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Pereira JH, Heins RA, Gall DL, McAndrew RP, Deng K, Holland KC, Donohue TJ, Noguera DR, Simmons BA, Sale KL, Ralph J, Adams PD. Structural and Biochemical Characterization of the Early and Late Enzymes in the Lignin β-Aryl Ether Cleavage Pathway from Sphingobium sp. SYK-6. J Biol Chem 2016; 291:10228-38. [PMID: 26940872 PMCID: PMC4858972 DOI: 10.1074/jbc.m115.700427] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Indexed: 12/23/2022] Open
Abstract
There has been great progress in the development of technology for the conversion of lignocellulosic biomass to sugars and subsequent fermentation to fuels. However, plant lignin remains an untapped source of materials for production of fuels or high value chemicals. Biological cleavage of lignin has been well characterized in fungi, in which enzymes that create free radical intermediates are used to degrade this material. In contrast, a catabolic pathway for the stereospecific cleavage of β-aryl ether units that are found in lignin has been identified in Sphingobium sp. SYK-6 bacteria. β-Aryl ether units are typically abundant in lignin, corresponding to 50–70% of all of the intermonomer linkages. Consequently, a comprehensive understanding of enzymatic β-aryl ether (β-ether) cleavage is important for future efforts to biologically process lignin and its breakdown products. The crystal structures and biochemical characterization of the NAD-dependent dehydrogenases (LigD, LigO, and LigL) and the glutathione-dependent lyase LigG provide new insights into the early and late enzymes in the β-ether degradation pathway. We present detailed information on the cofactor and substrate binding sites and on the catalytic mechanisms of these enzymes, comparing them with other known members of their respective families. Information on the Lig enzymes provides new insight into their catalysis mechanisms and can inform future strategies for using aromatic oligomers derived from plant lignin as a source of valuable aromatic compounds for biofuels and other bioproducts.
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Affiliation(s)
- Jose Henrique Pereira
- From the Joint BioEnergy Institute, Emeryville, California 94608, the Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Richard A Heins
- From the Joint BioEnergy Institute, Emeryville, California 94608, the Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, California 94551
| | - Daniel L Gall
- the United States Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726, the Departments of Civil and Environmental Engineering and
| | - Ryan P McAndrew
- From the Joint BioEnergy Institute, Emeryville, California 94608, the Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Kai Deng
- From the Joint BioEnergy Institute, Emeryville, California 94608, the Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, California 94551
| | - Keefe C Holland
- From the Joint BioEnergy Institute, Emeryville, California 94608, the Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, California 94551
| | - Timothy J Donohue
- the United States Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726, Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, and
| | - Daniel R Noguera
- the United States Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726, the Departments of Civil and Environmental Engineering and
| | - Blake A Simmons
- From the Joint BioEnergy Institute, Emeryville, California 94608, the Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, California 94551
| | - Kenneth L Sale
- From the Joint BioEnergy Institute, Emeryville, California 94608, the Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, California 94551
| | - John Ralph
- the United States Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726, Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, and
| | - Paul D Adams
- From the Joint BioEnergy Institute, Emeryville, California 94608, the Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, the Department of Bioengineering, University of California, Berkeley, California 94720
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Helmich KE, Pereira JH, Gall DL, Heins RA, McAndrew RP, Bingman C, Deng K, Holland KC, Noguera DR, Simmons BA, Sale KL, Ralph J, Donohue TJ, Adams PD, Phillips GN. Structural Basis of Stereospecificity in the Bacterial Enzymatic Cleavage of β-Aryl Ether Bonds in Lignin. J Biol Chem 2015; 291:5234-46. [PMID: 26637355 PMCID: PMC4777856 DOI: 10.1074/jbc.m115.694307] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Indexed: 11/23/2022] Open
Abstract
Lignin is a combinatorial polymer comprising monoaromatic units that are linked via covalent bonds. Although lignin is a potential source of valuable aromatic chemicals, its recalcitrance to chemical or biological digestion presents major obstacles to both the production of second-generation biofuels and the generation of valuable coproducts from lignin's monoaromatic units. Degradation of lignin has been relatively well characterized in fungi, but it is less well understood in bacteria. A catabolic pathway for the enzymatic breakdown of aromatic oligomers linked via β-aryl ether bonds typically found in lignin has been reported in the bacterium Sphingobium sp. SYK-6. Here, we present x-ray crystal structures and biochemical characterization of the glutathione-dependent β-etherases, LigE and LigF, from this pathway. The crystal structures show that both enzymes belong to the canonical two-domain fold and glutathione binding site architecture of the glutathione S-transferase family. Mutagenesis of the conserved active site serine in both LigE and LigF shows that, whereas the enzymatic activity is reduced, this amino acid side chain is not absolutely essential for catalysis. The results include descriptions of cofactor binding sites, substrate binding sites, and catalytic mechanisms. Because β-aryl ether bonds account for 50–70% of all interunit linkages in lignin, understanding the mechanism of enzymatic β-aryl ether cleavage has significant potential for informing ongoing studies on the valorization of lignin.
