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Raheja Y, Singh V, Sharma G, Tsang A, Chadha BS. A thermostable and inhibitor resistant β-glucosidase from Rasamsonia emersonii for efficient hydrolysis of lignocellulosics biomass. Bioprocess Biosyst Eng 2024; 47:567-582. [PMID: 38470501 DOI: 10.1007/s00449-024-02988-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 02/20/2024] [Indexed: 03/14/2024]
Abstract
The present study reports a highly thermostable β-glucosidase (GH3) from Rasamsonia emersonii that was heterologously expressed in Pichia pastoris. Extracellular β-glucosidase was purified to homogeneity using single step affinity chromatography with molecular weight of ~ 110 kDa. Intriguingly, the purified enzyme displayed high tolerance to inhibitors mainly acetic acid, formic acid, ferulic acid, vanillin and 5-hydroxymethyl furfural at concentrations exceeding those present in acid steam pretreated rice straw slurry used for hydrolysis and subsequent fermentation in 2G ethanol plants. Characteristics of purified β-glucosidase revealed the optimal activity at 80 °C, pH 5.0 and displayed high thermostability over broad range of temperature 50-70 °C with maximum half-life of ~ 60 h at 50 °C, pH 5.0. The putative transglycosylation activity of β-glucosidase was appreciably enhanced in the presence of methanol as an acceptor. Using the transglycosylation ability of β-glucosidase, the generated low cost mixed glucose disaccharides resulted in the increased induction of R. emersonii cellulase under submerged fermentation. Scaling up the recombinant protein production at fermenter level using temporal feeding approach resulted in maximal β-glucosidase titres of 134,660 units/L. Furthermore, a developed custom made enzyme cocktail consisting of cellulase from R. emersonii mutant M36 supplemented with recombinant β-glucosidase resulted in significantly enhanced hydrolysis of pretreated rice straw slurry from IOCL industries (India). Our results suggest multi-faceted β-glucosidase from R. emersonii can overcome obstacles mainly high cost associated enzyme production, inhibitors that impair the sugar yields and thermal inactivation of enzyme.
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Affiliation(s)
- Yashika Raheja
- Department of Microbiology, Guru Nanak Dev University, Amritsar, 143005, Punjab, India
| | - Varinder Singh
- Department of Microbiology, Guru Nanak Dev University, Amritsar, 143005, Punjab, India
| | - Gaurav Sharma
- Department of Microbiology, Guru Nanak Dev University, Amritsar, 143005, Punjab, India
| | - Adrian Tsang
- Center for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, QC, H4B 1R6, Canada
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Kim SK, Bomble YJ, Westpheling J. Simultaneous expression of an endogenous spermidine synthase and a butanol dehydrogenase from Thermoanaerobacter pseudethanolicus in Clostridium thermocellum results in increased resistance to acetic acid and furans, increased ethanol production and an increase in thermotolerance. Biotechnol Biofuels Bioprod 2023; 16:46. [PMID: 36918887 PMCID: PMC10012442 DOI: 10.1186/s13068-023-02291-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 02/28/2023] [Indexed: 03/16/2023]
Abstract
BACKGROUND Sensitivity to inhibitors derived from the pretreatment of plant biomass is a barrier to the consolidated bioprocessing of these complex substrates to fuels and chemicals by microbes. Spermidine is a low molecular weight aliphatic nitrogen compound ubiquitous in microorganisms, plants, and animals and is often associated with tolerance to stress. We recently showed that overexpression of the endogenous spermidine synthase enhanced tolerance of the Gram-positive bacterium, Clostridium thermocellum to the furan derivatives furfural and HMF. RESULTS Here we show that co-expression with an NADPH-dependent heat-stable butanol dehydrogenase from Thermoanaerobacter pseudethanolicus further enhanced tolerance to furans and acetic acid and most strikingly resulted in an increase in thermotolerance at 65 °C. CONCLUSIONS Tolerance to fermentation inhibitors will facilitate the use of plant biomass substrates by thermophiles in general and this organism in particular. The ability to grow C. thermocellum at 65 °C has profound implications for metabolic engineering.
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Affiliation(s)
- Sun-Ki Kim
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA.,Oak Ridge National Laboratory, The BioEnergy Science Center and The Center for Bioenergy Innovation, Oak Ridge, TN, 37831, USA.,Department of Food Science and Technology, Chung-Ang University, Anseong, Gyeonggi, 17546, Republic of Korea
| | - Yannick J Bomble
- Oak Ridge National Laboratory, The BioEnergy Science Center and The Center for Bioenergy Innovation, Oak Ridge, TN, 37831, USA.,Biosciences Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Janet Westpheling
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA. .,Oak Ridge National Laboratory, The BioEnergy Science Center and The Center for Bioenergy Innovation, Oak Ridge, TN, 37831, USA.
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Sandoval-Nuñez D, Romero-Gutiérrez T, Gómez-Márquez C, Gshaedler A, Arellano-Plaza M, Amaya-Delgado L. Physiological and transcriptome analyses of Kluyveromyces marxianus reveal adaptive traits in stress response. Appl Microbiol Biotechnol 2023; 107:1421-38. [PMID: 36651929 DOI: 10.1007/s00253-022-12354-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 12/21/2022] [Accepted: 12/24/2022] [Indexed: 01/19/2023]
Abstract
Kluyveromyces marxianus is a non-conventional yeast with outstanding physiological characteristics and a high potential for lignocellulosic ethanol production. However, achieving high ethanol productivity requires overcoming several biotechnological challenges due to the cellular inhibition caused by the inhibitors present in the medium. In this work, K. marxianus SLP1 was adapted to increase its tolerance to a mix of inhibitory compounds using the adaptive laboratory evolution strategy to study the adaptation and stress response mechanisms used by this non-Saccharomyces yeast. The fermentative and physiological parameters demonstrated that the adapted K. marxianus P8 had a better response against the synergistic effects of multiple inhibitors because it reduced the lag phase from 12 to 4 h, increasing the biomass by 40% and improving the volumetric ethanol productivity 16-fold than the parental K. marxianus SLP1. To reveal the effect of adaptation process in P8, transcriptome analysis was carried out; the result showed that the basal gene expression in P8 changed, suggesting the biological capability of K. marxianus to activate the adaptative prediction mechanism. Similarly, we carried out physiologic and transcriptome analyses to reveal the mechanisms involved in the stress response triggered by furfural, the most potent inhibitor in K. marxianus. Stress response studies demonstrated that P8 had a better physiologic response than SLP1, since key genes related to furfural transformation (ALD4 and ALD6) and stress response (STL1) were upregulated. Our study demonstrates the rapid adaptability of K. marxianus to stressful environments, making this yeast a promising candidate to produce lignocellulosic ethanol. KEY POINTS: • K. marxianus was adapted to increase its tolerance to a mix of inhibitory compounds • The basal gene expression of K. marxianus changed after the adaptation process • Adapted K. marxianus showed a better physiological response to stress by inhibitors • Transcriptome analyses revealed key genes involved in the stress response.
