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Vanacloig-Pedros E, Fisher KJ, Liu L, Debrauske DJ, Young MKM, Place M, Hittinger CT, Sato TK, Gasch AP. Comparative chemical genomic profiling across plant-based hydrolysate toxins reveals widespread antagonism in fitness contributions. FEMS Yeast Res 2022; 21:6650360. [PMID: 35883225 PMCID: PMC9508847 DOI: 10.1093/femsyr/foac036] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/06/2022] [Accepted: 07/21/2022] [Indexed: 11/15/2022] Open
Abstract
The budding yeast Saccharomyces cerevisiae has been used extensively in fermentative industrial processes, including biofuel production from sustainable plant-based hydrolysates. Myriad toxins and stressors found in hydrolysates inhibit microbial metabolism and product formation. Overcoming these stresses requires mitigation strategies that include strain engineering. To identify shared and divergent mechanisms of toxicity and to implicate gene targets for genetic engineering, we used a chemical genomic approach to study fitness effects across a library of S. cerevisiae deletion mutants cultured anaerobically in dozens of individual compounds found in different types of hydrolysates. Relationships in chemical genomic profiles identified classes of toxins that provoked similar cellular responses, spanning inhibitor relationships that were not expected from chemical classification. Our results also revealed widespread antagonistic effects across inhibitors, such that the same gene deletions were beneficial for surviving some toxins but detrimental for others. This work presents a rich dataset relating gene function to chemical compounds, which both expands our understanding of plant-based hydrolysates and provides a useful resource to identify engineering targets.
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Affiliation(s)
- Elena Vanacloig-Pedros
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 53726, Madison, WI, United States
| | - Kaitlin J Fisher
- Laboratory of Genetics, University of Wisconsin-Madison, 53706, Madison, WI, United States
- Center for Genomic Science Innovation, University of Wisconsin-Madison, 53706, Madison, WI, United States
- J.F. Crow Institute for the Study of Evolution, 53706, Madison, WI, United States
| | - Lisa Liu
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 53726, Madison, WI, United States
| | - Derek J Debrauske
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 53726, Madison, WI, United States
| | - Megan K M Young
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 53726, Madison, WI, United States
| | - Michael Place
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 53726, Madison, WI, United States
| | - Chris Todd Hittinger
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 53726, Madison, WI, United States
- Laboratory of Genetics, University of Wisconsin-Madison, 53706, Madison, WI, United States
- Center for Genomic Science Innovation, University of Wisconsin-Madison, 53706, Madison, WI, United States
- J.F. Crow Institute for the Study of Evolution, 53706, Madison, WI, United States
| | - Trey K Sato
- Corresponding author: Trey K. Sato, Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 4117 Wisconsin Energy Institute, 1552 University Ave, Madison, WI 53726. Tel: (608) 890-2546; E-mail:
| | - Audrey P Gasch
- Corresponding author: Audrey P. Gasch, Center for Genomic Science Innovation, University of Wisconsin-Madison, 3422 Genetics-Biotechnology Center, 425 Henry Mall, Madison, WI 53704, United States. Tel: (608)265-0859; E-mail:
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Teymennet-Ramírez KV, Martínez-Morales F, Muñoz-Garay C, Bertrand B, Morales-Guzmán D, Trejo-Hernández MR. Laccase treatment of phenolic compounds for bioethanol production and the impact of these compounds on yeast physiology. BIOCATAL BIOTRANSFOR 2020. [DOI: 10.1080/10242422.2020.1856820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Karla V. Teymennet-Ramírez
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, México
| | - Fernando Martínez-Morales
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, México
| | - Carlos Muñoz-Garay
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México (ICF-UNAM), Cuernavaca, México
| | - Brandt Bertrand
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México (ICF-UNAM), Cuernavaca, México
| | - Daniel Morales-Guzmán
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, México
| | - María R. Trejo-Hernández
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, México
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Wu D, Wang D, Hong J. Effect of a Novel Alpha/Beta Hydrolase Domain Protein on Tolerance of K. marxianus to Lignocellulosic Biomass Derived Inhibitors. Front Bioeng Biotechnol 2020; 8:844. [PMID: 32850717 PMCID: PMC7396682 DOI: 10.3389/fbioe.2020.00844] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 04/22/2020] [Accepted: 06/30/2020] [Indexed: 01/12/2023] Open
Abstract
The multiple inhibitors tolerance of microorganism is important in bioconversion of lignocellulosic biomass which is a promising renewable and sustainable source for biofuels and other chemicals. The disruption of an unknown α/β hydrolase, which was termed KmYME and located in mitochondria in this study, resulted in the yeast more susceptible to lignocellulose-derived inhibitors, particularly to acetic acid, furfural and 5-HMF. The KmYME disrupted strain lost more mitochondrial membrane potential, showed increased plasma membrane permeability, severer redox ratio imbalance, and increased ROS accumulation, compared with those of the non-disrupted strain in the presence of the same inhibitors. The intracellular concentration of ATP, NAD and NADP in the KmYME disrupted strain was decreased. However, disruption of KmYME did not result in a significant change of gene expression at the transcriptional level. The KmYME possessed esterase/thioesterase activity which was necessary for the resistance to inhibitors. In addition, KmYME was also required for the resistance to other stresses including ethanol, temperature, and osmotic pressure. Disruption of two possible homologous genes in S. cerevisiae also reduced its tolerance to inhibitors.
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Affiliation(s)
- Dan Wu
- School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Dongmei Wang
- School of Life Sciences, University of Science and Technology of China, Hefei, China
- Hefei National Laboratory for Physical Sciences at the Microscale, Hefei, China
| | - Jiong Hong
- School of Life Sciences, University of Science and Technology of China, Hefei, China
- Hefei National Laboratory for Physical Sciences at the Microscale, Hefei, China
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Kay JE, Jewett MC. A cell-free system for production of 2,3-butanediol is robust to growth-toxic compounds. Metab Eng Commun 2020; 10:e00114. [PMID: 31934547 PMCID: PMC6951449 DOI: 10.1016/j.mec.2019.e00114] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 11/14/2019] [Accepted: 11/19/2019] [Indexed: 11/23/2022] Open
Abstract
The need for sustainable, low-cost production of bioenergy and commodity chemicals is increasing. Unfortunately, the engineering potential of whole-cell catalysts to address this need can be hampered by cellular toxicity. When such bottlenecks limit the commercial feasibility of whole-cell fermentation, cell-free, or in vitro, based approaches may offer an alternative. Here, we assess the impact of three classes of growth toxic compounds on crude extract-based, cell-free chemical conversions. As a model system, we test a metabolic pathway for conversion of glucose to 2,3-butanediol (2,3-BDO) in lysates of Escherichia coli. First, we characterized 2,3-BDO production with different classes of antibiotics and found, as expected, that the system is uninhibited by compounds that prevent cell growth by means of cell wall replication and DNA, RNA, and protein synthesis. Second, we considered the impact of polar solvent addition (e.g., methanol, n-butanol). We observed that volumetric productivities (g/L/h) were slowed with increasing hydrophobicity of added alcohols. Finally, we investigated the effects of using pretreated biomass hydrolysate as a feed stock, observing a 25% reduction in 2,3-BDO production as a result of coumaroyl and feruloyl amides. Overall, we find the cell-free system to be robust to working concentrations of antibiotics and other compounds that are toxic to cell growth, but do not denature or inhibit relevant enzymes.
