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Angov E. Codon usage: nature's roadmap to expression and folding of proteins. Biotechnol J 2011; 6:650-9. [PMID: 21567958 PMCID: PMC3166658 DOI: 10.1002/biot.201000332] [Citation(s) in RCA: 153] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Revised: 04/11/2011] [Accepted: 04/13/2011] [Indexed: 02/06/2023]
Abstract
Biomedical and biotechnological research relies on processes leading to the successful expression and production of key biological products. High-quality proteins are required for many purposes, including protein structural and functional studies. Protein expression is the culmination of multistep processes involving regulation at the level of transcription, mRNA turnover, protein translation, and post-translational modifications leading to the formation of a stable product. Although significant strides have been achieved over the past decade, advances toward integrating genomic and proteomic information are essential, and until such time, many target genes and their products may not be fully realized. Thus, the focus of this review is to provide some experimental support and a brief overview of how codon usage bias has evolved relative to regulating gene expression levels.
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Affiliation(s)
- Evelina Angov
- Division of Malaria Vaccine Development, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA.
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202
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Shankar S, Pillai MR. Translating cancer research by synthetic biology. MOLECULAR BIOSYSTEMS 2011; 7:1802-10. [PMID: 21437339 DOI: 10.1039/c1mb05016h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Synthetic biology concerns applying engineering principles to biological systems. Engineering properties such as fine tuning, novel specificity, and modularity could be components of a synthetic toolkit that can be exploited to explore various issues in cancer research such as elucidation of mechanisms and pathways, creating new diagnostic tools and novel therapeutic approaches. A repertoire of synthetic biology toolkits involving DNA, RNA and protein bio-parts, have been applied to address the issues of drug target identification, drug discovery and therapeutic treatment in cancer research, thereby projecting a new dimension in oncology research.
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Affiliation(s)
- Sumitra Shankar
- Integrated Cancer Research Program, Rajiv Gandhi Centre for Biotechnology, Thycaud. PO, Thiruvananthapuram, 695 014, Kerala State, India
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203
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Waite JC, Leiner I, Lauer P, Rae CS, Barbet G, Zheng H, Portnoy DA, Pamer EG, Dustin ML. Dynamic imaging of the effector immune response to listeria infection in vivo. PLoS Pathog 2011; 7:e1001326. [PMID: 21455492 PMCID: PMC3063765 DOI: 10.1371/journal.ppat.1001326] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Accepted: 02/25/2011] [Indexed: 11/18/2022] Open
Abstract
Host defense against the intracellular pathogen Listeria monocytogenes (Lm) requires innate and adaptive immunity. Here, we directly imaged immune cell dynamics at Lm foci established by dendritic cells in the subcapsular red pulp (scDC) using intravital microscopy. Blood borne Lm rapidly associated with scDC. Myelomonocytic cells (MMC) swarmed around non-motile scDC forming foci from which blood flow was excluded. The depletion of scDC after foci were established resulted in a 10-fold reduction in viable Lm, while graded depletion of MMC resulted in 30-1000 fold increase in viable Lm in foci with enhanced blood flow. Effector CD8+ T cells at sites of infection displayed a two-tiered reduction in motility with antigen independent and antigen dependent components, including stable interactions with infected and non-infected scDC. Thus, swarming MMC contribute to control of Lm prior to development of T cell immunity by direct killing and sequestration from blood flow, while scDC appear to promote Lm survival while preferentially interacting with CD8+ T cells in effector sites.
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Affiliation(s)
- Janelle C. Waite
- Program in Molecular Pathogenesis, Helen L. and Martin S. Kimmel Center for Biology and Medicine of the Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York City, New York, United States of America
| | - Ingrid Leiner
- Infectious Disease Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, Immunology Program, Sloan-Kettering Institute, New York City, New York, United States of America
| | - Peter Lauer
- Aduro BioTech, Berkeley, California, United States of America
| | - Chris S. Rae
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Gaetan Barbet
- Program in Molecular Pathogenesis, Helen L. and Martin S. Kimmel Center for Biology and Medicine of the Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York City, New York, United States of America
| | - Huan Zheng
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Daniel A. Portnoy
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America
- School of Public Health, University of California, Berkeley, Berkeley, California, United State of America
| | - Eric G. Pamer
- Infectious Disease Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, Immunology Program, Sloan-Kettering Institute, New York City, New York, United States of America
| | - Michael L. Dustin
- Program in Molecular Pathogenesis, Helen L. and Martin S. Kimmel Center for Biology and Medicine of the Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York City, New York, United States of America
- * E-mail:
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204
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Glykys DJ, Szilvay GR, Tortosa P, Suárez Diez M, Jaramillo A, Banta S. Pushing the limits of automatic computational protein design: design, expression, and characterization of a large synthetic protein based on a fungal laccase scaffold. SYSTEMS AND SYNTHETIC BIOLOGY 2011; 5:45-58. [PMID: 22654993 DOI: 10.1007/s11693-011-9080-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Revised: 11/12/2010] [Accepted: 02/19/2011] [Indexed: 01/29/2023]
Abstract
UNLABELLED The de novo engineering of new proteins will allow the design of complex systems in synthetic biology. But the design of large proteins is very challenging due to the large combinatorial sequence space to be explored and the lack of a suitable selection system to guide the evolution and optimization. One way to approach this challenge is to use computational design methods based on the current crystallographic data and on molecular mechanics. We have used a laccase protein fold as a scaffold to design a new protein sequence that would adopt a 3D conformation in solution similar to a wild-type protein, the Trametes versicolor (TvL) fungal laccase. Laccases are multi-copper oxidases that find utility in a variety of industrial applications. The laccases with highest activity and redox potential are generally secreted fungal glycoproteins. Prokaryotic laccases have been identified with some desirable features, but they often exhibit low redox potentials. The designed sequence (DLac) shares a 50% sequence identity to the original TvL protein. The new DLac gene was overexpressed in E. coli and the majority of the protein was found in inclusion bodies. Both soluble protein and refolded insoluble protein were purified, and their identity was verified by mass spectrometry. Neither protein exhibited the characteristic T1 copper absorbance, neither bound copper by atomic absorption, and neither was active using a variety of laccase substrates over a range of pH values. Circular dichroism spectroscopy studies suggest that the DLac protein adopts a molten globule structure that is similar to the denatured and refolded native fungal TvL protein, which is significantly different from the natively secreted fungal protein. Taken together, these results indicate that the computationally designed DLac expressed in E. coli is unable to utilize the same folding pathway that is used in the expression of the parent TvL protein or the prokaryotic laccases. This sequence can be used going forward to help elucidate the sequence requirements needed for prokaryotic multi-copper oxidase expression. ELECTRONIC SUPPLEMENTARY MATERIAL The online version of this article (doi:10.1007/s11693-011-9080-9) contains supplementary material, which is available to authorized users.
