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Shokravi H, Shokravi Z, Heidarrezaei M, Ong HC, Rahimian Koloor SS, Petrů M, Lau WJ, Ismail AF. Fourth generation biofuel from genetically modified algal biomass: Challenges and future directions. CHEMOSPHERE 2021; 285:131535. [PMID: 34329137 DOI: 10.1016/j.chemosphere.2021.131535] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/27/2021] [Accepted: 07/09/2021] [Indexed: 06/13/2023]
Abstract
Genetic engineering applications in the field of biofuel are rapidly expanding due to their potential to boost biomass productivity while lowering its cost and enhancing its quality. Recently, fourth-generation biofuel (FGB), which is biofuel obtained from genetically modified (GM) algae biomass, has gained considerable attention from academic and industrial communities. However, replacing fossil resources with FGB is still beset with many challenges. Most notably, technical aspects of genetic modification operations need to be more fully articulated and elaborated. However, relatively little attention has been paid to GM algal biomass. There is a limited number of reviews on the progress and challenges faced in the algal genetics of FGB. Therefore, the present review aims to fill this gap in the literature by recapitulating the findings of recent studies and achievements on safe and efficient genetic manipulation in the production of FGB. Then, the essential issues and parameters related to genome editing in algal strains are highlighted. Finally, the main challenges to FGB pertaining to the diffusion risk and regulatory frameworks are addressed. This review concluded that the technical and biosafety aspects of FGB, as well as the complexity and diversity of the related regulations, legitimacy concerns, and health and environmental risks, are among the most important challenges that require a strong commitment at the national/international levels to reach a global consensus.
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Affiliation(s)
- Hoofar Shokravi
- School of Civil Engineering, Faculty of Engineering, Universiti Teknologi Malaysia, 81310, UTM Skudai, Johor Bahru, Johor, Malaysia
| | - Zahra Shokravi
- Department of Microbiology, Faculty of Basic Science, Islamic Azad University, Science and Research Branch of Tehran, Markazi, Iran
| | - Mahshid Heidarrezaei
- School of Chemical & Energy Engineering, Faculty of Engineering, Universiti Teknologi Malaysia, 81310, UTM Skudai, Johor Bahru, Johor, Malaysia; Institute of Bioproduct Development (IBD), Universiti Teknologi Malaysia, Johor Bahru, 81310, Malaysia
| | - Hwai Chyuan Ong
- Centre for Green Technology, Faculty of Engineering and Information Technology, University of Technology Sydney, NSW, 2007, Australia.
| | - Seyed Saeid Rahimian Koloor
- Institute for Nanomaterials, Advanced Technologies, and Innovation (CXI), Technical University of Liberec (TUL), Studentska 2, 461 17, Liberec, Czech Republic
| | - Michal Petrů
- Institute for Nanomaterials, Advanced Technologies, and Innovation (CXI), Technical University of Liberec (TUL), Studentska 2, 461 17, Liberec, Czech Republic
| | - Woei Jye Lau
- School of Chemical & Energy Engineering, Faculty of Engineering, Universiti Teknologi Malaysia, 81310, UTM Skudai, Johor Bahru, Johor, Malaysia; Advanced Membrane Technology Research Centre (AMTEC), Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | - Ahmad Fauzi Ismail
- School of Chemical & Energy Engineering, Faculty of Engineering, Universiti Teknologi Malaysia, 81310, UTM Skudai, Johor Bahru, Johor, Malaysia; Advanced Membrane Technology Research Centre (AMTEC), Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
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Li P, Fu X, Li S, Zhang L. Engineering TATA-binding protein Spt15 to improve ethanol tolerance and production in Kluyveromyces marxianus. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:207. [PMID: 30061929 PMCID: PMC6058363 DOI: 10.1186/s13068-018-1206-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 07/16/2018] [Indexed: 05/26/2023]
Abstract
BACKGROUND Low ethanol tolerance of Kluyveromyces marxianus limits its application in high-temperature ethanol fermentation. As a complex phenotype, ethanol tolerance involves synergistic actions of many genes that are widely distributed throughout the genome, thereby being difficult to engineer. TATA-binding protein is the most common target of global transcription machinery engineering for improvement of complex phenotypes. RESULTS A random mutagenesis library of K. marxianus TATA-binding protein Spt15 was constructed and subjected to screening under ethanol stress. Two mutant strains with improved ethanol tolerance were identified, one of which (denoted as M2) exhibited increased ethanol productivity. The mutant of Spt15 in strain M2 (denoted as Spt15-M2) has a single amino acid substitution