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Affiliation(s)
- Jennifer E. Kay
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
- Robert H. Lurie Comprehensive Cancer Center and Northwestern University, Chicago, IL, 60611, USA
- Simpson Querrey Institute, Northwestern University, Chicago, IL, 60611, USA
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Chen X, Zhai R, Li Y, Yuan X, Liu ZH, Jin M. Understanding the structural characteristics of water-soluble phenolic compounds from four pretreatments of corn stover and their inhibitory effects on enzymatic hydrolysis and fermentation. Biotechnol Biofuels 2020; 13:44. [PMID: 32175010 PMCID: PMC7065323 DOI: 10.1186/s13068-020-01686-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 10/21/2019] [Accepted: 02/22/2020] [Indexed: 06/10/2023]
Abstract
BACKGROUND For bioethanol production from lignocellulosic biomass, phenolics derived from pretreatment have been generally considered as highly inhibitory towards enzymatic hydrolysis and fermentation. As phenolics are produced from lignin degradation during pretreatment, it is likely that the pretreatment will exert a strong impact on the structure of phenolics, resulting in varied levels of inhibition of the bioconversion process. Despite the extensive studies on pretreatment, it remains unclear how pretreatment process affects the properties of generated phenolics and how the inhibitory effect of phenolics from different pretreatment varies on enzymatic hydrolysis and fermentation. RESULTS In this study, the structural properties of phenolic compounds derived from four typical pretreatment [dilute acid (DA), liquid hot water pretreatment (LHW), ammonia fiber expansion (AFEX) and alkaline pretreatment (AL)] were characterized, and their effect on both enzymatic hydrolysis and fermentation were evaluated. The inhibitory effect of phenolics on enzymatic hydrolysis followed the order: AFEX > LHW > DA > AL, while the inhibitory effect of phenolics on Zymomonas mobilis 8b strain fermentation followed the order: AL > LHW > DA > AFEX. Interestingly, this study revealed that phenolics derived from AFEX showed more severe inhibitory effect on enzymatic hydrolysis than those from the other pretreatments at the same phenolics concentrations (note: AFEX produced much less amount of phenolics compared to AL and DA), while they exhibited the lowest inhibitory effect on fermentation. The composition of phenolics from different pretreatments was analyzed and model phenolics were applied to explore the reason for this difference. The results suggested that the amide group in phenolics might account for this difference. CONCLUSIONS Pretreatment process greatly affects the properties of generated phenolics and the inhibitory effects of phenolics on enzymatic hydrolysis and fermentation. This study provides new insight for further pretreatment modification and hydrolysate detoxification to minimize phenolics-caused inhibition and enhance the efficiency of enzymatic hydrolysis and fermentation.
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Affiliation(s)
- Xiangxue Chen
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei Street, Xuanwu District, Nanjing, 210094 China
| | - Rui Zhai
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei Street, Xuanwu District, Nanjing, 210094 China
| | - Ying Li
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei Street, Xuanwu District, Nanjing, 210094 China
| | - Xinchuan Yuan
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei Street, Xuanwu District, Nanjing, 210094 China
| | - Zhi-Hua Liu
- Department of Plant Pathology and Microbiology, College of Agriculture and Life Sciences, Texas A&M University, College Station, TX 77843 USA
| | - Mingjie Jin
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei Street, Xuanwu District, Nanjing, 210094 China
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Bhatia SK, Jagtap SS, Bedekar AA, Bhatia RK, Patel AK, Pant D, Rajesh Banu J, Rao CV, Kim YG, Yang YH. Recent developments in pretreatment technologies on lignocellulosic biomass: Effect of key parameters, technological improvements, and challenges. Bioresour Technol 2020; 300:122724. [PMID: 31926792 DOI: 10.1016/j.biortech.2019.122724] [Citation(s) in RCA: 203] [Impact Index Per Article: 50.8] [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: 10/23/2019] [Revised: 12/27/2019] [Accepted: 12/30/2019] [Indexed: 05/12/2023]
Abstract
Lignocellulosic biomass is an inexpensive renewable source that can be used to produce biofuels and bioproducts. The recalcitrance nature of biomass hampers polysaccharide accessibility for enzymes and microbes. Several pretreatment methods have been developed for the conversion of lignocellulosic biomass into value-added products. However, these pretreatment methods also produce a wide range of secondary compounds, which are inhibitory to enzymes and microorganisms. The selection of an effective and efficient pretreatment method discussed in the review and its process optimization can significantly reduce the production of inhibitory compounds and may lead to enhanced production of fermentable sugars and biochemicals. Moreover, evolutionary and genetic engineering approaches are being used for the improvement of microbial tolerance towards inhibitors. Advancements in pretreatment and detoxification technologies may help to increase the productivity of lignocellulose-based biorefinery. In this review, we discuss the recent advancements in lignocellulosic biomass pretreatment technologies and strategies for the removal of inhibitors.
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Affiliation(s)
- Shashi Kant Bhatia
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea; Institute for Ubiquitous Information Technology and Application, Konkuk University, Seoul 05029, Republic of Korea
| | - Sujit Sadashiv Jagtap
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, IL 61801, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, IL 61801, USA
| | - Ashwini Ashok Bedekar
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, IL 61801, USA
| | - Ravi Kant Bhatia
- Department of Biotechnology, Himachal Pradesh University, Summer Hill-171005 (H.P), India
| | - Anil Kumar Patel
- Department of Chemical and Biological Engineering, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Deepak Pant
- Department of Chemistry, Central University of Haryana, Mahendragarh, Haryana 123031, India
| | - J Rajesh Banu
- Department of Civil Engineering, Anna University Regional Campus, Tirunelveli, India
| | - Christopher V Rao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, IL 61801, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave, Urbana, IL 61801, USA
| | - Yun-Gon Kim
- Department of Chemical Engineering, Soongsil University, 06978 Seoul, 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 Application, Konkuk University, Seoul 05029, Republic of Korea.
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Oshlag JZ, Ma Y, Morse K, Burger BT, Lemke RA, Karlen SD, Myers KS, Donohue TJ, Noguera DR. Anaerobic Degradation of Syringic Acid by an Adapted Strain of Rhodopseudomonas palustris. Appl Environ Microbiol 2020; 86:e01888-19. [PMID: 31732577 DOI: 10.1128/AEM.01888-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 08/16/2019] [Accepted: 11/13/2019] [Indexed: 01/06/2023] Open
Abstract
Lignin is the most abundant aromatic polymer on Earth and a resource that could eventually substitute for fossil fuels as a source of aromatic compounds for industrial and biotechnological applications. Engineering microorganisms for the production of aromatic-based biochemicals requires detailed knowledge of the metabolic pathways for the degradation of aromatics that are present in lignin. Our isolation and analysis of a Rhodopseudomonas palustris strain capable of syringic acid degradation reveal a previously unknown metabolic route for aromatic degradation in R. palustris. This study highlights several key features of this pathway and sets the stage for a more complete understanding of the microbial metabolic repertoire required to metabolize aromatic compounds from lignin and other renewable sources. While lignin represents a major fraction of the carbon in plant biomass, biological strategies to convert the components of this heterogeneous polymer into products of industrial and biotechnological value are lacking. Syringic acid (3,5-dimethoxy-4-hydroxybenzoic acid) is a by-product of lignin degradation, appearing in lignocellulosic hydrolysates, deconstructed lignin streams, and other agricultural products. Rhodopseudomonas palustris CGA009 is a known degrader of phenolic compounds under photoheterotrophic conditions via the benzoyl coenzyme A (CoA) degradation (BAD) pathway. However, R. palustris CGA009 is reported to be unable to metabolize meta-methoxylated phenolics, such as syringic acid. We isolated a strain of R. palustris (strain SA008.1.07), adapted from CGA009, which can grow on syringic acid under photoheterotrophic conditions, utilizing it as a sole source of organic carbon and reducing power. An SA008.1.07 mutant with an inactive benzoyl-CoA reductase structural gene was able to grow on syringic acid, demonstrating that the metabolism of this aromatic compound is not through the BAD pathway. Comparative gene expression analyses of SA008.1.07 implicated the involvement of products of the vanARB operon (rpa3619, rpa3620, rpa3621), which has been described as catalyzing aerobic aromatic ring demethylation in other bacteria, in anaerobic syringic acid degradation. In addition, experiments with a vanARB deletion mutant demonstrated the involvement of the vanARB operon in anaerobic syringic acid degradation. These observations provide new insights into the anaerobic degradation of meta-methoxylated and other aromatics by R. palustris. IMPORTANCE Lignin is the most abundant aromatic polymer on Earth and a resource that could eventually substitute for fossil fuels as a source of aromatic compounds for industrial and biotechnological applications. Engineering microorganisms for the production of aromatic-based biochemicals requires detailed knowledge of the metabolic pathways for the degradation of aromatics that are present in lignin. Our isolation and analysis of a Rhodopseudomonas palustris strain capable of syringic acid degradation reveal a previously unknown metabolic route for aromatic degradation in R. palustris. This study highlights several key features of this pathway and sets the stage for a more complete understanding of the microbial metabolic repertoire required to metabolize aromatic compounds from lignin and other renewable sources.