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205
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Invasive extravillous trophoblasts restrict intracellular growth and spread of Listeria monocytogenes. PLoS Pathog 2011; 7:e1002005. [PMID: 21408203 PMCID: PMC3048367 DOI: 10.1371/journal.ppat.1002005] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2010] [Accepted: 12/29/2010] [Indexed: 11/19/2022] Open
Abstract
Listeria monocytogenes is a facultative intracellular bacterial pathogen that can infect the placenta, a chimeric organ made of maternal and fetal cells. Extravillous trophoblasts (EVT) are specialized fetal cells that invade the uterine implantation site, where they come into direct contact with maternal cells. We have shown previously that EVT are the preferred site of initial placental infection. In this report, we infected primary human EVT with L. monocytogenes. EVT eliminated ∼80% of intracellular bacteria over 24-hours. Bacteria were unable to escape into the cytoplasm and remained confined to vacuolar compartments that became acidified and co-localized with LAMP1, consistent with bacterial degradation in lysosomes. In human placental organ cultures bacterial vacuolar escape rates differed between specific trophoblast subpopulations. The most invasive EVT—those that would be in direct contact with maternal cells in vivo—had lower escape rates than trophoblasts that were surrounded by fetal cells and tissues. Our results suggest that EVT present a bottleneck in the spread of L. monocytogenes from mother to fetus by inhibiting vacuolar escape, and thus intracellular bacterial growth. However, if L. monocytogenes is able to spread beyond EVT it can find a more hospitable environment. Our results elucidate a novel aspect of the maternal-fetal barrier. Infection of the placenta and fetus is an important cause of pregnancy complications and fetal and neonatal morbidity and mortality. Listeria monocytogenes is an intracellular bacterial pathogen that causes pregnancy-related infections in humans. The pathogenesis of listeriosis during pregnancy is poorly understood. We have previously shown that transmission of L. monocytogenes from maternal cells and tissues to fetal cells occurs in the uterine implantation site, and that a small subpopulation of specialized fetal cells called extravillous trophoblasts are the preferred initial site of infection. Here we use primary human placental organ and cell culture systems to characterize the intracellular fate of L. monocytogenes in extravillous trophoblasts. We found that these cells entrap bacteria in vacuolar compartments where they are degraded and therefore reduce bacterial dissemination into deeper structures of the placenta. Our study provides new insights into the nature of the maternal-fetal barrier. Extravillous trophoblasts that are accessible to infection with intracellular pathogens from infected maternal cells have host defense mechanisms that constitute a bottleneck in maternal-fetal transmission.
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206
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Menzella HG. Comparison of two codon optimization strategies to enhance recombinant protein production in Escherichia coli. Microb Cell Fact 2011; 10:15. [PMID: 21371320 PMCID: PMC3056764 DOI: 10.1186/1475-2859-10-15] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Accepted: 03/03/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Variations in codon usage between species are one of the major causes affecting recombinant protein expression levels, with a significant impact on the economy of industrial enzyme production processes. The use of codon-optimized genes may overcome this problem. However, designing a gene for optimal expression requires choosing from a vast number of possible DNA sequences and different codon optimization methods have been used in the past decade. Here, a comparative study of the two most common methods is presented using calf prochymosin as a model. RESULTS Seven sequences encoding calf prochymosin have been designed, two using the "one amino acid-one codon" method and five using a "codon randomization" strategy. When expressed in Escherichia coli, the variants optimized by the codon randomization approach produced significantly more proteins than the native sequence including one gene that produced an increase of 70% in the amount of prochymosin accumulated. On the other hand, no significant improvement in protein expression was observed for the variants designed with the one amino acid-one codon method. The use of codon-optimized sequences did not affect the quality of the recovered inclusion bodies. CONCLUSIONS The results obtained in this study indicate that the codon randomization method is a superior strategy for codon optimization. A significant improvement in protein expression was obtained for the largely established process of chymosin production, showing the power of this strategy to reduce production costs of industrial enzymes in microbial hosts.
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Affiliation(s)
- Hugo G Menzella
- Genetic Engineering & Fermentation Technology, CONICET, Facultad de Ciencias Bioquimicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531 Rosario 2000, Republica Argentina.
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207
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Real-time PCR assay and a synthetic positive control for the rapid and sensitive detection of the emerging resistance gene New Delhi Metallo-β-lactamase-1 (bla NDM-1). Med Microbiol Immunol 2011; 200:137-41. [DOI: 10.1007/s00430-011-0189-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Indexed: 11/25/2022]
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208
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Abstract
The evolution of phenotype is often based on changes in gene expression rather than changes in protein-coding sequence. Gene expression is controlled by complex networks of interacting regulators that act through a variety of biochemical mechanisms. Perturbation of these networks can have profound effects on the fitness of organisms. This highlights an important challenge: the investigation of whether the mechanisms and network architectures we observe in Nature evolved in response to selective pressure--and, if so, what that pressure might have been--or whether the architectures are a result of non-adaptive forces. Synthetic biologists aim to construct artificial genetic and biological systems to increase our understanding of Nature as well as for a number of biotechnological applications. In this review, I will highlight how engineering 'synthetic' control of gene expression provides a way to test evolutionary hypotheses. Synthetic biology might allow us to investigate experimentally the evolutionary paths not taken by extant organisms.
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Affiliation(s)
- Travis S Bayer
- Centre for Synthetic Biology and Innovation, Imperial College London, London, UK.
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209
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Wells MA, Mercer J, Mott RA, Pereira-Medrano AG, Burja AM, Radianingtyas H, Wright PC. Engineering a non-native hydrogen production pathway into Escherichia coli via a cyanobacterial [NiFe] hydrogenase. Metab Eng 2011; 13:445-53. [PMID: 21276867 DOI: 10.1016/j.ymben.2011.01.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Revised: 12/05/2010] [Accepted: 01/13/2011] [Indexed: 10/18/2022]
Abstract
Biotechnology is a promising approach for the generation of hydrogen, but is not yet commercially viable. Metabolic engineering is a potential solution, but has largely been limited to native pathway optimisation. To widen opportunities for use of non-native [NiFe] hydrogenases for improved hydrogen production, we introduced a cyanobacterial hydrogen production pathway and associated maturation factors into Escherichia coli. Hydrogen production is observed in vivo in a hydrogenase null host, demonstrating coupling to host electron transfer systems. Hydrogenase activity is also detected in vitro. Hydrogen output is increased when formate production is abolished, showing that the new pathway is distinct from the native formate dependent pathway and supporting the conclusion that it couples cellular NADH and NADPH pools to molecular hydrogen. This work demonstrates non-native hydrogen production in E. coli, showing the wide portability of [NiFe] hydrogenase pathways and the potential for metabolic engineering to improve hydrogen yields.
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Affiliation(s)
- Mark A Wells
- ChELSI Institute, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, UK
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210
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Abstract
DNA synthesis techniques and technologies are quickly becoming a cornerstone of modern molecular biology and play a pivotal role in the field of synthetic biology. The ability to synthesize whole genes, novel genetic pathways, and even entire genomes is no longer the dream it was 30 years ago. Using little more than a thermocycler, commercially synthesized oligonucleotides, and DNA polymerases, a standard molecular biology laboratory can synthesize several kilobase pairs of synthetic DNA in a week using existing techniques. Herein, we review the techniques used in the generation of synthetic DNA, from the chemical synthesis of oligonucleotides to their assembly into long, custom sequences. Software and websites to facilitate the execution of these approaches are explored, and applications of DNA synthesis techniques to gene expression and synthetic biology are discussed. Finally, an example of automated gene synthesis from our own laboratory is provided.
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Affiliation(s)
- Randall A Hughes
- Applied Research Laboratories, The University of Texas at Austin, Austin, Texas, USA
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211
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Jaschke PR, Saer RG, Noll S, Beatty JT. Modification of the genome of Rhodobacter sphaeroides and construction of synthetic operons. Methods Enzymol 2011; 497:519-38. [PMID: 21601102 DOI: 10.1016/b978-0-12-385075-1.00023-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The α-proteobacterium Rhodobacter sphaeroides is an exemplary model organism for the creation and study of novel protein expression systems, especially membrane protein complexes that harvest light energy to yield electrical energy. Advantages of this organism include a sequenced genome, tools for genetic engineering, a well-characterized metabolism, and a large membrane surface area when grown under hypoxic or anoxic conditions. This chapter provides a framework for the utilization of R. sphaeroides as a model organism for membrane protein expression, highlighting key advantages and shortcomings. Procedures covered in this chapter include the creation of chromosomal gene deletions, disruptions, and replacements, as well as the construction of a synthetic operon using a model promoter to induce expression of modified photosynthetic reaction center proteins for structural and functional analysis.
