151
|
Roche CM, Glass NL, Blanch HW, Clark DS. Engineering the filamentous fungusNeurospora crassafor lipid production from lignocellulosic biomass. Biotechnol Bioeng 2014; 111:1097-107. [DOI: 10.1002/bit.25211] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 02/03/2014] [Accepted: 02/06/2014] [Indexed: 01/14/2023]
Affiliation(s)
- Christine M. Roche
- The Chemical and Biomolecular Engineering Department; The University of California; Berkeley California 94720
- The Energy Biosciences Institute; The University of California; Berkeley California 94720
| | - N. Louise Glass
- The Energy Biosciences Institute; The University of California; Berkeley California 94720
- The Plant and Microbial Biology Department; The University of California; Berkeley California
| | - Harvey W. Blanch
- The Chemical and Biomolecular Engineering Department; The University of California; Berkeley California 94720
- The Energy Biosciences Institute; The University of California; Berkeley California 94720
| | - Douglas S. Clark
- The Chemical and Biomolecular Engineering Department; The University of California; Berkeley California 94720
- The Energy Biosciences Institute; The University of California; Berkeley California 94720
| |
Collapse
|
152
|
Gawand P, Mahadevan R. EngineeringEscherichia colifor D-Ribose Production from Glucose-Xylose Mixtures. Ind Biotechnol (New Rochelle N Y) 2014. [DOI: 10.1089/ind.2013.0028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Pratish Gawand
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Canada
- Institute of Biomaterials and Biomedical Engineering, University of Toronto, Canada
| |
Collapse
|
153
|
Royce LA, Boggess E, Fu Y, Liu P, Shanks JV, Dickerson J, Jarboe LR. Transcriptomic analysis of carboxylic acid challenge in Escherichia coli: beyond membrane damage. PLoS One 2014; 9:e89580. [PMID: 24586888 PMCID: PMC3938484 DOI: 10.1371/journal.pone.0089580] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 01/21/2014] [Indexed: 11/18/2022] Open
Abstract
Carboxylic acids are an attractive biorenewable chemical. Enormous progress has been made in engineering microbes for production of these compounds though titers remain lower than desired. Here we used transcriptome analysis of Escherichia coli during exogenous challenge with octanoic acid (C8) at pH 7.0 to probe mechanisms of toxicity. This analysis highlights the intracellular acidification and membrane damage caused by C8 challenge. Network component analysis identified transcription factors with altered activity including GadE, the activator of the glutamate-dependent acid resistance system (AR2) and Lrp, the amino acid biosynthesis regulator. The intracellular acidification was quantified during exogenous challenge, but was not observed in a carboxylic acid producing strain, though this may be due to lower titers than those used in our exogenous challenge studies. We developed a framework for predicting the proton motive force during adaptation to strong inorganic acids and carboxylic acids. This model predicts that inorganic acid challenge is mitigated by cation accumulation, but that carboxylic acid challenge inverts the proton motive force and requires anion accumulation. Utilization of native acid resistance systems was not useful in terms of supporting growth or alleviating intracellular acidification. AR2 was found to be non-functional, possibly due to membrane damage. We proposed that interaction of Lrp and C8 resulted in repression of amino acid biosynthesis. However, this hypothesis was not supported by perturbation of lrp expression or amino acid supplementation. E. coli strains were also engineered for altered cyclopropane fatty acid content in the membrane, which had a dramatic effect on membrane properties, though C8 tolerance was not increased. We conclude that achieving higher production titers requires circumventing the membrane damage. As higher titers are achieved, acidification may become problematic.
Collapse
Affiliation(s)
- Liam A. Royce
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, United States of America
| | - Erin Boggess
- Department of Electrical and Computer Engineering, Iowa State University, Ames, Iowa, United States of America
| | - Yao Fu
- Department of Electrical and Computer Engineering, Iowa State University, Ames, Iowa, United States of America
| | - Ping Liu
- Interdepartmental Microbiology Program, Iowa State University, Ames, Iowa, United States of America
| | - Jacqueline V. Shanks
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, United States of America
| | - Julie Dickerson
- Department of Electrical and Computer Engineering, Iowa State University, Ames, Iowa, United States of America
| | - Laura R. Jarboe
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa, United States of America
- Interdepartmental Microbiology Program, Iowa State University, Ames, Iowa, United States of America
- * E-mail:
| |
Collapse
|
154
|
Glebes TY, Sandoval NR, Reeder PJ, Schilling KD, Zhang M, Gill RT. Genome-wide mapping of furfural tolerance genes in Escherichia coli. PLoS One 2014; 9:e87540. [PMID: 24489935 PMCID: PMC3905028 DOI: 10.1371/journal.pone.0087540] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 12/30/2013] [Indexed: 11/19/2022] Open
Abstract
Advances in genomics have improved the ability to map complex genotype-to-phenotype relationships, like those required for engineering chemical tolerance. Here, we have applied the multiSCale Analysis of Library Enrichments (SCALEs; Lynch et al. (2007) Nat. Method.) approach to map, in parallel, the effect of increased dosage for >10(5) different fragments of the Escherichia coli genome onto furfural tolerance (furfural is a key toxin of lignocellulosic hydrolysate). Only 268 of >4,000 E. coli genes (∼ 6%) were enriched after growth selections in the presence of furfural. Several of the enriched genes were cloned and tested individually for their effect on furfural tolerance. Overexpression of thyA, lpcA, or groESL individually increased growth in the presence of furfural. Overexpression of lpcA, but not groESL or thyA, resulted in increased furfural reduction rate, a previously identified mechanism underlying furfural tolerance. We additionally show that plasmid-based expression of functional LpcA or GroESL is required to confer furfural tolerance. This study identifies new furfural tolerant genes, which can be applied in future strain design efforts focused on the production of fuels and chemicals from lignocellulosic hydrolysate.
Collapse
Affiliation(s)
- Tirzah Y. Glebes
- Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Nicholas R. Sandoval
- Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Philippa J. Reeder
- Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Katherine D. Schilling
- Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Min Zhang
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, Colorado, United States of America
| | - Ryan T. Gill
- Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado, United States of America
- * E-mail:
| |
Collapse
|
155
|
Liu Y, Ashok S, Seol E, Bao J, Park S. Comparison of three Pediococcus strains for lactic acid production from glucose in the presence of inhibitors generated by acid hydrolysis of lignocellulosic biomass. BIOTECHNOL BIOPROC E 2014. [DOI: 10.1007/s12257-013-0360-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
156
|
Yang S, Franden MA, Brown SD, Chou YC, Pienkos PT, Zhang M. Insights into acetate toxicity in Zymomonas mobilis 8b using different substrates. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:140. [PMID: 25298783 PMCID: PMC4189746 DOI: 10.1186/s13068-014-0140-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 09/11/2014] [Indexed: 05/19/2023]
Abstract
BACKGROUND Lignocellulosic biomass is a promising renewable feedstock for biofuel production. Acetate is one of the major inhibitors liberated from hemicelluloses during hydrolysis. An understanding of the toxic effects of acetate on the fermentation microorganism and the efficient utilization of mixed sugars of glucose and xylose in the presence of hydrolysate inhibitors is crucial for economic biofuel production. RESULTS A new microarray was designed including both coding sequences and intergenic regions to investigate the acetate stress responses of Zymomonas mobilis 8b when using single carbon sources of glucose or xylose, or mixed sugars of both glucose and xylose. With the supplementation of exogenous acetate, 8b can utilize all the glucose with a similar ethanol yield, although the growth, final biomass, and ethanol production rate were reduced. However, xylose utilization was inhibited in both media containing xylose or a mixed sugar of glucose and xylose, although the performance of 8b was better in mixed sugar than xylose-only media. The presence of acetate caused genes related to biosynthesis, the flagellar system, and glycolysis to be downregulated, and genes related to stress responses and energy metabolism to be upregulated. Unexpectedly, xylose seems to pose more stress on 8b, recruiting more genes for xylose utilization, than does acetate. Several gene candidates based on transcriptome results were selected for genetic manipulation, and a TonB-dependent receptor knockout mutant was confirmed to have a slight advantage regarding acetate tolerance. CONCLUSIONS Our results indicate Z. mobilis utilized a different mechanism for xylose utilization, with an even more severe impact on Z. mobilis than that caused by acetate treatment. Our study also suggests redox imbalance caused by stressful conditions may trigger a metabolic reaction leading to the accumulation of toxic intermediates such as xylitol, but Z. mobilis manages its carbon and energy metabolism through the control of individual reactions to mitigate the stressful conditions. We have thus provided extensive transcriptomic datasets and gained insights into the molecular responses of Z. mobilis to the inhibitor acetate when grown in different sugar sources, which will facilitate future metabolic modeling studies and strain improvement efforts for better xylose utilization and acetate tolerance.