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Zhang Y, Vera JM, Xie D, Serate J, Pohlmann E, Russell JD, Hebert AS, Coon JJ, Sato TK, Landick R. Multiomic Fermentation Using Chemically Defined Synthetic Hydrolyzates Revealed Multiple Effects of Lignocellulose-Derived Inhibitors on Cell Physiology and Xylose Utilization in Zymomonas mobilis. Front Microbiol 2019; 10:2596. [PMID: 31787963 PMCID: PMC6853872 DOI: 10.3389/fmicb.2019.02596] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 08/28/2019] [Accepted: 10/25/2019] [Indexed: 01/14/2023] Open
Abstract
Utilization of both C5 and C6 sugars to produce biofuels and bioproducts is a key goal for the development of integrated lignocellulosic biorefineries. Previously we found that although engineered Zymomonas mobilis 2032 was able to ferment glucose to ethanol when fermenting highly concentrated hydrolyzates such as 9% glucan-loading AFEX-pretreated corn stover hydrolyzate (9% ACSH), xylose conversion after glucose depletion was greatly impaired. We hypothesized that impaired xylose conversion was caused by lignocellulose-derived inhibitors (LDIs) in hydrolyzates. To investigate the effects of LDIs on the cellular physiology of Z. mobilis during fermentation of hydrolyzates, including impacts on xylose utilization, we generated synthetic hydrolyzates (SynHs) that contained nutrients and LDIs at concentrations found in 9% ACSH. Comparative fermentations of Z. mobilis 2032 using SynH with or without LDIs were performed, and samples were collected for end product, transcriptomic, metabolomic, and proteomic analyses. Several LDI-specific effects were observed at various timepoints during fermentation including upregulation of sulfur assimilation and cysteine biosynthesis, upregulation of RND family efflux pump systems (ZMO0282-0285) and ZMO1429-1432, downregulation of a Type I secretion system (ZMO0252-0255), depletion of reduced glutathione, and intracellular accumulation of mannose-1P and mannose-6P. Furthermore, when grown in SynH containing LDIs, Z. mobilis 2032 only metabolized ∼50% of xylose, compared to ∼80% in SynH without LDIs, recapitulating the poor xylose utilization observed in 9% ACSH. Our metabolomic data suggest that the overall flux of xylose metabolism is reduced in the presence of LDIs. However, the expression of most genes involved in glucose and xylose assimilation was not affected by LDIs, nor did we observe blocks in glucose and xylose metabolic pathways. Accumulations of intracellular xylitol and xylonic acid was observed in both SynH with and without LDIs, which decreased overall xylose-to-ethanol conversion efficiency. Our results suggest that xylose metabolism in Z. mobilis 2032 may not be able to support the cellular demands of LDI mitigation and detoxification during fermentation of highly concentrated lignocellulosic hydrolyzates with elevated levels of LDIs. Together, our findings identify several cellular responses to LDIs and possible causes of impaired xylose conversion that will enable future strain engineering of Z. mobilis.
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Affiliation(s)
- Yaoping Zhang
- DOE-Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Jessica M Vera
- DOE-Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Dan Xie
- DOE-Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Jose Serate
- DOE-Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Edward Pohlmann
- DOE-Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Jason D Russell
- DOE-Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Alexander S Hebert
- DOE-Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Joshua J Coon
- DOE-Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Trey K Sato
- DOE-Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States
| | - Robert Landick
- DOE-Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, United States
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Kim J, Tremaine M, Grass JA, Purdy HM, Landick R, Kiley PJ, Reed JL. Systems Metabolic Engineering of Escherichia coli Improves Coconversion of Lignocellulose-Derived Sugars. Biotechnol J 2019; 14:e1800441. [PMID: 31297978 DOI: 10.1002/biot.201800441] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 01/21/2019] [Revised: 07/08/2019] [Indexed: 11/10/2022]
Abstract
Currently, microbial conversion of lignocellulose-derived glucose and xylose to biofuels is hindered by the fact that most microbes (including Escherichia coli [E. coli], Saccharomyces cerevisiae, and Zymomonas mobilis) preferentially consume glucose first and consume xylose slowly after glucose is depleted in lignocellulosic hydrolysates. In this study, E. coli strains are developed that simultaneously utilize glucose and xylose in lignocellulosic biomass hydrolysate using genome-scale models and adaptive laboratory evolution. E. coli strains are designed and constructed that coutilize glucose and xylose and adaptively evolve them to improve glucose and xylose utilization. Whole-genome resequencing of the evolved strains find relevant mutations in metabolic and regulatory genes and the mutations' involvement in sugar coutilization is investigated. The developed strains show significantly improved coconversion of sugars in lignocellulosic biomass hydrolysates and provide a promising platform for producing next-generation biofuels.
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Affiliation(s)
- Joonhoon Kim
- US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53711, USA.,Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Dr, Madison, WI, 53711, USA
| | - Mary Tremaine
- US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53711, USA
| | - Jeffrey A Grass
- US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53711, USA
| | - Hugh M Purdy
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Dr, Madison, WI, 53711, USA
| | - Robert Landick
- US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53711, USA.,Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53711, USA.,Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53711, USA
| | - Patricia J Kiley
- US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53711, USA.,Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53711, USA
| | - Jennifer L Reed
- US Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53711, USA.,Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Dr, Madison, WI, 53711, USA
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10
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Vitkin E, Solomon O, Sultan S, Yakhini Z. Genome-wide analysis of fitness data and its application to improve metabolic models. BMC Bioinformatics 2018; 19:368. [PMID: 30305012 PMCID: PMC6180484 DOI: 10.1186/s12859-018-2341-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 01/03/2018] [Accepted: 08/28/2018] [Indexed: 11/17/2022] Open
Abstract
Background Synthetic biology and related techniques enable genome scale high-throughput investigation of the effect on organism fitness of different gene knock-downs/outs and of other modifications of genomic sequence. Results We develop statistical and computational pipelines and frameworks for analyzing high throughput fitness data over a genome scale set of sequence variants. Analyzing data from a high-throughput knock-down/knock-out bacterial study, we investigate differences and determinants of the effect on fitness in different conditions. Comparing fitness vectors of genes, across tens of conditions, we observe that fitness consequences strongly depend on genomic location and more weakly depend on gene sequence similarity and on functional relationships. In analyzing promoter sequences, we identified motifs associated with conditions studied in bacterial media such as Casaminos, D-glucose, Sucrose, and other sugars and amino-acid sources. We also use fitness data to infer genes associated with orphan metabolic reactions in the iJO1366 E. coli metabolic model. To do this, we developed a new computational method that integrates gene fitness and gene expression profiles within a given reaction network neighborhood to associate this reaction with a set of genes that potentially encode the catalyzing proteins. We then apply this approach to predict candidate genes for 107 orphan reactions in iJO1366. Furthermore - we validate our methodology with known reactions using a leave-one-out approach. Specifically, using top-20 candidates selected based on combined fitness and expression datasets, we correctly reconstruct 39.7% of the reactions, as compared to 33% based on fitness and to 26% based on expression separately, and to 4.02% as a random baseline. Our model improvement results include a novel association of a gene to an orphan cytosine nucleosidation reaction. Conclusion Our pipeline for metabolic modeling shows a clear benefit of using fitness data for predicting genes of orphan reactions. Along with the analysis pipelines we developed, it can be used to analyze similar high-throughput data. Electronic supplementary material The online version of this article (10.1186/s12859-018-2341-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Edward Vitkin
- Department of Computer Science, Technion, Haifa, Israel
| | - Oz Solomon
- Faculty of Biotechnology and Food Engineering, Technion, Haifa, Israel. .,School of Computer Science, The Interdisciplinary Center, Herzliya, Israel.
| | - Sharon Sultan
- School of Computer Science, The Interdisciplinary Center, Herzliya, Israel
| | - Zohar Yakhini
- Department of Computer Science, Technion, Haifa, Israel. .,School of Computer Science, The Interdisciplinary Center, Herzliya, Israel.
