The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform
Zhen Cai - One of the best experts on this subject based on the ideXlab platform.
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genome replication engineering assisted continuous evolution greace to improve microbial tolerance for biofuels production
Biotechnology for Biofuels, 2013Co-Authors: Guodong Luan, Zhen CaiAbstract:Background Microbial production of biofuels requires robust cell growth and metabolism under tough conditions. Conventionally, such tolerance phenotypes were engineered through evolutionary engineering using the principle of “Mutagenesis followed-by Selection”. The iterative rounds of mutagenesis-selection and frequent manual interventions resulted in discontinuous and inefficient Strain Improvement processes. This work aimed to develop a more continuous and efficient evolutionary engineering method termed as “Genome Replication Engineering Assisted Continuous Evolution” (GREACE) using “Mutagenesis coupled-with Selection” as its core principle.
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genome replication engineering assisted continuous evolution greace to improve microbial tolerance for biofuels production
Biotechnology for Biofuels, 2013Co-Authors: Guodong Luan, Zhen CaiAbstract:Microbial production of biofuels requires robust cell growth and metabolism under tough conditions. Conventionally, such tolerance phenotypes were engineered through evolutionary engineering using the principle of “Mutagenesis followed-by Selection”. The iterative rounds of mutagenesis-selection and frequent manual interventions resulted in discontinuous and inefficient Strain Improvement processes. This work aimed to develop a more continuous and efficient evolutionary engineering method termed as “Genome Replication Engineering Assisted Continuous Evolution” (GREACE) using “Mutagenesis coupled-with Selection” as its core principle. The core design of GREACE is to introduce an in vivo continuous mutagenesis mechanism into microbial cells by introducing a group of genetically modified proofreading elements of the DNA polymerase complex to accelerate the evolution process under stressful conditions. The genotype stability and phenotype heritability can be stably maintained once the genetically modified proofreading element is removed, thus scarless mutants with desired phenotypes can be obtained. Kanamycin resistance of E. coli was rapidly improved to confirm the concept and feasibility of GREACE. Intrinsic mechanism analysis revealed that during the continuous evolution process, the accumulation of genetically modified proofreading elements with mutator activities endowed the host cells with enhanced adaptation advantages. We further showed that GREACE can also be applied to engineer n-butanol and acetate tolerances. In less than a month, an E. coli Strain capable of growing under an n-butanol concentration of 1.25% was isolated. As for acetate tolerance, cell growth of the evolved E. coli Strain increased by 8-fold under 0.1% of acetate. In addition, we discovered that adaptation to specific stresses prefers accumulation of genetically modified elements with specific mutator strengths. We developed a novel GREACE method using “Mutagenesis coupled-with Selection” as core principle. Successful isolation of E. coli Strains with improved n-butanol and acetate tolerances demonstrated the potential of GREACE as a promising method for Strain Improvement in biofuels production.
Gregory Stephanopoulos - One of the best experts on this subject based on the ideXlab platform.
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method for designing and optimizing random search libraries for Strain Improvement
Applied and Environmental Microbiology, 2010Co-Authors: Daniel Kleinmarcuschamer, Gregory StephanopoulosAbstract:Random searches have been the hallmark of directed evolution and have been extensively employed in the Improvement of complex or poorly understood phenotypes such as tolerance to toxic compounds in the context of cellular engineering. While genome-wide mutagenesis followed by selection or screening has been a traditional means of phenotype Improvement, the list of experimental methods for cellular engineering based on random searches is rapidly expanding. Adding to the confusion is the element of chance, which lengthens the process and most notably adds to the cost of phenotypic Improvement programs. Here we present a method to systematize the effort of finding superior mutants by successively improving random libraries. The method, based on the quantification of phenotypic diversity, is then used to isolate more-robust Strains.
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Strain Improvement by metabolic engineering lysine production as a case study for systems biology
Current Opinion in Biotechnology, 2005Co-Authors: Mattheos A G Koffas, Gregory StephanopoulosAbstract:A central goal of systems biology is the elucidation of cell function and physiology through the integrated use of broad based genomic and physiological data. Such systemic approaches have been employed extensively in the past, as they are a central element of metabolic flux analysis, the distribution of kinetic control in pathways, and the key differentiating characteristic of metabolic engineering. In one case study, these tools have been applied to the Improvement of lysine-producing Strains of Corynebacterium glutamicum. The systematic study of the physiology of this organism allowed the identification of specific metabolic targets and subsequently led to significant Improvements in product yield and productivity. This case study can serve as a guide for the development of systems biology tools for the utilization of large volumes of cell- and genome-wide transcriptional and physiological data.
