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Wei Z, Li S, Gao P. Reactivity of surface oxygen vacancy sites and frustrated Lewis acid-base pairs of In 2O 3 catalysts in CO 2 hydrogenation. Phys Chem Chem Phys 2024; 26:16449-16453. [PMID: 38817205 DOI: 10.1039/d4cp00895b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
The effects of oxygen vacancy (VO) formation energy and surface frustrated Lewis acid-base pairs (SFLPs) on the CO2 hydrogenation activity of In2O3 catalysts were studied using density functional theory calculations. The VO formation energy of 2.8-3.3 eV was found to favor HCOO formation, whereas the presence of SFLPs is conducive to CO formation.
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Affiliation(s)
- Zhangqian Wei
- CAS Key Laboratory of Low-Carbon Conversion Science and Engineering, Shanghai Advanced Research Institute, Chinese Academy of Sciences, 100 Haike Road, Shanghai 201210, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shenggang Li
- CAS Key Laboratory of Low-Carbon Conversion Science and Engineering, Shanghai Advanced Research Institute, Chinese Academy of Sciences, 100 Haike Road, Shanghai 201210, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
- State Key Laboratory of Low Carbon Catalysis and Carbon Dioxide Utilization, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Peng Gao
- CAS Key Laboratory of Low-Carbon Conversion Science and Engineering, Shanghai Advanced Research Institute, Chinese Academy of Sciences, 100 Haike Road, Shanghai 201210, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Low Carbon Catalysis and Carbon Dioxide Utilization, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
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Wang XW, Benoit I, Groenewald JZ, Houbraken J, Dai X, Peng M, Yang X, Han DY, Gao C, Guo LD. Community dynamics of Neocallimastigomycetes in the rumen of yak feeding on wheat straw revealed by different primer sets. FUNGAL ECOL 2019. [DOI: 10.1016/j.funeco.2019.03.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Zhang Z, Lin L, Tang H, Zeng S, Guo Y, Wei Y, Huang R, Pang H, Du L. A Convenient Fluorescence-Based Assay for the Detection of Sucrose Transport and the Introduction of a Sucrose Transporter from Potato into Clostridium Strains. Molecules 2019; 24:molecules24193495. [PMID: 31561523 PMCID: PMC6803915 DOI: 10.3390/molecules24193495] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 09/23/2019] [Accepted: 09/24/2019] [Indexed: 11/16/2022] Open
Abstract
A convenient and effective sucrose transport assay for Clostridium strains is needed. Traditional methods, such as 14C-sucrose isotope labelling, use radioactive materials and are not convenient for many laboratories. Here, a sucrose transporter from potato was introduced into Clostridium, and a fluorescence assay based on esculin was used for the analysis of sucrose transport in Clostridium strains. This showed that the heterologously expressed potato sucrose transporter is functional in Clostridium. Recombinant engineering of high-level sucrose transport would aid sucrose fermentation in Clostridium strains. The assay described herein provides an important technological platform for studying sucrose transporter function following heterologous expression in Clostridium.
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Affiliation(s)
- Zhikai Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzymatic Technology, College of Life Science and Technology, Guangxi University, Daxue Road No. 100, Nanning 530005, China.
| | - Lihua Lin
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Bio-refinery, Guangxi Academy of Sciences, Daling Road No. 98, Nanning 530007, China.
| | - Hongchi Tang
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Bio-refinery, Guangxi Academy of Sciences, Daling Road No. 98, Nanning 530007, China.
| | - Shaowei Zeng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzymatic Technology, College of Life Science and Technology, Guangxi University, Daxue Road No. 100, Nanning 530005, China.
| | - Yuan Guo
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Bio-refinery, Guangxi Academy of Sciences, Daling Road No. 98, Nanning 530007, China.
| | - Yutuo Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzymatic Technology, College of Life Science and Technology, Guangxi University, Daxue Road No. 100, Nanning 530005, China.
| | - Ribo Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzymatic Technology, College of Life Science and Technology, Guangxi University, Daxue Road No. 100, Nanning 530005, China.
| | - Hao Pang
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Bio-refinery, Guangxi Academy of Sciences, Daling Road No. 98, Nanning 530007, China.
| | - Liqin Du
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi Research Center for Microbial and Enzymatic Technology, College of Life Science and Technology, Guangxi University, Daxue Road No. 100, Nanning 530005, China.
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Characterisation of novel biomass degradation enzymes from the genome of Cellulomonas fimi. Enzyme Microb Technol 2018; 113:9-17. [PMID: 29602392 PMCID: PMC5892457 DOI: 10.1016/j.enzmictec.2018.02.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 12/11/2017] [Accepted: 02/12/2018] [Indexed: 01/06/2023]
Abstract
Identified over 90 putative polysaccharide degrading ORFs in C. fimi genome. Cloned 14 putative cellulolytic ORFs as BioBricks, screened them for activity. Partially purified AfsB, BxyF, BxyH and XynF and characterised them further. BxyH proved highly temperature and alkaline pH tolerant. BioBricks are an easy method for screening genes for specific activities.
Recent analyses of genome sequences belonging to cellulolytic bacteria have revealed many genes potentially coding for cellulosic biomass degradation enzymes. Annotation of these genes however, is based on few biochemically characterised examples. Here we present a simple strategy based on BioBricks for the rapid screening of candidate genes expressed in Escherichia coli. As proof of principle we identified over 70 putative biomass degrading genes from bacterium Cellulomonas fimi, expressing a subset of these in BioBrick format. Six novel genes showed activity in E. coli. Four interesting enzymes were characterised further. α-l-arabinofuranosidase AfsB, β-xylosidases BxyF and BxyH and multi-functional β-cellobiosidase/xylosidase XynF were partially purified to determine their optimum pH, temperature and kinetic parameters. One of these enzymes, BxyH, was unexpectedly found to be highly active at strong alkaline pH and at temperatures as high as 100 °C. This report demonstrates a simple method of quickly screening and characterising putative genes as BioBricks.
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Biswas S, Katiyar R, Gurjar BR, Pruthi V. Role of Different Feedstocks on the Butanol Production Through Microbial and Catalytic Routes. INTERNATIONAL JOURNAL OF CHEMICAL REACTOR ENGINEERING 2018. [DOI: 10.1515/ijcre-2016-0215] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Among the renewable fuels, butanol has become an attractive, economic and sustainable choice because of cost elevation in petroleum fuel, diminishing the oil reserves and an increase of green house effect. Butanol can be derived from renewable sources by using the natural bio-resources and agro-wastes such as orchard wastes, peanut wastes, wheat straw, barley straw and grasses via Acetone Butanol Ethanol (ABE) process. On the other hand, butanol can be directly formed from chemical route involving catalysts also such as from ethanol through aldol condensation. This review presents extensive evaluation for the production of butanol deploying microbial and catalytic routes.