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Henson WR, Campbell T, DeLorenzo DM, Gao Y, Berla B, Kim SJ, Foston M, Moon TS, Dantas G. Multi-omic elucidation of aromatic catabolism in adaptively evolved Rhodococcus opacus. Metab Eng 2018; 49:69-83. [DOI: 10.1016/j.ymben.2018.06.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 05/29/2018] [Accepted: 06/14/2018] [Indexed: 12/30/2022]
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12
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Higgins DA, Young MKM, Tremaine M, Sardi M, Fletcher JM, Agnew M, Liu L, Dickinson Q, Peris D, Wrobel RL, Hittinger CT, Gasch AP, Singer SW, Simmons BA, Landick R, Thelen MP, Sato TK. Natural Variation in the Multidrug Efflux Pump SGE1 Underlies Ionic Liquid Tolerance in Yeast. Genetics 2018; 210:219-234. [PMID: 30045857 PMCID: PMC6116967 DOI: 10.1534/genetics.118.301161] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 07/23/2018] [Indexed: 01/20/2023] Open
Abstract
Imidazolium ionic liquids (IILs) have a range of biotechnological applications, including as pretreatment solvents that extract cellulose from plant biomass for microbial fermentation into sustainable bioenergy. However, residual levels of IILs, such as 1-ethyl-3-methylimidazolium chloride ([C2C1im]Cl), are toxic to biofuel-producing microbes, including the yeast Saccharomyces cerevisiae. S. cerevisiae strains isolated from diverse ecological niches differ in genomic sequence and in phenotypes potentially beneficial for industrial applications, including tolerance to inhibitory compounds present in hydrolyzed plant feedstocks. We evaluated >100 genome-sequenced S. cerevisiae strains for tolerance to [C2C1im]Cl and identified one strain with exceptional tolerance. By screening a library of genomic DNA fragments from the [C2C1im]Cl-tolerant strain for improved IIL tolerance, we identified SGE1, which encodes a plasma membrane multidrug efflux pump, and a previously uncharacterized gene that we named ionic liquid tolerance 1 (ILT1), which encodes a predicted membrane protein. Analyses of SGE1 sequences from our panel of S. cerevisiae strains together with growth phenotypes implicated two single nucleotide polymorphisms (SNPs) that associated with IIL tolerance and sensitivity. We confirmed these phenotypic effects by transferring the SGE1 SNPs into a [C2C1im]Cl-sensitive yeast strain using CRISPR/Cas9 genome editing. Further studies indicated that these SNPs affect Sge1 protein stability and cell surface localization, influencing the amount of toxic IILs that cells can pump out of the cytoplasm. Our results highlight the general potential for discovering useful biotechnological functions from untapped natural sequence variation and provide functional insight into emergent SGE1 alleles with reduced capacities to protect against IIL toxicity.
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Affiliation(s)
- Douglas A Higgins
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California 94608
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, California 94550
| | - Megan K M Young
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Mary Tremaine
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Maria Sardi
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53726
| | - Jenna M Fletcher
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Margaret Agnew
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Lisa Liu
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Quinn Dickinson
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - David Peris
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53726
| | - Russell L Wrobel
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53726
| | - Chris Todd Hittinger
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53726
| | - Audrey P Gasch
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53726
| | - Steven W Singer
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California 94608
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, California 94720
| | - Blake A Simmons
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California 94608
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, California 94550
| | - Robert Landick
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
- Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53726
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53726
| | - Michael P Thelen
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, California 94608
- Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, California 94550
| | - Trey K Sato
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
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13
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Siroli L, Braschi G, de Jong A, Kok J, Patrignani F, Lanciotti R. Transcriptomic approach and membrane fatty acid analysis to study the response mechanisms of Escherichia coli to thyme essential oil, carvacrol, 2-(E)-hexanal and citral exposure. J Appl Microbiol 2018; 125:1308-1320. [PMID: 30028070 DOI: 10.1111/jam.14048] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [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: 04/18/2018] [Revised: 06/21/2018] [Accepted: 07/15/2018] [Indexed: 12/18/2022]
Abstract
AIMS The application of essential oils (EOs) and their components as food preservatives is promising but requires a deeper understanding of their mechanisms of action. This study aims to evaluate the effects of thyme EO, carvacrol, citral and 2-(E)-hexenal, on whole-genome gene expression (the transcriptome), as well as the fatty acid (FA) composition of the cell membranes of Escherichia coli K12. METHODS AND RESULTS Therefore, we studied the response against 1 h of exposure to sublethal concentrations of natural antimicrobials, of exponentially growing E. coli K12, using DNA microarray technology and a gas chromatographic method. The results show that treatment with a sublethal concentration of the antimicrobials strongly affects global gene expression in E. coli for all antimicrobials used. Major changes in the expression of genes involved in metabolic pathways as well as in FA biosynthesis and protection against oxidative stress were evidenced. Moreover, the sublethal treatments resulted in increased levels of unsaturated and cyclic FAs as well as an increase in the chain length compared to the controls. CONCLUSIONS The down-regulation of genes involved in aerobic metabolism indicates a shift from respiration to fermentative growth. Moreover, the results obtained suggest that the cytoplasmic membrane of E. coli is the major cellular target of EOs and their components. In addition, the key role of membrane unsaturated FAs in the response mechanisms of E. coli to natural antimicrobials has been confirmed in this study. SIGNIFICANCE AND IMPACT OF THE STUDY The transcriptomic data obtained signify a further step to understand the mechanisms of action of natural antimicrobials also when sublethal concentrations and short-term exposure. In addition, this research goes in deep correlating the transcriptomic modification with the changes in E. coli FA composition of cell membrane identified as the main target of the natural antimicrobials.
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Affiliation(s)
- L Siroli
- Department of Agricultural and Food Sciences, Alma Mater Studiorum, University of Bologna, Campus of Food Science, Cesena, Italy.,Interdipartimental Centre for Industrial Research-CIRI-AGRIFOOD, Alma Mater Studiorum, University of Bologna, Cesena (FC), Italy
| | - G Braschi
- Department of Agricultural and Food Sciences, Alma Mater Studiorum, University of Bologna, Campus of Food Science, Cesena, Italy
| | - A de Jong
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, AG Groningen, The Netherlands
| | - J Kok
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, AG Groningen, The Netherlands
| | - F Patrignani
- Department of Agricultural and Food Sciences, Alma Mater Studiorum, University of Bologna, Campus of Food Science, Cesena, Italy.,Interdipartimental Centre for Industrial Research-CIRI-AGRIFOOD, Alma Mater Studiorum, University of Bologna, Cesena (FC), Italy
| | - R Lanciotti
- Department of Agricultural and Food Sciences, Alma Mater Studiorum, University of Bologna, Campus of Food Science, Cesena, Italy.,Interdipartimental Centre for Industrial Research-CIRI-AGRIFOOD, Alma Mater Studiorum, University of Bologna, Cesena (FC), Italy
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Xue S, Jones AD, Sousa L, Piotrowski J, Jin M, Sarks C, Dale BE, Balan V. Water-soluble phenolic compounds produced from extractive ammonia pretreatment exerted binary inhibitory effects on yeast fermentation using synthetic hydrolysate. PLoS One 2018; 13:e0194012. [PMID: 29543873 DOI: 10.1371/journal.pone.0194012] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Accepted: 02/22/2018] [Indexed: 11/19/2022] Open
Abstract
Biochemical conversion of lignocellulosic biomass to liquid fuels requires pretreatment and enzymatic hydrolysis of the biomass to produce fermentable sugars. Degradation products produced during thermochemical pretreatment, however, inhibit the microbes with regard to both ethanol yield and cell growth. In this work, we used synthetic hydrolysates (SynH) to study the inhibition of yeast fermentation by water-soluble components (WSC) isolated from lignin streams obtained after extractive ammonia pretreatment (EA). We found that SynH with 20g/L WSC mimics real hydrolysate in cell growth, sugar consumption and ethanol production. However, a long lag phase was observed in the first 48 h of fermentation of SynH, which is not observed during fermentation with the crude extraction mixture. Ethyl acetate extraction was conducted to separate phenolic compounds from other water-soluble components. These phenolic compounds play a key inhibitory role during ethanol fermentation. The most abundant compounds were identified by Liquid Chromatography followed by Mass Spectrometry (LC-MS) and Gas Chromatography followed by Mass Spectrometry (GC-MS), including coumaroyl amide, feruloyl amide and coumaroyl glycerol. Chemical genomics profiling was employed to fingerprint the gene deletion response of yeast to different groups of inhibitors in WSC and AFEX-Pretreated Corn Stover Hydrolysate (ACSH). The sensitive/resistant genes cluster patterns for different fermentation media revealed their similarities and differences with regard to degradation compounds.