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Affiliation(s)
- Paul R Jaschke
- Department of Microbiology and Immunology, University of British Columbia, Life Sciences Centre, Vancouver, British Columbia, Canada
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212
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213
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Abstract
Despite their name, synonymous mutations have significant consequences for cellular processes in all taxa. As a result, an understanding of codon bias is central to fields as diverse as molecular evolution and biotechnology. Although recent advances in sequencing and synthetic biology have helped to resolve longstanding questions about codon bias, they have also uncovered striking patterns that suggest new hypotheses about protein synthesis. Ongoing work to quantify the dynamics of initiation and elongation is as important for understanding natural synonymous variation as it is for designing transgenes in applied contexts.
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Affiliation(s)
- Joshua B Plotkin
- Department of Biology and Program in Applied Mathematics and Computational Science, University of Pennsylvania, 433 South University Avenue, Philadelphia, Pennsylvania 19104, USA.
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214
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Construction of a genetic multiplexer to toggle between chemosensory pathways in Escherichia coli. J Mol Biol 2010; 406:215-27. [PMID: 21185306 DOI: 10.1016/j.jmb.2010.12.019] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2010] [Revised: 12/05/2010] [Accepted: 12/08/2010] [Indexed: 11/20/2022]
Abstract
Many applications require cells to switch between discrete phenotypic states. Here, we harness the FimBE inversion switch to flip a promoter, allowing expression to be toggled between two genes oriented in opposite directions. The response characteristics of the switch are characterized using two-color cytometry. This switch is used to toggle between orthogonal chemosensory pathways by controlling the expression of CheW and CheW*, which interact with the Tar (aspartate) and Tsr* (serine) chemoreceptors, respectively. CheW* and Tsr* each contain a mutation at their protein-protein interface such that they interact with each other. The complete genetic program containing an arabinose-inducible FimE controlling CheW/CheW* (and constitutively expressed tar/tsr*) is transformed into an Escherichia coli strain lacking all native chemoreceptors. This program enables bacteria to swim toward serine or aspartate in the absence or in the presence of arabinose, respectively. Thus, the program functions as a multiplexer with arabinose as the selector. This demonstrates the ability of synthetic genetic circuits to connect to a natural signaling network to switch between phenotypes.
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215
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Grand challenge commentary: Transforming biosynthesis into an information science. Nat Chem Biol 2010; 6:859-61. [PMID: 21079588 DOI: 10.1038/nchembio.487] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Engineering biosynthetic pathways to natural products is a challenging endeavor that promises to provide new therapeutics and tools to manipulate biology. Information-guided design strategies and tools could unlock the creativity of a wide spectrum of scientists and engineers by decoupling expertise from implementation.
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216
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Enhanced periplasmic expression of high affinity humanized scFv against Hepatitis B surface antigen by codon optimization. Protein Expr Purif 2010; 74:272-9. [DOI: 10.1016/j.pep.2010.06.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Revised: 06/10/2010] [Accepted: 06/10/2010] [Indexed: 02/02/2023]
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217
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Widmaier DM, Voigt CA. Quantification of the physiochemical constraints on the export of spider silk proteins by Salmonella type III secretion. Microb Cell Fact 2010; 9:78. [PMID: 20973967 PMCID: PMC2987917 DOI: 10.1186/1475-2859-9-78] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Accepted: 10/25/2010] [Indexed: 01/28/2023] Open
Abstract
Background The type III secretion system (T3SS) is a molecular machine in gram negative bacteria that exports proteins through both membranes to the extracellular environment. It has been previously demonstrated that the T3SS encoded in Salmonella Pathogenicity Island 1 (SPI-1) can be harnessed to export recombinant proteins. Here, we demonstrate the secretion of a variety of unfolded spider silk proteins and use these data to quantify the constraints of this system with respect to the export of recombinant protein. Results To test how the timing and level of protein expression affects secretion, we designed a hybrid promoter that combines an IPTG-inducible system with a natural genetic circuit that controls effector expression in Salmonella (psicA). LacO operators are placed in various locations in the psicA promoter and the optimal induction occurs when a single operator is placed at the +5nt (234-fold) and a lower basal level of expression is achieved when a second operator is placed at -63nt to take advantage of DNA looping. Using this tool, we find that the secretion efficiency (protein secreted divided by total expressed) is constant as a function of total expressed. We also demonstrate that the secretion flux peaks at 8 hours. We then use whole gene DNA synthesis to construct codon optimized spider silk genes for full-length (3129 amino acids) Latrodectus hesperus dragline silk, Bombyx mori cocoon silk, and Nephila clavipes flagelliform silk and PCR is used to create eight truncations of these genes. These proteins are all unfolded polypeptides and they encompass a variety of length, charge, and amino acid compositions. We find those proteins fewer than 550 amino acids reliably secrete and the probability declines significantly after ~700 amino acids. There also is a charge optimum at -2.4, and secretion efficiency declines for very positively or negatively charged proteins. There is no significant correlation with hydrophobicity. Conclusions We show that the natural system encoded in SPI-1 only produces high titers of secreted protein for 4-8 hours when the natural psicA promoter is used to drive expression. Secretion efficiency can be high, but declines for charged or large sequences. A quantitative characterization of these constraints will facilitate the effective use and engineering of this system.
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218
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Lu W, Ness JE, Xie W, Zhang X, Minshull J, Gross RA. Biosynthesis of Monomers for Plastics from Renewable Oils. J Am Chem Soc 2010; 132:15451-5. [DOI: 10.1021/ja107707v] [Citation(s) in RCA: 167] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Wenhua Lu
- Polytechnic Institute of New York University, 6 Metrotech Center, Brooklyn, New York 11201, United States and DNA2.0 Incorporated, 1430 O’Brien Drive, Menlo Park, California 94025, United States
| | - Jon E. Ness
- Polytechnic Institute of New York University, 6 Metrotech Center, Brooklyn, New York 11201, United States and DNA2.0 Incorporated, 1430 O’Brien Drive, Menlo Park, California 94025, United States
| | - Wenchun Xie
- Polytechnic Institute of New York University, 6 Metrotech Center, Brooklyn, New York 11201, United States and DNA2.0 Incorporated, 1430 O’Brien Drive, Menlo Park, California 94025, United States
| | - Xiaoyan Zhang
- Polytechnic Institute of New York University, 6 Metrotech Center, Brooklyn, New York 11201, United States and DNA2.0 Incorporated, 1430 O’Brien Drive, Menlo Park, California 94025, United States
| | - Jeremy Minshull
- Polytechnic Institute of New York University, 6 Metrotech Center, Brooklyn, New York 11201, United States and DNA2.0 Incorporated, 1430 O’Brien Drive, Menlo Park, California 94025, United States
| | - Richard A. Gross
- Polytechnic Institute of New York University, 6 Metrotech Center, Brooklyn, New York 11201, United States and DNA2.0 Incorporated, 1430 O’Brien Drive, Menlo Park, California 94025, United States
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219
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Lu Z, Xie P, Qin Z. Promotion of markerless deletion of the actinorhodin biosynthetic gene cluster in Streptomyces coelicolor. Acta Biochim Biophys Sin (Shanghai) 2010; 42:717-21. [PMID: 20810535 DOI: 10.1093/abbs/gmq080] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The standard gene disruption and replacement to delete the actinorhodin biosynthetic gene cluster (Act) in Streptomyces coelicolor was inefficient, and the polymerase chain reaction-targeting of the cosmid could efficiently delete the Act, but still was a time-consuming procedure for markerless gene replacement. By using optimal Streptomyces codons, we synthesized a sceS gene encoding identical amino acid sequence as the chromosome rare-cutting meganuclease I-sce I of the Saccharomyces cerevisiae mitochondria. Expression of sceS gene in S. coelicolor resulted in promotion of homologous recombination and subsequently, successful achieved markerless deletion of the Act. The sceS system may be useful for the sequential markerless deletions of chromosomal segments in Streptomyces.