Collapse
Affiliation(s)
- Shihui Yang
- />National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Mary Ann Franden
- />National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Steven D Brown
- />Biosciences Division, Oak Ridge, TN 37831 USA
- />BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Yat-Chen Chou
- />National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Philip T Pienkos
- />National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Min Zhang
- />National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| |
Collapse
|
157
|
Clarkson SM, Hamilton-Brehm SD, Giannone RJ, Engle NL, Tschaplinski TJ, Hettich RL, Elkins JG. A comparative multidimensional LC-MS proteomic analysis reveals mechanisms for furan aldehyde detoxification in Thermoanaerobacter pseudethanolicus 39E. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:165. [PMID: 25506391 PMCID: PMC4265447 DOI: 10.1186/s13068-014-0165-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 11/07/2014] [Indexed: 05/07/2023]
Abstract
BACKGROUND Chemical and physical pretreatment of lignocellulosic biomass improves substrate reactivity for increased microbial biofuel production, but also restricts growth via the release of furan aldehydes, such as furfural and 5-hydroxymethylfurfural (5-HMF). The physiological effects of these inhibitors on thermophilic, fermentative bacteria are important to understand; especially as cellulolytic strains are being developed for consolidated bioprocessing (CBP) of lignocellulosic feedstocks. Identifying mechanisms for detoxification of aldehydes in naturally resistant strains, such as Thermoanaerobacter spp., may also enable improvements in candidate CBP microorganisms. RESULTS Thermoanaerobacter pseudethanolicus 39E, an anaerobic, saccharolytic thermophile, was found to grow readily in the presence of 30 mM furfural and 20 mM 5-HMF and reduce these aldehydes to their respective alcohols in situ. The proteomes of T. pseudethanolicus 39E grown in the presence or absence of 15 mM furfural were compared to identify upregulated enzymes potentially responsible for the observed reduction. A total of 225 proteins were differentially regulated in response to the 15 mM furfural treatment with 152 upregulated versus 73 downregulated. Only 87 proteins exhibited a twofold or greater change in abundance in either direction. Of these, 54 were upregulated in the presence of furfural and 33 were downregulated. Two oxidoreductases were upregulated at least twofold by furfural and were targeted for further investigation. Teth39_1597 encodes a predicted butanol dehydrogenase (BdhA) and Teth39_1598, a predicted aldo/keto reductase (AKR). Both genes were cloned from T. pseudethanolicus 39E, with the respective enzymes overexpressed in E. coli and specific activities determined against a variety of aldehydes. Overexpressed BdhA showed significant activity with all aldehydes tested, including furfural and 5-HMF, using NADPH as the cofactor. Cell extracts with AKR also showed activity with NADPH, but only with four-carbon butyraldehyde and isobutyraldehyde. CONCLUSIONS T. pseudethanolicus 39E displays intrinsic tolerance to the common pretreatment inhibitors furfural and 5-HMF. Multidimensional proteomic analysis was used as an effective tool to identify putative mechanisms for detoxification of furfural and 5-HMF. T. pseudethanolicus was found to upregulate an NADPH-dependent alcohol dehydrogenase 6.8-fold in response to furfural. In vitro enzyme assays confirmed the reduction of furfural and 5-HMF to their respective alcohols.
Collapse
Affiliation(s)
- Sonya M Clarkson
- />BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6341 USA
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6341 USA
| | - Scott D Hamilton-Brehm
- />BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6341 USA
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6341 USA
- />Current address: Division of Earth and Ecosystem Sciences, Desert Research Institute, Las Vegas, NV USA
| | - Richard J Giannone
- />BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6341 USA
- />Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6341 USA
| | - Nancy L Engle
- />BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6341 USA
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6341 USA
| | - Timothy J Tschaplinski
- />BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6341 USA
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6341 USA
| | - Robert L Hettich
- />BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6341 USA
- />Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6341 USA
| | - James G Elkins
- />BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6341 USA
- />Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6341 USA
| |
Collapse
|
158
|
Xiao H, Zhao H. Genome-wide RNAi screen reveals the E3 SUMO-protein ligase gene SIZ1 as a novel determinant of furfural tolerance in Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:78. [PMID: 24904688 PMCID: PMC4045865 DOI: 10.1186/1754-6834-7-78] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 05/12/2014] [Indexed: 05/15/2023]
Abstract
BACKGROUND Furfural is a major growth inhibitor in lignocellulosic hydrolysates and improving furfural tolerance of microorganisms is critical for rapid and efficient fermentation of lignocellulosic biomass. In this study, we used the RNAi-Assisted Genome Evolution (RAGE) method to select for furfural resistant mutants of Saccharomyces cerevisiae, and identified a new determinant of furfural tolerance. RESULTS By using a genome-wide RNAi (RNA-interference) screen in S. cerevisiae for genes involved in furfural tolerance, we identified SIZ1, a gene encoding an E3 SUMO-protein ligase. Disruption of SIZ1 gene function by knockdown or deletion conferred significantly higher furfural tolerance compared to other previously reported metabolic engineering strategies in S. cerevisiae. This improved furfural tolerance of siz1Δ cells is accompanied by rapid furfural reduction to furfuryl alcohol and leads to higher ethanol productivity in the presence of furfural. In addition, the siz1Δ mutant also exhibited tolerance towards oxidative stress, suggesting that oxidative stress tolerance related proteins may be under the SUMO regulation of SIZ1p and responsible for furfural tolerance. CONCLUSIONS Using a genome-wide approach, we identified a novel determinant for furfural tolerance, providing valuable insights into the design of recombinant microbes for efficient lignocellulose fermentation.
Collapse
Affiliation(s)
- Han Xiao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Departments of Chemistry, Biochemistry, and Bioengineering, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| |
Collapse
|
159
|
Chen X, Zhou L, Tian K, Kumar A, Singh S, Prior BA, Wang Z. Metabolic engineering of Escherichia coli: A sustainable industrial platform for bio-based chemical production. Biotechnol Adv 2013; 31:1200-23. [DOI: 10.1016/j.biotechadv.2013.02.009] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 02/04/2013] [Accepted: 02/25/2013] [Indexed: 12/20/2022]
|
160
|
Peng L, Wang L, Che C, Yang G, Yu B, Ma Y. Bacillus sp. strain P38: an efficient producer of L-lactate from cellulosic hydrolysate, with high tolerance for 2-furfural. BIORESOURCE TECHNOLOGY 2013; 149:169-76. [PMID: 24096283 DOI: 10.1016/j.biortech.2013.09.047] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 09/09/2013] [Accepted: 09/11/2013] [Indexed: 05/13/2023]
Abstract
In this study, efficient polymer-grade L-lactic acid production was achieved with the strain Bacillus sp. P38 by using cellulosic hydrolysate as the sole carbon source. In fed-batch fermentation, 180 g L(-1)L-lactic acid was obtained with a volumetric productivity of 2.4 g L(-1)h(-1) and a yield of 0.96 g g(-1) total reducing sugars. No D-isomer of lactic acid was detected in the broth. Strain P38 tolerated up to 10 g L(-1) 2-furfural, and lactate production was sharply inhibited only when the 2-furfural concentration was higher than 6 g L(-1). Moreover, strain P38 also tolerated high concentrations (>6 g L(-1)) of other fermentation inhibitors in cellulosic hydrolysate, such as vanillin and acetic acid, although it was slightly sensitive to formic acid. The efficient L-lactic acid production, combined with high inhibitor tolerance and efficient pentose utilization, indicate that Bacillus sp. P38 is a promising producer of polymer-grade L-lactic acid from cellulosic biomass.
Collapse
Affiliation(s)
- Lili Peng
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; College of Life Science, Qufu Normal University, Qufu 273165, China
| | | | | | | | | | | |
Collapse
|
161
|
Pflügl S, Marx H, Mattanovich D, Sauer M. Heading for an economic industrial upgrading of crude glycerol from biodiesel production to 1,3-propanediol by Lactobacillus diolivorans. BIORESOURCE TECHNOLOGY 2013; 152:499-504. [PMID: 24333679 DOI: 10.1016/j.biortech.2013.11.041] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 11/11/2013] [Accepted: 11/14/2013] [Indexed: 06/03/2023]
Abstract
Lactobacillus diolivorans was evaluated as a potential organism for production of 1,3-propanediol under industrially relevant conditions. Crude glycerol of different origins has been tested and showed no inhibitory effects on growth or production. Using crude glycerol from biodiesel production from palm oil 85 g/l 1,3-propanediol have been obtained with a productivity of 0.45 g/lh in a fed-batch cultivation. Sugar necessary for the formation of biomass was replaced with a hydrolysate from lignocellulosic material resulting in 75 g/l 1,3-propanediol and a productivity of 0.36 g/lh. Lignocellulosic hydrolysate contained the potential inhibitors furfural and 5-hydroxymethylfurfural at concentrations of 0.7 and 0.3 g/l, respectively. Addition of furfural and 5-hydroxymethylfurfural to batch cultures in said concentrations did not show inhibitory effects on growth or 1,3-propanediol production.
