501
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Kim JH, Feng Z, Bauer JD, Kallifidas D, Calle PY, Brady SF. Cloning large natural product gene clusters from the environment: piecing environmental DNA gene clusters back together with TAR. Biopolymers 2010; 93:833-44. [PMID: 20577994 PMCID: PMC2895911 DOI: 10.1002/bip.21450] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A single gram of soil can contain thousands of unique bacterial species, of which only a small fraction is regularly cultured in the laboratory. Although the fermentation of cultured microorganisms has provided access to numerous bioactive secondary metabolites, with these same methods it is not possible to characterize the natural products encoded by the uncultured majority. The heterologous expression of biosynthetic gene clusters cloned from DNA extracted directly from environmental samples (eDNA) has the potential to provide access to the chemical diversity encoded in the genomes of uncultured bacteria. One of the challenges facing this approach has been that many natural product biosynthetic gene clusters are too large to be readily captured on a single fragment of cloned eDNA. The reassembly of large eDNA-derived natural product gene clusters from collections of smaller overlapping clones represents one potential solution to this problem. Unfortunately, traditional methods for the assembly of large DNA sequences from multiple overlapping clones can be technically challenging. Here we present a general experimental framework that permits the recovery of large natural product biosynthetic gene clusters on overlapping soil-derived eDNA cosmid clones and the reassembly of these large gene clusters using transformation-associated recombination (TAR) in Saccharomyces cerevisiae. The development of practical methods for the rapid assembly of biosynthetic gene clusters from collections of overlapping eDNA clones is an important step toward being able to functionally study larger natural product gene clusters from uncultured bacteria. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 833–844, 2010.
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Affiliation(s)
- Jeffrey H Kim
- Howard Hughes Medical Institute, Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
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502
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Du J, Li S, Zhao H. Discovery and characterization of novel d-xylose-specific transporters from Neurospora crassa and Pichia stipitis. MOLECULAR BIOSYSTEMS 2010; 6:2150-6. [PMID: 20714641 DOI: 10.1039/c0mb00007h] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Saccharomyces cerevisiae is considered one of the most promising organisms for ethanol production from lignocellulosic feedstock. Unfortunately, pentose sugars, which comprise up to 30% of lignocellulose, cannot be utilized by wild type S. cerevisiae. Heterologous pathways were introduced into S. cerevisiae to enable utilization of d-xylose, the most abundant pentose sugar. However, the resulting recombinant S. cerevisiae strains exhibited a slow growth rate and poor sugar utilization efficiency when grown on d-xylose as the sole carbon source. d-xylose uptake is the first step of d-xylose utilization. d-xylose can only enter yeast cells through hexose transporters, which have two orders of magnitude lower affinity towards d-xylose compared to hexoses. It was also shown that inefficient pentose uptake is the limiting step in some d-xylose metabolizing yeast strains. Here we report the cloning and characterization of two novel d-xylose-specific transporters from Neurospora crassa and Pichia stipitis. These two transporters were identified from a total of 18 putative pentose transporters. They were functionally expressed and properly localized in S. cerevisiae as indicated by HPLC analysis and fluorescence confocal microscopy, respectively. Kinetic parameters of the d-xylose-specific transporters were determined using a (14)C-labeled sugar uptake assay. Use of pentose-specific transporters should improve d-xylose consumption and ethanol production in fast d-xylose assimilating strains, thereby lowering the cost of lignocellulosic ethanol production.
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Affiliation(s)
- Jing Du
- Energy Biosciences Institute, Institute for Genomic Biology, Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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503
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Bikard D, Julié-Galau S, Cambray G, Mazel D. The synthetic integron: an in vivo genetic shuffling device. Nucleic Acids Res 2010; 38:e153. [PMID: 20534632 PMCID: PMC2926619 DOI: 10.1093/nar/gkq511] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
As the field of synthetic biology expands, strategies and tools for the rapid construction of new biochemical pathways will become increasingly valuable. Purely rational design of complex biological pathways is inherently limited by the current state of our knowledge. Selection of optimal arrangements of genetic elements from randomized libraries may well be a useful approach for successful engineering. Here, we propose the construction and optimization of metabolic pathways using the inherent gene shuffling activity of a natural bacterial site-specific recombination system, the integron. As a proof of principle, we constructed and optimized a functional tryptophan biosynthetic operon in Escherichia coli. The trpA-E genes along with ‘regulatory’ elements were delivered as individual recombination cassettes in a synthetic integron platform. Integrase-mediated recombination generated thousands of genetic combinations overnight. We were able to isolate a large number of arrangements displaying varying fitness and tryptophan production capacities. Several assemblages required as many as six recombination events and produced as much as 11-fold more tryptophan than the natural gene order in the same context.