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15
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Bottoms S, Dickinson Q, McGee M, Hinchman L, Higbee A, Hebert A, Serate J, Xie D, Zhang Y, Coon JJ, Myers CL, Landick R, Piotrowski JS. Chemical genomic guided engineering of gamma-valerolactone tolerant yeast. Microb Cell Fact 2018; 17:5. [PMID: 29329531 PMCID: PMC5767017 DOI: 10.1186/s12934-017-0848-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [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: 05/11/2017] [Accepted: 12/14/2017] [Indexed: 11/13/2022] Open
Abstract
Background Gamma valerolactone (GVL) treatment of lignocellulosic bomass is a promising technology for degradation of biomass for biofuel production; however, GVL is toxic to fermentative microbes. Using a combination of chemical genomics with the yeast (Saccharomyces cerevisiae) deletion collection to identify sensitive and resistant mutants, and chemical proteomics to monitor protein abundance in the presence of GVL, we sought to understand the mechanism toxicity and resistance to GVL with the goal of engineering a GVL-tolerant, xylose-fermenting yeast. Results Chemical genomic profiling of GVL predicted that this chemical affects membranes and membrane-bound processes. We show that GVL causes rapid, dose-dependent cell permeability, and is synergistic with ethanol. Chemical genomic profiling of GVL revealed that deletion of the functionally related enzymes Pad1p and Fdc1p, which act together to decarboxylate cinnamic acid and its derivatives to vinyl forms, increases yeast tolerance to GVL. Further, overexpression of Pad1p sensitizes cells to GVL toxicity. To improve GVL tolerance, we deleted PAD1 and FDC1 in a xylose-fermenting yeast strain. The modified strain exhibited increased anaerobic growth, sugar utilization, and ethanol production in synthetic hydrolysate with 1.5% GVL, and under other conditions. Chemical proteomic profiling of the engineered strain revealed that enzymes involved in ergosterol biosynthesis were more abundant in the presence of GVL compared to the background strain. The engineered GVL strain contained greater amounts of ergosterol than the background strain. Conclusions We found that GVL exerts toxicity to yeast by compromising cellular membranes, and that this toxicity is synergistic with ethanol. Deletion of PAD1 and FDC1 conferred GVL resistance to a xylose-fermenting yeast strain by increasing ergosterol accumulation in aerobically grown cells. The GVL-tolerant strain fermented sugars in the presence of GVL levels that were inhibitory to the unmodified strain. This strain represents a xylose fermenting yeast specifically tailored to GVL produced hydrolysates. Electronic supplementary material The online version of this article (10.1186/s12934-017-0848-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Scott Bottoms
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, USA.,Lehrstuhl für Chemie Biogener Rohstoffe, Technische Universität München, Schulgasse 16, 94315, Straubing, Germany
| | - Quinn Dickinson
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, USA.,School of Biology, Georgia Institute of Technology, Atlanta, GA, USA
| | - Mick McGee
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, USA
| | - Li Hinchman
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, USA
| | - Alan Higbee
- University of Wisconsin Biotechnology Center, Madison, WI, USA
| | - Alex Hebert
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Jose Serate
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, USA
| | - Dan Xie
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, USA
| | - Yaoping Zhang
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, USA
| | - Joshua J Coon
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA.,Morgridge Institute for Research, Madison, WI, USA.,Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA.,Genome Center of Wisconsin, Madison, WI, USA
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, USA
| | - Robert Landick
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, USA
| | - Jeff S Piotrowski
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, 1552 University Ave, Madison, WI, USA. .,Yumanity Therapeutics, 790 Memorial Drive, Suite 2C, Cambridge, MA, 02139, USA.
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Peris D, Moriarty RV, Alexander WG, Baker E, Sylvester K, Sardi M, Langdon QK, Libkind D, Wang QM, Bai FY, Leducq JB, Charron G, Landry CR, Sampaio JP, Gonçalves P, Hyma KE, Fay JC, Sato TK, Hittinger CT. Hybridization and adaptive evolution of diverse Saccharomyces species for cellulosic biofuel production. Biotechnol Biofuels 2017; 10:78. [PMID: 28360936 PMCID: PMC5369230 DOI: 10.1186/s13068-017-0763-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/18/2017] [Indexed: 06/01/2023]
Abstract
BACKGROUND Lignocellulosic biomass is a common resource across the globe, and its fermentation offers a promising option for generating renewable liquid transportation fuels. The deconstruction of lignocellulosic biomass releases sugars that can be fermented by microbes, but these processes also produce fermentation inhibitors, such as aromatic acids and aldehydes. Several research projects have investigated lignocellulosic biomass fermentation by the baker's yeast Saccharomyces cerevisiae. Most projects have taken synthetic biological approaches or have explored naturally occurring diversity in S. cerevisiae to enhance stress tolerance, xylose consumption, or ethanol production. Despite these efforts, improved strains with new properties are needed. In other industrial processes, such as wine and beer fermentation, interspecies hybrids have combined important traits from multiple species, suggesting that interspecies hybridization may also offer potential for biofuel research. RESULTS To investigate the efficacy of this approach for traits relevant to lignocellulosic biofuel production, we generated synthetic hybrids by crossing engineered xylose-fermenting strains of S. cerevisiae with wild strains from various Saccharomyces species. These interspecies hybrids retained important parental traits, such as xylose consumption and stress tolerance, while displaying intermediate kinetic parameters and, in some cases, heterosis (hybrid vigor). Next, we exposed them to adaptive evolution in ammonia fiber expansion-pretreated corn stover hydrolysate and recovered strains with improved fermentative traits. Genome sequencing showed that the genomes of these evolved synthetic hybrids underwent rearrangements, duplications, and deletions. To determine whether the genus Saccharomyces contains additional untapped potential, we screened a genetically diverse collection of more than 500 wild, non-engineered Saccharomyces isolates and uncovered a wide range of capabilities for traits relevant to cellulosic biofuel production. Notably, Saccharomyces mikatae strains have high innate tolerance to hydrolysate toxins, while some Saccharomyces species have a robust native capacity to consume xylose. CONCLUSIONS This research demonstrates that hybridization is a viable method to combine industrially relevant traits from diverse yeast species and that members of the genus Saccharomyces beyond S. cerevisiae may offer advantageous genes and traits of interest to the lignocellulosic biofuel industry.
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Affiliation(s)
- David Peris
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI USA
| | - Ryan V. Moriarty
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI USA
| | - William G. Alexander
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI USA
| | - EmilyClare Baker
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI USA
| | - Kayla Sylvester
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI USA
| | - Maria Sardi
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI USA
| | - Quinn K. Langdon
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI USA
| | - Diego Libkind
- Laboratorio de Microbiología Aplicada, Biotecnología y Bioinformática, Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales, IPATEC (CONICET-UNComahue), Centro Regional Universitario Bariloche, Bariloche, Río Negro Argentina
| | - Qi-Ming Wang
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI USA
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Feng-Yan Bai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jean-Baptiste Leducq
- Departement des Sciences Biologiques, Université de Montréal, Montreal, QC Canada
- Département de Biologie, PROTEO, Pavillon Charles-Eugène-Marchand, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC Canada
| | - Guillaume Charron
- Département de Biologie, PROTEO, Pavillon Charles-Eugène-Marchand, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC Canada
| | - Christian R. Landry
- Département de Biologie, PROTEO, Pavillon Charles-Eugène-Marchand, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, QC Canada
| | - José Paulo Sampaio
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Paula Gonçalves
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Katie E. Hyma
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University in St. Louis, St. Louis, MO USA
| | - Justin C. Fay
- Department of Genetics, Center for Genome Sciences and Systems Biology, Washington University in St. Louis, St. Louis, MO USA
| | - Trey K. Sato
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI USA
| | - Chris Todd Hittinger
- Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI USA
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Tran TNT, Breuer RJ, Avanasi Narasimhan R, Parreiras LS, Zhang Y, Sato TK, Durrett TP. Metabolic engineering of Saccharomyces cerevisiae to produce a reduced viscosity oil from lignocellulose. Biotechnol Biofuels 2017; 10:69. [PMID: 28331545 PMCID: PMC5359884 DOI: 10.1186/s13068-017-0751-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 03/09/2017] [Indexed: 05/23/2023]
Abstract
BACKGROUND Acetyl-triacylglycerols (acetyl-TAGs) are unusual triacylglycerol (TAG) molecules that contain an sn-3 acetate group. Compared to typical triacylglycerol molecules (here referred to as long chain TAGs; lcTAGs), acetyl-TAGs possess reduced viscosity and improved cold temperature properties, which may allow direct use as a drop-in diesel fuel. Their different chemical and physical properties also make acetyl-TAGs useful for other applications such as lubricants and plasticizers. Acetyl-TAGs can be synthesized by EaDAcT, a diacylglycerol acetyltransferase enzyme originally isolated from Euonymus alatus (Burning Bush). The heterologous expression of EaDAcT in different organisms, including Saccharomyces cerevisiae, resulted in the accumulation of acetyl-TAGs in storage lipids. Microbial conversion of lignocellulose into acetyl-TAGs could allow biorefinery production of versatile molecules for biofuel and bioproducts. RESULTS In order to produce acetyl-TAGs from abundant lignocellulose feedstocks, we expressed EaDAcT in S. cerevisiae previously engineered to utilize xylose as a carbon source. The resulting strains were capable of producing acetyl-TAGs when grown on different media. The highest levels of acetyl-TAG production were observed with growth on synthetic lab media containing glucose or xylose. Importantly, acetyl-TAGs were also synthesized by this strain in ammonia fiber expansion (AFEX)-pretreated corn stover hydrolysate (ACSH) at higher volumetric titers than previously published strains. The deletion of the four endogenous enzymes known to contribute to lcTAG production increased the proportion of acetyl-TAGs in the total storage lipids beyond that in existing strains, which will make purification of these useful lipids easier. Surprisingly, the strains containing the four deletions were still capable of synthesizing lcTAG, suggesting that the particular strain used in this study possesses additional undetermined diacylglycerol acyltransferase activity. Additionally, the carbon source used for growth influenced the accumulation of these residual lcTAGs, with higher levels in strains cultured on xylose containing media. CONCLUSION Our results demonstrate that S. cerevisiae can be metabolically engineered to produce acetyl-TAGs when grown on different carbon sources, including hydrolysate derived from lignocellulose. Deletion of four endogenous acyltransferases enabled a higher purity of acetyl-TAGs to be achieved, but lcTAGs were still synthesized. Longer incubation times also decreased the levels of acetyl-TAGs produced. Therefore, additional work is needed to further manipulate acetyl-TAG production in this strain of S. cerevisiae, including the identification of other TAG biosynthetic and lipolytic enzymes and a better understanding of the regulation of the synthesis and degradation of storage lipids.