Collapse
Affiliation(s)
- Stefan Pflügl
- School of Bioengineering, FH Campus Wien - University of Applied Sciences, Muthgasse 62, 1190 Vienna, Austria; Department of Biotechnology, BOKU - VIBT University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Hans Marx
- Department of Biotechnology, BOKU - VIBT University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria.
| | - Diethard Mattanovich
- Department of Biotechnology, BOKU - VIBT University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria; Austrian Centre of Industrial Biotechnology (ACIB GmbH), Muthgasse 11, 1190 Vienna, Austria
| | - Michael Sauer
- Department of Biotechnology, BOKU - VIBT University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria; Austrian Centre of Industrial Biotechnology (ACIB GmbH), Muthgasse 11, 1190 Vienna, Austria
| |
Collapse
|
162
|
Ertas M, Han Q, Jameel H, Chang HM. Enzymatic hydrolysis of autohydrolyzed wheat straw followed by refining to produce fermentable sugars. BIORESOURCE TECHNOLOGY 2013; 152:259-66. [PMID: 24300844 DOI: 10.1016/j.biortech.2013.11.026] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 11/07/2013] [Accepted: 11/10/2013] [Indexed: 05/23/2023]
Abstract
Wheat straw was pretreated using an autohydrolysis process with different temperatures (160-200 °C) and times (10-20 min) in order to allow the recovery of hemicellulose in the filtrate and help open up the structure of the biomass for improved accessibility of enzymes during enzymatic hydrolysis. Autohydrolysis at 190 °C for 10 min provided the highest overall sugar (12.2/100g raw wheat straw) in the autohydrolysis filtrate and recovered 62.3% of solid residue. Before enzymatic hydrolysis, the pulps obtained from each pretreatment condition were subjected to a refining post-treatment to improve enzyme accessibility. Enzymatic hydrolysis was performed for all the pretreated solids with and without refining post-treatment at the enzyme loadings of 4 and 10 FPU/g oven dry substrate for 96 h. A total of 30.4 g sugars can be recovered from 100g wheat straw at 180 °C for 20 min with 4 FPU/g enzyme charge.
Collapse
Affiliation(s)
- Murat Ertas
- Department of Forest Industry Engineering, Bursa Technical University, 16200 Bursa, Turkey.
| | - Qiang Han
- Department of Forest Biomaterials, North Carolina State University, Campus Box 8005, Raleigh, NC 27695-8005, USA
| | - Hasan Jameel
- Department of Forest Biomaterials, North Carolina State University, Campus Box 8005, Raleigh, NC 27695-8005, USA
| | - Hou-min Chang
- Department of Forest Biomaterials, North Carolina State University, Campus Box 8005, Raleigh, NC 27695-8005, USA
| |
Collapse
|
163
|
Zingaro KA, Nicolaou SA, Papoutsakis ET. Dissecting the assays to assess microbial tolerance to toxic chemicals in bioprocessing. Trends Biotechnol 2013; 31:643-53. [DOI: 10.1016/j.tibtech.2013.08.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 08/14/2013] [Accepted: 08/19/2013] [Indexed: 11/15/2022]
|
164
|
Garst A, Lynch M, Evans R, Gill RT. Strategies for the multiplex mapping of genes to traits. Microb Cell Fact 2013; 12:99. [PMID: 24171944 PMCID: PMC3842685 DOI: 10.1186/1475-2859-12-99] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 10/20/2013] [Indexed: 12/19/2022] Open
Abstract
Rewiring and optimization of metabolic networks to enable the production of commercially valuable chemicals is a central goal of metabolic engineering. This prospect is challenged by the complexity of metabolic networks, lack of complete knowledge of gene function(s), and the vast combinatorial genotype space that is available for exploration and optimization. Various approaches have thus been developed to aid in the efficient identification of genes that contribute to a variety of different phenotypes, allowing more rapid design and engineering of traits desired for industrial applications. This review will highlight recent technologies that have enhanced capabilities to map genotype-phenotype relationships on a genome wide scale and emphasize how such approaches enable more efficient design and engineering of complex phenotypes.
Collapse
Affiliation(s)
| | | | | | - Ryan T Gill
- Department of Chemical and Biological Engineering, University of Colorado, Campus Box 592, Boulder, CO 80303, USA.
| |
Collapse
|
165
|
Zeng Y, Zhao S, Yang S, Ding SY. Lignin plays a negative role in the biochemical process for producing lignocellulosic biofuels. Curr Opin Biotechnol 2013; 27:38-45. [PMID: 24863895 DOI: 10.1016/j.copbio.2013.09.008] [Citation(s) in RCA: 213] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 09/25/2013] [Indexed: 10/26/2022]
Abstract
A biochemical platform holds the most promising route toward lignocellulosic biofuels, in which polysaccharides are hydrolyzed by cellulase enzymes into simple sugars and fermented to ethanol by microbes. However, these polysaccharides are cross-linked in the plant cell walls with the hydrophobic network of lignin that physically impedes enzymatic deconstruction. A thermochemical pretreatment process is often required to remove or delocalize lignin, which may also generate inhibitors that hamper enzymatic hydrolysis and fermentation. Here we review recent advances in understanding lignin structure in the plant cell walls and the negative roles of lignin in the processes of converting biomass to biofuels. Perspectives and future directions to improve the biomass conversion process are also discussed.
Collapse
Affiliation(s)
- Yining Zeng
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Shuai Zhao
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Shihui Yang
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Shi-You Ding
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA.
| |
Collapse
|
166
|
Chong H, Yeow J, Wang I, Song H, Jiang R. Improving acetate tolerance of Escherichia coli by rewiring its global regulator cAMP receptor protein (CRP). PLoS One 2013; 8:e77422. [PMID: 24124618 PMCID: PMC3790751 DOI: 10.1371/journal.pone.0077422] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 09/10/2013] [Indexed: 11/18/2022] Open
Abstract
The presence of acetate exceeding 5 g/L is a major concern during E. coli fermentation due to its inhibitory effect on cell growth, thereby limiting high-density cell culture and recombinant protein production. Hence, engineered E. coli strains with enhanced acetate tolerance would be valuable for these bioprocesses. In this work, the acetate tolerance of E. coli was much improved by rewiring its global regulator cAMP receptor protein (CRP), which is reported to regulate 444 genes. Error-prone PCR method was employed to modify crp and the mutagenesis libraries (~3×10(6)) were subjected to M9 minimal medium supplemented with 5-10 g/L sodium acetate for selection. Mutant A2 (D138Y) was isolated and its growth rate in 15 g/L sodium acetate was found to be 0.083 h(-1), much higher than that of the control (0.016 h(-1)). Real-time PCR analysis via OpenArray(®) system revealed that over 400 CRP-regulated genes were differentially expressed in A2 with or without acetate stress, including those involved in the TCA cycle, phosphotransferase system, etc. Eight genes were chosen for overexpression and the overexpression of uxaB was found to lead to E. coli acetate sensitivity.
Collapse
Affiliation(s)
- Huiqing Chong
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, Singapore
| | | | - Ivy Wang
- Life Technologies R&D, Singapore, Singapore
| | - Hao Song
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, Singapore
| | - Rongrong Jiang
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, Singapore
- * E-mail:
| |
Collapse
|
167
|
Domestication and Screening of Saccharomyces Cerevisiae Strain Resistant to Inhibitors in Lignocellulosic Hydrolysates by Acclimatizing Inhibitory. ACTA ACUST UNITED AC 2013. [DOI: 10.4028/www.scientific.net/amm.448-453.1581] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In order to find the strains which can produce high ethanol yield as well as tolerate inhibitors on the lignocellulosic hydrolysates for developing the renewable bioenergy, the sepecial yeast must be explored. After acclimatizing 23 days and using five different acclimation media with sequential increase in the concentration of inhibitory compounds , a kind ofsaccharomyces cerevisiaestrain resistant to inhibitors was obtained . When the yeast resistant to drug and the parent strain grew in the same media which contained several inhibitory compounds 3.2 g/L acetic acid , 0.8 g/L furfural , 0.4 g/L formic acid , the new yeasts maximal ethanol yield can reach 0.428 g/g , up to 85.6% of theoretical ethanol yield. Compared with drug resistant yeast , the parent strains maximal ethanol production yield only can reach 0.246 g/g , up to 52.8% of theoretical ethanol yield . After 5 continuous ages , the average ability of producing ethanol was stable. Compared with parent strain, the yeast resistant to drug had good ability to ferment glucose and produce ethanol as well as tolerate inhibitors .The new yeast has extensive application prospect in the bioethanol production.
Collapse
|
168
|
Chin WC, Lin KH, Chang JJ, Huang CC. Improvement of n-butanol tolerance in Escherichia coli by membrane-targeted tilapia metallothionein. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:130. [PMID: 24020941 PMCID: PMC3848587 DOI: 10.1186/1754-6834-6-130] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 09/04/2013] [Indexed: 05/03/2023]
Abstract
BACKGROUND Though n-butanol has been proposed as a potential transportation biofuel, its toxicity often causes oxidative stress in the host microorganism and is considered one of the bottlenecks preventing its efficient mass production. RESULTS To relieve the oxidative stress in the host cell, metallothioneins (MTs), which are known as scavengers for reactive oxygen species (ROS), were engineered in E. coli hosts for both cytosolic and outer-membrane-targeted (osmoregulatory membrane protein OmpC fused) expression. Metallothioneins from human (HMT), mouse (MMT), and tilapia fish (TMT) were tested. The host strain expressing membrane-targeted TMT showed the greatest ability to reduce oxidative stresses induced by n-butanol, ethanol, furfural, hydroxymethylfurfural, and nickel. The same strain also allowed for an increased growth rate of recombinant E. coli under n-butanol stress. Further experiments indicated that the TMT-fused OmpC protein could not only function in ROS scavenging but also regulate either glycine betaine (GB) or glucose uptake via osmosis, and the dual functional fusion protein could contribute in an enhancement of the host microorganism's growth rate. CONCLUSIONS The abilities of scavenging intracellular or extracellular ROS by these engineering E. coli were examined, and TMT show the best ability among three MTs. Additionally, the membrane-targeted fusion protein, OmpC-TMT, improved host tolerance up to 1.5% n-butanol above that of TMT which is only 1%. These results presented indicate potential novel approaches for engineering stress tolerant microorganism strains.