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Zhang N, Shang Y, Wang F, Wang D, Hong J. Influence of prefoldin subunit 4 on the tolerance of Kluyveromyces marxianus to lignocellulosic biomass-derived inhibitors. Microb Cell Fact 2021; 20:224. [PMID: 34906148 PMCID: PMC8672639 DOI: 10.1186/s12934-021-01715-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 12/02/2021] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Kluyveromyces marxianus is a potentially excellent host for microbial cell factories using lignocellulosic biomass, due to its thermotolerance, high growth rate, and wide substrate spectrum. However, its tolerance to inhibitors derived from lignocellulosic biomass pretreatment needs to be improved. The prefoldin complex assists the folding of cytoskeleton which relates to the stress tolerance, moreover, several subunits of prefoldin have been verified to be involved in gene expression regulation. With the presence of inhibitors, the expression of a gene coding the subunit 4 of prefoldin (KmPFD4), a possible transcription factor, was significantly changed. Therefore, KmPFD4 was selected to evaluate its functions in inhibitors tolerance. RESULTS In this study, the disruption of the prefoldin subunit 4 gene (KmPFD4) led to increased concentration of intracellular reactive oxygen species (ROS) and disturbed the assembly of actin and tubulin in the presence of inhibitors, resulting in reduced inhibitor tolerance. Nuclear localization of KmPFD4 indicated that it could regulate gene expression. Transcriptomic analysis showed that upregulated gene expression related to ROS elimination, ATP production, and NAD+ synthesis, which is a response to the presence of inhibitors, disappeared in KmPFD4-disrupted cells. Thus, KmPFD4 impacts inhibitor tolerance by maintaining integration of the cytoskeleton and directly or indirectly affecting the expression of genes in response to inhibitors. Finally, overexpression of KmPFD4 enhanced ethanol fermentation with a 46.27% improvement in productivity in presence of the inhibitors. CONCLUSION This study demonstrated that KmPFD4 plays a positive role in the inhibitor tolerance and can be applied for the development of inhibitor-tolerant platform strains.
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Affiliation(s)
- Nini Zhang
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China
| | - Yingying Shang
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China
| | - Feier Wang
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China
| | - Dongmei Wang
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China.
- Biomedical Sciences and Health Laboratory of Anhui Province, University of Science & Technology of China, Hefei, 230027, China.
| | - Jiong Hong
- School of Life Sciences, University of Science and Technology of China, Hefei, 230027, Anhui, People's Republic of China.
- Hefei National Laboratory for Physical Science at the Microscale, Hefei, Anhui, 230026, People's Republic of China.
- Biomedical Sciences and Health Laboratory of Anhui Province, University of Science & Technology of China, Hefei, 230027, China.
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Lee HS, Lee HJ, Kim SH, Cho JY, Suh MJ, Ham S, Bhatia SK, Gurav R, Kim YG, Lee EY, Yang YH. Novel phasins from the Arctic Pseudomonas sp. B14-6 enhance the production of polyhydroxybutyrate and increase inhibitor tolerance. Int J Biol Macromol 2021; 190:722-729. [PMID: 34506862 DOI: 10.1016/j.ijbiomac.2021.08.236] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/18/2021] [Accepted: 08/31/2021] [Indexed: 01/17/2023]
Abstract
Phasin (PhaP), one of the polyhydroxyalkanoate granule-associated protein, enhances cell growth and polyhydroxybutyrate (PHB) biosynthesis by regulating the number and size of PHB granules. However, few studies have applied phasins to various PHB production conditions. In this study, we identified novel phasin genes from the genomic data of Arctic soil bacterium Pseudomonas sp. B14-6 and determined the role of phaP1Ps under different PHB production conditions. Transmission electron microscopy and gel permeation chromatography revealed small PHB granules with high-molecular weight, while differential scanning calorimetry showed that the extracted PHB films had similar thermal properties. The phasin protein derived from Pseudomonas sp. B14-6 revealed higher PHB production and exhibited higher tolerance to several lignocellulosic biosugar-based inhibitors than the phasin protein of Ralstonia eutropha H16 in a recombinant Escherichia coli strain. The increased tolerance to propionate, temperature, and other inhibitors was attributed to the introduction of phaP1Ps, which increased PHB production from lignocellulosic hydrolysate (2.39-fold) in the phaP1Ps strain. However, a combination of phasin proteins isolated from two different sources did not increase PHB production. These findings suggest that phasin could serve as a powerful means to increase robustness and PHB production in heterologous strains.
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Affiliation(s)
- Hye Soo Lee
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Hong-Ju Lee
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Sang Hyun Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Jang Yeon Cho
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Min Ju Suh
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Sion Ham
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Shashi Kant Bhatia
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea; Institute for Ubiquitous Information Technology and Applications, Konkuk University, Seoul 05029, Republic of Korea.
| | - Ranjit Gurav
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea.
| | - Yun-Gon Kim
- Department of Chemical Engineering, Soongsil University, Seoul 06978, Republic of Korea.
| | - Eun Yeol Lee
- Department of Chemical Engineering, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea.
| | - Yung-Hun Yang
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea; Institute for Ubiquitous Information Technology and Applications, Konkuk University, Seoul 05029, Republic of Korea.
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Chang D, Wang C, Ndayisenga F, Yu Z. Mutations in adaptively evolved Escherichia coli LGE2 facilitated the cost-effective upgrading of undetoxified bio-oil to bioethanol fuel. BIORESOUR BIOPROCESS 2021; 8:105. [PMID: 38650237 PMCID: PMC10991953 DOI: 10.1186/s40643-021-00459-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 10/11/2021] [Indexed: 11/10/2022] Open
Abstract
Levoglucosan is a promising sugar present in the lignocellulose pyrolysis bio-oil, which is a renewable and environment-friendly source for various value-added productions. Although many microbial catalysts have been engineered to produce biofuels and chemicals from levoglucosan, the demerits that these biocatalysts can only utilize pure levoglucosan while inhibited by the inhibitors co-existing with levoglucosan in the bio-oil have greatly limited the industrial-scale application of these biocatalysts in lignocellulose biorefinery. In this study, the previously engineered Escherichia coli LGE2 was evolved for enhanced inhibitor tolerance using long-term adaptive evolution under the stress of multiple inhibitors and finally, a stable mutant E. coli-H was obtained after ~ 374 generations' evolution. In the bio-oil media with an extremely acidic pH of 3.1, E. coli-H with high inhibitor tolerance exhibited remarkable levoglucosan consumption and ethanol production abilities comparable to the control, while the growth of the non-evolved strain was completely blocked even when the pH was adjusted to 7.0. Finally, 8.4 g/L ethanol was achieved by E. coli-H in the undetoxified bio-oil media with ~ 2.0% (w/v) levoglucosan, reaching 82% of the theoretical yield. Whole-genome re-sequencing to monitor the acquisition of mutations identified 4 new mutations within the globally regulatory genes rssB, yqhA, and basR, and the - 10 box of the putative promoter of yqhD-dgkA operon. Especially, yqhA was the first time to be revealed as a gene responsible for inhibitor tolerance. The mutations were all responsible for improved fitness, while basR mutation greatly contributed to the fitness improvement of E. coli-H. This study, for the first time, generated an inhibitor-tolerant levoglucosan-utilizing strain that could produce cost-effective bioethanol from the toxic bio-oil without detoxification process, and provided important experimental evidence and valuable genetic/proteinic information for the development of other robust microbial platforms involved in lignocellulose biorefining processes.