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Affiliation(s)
- Tam N. T. Tran
- Department of Biochemistry and Molecular Biophysics, Kansas State University, 141 Chalmers Hall, Manhattan, KS 66506 USA
| | - Rebecca J. Breuer
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726 USA
| | | | - Lucas S. Parreiras
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726 USA
| | - Yaoping Zhang
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726 USA
| | - Trey K. Sato
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726 USA
| | - Timothy P. Durrett
- Department of Biochemistry and Molecular Biophysics, Kansas State University, 141 Chalmers Hall, Manhattan, KS 66506 USA
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Sardi M, Rovinskiy N, Zhang Y, Gasch AP. Leveraging Genetic-Background Effects in Saccharomyces cerevisiae To Improve Lignocellulosic Hydrolysate Tolerance. Appl Environ Microbiol 2016; 82:5838-49. [PMID: 27451446 DOI: 10.1128/AEM.01603-16] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 07/14/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED A major obstacle to sustainable lignocellulosic biofuel production is microbe inhibition by the combinatorial stresses in pretreated plant hydrolysate. Chemical biomass pretreatment releases a suite of toxins that interact with other stressors, including high osmolarity and temperature, which together can have poorly understood synergistic effects on cells. Improving tolerance in industrial strains has been hindered, in part because the mechanisms of tolerance reported in the literature often fail to recapitulate in other strain backgrounds. Here, we explored and then exploited variations in stress tolerance, toxin-induced transcriptomic responses, and fitness effects of gene overexpression in different Saccharomyces cerevisiae (yeast) strains to identify genes and processes linked to tolerance of hydrolysate stressors. Using six different S. cerevisiae strains that together maximized phenotypic and genetic diversity, first we explored transcriptomic differences between resistant and sensitive strains to identify common and strain-specific responses. This comparative analysis implicated primary cellular targets of hydrolysate toxins, secondary effects of defective defense strategies, and mechanisms of tolerance. Dissecting the responses to individual hydrolysate components across strains pointed to synergistic interactions between osmolarity, pH, hydrolysate toxins, and nutrient composition. By characterizing the effects of high-copy gene overexpression in three different strains, we revealed the breadth of the background-specific effects of gene fitness contributions in synthetic hydrolysate. Our approach identified new genes for engineering improved stress tolerance in diverse strains while illuminating the effects of genetic background on molecular mechanisms. IMPORTANCE Recent studies on natural variation within Saccharomyces cerevisiae have uncovered substantial phenotypic diversity. Here, we took advantage of this diversity, using it as a tool to infer the effects of combinatorial stress found in lignocellulosic hydrolysate. By comparing sensitive and tolerant strains, we implicated primary cellular targets of hydrolysate toxins and elucidated the physiological states of cells when exposed to this stress. We also explored the strain-specific effects of gene overexpression to further identify strain-specific responses to hydrolysate stresses and to identify genes that improve hydrolysate tolerance independent of strain background. This study underscores the importance of studying multiple strains to understand the effects of hydrolysate stress and provides a method to find genes that improve tolerance across strain backgrounds.
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19
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Yang S, Fei Q, Zhang Y, Contreras LM, Utturkar SM, Brown SD, Himmel ME, Zhang M. Zymomonas mobilis as a model system for production of biofuels and biochemicals. Microb Biotechnol 2016; 9:699-717. [PMID: 27629544 PMCID: PMC5072187 DOI: 10.1111/1751-7915.12408] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 08/03/2016] [Accepted: 08/05/2016] [Indexed: 12/04/2022] Open
Abstract
Zymomonas mobilis is a natural ethanologen with many desirable industrial biocatalyst characteristics. In this review, we will discuss work to develop Z. mobilis as a model system for biofuel production from the perspectives of substrate utilization, development for industrial robustness, potential product spectrum, strain evaluation and fermentation strategies. This review also encompasses perspectives related to classical genetic tools and emerging technologies in this context.
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Affiliation(s)
- Shihui Yang
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA. .,Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, 430062, China.
| | - Qiang Fei
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.,School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Yaoping Zhang
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, WI, 53726, USA
| | - Lydia M Contreras
- McKetta Department of Chemical Engineering, University of Texas, Austin, TX, 78712, USA
| | - Sagar M Utturkar
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37919, USA
| | - Steven D Brown
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37919, USA.,BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Michael E Himmel
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Min Zhang
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.
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20
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Sarks C, Higbee A, Piotrowski J, Xue S, Coon JJ, Sato TK, Jin M, Balan V, Dale BE. Quantifying pretreatment degradation compounds in solution and accumulated by cells during solids and yeast recycling in the Rapid Bioconversion with Integrated recycling Technology process using AFEX™ corn stover. Bioresour Technol 2016; 205:24-33. [PMID: 26802184 DOI: 10.1016/j.biortech.2016.01.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 12/13/2015] [Revised: 01/03/2016] [Accepted: 01/05/2016] [Indexed: 05/09/2023]
Abstract
Effects of degradation products (low molecular weight compounds produced during pretreatment) on the microbes used in the RaBIT (Rapid Bioconversion with Integrated recycling Technology) process that reduces enzyme usage up to 40% by efficient enzyme recycling were studied. Chemical genomic profiling was performed, showing no yeast response differences in hydrolysates produced during RaBIT enzymatic hydrolysis. Concentrations of degradation products in solution were quantified after different enzymatic hydrolysis cycles and fermentation cycles. Intracellular degradation product concentrations were also measured following fermentation. Degradation product concentrations in hydrolysate did not change between RaBIT enzymatic hydrolysis cycles; the cell population retained its ability to oxidize/reduce (detoxify) aldehydes over five RaBIT fermentation cycles; and degradation products accumulated within or on the cells as RaBIT fermentation cycles increased. Synthetic hydrolysate was used to confirm that pretreatment degradation products are the sole cause of decreased xylose consumption during RaBIT fermentations.
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Affiliation(s)
- Cory Sarks
- Biomass Conversion Research Laboratory (BCRL), Department of Chemical Engineering and Materials Science, Michigan State University, 3815 Technology Boulevard, Lansing, MI 48910, United States; DOE Great Lakes Bioenergy Research Center (GLBRC), Michigan State University, East Lansing, MI 48824, United States.
| | - Alan Higbee
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53704, United States.
| | - Jeff Piotrowski
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53704, United States.
| | - Saisi Xue
- Biomass Conversion Research Laboratory (BCRL), Department of Chemical Engineering and Materials Science, Michigan State University, 3815 Technology Boulevard, Lansing, MI 48910, United States; DOE Great Lakes Bioenergy Research Center (GLBRC), Michigan State University, East Lansing, MI 48824, United States.
| | - Joshua J Coon
- Departments of Chemistry and Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53704, United States.
| | - Trey K Sato
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53704, United States.
| | - Mingjie Jin
- Biomass Conversion Research Laboratory (BCRL), Department of Chemical Engineering and Materials Science, Michigan State University, 3815 Technology Boulevard, Lansing, MI 48910, United States; DOE Great Lakes Bioenergy Research Center (GLBRC), Michigan State University, East Lansing, MI 48824, United States.
| | - Venkatesh Balan
- Biomass Conversion Research Laboratory (BCRL), Department of Chemical Engineering and Materials Science, Michigan State University, 3815 Technology Boulevard, Lansing, MI 48910, United States; DOE Great Lakes Bioenergy Research Center (GLBRC), Michigan State University, East Lansing, MI 48824, United States.
| | - Bruce E Dale
- Biomass Conversion Research Laboratory (BCRL), Department of Chemical Engineering and Materials Science, Michigan State University, 3815 Technology Boulevard, Lansing, MI 48910, United States; DOE Great Lakes Bioenergy Research Center (GLBRC), Michigan State University, East Lansing, MI 48824, United States.