Collapse
Affiliation(s)
- Wei-Chih Chin
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Kuo-Hsing Lin
- Vaccine Research and Development Center, National Institute of Infectious Disease and Vaccinology, NHRI, Miaoli, Taiwan
| | - Jui-Jen Chang
- Department of Medical Research, China Medical University Hospital, Taichung 402, Taiwan
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Chieh-Chen Huang
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan
| |
Collapse
|
169
|
Jarboe LR, Royce LA, Liu P. Understanding biocatalyst inhibition by carboxylic acids. Front Microbiol 2013; 4:272. [PMID: 24027566 PMCID: PMC3760142 DOI: 10.3389/fmicb.2013.00272] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 08/20/2013] [Indexed: 11/13/2022] Open
Abstract
Carboxylic acids are an attractive biorenewable chemical in terms of their flexibility and usage as precursors for a variety of industrial chemicals. It has been demonstrated that such carboxylic acids can be fermentatively produced using engineered microbes, such as Escherichia coli and Saccharomyces cerevisiae. However, like many other attractive biorenewable fuels and chemicals, carboxylic acids become inhibitory to these microbes at concentrations below the desired yield and titer. In fact, their potency as microbial inhibitors is highlighted by the fact that many of these carboxylic acids are routinely used as food preservatives. This review highlights the current knowledge regarding the impact that saturated, straight-chain carboxylic acids, such as hexanoic, octanoic, decanoic, and lauric acids can have on E. coli and S. cerevisiae, with the goal of identifying metabolic engineering strategies to increase robustness. Key effects of these carboxylic acids include damage to the cell membrane and a decrease of the microbial internal pH. Certain changes in cell membrane properties, such as composition, fluidity, integrity, and hydrophobicity, and intracellular pH are often associated with increased tolerance. The availability of appropriate exporters, such as Pdr12, can also increase tolerance. The effect on metabolic processes, such as maintaining appropriate respiratory function, regulation of Lrp activity and inhibition of production of key metabolites such as methionine, are also considered. Understanding the mechanisms of biocatalyst inhibition by these desirable products can aid in the engineering of robust strains with improved industrial performance.
Collapse
Affiliation(s)
- Laura R Jarboe
- Department of Chemical and Biological Engineering, Iowa State University Ames, IA, USA ; Department of Microbiology, Iowa State University Ames, IA, USA
| | | | | |
Collapse
|
170
|
Royce LA, Liu P, Stebbins MJ, Hanson BC, Jarboe LR. The damaging effects of short chain fatty acids on Escherichia coli membranes. Appl Microbiol Biotechnol 2013; 97:8317-27. [PMID: 23912117 PMCID: PMC3757260 DOI: 10.1007/s00253-013-5113-5] [Citation(s) in RCA: 134] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 07/08/2013] [Accepted: 07/09/2013] [Indexed: 12/19/2022]
Abstract
Carboxylic acids are an attractive biorenewable chemical. However, like many other fermentatively produced compounds, they are inhibitory to the biocatalyst. An understanding of the mechanism of toxicity can aid in mitigating this problem. Here, we show that hexanoic and octanoic acids are completely inhibitory to Escherichia coli MG1655 in minimal medium at a concentration of 40 mM, while decanoic acid was inhibitory at 20 mM. This growth inhibition is pH-dependent and is accompanied by a significant change in the fluorescence polarization (fluidity) and integrity. This inhibition and sensitivity to membrane fluidization, but not to damage of membrane integrity, can be at least partially mitigated during short-term adaptation to octanoic acid. This short-term adaptation was accompanied by a change in membrane lipid composition and a decrease in cell surface hydrophobicity. Specifically, the saturated/unsaturated lipid ratio decreased and the average lipid length increased. A fatty acid-producing strain exhibited an increase in membrane leakage as the product titer increased, but no change in membrane fluidity. These results highlight the importance of the cell membrane as a target for future metabolic engineering efforts for enabling resistance and tolerance of desirable biorenewable compounds, such as carboxylic acids. Knowledge of these effects can help in the engineering of robust biocatalysts for biorenewable chemicals production.
Collapse
Affiliation(s)
- Liam A. Royce
- Department of Chemical and Biological Engineering, Iowa State University, 3051 Sweeney Hall, Ames, IA 50011 USA
| | - Ping Liu
- Interdepartmental Microbiology Program, Iowa State University, Ames, IA 50011 USA
| | - Matthew J. Stebbins
- Department of Chemical and Biological Engineering, Iowa State University, 3051 Sweeney Hall, Ames, IA 50011 USA
| | - Benjamin C. Hanson
- Department of Chemical and Biological Engineering, Iowa State University, 3051 Sweeney Hall, Ames, IA 50011 USA
| | - Laura R. Jarboe
- Department of Chemical and Biological Engineering, Iowa State University, 3051 Sweeney Hall, Ames, IA 50011 USA
- Interdepartmental Microbiology Program, Iowa State University, Ames, IA 50011 USA
| |
Collapse
|
171
|
Sànchez i Nogué V, Narayanan V, Gorwa-Grauslund MF. Short-term adaptation improves the fermentation performance of Saccharomyces cerevisiae in the presence of acetic acid at low pH. Appl Microbiol Biotechnol 2013; 97:7517-25. [PMID: 23872959 PMCID: PMC3724974 DOI: 10.1007/s00253-013-5093-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 06/28/2013] [Accepted: 06/30/2013] [Indexed: 12/01/2022]
Abstract
The release of acetic acid due to deacetylation of the hemicellulose fraction during the treatment of lignocellulosic biomass contributes to the inhibitory character of the generated hydrolysates. In the present study, we identified a strain-independent adaptation protocol consisting of pre-cultivating the strain at pH 5.0 in the presence of at least 4 g L−1 acetic acid that enabled aerobic growth and improved fermentation performance of Saccharomyces cerevisiae cells at low pH (3.7) and in the presence of inhibitory levels of acetic acid (6 g L−1). During anaerobic cultivation with adapted cells of strain TMB3500, the specific ethanol production rate was increased, reducing the fermentation time to 48 %.
Collapse
Affiliation(s)
- Violeta Sànchez i Nogué
- Division of Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, SE 22100 Lund, Sweden
| | | | | |
Collapse
|
172
|
Franden MA, Pilath HM, Mohagheghi A, Pienkos PT, Zhang M. Inhibition of growth of Zymomonas mobilis by model compounds found in lignocellulosic hydrolysates. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:99. [PMID: 23837621 PMCID: PMC3716709 DOI: 10.1186/1754-6834-6-99] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 06/24/2013] [Indexed: 05/18/2023]
Abstract
BACKGROUND During the pretreatment of biomass feedstocks and subsequent conditioning prior to saccharification, many toxic compounds are produced or introduced which inhibit microbial growth and in many cases, production of ethanol. An understanding of the toxic effects of compounds found in hydrolysate is critical to improving sugar utilization and ethanol yields in the fermentation process. In this study, we established a useful tool for surveying hydrolysate toxicity by measuring growth rates in the presence of toxic compounds, and examined the effects of selected model inhibitors of aldehydes, organic and inorganic acids (along with various cations), and alcohols on growth of Zymomonas mobilis 8b (a ZM4 derivative) using glucose or xylose as the carbon source. RESULTS Toxicity strongly correlated to hydrophobicity in Z. mobilis, which has been observed in Escherichia coli and Saccharomyces cerevisiae for aldehydes and with some exceptions, organic acids. We observed Z. mobilis 8b to be more tolerant to organic acids than previously reported, although the carbon source and growth conditions play a role in tolerance. Growth in xylose was profoundly inhibited by monocarboxylic organic acids compared to growth in glucose, whereas dicarboxylic acids demonstrated little or no effects on growth rate in either substrate. Furthermore, cations can be ranked in order of their toxicity, Ca++ > > Na+ > NH4+ > K+. HMF (5-hydroxymethylfurfural), furfural and acetate, which were observed to contribute to inhibition of Z. mobilis growth in dilute acid pretreated corn stover hydrolysate, do not interact in a synergistic manner in combination. We provide further evidence that Z. mobilis 8b is capable of converting the aldehydes furfural, vanillin, 4-hydroxybenzaldehyde and to some extent syringaldehyde to their alcohol forms (furfuryl, vanillyl, 4-hydroxybenzyl and syringyl alcohol) during fermentation. CONCLUSIONS Several key findings in this report provide a mechanism for predicting toxic contributions of inhibitory components of hydrolysate and provide guidance for potential process development, along with potential future strain improvement and tolerance strategies.
