concept studies, often developed in academic settings, can be used for the development of robust strain platforms that meet the requirements for industrial application. Fermentation performance of current engineered industrial S. cerevisiae strains is no longer a bottleneck in efforts to achieve the projected outputs of the first large-scale second-generation ethanol plants. Academic and industrial yeast research will continue to strengthen the economic value position of second-generation ethanol production by further improving fermentation kinetics, product yield and cellular robustness under process conditions.
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Affiliation(s)
- Mickel L. A. Jansen
- DSM Biotechnology Centre, Alexander Fleminglaan 1, 2613 AX Delft, The
Netherlands
| | - Jasmine M. Bracher
- Department of Biotechnology, Delft University of Technology, Van der Maasweg
9, 2629 HZ Delft, The Netherlands
| | - Ioannis Papapetridis
- Department of Biotechnology, Delft University of Technology, Van der Maasweg
9, 2629 HZ Delft, The Netherlands
| | - Maarten D. Verhoeven
- Department of Biotechnology, Delft University of Technology, Van der Maasweg
9, 2629 HZ Delft, The Netherlands
| | - Hans de Bruijn
- DSM Biotechnology Centre, Alexander Fleminglaan 1, 2613 AX Delft, The
Netherlands
| | - Paul P. de Waal
- DSM Biotechnology Centre, Alexander Fleminglaan 1, 2613 AX Delft, The
Netherlands
| | - Antonius J. A. van Maris
- Department of Biotechnology, Delft University of Technology, Van der Maasweg
9, 2629 HZ Delft, The Netherlands
| | - Paul Klaassen
- DSM Biotechnology Centre, Alexander Fleminglaan 1, 2613 AX Delft, The
Netherlands
| | - Jack T. Pronk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg
9, 2629 HZ Delft, The Netherlands
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Liu J, Ma Z, Zhu H, Caiyin Q, Liang D, Wu H, Huang X, Qiao J. Improving xylose utilization of defatted rice bran for nisin production by overexpression of a xylose transcriptional regulator in Lactococcus lactis. BIORESOURCE TECHNOLOGY 2017; 238:690-697. [PMID: 28499254 DOI: 10.1016/j.biortech.2017.04.076] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 04/18/2017] [Accepted: 04/19/2017] [Indexed: 06/07/2023]
Abstract
Present investigation explores the potential of defatted rice bran (DRB) serving as sole carbon source and partial nitrogen source to support Lactococcus lactis growth and nisin production. To retain the nutrients in DRB, especially protein fractions, thermal pretreatment followed by enzymatic hydrolysis without washing step was applied for saccharification. A maximum of 45.64g reducing sugar mainly containing 30.26g glucose and 5.66g xylose from 100g DRB was attained in hydrolysates of DRB (HD). A novel strategy of xylR (xylose transcriptional regulator) overexpression followed by evolutionary engineering was proposed, which significantly increased the capacity of L. lactis to metabolize xylose. Subsequently, RT-PCR results indicated that xylR overexpression stimulated expression of xylose assimilation genes synergistically with exposure to xylose. In HD medium, the highest nisin titer of the engineered strain FEXR was 3824.53IU/mL, which was 1.37 times of that in sucrose medium by the original strain F44.
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Affiliation(s)
- Jiaheng Liu
- Key Laboratory of Systems Bioengineering, Ministry of Education (Tianjin University), Tianjin 300072, China; School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
| | - Zelin Ma
- Key Laboratory of Systems Bioengineering, Ministry of Education (Tianjin University), Tianjin 300072, China; School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
| | - Hongji Zhu
- Key Laboratory of Systems Bioengineering, Ministry of Education (Tianjin University), Tianjin 300072, China; School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Qinggele Caiyin
- Key Laboratory of Systems Bioengineering, Ministry of Education (Tianjin University), Tianjin 300072, China; School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Dongmei Liang
- Key Laboratory of Systems Bioengineering, Ministry of Education (Tianjin University), Tianjin 300072, China; School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
| | - Hao Wu
- Key Laboratory of Systems Bioengineering, Ministry of Education (Tianjin University), Tianjin 300072, China; School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
| | - Xu Huang
- China Oil & Foodstuffs Corporation (COFCO), Nutrition and Health Research Institute, China
| | - Jianjun Qiao
- Key Laboratory of Systems Bioengineering, Ministry of Education (Tianjin University), Tianjin 300072, China; School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China.