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Affiliation(s)
- Shalini Biswas
- Centre for Transportation Systems , Indian Institute of Technology Roorkee , Roorkee , Uttarakhand 247667 , India
| | - Richa Katiyar
- Centre for Transportation Systems , Indian Institute of Technology Roorkee , Roorkee , Uttarakhand 247667 , India
| | - B. R. Gurjar
- Centre for Transportation Systems , Indian Institute of Technology Roorkee , Roorkee , Uttarakhand 247667 , India
| | - Vikas Pruthi
- Centre for Transportation Systems , Indian Institute of Technology Roorkee , Roorkee , Uttarakhand 247667 , India
- Department of Biotechnology , Indian Institute of Technology Roorkee , Roorkee , Uttarakhand 247667 , India
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7
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Yamaguchi S, Kawada Y, Yuge H, Tanaka K, Imamura S. Development of New Carbon Resources: Production of Important Chemicals from Algal Residue. Sci Rep 2017; 7:855. [PMID: 28405002 PMCID: PMC5429806 DOI: 10.1038/s41598-017-00979-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 03/17/2017] [Indexed: 12/19/2022] Open
Abstract
Algal biomass has received attention as an alternative carbon resource owing not only to its high oil production efficiency but also, unlike corn starch, to its lack of demand in foods. However, algal residue is commonly discarded after the abstraction of oil. The utilization of the residue to produce chemicals will therefore increase the value of using algal biomass instead of fossil fuels. Here, we report the use of algal residue as a new carbon resource to produce important chemicals. The application of different homogeneous catalysts leads to the selective production of methyl levulinate or methyl lactate. These results demonstrate the successful development of new carbon resources as a solution for the depletion of fossil fuels.
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Affiliation(s)
- Sho Yamaguchi
- Department of Chemical Science and Engineering, School of Materials and Chemical Technology, Tokyo Institute of Technology, 4259-G1-14 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8502, Japan.
| | - Yuuki Kawada
- Department of Chemistry, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Hidetaka Yuge
- Department of Chemistry, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Kan Tanaka
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259-R1-30 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8502, Japan.,Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Saitama, 332-0012, Japan
| | - Sousuke Imamura
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259-R1-30 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8502, Japan.,Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Saitama, 332-0012, Japan
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8
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Demkina EV, Shanenko EF, Nikolaev YA, El’-Registan GI. Model of the regulation of activity of immobilized enzymes (amylases) in soil. Microbiology (Reading) 2017. [DOI: 10.1134/s0026261717020060] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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9
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Winfough M, Yao R, Ng M, Catani K, Meloni G. Synchrotron Photoionization Investigation of the Oxidation of Ethyl tert-Butyl Ether. J Phys Chem A 2017; 121:1460-1469. [PMID: 28152311 DOI: 10.1021/acs.jpca.6b11507] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The oxidation of ethyl tert-butyl ether (ETBE), a widely used fuel oxygenated additive, is investigated using Cl atoms as initiators in the presence of oxygen. The reaction is carried out at 293, 550, and 700 K. Reaction products are probed by a multiplexed chemical kinetics photoionization mass spectrometer coupled with the synchrotron radiation produced at the Advanced Light Source (ALS) of the Lawrence Berkeley National Laboratory. Products are identified on the basis of mass-to-charge ratio, ionization energies, and shape of photoionization spectra. Reaction pathways are proposed together with detected primary products.
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Affiliation(s)
- Matthew Winfough
- Department of Chemistry, University of San Francisco , San Francisco, California 94117-1080, United States
| | - Rong Yao
- Department of Chemistry, University of San Francisco , San Francisco, California 94117-1080, United States
| | - Martin Ng
- Department of Chemistry, University of San Francisco , San Francisco, California 94117-1080, United States
| | - Katherine Catani
- Department of Chemistry, University of San Francisco , San Francisco, California 94117-1080, United States
| | - Giovanni Meloni
- Department of Chemistry, University of San Francisco , San Francisco, California 94117-1080, United States
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10
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Liang M, Zhou X, Xu C. Systems biology in biofuel. PHYSICAL SCIENCES REVIEWS 2016. [DOI: 10.1515/psr-2016-0047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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11
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Salamanca-Cardona L, Scheel RA, Bergey NS, Stipanovic AJ, Matsumoto K, Taguchi S, Nomura CT. Consolidated bioprocessing of poly(lactate-co-3-hydroxybutyrate) from xylan as a sole feedstock by genetically-engineered Escherichia coli. J Biosci Bioeng 2016; 122:406-14. [PMID: 27067372 DOI: 10.1016/j.jbiosc.2016.03.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 03/09/2016] [Accepted: 03/14/2016] [Indexed: 10/22/2022]
Abstract
Consolidated bioprocessing of lignocellulose is an attractive strategy for the sustainable production of petroleum-based alternatives. One of the underutilized sources of carbon in lignocellulose is the hemicellulosic fraction which largely consists of the polysaccharide xylan. In this study, Escherichia coli JW0885 (pyruvate formate lyase activator protein mutant, pflA(-)) was engineered to express recombinant xylanases and polyhydroxyalkanoate (PHA)-producing enzymes for the biosynthesis of poly(lactate-co-3-hydroxybutyrate) [P(LA-co-3HB)] from xylan as a consolidated bioprocess. The results show that E. coli JW0885 was capable of producing P(LA-co-3HB) when xylan was the only feedstock and different feeding and growth parameters were examined in order to improve upon initial yields. The highest yields of P(LA-co-3HB) copolymer obtained in this study occurred when xylan was added during mid-exponential growth after cells had been grown at high shaking-speeds (290 rpm). The results showed an inverse relationship between total PHA production and LA-monomer incorporation into the copolymer. Proton nuclear magnetic resonance ((1)H NMR), gel permeation chromatography (GPC), and differential scanning calorimetry (DSC) analyses corroborate that the polymers produced maintain physical properties characteristic of LA-incorporating PHB-based copolymers. The present study achieves the first ever engineering of a consolidated bioprocessing bacterial system for the production of a bioplastic from a hemicelluosic feedstock.
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Affiliation(s)
- Lucia Salamanca-Cardona
- Department of Chemistry, State University of New York, College of Environmental Science and Forestry, Syracuse, NY 13210, USA
| | - Ryan A Scheel
- Department of Chemistry, State University of New York, College of Environmental Science and Forestry, Syracuse, NY 13210, USA
| | - Norman Scott Bergey
- Department of Chemistry, State University of New York, College of Environmental Science and Forestry, Syracuse, NY 13210, USA
| | - Arthur J Stipanovic
- Department of Chemistry, State University of New York, College of Environmental Science and Forestry, Syracuse, NY 13210, USA
| | - Ken'ichiro Matsumoto
- Division of Biotechnology and Macromolecular Chemistry, Graduate School of Engineering, Hokkaido University, N13-28, Kita-ku, Sapporo 060-8638, Japan
| | - Seiichi Taguchi
- Division of Biotechnology and Macromolecular Chemistry, Graduate School of Engineering, Hokkaido University, N13-28, Kita-ku, Sapporo 060-8638, Japan; CREST, JST, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Christopher T Nomura
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, College of Life Sciences, Hubei University, Wuhan 430062, People's Republic of China; Department of Chemistry, State University of New York, College of Environmental Science and Forestry, Syracuse, NY 13210, USA; Center for Applied Microbiology, State University of New York, College of Environmental Science and Forestry, Syracuse, NY 13210, USA.