at position 31 (Lys → Glu). RNA-Seq-based transcriptomic analysis revealed cellular transcription profile changes resulting from Spt15-M2. Spt15-M2 caused changes in transcriptional level of most of the genes in the central carbon metabolism network. Compared with control strain, 444 differentially expressed genes (DEGs) were identified in strain M2 (fold change > 2, Padj < 0.05), including 48 up-regulated and 396 down-regulated. The up-regulated DEGs are involved in amino acid transport, long-chain fatty acid biosynthesis and MAPK signaling pathway, while the down-regulated DEGs are related to ribosome biogenesis, translation and protein synthesis. Five candidate genes (GAP1, GNP1, FAR1, STE2 and TEC1), which were found to be up-regulated in M2 strain, were overexpressed for a gain-of-function assay. However, the overexpression of no single gene helped improve ethanol tolerance as SPT15-M2 did. CONCLUSIONS This work demonstrates that ethanol tolerance of K. marxianus can be improved by engineering its TATA-binding protein. A single amino acid substitution (K31E) of TATA-binding protein Spt15 is able to bring differential expression of hundreds of genes that acted as an interconnected network for the phenotype of ethanol tolerance. Future perspectives of this technique in K. marxianus were discussed.
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Affiliation(s)
- Pengsong Li
- Institute of New Energy Technology, MOST-USDA Joint Research Center for Biofuels, Beijing Engineering Research Center for Biofuels, Tsinghua University, Beijing, 100084 China
| | - Xiaofen Fu
- Institute of New Energy Technology, MOST-USDA Joint Research Center for Biofuels, Beijing Engineering Research Center for Biofuels, Tsinghua University, Beijing, 100084 China
| | - Shizhong Li
- Institute of New Energy Technology, MOST-USDA Joint Research Center for Biofuels, Beijing Engineering Research Center for Biofuels, Tsinghua University, Beijing, 100084 China
| | - Lei Zhang
- Institute of New Energy Technology, MOST-USDA Joint Research Center for Biofuels, Beijing Engineering Research Center for Biofuels, Tsinghua University, Beijing, 100084 China
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Li P, Fu X, Zhang L, Zhang Z, Li J, Li S. The transcription factors Hsf1 and Msn2 of thermotolerant Kluyveromyces marxianus promote cell growth and ethanol fermentation of Saccharomyces cerevisiae at high temperatures. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:289. [PMID: 29213328 PMCID: PMC5713069 DOI: 10.1186/s13068-017-0984-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 11/26/2017] [Indexed: 05/18/2023]
Abstract
BACKGROUND High temperature inhibits cell growth and ethanol fermentation of Saccharomyces cerevisiae. As a complex phenotype, thermotolerance usually involves synergistic actions of many genes, thereby being difficult to engineer. The overexpression of either endogenous or exogenous stress-related transcription factor genes in yeasts was found to be able to improve relevant stress tolerance of the hosts. RESULTS To increase ethanol yield of high-temperature fermentation, we constructed a series of strains of S. cerevisiae by expressing 8 transcription factor genes from S. cerevisiae and 7 transcription factor genes from thermotolerant K. marxianus in S. cerevisiae. The results of growth curve measurements and spotting test show that KmHsf1 and KmMsn2 can enhance cell growth of S. cerevisiae at 40-42 °C. According to the results of batch fermentation at 43 °C with an initial glucose concentration of 104.8 g/l, the fermentation broths of KmHSF1 and KmMSN2-expressing strains could reach final ethanol concentrations of 27.2 ± 1.4 and 27.6 ± 1.2 g/l, respectively, while the control strain just produced 18.9 ± 0.3 g/l ethanol. Transcriptomic analysis found that the expression of KmHSF1 and KmMSN2 resulted in 55 (including 31 up-regulated and 24 down-regulated) and 50 (including 32 up-regulated and 18 down-regulated) genes with different expression levels, respectively (padj < 0.05). The results of transcriptomic analysis also reveal that KmHsf1 might increase ethanol production by regulating genes related to transporter activity to limit excessive ATP consumption and promote the uptake of glucose; while KmMsn2 might promote ethanol fermentation by regulating genes associated with glucose metabolic process and glycolysis/gluconeogenesis. In addition, KmMsn2 might also help to cope with high temperature by regulating genes associated with lipid metabolism to change the membrane fluidity. CONCLUSIONS The transcription factors KmHsf1 and KmMsn2 of thermotolerant K. marxianus can promote both cell growth and ethanol fermentation of S. cerevisiae at high temperatures. Different mechanisms of KmHsf1 and KmMsn2 in promoting high-temperature ethanol fermentation of S. cerevisiae were revealed by transcriptomic analysis.