Collapse
Affiliation(s)
- Mary Ann Franden
- National Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
| | - Heidi M Pilath
- National Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
| | - Ali Mohagheghi
- National Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
| | - Philip T Pienkos
- National Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
| | - Min Zhang
- National Bioenergy Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA
| |
Collapse
|
173
|
Ibraheem O, Ndimba BK. Molecular adaptation mechanisms employed by ethanologenic bacteria in response to lignocellulose-derived inhibitory compounds. Int J Biol Sci 2013; 9:598-612. [PMID: 23847442 PMCID: PMC3708040 DOI: 10.7150/ijbs.6091] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 04/26/2013] [Indexed: 11/12/2022] Open
Abstract
Current international interest in finding alternative sources of energy to the diminishing supplies of fossil fuels has encouraged research efforts in improving biofuel production technologies. In countries which lack sufficient food, the use of sustainable lignocellulosic feedstocks, for the production of bioethanol, is an attractive option. In the pre-treatment of lignocellulosic feedstocks for ethanol production, various chemicals and/or enzymatic processes are employed. These methods generally result in a range of fermentable sugars, which are subjected to microbial fermentation and distillation to produce bioethanol. However, these methods also produce compounds that are inhibitory to the microbial fermentation process. These compounds include products of sugar dehydration and lignin depolymerisation, such as organic acids, derivatised furaldehydes and phenolic acids. These compounds are known to have a severe negative impact on the ethanologenic microorganisms involved in the fermentation process by compromising the integrity of their cell membranes, inhibiting essential enzymes and negatively interact with their DNA/RNA. It is therefore important to understand the molecular mechanisms of these inhibitions, and the mechanisms by which these microorganisms show increased adaptation to such inhibitors. Presented here is a concise overview of the molecular adaptation mechanisms of ethanologenic bacteria in response to lignocellulose-derived inhibitory compounds. These include general stress response and tolerance mechanisms, which are typically those that maintain intracellular pH homeostasis and cell membrane integrity, activation/regulation of global stress responses and inhibitor substrate-specific degradation pathways. We anticipate that understanding these adaptation responses will be essential in the design of 'intelligent' metabolic engineering strategies for the generation of hyper-tolerant fermentation bacteria strains.
Collapse
Affiliation(s)
- Omodele Ibraheem
- Research and Services Unit, Agricultural Research Council/Infruitech & The University of Western Cape, Biotechnology Department, Private Bag X17, Bellville, Cape Town, South Africa
| | | |
Collapse
|
174
|
Lee JS, Chi WJ, Hong SK, Yang JW, Chang YK. Bioethanol production by heterologous expression of Pdc and AdhII in Streptomyces lividans. Appl Microbiol Biotechnol 2013; 97:6089-97. [PMID: 23681589 DOI: 10.1007/s00253-013-4951-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Revised: 04/22/2013] [Accepted: 04/24/2013] [Indexed: 11/24/2022]
Abstract
Two genes from Zymomonas mobilis that are responsible for ethanol production, pyruvate decarboxylase (pdc) and alcohol dehydrogenase II (adhII), were heterologously expressed in the Gram-positive bacterium Streptomyces lividans TK24. An examination of carbon distribution revealed that a significant portion of carbon metabolism was switched from biomass and organic acid biosynthesis to ethanol production upon the expression of pdc and adhII. The recombinant S. lividans TK24 produced ethanol from glucose with a yield of 23.7% based on the carbohydrate consumed. The recombinant was able to produce ethanol from xylose, L-arabinose, mannose, L-rhamnose, galactose, ribose, and cellobiose with yields of 16.0, 25.6, 21.5, 33.6, 30.6, 14.6, and 33.3%, respectively. Polymeric substances such as starch and xylan were directly converted to ethanol by the recombinant with ethanol yields of 18.9 and 8.8%, respectively. The recombinant S. lividans TK24/Tpet developed in this study is potentially a useful microbial resource for ethanol production from various sources of biomasses, especially microalgae.
Collapse
Affiliation(s)
- Jae Sun Lee
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology, 373-1, Guseong-dong, Yuseong-gu, Daejeon 305-701, South Korea
| | | | | | | | | |
Collapse
|
175
|
Zhang Y, Ezeji TC. Transcriptional analysis of Clostridium beijerinckii NCIMB 8052 to elucidate role of furfural stress during acetone butanol ethanol fermentation. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:66. [PMID: 23642190 PMCID: PMC3681630 DOI: 10.1186/1754-6834-6-66] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2012] [Accepted: 04/29/2013] [Indexed: 05/04/2023]
Abstract
BACKGROUND Furfural is the prevalent microbial inhibitor generated during pretreatment and hydrolysis of lignocellulose biomass to monomeric sugars, but the response of acetone butanol ethanol (ABE) producing Clostridium beijerinckii NCIMB 8052 to this compound at the molecular level is unknown. To discern the effect of furfural on C. beijerinckii and to gain insight into molecular mechanisms of action and detoxification, physiological changes of furfural-stressed cultures during acetone butanol ethanol (ABE) fermentation were studied, and differentially expressed genes were profiled by genome-wide transcriptional analysis. RESULTS A total of 5,003 C. beijerinckii NCIMB 8052 genes capturing about 99.7% of the genome were examined. About 111 genes were differentially expressed (up- or down-regulated) by C. beijerinckii when it was challenged with furfural at acidogenic growth phase compared with 721 genes that were differentially expressed (up- or down-regulated) when C. beijerinckii was challenged with furfural at solventogenic growth phase. The differentially expressed genes include genes related to redox and cofactors, membrane transporters, carbohydrate, amino sugar and nucleotide sugar metabolisms, heat shock proteins, DNA repair, and two-component signal transduction system. While C. beijerinckii exposed to furfural stress during the acidogenic growth phase produced 13% more ABE than the unstressed control, ABE production by C. beijerinckii ceased following exposure to furfural stress during the solventogenic growth phase. CONCLUSION Genome-wide transcriptional response of C. beijerinckii to furfural stress was investigated for the first time using microarray analysis. Stresses emanating from ABE accumulation in the fermentation medium; redox balance perturbations; and repression of genes that code for the phosphotransferase system, cell motility and flagellar proteins (and combinations thereof) may have caused the premature termination of C. beijerinckii 8052 growth and ABE production following furfural challenge at the solventogenic phase.This study provides insights into basis for metabolic engineering of C. beijerinckii NCIMB 8052 for enhanced tolerance of lignocellulose-derived microbial inhibitory compounds, thereby improving bioconversion of lignocellulose biomass hydrolysates to biofuels and chemicals. Indeed, two enzymes encoded by Cbei_3974 and Cbei_3904 belonging to aldo/keto reductase (AKR) and short-chain dehydrogenase/reductase (SDR) families have been identified to be involved in furfural detoxification and tolerance.
Collapse
Affiliation(s)
- Yan Zhang
- The Ohio State University, Department of Animal Sciences and Ohio Agricultural Research and Development Center (OARDC), 305 Gerlaugh Hall, 1680 Madison Avenue, Wooster, OH 44691, USA
| | - Thaddeus Chukwuemeka Ezeji
- The Ohio State University, Department of Animal Sciences and Ohio Agricultural Research and Development Center (OARDC), 305 Gerlaugh Hall, 1680 Madison Avenue, Wooster, OH 44691, USA
| |
Collapse
|
176
|
Polysaccharide hydrolysis with engineered Escherichia coli for the production of biocommodities. ACTA ACUST UNITED AC 2013; 40:401-10. [DOI: 10.1007/s10295-013-1245-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2012] [Accepted: 02/13/2013] [Indexed: 02/06/2023]
Abstract
Abstract
Escherichia coli can ferment a broad range of sugars, including pentoses, hexoses, uronic acids, and polyols. These features make E. coli a suitable microorganism for the development of biocatalysts to be used in the production of biocommodities and biofuels by metabolic engineering. E. coli cannot directly ferment polysaccharides because it does not produce and secrete the necessary saccharolytic enzymes; however, there are many genetic tools that can be used to confer this ability on this prokaryote. The construction of saccharolytic E. coli strains will reduce costs and simplify the production process because the saccharification and fermentation can be conducted in a single reactor with a reduced concentration or absence of additional external saccharolytic enzymes. Recent advances in metabolic engineering, surface display, and excretion of hydrolytic enzymes provide a framework for developing E. coli strains for the so-called consolidated bioprocessing. This review presents the different strategies toward the development of E. coli strains that have the ability to display and secrete saccharolytic enzymes to hydrolyze different sugar-polymeric substrates and reduce the loading of saccharolytic enzymes.
Collapse
|
177
|
Improving Escherichia coli FucO for furfural tolerance by saturation mutagenesis of individual amino acid positions. Appl Environ Microbiol 2013; 79:3202-8. [PMID: 23475621 DOI: 10.1128/aem.00149-13] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Furfural is an inhibitory side product formed during the depolymerization of hemicellulose with mineral acids. In Escherichia coli, furfural tolerance can be increased by expressing the native fucO gene (encoding lactaldehyde oxidoreductase). This enzyme also catalyzes the NADH-dependent reduction of furfural to the less toxic alcohol. Saturation mutagenesis was combined with growth-based selection to isolate a mutated form of fucO that confers increased furfural tolerance. The mutation responsible, L7F, is located within the interfacial region of FucO homodimers, replacing the most abundant codon for leucine with the most abundant codon for phenylalanine. Plasmid expression of the mutant gene increased FucO activity by more than 10-fold compared to the wild-type fucO gene and doubled the rate of furfural metabolism during fermentation. No inclusion bodies were evident with either the native or the mutated gene. mRNA abundance for the wild-type and mutant fucO genes differed by less than 2-fold. The Km (furfural) for the mutant enzyme was 3-fold lower than that for the native enzyme, increasing efficiency at low substrate concentrations. The L7F mutation is located near the FucO N terminus, within the ribosomal binding region associated with translational initiation. Free-energy calculations for mRNA folding in this region (nucleotides -7 to +37) were weak for the native gene (-4.1 kcal mol(-1)) but weaker still for the fucO mutant (-1.0 to -0.1 kcal mol(-1)). The beneficial L7F mutation in FucO is proposed to increase furfural tolerance by improving gene expression and increasing enzyme effectiveness at low substrate levels.