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Affiliation(s)
- Kate E Helmich
- From the Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, the United States Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726
| | - Jose Henrique Pereira
- the Joint BioEnergy Institute, Emeryville, California 94608, the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Daniel L Gall
- the United States Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726, the Departments of Civil and Environmental Engineering and
| | - Richard A Heins
- the Joint BioEnergy Institute, Emeryville, California 94608, the Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, California 94551
| | - Ryan P McAndrew
- the Joint BioEnergy Institute, Emeryville, California 94608, the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Craig Bingman
- From the Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Kai Deng
- the Joint BioEnergy Institute, Emeryville, California 94608, the Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, California 94551
| | - Keefe C Holland
- the Joint BioEnergy Institute, Emeryville, California 94608, the Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, California 94551
| | - Daniel R Noguera
- the United States Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726, the Departments of Civil and Environmental Engineering and
| | - Blake A Simmons
- the Joint BioEnergy Institute, Emeryville, California 94608, the Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, California 94551
| | - Kenneth L Sale
- the Joint BioEnergy Institute, Emeryville, California 94608, the Biological and Engineering Sciences Center, Sandia National Laboratories, Livermore, California 94551
| | - John Ralph
- From the Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, the United States Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726
| | - Timothy J Donohue
- the United States Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin 53726, Bacteriology, University of Wisconsin, Madison, Wisconsin 53706,
| | - Paul D Adams
- the Joint BioEnergy Institute, Emeryville, California 94608, the Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, the Department of Bioengineering, University of California, Berkeley, California 94720, and
| | - George N Phillips
- the Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77251
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Heins RA, Cheng X, Nath S, Deng K, Bowen BP, Chivian DC, Datta S, Friedland GD, D’Haeseleer P, Wu D, Tran-Gyamfi M, Scullin CS, Singh S, Shi W, Hamilton MG, Bendall ML, Sczyrba A, Thompson J, Feldman T, Guenther JM, Gladden JM, Cheng JF, Adams PD, Rubin EM, Simmons BA, Sale KL, Northen TR, Deutsch S. Phylogenomically guided identification of industrially relevant GH1 β-glucosidases through DNA synthesis and nanostructure-initiator mass spectrometry. ACS Chem Biol 2014; 9:2082-91. [PMID: 24984213 PMCID: PMC4168791 DOI: 10.1021/cb500244v] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Harnessing the biotechnological potential of the large number of proteins available in sequence databases requires scalable methods for functional characterization. Here we propose a workflow to address this challenge by combining phylogenomic guided DNA synthesis with high-throughput mass spectrometry and apply it to the systematic characterization of GH1 β-glucosidases, a family of enzymes necessary for biomass hydrolysis, an important step in the conversion of lignocellulosic feedstocks to fuels and chemicals. We synthesized and expressed 175 GH1s, selected from over 2000 candidate sequences to cover maximum sequence diversity. These enzymes were functionally characterized over a range of temperatures and pHs using nanostructure-initiator mass spectrometry (NIMS), generating over 10,000 data points. When combined with HPLC-based sugar profiling, we observed GH1 enzymes active over a broad temperature range and toward many different β-linked disaccharides. For some GH1s we also observed activity toward laminarin, a more complex oligosaccharide present as a major component of macroalgae. An area of particular interest was the identification of GH1 enzymes compatible with the ionic liquid 1-ethyl-3-methylimidazolium acetate ([C2mim][OAc]), a next-generation biomass pretreatment technology. We thus searched for GH1 enzymes active at 70 °C and 20% (v/v) [C2mim][OAc] over the course of a 24-h saccharification reaction. Using our unbiased approach, we identified multiple enzymes of different phylogentic origin with such activities. Our approach of characterizing sequence diversity through targeted gene synthesis coupled to high-throughput screening technologies is a broadly applicable paradigm for a wide range of biological problems.