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Affiliation(s)
- Zhiqun Lu
- Shanghai Institute of Plant Physiology and Ecology, The Chinese Academy of Sciences, China
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220
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Raab D, Graf M, Notka F, Schödl T, Wagner R. The GeneOptimizer Algorithm: using a sliding window approach to cope with the vast sequence space in multiparameter DNA sequence optimization. SYSTEMS AND SYNTHETIC BIOLOGY 2010; 4:215-25. [PMID: 21189842 PMCID: PMC2955205 DOI: 10.1007/s11693-010-9062-3] [Citation(s) in RCA: 138] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2009] [Revised: 07/16/2010] [Accepted: 08/02/2010] [Indexed: 11/25/2022]
Abstract
One of the main advantages of de novo gene synthesis is the fact that it frees the researcher from any limitations imposed by the use of natural templates. To make the most out of this opportunity, efficient algorithms are needed to calculate a coding sequence, combining different requirements, such as adapted codon usage or avoidance of restriction sites, in the best possible way. We present an algorithm where a “variation window” covering several amino acid positions slides along the coding sequence. Candidate sequences are built comprising the already optimized part of the complete sequence and all possible combinations of synonymous codons representing the amino acids within the window. The candidate sequences are assessed with a quality function, and the first codon of the best candidates’ variation window is fixed. Subsequently the window is shifted by one codon position. As an example of a freely accessible software implementing the algorithm, we present the Mr. Gene web-application. Additionally two experimental applications of the algorithm are shown.
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221
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Abstract
A wide variety of biological experiments rely on the ability to express an exogenous gene in a transgenic animal at a defined level and in a spatially and temporally controlled pattern. We describe major improvements of the methods available for achieving this objective in Drosophila melanogaster. We have systematically varied core promoters, UTRs, operator sequences, and transcriptional activating domains used to direct gene expression with the GAL4, LexA, and Split GAL4 transcription factors and the GAL80 transcriptional repressor. The use of site-specific integration allowed us to make quantitative comparisons between different constructs inserted at the same genomic location. We also characterized a set of PhiC31 integration sites for their ability to support transgene expression of both drivers and responders in the nervous system. The increased strength and reliability of these optimized reagents overcome many of the previous limitations of these methods and will facilitate genetic manipulations of greater complexity and sophistication.
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222
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Heterologous expression and extracellular secretion of cellulolytic enzymes by Zymomonas mobilis. Appl Environ Microbiol 2010; 76:6360-9. [PMID: 20693448 DOI: 10.1128/aem.00230-10] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Development of the strategy known as consolidated bioprocessing (CBP) involves the use of a single microorganism to convert pretreated lignocellulosic biomass to ethanol through the simultaneous production of saccharolytic enzymes and fermentation of the liberated monomeric sugars. In this report, the initial steps toward achieving this goal in the fermentation host Zymomonas mobilis were investigated by expressing heterologous cellulases and subsequently examining the potential to secrete these cellulases extracellularly. Numerous strains of Z. mobilis were found to possess endogenous extracellular activities against carboxymethyl cellulose, suggesting that this microorganism may harbor a favorable environment for the production of additional cellulolytic enzymes. The heterologous expression of two cellulolytic enzymes, E1 and GH12 from Acidothermus cellulolyticus, was examined. Both proteins were successfully expressed as soluble, active enzymes in Z. mobilis although to different levels. While the E1 enzyme was less abundantly expressed, the GH12 enzyme comprised as much as 4.6% of the total cell protein. Additionally, fusing predicted secretion signals native to Z. mobilis to the N termini of E1 and GH12 was found to direct the extracellular secretion of significant levels of active E1 and GH12 enzymes. The subcellular localization of the intracellular pools of cellulases revealed that a significant portion of both the E1 and GH12 secretion constructs resided in the periplasmic space. Our results strongly suggest that Z. mobilis is capable of supporting the expression and secretion of high levels of cellulases relevant to biofuel production, thereby serving as a foundation for developing Z. mobilis into a CBP platform organism.
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223
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Clancy K, Voigt CA. Programming cells: towards an automated 'Genetic Compiler'. Curr Opin Biotechnol 2010; 21:572-81. [PMID: 20702081 PMCID: PMC2950163 DOI: 10.1016/j.copbio.2010.07.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2010] [Accepted: 07/08/2010] [Indexed: 10/19/2022]
Abstract
One of the visions of synthetic biology is to be able to program cells using a language that is similar to that used to program computers or robotics. For large genetic programs, keeping track of the DNA on the level of nucleotides becomes tedious and error prone, requiring a new generation of computer-aided design (CAD) software. To push the size of projects, it is important to abstract the designer from the process of part selection and optimization. The vision is to specify genetic programs in a higher-level language, which a genetic compiler could automatically convert into a DNA sequence. Steps towards this goal include: defining the semantics of the higher-level language, algorithms to select and assemble parts, and biophysical methods to link DNA sequence to function. These will be coupled to graphic design interfaces and simulation packages to aid in the prediction of program dynamics, optimize genes, and scan projects for errors.
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Affiliation(s)
- Kevin Clancy
- Life Technologies, 5791 Van Allen Way, Carlsbad, CA, 90028
| | - Christopher A. Voigt
- Department of Pharmaceutical Chemistry, University of California-San Francisco, MC 2540, Room 408C, 1700 4 Street, San Francisco, CA 94158
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224
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H-NS silences gfp, the green fluorescent protein gene: gfpTCD is a genetically Remastered gfp gene with reduced susceptibility to H-NS-mediated transcription silencing and with enhanced translation. J Bacteriol 2010; 192:4790-3. [PMID: 20639321 DOI: 10.1128/jb.00531-10] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The bacterial nucleoid-associated protein H-NS, which preferentially targets and silences A+T-rich genes, binds the ubiquitous reporter gene gfp and dramatically reduces local transcription. We have redesigned gfp to reduce H-NS-mediated transcription silencing and simultaneously improve translation in vivo without altering the amino acid sequence of the GFP protein.
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225
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Gabilly ST, Dreyfuss BW, Karamoko M, Corvest V, Kropat J, Page MD, Merchant SS, Hamel PP. CCS5, a thioredoxin-like protein involved in the assembly of plastid c-type cytochromes. J Biol Chem 2010; 285:29738-49. [PMID: 20628047 DOI: 10.1074/jbc.m109.099069] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The c-type cytochromes are metalloproteins with a heme molecule covalently linked to the sulfhydryls of a CXXCH heme-binding site. In plastids, at least six assembly factors are required for heme attachment to the apo-forms of cytochrome f and cytochrome c(6) in the thylakoid lumen. CCS5, controlling plastid cytochrome c assembly, was identified through insertional mutagenesis in the unicellular green alga Chlamydomonas reinhardtii. The complementing gene encodes a protein with similarity to Arabidopsis thaliana HCF164, which is a thylakoid membrane-anchored protein with a lumen-facing thioredoxin-like domain. HCF164 is required for cytochrome b(6)f biogenesis, but its activity and site of action in the assembly process has so far remained undeciphered. We show that CCS5 is a component of a trans-thylakoid redox pathway and operates by reducing the CXXCH heme-binding site of apocytochrome c prior to the heme ligation reaction. The proposal is based on the following findings: 1) the ccs5 mutant is rescued by exogenous thiols; 2) CCS5 interacts with apocytochrome f and c(6) in a yeast two-hybrid assay; and 3) recombinant CCS5 is able to reduce a disulfide in the CXXCH heme-binding site of apocytochrome f.
