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Abstract
Biofuel consists of non-fossil fuel derived from the organic biomass of renewable resources, including plants, animals, microorganisms, and waste. Energy derived from biofuel is known as bioenergy. The reserve of fossil fuels is now limited and continuing to decrease, while at the same time demand for energy is increasing. In order to overcome this scarcity, it is vital for human beings to transfer their dependency on fossil fuels to alternative types of fuel, including biofuels, which are effective methods of fulfilling present and future demands. The current review therefore focusses on second-generation lignocellulosic biofuels obtained from non-edible plant biomass (i.e., cellulose, lignin, hemi-celluloses, non-food material) in a more sustainable manner. The conversion of lignocellulosic feedstock is an important step during biofuel production. It is, however, important to note that, as a result of various technical restrictions, biofuel production is not presently cost efficient, thus leading to the need for improvement in the methods employed. There remain a number of challenges for the process of biofuel production, including cost effectiveness and the limitations of various technologies employed. This leads to a vital need for ongoing and enhanced research and development, to ensure market level availability of lignocellulosic biofuel.
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2
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Lu H, Yadav V, Bilal M, Iqbal HMN. Bioprospecting microbial hosts to valorize lignocellulose biomass - Environmental perspectives and value-added bioproducts. CHEMOSPHERE 2022; 288:132574. [PMID: 34656619 DOI: 10.1016/j.chemosphere.2021.132574] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 10/09/2021] [Accepted: 10/13/2021] [Indexed: 02/08/2023]
Abstract
Current biorefinery approaches comprehend diverse biomass feedstocks and various conversion techniques to produce a variety of high-value biochemicals and biofuels. Lignocellulose is among the most abundant, bio-renewable, and sustainable bioresources on earth. It is regarded as a prodigious alternative raw feedstock to produce a large number of chemicals and biofuels. Producing biofuels and platform chemicals from lignocellulosic biomasses represent advantages in terms of energy and environmental perspectives. Lignocellulose is a main structural constituent of non-woody and woody plants consisting of lignin, cellulose, and hemicellulose. Efficient exploitation of all these components is likely to play a considerable contribution to the economic viability of the processes since lignocellulosic biomass often necessitate pretreatment for liberating fermentable sugars and added value products that might serve as feedstocks for microbial strains to produce biofuels and biochemicals. Developing robust microbial culture and advancements in metabolic engineering approaches might lead to the rapid construction of cell factories for the effective biotechnological transformation of biomass feedstocks to produce biorefinery products. In this comprehensive review, we discuss the recent progress in the valorization of agro-industrial wastes as prospective microbial feedstocks to produce a spectrum of high-value products, such as microbial pigments, biopolymers, industrial biocatalysts, biofuels, biologically active compounds, bioplastics, biosurfactants, and biocontrol agents with therapeutic and industrial potentialities. Lignocellulosic biomass architecture, compositional aspects, revalorization, and pretreatment strategies are outlined for efficient conversion of lignocellulosic biomass. Moreover, metabolic engineering approaches are briefly highlighted to develop cell factories to make the lignocellulose biorefinery platforms appealing.
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Affiliation(s)
- Hedong Lu
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an, Jiangsu, 223003, China; School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Vivek Yadav
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, 712100, China
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an, Jiangsu, 223003, China.
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, 64849, Mexico.
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3
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Yan Y, Chen H, Sun L, Zhang W, Lu X, Li Z, Xu J, Ren Q. The changes of microbial diversity and flavor compounds during the fermentation of millet Huangjiu, a traditional Chinese beverage. PLoS One 2022; 17:e0262353. [PMID: 34986204 PMCID: PMC8730391 DOI: 10.1371/journal.pone.0262353] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 12/21/2021] [Indexed: 02/01/2023] Open
Abstract
Huangjiu is a national alcoholic beverage in China. Millet has congenital advantages in development and utilization of nutrient. Brewing Huangjiu with millet can increase the value of millet. Microbial community plays crucial roles in millet Huangjiu fermentation. Flavor compounds reflect the quality and health function of Huangjiu. The flavor compounds of Huangjiu are complex and their formation is closely associated with microorganisms, but the relationship between them during fermentation has been unknown. In this research, this relationship during millet Huangjiu fermentation were deeply investigated. Totally 86 volatile compounds were detected. Bacillus, Weissella, Paenibacillus, Klebsiella, Prevotella was investigated as the dominant microbes through high-throughput sequencing. 537 correlations between major flavor compounds and microbes were established to reflect the dynamic change during millet Huangjiu fermentation. The top five dominant genus of flavor producing microbes were Chryseobacterium, Sporolactobacillus, Psychrobacter, Sphingobium and Anoxybacillus. The content of malic acid and citric acid was gradually improved all through the millet Huangjiu fermentation. Malic acid and citric acid generated from millet Huangjiu fermentation shows healthy properties as liver protection and eliminating fatigue. Our research provides essential information on microbial community succession and the flavor formation during millet Huangjiu fermentation, and beneficial for development of Huangjiu products.