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Affiliation(s)
- David Bikard
- Institut Pasteur, Département Génomes et Génétique, Paris, France
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504
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Densmore D, Hsiau THC, Kittleson JT, DeLoache W, Batten C, Anderson JC. Algorithms for automated DNA assembly. Nucleic Acids Res 2010; 38:2607-16. [PMID: 20335162 PMCID: PMC2860133 DOI: 10.1093/nar/gkq165] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Generating a defined set of genetic constructs within a large combinatorial space provides a powerful method for engineering novel biological functions. However, the process of assembling more than a few specific DNA sequences can be costly, time consuming and error prone. Even if a correct theoretical construction scheme is developed manually, it is likely to be suboptimal by any number of cost metrics. Modular, robust and formal approaches are needed for exploring these vast design spaces. By automating the design of DNA fabrication schemes using computational algorithms, we can eliminate human error while reducing redundant operations, thus minimizing the time and cost required for conducting biological engineering experiments. Here, we provide algorithms that optimize the simultaneous assembly of a collection of related DNA sequences. We compare our algorithms to an exhaustive search on a small synthetic dataset and our results show that our algorithms can quickly find an optimal solution. Comparison with random search approaches on two real-world datasets show that our algorithms can also quickly find lower-cost solutions for large datasets.
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Affiliation(s)
- Douglas Densmore
- Department of Fuel Synthesis, Joint BioEnergy Institute, 5885 Hollis St., Fourth Floor, Emeryville CA 94608, USA.
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505
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Affiliation(s)
- Robert Carlson
- Robert Carlson is at Biodesic, Seattle, Washington, USA.
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506
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Synthetic biology: tools to design, build, and optimize cellular processes. J Biomed Biotechnol 2010; 2010:130781. [PMID: 20150964 PMCID: PMC2817555 DOI: 10.1155/2010/130781] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2009] [Accepted: 10/28/2009] [Indexed: 11/17/2022] Open
Abstract
The general central
dogma frames the emergent properties of life,
which make biology both necessary and difficult
to engineer. In a process engineering paradigm,
each biological process stream and process unit
is heavily influenced by regulatory interactions
and interactions with the surrounding
environment. Synthetic biology is developing the
tools and methods that will increase control
over these interactions, eventually resulting in
an integrative synthetic biology that will allow
ground-up cellular optimization. In this review,
we attempt to contextualize the areas of
synthetic biology into three tiers: (1) the
process units and associated streams of the
central dogma, (2) the intrinsic regulatory
mechanisms, and (3) the extrinsic physical and
chemical environment. Efforts at each of these
three tiers attempt to control cellular systems
and take advantage of emerging tools and
approaches. Ultimately, it will be possible to
integrate these approaches and realize the
vision of integrative synthetic biology when
cells are completely rewired for
biotechnological goals. This review will
highlight progress towards this goal as well as
areas requiring further research.
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507
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Li S, Du J, Sun J, Galazka JM, Glass NL, Cate JHD, Yang X, Zhao H. Overcoming glucose repression in mixed sugar fermentation by co-expressing a cellobiose transporter and a β-glucosidase in Saccharomyces cerevisiae. MOLECULAR BIOSYSTEMS 2010; 6:2129-32. [DOI: 10.1039/c0mb00063a] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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508
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Yeast surface display of trifunctional minicellulosomes for simultaneous saccharification and fermentation of cellulose to ethanol. Appl Environ Microbiol 2009; 76:1251-60. [PMID: 20023102 DOI: 10.1128/aem.01687-09] [Citation(s) in RCA: 152] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
By combining cellulase production, cellulose hydrolysis, and sugar fermentation into a single step, consolidated bioprocessing (CBP) represents a promising technology for biofuel production. Here we report engineering of Saccharomyces cerevisiae strains displaying a series of uni-, bi-, and trifunctional minicellulosomes. These minicellulosomes consist of (i) a miniscaffoldin containing a cellulose-binding domain and three cohesin modules, which was tethered to the cell surface through the yeast a-agglutinin adhesion receptor, and (ii) up to three types of cellulases, an endoglucanase, a cellobiohydrolase, and a beta-glucosidase, each bearing a C-terminal dockerin. Cell surface assembly of the minicellulosomes was dependent on expression of the miniscaffoldin, indicating that formation of the complex was dictated by the high-affinity interactions between cohesins and dockerins. Compared to the unifunctional and bifunctional minicellulosomes, the quaternary trifunctional complexes showed enhanced enzyme-enzyme synergy and enzyme proximity synergy. More importantly, surface display of the trifunctional minicellulosomes gave yeast cells the ability to simultaneously break down and ferment phosphoric acid-swollen cellulose to ethanol with a titer of approximately 1.8 g/liter. To our knowledge, this is the first report of a recombinant yeast strain capable of producing cell-associated trifunctional minicellulosomes. The strain reported here represents a useful engineering platform for developing CBP-enabling microorganisms and elucidating principles of cellulosome construction and mode of action.