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Affiliation(s)
- Dongdong Chang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Cong Wang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Fabrice Ndayisenga
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Zhisheng Yu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.
- RCEES-IMCAS-UCAS Joint-Lab of Microbial Technology for Environmental Science, Beijing, 100085, People's Republic of China.
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Konzock O, Zaghen S, Norbeck J. Tolerance of Yarrowia lipolytica to inhibitors commonly found in lignocellulosic hydrolysates. BMC Microbiol 2021; 21:77. [PMID: 33685391 PMCID: PMC7938539 DOI: 10.1186/s12866-021-02126-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 02/15/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Lignocellulosic material is a suitable renewable carbon and energy source for microbial cell factories, such as Yarrowia lipolytica. To be accessible for microorganisms, the constituent sugars need to be released in a hydrolysis step, which as a side effect leads to the formation of various inhibitory compounds. However, the effects of these inhibitory compounds on the growth of Y. lipolytica have not been thoroughly investigated. RESULTS Here we show the individual and combined effect of six inhibitors from three major inhibitor groups on the growth of Y. lipolytica. We engineered a xylose consuming strain by overexpressing the three native genes XR, XDH, and XK and found that the inhibitor tolerance of Y. lipolytica is similar in glucose and in xylose. Aromatic compounds could be tolerated at high concentrations, while furfural linearly increased the lag phase of the cultivation, and hydroxymethylfurfural only inhibited growth partially. The furfural induced increase in lag phase can be overcome by an increased volume of inoculum. Formic acid only affected growth at concentrations above 25 mM. In a synthetic hydrolysate, formic acid, furfural, and coniferyl aldehyde were identified as the major growth inhibitors. CONCLUSION We showed the individual and combined effect of inhibitors found in hydrolysate on the growth of Y. lipolytica. Our study improves understanding of the growth limiting inhibitors found in hydrolysate and enables a more targeted engineering approach to increase the inhibitor tolerance of Y. lipolytica. This will help to improve the usage of Y. lipolytica as a sustainable microbial cell factory.
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Affiliation(s)
- Oliver Konzock
- Department of Biology and Biological Engineering, division of Systems and Synthetic Biology, Chalmers University of Technology, Göteborg, Sweden
| | - Simone Zaghen
- Department of Biology and Biological Engineering, division of Systems and Synthetic Biology, Chalmers University of Technology, Göteborg, Sweden
| | - Joakim Norbeck
- Department of Biology and Biological Engineering, division of Systems and Synthetic Biology, Chalmers University of Technology, Göteborg, Sweden.
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van Dijk M, Mierke F, Nygård Y, Olsson L. Nutrient-supplemented propagation of Saccharomyces cerevisiae improves its lignocellulose fermentation ability. AMB Express 2020; 10:157. [PMID: 32857229 PMCID: PMC7455642 DOI: 10.1186/s13568-020-01070-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 07/18/2020] [Indexed: 12/21/2022] Open
Abstract
Propagation conditions have been shown to be of considerable importance for the fermentation ability of Saccharomyces cerevisiae. The limited tolerance of yeast to inhibitors present in lignocellulosic hydrolysates is a major challenge in second-generation bioethanol production. We have investigated the hypothesis that the addition of nutrients during propagation leads to yeast cultures with improved ability to subsequently ferment lignocellulosic materials. This hypothesis was tested with and without short-term adaptation to wheat straw or corn stover hydrolysates during propagation of the yeast. The study was performed using the industrial xylose-fermenting S. cerevisiae strain CR01. Adding a mixture of pyridoxine, thiamine, and biotin to unadapted propagation cultures improved cell growth and ethanol yields during fermentation in wheat straw hydrolysate from 0.04 g g−1 to 0.19 g g−1 and in corn stover hydrolysate from 0.02 g g−1 to 0.08 g g−1. The combination of short–term adaptation and supplementation with the vitamin mixture during propagation led to ethanol yields of 0.43 g g−1 in wheat straw hydrolysate fermentation and 0.41 g g−1 in corn stover hydrolysate fermentation. These ethanol yields were improved compared to ethanol yields from cultures that were solely short-term adapted (0.37 and 0.33 g g−1). Supplementing the propagation medium with nutrients in combination with short-term adaptation was thus demonstrated to be a promising strategy to improve the efficiency of industrial lignocellulosic fermentation.
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Milessi TS, Perez CL, Zangirolami TC, Corradini FAS, Sandri JP, Foulquié-Moreno MR, Giordano RC, Thevelein JM, Giordano RLC. Repeated batches as a strategy for high 2G ethanol production from undetoxified hemicellulose hydrolysate using immobilized cells of recombinant Saccharomyces cerevisiae in a fixed-bed reactor. Biotechnol Biofuels 2020; 13:85. [PMID: 32426034 PMCID: PMC7216711 DOI: 10.1186/s13068-020-01722-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 04/27/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND The search for sustainable energy sources has become a worldwide issue, making the development of efficient biofuel production processes a priority. Immobilization of second-generation (2G) xylose-fermenting Saccharomyces cerevisiae strains is a promising approach to achieve economic viability of 2G bioethanol production from undetoxified hydrolysates through operation at high cell load and mitigation of inhibitor toxicity. In addition, the use of a fixed-bed reactor can contribute to establish an efficient process because of its distinct advantages, such as high conversion rate per weight of biocatalyst and reuse of biocatalyst. RESULTS This work assessed the influence of alginate entrapment on the tolerance of recombinant S. cerevisiae to acetic acid. Encapsulated GSE16-T18SI.1 (T18) yeast showed an outstanding performance in repeated batch fermentations with cell recycling in YPX medium supplemented with 8 g/L acetic acid (pH 5.2), achieving 10 cycles without significant loss of productivity. In the fixed-bed bioreactor, a high xylose fermentation rate with ethanol yield and productivity values of 0.38 gethanol/gsugars and 5.7 g/L/h, respectively were achieved in fermentations using undetoxified sugarcane bagasse hemicellulose hydrolysate, with and without medium recirculation. CONCLUSIONS The performance of recombinant strains developed for 2G ethanol production can be boosted strongly by cell immobilization in alginate gels. Yeast encapsulation allows conducting fermentations in repeated batch mode in fixed-bed bioreactors with high xylose assimilation rate and high ethanol productivity using undetoxified hemicellulose hydrolysate.