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Affiliation(s)
- Pengsong Li
- Institute of New Energy Technology, Tsinghua University, Beijing, 100084 China
| | - Xiaofen Fu
- Institute of New Energy Technology, Tsinghua University, Beijing, 100084 China
| | - Lei Zhang
- Institute of New Energy Technology, Tsinghua University, Beijing, 100084 China
| | - Zhiyu Zhang
- Institute of New Energy Technology, Tsinghua University, Beijing, 100084 China
| | - Jihong Li
- Institute of New Energy Technology, Tsinghua University, Beijing, 100084 China
| | - Shizhong Li
- Institute of New Energy Technology, Tsinghua University, Beijing, 100084 China
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Kumar A, Mosa KA, Ji L, Kage U, Dhokane D, Karre S, Madalageri D, Pathania N. Metabolomics-assisted biotechnological interventions for developing plant-based functional foods and nutraceuticals. Crit Rev Food Sci Nutr 2017; 58:1791-1807. [PMID: 28272908 DOI: 10.1080/10408398.2017.1285752] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Today, the dramatic changes in types of food consumed have led to an increased burden of chronic diseases. Therefore, the emphasis of food research is not only to ensure quality food that can supply adequate nutrients to prevent nutrition related diseases, but also to ensure overall physical and mental-health. This has led to the concept of functional foods and nutraceuticals (FFNs), which can be ideally produced and delivered through plants. Metabolomics can help in getting the most relevant functional information, and thus has been considered the greatest -OMICS technology to date. However, metabolomics has not been exploited to the best potential in plant sciences. The technology can be leveraged to identify the health promoting compounds and metabolites that can be used for the development of FFNs. This article reviews (i) plant-based FFNs-related metabolites and their health benefits; (ii) use of different analytic platforms for targeted and non-targeted metabolite profiling along with experimental considerations; (iii) exploitation of metabolomics to develop FFNs in plants using various biotechnological tools; and (iv) potential use of metabolomics in plant breeding. We have also provided some insights into integration of metabolomics with latest genome editing tools for metabolic pathway regulation in plants.
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Affiliation(s)
- Arun Kumar
- a Department of Horticulture , University of Wisconsin-Madison , Madison , Wisconsin , USA
| | - Kareem A Mosa
- b Department of Applied Biology , College of Sciences, University of Sharjah , Sharjah , United Arab Emirates.,c Department of Biotechnology , Faculty of Agriculture, Al-Azhar University , Cairo , Egypt
| | - Liyao Ji
- d Plant Science Department , McGill University , Quebec , Canada
| | - Udaykumar Kage
- d Plant Science Department , McGill University , Quebec , Canada
| | | | - Shailesh Karre
- d Plant Science Department , McGill University , Quebec , Canada
| | - Deepa Madalageri
- e Department of Food Science and Nutrition , College of Home Science, University of Agricultural Science , Dharwad , India
| | - Neemisha Pathania
- f Department of Soil Sciences , Punjab Agricultural University , Ludhiana , India
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Zhang G, Lin Y, Qi X, Li L, Wang Q, Ma Y. TALENs-Assisted Multiplex Editing for Accelerated Genome Evolution To Improve Yeast Phenotypes. ACS Synth Biol 2015; 4:1101-11. [PMID: 26011297 DOI: 10.1021/acssynbio.5b00074] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Genome editing is an important tool for building novel genotypes with a desired phenotype. However, the fundamental challenge is to rapidly generate desired alterations on a genome-wide scale. Here, we report TALENs (transcription activator-like effector nucleases)-assisted multiplex editing (TAME), based on the interaction of designed TALENs with the DNA sequences between the critical TATA and GC boxes, for generating multiple targeted genomic modifications. Through iterative cycles of TAME to induce abundant semirational indels coupled with efficient screening using a reporter, the targeted fluorescent trait can be continuously and rapidly improved by accumulating multiplex beneficial genetic modifications in the evolving yeast genome. To further evaluate its efficiency, we also demonstrate the application of TAME for significantly improving ethanol tolerance of yeast in a short amount of time. Therefore, TAME is a broadly generalizable platform for accelerated genome evolution to rapidly improve yeast phenotypes.