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Affiliation(s)
- Stéphane T Gabilly
- From the Department of Molecular Genetics and Department of Molecular Cellular Biochemistry and
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226
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227
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Richardson SM, Nunley PW, Yarrington RM, Boeke JD, Bader JS. GeneDesign 3.0 is an updated synthetic biology toolkit. Nucleic Acids Res 2010; 38:2603-6. [PMID: 20211837 PMCID: PMC2860129 DOI: 10.1093/nar/gkq143] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
GeneDesign is a set of web applications that provides public access to a nucleotide manipulation pipeline for synthetic biology. The server is public and freely accessible, and the source is available for download under the New BSD License. Since GeneDesign was published and made publicly available 3 years ago, we have made its code base more efficient, added several algorithms and modules, updated the restriction enzyme library, added batch processing capabilities, and added several command line modules, all of which we briefly describe here.
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Affiliation(s)
- Sarah M Richardson
- McKusick-Nathans Institute of Genetic Medicine, High Throughput Biology Center, Johns Hopkins University School of Medicine, 733 North Broadway, Baltimore, MD 21205, USA.
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228
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Cai Y, Wilson ML, Peccoud J. GenoCAD for iGEM: a grammatical approach to the design of standard-compliant constructs. Nucleic Acids Res 2010; 38:2637-44. [PMID: 20167639 PMCID: PMC2860117 DOI: 10.1093/nar/gkq086] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
One of the foundations of synthetic biology is the project to develop libraries of standardized genetic parts that could be assembled quickly and cheaply into large systems. The limitations of the initial BioBrick standard have prompted the development of multiple new standards proposing different avenues to overcome these shortcomings. The lack of compatibility between standards, the compliance of parts with only some of the standards or even the type of constructs that each standard supports have significantly increased the complexity of assembling constructs from standardized parts. Here, we describe computer tools to facilitate the rigorous description of part compositions in the context of a rapidly changing landscape of physical construction methods and standards. A context-free grammar has been developed to model the structure of constructs compliant with six popular assembly standards. Its implementation in GenoCAD makes it possible for users to quickly assemble from a rich library of genetic parts, constructs compliant with any of six existing standards.
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Affiliation(s)
| | | | - Jean Peccoud
- *To whom correspondence should be addressed. Tel: +1 540 231 0403; Fax: +1 540 231 2606;
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229
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Lai H, Engle M, Fuchs A, Keller T, Johnson S, Gorlatov S, Diamond MS, Chen Q. Monoclonal antibody produced in plants efficiently treats West Nile virus infection in mice. Proc Natl Acad Sci U S A 2010; 107:2419-24. [PMID: 20133644 PMCID: PMC2823901 DOI: 10.1073/pnas.0914503107] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Over the past decade, West Nile virus (WNV) has spread to all 48 of the lower United States as well as to parts of Canada, Mexico, the Caribbean, and South America, with outbreaks of neuroinvasive disease occurring annually. At present, no therapeutic or vaccine is available for human use. Epidemics of WNV and other emerging infectious disease threats demand cost-efficient and scalable production technologies that can rapidly transfer effective therapeutics into the clinical setting. We have previously reported that Hu-E16, a humanized anti-WNV mAb, binds to a highly conserved epitope on the envelope protein, blocks viral fusion, and shows promising postexposure therapeutic activity. Herein, we generated a plant-derived Hu-E16 mAb that can be rapidly scaled up for commercial production. Plant Hu-E16 was expressed at high levels within 8 days of infiltration in Nicotiana benthamiana plants and retained high-affinity binding and potent neutralizing activity in vitro against WNV. A single dose of plant Hu-E16 protected mice against WNV-induced mortality even 4 days after infection at rates that were indistinguishable from mammalian-cell-produced Hu-E16. This study demonstrates the efficacy of a plant-produced mAb against a potentially lethal infection several days after exposure in an animal challenge model and provides a proof of principle for the development of plant-derived mAbs as therapy against emerging infectious diseases.
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Affiliation(s)
- Huafang Lai
- The Biodesign Institute, Arizona State University, Tempe, AZ 85287
| | | | | | - Thomas Keller
- The Biodesign Institute, Arizona State University, Tempe, AZ 85287
| | | | | | - Michael S. Diamond
- Departments of Medicine
- Molecular Microbiology, and
- Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110; and
| | - Qiang Chen
- The Biodesign Institute, Arizona State University, Tempe, AZ 85287
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230
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Recombinant respiratory syncytial virus F protein expression is hindered by inefficient nuclear export and mRNA processing. Virus Genes 2010; 40:212-21. [PMID: 20111897 DOI: 10.1007/s11262-010-0449-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2009] [Accepted: 01/11/2010] [Indexed: 11/26/2022]
Abstract
Studies of the fusion activity of respiratory syncytial virus (RSV) F protein are significantly hindered by low recombinant expression levels. While infection produces F protein levels detectable by western blot, recombinant expression produces undetectable to low levels of F protein. Identifying the obstacles that hinder recombinant F protein expression may lead to improved expression and facilitate the study of F protein function. We hypothesized that nuclear localization and/or inefficient RNA polymerase II-mediated transcription contribute to poor recombinant F protein expression. This study shows a combination of stalled nuclear export, premature polyadenylation, and low mRNA abundance all contribute to low recombinant F protein expression levels. In addition, this study provides an expression optimization strategy that results in greater F protein expression levels than observed by codon-optimization of the F protein gene, which will be useful for future studies of F protein function.
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231
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Torres Pazmiño DE, Riebel A, de Lange J, Rudroff F, Mihovilovic MD, Fraaije MW. Efficient biooxidations catalyzed by a new generation of self-sufficient Baeyer-Villiger monooxygenases. Chembiochem 2010; 10:2595-8. [PMID: 19795432 DOI: 10.1002/cbic.200900480] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Daniel E Torres Pazmiño
- Laboratory of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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232
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Automated Design of Assemblable, Modular, Synthetic Chromosomes. PARALLEL PROCESSING AND APPLIED MATHEMATICS 2010. [DOI: 10.1007/978-3-642-14403-5_30] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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233
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Schloendorn J, Webb T, Kemmish K, Hamalainen M, Jackemeyer D, Jiang L, Mathieu J, Rebo J, Sankman J, Sherman L, Tontson L, Qureshi A, Alvarez P, Rittmann B. Medical Bioremediation: A Concept Moving Toward Reality. Rejuvenation Res 2009; 12:411-9. [DOI: 10.1089/rej.2009.0917] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- John Schloendorn
- Biodesign Institute at Arizona State University, Tempe, Arizona
- SENS Foundation Research Center, Sunnyvale, California
| | - Tim Webb
- SENS Foundation Research Center, Sunnyvale, California
| | | | | | | | - Lijing Jiang
- Biodesign Institute at Arizona State University, Tempe, Arizona
| | - Jacques Mathieu
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas
| | - Justin Rebo
- SENS Foundation Research Center, Sunnyvale, California
- Department of Microbiology, St. George's University School of Medicine, Grenada, Wisconsin
| | | | - Lindsey Sherman
- Biodesign Institute at Arizona State University, Tempe, Arizona
| | - Lauri Tontson
- Biodesign Institute at Arizona State University, Tempe, Arizona
| | - Ateef Qureshi
- Department of Microbiology, St. George's University School of Medicine, Grenada, Wisconsin
| | - Pedro Alvarez
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas
| | - Bruce Rittmann
- Biodesign Institute at Arizona State University, Tempe, Arizona
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234
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Marchisio MA, Stelling J. Computational design tools for synthetic biology. Curr Opin Biotechnol 2009; 20:479-85. [PMID: 19758796 DOI: 10.1016/j.copbio.2009.08.007] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2009] [Revised: 08/19/2009] [Accepted: 08/23/2009] [Indexed: 10/20/2022]
Abstract
Computer-aided design, pervasive in other engineering disciplines, is currently developing in synthetic biology. Concepts for standardization and hierarchies of parts, devices and systems provide a basis for efficient engineering in biology. Recently developed computational tools, for instance, enable rational (and graphical) composition of genetic circuits from standard parts, and subsequent simulation for testing the predicted functions in silico. The computational design of DNA and proteins with predetermined quantitative functions has made similar advances. The biggest challenge, however, is the integration of tools and methods into powerful and intuitively usable workflows-and the field is only starting to address it.