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Deneyer A, Renders T, Van Aelst J, Van den Bosch S, Gabriëls D, Sels BF. Alkane production from biomass: chemo-, bio- and integrated catalytic approaches. Curr Opin Chem Biol 2015; 29:40-8. [DOI: 10.1016/j.cbpa.2015.08.010] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 08/12/2015] [Accepted: 08/17/2015] [Indexed: 10/23/2022]
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Wallenstein MD, Burns RG. Ecology of Extracellular Enzyme Activities and Organic Matter Degradation in Soil: A Complex Community-Driven Process. SSSA BOOK SERIES 2015. [DOI: 10.2136/sssabookser9.c2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Affiliation(s)
| | - Richard G. Burns
- School of Agriculture and Food Sciences; University of Queensland; Brisbane Australia
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Ndaba B, Chiyanzu I, Marx S. n-Butanol derived from biochemical and chemical routes: A review. ACTA ACUST UNITED AC 2015; 8:1-9. [PMID: 28352567 PMCID: PMC4980751 DOI: 10.1016/j.btre.2015.08.001] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 07/24/2015] [Accepted: 08/01/2015] [Indexed: 10/31/2022]
Abstract
Traditionally, bio-butanol is produced with the ABE (Acetone Butanol Ethanol) process using Clostridium species to ferment sugars from biomass. However, the route is associated with some disadvantages such as low butanol yield and by-product formation (acetone and ethanol). On the other hand, butanol can be directly produced from ethanol through aldol condensation over metal oxides/ hydroxyapatite catalysts. This paper suggests that the chemical conversion route is more preferable than the ABE process, because the reaction proceeds more quickly compared to the fermentation route and fewer steps are required to get to the product.
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Affiliation(s)
- B Ndaba
- Focus area: Energy system, School of Chemical and Minerals Engineering, North-West University (Potchefstroom Campus), Potchefstroom, South Africa
| | - I Chiyanzu
- Focus area: Energy system, School of Chemical and Minerals Engineering, North-West University (Potchefstroom Campus), Potchefstroom, South Africa
| | - S Marx
- Focus area: Energy system, School of Chemical and Minerals Engineering, North-West University (Potchefstroom Campus), Potchefstroom, South Africa
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Kim DY, Shin DH, Jung S, Lee JS, Cho HY, Bae KS, Sung CK, Rhee YH, Son KH, Park HY. Biocatalytic properties and substrate-binding ability of a modular GH10 β-1,4-xylanase from an insect-symbiotic bacterium, Streptomyces mexicanus HY-14. J Microbiol 2014; 52:863-70. [PMID: 25269606 DOI: 10.1007/s12275-014-4390-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 09/11/2014] [Accepted: 09/15/2014] [Indexed: 11/29/2022]
Abstract
The gene (1350-bp) encoding a modular β-1,4-xylanase (XylU), which consists of an N-terminal catalytic GH10 domain and a C-terminal carbohydrate-binding module 2 (CBM 2), from Streptomyces mexicanus HY-14 was cloned and functionally characterized. The purified His-tagged recombinant enzyme (rXylU, 44.0 kDa) was capable of efficiently hydrolyze diverse xylosidic compounds, p-nitrophenyl-cellobioside, and p-nitrophenyl-xylopyranoside when incubated at pH 5.5 and 65°C. Especially, the specific activities (649.8 U/mg and 587.0 U/mg, respectively) of rXylU toward oat spelts xylan and beechwood xylan were relatively higher than those (<500.0 U/mg) of many other GH10 homologs toward the same substrates. The results of enzymatic degradation of birchwood xylan and xylooligosaccharides (xylotriose to xylohexaose) revealed that rXylU preferentially hydrolyzed the substrates to xylobiose (>75%) as the primary degradation product. Moreover, a small amount (4%<) of xylose was detected as the degradation product of the evaluated xylosidic substrates, indicating that rXylU was a peculiar GH10 β-1,4-xylanase with substrate specificity, which was different from its retaining homologs. A significant reduction of the binding ability of rXylU caused by deletion of the C-terminal CBM 2 to various insoluble substrates strongly suggested that the additional domain might considerably contribute to the enzyme-substrate interaction.
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Affiliation(s)
- Do Young Kim
- Industrial Bio-materials Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 305-806, Republic of Korea
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Correcting direct effects of ethanol on translation and transcription machinery confers ethanol tolerance in bacteria. Proc Natl Acad Sci U S A 2014; 111:E2576-85. [PMID: 24927582 DOI: 10.1073/pnas.1401853111] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The molecular mechanisms of ethanol toxicity and tolerance in bacteria, although important for biotechnology and bioenergy applications, remain incompletely understood. Genetic studies have identified potential cellular targets for ethanol and have revealed multiple mechanisms of tolerance, but it remains difficult to separate the direct and indirect effects of ethanol. We used adaptive evolution to generate spontaneous ethanol-tolerant strains of Escherichia coli, and then characterized mechanisms of toxicity and resistance using genome-scale DNAseq, RNAseq, and ribosome profiling coupled with specific assays of ribosome and RNA polymerase function. Evolved alleles of metJ, rho, and rpsQ recapitulated most of the observed ethanol tolerance, implicating translation and transcription as key processes affected by ethanol. Ethanol induced miscoding errors during protein synthesis, from which the evolved rpsQ allele protected cells by increasing ribosome accuracy. Ribosome profiling and RNAseq analyses established that ethanol negatively affects transcriptional and translational processivity. Ethanol-stressed cells exhibited ribosomal stalling at internal AUG codons, which may be ameliorated by the adaptive inactivation of the MetJ repressor of methionine biosynthesis genes. Ethanol also caused aberrant intragenic transcription termination for mRNAs with low ribosome density, which was reduced in a strain with the adaptive rho mutation. Furthermore, ethanol inhibited transcript elongation by RNA polymerase in vitro. We propose that ethanol-induced inhibition and uncoupling of mRNA and protein synthesis through direct effects on ribosomes and RNA polymerase conformations are major contributors to ethanol toxicity in E. coli, and that adaptive mutations in metJ, rho, and rpsQ help protect these central dogma processes in the presence of ethanol.