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Affiliation(s)
- Thais S. Milessi
- Department of Chemical Engineering, Federal University of São Carlos, Rodovia Washington Luís, km 235, 13565-905 São Carlos, SP Brazil
- Institute of Natural Resources, Federal University of Itajubá, Av. Benedito Pereira dos Santos, 1303, 37500-903 Itajubá, MG Brazil
| | - Caroline L. Perez
- Graduate Program of Chemical Engineering, Federal University of São Carlos (PPGEQ-UFSCar), Rodovia Washington Luís, km 235, 13565-905 São Carlos, SP Brazil
| | - Teresa C. Zangirolami
- Department of Chemical Engineering, Federal University of São Carlos, Rodovia Washington Luís, km 235, 13565-905 São Carlos, SP Brazil
- Graduate Program of Chemical Engineering, Federal University of São Carlos (PPGEQ-UFSCar), Rodovia Washington Luís, km 235, 13565-905 São Carlos, SP Brazil
| | - Felipe A. S. Corradini
- Graduate Program of Chemical Engineering, Federal University of São Carlos (PPGEQ-UFSCar), Rodovia Washington Luís, km 235, 13565-905 São Carlos, SP Brazil
| | - Juliana P. Sandri
- Graduate Program of Chemical Engineering, Federal University of São Carlos (PPGEQ-UFSCar), Rodovia Washington Luís, km 235, 13565-905 São Carlos, SP Brazil
| | - Maria R. Foulquié-Moreno
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Kasteelpark Arenberg 31, 3001 Leuven-Heverlee, Flanders Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, 3001 Leuven-Heverlee, Flanders Belgium
| | - Roberto C. Giordano
- Department of Chemical Engineering, Federal University of São Carlos, Rodovia Washington Luís, km 235, 13565-905 São Carlos, SP Brazil
- Graduate Program of Chemical Engineering, Federal University of São Carlos (PPGEQ-UFSCar), Rodovia Washington Luís, km 235, 13565-905 São Carlos, SP Brazil
| | - Johan M. Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Kasteelpark Arenberg 31, 3001 Leuven-Heverlee, Flanders Belgium
- Center for Microbiology, VIB, Kasteelpark Arenberg 31, 3001 Leuven-Heverlee, Flanders Belgium
| | - Raquel L. C. Giordano
- Department of Chemical Engineering, Federal University of São Carlos, Rodovia Washington Luís, km 235, 13565-905 São Carlos, SP Brazil
- Graduate Program of Chemical Engineering, Federal University of São Carlos (PPGEQ-UFSCar), Rodovia Washington Luís, km 235, 13565-905 São Carlos, SP Brazil
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Sitepu I, Enriquez L, Nguyen V, Fry R, Simmons B, Singer S, Simmons C, Boundy-Mills KL. Ionic Liquid Tolerance of Yeasts in Family Dipodascaceae and Genus Wickerhamomyces. Appl Biochem Biotechnol 2020; 191:1580-1593. [PMID: 32185613 DOI: 10.1007/s12010-020-03293-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 02/13/2020] [Indexed: 11/26/2022]
Abstract
In previous studies of ionic liquid (IL) tolerance of numerous species of ascomycetous yeasts, two strains of Wickerhamomyces ciferrii and Galactomyces candidus had unusually high tolerance in media containing up to 5% (w/v) of the 1-ethyl-3-methylimidazolium acetate ([C2C1Im][OAc]). The study aimed at investigating whether additional strains of these species, and additional species in the Dipodascaceae family, also possess IL tolerance, and to compare sensitivity to the acetate and chloride versions of the ionic liquid. Fifty five yeast strains in the family Dipodascaceae, which encompasses genera Galactomyces, Geotrichum, and Dipodascus, and seven yeast strains of species Wickerhamomyces ciferrii were tested for ability to grow in laboratory medium containing no IL, 242 mM [C2C1Im][OAc], or 242 mM [C2C1Im]Cl, and in IL-pretreated switchgrass hydrolysate. Many yeasts exhibited tolerance of one or both ILs, with higher tolerance of the chloride anion than of the acetate anion. Different strains of the same species exhibited varying degrees of IL tolerance. Galactomyces candidus, UCDFSTs 52-260, and 50-64, had exceptionally robust growth in [C2C1Im][OAc], and also grew well in the switchgrass hydrolysate. Identification of IL tolerant and IL resistant yeast strains will facilitate studies of the mechanism of IL tolerance, which could include superior efflux, metabolism or exclusion.
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Affiliation(s)
- Irnayuli Sitepu
- Department of Food Science and Technology, University of California Davis, One Shields Ave, Davis, CA, 95616, USA
| | - Lauren Enriquez
- Department of Food Science and Technology, University of California Davis, One Shields Ave, Davis, CA, 95616, USA
| | - Valerie Nguyen
- Department of Food Science and Technology, University of California Davis, One Shields Ave, Davis, CA, 95616, USA
| | - Russell Fry
- Department of Food Science and Technology, University of California Davis, One Shields Ave, Davis, CA, 95616, USA
| | - Blake Simmons
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94550, USA
| | - Steve Singer
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA
- Department of Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, CA, 94550, USA
| | - Christopher Simmons
- Department of Food Science and Technology, University of California Davis, One Shields Ave, Davis, CA, 95616, USA
| | - Kyria L Boundy-Mills
- Department of Food Science and Technology, University of California Davis, One Shields Ave, Davis, CA, 95616, USA.
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Wu Y, Bai Y, Zhang D, Cheng C, Chen L, Bai F, Xue C. Pleiotropic regulation of a glucose-specific PTS in Clostridium acetobutylicum for high-efficient butanol production from corn stover without detoxification. Biotechnol Biofuels 2019; 12:264. [PMID: 31709013 PMCID: PMC6836401 DOI: 10.1186/s13068-019-1604-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 10/29/2019] [Indexed: 05/26/2023]
Abstract
BACKGROUND Corn stover (CS) is evaluated as the most favorable candidate feedstock for butanol production via microbial acetone-butanol-ethanol (ABE) fermentation by Clostridium acetobutylicum. By independent acid pretreatment and enzymatic hydrolysis, fermentable sugars (mainly glucose and xylose) were released, of which glucose was naturally utilized as the most preferred carbon source by C. acetobutylicum. However, the ABE fermentation using corn stover hydrolysate (CSH) without detoxification is typically limited to poor sugars utilization, butanol production and productivity. In the presence of pretreatment-derived inhibitors, the intracellular ATP and NADH, as important factors involved in cell growth, solventogenesis initiation and stress response, are exceedingly challenged owing to disrupted glucose phosphotransferase system (PTS). Therefore, there is a necessity to develop effective engineering approaches to overcome these limitations for high-efficient butanol production from CSH without detoxification. RESULTS PTS-engineered C. acetobutylicum strains were constructed via overexpression and knockout of gene glcG encoding glucose-specific PTS IICBA, which pleiotropically regulated glucose utilization, cell growth, solventogenesis and inhibitors tolerance. The PTSGlcG-overexpressing strain exhibited high fermentation efficiency, wherein butanol production and productivity was 11.1 g/L and 0.31 g/L/h, compared to those of 11.0 g/L and 0.15 g/L/h with the PTSGlcG-deficient strain. During CSH culture without detoxification, the PTSGlcG-overexpressing strain exhibited desirable inhibitors tolerance and solventogenesis with butanol production of 10.0 g/L, increased by 300% and 400% compared to those of 2.5 and 2.0 g/L with the control and PTSGlcG-deficient strains, respectively. As a result of extra glucose and 10 g/L CaCO3 addition into CSH, butanol production and productivity were further maximized to 12.5 g/L and 0.39 g/L/h. These validated improvements on the PTSGlcG-overexpressing strain were ascribed to not only efficient glucose transport but also its cascading effects on intracellular ATP and NADH generation, solventogenesis initiation and inhibitors tolerance at the exponential growth phase. CONCLUSION The PTSGluG regulation could be an effective engineering approach for high-efficient ABE fermentation from lignocellulosic hydrolysates without detoxification or wastewater generation, providing fundamental information for economically sustainable butanol production with high productivity.