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Affiliation(s)
- Richard A. Heins
- Joint Bioenergy
Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Sandia National
Laboratories, 7011 East Avenue, Livermore, California 94551, United States
| | - Xiaoliang Cheng
- Joint Bioenergy
Institute, 5885 Hollis Street, Emeryville, California 94608, United States
| | - Sangeeta Nath
- Joint Genome Institute, 2800 Mitchell Drive, Walnut
Creek, California 94598, United States
| | - Kai Deng
- Joint Bioenergy
Institute, 5885 Hollis Street, Emeryville, California 94608, United States
| | - Benjamin P. Bowen
- Lawrence Berkeley
National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Dylan C. Chivian
- Joint Bioenergy
Institute, 5885 Hollis Street, Emeryville, California 94608, United States
| | - Supratim Datta
- Joint Bioenergy
Institute, 5885 Hollis Street, Emeryville, California 94608, United States
| | - Gregory D. Friedland
- Joint Bioenergy
Institute, 5885 Hollis Street, Emeryville, California 94608, United States
| | - Patrik D’Haeseleer
- Joint Bioenergy
Institute, 5885 Hollis Street, Emeryville, California 94608, United States
| | - Dongying Wu
- Joint Genome Institute, 2800 Mitchell Drive, Walnut
Creek, California 94598, United States
| | - Mary Tran-Gyamfi
- Sandia National
Laboratories, 7011 East Avenue, Livermore, California 94551, United States
| | - Chessa S. Scullin
- Joint Bioenergy
Institute, 5885 Hollis Street, Emeryville, California 94608, United States
| | - Seema Singh
- Joint Bioenergy
Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Sandia National
Laboratories, 7011 East Avenue, Livermore, California 94551, United States
| | - Weibing Shi
- Joint Genome Institute, 2800 Mitchell Drive, Walnut
Creek, California 94598, United States
| | - Matthew G. Hamilton
- Joint Genome Institute, 2800 Mitchell Drive, Walnut
Creek, California 94598, United States
| | - Matthew L. Bendall
- Joint Genome Institute, 2800 Mitchell Drive, Walnut
Creek, California 94598, United States
| | - Alexander Sczyrba
- Joint Genome Institute, 2800 Mitchell Drive, Walnut
Creek, California 94598, United States
| | - John Thompson
- NIDCR, NIH, Oral
Infection and Immunity Branch, 30 Convent
Drive, Bethesda, Maryland 20892, United States
| | - Taya Feldman
- Joint Bioenergy
Institute, 5885 Hollis Street, Emeryville, California 94608, United States
| | - Joel M. Guenther
- Joint Bioenergy
Institute, 5885 Hollis Street, Emeryville, California 94608, United States
| | - John M. Gladden
- Joint Bioenergy
Institute, 5885 Hollis Street, Emeryville, California 94608, United States
| | - Jan-Fang Cheng
- Joint Genome Institute, 2800 Mitchell Drive, Walnut
Creek, California 94598, United States
| | - Paul D. Adams
- Lawrence Berkeley
National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Edward M. Rubin
- Joint Genome Institute, 2800 Mitchell Drive, Walnut
Creek, California 94598, United States
- Lawrence Berkeley
National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Blake A. Simmons
- Joint Bioenergy
Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Sandia National
Laboratories, 7011 East Avenue, Livermore, California 94551, United States
| | - Kenneth L. Sale
- Joint Bioenergy
Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Sandia National
Laboratories, 7011 East Avenue, Livermore, California 94551, United States
| | - Trent R. Northen
- Joint Bioenergy
Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Lawrence Berkeley
National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Samuel Deutsch
- Joint Genome Institute, 2800 Mitchell Drive, Walnut
Creek, California 94598, United States
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Reyes-Ortiz V, Heins RA, Cheng G, Kim EY, Vernon BC, Elandt RB, Adams PD, Sale KL, Hadi MZ, Simmons BA, Kent MS, Tullman-Ercek D. Addition of a carbohydrate-binding module enhances cellulase penetration into cellulose substrates. Biotechnol Biofuels 2013; 6:93. [PMID: 23819686 PMCID: PMC3716932 DOI: 10.1186/1754-6834-6-93] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 06/18/2013] [Indexed: 05/03/2023]
Abstract