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Affiliation(s)
- Mario A Marchisio
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland.
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235
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Welch M, Govindarajan S, Ness JE, Villalobos A, Gurney A, Minshull J, Gustafsson C. Design parameters to control synthetic gene expression in Escherichia coli. PLoS One 2009; 4:e7002. [PMID: 19759823 PMCID: PMC2736378 DOI: 10.1371/journal.pone.0007002] [Citation(s) in RCA: 259] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Accepted: 08/17/2009] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Production of proteins as therapeutic agents, research reagents and molecular tools frequently depends on expression in heterologous hosts. Synthetic genes are increasingly used for protein production because sequence information is easier to obtain than the corresponding physical DNA. Protein-coding sequences are commonly re-designed to enhance expression, but there are no experimentally supported design principles. PRINCIPAL FINDINGS To identify sequence features that affect protein expression we synthesized and expressed in E. coli two sets of 40 genes encoding two commercially valuable proteins, a DNA polymerase and a single chain antibody. Genes differing only in synonymous codon usage expressed protein at levels ranging from undetectable to 30% of cellular protein. Using partial least squares regression we tested the correlation of protein production levels with parameters that have been reported to affect expression. We found that the amount of protein produced in E. coli was strongly dependent on the codons used to encode a subset of amino acids. Favorable codons were predominantly those read by tRNAs that are most highly charged during amino acid starvation, not codons that are most abundant in highly expressed E. coli proteins. Finally we confirmed the validity of our models by designing, synthesizing and testing new genes using codon biases predicted to perform well. CONCLUSION The systematic analysis of gene design parameters shown in this study has allowed us to identify codon usage within a gene as a critical determinant of achievable protein expression levels in E. coli. We propose a biochemical basis for this, as well as design algorithms to ensure high protein production from synthetic genes. Replication of this methodology should allow similar design algorithms to be empirically derived for any expression system.
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236
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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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237
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Bayer TS, Widmaier DM, Temme K, Mirsky EA, Santi DV, Voigt CA. Synthesis of methyl halides from biomass using engineered microbes. J Am Chem Soc 2009; 131:6508-15. [PMID: 19378995 DOI: 10.1021/ja809461u] [Citation(s) in RCA: 163] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Methyl halides are used as agricultural fumigants and are precursor molecules that can be catalytically converted to chemicals and fuels. Plants and microorganisms naturally produce methyl halides, but these organisms produce very low yields or are not amenable to industrial production. A single methyl halide transferase (MHT) enzyme transfers the methyl group from the ubiquitous metabolite S-adenoyl methionine (SAM) to a halide ion. Using a synthetic metagenomic approach, we chemically synthesized all 89 putative MHT genes from plants, fungi, bacteria, and unidentified organisms present in the NCBI sequence database. The set was screened in Escherichia coli to identify the rates of CH(3)Cl, CH(3)Br, and CH(3)I production, with 56% of the library active on chloride, 85% on bromide, and 69% on iodide. Expression of the highest activity MHT and subsequent engineering in Saccharomyces cerevisiae results in productivity of 190 mg/L-h from glucose and sucrose. Using a symbiotic co-culture of the engineered yeast and the cellulolytic bacterium Actinotalea fermentans, we are able to achieve methyl halide production from unprocessed switchgrass (Panicum virgatum), corn stover, sugar cane bagasse, and poplar (Populus sp.). These results demonstrate the potential of producing methyl halides from non-food agricultural resources.
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Affiliation(s)
- Travis S Bayer
- Department of Pharmaceutical Chemistry, University of California, San Francisco, MC 2540, Room 408C, 1700 4th Street, San Francisco, California 94158-2330, USA
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238
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Czar MJ, Cai Y, Peccoud J. Writing DNA with GenoCAD. Nucleic Acids Res 2009; 37:W40-7. [PMID: 19429897 PMCID: PMC2703884 DOI: 10.1093/nar/gkp361] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2009] [Revised: 04/21/2009] [Accepted: 04/22/2009] [Indexed: 01/20/2023] Open
Abstract
Chemical synthesis of custom DNA made to order calls for software streamlining the design of synthetic DNA sequences. GenoCAD (www.genocad.org) is a free web-based application to design protein expression vectors, artificial gene networks and other genetic constructs composed of multiple functional blocks called genetic parts. By capturing design strategies in grammatical models of DNA sequences, GenoCAD guides the user through the design process. By successively clicking on icons representing structural features or actual genetic parts, complex constructs composed of dozens of functional blocks can be designed in a matter of minutes. GenoCAD automatically derives the construct sequence from its comprehensive libraries of genetic parts. Upon completion of the design process, users can download the sequence for synthesis or further analysis. Users who elect to create a personal account on the system can customize their workspace by creating their own parts libraries, adding new parts to the libraries, or reusing designs to quickly generate sets of related constructs.
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Affiliation(s)
| | | | - Jean Peccoud
- Virginia Bioinformatics Institute at Virginia Polytechnic and State University, Blacksburg, VA 24061, USA
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239
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Martin CH, Nielsen DR, Solomon KV, Prather KLJ. Synthetic metabolism: engineering biology at the protein and pathway scales. ACTA ACUST UNITED AC 2009; 16:277-86. [PMID: 19318209 DOI: 10.1016/j.chembiol.2009.01.010] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2008] [Revised: 01/21/2009] [Accepted: 01/22/2009] [Indexed: 11/25/2022]
Abstract
Biocatalysis has become a powerful tool for the synthesis of high-value compounds, particularly so in the case of highly functionalized and/or stereoactive products. Nature has supplied thousands of enzymes and assembled them into numerous metabolic pathways. Although these native pathways can be use to produce natural bioproducts, there are many valuable and useful compounds that have no known natural biochemical route. Consequently, there is a need for both unnatural metabolic pathways and novel enzymatic activities upon which these pathways can be built. Here, we review the theoretical and experimental strategies for engineering synthetic metabolic pathways at the protein and pathway scales, and highlight the challenges that this subfield of synthetic biology currently faces.