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Affiliation(s)
- Yi Yan
- School of Light Industry, Beijing Technology and Business University, Beijing, China
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing, China
| | - Haiyan Chen
- School of Light Industry, Beijing Technology and Business University, Beijing, China
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing, China
| | - Leping Sun
- School of Light Industry, Beijing Technology and Business University, Beijing, China
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing, China
| | - Wei Zhang
- College of Food Science and Technology, Hebei Agricultural University, Baoding, China
| | - Xin Lu
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhenpeng Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jialiang Xu
- School of Light Industry, Beijing Technology and Business University, Beijing, China
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing, China
| | - Qing Ren
- School of Light Industry, Beijing Technology and Business University, Beijing, China
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing, China
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4
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de Paula RG, Antoniêto ACC, Ribeiro LFC, Srivastava N, O'Donovan A, Mishra PK, Gupta VK, Silva RN. Engineered microbial host selection for value-added bioproducts from lignocellulose. Biotechnol Adv 2019; 37:107347. [PMID: 30771467 DOI: 10.1016/j.biotechadv.2019.02.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 01/27/2019] [Accepted: 02/08/2019] [Indexed: 12/12/2022]
Abstract
Lignocellulose is a rich and sustainable globally available carbon source and is considered a prominent alternative raw material for producing biofuels and valuable chemical compounds. Enzymatic hydrolysis is one of the crucial steps of lignocellulose degradation. Cellulolytic and hemicellulolytic enzyme mixes produced by different microorganisms including filamentous fungi, yeasts and bacteria, are used to degrade the biomass to liberate monosaccharides and other compounds for fermentation or conversion to value-added products. During biomass pretreatment and degradation, toxic compounds are produced, and undesirable carbon catabolic repression (CCR) can occur. In order to solve this problem, microbial metabolic pathways and transcription factors involved have been investigated along with the application of protein engineering to optimize the biorefinery platform. Engineered Microorganisms have been used to produce specific enzymes to breakdown biomass polymers and metabolize sugars to produce ethanol as well other biochemical compounds. Protein engineering strategies have been used for modifying lignocellulolytic enzymes to overcome enzymatic limitations and improving both their production and functionality. Furthermore, promoters and transcription factors, which are key proteins in this process, are modified to promote microbial gene expression that allows a maximum performance of the hydrolytic enzymes for lignocellulosic degradation. The present review will present a critical discussion and highlight the aspects of the use of microorganisms to convert lignocellulose into value-added bioproduct as well combat the bottlenecks to make the biorefinery platform from lignocellulose attractive to the market.
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Affiliation(s)
- Renato Graciano de Paula
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | | | - Liliane Fraga Costa Ribeiro
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Neha Srivastava
- Department of Chemical Engineering & Technology, IIT (BHU), Varanasi 221005, U.P, India
| | - Anthonia O'Donovan
- School of Science and Computing, Galway-Mayo Institute of Technology, Galway, Ireland
| | - P K Mishra
- Department of Chemical Engineering & Technology, IIT (BHU), Varanasi 221005, U.P, India
| | - Vijai K Gupta
- ERA Chair of Green Chemistry, Department of Chemistry and Biotechnology, Tallinn University of Technology, 12618 Tallinn, Estonia.
| | - Roberto N Silva
- Department of Biochemistry and Immunology, Ribeirao Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil.