INTRODUCTION Cellulases are of great interest for application in biomass degradation, yet the molecular details of the mode of action of glycoside hydrolases during degradation of insoluble cellulose remain elusive. To further improve these enzymes for application at industrial conditions, it is critical to gain a better understanding of not only the details of the degradation process, but also the function of accessory modules. METHOD We fused a carbohydrate-binding module (CBM) from family 2a to two thermophilic endoglucanases. We then applied neutron reflectometry to determine the mechanism of the resulting enhancements. RESULTS Catalytic activity of the chimeric enzymes was enhanced up to three fold on insoluble cellulose substrates as compared to wild type. Importantly, we demonstrate that the wild type enzymes affect primarily the surface properties of an amorphous cellulose film, while the chimeras containing a CBM alter the bulk properties of the amorphous film. CONCLUSION Our findings suggest that the CBM improves the efficiency of these cellulases by enabling digestion within the bulk of the film.
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Affiliation(s)
- Vimalier Reyes-Ortiz
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA 94608, US
- Department of Bioengineering, University of California, Berkeley, CA 94720, US
| | - Richard A Heins
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA 94608, US
- Sandia National Laboratories, Livermore, CA 94550, US
| | - Gang Cheng
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA 94608, US
- Sandia National Laboratories, Livermore, CA 94550, US
| | - Edward Y Kim
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, US
| | - Briana C Vernon
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA 94608, US
- Sandia National Laboratories, Albuquerque, NM 87185, US
| | - Ryan B Elandt
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA 94608, US
| | - Paul D Adams
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA 94608, US
- Department of Bioengineering, University of California, Berkeley, CA 94720, US
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, US
| | - Kenneth L Sale
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA 94608, US
- Sandia National Laboratories, Livermore, CA 94550, US
| | - Masood Z Hadi
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA 94608, US
- Sandia National Laboratories, Livermore, CA 94550, US
| | - Blake A Simmons
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA 94608, US
- Sandia National Laboratories, Livermore, CA 94550, US
| | - Michael S Kent
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA 94608, US
- Sandia National Laboratories, Albuquerque, NM 87185, US
| | - Danielle Tullman-Ercek
- Deconstruction Division, Joint BioEnergy Institute, Emeryville, CA 94608, US
- Department of Bioengineering, University of California, Berkeley, CA 94720, US
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, US
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, US
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McAndrew RP, Park JI, Heins RA, Reindl W, Friedland GD, D'haeseleer P, Northen T, Sale KL, Simmons BA, Adams PD. From soil to structure, a novel dimeric β-glucosidase belonging to glycoside hydrolase family 3 isolated from compost using metagenomic analysis. J Biol Chem 2013; 288:14985-92. [PMID: 23580647 DOI: 10.1074/jbc.m113.458356] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A recent metagenomic analysis sequenced a switchgrass-adapted compost community to identify enzymes from microorganisms that were specifically adapted to switchgrass under thermophilic conditions. These enzymes are being examined as part of the pretreatment process for the production of "second-generation" biofuels. Among the enzymes discovered was JMB19063, a novel three-domain β-glucosidase that belongs to the GH3 (glycoside hydrolase 3) family. Here, we report the structure of JMB19063 in complex with glucose and the catalytic variant D261N crystallized in the presence of cellopentaose. JMB19063 is first structure of a dimeric member of the GH3 family, and we demonstrate that dimerization is required for catalytic activity. Arg-587 and Phe-598 from the C-terminal domain of the opposing monomer are shown to interact with bound ligands in the D261N structure. Enzyme assays confirmed that these residues are absolutely essential for full catalytic activity.