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Affiliation(s)
- Youduo Wu
- School of Bioengineering, Dalian University of Technology, No 2 Linggong Road, Dalian, 116024 China
| | - Yidi Bai
- School of Bioengineering, Dalian University of Technology, No 2 Linggong Road, Dalian, 116024 China
| | - Daojing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237 China
| | - Chi Cheng
- School of Bioengineering, Dalian University of Technology, No 2 Linggong Road, Dalian, 116024 China
| | - Lijie Chen
- School of Bioengineering, Dalian University of Technology, No 2 Linggong Road, Dalian, 116024 China
| | - Fengwu Bai
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Chuang Xue
- School of Bioengineering, Dalian University of Technology, No 2 Linggong Road, Dalian, 116024 China
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12
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Palakawong Na Ayutthaya P, Charoenrat T, Krusong W, Pornpukdeewattana S. Repeated cultures of Saccharomyces cerevisiae SC90 to tolerate inhibitors generated during cassava processing waste hydrolysis for bioethanol production. 3 Biotech 2019; 9:76. [PMID: 30800587 PMCID: PMC6370576 DOI: 10.1007/s13205-019-1607-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 02/01/2019] [Indexed: 12/29/2022] Open
Abstract
Large amount of cassava pulp is produced as by-product of industrial tapioca production. The value-added process of this low-cost waste is to use it as a substrate for bioethanol production. However, during the pulp pretreatment by acidification combined with steam explosion, many yeast inhibitors including acetic acid, formic acid, levulinic acid, furfural and 5-hydroxymethylfurfural are generated and these compounds have negative effects on the subsequent fermentation step. Therefore, the objective of this study was to investigate whether the repeated cultures of Saccharomyces cerevisiae SC90 could alleviate this problem. To obtain the inhibitor tolerable cells, the repeated culture was performed by growing yeast cells to a specific growth rate (µ) of 0.22 h-1 or higher (80% of the µ in control) and then transferring them to progressively higher concentrations of hydrolysate ranging from 20 to 100% (v/v). The results showed a tendency of longer lag phase as well as time to reach maximum cell number (t maxc) with an increase in hydrolysate concentration. However, the repeated culture at the same hydrolysate concentration could shorten both lag period and t maxc. Interestingly, the growth and fermentation efficiency of adapted cells in 100% hydrolysate were significantly higher (p ≤ 0.05) than those of non-adapted cells by 38% and 27%, respectively.
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Affiliation(s)
- Pakathamon Palakawong Na Ayutthaya
- Division of Fermentation Technology, Faculty of Agro-Industry, King Mongkut’s Institute of Technology Ladkrabang, Bangkok, 10520 Thailand
| | - Theppanya Charoenrat
- Department of Biotechnology, Faculty of Science and Technology, Thammasat University (Rangsit Center), Pathum Thani, 12120 Thailand
| | - Warawut Krusong
- Division of Fermentation Technology, Faculty of Agro-Industry, King Mongkut’s Institute of Technology Ladkrabang, Bangkok, 10520 Thailand
| | - Soisuda Pornpukdeewattana
- Division of Fermentation Technology, Faculty of Agro-Industry, King Mongkut’s Institute of Technology Ladkrabang, Bangkok, 10520 Thailand
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Wu B, Qin H, Yang Y, Duan G, Yang S, Xin F, Zhao C, Shao H, Wang Y, Zhu Q, Tan F, Hu G, He M. Engineered Zymomonas mobilis tolerant to acetic acid and low pH via multiplex atmospheric and room temperature plasma mutagenesis. Biotechnol Biofuels 2019; 12:10. [PMID: 30627218 PMCID: PMC6321654 DOI: 10.1186/s13068-018-1348-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 12/24/2018] [Indexed: 05/19/2023]
Abstract
BACKGROUND Cellulosic biofuels are sustainable compared to fossil fuels. However, inhibitors, such as acetic acid generated during lignocellulose pretreatment and hydrolysis, would significantly inhibit microbial fermentation efficiency. Microbial mutants able to tolerate high concentration of acetic acid are needed urgently to alleviate this inhibition. RESULTS Zymomonas mobilis mutants AQ8-1 and AC8-9 with enhanced tolerance against acetic acid were generated via a multiplex atmospheric and room temperature plasma (mARTP) mutagenesis. The growth and ethanol productivity of AQ8-1 and AC8-9 were both improved in the presence of 5.0-8.0 g/L acetic acid. Ethanol yield reached 84% of theoretical value in the presence of 8.0 g/L acetic acid (~ pH 4.0). Furthermore, a mutant tolerant to pH 3.5, named PH1-29, was generated via the third round of ARTP mutagenesis. PH1-29 showed enhanced growth and ethanol production under both sterilized/unsterilized conditions at pH 4.0 or 3.5. Intracellular NAD levels revealed that mARTP mutants could modulate NADH/NAD+ ratio to respond to acetic acid and low pH stresses. Moreover, genomic re-sequencing revealed that eleven single nucleic variations (SNVs) were likely related to acetic acid and low pH tolerance. Most SNVs were targeted in regions between genes ZMO0952 and ZMO0956, ZMO0152 and ZMO0153, and ZMO0373 and ZMO0374. CONCLUSIONS The multiplex mutagenesis strategy mARTP was efficient for enhancing the tolerance in Z. mobilis. The ARTP mutants generated in this study could serve as potential cellulosic ethanol producers.
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Affiliation(s)
- Bo Wu
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture), Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin Rd. South, Chengdu, 610041 China
| | - Han Qin
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture), Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin Rd. South, Chengdu, 610041 China
| | - Yiwei Yang
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture), Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin Rd. South, Chengdu, 610041 China
| | - Guowei Duan
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture), Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin Rd. South, Chengdu, 610041 China
| | - Shihui Yang
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 Puzhu Rd, Pukou District, Nanjing, 211816 China
| | - Chunyan Zhao
- College of Life Science, Sichuan Normal University, Section 2-1819, Chenglong Avenue, Chengdu, 610101 China
| | - Huanhuan Shao
- College of Life Science, Sichuan Normal University, Section 2-1819, Chenglong Avenue, Chengdu, 610101 China
| | - Yanwei Wang
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture), Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin Rd. South, Chengdu, 610041 China
| | - Qili Zhu
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture), Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin Rd. South, Chengdu, 610041 China
| | - Furong Tan
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture), Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin Rd. South, Chengdu, 610041 China
| | - Guoquan Hu
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture), Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin Rd. South, Chengdu, 610041 China
| | - Mingxiong He
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture), Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin Rd. South, Chengdu, 610041 China
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14
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Wang W, Wu B, Qin H, Liu P, Qin Y, Duan G, Hu G, He M. Genome shuffling enhances stress tolerance of Zymomonas mobilis to two inhibitors. Biotechnol Biofuels 2019; 12:288. [PMID: 31890016 PMCID: PMC6913010 DOI: 10.1186/s13068-019-1631-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 12/05/2019] [Indexed: 05/19/2023]
Abstract
BACKGROUND Furfural and acetic acid are the two major inhibitors generated during lignocellulose pretreatment and hydrolysis, would severely inhibit the cell growth, metabolism, and ethanol fermentation efficiency of Zymomonas mobilis. Effective genome shuffling mediated by protoplast electrofusion was developed and then applied to Z. mobilis. RESULTS After two rounds of genome shuffling, 10 different mutants with improved cell growth and ethanol yield in the presence of 5.0 g/L acetic acid and 3.0 g/L furfural were obtained. The two most prominent genome-shuffled strains, 532 and 533, were further investigated along with parental strains in the presence of 7.0 g/L acetic acid and 3.0 g/L furfural. The results showed that mutants 532 and 533 were superior to the parental strain AQ8-1 in the presence of 7.0 g/L acetic acid, with a shorter fermentation time (30 h) and higher productivity than AQ8-1. Mutant 533 exhibited subtle differences from parental strain F34 in the presence of 3.0 g/L furfural. Mutations present in 10 genome-shuffled strains were identified via whole-genome resequencing, and the source of each mutation was identified as either de novo mutation or recombination of the parent genes. CONCLUSIONS These results indicate that genome shuffling is an efficient method for enhancing stress tolerance in Z. mobilis. The engineered strains generated in this study could be potential cellulosic ethanol producers in the future.