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5
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Microbial Production of Fatty Acid via Metabolic Engineering and Synthetic Biology. BIOTECHNOL BIOPROC E 2019. [DOI: 10.1007/s12257-018-0374-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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6
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Syed MS, Rafeie M, Vandamme D, Asadnia M, Henderson R, Taylor RA, Warkiani ME. Selective separation of microalgae cells using inertial microfluidics. BIORESOURCE TECHNOLOGY 2018; 252:91-99. [PMID: 29306136 DOI: 10.1016/j.biortech.2017.12.065] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 12/19/2017] [Accepted: 12/20/2017] [Indexed: 05/08/2023]
Abstract
Microalgae represent the most promising new source of biomass for the world's growing demands. However, the biomass productivity and quality is significantly decreased by the presence of bacteria or other invading microalgae species in the cultures. We therefore report a low-cost spiral-microchannel that can effectively separate and purify Tetraselmis suecica (lipid-rich microalgae) cultures from Phaeodactylum tricornutum (invasive diatom). Fluorescent polystyrene-microbeads of 6 μm and 10 μm diameters were first used as surrogate particles to optimize the microchannel design by mimicking the microalgae cell behaviour. Using the optimum flowrate, up to 95% of the P. tricornutum cells were separated from the culture without affecting the cell viability. This study shows, for the first time, the potential of inertial microfluidics to sort microalgae species with minimal size difference. Additionally, this approach can also be applied as a pre-sorting technique for water quality analysis.
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Affiliation(s)
- Maira S Syed
- School of Mechanical and Manufacturing Engineering, University of New South Wales, Australia; Biomass Lab, School of Chemical Engineering, University of New South Wales, Australia.
| | - Mehdi Rafeie
- School of Mechanical and Manufacturing Engineering, University of New South Wales, Australia
| | - Dries Vandamme
- Biomass Lab, School of Chemical Engineering, University of New South Wales, Australia; Laboratory for Aquatic Biology, KU Leuven, Campus Kulak, Belgium
| | - Mohsen Asadnia
- Department of Engineering, Macquarie University, Sydney, New South Wales, Australia
| | - Rita Henderson
- Biomass Lab, School of Chemical Engineering, University of New South Wales, Australia
| | - Robert A Taylor
- School of Mechanical and Manufacturing Engineering, University of New South Wales, Australia; School of Photovoltaic and Renewable Energy Engineering, University of New South Wales, Australia
| | - Majid E Warkiani
- School of Biomedical Engineering, University of Technology Sydney, Australia; Center for Health Technologies, University of Technology Sydney, Australia.
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7
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Wang C, Zhao C, Hu L, Chen H. Calculated Mechanism of Cyanobacterial Aldehyde-Deformylating Oxygenase: Asymmetric Aldehyde Activation by a Symmetric Diiron Cofactor. J Phys Chem Lett 2016; 7:4427-4432. [PMID: 27775357 DOI: 10.1021/acs.jpclett.6b02061] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Cyanobacterial aldehyde-deformylating oxygenase (cADO) is a nonheme diiron enzyme that catalyzes the conversion of aldehyde to alk(a/e)ne, an important transformation in biofuel research. In this work, we report a highly desired computational study for probing the mechanism of cADO. By combining our QM/MM results with the available 57Fe Mössbauer spectroscopic data, the gained detailed structural information suggests construction of asymmetry from the symmetric diiron cofactor in an aldehyde substrate and O2 activation. His160, one of the two iron-coordinate histidine residues in cADO, plays a pivotal role in this asymmetric aldehyde activation process by unprecedented reversible dissociation from the diiron cofactor, a behavior unknown in any other nonheme dinuclear or mononuclear enzymes. The revealed intrinsically asymmetric interactions of the substrate/O2 with the symmetric cofactor in cADO are inspirational for exploring diiron subsite resolution in other nonheme diiron enzymes.
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Affiliation(s)
- Chao Wang
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, People's Republic of China
- University of Chinese Academy of Sciences , Beijing 100049, People's Republic of China
| | - Chongyang Zhao
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, People's Republic of China
- University of Chinese Academy of Sciences , Beijing 100049, People's Republic of China
| | - Lianrui Hu
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, People's Republic of China
- University of Chinese Academy of Sciences , Beijing 100049, People's Republic of China
| | - Hui Chen
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, People's Republic of China
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8
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Juang YJ, Chang JS. Applications of microfluidics in microalgae biotechnology: A review. Biotechnol J 2016; 11:327-35. [DOI: 10.1002/biot.201500278] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 10/29/2015] [Accepted: 12/25/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Yi-Je Juang
- Department of Chemical Engineering; National Cheng Kung University; Tainan Taiwan
| | - Jo-Shu Chang
- Department of Chemical Engineering; National Cheng Kung University; Tainan Taiwan
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9
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Shokri A, Que L. Conversion of Aldehyde to Alkane by a Peroxoiron(III) Complex: A Functional Model for the Cyanobacterial Aldehyde-Deformylating Oxygenase. J Am Chem Soc 2015; 137:7686-91. [PMID: 26030345 DOI: 10.1021/jacs.5b01053] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cyanobacterial aldehyde-deformylating oxygenase (cADO) converts long-chain fatty aldehydes to alkanes via a proposed diferric-peroxo intermediate that carries out the oxidative deformylation of the substrate. Herein, we report that the synthetic iron(III)-peroxo complex [Fe(III)(η(2)-O2)(TMC)](+) (TMC = tetramethylcyclam) causes a similar transformation in the presence of a suitable H atom donor, thus serving as a functional model for cADO. Mechanistic studies suggest that the H atom donor can intercept the incipient alkyl radical formed in the oxidative deformylation step in competition with the oxygen rebound step typically used by most oxygenases for forming C-O bonds.