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exploiting biological complexity for Strain Improvement through systems biology
Nature Biotechnology, 2004Co-Authors: Gregory Stephanopoulos, Hal S Alper, Joel MoxleyAbstract:Cellular complexity makes it difficult to build a complete understanding of cellular function but also offers innumerable possibilities for modifying the cellular machinery to achieve a specific purpose. The exploitation of cellular complexity for Strain Improvement has been a challenging goal for applied biological research because it requires the coordinated understanding of multiple cellular processes. It is therefore pursued most efficiently in the framework of systems biology. Progress in Strain Improvement will depend not only on advances in technologies for high-throughput measurements but, more importantly, on the development of theoretical methods that increase the information content of these measurements and, as such, facilitate the elucidation of mechanisms and the identification of genetic targets for modification.
Monika Schmoll - One of the best experts on this subject based on the ideXlab platform.
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a versatile toolkit for high throughput functional genomics with trichoderma reesei
Biotechnology for Biofuels, 2012Co-Authors: Andre Schuster, Kenneth S Bruno, James R Collett, Scott E Baker, Bernhard Seiboth, Christian P Kubicek, Monika SchmollAbstract:Background The ascomycete fungus, Trichoderma reesei (anamorph of Hypocrea jecorina), represents a biotechnological workhorse and is currently one of the most proficient cellulase producers. While Strain Improvement was traditionally accomplished by random mutagenesis, a detailed understanding of cellulase regulation can only be gained using recombinant technologies.
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sexual development in the industrial workhorse trichoderma reesei
Proceedings of the National Academy of Sciences of the United States of America, 2009Co-Authors: Verena Seidl, Christian P Kubicek, Christian Seibel, Monika SchmollAbstract:Filamentous fungi are indispensable biotechnological tools for the production of organic chemicals, enzymes, and antibiotics. Most of the Strains used for industrial applications have been—and still are—screened and improved by classical mutagenesis. Sexual crossing approaches would yield considerable advantages for research and industrial Strain Improvement, but interestingly, industrially applied filamentous fungal species have so far been considered to be largely asexual. This is also true for the ascomycete Trichoderma reesei (anamorph of Hypocrea jecorina), which is used for production of cellulolytic and hemicellulolytic enzymes. In this study, we report that T. reesei QM6a has a MAT1-2 mating type locus, and the identification of its respective mating type counterpart, MAT1-1, in natural isolates of H. jecorina, thus proving that this is a heterothallic species. After being considered asexual since its discovery more than 50 years ago, we were now able to induce sexual reproduction of T. reesei QM6a and obtained fertilized stromata and mature ascospores. This sexual crossing approach therefore opens up perspectives for biotechnologically important fungi. Our findings provide a tool for fast and efficient industrial Strain Improvement in T. reesei, thus boosting research toward economically feasible biofuel production. In addition, knowledge of MAT-loci and sexual crossing techniques will facilitate research with other Trichoderma spp. relevant for agriculture and human health.
Dongyup Lee - One of the best experts on this subject based on the ideXlab platform.
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genome scale metabolic reconstruction and in silico analysis of methylotrophic yeast pichia pastoris for Strain Improvement
Microbial Cell Factories, 2010Co-Authors: Bevan Ks Chung, Suresh Selvarasu, Andrea Camattari, Jimyoung Ryu, Hyeokweon Lee, Jungoh Ahn, Hongw Eon Lee, Dongyup LeeAbstract:Background: Pichia pastoris has been recognized as an effective host for recombinant protein production. A number of studies have been reported for improving this expression system. However, its physiology and cellular metabolism still remained largely uncharacterized. Thus, it is highly desirable to establish a systems biotechnological framework, in which a comprehensive in silico model of P. pastoris can be employed together with high throughput experimental data analysis, for better understanding of the methylotrophic yeast's metabolism. Results: A fully compartmentalized metabolic model of P. pastoris (iPP668), composed of 1,361 reactions and 1,177 metabolites, was reconstructed based on its genome annotation and biochemical information. The conStraints-based flux analysis was then used to predict achievable growth rate which is consistent with the cellular phenotype of P. pastoris observed during chemostat experiments. Subsequent in silico analysis further explored the effect of various carbon sources on cell growth, revealing sorbitol as a promising candidate for culturing recombinant P. pastoris Strains producing heterologous proteins. Interestingly, methanol consumption yields a high regeneration rate of reducing equivalents which is substantial for the synthesis of valuable pharmaceutical precursors. Hence, as a case study, we examined the applicability of P. pastoris system to whole-cell biotransformation and also identified relevant metabolic engineering targets that have been experimentally verified. Conclusion: The genome-scale metabolic model characterizes the cellular physiology of P. pastoris, thus allowing us to gain valuable insights into the metabolism of methylotrophic yeast and devise possible strategies for Strain Improvement through in silico simulations. This computational approach, combined with synthetic biology techniques, potentially forms a basis for rational analysis and design of P. pastoris metabolic network to enhance humanized glycoprotein production.