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Dahmen I, Chtourou H, Jebali A, Daassi D, Karray F, Hassairi I, Sayadi S, Abdelkafi S, Dhouib A. Optimisation of the critical medium components for better growth of Picochlorum sp. and the role of stressful environments for higher lipid production. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2014; 94:1628-1638. [PMID: 24301903 DOI: 10.1002/jsfa.6470] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 10/09/2013] [Accepted: 11/04/2013] [Indexed: 06/02/2023]
Abstract
BACKGROUND Coastal countries that suffer from a scarcity of water, such as Tunisia, have to cultivate marine microalgae on non-arable land in order to produce feedstock and overcome their demands of nutrition and energy. In this framework, a green microalga, CTM 20019, was isolated, identified as Picochlorum sp. and tested for its lipid production. RESULTS The dry weight of Picochlorum sp. is composed of 163 g kg(-1) lipids, 225 g kg(-1) total sugars, 440 g kg(-1) proteins and 112 g kg(-1) ash rich in potassium, calcium, iron, magnesium and zinc. Gas chromatography-mass spectrometry analysis showed that the main fatty acids were palmitic acid (29%), linolenic acid (26.5%), linoleic acid (23.5%), hexadecatrienoic acid (11%) and hexadecadienoic acid (8.5%). As it is known that culture conditions greatly influence the composition of microalgae, the experiments were designed to optimise the composition of the medium in order to increase Picochlorum sp. growth from OD680nm = 0.53 to OD680nm = 2.2 and lipid accumulation from 163 g kg(-1) to 190 g kg(-1) . The highest lipid contents of 570 and 585 g kg(-1) were achieved under phosphate starvation and sodium carbonate supplementation, respectively. Under these conditions, the fatty acid profile is dominated by mono-unsaturated and polyunsaturated acids, and is therefore suitable for aqua-culture feeding. However, under high salinity, growth and lipid synthesis are inhibited, and the fatty acids are saturate, and the product is therefore suitable for biodiesel. CONCLUSION This high lipid content rich in essential fatty acids, omega-6 and omega-3, endorses this wild strain of Picochlorum sp. as a promising feedstock for aqua-culture and human nutrition or for the production of biodiesel. © 2013 Society of Chemical Industry.
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Affiliation(s)
- Ines Dahmen
- Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, University of Sfax, Sidi Mansour Road Km 6, P.O. Box «1177», 3018, Sfax, Tunisia
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Liu Y, Tan H, Deng Q, Cao L. Characterization of fibrolytic and lipid accumulating fungi isolated from fresh cattle feces. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2014; 21:9228-9233. [PMID: 24710729 DOI: 10.1007/s11356-014-2846-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Accepted: 03/26/2014] [Indexed: 06/03/2023]
Abstract
To characterize coprophilous fungi for converting lignocellulose into lipids, four fungal strains utilizing cellulose microcrystalline and xylan were screened. The fungi were identified as Cladosporium sp. F1, Circinella sp. F6, Mycocladus sp. F49, and Byssochlamys sp. F52 based on the ITS1-5.8S-ITS2 sequence similarity. The strain F52 accumulated 336.0 mg/L reducing sugars on cottonseed shells treated with ethanol. The combination of F1+F52 increased the reducing sugar accumulating rates. However, the activities of avicelase and xylanase were not correlated with the reducing sugars accumulated by the test strains. Strains F6 and F52 produced higher cellular lipids (above 530.7 mg/L) than other strains. However, the strain F52 could produce more cellular lipids with xylose and mannose as the sole carbon sources. The results indicated that the reducing sugar contents accumulated by the different strains were influenced by the fungal taxa and ligocellulosic types. With fibrolytic and lipid accumulating activities, diverse fungi harboring in herbivore feces need to be further characterized.
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Affiliation(s)
- Yupei Liu
- School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
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Liu Y, Wang C, Yan J, Zhang W, Guan W, Lu X, Li S. Hydrogen peroxide-independent production of α-alkenes by OleTJE P450 fatty acid decarboxylase. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:28. [PMID: 24565055 PMCID: PMC3937522 DOI: 10.1186/1754-6834-7-28] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 02/10/2014] [Indexed: 05/21/2023]
Abstract
BACKGROUND Cytochrome P450 OleTJE from Jeotgalicoccus sp. ATCC 8456, a new member of the CYP152 peroxygenase family, was recently found to catalyze the unusual decarboxylation of long-chain fatty acids to form α-alkenes using H2O2 as the sole electron and oxygen donor. Because aliphatic α-alkenes are important chemicals that can be used as biofuels to replace fossil fuels, or for making lubricants, polymers and detergents, studies on OleTJE fatty acid decarboxylase are significant and may lead to commercial production of biogenic α-alkenes in the future, which are renewable and more environmentally friendly than petroleum-derived equivalents. RESULTS We report the H2O2-independent activity of OleTJE for the first time. In the presence of NADPH and O2, this P450 enzyme efficiently decarboxylates long-chain fatty acids (C12 to C20) in vitro when partnering with either the fused P450 reductase domain RhFRED from Rhodococcus sp. or the separate flavodoxin/flavodoxin reductase from Escherichia coli. In vivo, expression of OleTJE or OleTJE-RhFRED in different E. coli strains overproducing free fatty acids resulted in production of variant levels of multiple α-alkenes, with a highest total hydrocarbon titer of 97.6 mg·l-1. CONCLUSIONS The discovery of the H2O2-independent activity of OleTJE not only raises a number of fundamental questions on the monooxygenase-like mechanism of this peroxygenase, but also will direct the future metabolic engineering work toward improvement of O2/redox partner(s)/NADPH for overproduction of α-alkenes by OleTJE.
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Affiliation(s)
- Yi Liu
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cong Wang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong 266101, China
| | - Jinyong Yan
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong 266101, China
| | - Wei Zhang
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong 266101, China
| | - Wenna Guan
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong 266101, China
| | - Xuefeng Lu
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong 266101, China
| | - Shengying Li
- Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong 266101, China
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Nikel PI, de Lorenzo V. Robustness of Pseudomonas putida KT2440 as a host for ethanol biosynthesis. N Biotechnol 2014; 31:562-71. [PMID: 24572656 DOI: 10.1016/j.nbt.2014.02.006] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 02/10/2014] [Accepted: 02/15/2014] [Indexed: 12/01/2022]
Abstract
Expansion of the burgeoning biofuels agenda involves not only the design of suitable genetic and metabolic devices but also their deployment into suitable hosts that can endure the stress brought about by the products themselves. The microorganisms that are easiest to genetically manipulate for these endeavors (e.g. Escherichia coli) are often afflicted by an undesirable sensitivity to the very product that they are engineered to synthesize. In this context, we have examined the resistance to the stress arising from ethanol synthesis and/or its addition to cultures of recombinant Pseudomonas putida, using as a benchmark the same trait in an E. coli strain. To this end, ethanologenic strains of these two species were constructed by functionally expressing pdc (pyruvate decarboxylase) and adhB (alcohol dehydrogenase) from Zymomonas mobilis. Recombinants were compared under anoxic conditions as ethanol producers, and cell survival, stress resistance, and phenotypic stability were quantified in each case. P. putida consistently outperformed E. coli in every ethanol tolerance test conducted - whether the alcohol was produced endogenously or added exogenously. These results highlight the value of this bacterium as a microbial cell factory for the production of biofuels owing to its naturally pre-evolved ability to withstand different kinds of chemical stresses.