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509
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Toward engineering synthetic microbial metabolism. J Biomed Biotechnol 2009; 2010:459760. [PMID: 20037734 PMCID: PMC2796345 DOI: 10.1155/2010/459760] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2009] [Accepted: 10/09/2009] [Indexed: 11/18/2022] Open
Abstract
The generation of well-characterized parts and the formulation of biological design principles in synthetic biology are laying the foundation for more complex and advanced microbial metabolic engineering. Improvements in de novo DNA synthesis and codon-optimization alone are already contributing to the manufacturing of pathway enzymes with improved or novel function. Further development of analytical and computer-aided design tools should accelerate the forward engineering of precisely regulated synthetic pathways by providing a standard framework for the predictable design of biological systems from well-characterized parts. In this review we discuss the current state of synthetic biology within a four-stage framework (design, modeling, synthesis, analysis) and highlight areas requiring further advancement to facilitate true engineering of synthetic microbial metabolism.
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510
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511
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Alterovitz G, Muso T, Ramoni MF. The challenges of informatics in synthetic biology: from biomolecular networks to artificial organisms. Brief Bioinform 2009; 11:80-95. [PMID: 19906839 DOI: 10.1093/bib/bbp054] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The field of synthetic biology holds an inspiring vision for the future; it integrates computational analysis, biological data and the systems engineering paradigm in the design of new biological machines and systems. These biological machines are built from basic biomolecular components analogous to electrical devices, and the information flow among these components requires the augmentation of biological insight with the power of a formal approach to information management. Here we review the informatics challenges in synthetic biology along three dimensions: in silico, in vitro and in vivo. First, we describe state of the art of the in silico support of synthetic biology, from the specific data exchange formats, to the most popular software platforms and algorithms. Next, we cast in vitro synthetic biology in terms of information flow, and discuss genetic fidelity in DNA manipulation, development strategies of biological parts and the regulation of biomolecular networks. Finally, we explore how the engineering chassis can manipulate biological circuitries in vivo to give rise to future artificial organisms.
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Affiliation(s)
- Gil Alterovitz
- Children's Hospital Informatics Program, Harvard/MITDivision of Health Sciences and Technology, USA
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512
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Gibson DG. Synthesis of DNA fragments in yeast by one-step assembly of overlapping oligonucleotides. Nucleic Acids Res 2009; 37:6984-90. [PMID: 19745056 PMCID: PMC2777417 DOI: 10.1093/nar/gkp687] [Citation(s) in RCA: 202] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Here it is demonstrated that the yeast Saccharomyces cerevisiae can take up and assemble at least 38 overlapping single-stranded oligonucleotides and a linear double-stranded vector in one transformation event. These oligonucleotides can overlap by as few as 20 bp, and can be as long as 200 nucleotides in length. This straightforward scheme for assembling chemically-synthesized oligonucleotides could be a useful tool for building synthetic DNA molecules.
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Affiliation(s)
- Daniel G Gibson
- The J Craig Venter Institute, Synthetic Biology Group, 9704 Medical Center Drive, Rockville, MD 20850, USA.
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513
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Wen F, Nair NU, Zhao H. Protein engineering in designing tailored enzymes and microorganisms for biofuels production. Curr Opin Biotechnol 2009; 20:412-9. [PMID: 19660930 DOI: 10.1016/j.copbio.2009.07.001] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2009] [Accepted: 07/02/2009] [Indexed: 10/20/2022]
Abstract
Lignocellulosic biofuels represent a sustainable, renewable, and the only foreseeable alternative energy source to transportation fossil fuels. However, the recalcitrant nature of lignocellulose poses technical hurdles to an economically viable biorefinery. Low enzymatic hydrolysis efficiency and low productivity, yield, and titer of biofuels are among the top cost contributors. Protein engineering has been used to improve the performance of lignocellulose-degrading enzymes, as well as proteins involved in biofuel synthesis pathways. Unlike its great success seen in other industrial applications, protein engineering has achieved only modest results in improving the lignocellulose-to-biofuels efficiency. This review will discuss the unique challenges that protein engineering faces in the process of converting lignocellulose to biofuels and how they are addressed by recent advances in this field.
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Affiliation(s)
- Fei Wen
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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514
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Synthetic gene networks: the next wave in biotechnology? Trends Biotechnol 2009; 27:368-74. [PMID: 19409633 DOI: 10.1016/j.tibtech.2009.03.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2008] [Revised: 02/24/2009] [Accepted: 03/02/2009] [Indexed: 11/22/2022]
Abstract
Engineering novel, reusable gene networks to provide greater control over cellular processes is one of the goals of the emerging discipline of synthetic biology. This article reviews the landmark literature pertaining to the development of synthetic gene networks, the engineering framework used to design and characterize them and the technological developments on the horizon that could potentially advance the field in new directions. As gene network engineering enters its second decade, an attempt is also made to outline the challenges in advancing this nascent field, especially with regard to the practical limitations of component reusability and reliability and the opportunities that present themselves in the development of novel gene expression controllers and single-cell biosensors.
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