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Affiliation(s)
- Ryan P McAndrew
- Joint BioEnergy Institute, Emeryville, California 94608, USA
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Heins RA, Choi JH, Sohka T, Ostermeier M. In vitro recombination of non-homologous genes can result in gene fusions that confer a switching phenotype to cells. PLoS One 2011; 6:e27302. [PMID: 22096548 PMCID: PMC3214044 DOI: 10.1371/journal.pone.0027302] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2011] [Accepted: 10/13/2011] [Indexed: 11/18/2022] Open
Abstract
Regulation of protein activity is central to the complexity of life. The ability to regulate protein activity through exogenously added molecules has biotechnological/biomedical applications and offers tools for basic science. Such regulation can be achieved by establishing a means to modulate the specific activity of the protein (i.e. allostery). An alternative strategy for intracellular regulation of protein activity is to control the amount of protein through effects on its production, accumulation, and degradation. We have previously demonstrated that the non-homologous recombination of the genes encoding maltose binding protein (MBP) and TEM1 β-lactamase (BLA) can result in fusion proteins in which β-lactamase enzyme activity is allosterically regulated by maltose. Here, through use of a two-tiered genetic selection scheme, we demonstrate that such recombination can result in genes that confer maltose-dependent resistance to β-lactam even though they do not encode allosteric enzymes. These ‘phenotypic switch’ genes encode fusion proteins whose accumulation is a result of a specific interaction with maltose. Phenotypic switches represent an important class of proteins for basic science and biotechnological applications in vivo.
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Affiliation(s)
- Richard A. Heins
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Jay H. Choi
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Takayuki Sohka
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Marc Ostermeier
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail:
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Sohka T, Heins RA, Ostermeier M. Morphogen-defined patterning of Escherichia coli enabled by an externally tunable band-pass filter. J Biol Eng 2009; 3:10. [PMID: 19586541 PMCID: PMC2715369 DOI: 10.1186/1754-1611-3-10] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2009] [Accepted: 07/08/2009] [Indexed: 11/10/2022] Open
Abstract
Background Gradients of morphogens pattern cell fate – a phenomenon that is especially important during development. A simple model system for studying how morphogens pattern cell behavior would overcome difficulties inherent in the study of natural morphogens in vivo. A synthetic biology approach to building such a system is attractive. Results Using an externally-tunable band-pass filter paradigm, we engineered Escherichia coli cells to function as a model system for the study of how multiple morphogens can pattern cell behavior. We demonstrate how our system exhibits behavior such as morphogen crosstalk and how the cells' growth and fluorescence can be patterned in a number of complex patterns. We extend our cell patterning from 2D cultures on the surface of plates to 3D cultures in soft agarose medium. Conclusion Our system offers a convenient, well-defined model system for fundamental studies on how multiple morphogen gradients can affect cell fate and lead to pattern formation. Our design principles could be applied to eukaryotic cells to develop other models systems for studying development or for enabling the patterning of cells for applications such as tissue engineering and biomaterials.
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Affiliation(s)
- Takayuki Sohka
- Department of Chemical & Biomolecular Engineering, Johns Hopkins University, 3400 N. Charles St, Baltimore, MD 21212, USA.
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Abstract
Proteins that behave as switches help to establish the complex molecular logic that is central to biological systems. Aspiring to be nature's equal, researchers have successfully created protein switches of their own design; in particular, numerous and varied zinc-triggered switches have been made. Recent studies in which such switches have been readily identified from combinatorial protein libraries support the notion that proteins are primed to show allosteric behavior and that newly created ligand-binding sites will often be functionally coupled to the original activity of the protein. If true, this notion suggests that switch engineering might be more tractable than previously thought, boding well for the basic science, sensing and biomedical applications for which protein switches hold much promise.
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Affiliation(s)
- Chapman M Wright
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218-2681, USA
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