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Affiliation(s)
- Alireza Shokri
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Lawrence Que
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
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10
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Buer B, Paul B, Das D, Stuckey JA, Marsh ENG. Insights into substrate and metal binding from the crystal structure of cyanobacterial aldehyde deformylating oxygenase with substrate bound. ACS Chem Biol 2014; 9:2584-93. [PMID: 25222710 PMCID: PMC4245163 DOI: 10.1021/cb500343j] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 09/02/2014] [Indexed: 11/28/2022]
Abstract
The nonheme diiron enzyme cyanobacterial aldehyde deformylating oxygenase, cADO, catalyzes the highly unusual deformylation of aliphatic aldehydes to alkanes and formate. We have determined crystal structures for the enzyme with a long-chain water-soluble aldehyde and medium-chain carboxylic acid bound to the active site. These structures delineate a hydrophobic channel that connects the solvent with the deeply buried active site and reveal a mode of substrate binding that is different from previously determined structures with long-chain fatty acids bound. The structures also identify a water channel leading to the active site that could facilitate the entry of protons required in the reaction. NMR studies examining 1-[(13)C]-octanal binding to cADO indicate that the enzyme binds the aldehyde form rather than the hydrated form. Lastly, the fortuitous cocrystallization of the metal-free form of the protein with aldehyde bound has revealed protein conformation changes that are involved in binding iron.
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Affiliation(s)
- Benjamin
C. Buer
- Department of Chemistry, Life Sciences Institute, and Department of Biological
Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Bishwajit Paul
- Department of Chemistry, Life Sciences Institute, and Department of Biological
Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Debasis Das
- Department of Chemistry, Life Sciences Institute, and Department of Biological
Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jeanne A. Stuckey
- Department of Chemistry, Life Sciences Institute, and Department of Biological
Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - E. Neil G. Marsh
- Department of Chemistry, Life Sciences Institute, and Department of Biological
Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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11
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Lisha KP, Sarkar D. In silico analysis of bioethanol production from glucose/xylose mixtures during fed-batch fermentation of co-culture and mono-culture systems. BIOTECHNOL BIOPROC E 2014. [DOI: 10.1007/s12257-014-0320-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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12
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Waugh MW, Marsh ENG. Solvent isotope effects on alkane formation by cyanobacterial aldehyde deformylating oxygenase and their mechanistic implications. Biochemistry 2014; 53:5537-43. [PMID: 25142631 PMCID: PMC4151702 DOI: 10.1021/bi5005766] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The reaction catalyzed by cyanobacterial aldehyde deformylating oxygenase is of interest both because of its potential application to the production of biofuels and because of the highly unusual nature of the deformylation reaction it catalyzes. Whereas the proton in the product alkane derives ultimately from the solvent, the identity of the proton donor in the active site remains unclear. To investigate the proton transfer step, solvent isotope effect (SIE) studies were undertaken. The rate of alkane formation was found to be maximal at pH 6.8 and to be the same in D2O or H2O within experimental error, implying that proton transfer is not a kinetically significant step. However, when the ratio of protium to deuterium in the product alkane was measured as a function of the mole fraction of D2O, a (D2O)SIEobs of 2.19 ± 0.02 was observed. The SIE was invariant with the mole fraction of D2O, indicating the involvement of a single protic site in the reaction. We interpret this SIE as most likely arising from a reactant state equilibrium isotope effect on a proton donor with an inverse fractionation factor, for which Φ = 0.45. These observations are consistent with an iron-bound water molecule being the proton donor to the alkane in the reaction.