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Affiliation(s)
- Weiting Wang
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041 People’s Republic of China
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081 People’s Republic of China
| | - Bo Wu
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041 People’s Republic of China
| | - Han Qin
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041 People’s Republic of China
| | - Panting Liu
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041 People’s Republic of China
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081 People’s Republic of China
| | - Yao Qin
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041 People’s Republic of China
- College of Pharmacy and Biological Engineering, Chengdu University, Chengdu, 610041 People’s Republic of China
| | - Guowei Duan
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041 People’s Republic of China
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081 People’s Republic of China
| | - Guoquan Hu
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041 People’s Republic of China
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081 People’s Republic of China
| | - Mingxiong He
- Biomass Energy Technology Research Centre, Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture and Rural Affairs), Biogas Institute of Ministry of Agriculture and Rural Affairs, Section 4-13, Renmin Rd. South, Chengdu, 610041 People’s Republic of China
- Graduate School of Chinese Academy of Agricultural Science, Beijing, 100081 People’s Republic of China
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15
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Wordofa GG, Kristensen M. Tolerance and metabolic response of Pseudomonas taiwanensis VLB120 towards biomass hydrolysate-derived inhibitors. Biotechnol Biofuels 2018; 11:199. [PMID: 30034525 PMCID: PMC6052574 DOI: 10.1186/s13068-018-1192-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 07/06/2018] [Indexed: 05/10/2023]
Abstract
BACKGROUND Bio-conversion of lignocellulosic biomass to high-value products offers numerous benefits; however, its development is hampered by chemical inhibitors generated during the pretreatment process. A better understanding of how microbes naturally respond to those inhibitors is valuable in the process of designing microorganisms with improved tolerance. Pseudomonas taiwanensis VLB120 is a natively tolerant strain that utilizes a wide range of carbon sources including pentose and hexose sugars. To this end, we investigated the tolerance and metabolic response of P. taiwanensis VLB120 towards biomass hydrolysate-derived inhibitors including organic acids (acetic acid, formic acid, and levulinic acid), furans (furfural, 5-hydroxymethylfurfural), and phenols (vanillin). RESULTS The inhibitory effect of the tested compounds varied with respect to lag phase, specific growth rate, and biomass yield compared to the control cultures grown under the same conditions without addition of inhibitors. However, P. taiwanensis was able to oxidize vanillin and furfural to vanillic acid and 2-furoic acid, respectively. Vanillic acid was further metabolized, whereas 2-furoic acid was secreted outside the cells and remained in the fermentation broth without further conversion. Acetic acid and formic acid were completely consumed from the fermentation broth, while concentration of levulinic acid remained constant throughout the fermentation process. Analysis of free intracellular metabolites revealed varying levels when P. taiwanensis VLB120 was exposed to inhibitory compounds. This resulted in increased levels of ATP to export inhibitors from the cell and NADPH/NADP ratio that provides reducing power to deal with the oxidative stress caused by the inhibitors. Thus, adequate supply of these metabolites is essential for the survival and reproduction of P. taiwanensis in the presence of biomass-derived inhibitors. CONCLUSIONS In this study, the tolerance and metabolic response of P. taiwanensis VLB120 to biomass hydrolysate-derived inhibitors was investigated. P. taiwanensis VLB120 showed high tolerance towards biomass hydrolysate-derived inhibitors compared to most wild-type microbes reported in the literature. It adopts different resistance mechanisms, including detoxification, efflux, and repair, which require additional energy and resources. Thus, targeting redox and energy metabolism in strain engineering may be a successful strategy to overcome inhibition during biomass hydrolysate conversion and lead to development of more robust strains.
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Affiliation(s)
- Gossa G. Wordofa
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Mette Kristensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
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16
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Abstract
Cerebrospinal fluid (CSF) contains molecules directly linked with brain function because it permeates brain tissue. The analysis of protein biomarkers in CSF is currently recommended for the diagnosis of neurodegenerative disorders, but the clinical sensitivity and specificity are still being investigated. A major drawback is that most of the currently used biomarkers of neurodegenerative diseases are proteins that are found at very low concentrations in CSF and need to be measured by immunoassays that provide relative values, which sometimes are difficult to reproduce between laboratories. In contrast, the recent availability of digital PCR platforms allows the absolute quantification of nucleic acids at single-molecule resolution, but their presence in CSF has not been characterized. CSF contains cell-free mitochondrial DNA (mtDNA) and changes in the concentration of this nucleic acid are linked to neurodegeneration. Here we describe a method to measure the concentration of cell-free circulating mtDNA directly in unpurified CSF using droplet digital PCR with either hydrolysis probes or fluorescent DNA-binding dye methods. This protocol allows the detection and absolute quantification of mtDNA content in the CSF with high analytical sensitivity, specificity, and accuracy.
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17
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Abstract
RNA interference (RNAi)-assisted genome evolution (RAGE) applies directed evolution principles to engineer Saccharomyces cerevisiae genomes. Here, we use acetic acid tolerance as a target trait to describe the key steps of RAGE. Briefly, iterative cycles of RNAi screening are performed to accumulate multiplex knockdown modifications, enabling directed evolution of the yeast genome and continuous improvement of a target phenotype. Detailed protocols are provided on the reconstitution of RNAi machinery, creation of genome-wide RNAi libraries, identification and integration of beneficial knockdown cassettes, and repeated RAGE cycles.
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Affiliation(s)
- Tong Si
- Carl R Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Huimin Zhao
- Carl R Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. .,Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. .,Departments of Chemistry, Biochemistry, and Bioengineering, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL, 61801, USA.