Collapse
|
178
|
Engineering furfural tolerance in Escherichia coli improves the fermentation of lignocellulosic sugars into renewable chemicals. Proc Natl Acad Sci U S A 2013; 110:4021-6. [PMID: 23431191 DOI: 10.1073/pnas.1217958110] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Pretreatments such as dilute acid at elevated temperature are effective for the hydrolysis of pentose polymers in hemicellulose and also increase the access of enzymes to cellulose fibers. However, the fermentation of resulting syrups is hindered by minor reaction products such as furfural from pentose dehydration. To mitigate this problem, four genetic traits have been identified that increase furfural tolerance in ethanol-producing Escherichia coli LY180 (strain W derivative): increased expression of fucO, ucpA, or pntAB and deletion of yqhD. Plasmids and integrated strains were used to characterize epistatic interactions among traits and to identify the most effective combinations. Furfural resistance traits were subsequently integrated into the chromosome of LY180 to construct strain XW129 (LY180 ΔyqhD ackA::PyadC'fucO-ucpA) for ethanol. This same combination of traits was also constructed in succinate biocatalysts (Escherichia coli strain C derivatives) and found to increase furfural tolerance. Strains engineered for resistance to furfural were also more resistant to the mixture of inhibitors in hemicellulose hydrolysates, confirming the importance of furfural as an inhibitory component. With resistant biocatalysts, product yields (ethanol and succinate) from hemicellulose syrups were equal to control fermentations in laboratory media without inhibitors. The combination of genetic traits identified for the production of ethanol (strain W derivative) and succinate (strain C derivative) may prove useful for other renewable chemicals from lignocellulosic sugars.
Collapse
|
179
|
Monnappa AK, Lee S, Mitchell RJ. Sensing of plant hydrolysate-related phenolics with an aaeXAB::luxCDABE bioreporter strain of Escherichia coli. BIORESOURCE TECHNOLOGY 2013; 127:429-434. [PMID: 23138066 DOI: 10.1016/j.biortech.2012.09.086] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Revised: 08/06/2012] [Accepted: 09/21/2012] [Indexed: 06/01/2023]
Abstract
A bioluminescent Escherichia coli bioreporter strain to detect hydrolysate related phenolics was developed by cloning the aaeXAB promoter from E. coli upstream of the luxCDABE genes. E. coli str. DH5α carrying this plasmid (pDMA3) was responsive to sub-inhibitory concentrations of plant hydrolysate-related phenolics, such as ferulic and vanillic acids, responding to these compounds at concentrations as low as 9.8 and 4.9 mg/L, respectively. Experiments with a mixture of the compounds showed similar responses as with single compound tests, with a minimum detectable concentration of 19.5mg/L. Finally, tests using rice straw hydrolysates were conducted, with E. coli str. DH5α/pDMA3 showing a maximum induction of 33-fold and a minimum detectable phenolic concentration of 9.3mg/L, based upon Folin-Ciocalteu's reagent. These results demonstrate that this bioreporter maintains its sensitivity even with hydrolysate samples and that it can be potentially applied within biofuel industries to detect phenolics present within plant hydrolysates.
Collapse
Affiliation(s)
- Ajay Kalanjana Monnappa
- Dept of Nano-Bioscience and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan, South Korea
| | | | | |
Collapse
|
180
|
Varanasi P, Singh P, Arora R, Adams PD, Auer M, Simmons BA, Singh S. Understanding changes in lignin of Panicum virgatum and Eucalyptus globulus as a function of ionic liquid pretreatment. BIORESOURCE TECHNOLOGY 2012; 126:156-61. [PMID: 23073103 DOI: 10.1016/j.biortech.2012.08.070] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 08/16/2012] [Accepted: 08/18/2012] [Indexed: 05/08/2023]
Abstract
Ionic liquids (ILs) have shown great potential for the reduction of lignin in biomass after pretreatment. Although dilute acid and base pretreatments have been shown to result in pretreated biomass with substantially different lignin composition, there is scarce information on the composition of lignin of IL pretreated biomass. In this work, temperature dependent compositional changes in lignin after IL pretreatment were studied to develop a mechanistic understanding of the process. Panicum virgatum and Eucalyptus globulus were pretreated with 1-ethyl-3-methylimidazolium acetate ([C(2)mim][OAc]). Measurement of syringyl and guaiacyl ratio using pyrolysis-GC/MS and Kamlet-Taft properties of [C(2)mim][OAc] at 120 °C and 160 °C strongly suggest two different modes of IL pretreatment. Preferential breakdown of S-lignin in both eucalyptus and switchgrass at high pretreatment temperature (160 °C) and breakdown of G-lignin for eucalyptus and no preferential break down of either S- or G-lignin in switchgrass was observed at lower pretreatment temperatures (120 °C).
Collapse
Affiliation(s)
- Patanjali Varanasi
- Joint BioEnergy Institute, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Emeryville, CA, United States
| | | | | | | | | | | | | |
Collapse
|
181
|
Freitas C, Neves E, Reis A, Passarinho PC, da Silva TL. Effect of Acetic Acid on Saccharomyces Carlsbergensis ATCC 6269 Batch Ethanol Production Monitored by Flow Cytometry. Appl Biochem Biotechnol 2012; 168:1501-15. [DOI: 10.1007/s12010-012-9873-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 08/28/2012] [Indexed: 11/24/2022]
|
182
|
Fernández-Sandoval MT, Huerta-Beristain G, Trujillo-Martinez B, Bustos P, González V, Bolivar F, Gosset G, Martinez A. Laboratory metabolic evolution improves acetate tolerance and growth on acetate of ethanologenic Escherichia coli under non-aerated conditions in glucose-mineral medium. Appl Microbiol Biotechnol 2012; 96:1291-300. [DOI: 10.1007/s00253-012-4177-y] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Revised: 05/14/2012] [Accepted: 05/14/2012] [Indexed: 11/28/2022]
|
183
|
Lee S, Nam D, Jung JY, Oh MK, Sang BI, Mitchell RJ. Identification of Escherichia coli biomarkers responsive to various lignin-hydrolysate compounds. BIORESOURCE TECHNOLOGY 2012; 114:450-456. [PMID: 22445268 DOI: 10.1016/j.biortech.2012.02.085] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Revised: 02/16/2012] [Accepted: 02/17/2012] [Indexed: 05/31/2023]
Abstract
Aberrations in the growth and transcriptome of Escherichia coli str. BL21(DE3) were determined when exposed to varying concentrations of ferulic acid (0.25-1 g/L), an aromatic carboxylic acid identified within lignin-cellulose hydrolysate samples. The expression of several individual genes (aaeA, aaeB, inaA and marA) was significantly induced, i.e., more than 4-fold, and thus these genes and the heat shock response gene htpG were selected as biomarkers to monitor E. coli's responses to five additional hydrolysate-related compounds, including vanillic acid, coumaric acid, 4-hydroxybenzoic acid, ferulaldehyde and furfural. While all of the biomarkers showed dose-dependent responses to most of the compounds, expression of aaeA and aaeB showed the greatest induction (5-30-fold) for all compounds tested except furfural. Lastly, the marA, inaA and htpG genes all showed higher expression levels when the culture was exposed to spruce hydrolysate samples, demonstrating the potential use of these genes as biomarkers.
Collapse
Affiliation(s)
- Siseon Lee
- School of Nano-Bioscience and Chemical Engineering, Ulsan National Institute of Science and Technology, 100 Banyeon-ri, Eonyang-eup, Ulsan 689-805, Republic of Korea
| | | | | | | | | | | |
Collapse
|
184
|
He MX, Wu B, Shui ZX, Hu QC, Wang WG, Tan FR, Tang XY, Zhu QL, Pan K, Li Q, Su XH. Transcriptome profiling of Zymomonas mobilis under furfural stress. Appl Microbiol Biotechnol 2012; 95:189-99. [PMID: 22592554 DOI: 10.1007/s00253-012-4155-4] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Revised: 05/03/2012] [Accepted: 05/03/2012] [Indexed: 11/24/2022]
Abstract
Furfural from lignocellulosic hydrolysates is the prevalent inhibitor to microorganisms during cellulosic ethanol production, but the molecular mechanisms of tolerance to this inhibitor in Zymomonas mobilis are still unclear. In this study, genome-wide transcriptional responses to furfural were investigated in Z. mobilis using microarray analysis. We found that 433 genes were differentially expressed in response to furfural. Furfural up- or down-regulated genes related to cell wall/membrane biogenesis, metabolism, and transcription. However, furfural has a subtle negative effect on Entner-Doudoroff pathway mRNAs. Our results revealed that furfural had effects on multiple aspects of cellular metabolism at the transcriptional level and that membrane might play important roles in response to furfural. This research has provided insights into the molecular response to furfural in Z. mobilis, and it will be helpful to construct more furfural-resistant strains for cellulosic ethanol production.