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Wang C, Li Y, Qiu C, Wang S, Ma J, Shen Y, Zhang Q, Du B, Ding Y, Bao X. Identification of Important Amino Acids in Gal2p for Improving the L-arabinose Transport and Metabolism in Saccharomyces cerevisiae. Front Microbiol 2017; 8:1391. [PMID: 28785254 PMCID: PMC5519586 DOI: 10.3389/fmicb.2017.01391] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 07/10/2017] [Indexed: 11/29/2022] Open
Abstract
Efficient and cost-effective bioethanol production from lignocellulosic materials requires co-fermentation of the main hydrolyzed sugars, including glucose, xylose, and L-arabinose. Saccharomyces cerevisiae is a glucose-fermenting yeast that is traditionally used for ethanol production. Fermentation of L-arabinose is also possible after metabolic engineering. Transport into the cell is the first and rate-limiting step for L-arabinose metabolism. The galactose permease, Gal2p, is a non-specific, endogenous monosaccharide transporter that has been shown to transport L-arabinose. However, Gal2p-mediated transport of L-arabinose occurs at a low efficiency. In this study, homologous modeling and L-arabinose docking were used to predict amino acids in Gal2p that are crucial for L-arabinose transport. Nine amino acid residues in Gal2p were identified and were the focus for site-directed mutagenesis. In the Gal2p transport-deficient chassis cells, the capacity for L-arabinose transport of the different Gal2p mutants was compared by testing growth rates using L-arabinose as the sole carbon source. Almost all the tested mutations affected L-arabinose transport capacity. Among them, F85 is a unique site. The F85S, F85G, F85C, and F85T point mutations significantly increased L-arabinose transport activities, while, the F85E and F85R mutations decreased L-arabinose transport activities compared to the Gal2p-expressing wild-type strain. These results verified F85 as a key residue in L-arabinose transport. The F85S mutation, having the most significant effect, elevated the exponential growth rate by 40%. The F85S mutation also improved xylose transport efficiency and weakened the glucose transport preference. Overall, enhancing the L-arabinose transport capacity further improved the L-arabinose metabolism of engineered S. cerevisiae.
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Affiliation(s)
- Chengqiang Wang
- College of Life Sciences/Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural UniversityTai'an, China.,The State Key Laboratory of Microbial Technology/Environment Research Institute, Shandong UniversityJinan, China
| | - Yanwei Li
- The State Key Laboratory of Microbial Technology/Environment Research Institute, Shandong UniversityJinan, China
| | - Chenxi Qiu
- College of Life Sciences/Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural UniversityTai'an, China.,The State Key Laboratory of Microbial Technology/Environment Research Institute, Shandong UniversityJinan, China
| | - Shihao Wang
- College of Life Sciences/Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural UniversityTai'an, China.,The State Key Laboratory of Microbial Technology/Environment Research Institute, Shandong UniversityJinan, China
| | - Jinjin Ma
- College of Life Sciences/Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural UniversityTai'an, China
| | - Yu Shen
- The State Key Laboratory of Microbial Technology/Environment Research Institute, Shandong UniversityJinan, China
| | - Qingzhu Zhang
- The State Key Laboratory of Microbial Technology/Environment Research Institute, Shandong UniversityJinan, China
| | - Binghai Du
- College of Life Sciences/Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural UniversityTai'an, China
| | - Yanqin Ding
- College of Life Sciences/Shandong Key Laboratory of Agricultural Microbiology, Shandong Agricultural UniversityTai'an, China
| | - Xiaoming Bao
- The State Key Laboratory of Microbial Technology/Environment Research Institute, Shandong UniversityJinan, China.,College of Bioengineering, Qilu University of TechnologyJinan, China
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35
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Hope EA, Amorosi CJ, Miller AW, Dang K, Heil CS, Dunham MJ. Experimental Evolution Reveals Favored Adaptive Routes to Cell Aggregation in Yeast. Genetics 2017; 206:1153-1167. [PMID: 28450459 PMCID: PMC5499169 DOI: 10.1534/genetics.116.198895] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 04/06/2017] [Indexed: 02/02/2023] Open
Abstract
Yeast flocculation is a community-building cell aggregation trait that is an important mechanism of stress resistance and a useful phenotype for brewers; however, it is also a nuisance in many industrial processes, in clinical settings, and in the laboratory. Chemostat-based evolution experiments are impaired by inadvertent selection for aggregation, which we observe in 35% of populations. These populations provide a testing ground for understanding the breadth of genetic mechanisms Saccharomyces cerevisiae uses to flocculate, and which of those mechanisms provide the biggest adaptive advantages. In this study, we employed experimental evolution as a tool to ask whether one or many routes to flocculation are favored, and to engineer a strain with reduced flocculation potential. Using a combination of whole genome sequencing and bulk segregant analysis, we identified causal mutations in 23 independent clones that had evolved cell aggregation during hundreds of generations of chemostat growth. In 12 of those clones, we identified a transposable element insertion in the promoter region of known flocculation gene FLO1, and, in an additional five clones, we recovered loss-of-function mutations in transcriptional repressor TUP1, which regulates FLO1 and other related genes. Other causal mutations were found in genes that have not been previously connected to flocculation. Evolving a flo1 deletion strain revealed that this single deletion reduces flocculation occurrences to 3%, and demonstrated the efficacy of using experimental evolution as a tool to identify and eliminate the primary adaptive routes for undesirable traits.