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Affiliation(s)
- Matthew W Waugh
- Department of Chemistry and ‡Department of Biological Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
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13
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Das D, Ellington B, Paul B, Marsh ENG. Mechanistic insights from reaction of α-oxiranyl-aldehydes with cyanobacterial aldehyde deformylating oxygenase. ACS Chem Biol 2014; 9:570-7. [PMID: 24313866 DOI: 10.1021/cb400772q] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The biosynthesis of long-chain aliphatic hydrocarbons, which are derived from fatty acids, is widespread in Nature. The last step in this pathway involves the decarbonylation of fatty aldehydes to the corresponding alkanes or alkenes. In cyanobacteria, this is catalyzed by an aldehyde deformylating oxygenase. We have investigated the mechanism of this enzyme using substrates bearing an oxirane ring adjacent to the aldehyde carbon. The enzyme catalyzed the deformylation of these substrates to produce the corresponding oxiranes. Performing the reaction in D2O allowed the facial selectivity of proton addition to be examined by (1)H NMR spectroscopy. The proton is delivered with equal probability to either face of the oxirane ring, indicating the formation of an oxiranyl radical intermediate that is free to rotate during the reaction. Unexpectedly, the enzyme also catalyzes a side reaction in which oxiranyl-aldehydes undergo tandem deformylation to furnish alkanes two carbons shorter. We present evidence that this involves the rearrangement of the intermediate oxiranyl radical formed in the first step, resulting in aldehyde that is further deformylated in a second step. These observations provide support for a radical mechanism for deformylation and, furthermore, allow the lifetime of the radical intermediate to be estimated based on prior measurements of rate constants for the rearrangement of oxiranyl radicals.
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Affiliation(s)
- Debasis Das
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Benjamin Ellington
- Department
of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Bishwajit Paul
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - E. Neil G. Marsh
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department
of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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14
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Marsh ENG, Waugh MW. Aldehyde Decarbonylases: Enigmatic Enzymes of Hydrocarbon Biosynthesis. ACS Catal 2013; 3. [PMID: 24319622 DOI: 10.1021/cs400637t] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- E. Neil G. Marsh
- Department of Chemistry and ‡Department of
Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Matthew W. Waugh
- Department of Chemistry and ‡Department of
Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
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15
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Lim HG, Seo SW, Jung GY. Engineered Escherichia coli for simultaneous utilization of galactose and glucose. BIORESOURCE TECHNOLOGY 2013; 135:564-7. [PMID: 23246298 DOI: 10.1016/j.biortech.2012.10.124] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Revised: 10/09/2012] [Accepted: 10/10/2012] [Indexed: 05/20/2023]
Abstract
In this study, the Leloir pathway of galactose metabolism was rebuilt in Escherichia coli to remove CCR and amplify galactose utilization rate. All genes encoding pathway enzymes were expressed under the control of a synthetic module that included promoters, 5'-untranslated regions, and terminators as a re-organized single operon in the chromosome. The engineered strain showed both an enhanced galactose utilization rate and the capacity to simultaneously assimilate galactose and glucose. This work demonstrates the feasibility of using synthetic biology tools to re-build biological systems for engineering purpose.
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Affiliation(s)
- Hyun Gyu Lim
- Department of Chemical Engineering, Pohang University of Science and Technology, San 31, Hyoja-dong, Nam-gu, Pohang, Gyeongbuk 790-784, South Korea
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16
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Paul B, Das D, Ellington B, Marsh ENG. Probing the mechanism of cyanobacterial aldehyde decarbonylase using a cyclopropyl aldehyde. J Am Chem Soc 2013; 135:5234-7. [PMID: 23514600 DOI: 10.1021/ja3115949] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Cyanobacterial aldehyde decarbonylase (cAD) is a non-heme diiron oxygenase that catalyzes the conversion of fatty aldehydes to alkanes and formate. The mechanism of this chemically unusual reaction is poorly understood. We have investigated the mechanism of C1-C2 bond cleavage by cAD using a fatty aldehyde that incorporates a cyclopropyl group, which can act as a radical clock. When reacted with cAD, the cyclopropyl aldehyde produces 1-octadecene as the rearranged product, providing evidence for a radical mechanism for C-C bond scission. In an alternate pathway, the cyclopropyl aldehyde acts as a mechanism-based irreversible inhibitor of cAD through covalent binding of the alkyl chain to the enzyme.
