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Synthetic Biology Applications in Industrial Microbiology SYNTHETIC BIOLOGY APPLICATIONS IN INDUSTRIAL MICROBIOLOGY Topic Editors Weiwen Zhang and David R. Nielsen MICROBIOLOGY FRONTIERS COPYRIGHT STATEMENT ABOUT FRONTIERS © Copyright 2007-2014 Frontiers is more than just an open-access publisher of scholarly articles: it is a pioneering Frontiers Media SA. All rights reserved. approach to the world of academia, radically improving the way scholarly research is managed. All content included on this site, such as The grand vision of Frontiers is a world where all people have an equal opportunity to seek, share text, graphics, logos, button icons, images, and generate knowledge. 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ISBN 978-2-88919-342-4 Find out more on how to host your own Frontiers Research Topic or contribute to one as an DOI 10.3389/978-2-88919-342-4 author by contacting the Frontiers Editorial Office: [email protected] Frontiers in Microbiology December 2014 | Synthetic biology applications in industrial microbiology | 1 SYNTHETIC BIOLOGY APPLICATIONS IN INDUSTRIAL MICROBIOLOGY Topic Editors: Weiwen Zhang, Tianjin University, China David R. Nielsen, Arizona State University, USA Exponentially increasing information on biological organisms coupled with increasing computational power in the past decade have broadened the perspective of fundamental biological research, bringing about considerable promise and unprecedented potential for practical applications in biotechnology. As one emergent discipline, synthetic biology aims to design and engineer novel biologically-based parts, devices, and systems, in addition to redesigning existing, natural biological systems. Although previously relegated to demonstration studies, more recent research in synthetic biology has focused on the rational engineering of industrial microorganisms with the potential to address many of society’s critical challenges. Within the realm of industrial microbiology, progress in the field of synthetic biology has enabled the development of, for example, new biosynthetic pathways for the production of renewable fuels and chemicals, programmable logic controls to regulate and optimize cell function, and robust microbes for the destruction of harmful environmental contaminants. Some of the exciting examples included producing anti-malarial drug, anti- cancer taxol precursor and various biofuel molecules in E. coli and yeast. In addition, these researches have also greatly enhanced our understanding of the cellular machinery and its regulation in some of the industry important microbes, laying an important foundation for further design and engineering of biological function for even greater application. For these reasons, we present here a collection of articles from the leading edge of the field of synthetic biology, with a specific focus on the development in industrial microorganisms. It is the intent of this collection to reach a wide audience whose interests and expertise spans from development of novel synthetic biology methodologies and theories (both experimental and computational) to practical applications seeking to address issues facing the world today. Frontiers in Microbiology December 2014 | Synthetic biology applications in industrial microbiology | 2 Table of Contents 04 Synthetic Biology Applications in Industrial Microbiology Weiwen Zhang and David R. Nielsen 06 Recent Progress in Synthetic Biology for Microbial Production of C3–C10 Alcohols Edna N. Lamsen and Shota Atsumi 19 Visualizing Evolution in Real-Time Method for Strain Engineering Luis H. Reyes, James Winkler and Katy C. Kao 25 Engineering Microbial Consortia to Enhance Biomining and Bioremediation Karl D. Brune and Travis S. Bayer 31 Engineering Microbial Chemical Factories to Produce Renewable “Biomonomers” Jake Adkins, Shawn Pugh, Rebekah McKenna and David R. Nielsen 43 Application of Synthetic Biology in Cyanobacteria and Algae Bo Wang, Jiangxin Wang, Weiwen Zhang and Deirdre R. Meldrum 58 Synthetic Feedback Loop Model for Increasing Microbial Biofuel Production Using a Biosensor Mary E. Harrison and Mary J. Dunlop 67 Balance of XYL1 and XYL2 Expression in Different Yeast Chassis for Improved xylose Fermentation Jian Zha, Meng-Long Hu, Ming-Hua Shen, Bing-Zhi Li, Jing-Yu Wang and Ying-Jin Yuan 77 Preparing Synthetic Biology for the World Gerd H. G. Moe-Behrens, Rene Davis and Karmella A. Haynes 87 Design and Development of Synthetic Microbial Platform Cells for Bioenergy Sang Jun Lee, Sang-Jae Lee and Dong-Woo Lee 100 Microbial Production of Isoprenoids Enabled by Synthetic Biology Cheryl M. Immethun, Allison G. Hoynes-O’Connor, Andrea Balassy and Tae Seok Moon 108 Metabolic Analyses Elucidate Non-Trivial Gene Targets for Amplifying Dihydroartemisinic Acid Production in Yeast Ashish Misra, Matthew F. Conway, Joseph Johnnie, Tabish M. Qureshi, Bao Lige, Anne M. Derrick, Eddy C. Agbo and Ganesh Sriram 123 Chemical Synthetic Biology: A Mini-Review Cristiano Chiarabelli, Pasquale Stano and Pier Luigi Luisi Frontiers in Microbiology December 2014 | Synthetic biology applications in industrial microbiology | 3 EDITORIAL published: 26 August 2014 doi: 10.3389/fmicb.2014.00451 Synthetic biology applications in industrial microbiology Weiwen Zhang 1* and David R. Nielsen 2* 1 Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China 2 Department of Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ, USA *Correspondence: [email protected]; [email protected] Edited by: Peter Neubauer, Technische Universität Berlin, Germany Reviewed by: Dong-Yup Lee, National University of Singapore, Singapore Stephen Fong, Virginia Commonwealth University, USA Pablo Carbonell, University of Evry, France Pattanathu K. S. M. Rahman, Teesside University, UK Keywords: chemicals, microbial systems, synthetic biology, industrial microbiology, biotechnology With the ability to perform a multitude of unique and complex understandings of
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