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Affiliation(s)
- Elyse A Hope
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195
| | - Clara J Amorosi
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195
| | - Aaron W Miller
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195
| | - Kolena Dang
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195
| | - Caiti Smukowski Heil
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195
| | - Maitreya J Dunham
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195
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36
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Bonturi N, Crucello A, Viana AJC, Miranda EA. Microbial oil production in sugarcane bagasse hemicellulosic hydrolysate without nutrient supplementation by a Rhodosporidium toruloides adapted strain. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.03.007] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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37
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Deparis Q, Claes A, Foulquié-Moreno MR, Thevelein JM. Engineering tolerance to industrially relevant stress factors in yeast cell factories. FEMS Yeast Res 2017; 17:3861662. [PMID: 28586408 PMCID: PMC5812522 DOI: 10.1093/femsyr/fox036] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/04/2017] [Indexed: 01/01/2023] Open
Abstract
The main focus in development of yeast cell factories has generally been on establishing optimal activity of heterologous pathways and further metabolic engineering of the host strain to maximize product yield and titer. Adequate stress tolerance of the host strain has turned out to be another major challenge for obtaining economically viable performance in industrial production. Although general robustness is a universal requirement for industrial microorganisms, production of novel compounds using artificial metabolic pathways presents additional challenges. Many of the bio-based compounds desirable for production by cell factories are highly toxic to the host cells in the titers required for economic viability. Artificial metabolic pathways also turn out to be much more sensitive to stress factors than endogenous pathways, likely because regulation of the latter has been optimized in evolution in myriads of environmental conditions. We discuss different environmental and metabolic stress factors with high relevance for industrial utilization of yeast cell factories and the experimental approaches used to engineer higher stress tolerance. Improving stress tolerance in a predictable manner in yeast cell factories should facilitate their widespread utilization in the bio-based economy and extend the range of products successfully produced in large scale in a sustainable and economically profitable way.
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Affiliation(s)
- Quinten Deparis
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, B-3001 KU Leuven, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Arne Claes
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, B-3001 KU Leuven, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Maria R. Foulquié-Moreno
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, B-3001 KU Leuven, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
| | - Johan M. Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, B-3001 KU Leuven, Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, B-3001 Leuven-Heverlee, Flanders, Belgium
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38
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Caballero A, Ramos JL. Enhancing ethanol yields through d-xylose and l-arabinose co-fermentation after construction of a novel high efficient l-arabinose-fermenting Saccharomyces cerevisiae strain. Microbiology (Reading) 2017; 163:442-452. [DOI: 10.1099/mic.0.000437] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Antonio Caballero
- Abengoa Research, Department of Biotechnology, Campus de Palmas Altas, c/Energia Solar number 1, 41004 Sevilla, Spain
- BacMine, C/de Santiago Grisolía 28760 Tres Cantos, Spain
| | - Juan Luis Ramos
- Abengoa Research, Department of Biotechnology, Campus de Palmas Altas, c/Energia Solar number 1, 41004 Sevilla, Spain
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Coutilization of D-Glucose, D-Xylose, and L-Arabinose in Saccharomyces cerevisiae by Coexpressing the Metabolic Pathways and Evolutionary Engineering. BIOMED RESEARCH INTERNATIONAL 2017; 2017:5318232. [PMID: 28459063 PMCID: PMC5385224 DOI: 10.1155/2017/5318232] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 03/04/2017] [Accepted: 03/20/2017] [Indexed: 11/23/2022]
Abstract
Efficient and cost-effective fuel ethanol production from lignocellulosic materials requires simultaneous cofermentation of all hydrolyzed sugars, mainly including D-glucose, D-xylose, and L-arabinose. Saccharomyces cerevisiae is a traditional D-glucose fermenting strain and could utilize D-xylose and L-arabinose after introducing the initial metabolic pathways. The efficiency and simultaneous coutilization of the two pentoses and D-glucose for ethanol production in S. cerevisiae still need to be optimized. Previously, we constructed an L-arabinose-utilizing S. cerevisiae BSW3AP. In this study, we further introduced the XI and XR-XDH metabolic pathways of D-xylose into BSW3AP to obtain D-glucose, D-xylose, and L-arabinose cofermenting strain. Benefits of evolutionary engineering: the resulting strain BSW4XA3 displayed a simultaneous coutilization of D-xylose and L-arabinose with similar consumption rates, and the D-glucose metabolic capacity was not decreased. After 120 h of fermentation on mixed D-glucose, D-xylose, and L-arabinose, BSW4XA3 consumed 24% more amounts of pentoses and the ethanol yield of mixed sugars was increased by 30% than that of BSW3AP. The resulting strain BSW4XA3 was a useful chassis for further enhancing the coutilization efficiency of mixed sugars for bioethanol production.