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Affiliation(s)
- Bishwajit Paul
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
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17
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Heterologous expression of plant cell wall degrading enzymes for effective production of cellulosic biofuels. J Biomed Biotechnol 2012; 2012:405842. [PMID: 22911272 PMCID: PMC3403577 DOI: 10.1155/2012/405842] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2012] [Accepted: 05/20/2012] [Indexed: 11/17/2022] Open
Abstract
A major technical challenge in the cost-effective production of cellulosic biofuel is the need to lower the cost of plant cell wall degrading enzymes (PCDE), which is required for the production of sugars from biomass. Several competitive, low-cost technologies have been developed to produce PCDE in different host organisms such as Escherichia coli, Zymomonas mobilis, and plant. Selection of an ideal host organism is very important, because each host organism has its own unique features. Synthetic biology-aided tools enable heterologous expression of PCDE in recombinant E. coli or Z. mobilis and allow successful consolidated bioprocessing (CBP) in these microorganisms. In-planta expression provides an opportunity to simplify the process of enzyme production and plant biomass processing and leads to self-deconstruction of plant cell walls. Although the future of currently available technologies is difficult to predict, a complete and viable platform will most likely be available through the integration of the existing approaches with the development of breakthrough technologies.
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18
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Vinuselvi P, Kim MK, Lee SK, Ghim CM. Rewiring carbon catabolite repression for microbial cell factory. BMB Rep 2012; 45:59-70. [PMID: 22360882 DOI: 10.5483/bmbrep.2012.45.2.59] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Carbon catabolite repression (CCR) is a key regulatory system found in most microorganisms that ensures preferential utilization of energy-efficient carbon sources. CCR helps microorganisms obtain a proper balance between their metabolic capacity and the maximum sugar uptake capability. It also constrains the deregulated utilization of a preferred cognate substrate, enabling microorganisms to survive and dominate in natural environments. On the other side of the same coin lies the tenacious bottleneck in microbial production of bioproducts that employs a combination of carbon sources in varied proportion, such as lignocellulose-derived sugar mixtures. Preferential sugar uptake combined with the transcriptional and/or enzymatic exclusion of less preferred sugars turns out one of the major barriers in increasing the yield and productivity of fermentation process. Accumulation of the unused substrate also complicates the downstream processes used to extract the desired product. To overcome this difficulty and to develop tailor-made strains for specific metabolic engineering goals, quantitative and systemic understanding of the molecular interaction map behind CCR is a prerequisite. Here we comparatively review the universal and strain-specific features of CCR circuitry and discuss the recent efforts in developing synthetic cell factories devoid of CCR particularly for lignocellulose- based biorefinery.
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Affiliation(s)
- Parisutham Vinuselvi
- School of Nano-Bioscience and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 689-798, Korea
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Hoover SW, Youngquist JT, Angart PA, Withers ST, Lennen RM, Pfleger BF. Isolation of improved free fatty acid overproducing strains of Escherichia coli via Nile red based high-throughput screening. ENVIRONMENTAL PROGRESS & SUSTAINABLE ENERGY 2012; 31:17-23. [PMID: 30034576 PMCID: PMC6051543 DOI: 10.1002/ep.10599] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Biological production of hydrocarbons is an attractive strategy to produce drop-in replacement transportation fuels. Several methods for converting microbially-produced fatty acids into reduced compounds compatible with petrodiesel have been reported. For these processes to become economically viable, microorganisms must be engineered to approach the theoretical yield of fatty acid products from renewable feedstocks such as glucose. Strains with increased titers can be obtained through both rational and random approaches. While powerful, random approaches require a genetic selection or facile screen that is amenable to high throughput platforms. Here, we present the use of a high throughput screen for fatty acids based on the hydrophobic dye Nile red. The method was applied to screening a transposon library of a free fatty acid overproducing strain of Escherichia coli in search of high producing mutants. Ten gene targets were identified via primary and secondary screening. A strain comprising a clean knockout of one of the identified genes led to a 20% increase in titer over the baseline strain. A selection strategy that combines these findings and can act in an iterative fashion has been developed and can be used for future strain optimization in hydrocarbon producing strains.