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systems biotechnology for Strain Improvement
Trends in Biotechnology, 2005Co-Authors: Sang Yup Lee, Dongyup Lee, Tae Yong KimAbstract:Various high-throughput experimental techniques are routinely used for generating large amounts of omics data. In parallel, in silico modelling and simulation approaches are being developed for quantitatively analyzing cellular metabolism at the systems level. Thus informative high-throughput analysis and predictive computational modelling or simulation can be combined to generate new knowledge through iterative modification of an in silico model and experimental design. On the basis of such global cellular information we can design cells that have improved metabolic properties for industrial applications. This article highlights the recent developments in these systems approaches, which we call systems biotechnology, and discusses future prospects.
Guodong Luan - One of the best experts on this subject based on the ideXlab platform.
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genome replication engineering assisted continuous evolution greace to improve microbial tolerance for biofuels production
Biotechnology for Biofuels, 2013Co-Authors: Guodong Luan, Zhen CaiAbstract:Background Microbial production of biofuels requires robust cell growth and metabolism under tough conditions. Conventionally, such tolerance phenotypes were engineered through evolutionary engineering using the principle of “Mutagenesis followed-by Selection”. The iterative rounds of mutagenesis-selection and frequent manual interventions resulted in discontinuous and inefficient Strain Improvement processes. This work aimed to develop a more continuous and efficient evolutionary engineering method termed as “Genome Replication Engineering Assisted Continuous Evolution” (GREACE) using “Mutagenesis coupled-with Selection” as its core principle.
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genome replication engineering assisted continuous evolution greace to improve microbial tolerance for biofuels production
Biotechnology for Biofuels, 2013Co-Authors: Guodong Luan, Zhen CaiAbstract:Microbial production of biofuels requires robust cell growth and metabolism under tough conditions. Conventionally, such tolerance phenotypes were engineered through evolutionary engineering using the principle of “Mutagenesis followed-by Selection”. The iterative rounds of mutagenesis-selection and frequent manual interventions resulted in discontinuous and inefficient Strain Improvement processes. This work aimed to develop a more continuous and efficient evolutionary engineering method termed as “Genome Replication Engineering Assisted Continuous Evolution” (GREACE) using “Mutagenesis coupled-with Selection” as its core principle. The core design of GREACE is to introduce an in vivo continuous mutagenesis mechanism into microbial cells by introducing a group of genetically modified proofreading elements of the DNA polymerase complex to accelerate the evolution process under stressful conditions. The genotype stability and phenotype heritability can be stably maintained once the genetically modified proofreading element is removed, thus scarless mutants with desired phenotypes can be obtained. Kanamycin resistance of E. coli was rapidly improved to confirm the concept and feasibility of GREACE. Intrinsic mechanism analysis revealed that during the continuous evolution process, the accumulation of genetically modified proofreading elements with mutator activities endowed the host cells with enhanced adaptation advantages. We further showed that GREACE can also be applied to engineer n-butanol and acetate tolerances. In less than a month, an E. coli Strain capable of growing under an n-butanol concentration of 1.25% was isolated. As for acetate tolerance, cell growth of the evolved E. coli Strain increased by 8-fold under 0.1% of acetate. In addition, we discovered that adaptation to specific stresses prefers accumulation of genetically modified elements with specific mutator strengths. We developed a novel GREACE method using “Mutagenesis coupled-with Selection” as core principle. Successful isolation of E. coli Strains with improved n-butanol and acetate tolerances demonstrated the potential of GREACE as a promising method for Strain Improvement in biofuels production.