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Affiliation(s)
- Pablo I Nikel
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Madrid 28049, Spain
| | - Víctor de Lorenzo
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Madrid 28049, Spain.
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21
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Phukan MM, Singh SP, Phukon P, Borah T, Konwar BK, Dutta N. Production and statistical optimization of biodiesel from kitchen chimney dump lard. ACTA ACUST UNITED AC 2013. [DOI: 10.1186/2043-7129-1-12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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22
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Polyester synthesis genes associated with stress resistance are involved in an insect-bacterium symbiosis. Proc Natl Acad Sci U S A 2013; 110:E2381-9. [PMID: 23757494 DOI: 10.1073/pnas.1303228110] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Many bacteria accumulate granules of polyhydroxyalkanoate (PHA) within their cells, which confer resistance to nutritional depletion and other environmental stresses. Here, we report an unexpected involvement of the bacterial endocellular storage polymer, PHA, in an insect-bacterium symbiotic association. The bean bug Riptortus pedestris harbors a beneficial and specific gut symbiont of the β-proteobacterial genus Burkholderia, which is orally acquired by host nymphs from the environment every generation and easily cultivable and genetically manipulatable. Biochemical and cytological comparisons between symbiotic and cultured Burkholderia detected more PHA granules consisting of poly-3-hydroxybutyrate and associated phasin (PhaP) protein in the symbiotic Burkholderia. Among major PHA synthesis genes, phaB and phaC were disrupted by homologous recombination together with the phaP gene, whereby ΔphaB, ΔphaC, and ΔphaP mutants were generated. Both in culture and in symbiosis, accumulation of PHA granules was strongly suppressed in ΔphaB and ΔphaC, but only moderately in ΔphaP. In symbiosis, the host insects infected with ΔphaB and ΔphaC exhibited significantly lower symbiont densities and smaller body sizes. These deficient phenotypes associated with ΔphaB and ΔphaC were restored by complementation of the mutants with plasmids encoding a functional phaB/phaC gene. Retention analysis of the plasmids revealed positive selection acting on the functional phaB/phaC in symbiosis. These results indicate that the PHA synthesis genes of the Burkholderia symbiont are required for normal symbiotic association with the Riptortus host. In vitro culturing analyses confirmed vulnerability of the PHA gene mutants to environmental stresses, suggesting that PHA may play a role in resisting stress under symbiotic conditions.
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Chan JMW, Bauer S, Sorek H, Sreekumar S, Wang K, Toste FD. Studies on the Vanadium-Catalyzed Nonoxidative Depolymerization of Miscanthus giganteus-Derived Lignin. ACS Catal 2013. [DOI: 10.1021/cs400333q] [Citation(s) in RCA: 139] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Julian M. W. Chan
- Department of Chemistry, University of California, Berkeley, Berkeley, California
94720, United States
- Energy Biosciences Institute (EBI), Berkeley, California 94720, United
States
| | - Stefan Bauer
- Energy Biosciences Institute (EBI), Berkeley, California 94720, United
States
| | - Hagit Sorek
- Energy Biosciences Institute (EBI), Berkeley, California 94720, United
States
| | - Sanil Sreekumar
- Department of Chemistry, University of California, Berkeley, Berkeley, California
94720, United States
- Energy Biosciences Institute (EBI), Berkeley, California 94720, United
States
| | - Kun Wang
- Department of Chemistry, University of California, Berkeley, Berkeley, California
94720, United States
- Institute of Biomass
Chemistry
and Technology, Beijing Forestry University, Beijing 100083, China
| | - F. Dean Toste
- Department of Chemistry, University of California, Berkeley, Berkeley, California
94720, United States
- Energy Biosciences Institute (EBI), Berkeley, California 94720, United
States
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Kim HJ, Turner TL, Jin YS. Combinatorial genetic perturbation to refine metabolic circuits for producing biofuels and biochemicals. Biotechnol Adv 2013; 31:976-85. [PMID: 23562845 DOI: 10.1016/j.biotechadv.2013.03.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 03/18/2013] [Accepted: 03/28/2013] [Indexed: 12/25/2022]
Abstract
Recent advances in metabolic engineering have enabled microbial factories to compete with conventional processes for producing fuels and chemicals. Both rational and combinatorial approaches coupled with synthetic and systematic tools play central roles in metabolic engineering to create and improve a selected microbial phenotype. Compared to knowledge-based rational approaches, combinatorial approaches exploiting biological diversity and high-throughput screening have been demonstrated as more effective tools for improving various phenotypes of interest. In particular, identification of unprecedented targets to rewire metabolic circuits for maximizing yield and productivity of a target chemical has been made possible. This review highlights general principles and the features of the combinatorial approaches using various libraries to implement desired phenotypes for strain improvement. In addition, recent applications that harnessed the combinatorial approaches to produce biofuels and biochemicals will be discussed.
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Affiliation(s)
- Hyo Jin Kim
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, 1206 West Gregory Dr., Urbana, IL 61801, USA
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Chong H, Huang L, Yeow J, Wang I, Zhang H, Song H, Jiang R. Improving ethanol tolerance of Escherichia coli by rewiring its global regulator cAMP receptor protein (CRP). PLoS One 2013; 8:e57628. [PMID: 23469036 PMCID: PMC3585226 DOI: 10.1371/journal.pone.0057628] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 01/21/2013] [Indexed: 11/19/2022] Open
Abstract
A major challenge in bioethanol fermentation is the low tolerance of the microbial host towards the end product bioethanol. Here we report to improve the ethanol tolerance of E. coli from the transcriptional level by engineering its global transcription factor cAMP receptor protein (CRP), which is known to regulate over 400 genes in E. coli. Three ethanol tolerant CRP mutants (E1- E3) were identified from error-prone PCR libraries. The best ethanol-tolerant strain E2 (M59T) had the growth rate of 0.08 h(-1) in 62 g/L ethanol, higher than that of the control at 0.06 h(-1). The M59T mutation was then integrated into the genome to create variant iE2. When exposed to 150 g/l ethanol, the survival of iE2 after 15 min was about 12%, while that of BW25113 was <0.01%. Quantitative real-time reverse transcription PCR analysis (RT-PCR) on 444 CRP-regulated genes using OpenArray® technology revealed that 203 genes were differentially expressed in iE2 in the absence of ethanol, whereas 92 displayed differential expression when facing ethanol stress. These genes belong to various functional groups, including central intermediary metabolism (aceE, acnA, sdhD, sucA), iron ion transport (entH, entD, fecA, fecB), and general stress response (osmY, rpoS). Six up-regulated and twelve down-regulated common genes were found in both iE2 and E2 under ethanol stress, whereas over one hundred common genes showed differential expression in the absence of ethanol. Based on the RT-PCR results, entA, marA or bhsA was knocked out in iE2 and the resulting strains became more sensitive towards ethanol.