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Affiliation(s)
- Collin H Martin
- Department of Chemical Engineering, Synthetic Biology Engineering Research Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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240
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Raymond A, Lovell S, Lorimer D, Walchli J, Mixon M, Wallace E, Thompkins K, Archer K, Burgin A, Stewart L. Combined protein construct and synthetic gene engineering for heterologous protein expression and crystallization using Gene Composer. BMC Biotechnol 2009; 9:37. [PMID: 19383143 PMCID: PMC2680836 DOI: 10.1186/1472-6750-9-37] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2008] [Accepted: 04/21/2009] [Indexed: 01/29/2023] Open
Abstract
Background With the goal of improving yield and success rates of heterologous protein production for structural studies we have developed the database and algorithm software package Gene Composer. This freely available electronic tool facilitates the information-rich design of protein constructs and their engineered synthetic gene sequences, as detailed in the accompanying manuscript. Results In this report, we compare heterologous protein expression levels from native sequences to that of codon engineered synthetic gene constructs designed by Gene Composer. A test set of proteins including a human kinase (P38α), viral polymerase (HCV NS5B), and bacterial structural protein (FtsZ) were expressed in both E. coli and a cell-free wheat germ translation system. We also compare the protein expression levels in E. coli for a set of 11 different proteins with greatly varied G:C content and codon bias. Conclusion The results consistently demonstrate that protein yields from codon engineered Gene Composer designs are as good as or better than those achieved from the synonymous native genes. Moreover, structure guided N- and C-terminal deletion constructs designed with the aid of Gene Composer can lead to greater success in gene to structure work as exemplified by the X-ray crystallographic structure determination of FtsZ from Bacillus subtilis. These results validate the Gene Composer algorithms, and suggest that using a combination of synthetic gene and protein construct engineering tools can improve the economics of gene to structure research.
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Affiliation(s)
- Amy Raymond
- deCODE biostructures Inc, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA.
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241
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Lorimer D, Raymond A, Walchli J, Mixon M, Barrow A, Wallace E, Grice R, Burgin A, Stewart L. Gene composer: database software for protein construct design, codon engineering, and gene synthesis. BMC Biotechnol 2009; 9:36. [PMID: 19383142 PMCID: PMC2681465 DOI: 10.1186/1472-6750-9-36] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2008] [Accepted: 04/21/2009] [Indexed: 12/18/2022] Open
Abstract
Background To improve efficiency in high throughput protein structure determination, we have developed a database software package, Gene Composer, which facilitates the information-rich design of protein constructs and their codon engineered synthetic gene sequences. With its modular workflow design and numerous graphical user interfaces, Gene Composer enables researchers to perform all common bio-informatics steps used in modern structure guided protein engineering and synthetic gene engineering. Results An interactive Alignment Viewer allows the researcher to simultaneously visualize sequence conservation in the context of known protein secondary structure, ligand contacts, water contacts, crystal contacts, B-factors, solvent accessible area, residue property type and several other useful property views. The Construct Design Module enables the facile design of novel protein constructs with altered N- and C-termini, internal insertions or deletions, point mutations, and desired affinity tags. The modifications can be combined and permuted into multiple protein constructs, and then virtually cloned in silico into defined expression vectors. The Gene Design Module uses a protein-to-gene algorithm that automates the back-translation of a protein amino acid sequence into a codon engineered nucleic acid gene sequence according to a selected codon usage table with minimal codon usage threshold, defined G:C% content, and desired sequence features achieved through synonymous codon selection that is optimized for the intended expression system. The gene-to-oligo algorithm of the Gene Design Module plans out all of the required overlapping oligonucleotides and mutagenic primers needed to synthesize the desired gene constructs by PCR, and for physically cloning them into selected vectors by the most popular subcloning strategies. Conclusion We present a complete description of Gene Composer functionality, and an efficient PCR-based synthetic gene assembly procedure with mis-match specific endonuclease error correction in combination with PIPE cloning. In a sister manuscript we present data on how Gene Composer designed genes and protein constructs can result in improved protein production for structural studies.
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Affiliation(s)
- Don Lorimer
- deCODE biostructures, Inc 7869 NE Day Road West, Bainbridge Island, WA 98110, USA.
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242
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Welch M, Villalobos A, Gustafsson C, Minshull J. You're one in a googol: optimizing genes for protein expression. J R Soc Interface 2009; 6 Suppl 4:S467-76. [PMID: 19324676 DOI: 10.1098/rsif.2008.0520.focus] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A vast number of different nucleic acid sequences can all be translated by the genetic code into the same amino acid sequence. These sequences are not all equally useful however; the exact sequence chosen can have profound effects on the expression of the encoded protein. Despite the importance of protein-coding sequences, there has been little systematic study to identify parameters that affect expression. This is probably because protein expression has largely been tackled on an ad hoc basis in many independent projects: once a sequence has been obtained that yields adequate expression for that project, there is little incentive to continue work on the problem. Synthetic biology may now provide the impetus to transform protein expression folklore into design principles, so that DNA sequences may easily be designed to express any protein in any system. In this review, we offer a brief survey of the literature, outline the major challenges in interpreting existing data and constructing robust design algorithms, and propose a way to proceed towards the goal of rational sequence engineering.
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Affiliation(s)
- Mark Welch
- DNA 2.0, Inc., 1430 O'Brien Drive, Menlo Park, CA 94025, USA
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243
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Williams JA, Carnes AE, Hodgson CP. Plasmid DNA vaccine vector design: impact on efficacy, safety and upstream production. Biotechnol Adv 2009; 27:353-70. [PMID: 19233255 DOI: 10.1016/j.biotechadv.2009.02.003] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2008] [Revised: 02/02/2009] [Accepted: 02/07/2009] [Indexed: 10/21/2022]
Abstract
Critical molecular and cellular biological factors impacting design of licensable DNA vaccine vectors that combine high yield and integrity during bacterial production with increased expression in mammalian cells are reviewed. Food and Drug Administration (FDA), World Health Organization (WHO) and European Medical Agencies (EMEA) regulatory guidance's are discussed, as they relate to vector design and plasmid fermentation. While all new vectors will require extensive preclinical testing to validate safety and performance prior to clinical use, regulatory testing burden for follow-on products can be reduced by combining carefully designed synthetic genes with existing validated vector backbones. A flowchart for creation of new synthetic genes, combining rationale design with bioinformatics, is presented. The biology of plasmid replication is reviewed, and process engineering strategies that reduce metabolic burden discussed. Utilizing recently developed low metabolic burden seed stock and fermentation strategies, optimized vectors can now be manufactured in high yields exceeding 2 g/L, with specific plasmid yields of 5% total dry cell weight.
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244
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Czar MJ, Anderson JC, Bader JS, Peccoud J. Gene synthesis demystified. Trends Biotechnol 2008; 27:63-72. [PMID: 19111926 DOI: 10.1016/j.tibtech.2008.10.007] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2008] [Revised: 10/09/2008] [Accepted: 10/16/2008] [Indexed: 11/18/2022]
Abstract
DNA fabrication of genetic cassettes at base-level precision is transforming genetic engineering from a laborious art to an information-driven discipline. Although substantial advances have been made in the development of DNA fabrication, the methods employed vary widely based on the length of the DNA. All of these methods are available commercially, but can also be performed at the molecular biology bench using typical reagents and procedures. Because the technology is not mature and is still evolving rapidly, it is helpful to gain some understanding of the different steps in this process and the associated technical challenges to successfully take advantage of DNA fabrication in a research project.