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21
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Abstract
This review is a short synopsis of some of the latest breakthroughs in the areas of lignocellulosic conversion to fuels and utilization of oils for biodiesel. Although four lignocellulosic ethanol factories have opened in the USA and hundreds of biodiesel installations are active worldwide, technological improvements are being discovered that will rapidly evolve the biofuels industry into a new paradigm. These discoveries involve the feedstocks as well as the technologies to process them.
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Affiliation(s)
- Elizabeth E Hood
- College of Agriculture and Technology, Arkansas State University, Arkanas, AR, USA
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22
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Yoneda A, Henson WR, Goldner NK, Park KJ, Forsberg KJ, Kim SJ, Pesesky MW, Foston M, Dantas G, Moon TS. Comparative transcriptomics elucidates adaptive phenol tolerance and utilization in lipid-accumulating Rhodococcus opacus PD630. Nucleic Acids Res 2016; 44:2240-54. [PMID: 26837573 PMCID: PMC4797299 DOI: 10.1093/nar/gkw055] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 01/20/2016] [Indexed: 12/29/2022] Open
Abstract
Lignin-derived (e.g. phenolic) compounds can compromise the bioconversion of lignocellulosic biomass to fuels and chemicals due to their toxicity and recalcitrance. The lipid-accumulating bacterium Rhodococcus opacus PD630 has recently emerged as a promising microbial host for lignocellulose conversion to value-added products due to its natural ability to tolerate and utilize phenolics. To gain a better understanding of its phenolic tolerance and utilization mechanisms, we adaptively evolved R. opacus over 40 passages using phenol as its sole carbon source (up to 373% growth improvement over wild-type), and extensively characterized two strains from passages 33 and 40. The two adapted strains showed higher phenol consumption rates (∼20 mg/l/h) and ∼2-fold higher lipid production from phenol than the wild-type strain. Whole-genome sequencing and comparative transcriptomics identified highly-upregulated degradation pathways and putative transporters for phenol in both adapted strains, highlighting the important linkage between mechanisms of regulated phenol uptake, utilization, and evolved tolerance. Our study shows that the R. opacus mutants are likely to use their transporters to import phenol rather than export them, suggesting a new aromatic tolerance mechanism. The identified tolerance genes and pathways are promising candidates for future metabolic engineering in R. opacus for improved lignin conversion to lipid-based products.
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Affiliation(s)
- Aki Yoneda
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63108, USA Center for Genome Sciences & Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO 63108, USA
| | - William R Henson
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Nicholas K Goldner
- Center for Genome Sciences & Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO 63108, USA
| | - Kun Joo Park
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Kevin J Forsberg
- Center for Genome Sciences & Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO 63108, USA
| | - Soo Ji Kim
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Mitchell W Pesesky
- Center for Genome Sciences & Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO 63108, USA
| | - Marcus Foston
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Gautam Dantas
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63108, USA Center for Genome Sciences & Systems Biology, Washington University in St. Louis School of Medicine, St. Louis, MO 63108, USA Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA Department of Molecular Microbiology, Washington University in St. Louis School of Medicine, St. Louis, MO 63108, USA
| | - Tae Seok Moon
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
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23
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Dickinson Q, Bottoms S, Hinchman L, McIlwain S, Li S, Myers CL, Boone C, Coon JJ, Hebert A, Sato TK, Landick R, Piotrowski JS. Mechanism of imidazolium ionic liquids toxicity in Saccharomyces cerevisiae and rational engineering of a tolerant, xylose-fermenting strain. Microb Cell Fact 2016; 15:17. [PMID: 26790958 PMCID: PMC4721058 DOI: 10.1186/s12934-016-0417-7] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 01/08/2016] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Imidazolium ionic liquids (IILs) underpin promising technologies that generate fermentable sugars from lignocellulose for future biorefineries. However, residual IILs are toxic to fermentative microbes such as Saccharomyces cerevisiae, making IIL-tolerance a key property for strain engineering. To enable rational engineering, we used chemical genomic profiling to understand the effects of IILs on S. cerevisiae. RESULTS We found that IILs likely target mitochondria as their chemical genomic profiles closely resembled that of the mitochondrial membrane disrupting agent valinomycin. Further, several deletions of genes encoding mitochondrial proteins exhibited increased sensitivity to IIL. High-throughput chemical proteomics confirmed effects of IILs on mitochondrial protein levels. IILs induced abnormal mitochondrial morphology, as well as altered polarization of mitochondrial membrane potential similar to valinomycin. Deletion of the putative serine/threonine kinase PTK2 thought to activate the plasma-membrane proton efflux pump Pma1p conferred a significant IIL-fitness advantage. Conversely, overexpression of PMA1 conferred sensitivity to IILs, suggesting that hydrogen ion efflux may be coupled to influx of the toxic imidazolium cation. PTK2 deletion conferred resistance to multiple IILs, including [EMIM]Cl, [BMIM]Cl, and [EMIM]Ac. An engineered, xylose-converting ptk2∆ S. cerevisiae (Y133-IIL) strain consumed glucose and xylose faster and produced more ethanol in the presence of 1 % [BMIM]Cl than the wild-type PTK2 strain. We propose a model of IIL toxicity and resistance. CONCLUSIONS This work demonstrates the utility of chemical genomics-guided biodesign for development of superior microbial biocatalysts for the ever-changing landscape of fermentation inhibitors.
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Affiliation(s)
- Quinn Dickinson
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, USA.
| | - Scott Bottoms
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, USA.
| | - Li Hinchman
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, USA.
| | - Sean McIlwain
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, USA.
| | - Sheena Li
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan.
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN, USA.
| | - Charles Boone
- Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.
| | - Joshua J Coon
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, USA. .,Biomolecular Chemistry, University of Wisconsin, Madison, WI, USA.
| | - Alexander Hebert
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, USA. .,Biomolecular Chemistry, University of Wisconsin, Madison, WI, USA.
| | - Trey K Sato
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, USA.
| | - Robert Landick
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, USA. .,Departments of Biochemistry and Bacteriology, University of Wisconsin, Madison, WI, USA.
| | - Jeff S Piotrowski
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, USA.
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24
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Sawisit A, Jantama K, Zheng H, Yomano LP, York SW, Shanmugam KT, Ingram LO. Mutation in galP improved fermentation of mixed sugars to succinate using engineered Escherichia coli AS1600a and AM1 mineral salts medium. Bioresour Technol 2015; 193:433-441. [PMID: 26159300 DOI: 10.1016/j.biortech.2015.06.108] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [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: 05/26/2015] [Revised: 06/18/2015] [Accepted: 06/19/2015] [Indexed: 06/04/2023]
Abstract
Escherichia coli KJ122 was engineered to produce succinate from glucose using the wild type GalP for glucose uptake instead of the native phosphotransferase system (ptsI mutation). This strain now ferments 10% xylose poorly. Mutants were selected by serial transfers in AM1 mineral salts medium with 10% xylose. Clones from this population all exhibited a similar improvement, co-fermentation of an equal mixture of xylose and glucose. One of these, AS1600a, produced 84.26 ± 1.37 g/L succinate, equivalent to that produced by the parent (KJ122) from 10% glucose (85.46 ± 1.78 g/L). AS1600a was sequenced and found to contain a mutation in galactose permease (GalP, G236D). This mutation was shown to be responsible for the improvement in fermentation using KJΔgalP as the host and expression vectors with native galP and with mutant galP(∗). Strain AS1600a and KJΔgalP(pLOI5746; galP(∗)) also co-fermented a mixture of glucose, xylose, arabinose, and galactose in sugarcane bagasse hydrolysate using mineral salts medium.
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Affiliation(s)
- Apichai Sawisit
- Metabolic Engineering Research Unit, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Kaemwich Jantama
- Metabolic Engineering Research Unit, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Huabao Zheng
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Lorraine P Yomano
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Sean W York
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Keelnatham T Shanmugam
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Lonnie O Ingram
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA.