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Affiliation(s)
- Guoqiang Zhang
- Key
Laboratory of Systems Microbial Biotechnology, Tianjin Institute of
Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuping Lin
- Key
Laboratory of Systems Microbial Biotechnology, Tianjin Institute of
Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Xianni Qi
- Key
Laboratory of Systems Microbial Biotechnology, Tianjin Institute of
Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Lin Li
- Key
Laboratory of Systems Microbial Biotechnology, Tianjin Institute of
Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Qinhong Wang
- Key
Laboratory of Systems Microbial Biotechnology, Tianjin Institute of
Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yanhe Ma
- Key
Laboratory of Systems Microbial Biotechnology, Tianjin Institute of
Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
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Metabolic engineering of Escherichia coli using CRISPR–Cas9 meditated genome editing. Metab Eng 2015; 31:13-21. [DOI: 10.1016/j.ymben.2015.06.006] [Citation(s) in RCA: 267] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 06/19/2015] [Accepted: 06/22/2015] [Indexed: 12/17/2022]
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Affiliation(s)
- Kristin Hagen
- EA European Academy of Technology and Innovation Assessment GmbH, Bad Neuenahr-Ahrweiler, Germany
| | - Margret Engelhard
- EA European Academy of Technology and Innovation Assessment GmbH, Bad Neuenahr-Ahrweiler, Germany
| | - Georg Toepfer
- Center for Literary and Cultural Research Berlin, Berlin, Germany
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Si T, Luo Y, Bao Z, Zhao H. RNAi-assisted genome evolution in Saccharomyces cerevisiae for complex phenotype engineering. ACS Synth Biol 2015; 4:283-91. [PMID: 24758359 DOI: 10.1021/sb500074a] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A fundamental challenge in basic and applied biology is to reprogram cells with improved or novel traits on a genomic scale. However, the current ability to reprogram a cell on the genome scale is limited to bacterial cells. Here, we report RNA interference (RNAi)-assisted genome evolution (RAGE) as a generally applicable method for genome-scale engineering in the yeast Saccharomyces cerevisiae. Through iterative cycles of creating a library of RNAi induced reduction-of-function mutants coupled with high throughput screening or selection, RAGE can continuously improve target trait(s) by accumulating multiplex beneficial genetic modifications in an evolving yeast genome. To validate the RNAi library constructed with yeast genomic DNA and convergent-promoter expression cassette, we demonstrated RNAi screening in Saccharomyces cerevisiae for the first time by identifying two known and three novel suppressors of a telomerase-deficient mutation yku70Δ. We then showed the application of RAGE for improved acetic acid tolerance, a key trait for microbial production of chemicals and fuels. Three rounds of iterative RNAi screening led to the identification of three gene knockdown targets that acted synergistically to confer an engineered yeast strain with substantially improved acetic acid tolerance. RAGE should greatly accelerate the design and evolution of organisms with desired traits and provide new insights on genome structure, function, and evolution.
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Affiliation(s)
- Tong Si
- Department
of Chemical and Biomolecular Engineering, ‡Department of Biochemistry, §Departments of Chemistry
and Bioengineering, Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Yunzi Luo
- Department
of Chemical and Biomolecular Engineering, ‡Department of Biochemistry, §Departments of Chemistry
and Bioengineering, Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Zehua Bao
- Department
of Chemical and Biomolecular Engineering, ‡Department of Biochemistry, §Departments of Chemistry
and Bioengineering, Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Department
of Chemical and Biomolecular Engineering, ‡Department of Biochemistry, §Departments of Chemistry
and Bioengineering, Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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Tools for developing tolerance to toxic chemicals in microbial systems and perspectives on moving the field forward and into the industrial setting. Curr Opin Chem Eng 2014. [DOI: 10.1016/j.coche.2014.08.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Abstract
Genome engineering strategies--such as genome editing, reduction and shuffling, and de novo genome synthesis--enable the modification of specific genomic locations in a directed and combinatorial manner. These approaches offer an unprecedented opportunity to study central evolutionary issues in which natural genetic variation is limited or biased, which sheds light on the evolutionary forces driving complex and extremely slowly evolving traits; the selective constraints on genome architecture; and the reconstruction of ancestral states of cellular structures and networks.
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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.
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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:
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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.
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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:
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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.