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Affiliation(s)
- Spencer W Hoover
- University of Wisconsin-Madison, Department of Chemical and Biological Engineering
- Great Lakes Bioenergy Research Center
| | - J Tyler Youngquist
- University of Wisconsin-Madison, Department of Chemical and Biological Engineering
- Great Lakes Bioenergy Research Center
| | - Phil A Angart
- University of Wisconsin-Madison, Department of Chemical and Biological Engineering
- Great Lakes Bioenergy Research Center
| | - Sydnor T Withers
- University of Wisconsin-Madison, Department of Chemical and Biological Engineering
- Great Lakes Bioenergy Research Center
| | - Rebecca M Lennen
- University of Wisconsin-Madison, Department of Chemical and Biological Engineering
- Great Lakes Bioenergy Research Center
| | - Brian F Pfleger
- University of Wisconsin-Madison, Department of Chemical and Biological Engineering
- Great Lakes Bioenergy Research Center
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Lütke-Eversloh T, Bahl H. Metabolic engineering of Clostridium acetobutylicum: recent advances to improve butanol production. Curr Opin Biotechnol 2011; 22:634-47. [DOI: 10.1016/j.copbio.2011.01.011] [Citation(s) in RCA: 290] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Revised: 01/26/2011] [Accepted: 01/26/2011] [Indexed: 11/26/2022]
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Effects of deletion of glycerol-3-phosphate dehydrogenase and glutamate dehydrogenase genes on glycerol and ethanol metabolism in recombinant Saccharomyces cerevisiae. Bioprocess Biosyst Eng 2011; 35:49-54. [DOI: 10.1007/s00449-011-0590-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Accepted: 07/18/2011] [Indexed: 11/26/2022]
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Vinuselvi P, Lee SK. Engineering Escherichia coli for efficient cellobiose utilization. Appl Microbiol Biotechnol 2011; 92:125-32. [PMID: 21713510 DOI: 10.1007/s00253-011-3434-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Revised: 05/09/2011] [Accepted: 06/02/2011] [Indexed: 12/11/2022]
Abstract
Escherichia coli normally cannot utilize the β-glucoside sugar cellobiose as a carbon and energy source unless a stringent selection pressure for survival is present. The cellobiose-utilization phenotype can be conferred by mutations in the two cryptic operons, chb and asc. In this study, the cellobiose-utilization phenotype was conferred to E. coli by replacing the cryptic promoters of these endogenous operons with a constitutive promoter. Evolutionary adaptation of the engineered strain CP12CHBASC by repeated subculture in cellobiose-containing minimal medium led to an increase in the rate of cellobiose uptake and cell growth on cellobiose. An efficient cellobiose-metabolizing E. coli strain would be of great importance over glucose-metabolizing E. coli for a simultaneous saccharification and fermentation process, as the cost of the process would be reduced by eliminating one of the three enzymes needed to hydrolyze cellulose into simple sugars.
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Affiliation(s)
- Parisutham Vinuselvi
- School of Nano-Bioscience and Chemical Engineering, Ulsan National Institute of Science and Technology, Republic of Korea
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23
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Mitchell RJ, Lee SK, Kim T, Ghim CM. Microbial linguistics: perspectives and applications of microbial cell-to-cell communication. BMB Rep 2011; 44:1-10. [PMID: 21266100 DOI: 10.5483/bmbrep.2011.44.1.1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Inter-cellular communication via diffusible small molecules is a defining character not only of multicellular forms of life but also of single-celled organisms. A large number of bacterial genes are regulated by the change of chemical milieu mediated by the local population density of its own species or others. The cell density-dependent "autoinducer" molecules regulate the expression of those genes involved in genetic competence, biofilm formation and persistence, virulence, sporulation, bioluminescence, antibiotic production, and many others. Recent innovations in recombinant DNA technology and micro-/nano-fluidics systems render the genetic circuitry responsible for cell-to-cell communication feasible to and malleable via synthetic biological approaches. Here we review the current understanding of the molecular biology of bacterial intercellular communication and the novel experimental protocols and platforms used to investigate this phenomenon. A particular emphasis is given to the genetic regulatory circuits that provide the standard building blocks which constitute the syntax of the biochemical communication network. Thus, this review gives focus to the engineering principles necessary for rewiring bacterial chemo-communication for various applications, ranging from population-level gene expression control to the study of host-pathogen interactions.