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Affiliation(s)
- Huiqing Chong
- School of Chemical & Biomedical Engineering, Nanyang Technological University, Singapore
| | - Lei Huang
- Institute of Biological Engineering, Department of Chemical and Biological Engineering, Zhejiang University, Hangzhou, P. R. China
| | - Jianwei Yeow
- System Engineering, Life Technologies, Singapore
| | - Ivy Wang
- System Engineering, Life Technologies, Singapore
| | - Hongfang Zhang
- School of Chemical & Biomedical Engineering, Nanyang Technological University, Singapore
| | - Hao Song
- School of Chemical & Biomedical Engineering, Nanyang Technological University, Singapore
| | - Rongrong Jiang
- School of Chemical & Biomedical Engineering, Nanyang Technological University, Singapore
- * E-mail:
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Lertwattanasakul N, Murata M, Rodrussamee N, Limtong S, Kosaka T, Yamada M. Essentiality of respiratory activity for pentose utilization in thermotolerant yeast Kluyveromyces marxianus DMKU 3-1042. Antonie van Leeuwenhoek 2013; 103:933-45. [PMID: 23338601 DOI: 10.1007/s10482-012-9874-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2012] [Accepted: 12/31/2012] [Indexed: 11/26/2022]
Abstract
By random integrative mutagenesis with a kanMX4 cassette in Kluyveromyces marxianus DMKU 3-1042, we obtained three mutants of COX15, ATP25 and CYC3 encoding a cytochrome oxidase assembly factor (singleton), a transcription factor required for assembly of the Atp9p subunit of mitochondrial ATP synthase and cytochrome c heme lyase, respectively, as mutants lacking growth capability on xylose and/or arabinose. They exhibited incapability of growth on non-fermentable carbon sources, such as acetate or glycerol, and thermosensitiveness. Their biomass formation in glucose medium was reduced, but ethanol yields were increased with a high ethanol level in the medium, compared to those of the parental strain. Experiments with respiratory inhibitors showed that cox15 and cyc3, but not atp25, were able to grow in glucose medium containing antimycin A and that the atp25 mutant was KCN-resistant. Activities of NADH and ubiquinol oxidases in membrane fractions of each mutant became a half of that of the parent and negligible, respectively, and their remaining NADH oxidase activities were found to be resistant to KCN. Absolute absorption spectral analysis revealed that the peak corresponding to a + a 3 was very small in atp25 and negligible in cox15 and cyc3. These findings suggest that the K. marxianus strain possesses an alternative KCN-resistant oxidase that is located between primary dehydrogenases and the ubiquinone pool and that the respiratory activity is essential for utilization of pentoses.
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Affiliation(s)
- Noppon Lertwattanasakul
- Applied Molecular Bioscience, Graduate School of Medicine, Yamaguchi University, Ube, 755-8505, Japan.
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27
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Gu F, Yang L, Jin Y, Han Q, Chang HM, Jameel H, Phillips R. Green liquor pretreatment for improving enzymatic hydrolysis of corn stover. BIORESOURCE TECHNOLOGY 2012; 124:299-305. [PMID: 22989657 DOI: 10.1016/j.biortech.2012.08.054] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Revised: 08/12/2012] [Accepted: 08/14/2012] [Indexed: 05/06/2023]
Abstract
Green liquor consists of sodium carbonate and sodium sulfide and is readily available in any kraft mills. The green liquor pretreatment process for bioethanol production was developed for wood chips. This process uses only proven technology and equipment currently used in a kraft pulp mill and has several additional advantages such as high sugar recovery and concentration, no inhibitive substances produced, as compared to acid-based pretreatment methods. The liquor was used to pretreat corn stover for enhancing enzymatic hydrolysis in bioethanol production. Pulp yield of 70% with 45% lignin removal was achieved under optimized conditions (8% total titratable alkali, 40% sulfidity and 140°C). About 70% of the original polysaccharides were converted into fermentable sugars, using 20 FPU/g-pulp of enzyme in the subsequent enzymatic hydrolysis. The result indicates that green liquor is a feasible pretreatment to improve the enzymatic saccharification of corn stover for bioethanol production.
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Affiliation(s)
- Feng Gu
- Jiangsu Provincial Key Laboratory of Pulp and Paper Science and Technology, Nanjing Forestry University, Nanjing 210037, China.
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28
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Biomass Converting Enzymes as Industrial Biocatalysts for Fuels and Chemicals: Recent Developments. Catalysts 2012. [DOI: 10.3390/catal2020244] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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Mao S, Jia K, Zhang Y, Li Y. Use of proteomic tools in microbial engineering for biofuel production. Methods Mol Biol 2012; 834:137-51. [PMID: 22144358 DOI: 10.1007/978-1-61779-483-4_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The production of biofuels from renewable sources by microbial engineering has gained increased attention due to energy and environmental concerns. Butanol is one of the important gasoline-substitute fuels and can be produced by native microorganism Clostridium acetobutylicum. To develop a fundamental tool to understand C. acetobutylicum, a high resolution proteome reference map for this species has been established. To better understand the relationship between butanol tolerance and butanol yield, we performed a comparative proteomic analysis between the wild-type strain DSM 1731 and its mutant Rh8 at acidogenic and solventogenic phases, respectively. The 102 differentially expressed proteins that are mainly involved in protein folding, solvent formation, amino acid metabolism, protein synthesis, nucleotide metabolism, transport, and others were detected. Hierarchical clustering analysis revealed that over 70% of the 102 differentially expressed proteins in mutant Rh8 were either upregulated (e.g., chaperones and solvent formation related) or downregulated (e.g., amino acid metabolism and protein synthesis related) in both acidogenic and solventogenic phase, which, respectively, are only upregulated or downregulated in solventogenic phase in the wild-type strain.
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Affiliation(s)
- Shaoming Mao
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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30
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Efficiency of acetone-butanol-ethanol-water system separation by pervaporation. CHEMICAL AND PROCESS ENGINEERING 2012. [DOI: 10.2478/v10176-012-0012-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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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.