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40
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Goold HD, Kroukamp H, Williams TC, Paulsen IT, Varela C, Pretorius IS. Yeast's balancing act between ethanol and glycerol production in low-alcohol wines. Microb Biotechnol 2017; 10:264-278. [PMID: 28083938 PMCID: PMC5328816 DOI: 10.1111/1751-7915.12488] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 11/17/2016] [Accepted: 11/23/2016] [Indexed: 01/06/2023] Open
Abstract
Alcohol is fundamental to the character of wine, yet too much can put a wine off‐balance. A wine is regarded to be well balanced if its alcoholic strength, acidity, sweetness, fruitiness and tannin structure complement each other so that no single component dominates on the palate. Balancing a wine's positive fruit flavours with the optimal absolute and relative concentration of alcohol can be surprisingly difficult. Over the past three decades, consumers have increasingly demanded wine with richer and riper fruit flavour profiles. In response, grape and wine producers have extended harvest times to increase grape maturity and enhance the degree of fruit flavours and colour intensity. However, a higher degree of grape maturity results in increased grape sugar concentration, which in turn results in wines with elevated alcohol concentration. On average, the alcohol strength of red wines from many warm wine‐producing regions globally rose by about 2% (v/v) during this period. Notwithstanding that many of these ‘full‐bodied, fruit‐forward’ wines are well balanced and sought after, there is also a significant consumer market segment that seeks lighter styles with less ethanol‐derived ‘hotness’ on the palate. Consumer‐focussed wine producers are developing and implementing several strategies in the vineyard and winery to reduce the alcohol concentration in wines produced from well‐ripened grapes. In this context, Saccharomyces cerevisiae wine yeasts have proven to be a pivotal strategy to reduce ethanol formation during the fermentation of grape musts with high sugar content (> 240 g l−1). One of the approaches has been to develop ‘low‐alcohol’ yeast strains which work by redirecting their carbon metabolism away from ethanol production to other metabolites, such as glycerol. This article reviews the current challenges of producing glycerol at the expense of ethanol. It also casts new light on yeast strain development programmes which, bolstered by synthetic genomics, could potentially overcome these challenges.
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Affiliation(s)
- Hugh D Goold
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia.,New South Wales Department of Primary Industries, Locked Bag 21, Orange, NSW, 2800, Australia
| | - Heinrich Kroukamp
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Thomas C Williams
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Ian T Paulsen
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Cristian Varela
- The Australian Wine Research Institute, PO Box 197, Adelaide, SA, 5064, Australia
| | - Isak S Pretorius
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
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41
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Williams TC, Xu X, Ostrowski M, Pretorius IS, Paulsen IT. Positive-feedback, ratiometric biosensor expression improves high-throughput metabolite-producer screening efficiency in yeast. Synth Biol (Oxf) 2017; 2:ysw002. [PMID: 32995501 PMCID: PMC7513737 DOI: 10.1093/synbio/ysw002] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 11/14/2016] [Accepted: 11/29/2016] [Indexed: 11/23/2022] Open
Abstract
Biosensors are valuable and versatile tools in synthetic biology that are used to modulate gene expression in response to a wide range of stimuli. Ligand responsive transcription factors are a class of biosensor that can be used to couple intracellular metabolite concentration with gene expression to enable dynamic regulation and high-throughput metabolite producer screening. We have established the Saccharomyces cerevisiae WAR1 transcriptional regulator and PDR12 promoter as an organic acid biosensor that can be used to detect varying levels of para-hydroxybenzoic acid (PHBA) production from the shikimate pathway and output green fluorescent protein (GFP) expression in response. The dynamic range of GFP expression in response to PHBA was dramatically increased by engineering positive-feedback expression of the WAR1 transcriptional regulator from its target PDR12 promoter. In addition, the noise in GFP expression at the population-level was controlled by normalising GFP fluorescence to constitutively expressed mCherry fluorescence within each cell. These biosensor modifications increased the high-throughput screening efficiency of yeast cells engineered to produce PHBA by 5,000-fold, enabling accurate fluorescence activated cell sorting isolation of producer cells that were mixed at a ratio of 1 in 10,000 with non-producers. Positive-feedback, ratiometric transcriptional regulator expression is likely applicable to many other transcription-factor/promoter pairs used in synthetic biology and metabolic engineering for both dynamic regulation and high-throughput screening applications.
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Affiliation(s)
- Thomas C Williams
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Xin Xu
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Martin Ostrowski
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Isak S Pretorius
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Ian T Paulsen
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
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42
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Synthetic Evolution of Metabolic Productivity Using Biosensors. Trends Biotechnol 2016; 34:371-381. [DOI: 10.1016/j.tibtech.2016.02.002] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 02/01/2016] [Accepted: 02/01/2016] [Indexed: 11/23/2022]
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Brandenburg J, Blomqvist J, Pickova J, Bonturi N, Sandgren M, Passoth V. Lipid production from hemicellulose with Lipomyces starkeyi in a pH regulated fed-batch cultivation. Yeast 2016; 33:451-62. [PMID: 26945827 DOI: 10.1002/yea.3160] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 02/12/2016] [Accepted: 02/27/2016] [Indexed: 11/11/2022] Open
Abstract