Collapse
Affiliation(s)
- Ming-xiong He
- Biomass Energy Technology Research Centre, Biogas Institute of Ministry of Agriculture, Section 4-13, Renming Nanlu, Chengdu 610041, China.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
185
|
Degradation and assimilation of aromatic compounds by Corynebacterium glutamicum: another potential for applications for this bacterium? Appl Microbiol Biotechnol 2012; 95:77-89. [DOI: 10.1007/s00253-012-4139-4] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2012] [Revised: 04/24/2012] [Accepted: 04/24/2012] [Indexed: 11/26/2022]
|
186
|
Increase in furfural tolerance in ethanologenic Escherichia coli LY180 by plasmid-based expression of thyA. Appl Environ Microbiol 2012; 78:4346-52. [PMID: 22504824 DOI: 10.1128/aem.00356-12] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Furfural is an inhibitory side product formed during the depolymerization of hemicellulose by mineral acids. Genomic libraries from three different bacteria (Bacillus subtilis YB886, Escherichia coli NC3, and Zymomonas mobilis CP4) were screened for genes that conferred furfural resistance on plates. Beneficial plasmids containing the thyA gene (coding for thymidylate synthase) were recovered from all three organisms. Expression of this key gene in the de novo pathway for dTMP biosynthesis improved furfural resistance on plates and during fermentation. A similar benefit was observed by supplementation with thymine, thymidine, or the combination of tetrahydrofolate and serine (precursors for 5,10-methylenetetrahydrofolate, the methyl donor for ThyA). Supplementation with deoxyuridine provided a small benefit, and deoxyribose was of no benefit for furfural tolerance. A combination of thymidine and plasmid expression of thyA was no more effective than either alone. Together, these results demonstrate that furfural tolerance is increased by approaches that increase the supply of pyrimidine deoxyribonucleotides. However, ThyA activity was not directly affected by the addition of furfural. Furfural has been previously shown to damage DNA in E. coli and to activate a cellular response to oxidative damage in yeast. The added burden of repairing furfural-damaged DNA in E. coli would be expected to increase the cellular requirement for dTMP. Increased expression of thyA (E. coli, B. subtilis, or Z. mobilis), supplementation of cultures with thymidine, and supplementation with precursors for 5,10-methylenetetrahydrofolate (methyl donor) are each proposed to increase furfural tolerance by increasing the availability of dTMP for DNA repair.
Collapse
|
187
|
Complex physiology and compound stress responses during fermentation of alkali-pretreated corn stover hydrolysate by an Escherichia coli ethanologen. Appl Environ Microbiol 2012; 78:3442-57. [PMID: 22389370 DOI: 10.1128/aem.07329-11] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The physiology of ethanologenic Escherichia coli grown anaerobically in alkali-pretreated plant hydrolysates is complex and not well studied. To gain insight into how E. coli responds to such hydrolysates, we studied an E. coli K-12 ethanologen fermenting a hydrolysate prepared from corn stover pretreated by ammonia fiber expansion. Despite the high sugar content (∼6% glucose, 3% xylose) and relatively low toxicity of this hydrolysate, E. coli ceased growth long before glucose was depleted. Nevertheless, the cells remained metabolically active and continued conversion of glucose to ethanol until all glucose was consumed. Gene expression profiling revealed complex and changing patterns of metabolic physiology and cellular stress responses during an exponential growth phase, a transition phase, and the glycolytically active stationary phase. During the exponential and transition phases, high cell maintenance and stress response costs were mitigated, in part, by free amino acids available in the hydrolysate. However, after the majority of amino acids were depleted, the cells entered stationary phase, and ATP derived from glucose fermentation was consumed entirely by the demands of cell maintenance in the hydrolysate. Comparative gene expression profiling and metabolic modeling of the ethanologen suggested that the high energetic cost of mitigating osmotic, lignotoxin, and ethanol stress collectively limits growth, sugar utilization rates, and ethanol yields in alkali-pretreated lignocellulosic hydrolysates.
Collapse
|
188
|
Lee S, Mitchell RJ. Detection of toxic lignin hydrolysate-related compounds using an inaA::luxCDABE fusion strain. J Biotechnol 2012; 157:598-604. [DOI: 10.1016/j.jbiotec.2011.06.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 06/15/2011] [Accepted: 06/17/2011] [Indexed: 10/18/2022]
|
189
|
Increased furan tolerance in Escherichia coli due to a cryptic ucpA gene. Appl Environ Microbiol 2012; 78:2452-5. [PMID: 22267665 DOI: 10.1128/aem.07783-11] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Expression arrays were used to identify 4 putative oxidoreductases that were upregulated (>3-fold) by furfural (15 mM, 15 min). Plasmid expression of one (ucpA) increased furan tolerance in ethanologenic strain LY180 and wild-type strain W. Deleting ucpA decreased furfural tolerance. Although the mechanism remains unknown, the cryptic ucpA gene is now associated with a phenotype: furan resistance.
Collapse
|
190
|
Wierckx N, Koopman F, Ruijssenaars HJ, de Winde JH. Microbial degradation of furanic compounds: biochemistry, genetics, and impact. Appl Microbiol Biotechnol 2011; 92:1095-105. [PMID: 22031465 PMCID: PMC3223595 DOI: 10.1007/s00253-011-3632-5] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Revised: 09/29/2011] [Accepted: 10/06/2011] [Indexed: 11/16/2022]
Abstract
Microbial metabolism of furanic compounds, especially furfural and 5-hydroxymethylfurfural (HMF), is rapidly gaining interest in the scientific community. This interest can largely be attributed to the occurrence of toxic furanic aldehydes in lignocellulosic hydrolysates. However, these compounds are also widespread in nature and in human processed foods, and are produced in industry. Although several microorganisms are known to degrade furanic compounds, the variety of species is limited mostly to Gram-negative aerobic bacteria, with a few notable exceptions. Furanic aldehydes are highly toxic to microorganisms, which have evolved a wide variety of defense mechanisms, such as the oxidation and/or reduction to the furanic alcohol and acid forms. These oxidation/reduction reactions constitute the initial steps of the biological pathways for furfural and HMF degradation. Furfural degradation proceeds via 2-furoic acid, which is metabolized to the primary intermediate 2-oxoglutarate. HMF is converted, via 2,5-furandicarboxylic acid, into 2-furoic acid. The enzymes in these HMF/furfural degradation pathways are encoded by eight hmf genes, organized in two distinct clusters in Cupriavidus basilensis HMF14. The organization of the five genes of the furfural degradation cluster is highly conserved among microorganisms capable of degrading furfural, while the three genes constituting the initial HMF degradation route are organized in a highly diverse manner. The genetic and biochemical characterization of the microbial metabolism of furanic compounds holds great promises for industrial applications such as the biodetoxifcation of lignocellulosic hydrolysates and the production of value-added compounds such as 2,5-furandicarboxylic acid.
Collapse
|
191
|
Dunlop MJ. Engineering microbes for tolerance to next-generation biofuels. BIOTECHNOLOGY FOR BIOFUELS 2011; 4:32. [PMID: 21936941 PMCID: PMC3189103 DOI: 10.1186/1754-6834-4-32] [Citation(s) in RCA: 151] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Accepted: 09/21/2011] [Indexed: 05/02/2023]
Abstract
A major challenge when using microorganisms to produce bulk chemicals such as biofuels is that the production targets are often toxic to cells. Many biofuels are known to reduce cell viability through damage to the cell membrane and interference with essential physiological processes. Therefore, cells must trade off biofuel production and survival, reducing potential yields. Recently, there have been several efforts towards engineering strains for biofuel tolerance. Promising methods include engineering biofuel export systems, heat shock proteins, membrane modifications, more general stress responses, and approaches that integrate multiple tolerance strategies. In addition, in situ recovery methods and media supplements can help to ease the burden of end-product toxicity and may be used in combination with genetic approaches. Recent advances in systems and synthetic biology provide a framework for tolerance engineering. This review highlights recent targeted approaches towards improving microbial tolerance to next-generation biofuels with a particular emphasis on strategies that will improve production.
Collapse
Affiliation(s)
- Mary J Dunlop
- University of Vermont, School of Engineering, 33 Colchester Ave, Burlington, VT 05405, USA.
| |
Collapse
|
192
|
Winkler J, Kao KC. Transcriptional analysis of Lactobacillus brevis to N-butanol and ferulic acid stress responses. PLoS One 2011; 6:e21438. [PMID: 21829598 PMCID: PMC3149049 DOI: 10.1371/journal.pone.0021438] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Accepted: 05/27/2011] [Indexed: 11/19/2022] Open
Abstract
Background The presence of anti-microbial phenolic compounds, such as the model compound ferulic acid, in biomass hydrolysates pose significant challenges to the widespread use of biomass in conjunction with whole cell biocatalysis or fermentation. Currently, these inhibitory compounds must be removed through additional downstream processing or sufficiently diluted to create environments suitable for most industrially important microbial strains. Simultaneously, product toxicity must also be overcome to allow for efficient production of next generation biofuels such as n-butanol, isopropanol, and others from these low cost feedstocks. Methodology and Principal Findings This study explores the high ferulic acid and n-butanol tolerance in Lactobacillus brevis, a lactic acid bacterium often found in fermentation processes, by global transcriptional response analysis. The transcriptional profile of L. brevis reveals that the presence of ferulic acid triggers the expression of currently uncharacterized membrane proteins, possibly in an effort to counteract ferulic acid induced changes in membrane fluidity and ion leakage. In contrast to the ferulic acid stress response, n-butanol challenges to growing cultures primarily induce genes within the fatty acid synthesis pathway and reduced the proportion of 19∶1 cyclopropane fatty acid within the L. brevis membrane. Both inhibitors also triggered generalized stress responses. Separate attempts to alter flux through the Escherichia coli fatty acid synthesis by overexpressing acetyl-CoA carboxylase subunits and deleting cyclopropane fatty acid synthase (cfa) both failed to improve n-butanol tolerance in E. coli, indicating that additional components of the stress response are required to confer n-butanol resistance. Conclusions Several promising routes for understanding both ferulic acid and n-butanol tolerance have been identified from L. brevis gene expression data. These insights may be used to guide further engineering of model industrial organisms to better tolerate both classes of inhibitors to enable facile production of biofuels from lignocellulosic biomass.