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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:
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32
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Freese S, Passoth V, Klinner U. A mutation in the COX5 gene of the yeast Scheffersomyces stipitis alters utilization of amino acids as carbon source, ethanol formation and activity of cyanide insensitive respiration. Yeast 2011; 28:309-20. [PMID: 21456056 DOI: 10.1002/yea.1840] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2010] [Accepted: 11/26/2010] [Indexed: 11/06/2022] Open
Abstract
Scheffersomyces stipitis PJH was mutagenized by random integrative mutagenesis and the integrants were screened for lacking the ability to grow with glutamate as sole carbon source. One of the two isolated mutants was damaged in the COX5 gene, which encodes a subunit of the cytochrome c oxidase. BLAST searches in the genome of Sc. stipitis revealed that only one singular COX5 gene exists in Sc. stipitis, in contrast to Saccharomyces cerevisiae, where two homologous genes are present. Mutant cells had lost the ability to grow with the amino acids glutamate, proline or aspartate and other non-fermentable carbon sources, such as acetic acid and ethanol, as sole carbon sources. Biomass formation of the mutant cells in medium containing glucose or xylose as carbon source was lower compared with the wild-type cells. However, yields and specific ethanol formation of the mutant were much higher, especially under conditions of higher aeration. The mutant cells lacked both cytochrome c oxidase activity and cyanide-sensitive respiration, whereas ADH and PDC activities were distinctly enhanced. SHAM-sensitive respiration was obviously essential for the fermentative metabolism, because SHAM completely abolished growth of the mutant cells with both glucose or xylose as carbon source.
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Affiliation(s)
- Stefan Freese
- RWTH Aachen University, Department of Biology IV (Microbiology und Genetics), Unit Applied Microbiology, Germany.
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Potential of Arabidopsis systems biology to advance the biofuel field. Trends Biotechnol 2010; 28:543-7. [PMID: 20800303 DOI: 10.1016/j.tibtech.2010.07.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2010] [Revised: 07/20/2010] [Accepted: 07/20/2010] [Indexed: 01/01/2023]
Abstract
Plant biomass is a renewable and potentially sustainable resource for the production of liquid biofuels and a multitude of bio-based materials. To tailor plants for biofuel production, a powerful gene discovery program targeted to cell wall recalcitrance genes is needed. In parallel, a system is required that reveals the pleiotropic effects of gene modifications and that delivers the fundamental knowledge necessary for successful gene stacking. In our opinion, these objectives can be pioneered through a systems biology approach in Arabidopsis. We develop our ideas with a focus on the lignin biosynthetic pathway, because lignin is among the most important factors determining cell wall recalcitrance.
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Protein engineering for bioenergy and biomass-based chemicals. Curr Opin Struct Biol 2010; 20:527-32. [DOI: 10.1016/j.sbi.2010.06.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2010] [Accepted: 06/02/2010] [Indexed: 11/18/2022]
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35
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Tran HL, Kwon JS, Kim ZH, Oh Y, Lee CG. Statistical optimization of culture media for growth and lipid production of Botryococcus braunii LB572. BIOTECHNOL BIOPROC E 2010. [DOI: 10.1007/s12257-009-0127-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Boghigian BA, Shi H, Lee K, Pfeifer BA. Utilizing elementary mode analysis, pathway thermodynamics, and a genetic algorithm for metabolic flux determination and optimal metabolic network design. BMC SYSTEMS BIOLOGY 2010; 4:49. [PMID: 20416071 PMCID: PMC2880971 DOI: 10.1186/1752-0509-4-49] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2009] [Accepted: 04/23/2010] [Indexed: 12/25/2022]
Abstract
BACKGROUND Microbial hosts offer a number of unique advantages when used as production systems for both native and heterologous small-molecules. These advantages include high selectivity and benign environmental impact; however, a principal drawback is low yield and/or productivity, which limits economic viability. Therefore a major challenge in developing a microbial production system is to maximize formation of a specific product while sustaining cell growth. Tools to rationally reconfigure microbial metabolism for these potentially conflicting objectives remain limited. Exhaustively exploring combinations of genetic modifications is both experimentally and computationally inefficient, and can become intractable when multiple gene deletions or insertions need to be considered. Alternatively, the search for desirable gene modifications may be solved heuristically as an evolutionary optimization problem. In this study, we combine a genetic algorithm and elementary mode analysis to develop an optimization framework for evolving metabolic networks with energetically favorable pathways for production of both biomass and a compound of interest. RESULTS Utilization of thermodynamically-weighted elementary modes for flux reconstruction of E. coli central metabolism revealed two clusters of EMs with respect to their Delta Gp degrees. For proof of principle testing, the algorithm was applied to ethanol and lycopene production in E. coli. The algorithm was used to optimize product formation, biomass formation, and product and biomass formation simultaneously. Predicted knockouts often matched those that have previously been implemented experimentally for improved product formation. The performance of a multi-objective genetic algorithm showed that it is better to couple the two objectives in a single objective genetic algorithm. CONCLUSION A computationally tractable framework is presented for the redesign of metabolic networks for maximal product formation combining elementary mode analysis (a form of convex analysis), pathway thermodynamics, and a genetic algorithm to optimize the production of two industrially-relevant products, ethanol and lycopene, from E. coli. The designed algorithm can be applied to any small-scale model of cellular metabolism theoretically utilizing any substrate and applied towards the production of any product.
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Affiliation(s)
- Brett A Boghigian
- Tufts University, Department of Chemical & Biological Engineering, Science & Technology Center, 4 Colby Street, Medford, MA 02155, USA
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37
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38
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Li Q, Jiang X, He Y, Li L, Xian M, Yang J. Evaluation of the biocompatibile ionic liquid 1-methyl-3-methylimidazolium dimethylphosphite pretreatment of corn cob for improved saccharification. Appl Microbiol Biotechnol 2010; 87:117-26. [PMID: 20182710 DOI: 10.1007/s00253-010-2484-8] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2009] [Revised: 01/28/2010] [Accepted: 01/29/2010] [Indexed: 11/26/2022]
Affiliation(s)
- Qiang Li
- Key Laboratory of Biofuel, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266071, China
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Yoo C, Jun SY, Lee JY, Ahn CY, Oh HM. Selection of microalgae for lipid production under high levels carbon dioxide. BIORESOURCE TECHNOLOGY 2010; 101 Suppl 1:S71-4. [PMID: 19362826 DOI: 10.1016/j.biortech.2009.03.030] [Citation(s) in RCA: 265] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2008] [Revised: 03/10/2009] [Accepted: 03/12/2009] [Indexed: 05/09/2023]
Abstract
To select microalgae with a high biomass and lipid productivity, Botryococcus braunii, Chlorella vulgaris, and Scenedesmus sp. were cultivated with ambient air containing 10% CO(2) and flue gas. The biomass and lipid productivity for Scenedesmus sp. with 10% CO(2) were 217.50 and 20.65 mg L(-1)d(-1) (9% of biomass), while those for B. braunii were 26.55 and 5.51 mg L(-1)d(-1) (21% of biomass). With flue gas, the lipid productivity for Scenedesmus sp. and B. braunii was increased 1.9-fold (39.44 mg L(-1)d(-1)) and 3.7-fold (20.65 mg L(-1)d(-1)), respectively. Oleic acid, a main component of biodiesel, occupied 55% among the fatty acids in B. braunii. Therefore, the present results suggested that Scenedesmus sp. is appropriate for mitigating CO(2), due to its high biomass productivity and C-fixation ability, whereas B. braunii is appropriate for producing biodiesel, due to its high lipid content and oleic acid proportion.