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Affiliation(s)
- Robert J Mitchell
- School of Nano-Bioscience and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, Korea
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Chen T, Wang J, Yang R, Li J, Lin M, Lin Z. Laboratory-evolved mutants of an exogenous global regulator, IrrE from Deinococcus radiodurans, enhance stress tolerances of Escherichia coli. PLoS One 2011; 6:e16228. [PMID: 21267412 PMCID: PMC3022760 DOI: 10.1371/journal.pone.0016228] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Accepted: 12/09/2010] [Indexed: 01/28/2023] Open
Abstract
Background The tolerance of cells toward different stresses is very important for industrial strains of microbes, but difficult to improve by the manipulation of single genes. Traditional methods for enhancing cellular tolerances are inefficient and time-consuming. Recently, approaches employing global transcriptional or translational engineering methods have been increasingly explored. We found that an exogenous global regulator, irrE from an extremely radiation-resistant bacterium, Deinococcus radiodurans, has the potential to act as a global regulator in Escherichia coli, and that laboratory-evolution might be applied to alter this regulator to elicit different phenotypes for E. coli. Methodology/Principal Findings To extend the methodology for strain improvement and to obtain higher tolerances toward different stresses, we here describe an approach of engineering irrE gene in E. coli. An irrE library was constructed by randomly mutating the gene, and this library was then selected for tolerance to ethanol, butanol and acetate stresses. Several mutants showing significant tolerances were obtained and characterized. The tolerances of E. coli cells containing these mutants were enhanced 2 to 50-fold, based on cell growth tests using different concentrations of alcohols or acetate, and enhanced 10 to 100-fold based on ethanol or butanol shock experiments. Intracellular reactive oxygen species (ROS) assays showed that intracellular ROS levels were sharply reduced for cells containing the irrE mutants. Sequence analysis of the mutants revealed that the mutations distribute cross all three domains of the protein. Conclusions To our knowledge, this is the first time that an exogenous global regulator has been artificially evolved to suit its new host. The successes suggest the possibility of improving tolerances of industrial strains by introducing and engineering exogenous global regulators, such as those from extremophiles. This new approach can be applied alone or in combination with other global methods, such as global transcriptional machinery engineering (gTME) for strain improvements.
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Affiliation(s)
- Tingjian Chen
- Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Jianqing Wang
- Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Rong Yang
- Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Jicong Li
- Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Min Lin
- Key Laboratory of Crop Biotechnology, Ministry of Agriculture, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- * E-mail: (ZL); (ML)
| | - Zhanglin Lin
- Department of Chemical Engineering, Tsinghua University, Beijing, China
- * E-mail: (ZL); (ML)
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Skar-Gislinge N, Simonsen JB, Mortensen K, Feidenhans’l R, Sligar SG, Møller BL, Bjørnholm T, Arleth L. Elliptical structure of phospholipid bilayer nanodiscs encapsulated by scaffold proteins: casting the roles of the lipids and the protein. J Am Chem Soc 2010; 132:13713-22. [PMID: 20828154 PMCID: PMC4120756 DOI: 10.1021/ja1030613] [Citation(s) in RCA: 104] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Phospholipid bilayers host and support the function of membrane proteins and may be stabilized in disc-like nanostructures, allowing for unprecedented solution studies of the assembly, structure, and function of membrane proteins (Bayburt et al. Nano Lett. 2002, 2, 853-856). Based on small-angle neutron scattering in combination with variable-temperature studies of synchrotron small-angle X-ray scattering on nanodiscs in solution, we show that the fundamental nanodisc unit, consisting of a lipid bilayer surrounded by amphiphilic scaffold proteins, possesses intrinsically an elliptical shape. The temperature dependence of the curvature of the nanodiscs prepared with two different phospholipid types (DLPC and POPC) shows that it is the scaffold protein that determines the overall elliptical shape and that the nanodiscs become more circular with increasing temperature. Our data also show that the hydrophobic bilayer thickness is, to a large extent, dictated by the scaffolding protein and adjusted to minimize the hydrophobic mismatch between protein and phospholipid. Our conclusions result from a new comprehensive and molecular-based model of the nanodisc structure and the use of this to analyze the experimental scattering profile from nanodiscs. The model paves the way for future detailed structural studies of functional membrane proteins encapsulated in nanodiscs.
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Cho YK, Shin H, Lee SK, Kim T. Current application of micro/nano-interfaces to stimulate and analyze cellular responses. Ann Biomed Eng 2010; 38:2056-67. [PMID: 20213211 DOI: 10.1007/s10439-010-9984-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2009] [Accepted: 02/22/2010] [Indexed: 01/09/2023]
Abstract
Microfabrication technologies have a high potential for novel approaches to access living cells at a cellular or even at a molecular level. In the course of reviewing and discussing the current application of microinterface systems including nanointerfaces to stimulate and analyze cellular responses with subcellular resolution, this article focuses on interfaces based on microfluidics, nanoparticles, and scanning electrochemical microscopy (SECM). Micro/nanointerface systems provide a novel, attractive means for cell study because they are capable of regulating and monitoring cellular signals simultaneously and repeatedly, leading us to an enhanced understanding and interpretation of cellular responses. Therefore, it is hoped that the integrated micro/nanointerfaces presented in this review will contribute to future developments of cell biology and facilitate advanced biomedical applications.
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Affiliation(s)
- Yoon-Kyoung Cho
- School of Nano-Biotechnology and Chemical Engineering, Ulsan National Institute of Science and Technology, Banyeon-ri 100, Ulsan 689-798, Korea
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