This study investigated lipid production from the hemicellulosic fraction of birch wood by the oleaginous yeast Lipomyces starkeyi. Birch wood chips were thermochemically pretreated by hot water extraction, and the liquid phase, containing 45.1 g/l xylose as the major sugar, 13.1 g/l acetic acid and 4.7 g/l furfural, was used for cultivations of L. starkeyi CBS1807. The hydrolysate strongly inhibited yeast growth; the strain could only grow in medium containing 30% hydrolysate at pH 6. At pH 5, growth stopped already upon the addition of about 10% hydrolysate. In fed-batch cultures fed with hydrolysate or a model xylose-acetic acid mixture, co-consumption of xylose and acetic acid was observed, which resulted in a pH increase. This phenomenon was utilized to establish a pH-stat fed-batch cultivation in which, after an initial feeding, hydrolysate or model mixture was connected to the pH-regulation system of the bioreactor. Under these conditions we obtained growth and lipid production in cultures grown on either xylose or glucose during the batch phase. In cultivations fed with model mixture, a maximum lipid content of 60.5% of the cell dry weight (CDW) was obtained; however, not all xylose was consumed. When feeding hydrolysate, growth was promoted and carbon sources were completely consumed, resulting in higher CDW with maximum lipid content of 51.3%. In both cultures the lipid concentration was 8 g/l and a lipid yield of 0.1 g/g carbon source was obtained. Lipid composition was similar in all cultivations, with C18:1 and C16:0 being the most abundant fatty acids. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Jule Brandenburg
- Swedish University of Agricultural Sciences, Department of Chemistry and Biotechnology, BioCentre, Uppsala, Sweden
| | - Johanna Blomqvist
- Swedish University of Agricultural Sciences, Department of Chemistry and Biotechnology, BioCentre, Uppsala, Sweden
| | - Jana Pickova
- Swedish University of Agricultural Sciences, Department of Food Science, BioCentre, SLU, Uppsala, Sweden
| | - Nemailla Bonturi
- School of Chemical Engineering, State University of Campinas, UNICAMP, Department of Materials and Bioprocess Engineering, Campinas, Brazil
| | - Mats Sandgren
- Swedish University of Agricultural Sciences, Department of Chemistry and Biotechnology, BioCentre, Uppsala, Sweden
| | - Volkmar Passoth
- Swedish University of Agricultural Sciences, Department of Microbiology, BioCentre, SLU, Uppsala, Sweden
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44
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Metabolic Engineering Strategies for Co-Utilization of Carbon Sources in Microbes. Bioengineering (Basel) 2016; 3:bioengineering3010010. [PMID: 28952572 PMCID: PMC5597168 DOI: 10.3390/bioengineering3010010] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 01/25/2016] [Indexed: 11/17/2022] Open
Abstract
Co-utilization of carbon sources in microbes is an important topic in metabolic engineering research. It is not only a way to reduce microbial production costs but also an attempt for either improving the yields of target products or decreasing the formation of byproducts. However, there are barriers in co-utilization of carbon sources in microbes, such as carbon catabolite repression. To overcome the barriers, different metabolic engineering strategies have been developed, such as inactivation of the phosphotransferase system and rewiring carbon assimilation pathways. This review summarizes the most recent developments of different strategies that support microbes to utilize two or more carbon sources simultaneously. The main content focuses on the co-utilization of glucose and pentoses, major sugars in lignocellulose.
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45
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Guo W, Sheng J, Zhao H, Feng X. Metabolic engineering of Saccharomyces cerevisiae to produce 1-hexadecanol from xylose. Microb Cell Fact 2016; 15:24. [PMID: 26830023 PMCID: PMC4736120 DOI: 10.1186/s12934-016-0423-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 01/19/2016] [Indexed: 11/10/2022] Open
Abstract
Background An advantageous but challenging approach to overcome the limited supply of petroleum and relieve the greenhouse effect is to produce bulk chemicals from renewable materials. Fatty alcohols, with a billion-dollar global market, are important raw chemicals for detergents, emulsifiers, lubricants, and cosmetics production. Microbial production of fatty alcohols has been successfully achieved in several industrial microorganisms. However, most of the achievements were using glucose, an edible sugar, as the carbon source. To produce fatty alcohols in a renewable manner, non-edible sugars such as xylose will be a more appropriate feedstock. Results In this study, we aim to engineer a Saccharomyces cerevisiae strain that can efficiently convert xylose to fatty alcohols. To this end, we first introduced the fungal xylose utilization pathway consisting of xylose reductase (XR), xylitol dehydrogenase (XDH), and xylulose kinase (XKS) into a fatty alcohol-producing S. cerevisiae strain (XF3) that was developed in our previous studies to achieve 1-hexadecanol production from xylose at 0.4 g/L. We next applied promoter engineering on the xylose utilization pathway to optimize the expression levels of XR, XDH, and XKS, and increased the 1-hexadecanol titer by 171 %. To further improve the xylose-based fatty alcohol production, two optimized S. cerevisiae strains from promoter engineering were evolved with the xylose as the sole carbon source. We found that the cell growth rate was improved at the expense of decreased fatty alcohol production, which indicated 1-hexadecanol was mainly produced as a non-growth associated product. Finally, through fed-batch fermentation, we successfully achieved 1-hexadecanol production at over 1.2 g/L using xylose as the sole carbon source, which represents the highest titer of xylose-based 1-hexadecanol reported in microbes to date. Conclusions A fatty alcohol-producing S. cerevisiae strain was engineered in this study to produce 1-hexadecanol from xylose. Although the xylose pathway we developed in this study could be further improved, this proof-of-concept study, for the first time to our best knowledge, demonstrated that the xylose-based fatty alcohol could be produced in S. cerevisiae with potential applications in developing consolidated bioprocessing for producing other fatty acid-derived chemicals. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0423-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Weihua Guo
- Department of Biological Systems Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA.
| | - Jiayuan Sheng
- Department of Biological Systems Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA.