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18
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Li YC, Gou ZX, Zhang Y, Xia ZY, Tang YQ, Kida K. Inhibitor tolerance of a recombinant flocculating industrial Saccharomyces cerevisiae strain during glucose and xylose co-fermentation. Braz J Microbiol 2017. [PMID: 28629968 PMCID: PMC5628316 DOI: 10.1016/j.bjm.2016.11.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Lignocellulose-derived inhibitors have negative effects on the ethanol fermentation capacity of Saccharomyces cerevisiae. In this study, the effects of eight typical inhibitors, including weak acids, furans, and phenols, on glucose and xylose co-fermentation of the recombinant xylose-fermenting flocculating industrial S. cerevisiae strain NAPX37 were evaluated by batch fermentation. Inhibition on glucose fermentation, not that on xylose fermentation, correlated with delayed cell growth. The weak acids and the phenols showed additive effects. The effect of inhibitors on glucose fermentation was as follows (from strongest to weakest): vanillin > phenol > syringaldehyde > 5-HMF > furfural > levulinic acid > acetic acid > formic acid. The effect of inhibitors on xylose fermentation was as follows (from strongest to weakest): phenol > vanillin > syringaldehyde > furfural > 5-HMF > formic acid > levulinic acid > acetic acid. The NAPX37 strain showed substantial tolerance to typical inhibitors and showed good fermentation characteristics, when a medium with inhibitor cocktail or rape straw hydrolysate was used. This research provides important clues for inhibitors tolerance of recombinant industrial xylose-fermenting S. cerevisiae.
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Affiliation(s)
- Yun-Cheng Li
- College of Architecture and Environment, Sichuan University, Chengdu, China; College of Pharmacy and Bioengineering, Chengdu University, Chengdu, China
| | - Zi-Xi Gou
- College of Architecture and Environment, Sichuan University, Chengdu, China
| | - Ying Zhang
- College of Architecture and Environment, Sichuan University, Chengdu, China
| | - Zi-Yuan Xia
- College of Architecture and Environment, Sichuan University, Chengdu, China
| | - Yue-Qin Tang
- College of Architecture and Environment, Sichuan University, Chengdu, China.
| | - Kenji Kida
- College of Architecture and Environment, Sichuan University, Chengdu, China
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Hu BB, Zhu MJ. Direct hydrogen production from dilute-acid pretreated sugarcane bagasse hydrolysate using the newly isolated Thermoanaerobacterium thermosaccharolyticum MJ1. Microb Cell Fact 2017; 16:77. [PMID: 28468624 PMCID: PMC5415828 DOI: 10.1186/s12934-017-0692-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 04/26/2017] [Indexed: 11/23/2022] Open
Abstract
Background Energy shortage and environmental pollution are two severe global problems, and biological hydrogen production from lignocellulose shows great potential as a promising alternative biofuel to replace the fossil fuels. Currently, most studies on hydrogen production from lignocellulose concentrate on cellulolytic microbe, pretreatment method, process optimization and development of new raw materials. Due to no effective approaches to relieve the inhibiting effect of inhibitors, the acid pretreated lignocellulose hydrolysate was directly discarded and caused environmental problems, suggesting that isolation of inhibitor-tolerant strains may facilitate the utilization of acid pretreated lignocellulose hydrolysate. Results Thermophilic bacteria for producing hydrogen from various kinds of sugars were screened, and the new strain named MJ1 was isolated from paper sludge, with 99% identity to Thermoanaerobacterium thermosaccharolyticum by 16S rRNA gene analysis. The hydrogen yields of 11.18, 4.25 and 2.15 mol-H2/mol sugar can be reached at an initial concentration of 5 g/L cellobiose, glucose and xylose, respectively. The main metabolites were acetate and butyrate. More important, MJ1 had an excellent tolerance to inhibitors of dilute-acid (1%, g/v) pretreated sugarcane bagasse hydrolysate (DAPSBH) and could efficiently utilize DAPSBH for hydrogen production without detoxication, with a production higher than that of pure sugars. The hydrogen could be quickly produced with the maximum hydrogen production reached at 24 h. The hydrogen production reached 39.64, 105.42, 111.75 and 110.44 mM at 20, 40, 60 and 80% of DAPSBH, respectively. Supplementation of CaCO3 enhanced the hydrogen production by 21.32% versus the control. Conclusions These results demonstrate that MJ1 could directly utilize DAPSBH for biohydrogen production without detoxication and can serve as an excellent candidate for industrialization of hydrogen production from DAPSBH. The results also suggest that isolating unique strains from a particular environment offers an ideal way to conquer the related problems. Electronic supplementary material The online version of this article (doi:10.1186/s12934-017-0692-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bin-Bin Hu
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou Higher Education Mega Center, Panyu, Guangzhou, 510006, People's Republic of China
| | - Ming-Jun Zhu
- School of Bioscience and Bioengineering, South China University of Technology, Guangzhou Higher Education Mega Center, Panyu, Guangzhou, 510006, People's Republic of China. .,School of Life and Geographical Sciences, Kashi University, 29 Xueyuan Road, Kashi, 844006, Xinjiang Uygur Autonomous Region, People's Republic of China.
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Zhang H, Zhang J, Bao J. High titer gluconic acid fermentation by Aspergillus niger from dry dilute acid pretreated corn stover without detoxification. Bioresour Technol 2016; 203:211-9. [PMID: 26724553 DOI: 10.1016/j.biortech.2015.12.042] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 12/13/2015] [Accepted: 12/15/2015] [Indexed: 05/15/2023]
Abstract
This study reported a high titer gluconic acid fermentation using dry dilute acid pretreated corn stover (DDAP) hydrolysate without detoxification. The selected fermenting strain Aspergillus niger SIIM M276 was capable of inhibitor degradation thus no detoxification on pretreated corn stover was required. Parameters of gluconic acid fermentation in corn stover hydrolysate were optimized in flasks and in fermentors to achieve 76.67 g/L gluconic acid with overall yield of 94.91%. The sodium gluconate obtained from corn stover was used as additive for extending setting time of cement mortar and similar function was obtained with starch based sodium gluconate. This study provided the first high titer gluconic acid production from lignocellulosic feedstock with potential of industrial applications.
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Affiliation(s)
- Hongsen Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Jian Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Jie Bao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China.
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Thompson OA, Hawkins GM, Gorsich SW, Doran-Peterson J. Phenotypic characterization and comparative transcriptomics of evolved Saccharomyces cerevisiae strains with improved tolerance to lignocellulosic derived inhibitors. Biotechnol Biofuels 2016; 9:200. [PMID: 27679668 PMCID: PMC5029107 DOI: 10.1186/s13068-016-0614-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 09/07/2016] [Indexed: 05/15/2023]
Abstract
BACKGROUND Lignocellulosic biomass continues to be investigated as a viable source for bioethanol production. However, the pretreatment process generates inhibitory compounds that impair the growth and fermentation performance of microorganisms such as Saccharomyces cerevisiae. Pinewood specifically has been shown to be challenging in obtaining industrially relevant ethanol titers. An industrial S. cerevisiae strain was subjected to directed evolution and adaptation in pretreated pine biomass and resultant strains, GHP1 and GHP4, exhibited improved growth and fermentative ability on pretreated pine in the presence of related inhibitory compounds. A comparative transcriptomic approach was applied to identify and characterize differences in phenotypic stability of evolved strains. RESULTS Evolved strains displayed different fermentative capabilities with pretreated pine that appear to be influenced by the addition or absence of 13 inhibitory compounds during pre-culturing. GHP4 performance was consistent independent of culturing conditions, while GHP1 performance was dependent on culturing with inhibitors. Comparative transcriptomics revealed 52 genes potentially associated with stress responses to multiple inhibitors simultaneously. Fluorescence microscopy revealed improved cellular integrity of both strains with mitochondria exhibiting resistance to the damaging effects of inhibitors in contrast to the parent. CONCLUSIONS Multiple potentially novel genetic targets have been discovered for understanding stress tolerance through the characterization of our evolved strains. This study specifically examines the synergistic effects of multiple inhibitors and identified targets will guide future studies in remediating effects of inhibitors and further development of robust yeast strains for multiple industrial applications.