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Affiliation(s)
| | | | | | - Ryan T Gill
- Department of Chemical and Biological Engineering, University of Colorado, Campus Box 592, Boulder, CO 80303, USA.
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Lin L, Ji Y, Tu Q, Huang R, Teng L, Zeng X, Song H, Wang K, Zhou Q, Li Y, Cui Q, He Z, Zhou J, Xu J. Microevolution from shock to adaptation revealed strategies improving ethanol tolerance and production in Thermoanaerobacter. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:103. [PMID: 23875846 PMCID: PMC3751872 DOI: 10.1186/1754-6834-6-103] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 07/17/2013] [Indexed: 05/08/2023]
Abstract
INTRODUCTION The molecular links between shock-response and adaptation remain poorly understood, particularly for extremophiles. This has hindered rational engineering of solvent tolerance and correlated traits (e.g., productivity) in extremophiles. To untangle such molecular links, here we established a model that tracked the microevolution from shock to adaptation in thermophilic bacteria. METHOD Temporal dynamics of genomes and transcriptomes was tracked for Thermoanaerobacter sp. X514 which under increasing exogenous ethanol evolved from ethanol-sensitive wild-type (Strain X) to tolerance of 2%- (XI) and eventually 6%-ethanol (XII). Based on the reconstructed transcriptional network underlying stress tolerance, genetic engineering was employed to improve ethanol tolerance and production in Thermoanaerobacter. RESULTS The spontaneous genome mutation rate (μg) of Thermoanaerobacter sp. X514, calculated at 0.045, suggested a higher mutation rate in thermophile than previously thought. Transcriptomic comparison revealed that shock-response and adaptation were distinct in nature, whereas the transcriptomes of XII resembled those of the extendedly shocked X. To respond to ethanol shock, X employed fructose-specific phosphotransferase system (PTS), Arginine Deiminase (ADI) pathway, alcohol dehydrogenase (Adh) and a distinct mechanism of V-type ATPase. As an adaptation to exogenous ethanol, XI mobilized resistance-nodulation-cell division (RND) efflux system and Adh, whereas XII, which produced higher ethanol than XI, employed ECF-type ϭ24, an alcohol catabolism operon and phase-specific heat-shock proteins (Hsps), modulated hexose/pentose-transport operon structure and reinforced membrane rigidity. Exploiting these findings, we further showed that ethanol productivity and tolerance can be improved simultaneously by overexpressing adh or ϭ24 in X. CONCLUSION Our work revealed thermophilic-bacteria specific features of adaptive evolution and demonstrated a rational strategy to engineer co-evolving industrial traits. As improvements of shock-response, stress tolerance and productivity have been crucial aims in industrial applications employing thermophiles, our findings should be valuable not just to the production of ethanol but also to a wide variety of biofuels and biochemicals.
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Affiliation(s)
- Lu Lin
- BioEnergy Genome Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, P. R. China
| | - Yuetong Ji
- BioEnergy Genome Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, P. R. China
| | - Qichao Tu
- Institute for Environmental Genomics, and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Ranran Huang
- BioEnergy Genome Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, P. R. China
| | - Lin Teng
- BioEnergy Genome Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, P. R. China
| | - Xiaowei Zeng
- BioEnergy Genome Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, P. R. China
| | - Houhui Song
- BioEnergy Genome Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, P. R. China
| | - Kun Wang
- BioEnergy Genome Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, P. R. China
| | - Qian Zhou
- BioEnergy Genome Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, P. R. China
| | - Yifei Li
- BioEnergy Genome Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, P. R. China
| | - Qiu Cui
- BioEnergy Genome Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, P. R. China
| | - Zhili He
- Institute for Environmental Genomics, and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Jizhong Zhou
- Institute for Environmental Genomics, and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Jian Xu
- BioEnergy Genome Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, P. R. China
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Affiliation(s)
- Eleftherios T. Papoutsakis
- Dept. of Chemical and Biomolecular Engineering, Dept. of Biological Sciences, and the Delaware Biotechnology Institute; University of Delaware; 15 Innovation Way; Newark; DE; 19711
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Woodruff LB, May BL, Warner JR, Gill RT. Towards a metabolic engineering strain “commons”: AnEscherichia coliplatform strain for ethanol production. Biotechnol Bioeng 2013; 110:1520-6. [DOI: 10.1002/bit.24840] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Revised: 11/28/2012] [Accepted: 12/28/2012] [Indexed: 11/09/2022]