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Xueyang Feng
- Department of Biological Systems Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA.
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46
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Fletcher E, Krivoruchko A, Nielsen J. Industrial systems biology and its impact on synthetic biology of yeast cell factories. Biotechnol Bioeng 2015; 113:1164-70. [PMID: 26524089 DOI: 10.1002/bit.25870] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 10/01/2015] [Accepted: 10/28/2015] [Indexed: 02/04/2023]
Abstract
Engineering industrial cell factories to effectively yield a desired product while dealing with industrially relevant stresses is usually the most challenging step in the development of industrial production of chemicals using microbial fermentation processes. Using synthetic biology tools, microbial cell factories such as Saccharomyces cerevisiae can be engineered to express synthetic pathways for the production of fuels, biopharmaceuticals, fragrances, and food flavors. However, directing fluxes through these synthetic pathways towards the desired product can be demanding due to complex regulation or poor gene expression. Systems biology, which applies computational tools and mathematical modeling to understand complex biological networks, can be used to guide synthetic biology design. Here, we present our perspective on how systems biology can impact synthetic biology towards the goal of developing improved yeast cell factories. Biotechnol. Bioeng. 2016;113: 1164-1170. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Eugene Fletcher
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96 Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, SE-412 96 Gothenburg, Sweden
| | - Anastasia Krivoruchko
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96 Gothenburg, Sweden.,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, SE-412 96 Gothenburg, Sweden
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, SE-412 96 Gothenburg, Sweden. .,Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Kemivägen 10, SE-412 96 Gothenburg, Sweden. .,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2970, Hørsholm, Denmark.
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47
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Lindquist MR, López-Núñez JC, Jones MA, Cox EJ, Pinkelman RJ, Bang SS, Moser BR, Jackson MA, Iten LB, Kurtzman CP, Bischoff KM, Liu S, Qureshi N, Tasaki K, Rich JO, Cotta MA, Saha BC, Hughes SR. Irradiation of Yarrowia lipolytica NRRL YB-567 creating novel strains with enhanced ammonia and oil production on protein and carbohydrate substrates. Appl Microbiol Biotechnol 2015; 99:9723-43. [PMID: 26272089 PMCID: PMC4628078 DOI: 10.1007/s00253-015-6852-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 07/12/2015] [Accepted: 07/15/2015] [Indexed: 01/05/2023]
Abstract
Increased interest in sustainable production of renewable diesel and other valuable bioproducts is redoubling efforts to improve economic feasibility of microbial-based oil production. Yarrowia lipolytica is capable of employing a wide variety of substrates to produce oil and valuable co-products. We irradiated Y. lipolytica NRRL YB-567 with UV-C to enhance ammonia (for fertilizer) and lipid (for biodiesel) production on low-cost protein and carbohydrate substrates. The resulting strains were screened for ammonia and oil production using color intensity of indicators on plate assays. Seven mutant strains were selected (based on ammonia assay) and further evaluated for growth rate, ammonia and oil production, soluble protein content, and morphology when grown on liver infusion medium (without sugars), and for growth on various substrates. Strains were identified among these mutants that had a faster doubling time, produced higher maximum ammonia levels (enzyme assay) and more oil (Sudan Black assay), and had higher maximum soluble protein levels (Bradford assay) than wild type. When grown on plates with substrates of interest, all mutant strains showed similar results aerobically to wild-type strain. The mutant strain with the highest oil production and the fastest doubling time was evaluated on coffee waste medium. On this medium, the strain produced 0.12 g/L ammonia and 0.20 g/L 2-phenylethanol, a valuable fragrance/flavoring, in addition to acylglycerols (oil) containing predominantly C16 and C18 residues. These mutant strains will be investigated further for potential application in commercial biodiesel production.