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Affiliation(s)
| | - Gary M. Hawkins
- Department of Microbiology, University of Georgia, Athens, GA 30602 USA
| | - Steven W. Gorsich
- Department of Biology, Central Michigan University, Mount Pleasant, MI 48859 USA
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Hasunuma T, Sakamoto T, Kondo A. Inverse metabolic engineering based on transient acclimation of yeast improves acid-containing xylose fermentation and tolerance to formic and acetic acids. Appl Microbiol Biotechnol 2016; 100:1027-38. [PMID: 26521247 DOI: 10.1007/s00253-015-7094-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Revised: 09/28/2015] [Accepted: 10/11/2015] [Indexed: 02/02/2023]
Abstract
Improving the production of ethanol from xylose is an important goal in metabolic engineering of Saccharomyces cerevisiae. Furthermore, S. cerevisiae must produce ethanol in the presence of weak acids (formate and acetate) generated during pre-treatment of lignocellulosic biomass. In this study, weak acid-containing xylose fermentation was significantly improved using cells that were acclimated to the weak acids during pre-cultivation. Transcriptome analyses showed that levels of transcripts for transcriptional/translational machinery-related genes (RTC3 and ANB1) were enhanced by formate and acetate acclimation. Recombinant yeast strains overexpressing RTC3 and ANB1 demonstrated improved ethanol production from xylose in the presence of the weak acids, along with improved tolerance to the acids. Novel metabolic engineering strategy based on the combination of short-term acclimation and system-wide analysis was developed, which can develop stress-tolerant strains in a short period of time, although conventional evolutionary engineering approach has required long periods of time to isolate inhibitor-adapted strains.
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Affiliation(s)
- Tomohisa Hasunuma
- Organization of Advanced Science and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Takatoshi Sakamoto
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Akihiko Kondo
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.
- Biomass Engineering Program, RIKEN, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan.
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Zhu JQ, Qin L, Li WC, Zhang J, Bao J, Huang YD, Li BZ, Yuan YJ. Simultaneous saccharification and co-fermentation of dry diluted acid pretreated corn stover at high dry matter loading: Overcoming the inhibitors by non-tolerant yeast. Bioresour Technol 2015; 198:39-46. [PMID: 26363500 DOI: 10.1016/j.biortech.2015.08.140] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2015] [Revised: 08/20/2015] [Accepted: 08/21/2015] [Indexed: 05/15/2023]
Abstract
Dry dilute acid pretreatment (DDAP) is a promising method for lignocellulose bioconversion, although inhibitors generated during the pretreatment impede the fermentation severely. We developed the simultaneous saccharification and co-fermentation (SScF) of DDAP pretreated biomass at high solid loading using xylose fermenting Saccharomyces cerevisiae, SyBE005. Effect of temperature on SScF showed that ethanol yield at 34°C was 10.2% higher than that at 38°C. Ethanol concentration reached 29.5 g/L at 15% (w/w) dry matter loading, while SScF almost ceased at the beginning at 25% (w/w) dry matter loading of DDAP pretreated corn stover. According to the effect of the diluted hydrolysate on the fermentation of strain SyBE005, a fed-batch mode was developed for the SScF of DDAP pretreated corn stover with 25% dry matter loading without detoxification, and 40.0 g/L ethanol was achieved. In addition, high yeast inoculation improved xylose utilization and the final ethanol concentration reached 47.2 g/L.
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Affiliation(s)
- Jia-Qing Zhu
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, PR China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
| | - Lei Qin
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, PR China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
| | - Wen-Chao Li
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, PR China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
| | - Jian Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, PR China
| | - Jie Bao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, PR China
| | - Yao-Dong Huang
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, PR China
| | - Bing-Zhi Li
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, PR China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China.
| | - Ying-Jin Yuan
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, PR China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
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Li YC, Mitsumasu K, Gou ZX, Gou M, Tang YQ, Li GY, Wu XL, Akamatsu T, Taguchi H, Kida K. Xylose fermentation efficiency and inhibitor tolerance of the recombinant industrial Saccharomyces cerevisiae strain NAPX37. Appl Microbiol Biotechnol 2016; 100:1531-42. [PMID: 26603762 DOI: 10.1007/s00253-015-7167-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Revised: 10/19/2015] [Accepted: 11/06/2015] [Indexed: 01/01/2023]
Abstract
Industrial yeast strains with good xylose fermentation ability and inhibitor tolerance are important for economical lignocellulosic bioethanol production. The flocculating industrial Saccharomyces cerevisiae strain NAPX37, harboring the xylose reductase-xylitol dehydrogenase (XR-XDH)-based xylose metabolic pathway, displayed efficient xylose fermentation during batch and continuous fermentation. During batch fermentation, the xylose consumption rates at the first 36 h were similar (1.37 g/L/h) when the initial xylose concentrations were 50 and 75 g/L, indicating that xylose fermentation was not inhibited even when the xylose concentration was as high as 75 g/L. The presence of glucose, at concentrations of up to 25 g/L, did not affect xylose consumption rate at the first 36 h. Strain NAPX37 showed stable xylose fermentation capacity during continuous ethanol fermentation using xylose as the sole sugar, for almost 1 year. Fermentation remained stable at a dilution rate of 0.05/h, even though the xylose concentration in the feed was as high as 100 g/L. Aeration rate, xylose concentration, and MgSO4 concentration were found to affect xylose consumption and ethanol yield. When the xylose concentration in the feed was 75 g/L, a high xylose consumption rate of 6.62 g/L/h and an ethanol yield of 0.394 were achieved under an aeration rate of 0.1 vvm, dilution rate of 0.1/h, and 5 mM MgSO4. In addition, strain NAPX37 exhibited good tolerance to inhibitors such as weak acids, furans, and phenolics during xylose fermentation. These findings indicate that strain NAPX37 is a promising candidate for application in the industrial production of lignocellulosic bioethanol.
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Chen R, Dou J. Biofuels and bio-based chemicals from lignocellulose: metabolic engineering strategies in strain development. Biotechnol Lett 2016; 38:213-21. [PMID: 26466596 DOI: 10.1007/s10529-015-1976-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 10/07/2015] [Indexed: 12/22/2022]
Abstract
Interest in developing a sustainable technology for fuels and chemicals has unleashed tremendous creativity in metabolic engineering for strain development over the last few years. This is driven by the exceptionally recalcitrant substrate, lignocellulose, and the necessity to keep the costs down for commodity products. Traditional methods of gene expression and evolutionary engineering are more effectively used with the help of synthetic biology and -omics techniques. Compared to the last biomass research peak during the 1980s oil crisis, a more diverse range of microorganisms are being engineered for a greater variety of products, reflecting the broad applicability and effectiveness of today's gene technology. We review here several prominent and successful metabolic engineering strategies with emphasis on the following four areas: xylose catabolism, inhibitor tolerance, synthetic microbial consortium, and cellulosic oligomer assimilation.
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