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Woodruff LBA, Pandhal J, Ow SY, Karimpour-Fard A, Weiss SJ, Wright PC, Gill RT. Genome-scale identification and characterization of ethanol tolerance genes in Escherichia coli. Metab Eng 2012; 15:124-33. [PMID: 23164575 DOI: 10.1016/j.ymben.2012.10.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 09/17/2012] [Accepted: 10/03/2012] [Indexed: 11/30/2022]
Abstract
The identification of relevant gene targets for engineering a desired trait is a key step in combinatorial strain engineering. Here, we applied the multi-Scalar Analysis of Library Enrichments (SCALEs) approach to map ethanol tolerance onto 1,000,000 genomic-library clones in Escherichia coli. We assigned fitness scores to each of the ∼4,300 genes in E. coli, and through follow-up confirmatory studies identified 9 novel genetic targets (12 genes total) that increase E. coli ethanol tolerance (up to 6-fold improved growth). These genetic targets are involved in the processes related to cell membrane composition, translation, serine biosynthesis, and transcription regulation. Transcriptional profiling of the ethanol stress response in 5 of these ethanol-tolerant clones revealed a total of 700 genes with significantly altered expression (mapped to 615 significantly enriched gene ontology terms) across all five clones, with similar overall changes in global gene expression between two clone clusters. All ethanol-tolerant clones analyzed shared 6% of the overexpressed genes and showed enrichment for transcription regulation-related GO terms. iTRAQ-based proteomic analysis of ethanol-tolerant strains identified upregulation of proteins related to ROS mitigation, fatty acid biosynthesis, and vitamin biosynthesis as compared to the parent strain's ethanol response. The approach we outline here will be useful for engineering a variety of other traits and further improvements in alcohol tolerance.
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Affiliation(s)
- Lauren B A Woodruff
- Department of Chemical and Biological Engineering, University of Colorado at Boulder, Jennie Smoly Caruthers Biotechnology Building, UCB 596, Boulder, CO 80309, USA.
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Directed evolution: an evolving and enabling synthetic biology tool. Curr Opin Chem Biol 2012; 16:285-91. [PMID: 22673064 DOI: 10.1016/j.cbpa.2012.05.186] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Revised: 05/06/2012] [Accepted: 05/11/2012] [Indexed: 01/08/2023]
Abstract
Synthetic biology, with its goal of designing biological entities for wide-ranging purposes, remains a field of intensive research interest. However, the vast complexity of biological systems has heretofore rendered rational design prohibitively difficult. As a result, directed evolution remains a valuable tool for synthetic biology, enabling the identification of desired functionalities from large libraries of variants. This review highlights the most recent advances in the use of directed evolution in synthetic biology, focusing on new techniques and applications at the pathway and genome scale.
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19
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Leprince A, de Lorenzo V, Völler P, van Passel MWJ, Martins dos Santos VAP. Random and cyclical deletion of large DNA segments in the genome of Pseudomonas putida. Environ Microbiol 2012; 14:1444-53. [PMID: 22429517 PMCID: PMC3429869 DOI: 10.1111/j.1462-2920.2012.02730.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Cumulative site-directed mutagenesis is of limited suitability for the global analysis of the gene functions in the microbe's cellular network. In order to simplify and stabilize the genome of the soil bacterium Pseudomonas putida, we developed a recyclable three-step excision method based on the combination of customized mini-transposons and the FLP-FRT site-specific recombination system. To demonstrate the powerful potential of these tools, we first established insertion mutant libraries that allow users to study gene functions with respect either to phenotypic characteristics (single insertions) or to their involvement in predicted networks (double insertions). Based on these libraries, we generated as a proof-of-principle, single-deletion mutants lacking ∼ 4.1% of the genome (∼ 3.7% of the gene repertoire). A cyclical application of the method generated four double-deletion mutants of which a maximum of ∼ 7.4% of the chromosome (∼ 6.9% of the gene count) was excised. This procedure demonstrates a new strategy for rapid genome streamlining and gain of new insights into the molecular interactions and regulations.
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Affiliation(s)
- Audrey Leprince
- Systems and Synthetic Biology Group, Helmholtz-Centre for Infection Research, Braunschweig, Germany
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Cambray G, Mutalik VK, Arkin AP. Toward rational design of bacterial genomes. Curr Opin Microbiol 2011; 14:624-30. [DOI: 10.1016/j.mib.2011.08.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2011] [Revised: 08/02/2011] [Accepted: 08/07/2011] [Indexed: 02/02/2023]
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