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Affiliation(s)
- Mitch R Lindquist
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Center for Agricultural Utilization Research (NCAUR), Renewable Product Technology Research Unit, 1815 North University Street, Peoria, IL, 61604, USA
| | - Juan Carlos López-Núñez
- National Coffee Research Centre - Cenicafe, National Federation of Coffee Growers of Colombia - FNC, Cenicafé Planalto Km 4 vía Antigua Chinchiná, Manizales, Caldas, Colombia
| | - Marjorie A Jones
- 4160 Department of Chemistry, Illinois State University, 214 Julian Hall, Normal, IL, 61790-4160, USA
| | - Elby J Cox
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Center for Agricultural Utilization Research (NCAUR), Renewable Product Technology Research Unit, 1815 North University Street, Peoria, IL, 61604, USA
| | - Rebecca J Pinkelman
- South Dakota School of Mines & Technology, Chemical and Biological Engineering, 501 East Saint Joseph Street, Rapid City, SD, 57701-3995, USA
| | - Sookie S Bang
- South Dakota School of Mines & Technology, Chemical and Biological Engineering, 501 East Saint Joseph Street, Rapid City, SD, 57701-3995, USA
| | - Bryan R Moser
- USDA, ARS, NCAUR, Bio-oils Research Unit, 1815 North University Street, Peoria, IL, 61604, USA
| | - Michael A Jackson
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Center for Agricultural Utilization Research (NCAUR), Renewable Product Technology Research Unit, 1815 North University Street, Peoria, IL, 61604, USA
| | - Loren B Iten
- USDA, ARS, NCAUR, Bioenergy Research Unit, 1815 North University Street, Peoria, IL, 61604, USA
| | - Cletus P Kurtzman
- USDA, ARS, NCAUR, Bacterial Foodborne Pathogens and Mycology Research Unit, 1815 North University Street, Peoria, IL, 61604, USA
| | - Kenneth M Bischoff
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Center for Agricultural Utilization Research (NCAUR), Renewable Product Technology Research Unit, 1815 North University Street, Peoria, IL, 61604, USA
| | - Siqing Liu
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Center for Agricultural Utilization Research (NCAUR), Renewable Product Technology Research Unit, 1815 North University Street, Peoria, IL, 61604, USA
| | - Nasib Qureshi
- USDA, ARS, NCAUR, Bioenergy Research Unit, 1815 North University Street, Peoria, IL, 61604, USA
| | - Kenneth Tasaki
- Mitsubishi Chemical, USMC Research & Innovation, 410 Palos Verdes Blvd, Redondo Beach, CA, 90277, USA
| | - Joseph O Rich
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Center for Agricultural Utilization Research (NCAUR), Renewable Product Technology Research Unit, 1815 North University Street, Peoria, IL, 61604, USA
| | - Michael A Cotta
- USDA, ARS, NCAUR, Bioenergy Research Unit, 1815 North University Street, Peoria, IL, 61604, USA
| | - Badal C Saha
- USDA, ARS, NCAUR, Bioenergy Research Unit, 1815 North University Street, Peoria, IL, 61604, USA
| | - Stephen R Hughes
- United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Center for Agricultural Utilization Research (NCAUR), Renewable Product Technology Research Unit, 1815 North University Street, Peoria, IL, 61604, USA.
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Qi X, Zha J, Liu GG, Zhang W, Li BZ, Yuan YJ. Heterologous xylose isomerase pathway and evolutionary engineering improve xylose utilization in Saccharomyces cerevisiae. Front Microbiol 2015; 6:1165. [PMID: 26539187 PMCID: PMC4612707 DOI: 10.3389/fmicb.2015.01165] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2015] [Accepted: 10/08/2015] [Indexed: 12/24/2022] Open
Abstract
Xylose utilization is one key issue for the bioconversion of lignocelluloses. It is a promising approach to engineering heterologous pathway for xylose utilization in Saccharomyces cerevisiae. Here, we constructed a xylose-fermenting yeast SyBE001 through combinatorial fine-tuning the expression of XylA and endogenous XKS1. Additional overexpression of genes RKI1, RPE1, TKL1, and TAL1 in the non-oxidative pentose phosphate pathway (PPP) in SyBE001 increased the xylose consumption rate by 1.19-fold. By repetitive adaptation, the xylose utilization rate was further increased by ∼10-fold in the resultant strain SyBE003. Gene expression analysis identified a variety of genes with significantly changed expression in the PPP, glycolysis and the tricarboxylic acid cycle in SyBE003.
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Affiliation(s)
- Xin Qi
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University Tianjin, China ; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University Tianjin, China
| | - Jian Zha
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University Tianjin, China ; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University Tianjin, China
| | - Gao-Gang Liu
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University Tianjin, China ; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University Tianjin, China
| | - Weiwen Zhang
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University Tianjin, China ; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University Tianjin, China
| | - Bing-Zhi Li
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University Tianjin, China ; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University Tianjin, China
| | - Ying-Jin Yuan
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University Tianjin, China ; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University Tianjin, China
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Knoshaug EP, Vidgren V, Magalhães F, Jarvis EE, Franden MA, Zhang M, Singh A. Novel transporters from
Kluyveromyces marxianus
and
Pichia guilliermondii
expressed in
Saccharomyces cerevisiae
enable growth on
l
‐arabinose and