Collapse
Affiliation(s)
- James Winkler
- Department of Chemical Engineering, Texas A&M University, College Station, Texas, United States of America
| | - Katy C. Kao
- Department of Chemical Engineering, Texas A&M University, College Station, Texas, United States of America
- * E-mail:
| |
Collapse
|
193
|
|
194
|
Increased furfural tolerance due to overexpression of NADH-dependent oxidoreductase FucO in Escherichia coli strains engineered for the production of ethanol and lactate. Appl Environ Microbiol 2011; 77:5132-40. [PMID: 21685167 DOI: 10.1128/aem.05008-11] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Furfural is an important fermentation inhibitor in hemicellulose sugar syrups derived from woody biomass. The metabolism of furfural by NADPH-dependent oxidoreductases, such as YqhD (low K(m) for NADPH), is proposed to inhibit the growth and fermentation of xylose in Escherichia coli by competing with biosynthesis for NADPH. The discovery that the NADH-dependent propanediol oxidoreductase (FucO) can reduce furfural provided a new approach to improve furfural tolerance. Strains that produced ethanol or lactate efficiently as primary products from xylose were developed. These strains included chromosomal mutations in yqhD expression that permitted the fermentation of xylose broths containing up to 10 mM furfural. Expression of fucO from plasmids was shown to increase furfural tolerance by 50% and to permit the fermentation of 15 mM furfural. Product yields with 15 mM furfural were equivalent to those of control strains without added furfural (85% to 90% of the theoretical maximum). These two defined genetic traits can be readily transferred to enteric biocatalysts designed to produce other products. A similar strategy that minimizes the depletion of NADPH pools by native detoxification enzymes may be generally useful for other inhibitory compounds in lignocellulosic sugar streams and with other organisms.
Collapse
|
195
|
Geddes CC, Nieves IU, Ingram LO. Advances in ethanol production. Curr Opin Biotechnol 2011; 22:312-9. [DOI: 10.1016/j.copbio.2011.04.012] [Citation(s) in RCA: 184] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Accepted: 04/18/2011] [Indexed: 12/23/2022]
|
196
|
Nieves IU, Geddes CC, Miller EN, Mullinnix MT, Hoffman RW, Fu Z, Tong Z, Ingram LO. Effect of reduced sulfur compounds on the fermentation of phosphoric acid pretreated sugarcane bagasse by ethanologenic Escherichia coli. BIORESOURCE TECHNOLOGY 2011; 102:5145-5152. [PMID: 21353535 DOI: 10.1016/j.biortech.2011.02.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Revised: 01/31/2011] [Accepted: 02/01/2011] [Indexed: 05/30/2023]
Abstract
The addition of reduced sulfur compounds (thiosulfate, cysteine, sodium hydrosulfite, and sodium metabisulfite) increased growth and fermentation of dilute acid hydrolysate of sugarcane bagasse by ethanologenic Escherichia coli (strains LY180, EMFR9, and MM160). With sodium metabisulfite (0.5mM), toxicity was sufficiently reduced that slurries of pretreated biomass (10% dry weight including fiber and solubles) could be fermented by E. coli strain MM160 without solid-liquid separation or cleanup of sugars. A 6-h liquefaction step was added to improve mixing. Sodium metabisulfite also caused spectral changes at wavelengths corresponding to furfural and soluble products from lignin. Glucose and cellobiose were rapidly metabolized. Xylose utilization was improved by sodium metabisulfite but remained incomplete after 144 h. The overall ethanol yield for this liquefaction plus simultaneous saccharification and co-fermentation process was 0.20 g ethanol/g bagasse dry weight, 250 L/tonne (61 gal/US ton).
Collapse
Affiliation(s)
- I U Nieves
- Department of Microbiology & Cell Science, University of Florida, Box 110700, Gainesville, FL 32611, USA
| | | | | | | | | | | | | | | |
Collapse
|
197
|
Geddes CC, Mullinnix MT, Nieves IU, Peterson JJ, Hoffman RW, York SW, Yomano LP, Miller EN, Shanmugam KT, Ingram LO. Simplified process for ethanol production from sugarcane bagasse using hydrolysate-resistant Escherichia coli strain MM160. BIORESOURCE TECHNOLOGY 2011; 102:2702-11. [PMID: 21111615 DOI: 10.1016/j.biortech.2010.10.143] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Revised: 10/28/2010] [Accepted: 10/30/2010] [Indexed: 05/07/2023]
Abstract
Hexose and pentose sugars from phosphoric acid pretreated sugarcane bagasse were co-fermented to ethanol in a single vessel (SScF), eliminating process steps for solid-liquid separation and sugar cleanup. An initial liquefaction step (L) with cellulase was included to improve mixing and saccharification (L+SScF), analogous to a corn ethanol process. Fermentation was enabled by the development of a hydrolysate-resistant mutant of Escherichia coli LY180, designated MM160. Strain MM160 was more resistant than the parent to inhibitors (furfural, 5-hydroxymethylfurfural, and acetate) formed during pretreatment. Bagasse slurries containing 10% and 14% dry weight (fiber plus solubles) were tested using pretreatment temperatures of 160-190°C (1% phosphoric acid, 10 min). Enzymatic saccharification and inhibitor production both increased with pretreatment temperature. The highest titer (30 g/L ethanol) and yield (0.21 g ethanol/g bagasse dry weight) were obtained after incubation for 122 h using 14% dry weight slurries of pretreated bagasse (180°C).
Collapse
Affiliation(s)
- C C Geddes
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
198
|
Sandoval NR, Mills TY, Zhang M, Gill RT. Elucidating acetate tolerance in E. coli using a genome-wide approach. Metab Eng 2010; 13:214-24. [PMID: 21163359 DOI: 10.1016/j.ymben.2010.12.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Revised: 11/17/2010] [Accepted: 12/01/2010] [Indexed: 11/25/2022]
Abstract
Engineering organisms for improved performance using lignocellulose feedstocks is an important step towards a sustainable fuel and chemical industry. Cellulosic feedstocks contain carbon and energy in the form of cellulosic and hemicellulosic sugars that are not metabolized by most industrial microorganisms. Pretreatment processes that hydrolyze these polysaccharides often also result in the accumulation of growth inhibitory compounds, such as acetate and furfural among others. Here, we have applied a recently reported strategy for engineering tolerance towards the goal of increasing Escherichia coli growth in the presence of elevated acetate concentrations (Lynch et al., 2007). We performed growth selections upon an E. coli genome library developed using a moderate selection pressure to identify genomic regions implicated in acetate toxicity and tolerance. These studies identified a range of high-fitness genes that are normally involved in membrane and extracellular processes, are key regulated steps in pathways, and are involved in pathways that yield specific amino acids and nucleotides. Supplementation of the products and metabolically related metabolites of these pathways significantly increased growth rate (a 130% increase in specific growth) at inhibitory acetate concentrations. Our results suggest that acetate tolerance will not involve engineering of a single pathway; rather we observe a range of potential mechanisms for overcoming acetate based inhibition.
Collapse
Affiliation(s)
- Nicholas R Sandoval
- Department of Chemical and Biological Engineering, University of Colorado at Boulder, Boulder, CO 80309, USA.
| | | | | | | |
Collapse
|
199
|
Affiliation(s)
- Tiangang Liu
- Department of Chemistry, Stanford University, Stanford, California 94305
| | - Chaitan Khosla
- Department of Chemistry, Stanford University, Stanford, California 94305
- Department of Chemical Engineering, Stanford University, Stanford, California 94305
- Department of Biochemistry, Stanford University, Stanford, California 94305;
| |
Collapse
|
200
|
Li X, Kim TH, Nghiem NP. Bioethanol production from corn stover using aqueous ammonia pretreatment and two-phase simultaneous saccharification and fermentation (TPSSF). BIORESOURCE TECHNOLOGY 2010; 101:5910-6. [PMID: 20338749 DOI: 10.1016/j.biortech.2010.03.015] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Revised: 02/26/2010] [Accepted: 03/03/2010] [Indexed: 05/15/2023]
Abstract
An integrated bioconversion process was developed to convert corn stover derived pentose and hexose to ethanol effectively. In this study, corn stover was pretreated by soaking in aqueous ammonia (SAA), which retained glucan ( approximately 100%) and xylan (>80%) in the solids. The pretreated carbohydrates-rich corn stover was converted to ethanol via two-phase simultaneous saccharification and fermentation (TPSSF). This single-reactor process employed sequential simultaneous saccharification and fermentation (SSF), i.e. pentose conversion using recombinant Escherichia coli KO11 in the first phase, followed by hexose conversion with Saccharomyces cerevisiae D5A in the second phase. In the first phase, 88% of xylan digestibility was achieved through the synergistic action of xylanase and endo-glucanase with minimal glucan hydrolysis (10.5%). Overall, the TPSSF using 12-h SAA-treated corn stover resulted in the highest ethanol concentration (22.3g/L), which was equivalent to 84% of the theoretical ethanol yield based on the total carbohydrates (glucan+xylan) in the untreated corn stover.
Collapse
Affiliation(s)
- Xuan Li
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA 50011, USA
| | | | | |
Collapse
|