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Affiliation(s)
- Chan Yoo
- Environmental Biotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
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Adamczak M, Bornscheuer UT, Bednarski W. The application of biotechnological methods for the synthesis of biodiesel. EUR J LIPID SCI TECH 2009. [DOI: 10.1002/ejlt.200900078] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Uthoff S, Bröker D, Steinbüchel A. Current state and perspectives of producing biodiesel-like compounds by biotechnology. Microb Biotechnol 2009; 2:551-65. [PMID: 21255288 PMCID: PMC3815363 DOI: 10.1111/j.1751-7915.2009.00139.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The global demand for crude oil is expected to continue to rise in future while simultaneously oil production is currently reaching its peak. Subsequently, rising oil prices and their negative impacts on economy, together with an increased environmental awareness of our society, directed the focus also on the biotechnological production of fuels. Although a wide variety of such fuels has been suggested, only the production of ethanol and biodiesel has reached a certain economic feasibility and volume, yet. This review focuses on the current state and perspectives of biotechnological production of biodiesel‐like compounds. At present by far most of the produced biodiesel is obtained by chemical transesterification reactions, which cannot meet the demands of a totally ‘green’ fuel production. Therefore, also several biotechnological biodiesel production processes are currently being developed. Biotechnological production can be achieved by purified enzymes in the soluble state, which requires cost‐intensive protein preparation. Alternatively, enzymes could be immobilized on an appropriate matrix, enabling a reuse of the enzyme, although the formation of by‐products may provide difficulties to maintain the enzyme activity. Processes in presence of organic solvents like t‐butanol have been developed, which enhance by‐product solubility and therefore prevent loss of enzyme activity. As another approach the application of whole‐cell catalysis for the production of fatty acid ethyl esters, which is also referred to as ‘microdiesel’, by recombinant microorganisms has recently been suggested.
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Affiliation(s)
- Stefan Uthoff
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstrasse 3, D-48149 Münster, Germany
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Abstract
To move our economy onto a sustainable basis, it is essential that we find a replacement for fossil carbon as a source of liquid fuels and chemical industry feedstocks. Lignocellulosic biomass, available in enormous quantities, is the only feasible replacement. Many micro-organisms are capable of rapid and efficient degradation of biomass, employing a battery of specialized enzymes, but do not produce useful products. Attempts to transfer biomass-degrading capability to industrially useful organisms by heterologous expression of one or a few biomass-degrading enzymes have met with limited success. It seems probable that an effective biomass-degradation system requires the synergistic action of a large number of enzymes, the individual and collective actions of which are poorly understood. By offering the ability to combine any number of transgenes in a modular, combinatorial way, synthetic biology offers a new approach to elucidating the synergistic action of combinations of biomass-degrading enzymes in vivo and may ultimately lead to a transferable biomass-degradation system. Also, synthetic biology offers the potential for assembly of novel product-formation pathways, as well as mechanisms for increased solvent tolerance. Thus, synthetic biology may finally lead to cheap and effective processes for conversion of biomass to useful products.
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Mutagenesis of the bacterial RNA polymerase alpha subunit for improvement of complex phenotypes. Appl Environ Microbiol 2009; 75:2705-11. [PMID: 19251886 DOI: 10.1128/aem.01888-08] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Combinatorial or random methods for strain engineering have been extensively used for the improvement of multigenic phenotypes and other traits for which the underlying mechanism is not fully understood. Although the preferred method has traditionally been mutagenesis and selection, our laboratory has successfully used mutant transcription factors, which direct the RNA polymerase (RNAP) during transcription, to engineer complex phenotypes in microbial cells. Here, we show that it is also possible to impart new phenotypes by altering the RNAP core enzyme itself, in particular through mutagenesis of the alpha subunit of the bacterial polymerase. We present the use of this tool for improving tolerance of Escherichia coli to butanol and other solvents and for increasing the titers of two commercially relevant products, L-tyrosine and hyaluronic acid. In addition, we explore the underlying physiological changes that give rise to the solvent-tolerant mutant.
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Wohlgemuth R. The locks and keys to industrial biotechnology. N Biotechnol 2009; 25:204-13. [PMID: 19429540 DOI: 10.1016/j.nbt.2009.01.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2008] [Revised: 01/07/2009] [Accepted: 01/08/2009] [Indexed: 11/27/2022]
Abstract
The sustainable use of resources by Nature to synthesize the required products at the right place, when they are needed, continues to be the role model for total synthesis and production in general. The combination of molecular and engineering science and technology in the biotechnological approach needs no protecting groups at all and has therefore been established for numerous large-scale routes to both natural and synthetic products in industry. The use of biobased raw materials for chemical synthesis, and the economy of molecular transformations like atom economy and step economy are of growing importance. As safety, health and environmental issues are key drivers for process improvements in the chemical industry, the development of biocatalytic reactions or pathways replacing hazardous reagents is a major focus. The integration of the biocatalytic reaction and downstream processing with product isolation has led to a variety of in situ product recovery techniques and has found numerous successful applications. With the growing collection of biocatalytic reactions, the retrosynthetic thinking can be applied to biocatalysis as well. The introduction of biocatalytic reactions is uniquely suited to cost reductions and higher quality products, as well as to more sustainable processes. The transfer of Nature's simple and robust sensing and control principles as well as its reaction and separation organization into useful technical systems can be applied to different fermentations, biotransformations and downstream processes. Biocatalyst and pathway discovery and development is the key towards new synthetic transformations in industrial biotechnology.
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Affiliation(s)
- Roland Wohlgemuth
- Sigma-Aldrich, Research Specialities, Industriestrasse 25, 9470 Buchs, Switzerland.
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Mukhopadhyay A, Redding AM, Rutherford BJ, Keasling JD. Importance of systems biology in engineering microbes for biofuel production. Curr Opin Biotechnol 2008; 19:228-34. [PMID: 18515068 DOI: 10.1016/j.copbio.2008.05.003] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2008] [Revised: 05/05/2008] [Accepted: 05/07/2008] [Indexed: 01/23/2023]
Abstract
Microorganisms have been rich sources for natural products, some of which have found use as fuels, commodity chemicals, specialty chemicals, polymers, and drugs, to name a few. The recent interest in production of transportation fuels from renewable resources has catalyzed numerous research endeavors that focus on developing microbial systems for production of such natural products. Eliminating bottlenecks in microbial metabolic pathways and alleviating the stresses due to production of these chemicals are crucial in the generation of robust and efficient production hosts. The use of systems-level studies makes it possible to comprehensively understand the impact of pathway engineering within the context of the entire host metabolism, to diagnose stresses due to product synthesis, and provides the rationale to cost-effectively engineer optimal industrial microorganisms.
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