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Affiliation(s)
- Michael J Czar
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA
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245
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Meister GE, Chandrasegaran S, Ostermeier M. An engineered split M.HhaI-zinc finger fusion lacks the intended methyltransferase specificity. Biochem Biophys Res Commun 2008; 377:226-30. [PMID: 18835252 PMCID: PMC2586766 DOI: 10.1016/j.bbrc.2008.09.099] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2008] [Accepted: 09/24/2008] [Indexed: 11/20/2022]
Abstract
The ability to site-specifically methylate DNA in vivo would have wide applicability to the study of basic biomedical problems as well as enable studies on the potential of site-specific DNA methylation as a therapeutic strategy for the treatment of diseases. Natural DNA methyltransferases lack the specificity required for these applications. Nomura and Barbas [W. Nomura, C.F. Barbas 3rd, In vivo site-specific DNA methylation with a designed sequence-enabled DNA methylase, J. Am. Chem. Soc. 129 (2007) 8676-8677] have reported that an engineered DNA methyltransferase comprised of fragments of M.HhaI methyltransferase and zinc finger proteins has very high specificity for the chosen target site. Our analysis of this engineered enzyme shows that the fusion protein methylates target and non-target sites with similar efficiency.
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Affiliation(s)
- Glenna E. Meister
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218
| | - Srinivasan Chandrasegaran
- Department of Environmental Health Sciences, Bloomberg School of Public Health, Johns Hopkins University, 615 North Wolfe Street, Baltimore, MD 21205
| | - Marc Ostermeier
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218
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246
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Nilsson J, Yekezare M, Minshull J, Pines J. The APC/C maintains the spindle assembly checkpoint by targeting Cdc20 for destruction. Nat Cell Biol 2008; 10:1411-20. [PMID: 18997788 PMCID: PMC2635557 DOI: 10.1038/ncb1799] [Citation(s) in RCA: 231] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2008] [Accepted: 10/17/2008] [Indexed: 01/28/2023]
Abstract
The Spindle Assembly Checkpoint (SAC) is required to block sister chromatid separation until all chromosomes are properly attached to the mitotic apparatus. The SAC prevents cells entering anaphase by inhibiting the ubiquitination of cyclin B1 and securin by the Anaphase Promoting Complex/Cyclosome (APC/C) ubiquitin ligase. The target of the SAC is the essential APC/C activator, Cdc20. It is unclear how the SAC inactivates Cdc20 but current models mostly involve Cdc20 forming a stable complex with the Mad2 checkpoint protein. Here we show that most Cdc20 is not in a complex with Mad2; instead Mad2 is required for Cdc20 to form a complex with another checkpoint protein, BubR1. We further show that during the SAC the APC/C ubiquitinates Cdc20 to target it for degradation. Thus, ubiquitination of human Cdc20 is not required to release it from the checkpoint complex, but to degrade it to maintain mitotic arrest.
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Affiliation(s)
- Jakob Nilsson
- Wellcome/CR UK Gurdon Institute and Department of Zoology, Tennis Court Road, Cambridge CB2 1QN, UK
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247
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Ehren J, Govindarajan S, Morón B, Minshull J, Khosla C. Protein engineering of improved prolyl endopeptidases for celiac sprue therapy. Protein Eng Des Sel 2008; 21:699-707. [PMID: 18836204 DOI: 10.1093/protein/gzn050] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Due to their unique ability to cleave immunotoxic gluten peptides endoproteolytically, prolyl endopeptidases (PEPs) are attractive oral therapeutic candidates for protecting celiac sprue patients from the toxic effects of dietary gluten. Enhancing the activity and stability of PEPs under gastric conditions (low pH, high pepsin concentration) is a challenge for protein engineers. Using a combination of sequence- and structure-based approaches together with machine learning algorithms, we have identified improved variants of the Sphingomonas capsulata PEP, a target of clinical relevance. Through two rounds of iterative mutagenesis and analysis, variants with as much as 20% enhanced specific activity at pH 4.5 and 200-fold greater resistance to pepsin were identified. Our results vividly reinforce the concept that conservative changes in proteins, especially in hydrophobic residues within tightly packed regions, can profoundly influence protein structure and function in ways that are difficult to predict entirely from first principles and must therefore be optimized through iterative design and analytical cycles. Incubation with whole wheat bread under simulated gastric conditions also suggests that some variants have pharmacologically significant improvements in gluten detoxification activity.
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Affiliation(s)
- Jennifer Ehren
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
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248
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Goler JA, Bramlett BW, Peccoud J. Genetic design: rising above the sequence. Trends Biotechnol 2008; 26:538-44. [PMID: 18687496 DOI: 10.1016/j.tibtech.2008.06.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2007] [Revised: 06/19/2008] [Accepted: 06/23/2008] [Indexed: 10/21/2022]
Abstract
Genetic engineering has developed around technologies enabling the targeted in vitro recombination of DNA molecules found in living organisms. As a result, the development of new DNA molecules has been primarily focused on cloning strategies that allow their assembly from existing DNA fragments. As chemical gene synthesis matures, the design of synthetic DNA molecules becomes the bottleneck of many biotechnology projects. It becomes urgent to develop representations of synthetic genetic systems more abstract than their DNA sequence. Abstraction makes it possible to reuse simple components to build complex systems or to break down a complex engineering problem into manageable tasks. Specialized computer languages or a general purpose XCell Description Language are promising avenues to build abstraction hierarchies for synthetic biology.
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Affiliation(s)
- Jonathan A Goler
- Synthetic Biology Engineering Research Center, University of California Berkeley, CA 94720, USA
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249
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Abstract
Background The design and construction of novel biological systems by combining basic building blocks represents a dominant paradigm in synthetic biology. Creating and maintaining a database of these building blocks is a way to streamline the fabrication of complex constructs. The Registry of Standard Biological Parts (Registry) is the most advanced implementation of this idea. Methods/Principal Findings By analyzing inclusion relationships between the sequences of the Registry entries, we build a network that can be related to the Registry abstraction hierarchy. The distribution of entry reuse and complexity was extracted from this network. The collection of clones associated with the database entries was also analyzed. The plasmid inserts were amplified and sequenced. The sequences of 162 inserts could be confirmed experimentally but unexpected discrepancies have also been identified. Conclusions/Significance Organizational guidelines are proposed to help design and manage this new type of scientific resources. In particular, it appears necessary to compare the cost of ensuring the integrity of database entries and associated biological samples with their value to the users. The initial strategy that permits including any combination of parts irrespective of its potential value leads to an exponential and economically unsustainable growth that may be detrimental to the quality and long-term value of the resource to its users.
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250
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Taylor LE, Dai Z, Decker SR, Brunecky R, Adney WS, Ding SY, Himmel ME. Heterologous expression of glycosyl hydrolases in planta: a new departure for biofuels. Trends Biotechnol 2008; 26:413-24. [PMID: 18579242 DOI: 10.1016/j.tibtech.2008.05.002] [Citation(s) in RCA: 101] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2008] [Revised: 05/01/2008] [Accepted: 05/07/2008] [Indexed: 11/18/2022]
Abstract
The concept of expressing non-plant glycosyl hydrolase genes in plant tissue is nearly two decades old, yet relatively little work in this field has been reported. However, resurgent interest in technologies aimed at enabling processes that convert biomass to sugars and fuels has turned attention toward this intuitive solution. There are several challenges facing researchers in this field, including the development of better and more specifically targeted delivery systems for hydrolytic genes, the successful folding and post-translational modification of heterologous proteins and the development of cost-effective process strategies utilizing these transformed plants. The integration of these concepts, from the improvement of biomass production and conversion characteristics to the heterologous production of glycosyl hydrolases in a high yielding bioenergy crop, holds considerable promise for improving the lignocellulosic conversion of biomass to ethanol and subsequently to fuels.
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Affiliation(s)
- Larry E Taylor
- Chemical and Biosciences Center, National Renewable Energy Laboratory, 1617 Cole Blvd, Golden, CO 80401, USA
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