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25
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Austin S, Kontur WS, Ulbrich A, Oshlag Z, Zhang W, Higbee A, Zhang Y, Coon JJ, Hodge DB, Donohue TJ, Noguera DR. Metabolism of Multiple Aromatic Compounds in Corn Stover Hydrolysate by Rhodopseudomonas palustris. Environ Sci Technol 2015; 49:8914-22. [PMID: 26121369 PMCID: PMC5031247 DOI: 10.1021/acs.est.5b02062] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Lignocellulosic biomass hydrolysates hold great potential as a feedstock for microbial biofuel production, due to their high concentration of fermentable sugars. Present at lower concentrations are a suite of aromatic compounds that can inhibit fermentation by biofuel-producing microbes. We have developed a microbial-mediated strategy for removing these aromatic compounds, using the purple nonsulfur bacterium Rhodopseudomonas palustris. When grown photoheterotrophically in an anaerobic environment, R. palustris removes most of the aromatics from ammonia fiber expansion (AFEX) treated corn stover hydrolysate (ACSH), while leaving the sugars mostly intact. We show that R. palustris can metabolize a host of aromatic substrates in ACSH that have either been previously described as unable to support growth, such as methoxylated aromatics, and those that have not yet been tested, such as aromatic amides. Removing the aromatics from ACSH with R. palustris, allowed growth of a second microbe that could not grow in the untreated ACSH. By using defined mutants, we show that most of these aromatic compounds are metabolized by the benzoyl-CoA pathway. We also show that loss of enzymes in the benzoyl-CoA pathway prevents total degradation of the aromatics in the hydrolysate, and instead allows for biological transformation of this suite of aromatics into selected aromatic compounds potentially recoverable as an additional bioproduct.
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Affiliation(s)
- Samantha Austin
- Department of Civil and Environmental Engineering, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
| | - Wayne S. Kontur
- Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
| | - Arne Ulbrich
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
| | - Zachary Oshlag
- Department of Civil and Environmental Engineering, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
| | - Weiping Zhang
- Department of Civil and Environmental Engineering, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
| | - Alan Higbee
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
| | - Yaoping Zhang
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
| | - Joshua J. Coon
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
| | - David B. Hodge
- Department of Chemical Engineering & Materials Science, Michigan State University, East Lansing, Michigan 48824, United States
- Department of Biosystems & Agricultural Engineering, Michigan State University, East Lansing, Michigan 48824, United States
| | - Timothy J. Donohue
- Department of Bacteriology, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
| | - Daniel R. Noguera
- Department of Civil and Environmental Engineering, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
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26
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Pisithkul T, Jacobson TB, O'Brien TJ, Stevenson DM, Amador-Noguez D. Phenolic Amides Are Potent Inhibitors of De Novo Nucleotide Biosynthesis. Appl Environ Microbiol 2015; 81:5761-72. [PMID: 26070680 DOI: 10.1128/AEM.01324-15] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 06/09/2015] [Indexed: 12/17/2022] Open
Abstract
An outstanding challenge toward efficient production of biofuels and value-added chemicals from plant biomass is the impact that lignocellulose-derived inhibitors have on microbial fermentations. Elucidating the mechanisms that underlie their toxicity is critical for developing strategies to overcome them. Here, using Escherichia coli as a model system, we investigated the metabolic effects and toxicity mechanisms of feruloyl amide and coumaroyl amide, the predominant phenolic compounds in ammonia-pretreated biomass hydrolysates. Using metabolomics, isotope tracers, and biochemical assays, we showed that these two phenolic amides act as potent and fast-acting inhibitors of purine and pyrimidine biosynthetic pathways. Feruloyl or coumaroyl amide exposure leads to (i) a rapid buildup of 5-phosphoribosyl-1-pyrophosphate (PRPP), a key precursor in nucleotide biosynthesis, (ii) a rapid decrease in the levels of pyrimidine biosynthetic intermediates, and (iii) a long-term generalized decrease in nucleotide and deoxynucleotide levels. Tracer experiments using 13C-labeled sugars and [15N]ammonia demonstrated that carbon and nitrogen fluxes into nucleotides and deoxynucleotides are inhibited by these phenolic amides. We found that these effects are mediated via direct inhibition of glutamine amidotransferases that participate in nucleotide biosynthetic pathways. In particular, feruloyl amide is a competitive inhibitor of glutamine PRPP amidotransferase (PurF), which catalyzes the first committed step in de novo purine biosynthesis. Finally, external nucleoside supplementation prevents phenolic amide-mediated growth inhibition by allowing nucleotide biosynthesis via salvage pathways. The results presented here will help in the development of strategies to overcome toxicity of phenolic compounds and facilitate engineering of more efficient microbial producers of biofuels and chemicals.
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27
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Serate J, Xie D, Pohlmann E, Donald C, Shabani M, Hinchman L, Higbee A, Mcgee M, La Reau A, Klinger GE, Li S, Myers CL, Boone C, Bates DM, Cavalier D, Eilert D, Oates LG, Sanford G, Sato TK, Dale B, Landick R, Piotrowski J, Ong RG, Zhang Y. Controlling microbial contamination during hydrolysis of AFEX-pretreated corn stover and switchgrass: effects on hydrolysate composition, microbial response and fermentation. Biotechnol Biofuels 2015; 8:180. [PMID: 26583044 PMCID: PMC4650398 DOI: 10.1186/s13068-015-0356-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 10/09/2015] [Indexed: 05/04/2023]
Abstract
BACKGROUND Microbial conversion of lignocellulosic feedstocks into biofuels remains an attractive means to produce sustainable energy. It is essential to produce lignocellulosic hydrolysates in a consistent manner in order to study microbial performance in different feedstock hydrolysates. Because of the potential to introduce microbial contamination from the untreated biomass or at various points during the process, it can be difficult to control sterility during hydrolysate production. In this study, we compared hydrolysates produced from AFEX-pretreated corn stover and switchgrass using two different methods to control contamination: either by autoclaving the pretreated feedstocks prior to enzymatic hydrolysis, or by introducing antibiotics during the hydrolysis of non-autoclaved feedstocks. We then performed extensive chemical analysis, chemical genomics, and comparative fermentations to evaluate any differences between these two different methods used for producing corn stover and switchgrass hydrolysates. RESULTS Autoclaving the pretreated feedstocks could eliminate the contamination for a variety of feedstocks, whereas the antibiotic gentamicin was unable to control contamination consistently during hydrolysis. Compared to the addition of gentamicin, autoclaving of biomass before hydrolysis had a minimal effect on mineral concentrations, and showed no significant effect on the two major sugars (glucose and xylose) found in these hydrolysates. However, autoclaving elevated the concentration of some furanic and phenolic compounds. Chemical genomics analyses using Saccharomyces cerevisiae strains indicated a high correlation between the AFEX-pretreated hydrolysates produced using these two methods within the same feedstock, indicating minimal differences between the autoclaving and antibiotic methods. Comparative fermentations with S. cerevisiae and Zymomonas mobilis also showed that autoclaving the AFEX-pretreated feedstocks had no significant effects on microbial performance in these hydrolysates. CONCLUSIONS Our results showed that autoclaving the pretreated feedstocks offered advantages over the addition of antibiotics for hydrolysate production. The autoclaving method produced a more consistent quality of hydrolysate, and also showed negligible effects on microbial performance. Although the levels of some of the lignocellulose degradation inhibitors were elevated by autoclaving the feedstocks prior to enzymatic hydrolysis, no significant effects on cell growth, sugar utilization, or ethanol production were seen during bacterial or yeast fermentations in hydrolysates produced using the two different methods.
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Affiliation(s)
- Jose Serate
- />DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI USA
| | - Dan Xie
- />DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI USA
| | - Edward Pohlmann
- />DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI USA
| | - Charles Donald
- />DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI USA
| | - Mahboubeh Shabani
- />DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI USA
| | - Li Hinchman
- />DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI USA
| | - Alan Higbee
- />DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI USA
| | - Mick Mcgee
- />DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI USA
| | - Alex La Reau
- />DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI USA
| | - Grace E. Klinger
- />DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI USA
| | - Sheena Li
- />RIKEN Center for Sustainable Resource Science, Wako, Saitama Japan
| | - Chad L. Myers
- />Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, MN USA
| | - Charles Boone
- />Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON Canada
| | - Donna M. Bates
- />DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI USA
| | - Dave Cavalier
- />DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI USA
| | - Dustin Eilert
- />DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI USA
| | - Lawrence G. Oates
- />DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI USA
| | - Gregg Sanford
- />DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI USA
| | - Trey K. Sato
- />DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI USA
| | - Bruce Dale
- />DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI USA
| | - Robert Landick
- />DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI USA
| | - Jeff Piotrowski
- />DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI USA
| | - Rebecca Garlock Ong
- />DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI USA
| | - Yaoping Zhang
- />DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI USA
| |
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