d
‐xylose. Yeast 2015; 32:615-28. [DOI: 10.1002/yea.3084] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 05/11/2015] [Accepted: 06/23/2015] [Indexed: 11/08/2022] Open
Affiliation(s)
- Eric P. Knoshaug
- National Renewable Energy Laboratory National Bioenergy Centre Golden CO USA
| | - Virve Vidgren
- VTT Technical Research Centre of Finland PO Box 1000 FI‐02044 VTT Finland
| | | | - Eric E. Jarvis
- National Renewable Energy Laboratory National Bioenergy Centre Golden CO USA
| | - Mary Ann Franden
- National Renewable Energy Laboratory National Bioenergy Centre Golden CO USA
| | - Min Zhang
- National Renewable Energy Laboratory National Bioenergy Centre Golden CO USA
| | - Arjun Singh
- National Renewable Energy Laboratory National Bioenergy Centre Golden CO USA
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50
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Liaud N, Rosso MN, Fabre N, Crapart S, Herpoël-Gimbert I, Sigoillot JC, Raouche S, Levasseur A. L-lactic acid production by Aspergillus brasiliensis overexpressing the heterologous ldha gene from Rhizopus oryzae. Microb Cell Fact 2015; 14:66. [PMID: 25935554 PMCID: PMC4425913 DOI: 10.1186/s12934-015-0249-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 04/23/2015] [Indexed: 11/10/2022] Open
Abstract
Background Lactic acid is the building block of poly-lactic acid (PLA), a biopolymer that could be set to replace petroleum-based plastics. To make lactic acid production cost-effective, the production process should be carried out at low pH, in low-nutrient media, and with a low-cost carbon source. Yeasts have been engineered to produce high levels of lactic acid at low pH from glucose but not from carbohydrate polymers (e.g. cellulose, hemicellulose, starch). Aspergilli are versatile microbial cell factories able to naturally produce large amounts of organic acids at low pH and to metabolize cheap abundant carbon sources such as plant biomass. However, they have never been used for lactic acid production. Results To investigate the feasibility of lactic acid production with Aspergillus, the NAD-dependent lactate dehydrogenase (LDH) responsible for lactic acid production by Rhizopus oryzae was produced in Aspergillus brasiliensis BRFM103. Among transformants, the best lactic acid producer, A. brasiliensis BRFM1877, integrated 6 ldhA gene copies, and intracellular LDH activity was 9.2 × 10−2 U/mg. At a final pH of 1.6, lactic acid titer reached 13.1 g/L (conversion yield: 26%, w/w) at 138 h in glucose-ammonium medium. This extreme pH drop was subsequently prevented by switching nitrogen source from ammonium sulfate to Na-nitrate, leading to a final pH of 3 and a lactic acid titer of 17.7 g/L (conversion yield: 47%, w/w) at 90 h of culture. Final titer was further improved to 32.2 g/L of lactic acid (conversion yield: 44%, w/w) by adding 20 g/L glucose to the culture medium at 96 h. This strain was ultimately able to produce lactic acid from xylose, arabinose, starch and xylan. Conclusion We obtained the first Aspergillus strains able to produce large amounts of lactic acid by inserting recombinant ldhA genes from R. oryzae into a wild-type A. brasiliensis strain. pH regulation failed to significantly increase lactic acid production, but switching nitrogen source and changing culture feed enabled a 1.8-fold increase in conversion yields. The strain produced lactic acid from plant biomass. Our findings make A. brasiliensis a strong contender microorganism for low-pH acid production from various complex substrates, especially hemicellulose.
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Affiliation(s)
- Nadège Liaud
- INRA, UMR1163 Biodiversité et Biotechnologie Fongiques, Polytech' Marseille, 163 avenue de Luminy, CP 925, 13288, Marseille, Cedex 09, France. .,Aix-Marseille Université, UMR1163 Biodiversité et Biotechnologie Fongiques, Polytech' Marseille, 163 avenue de Luminy, CP 925, 13288, Marseille, Cedex 09, France. .,ARD Agro-Industrie Recherche et Développement, Route de Bazancourt, 51110, Pomacle, France.
| | - Marie-Noëlle Rosso
- INRA, UMR1163 Biodiversité et Biotechnologie Fongiques, Polytech' Marseille, 163 avenue de Luminy, CP 925, 13288, Marseille, Cedex 09, France.
| | - Nicolas Fabre
- ARD Agro-Industrie Recherche et Développement, Route de Bazancourt, 51110, Pomacle, France.
| | - Sylvaine Crapart
- ARD Agro-Industrie Recherche et Développement, Route de Bazancourt, 51110, Pomacle, France.
| | - Isabelle Herpoël-Gimbert
- INRA, UMR1163 Biodiversité et Biotechnologie Fongiques, Polytech' Marseille, 163 avenue de Luminy, CP 925, 13288, Marseille, Cedex 09, France. .,Aix-Marseille Université, UMR1163 Biodiversité et Biotechnologie Fongiques, Polytech' Marseille, 163 avenue de Luminy, CP 925, 13288, Marseille, Cedex 09, France.
| | - Jean-Claude Sigoillot
- INRA, UMR1163 Biodiversité et Biotechnologie Fongiques, Polytech' Marseille, 163 avenue de Luminy, CP 925, 13288, Marseille, Cedex 09, France. .,Aix-Marseille Université, UMR1163 Biodiversité et Biotechnologie Fongiques, Polytech' Marseille, 163 avenue de Luminy, CP 925, 13288, Marseille, Cedex 09, France.
| | - Sana Raouche
- INRA, UMR1163 Biodiversité et Biotechnologie Fongiques, Polytech' Marseille, 163 avenue de Luminy, CP 925, 13288, Marseille, Cedex 09, France. .,Aix-Marseille Université, UMR1163 Biodiversité et Biotechnologie Fongiques, Polytech' Marseille, 163 avenue de Luminy, CP 925, 13288, Marseille, Cedex 09, France.
| | - Anthony Levasseur
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS 7278, IRD 198, INSERM U1095, IHU Méditerranée Infection, Pôle des Maladies Infectieuses, Assistance Publique-Hôpitaux de Marseille, Faculté de Médecine, 27 Bd Jean Moulin, 13005, Marseille, France.
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