Synthetic Biology: engineering complexity and refactoring cell capabilities

Polymerase operations per second (PoPs) and ribosomes per second (RIPS) Describes information flow (input/output) from transcriptional-based logic devices Units cannot be directly measured May not capture biological processes at the mechanistic level Abstract level modeling Does not describe biological information that is sent throughlevel modeling Does not describe biological information that is sent through other mechanisms e.g., protein post-translational modifications

[1]  H. Alper,et al.  A molecular transporter engineering approach to improving xylose catabolism in Saccharomyces cerevisiae. , 2012, Metabolic engineering.

[2]  Jingwen Zhou,et al.  Characterization of a group of pyrroloquinoline quinone‐dependent dehydrogenases that are involved in the conversion of L‐sorbose to 2‐Keto‐L‐gulonic acid in Ketogulonicigenium vulgare WSH‐001 , 2013, Biotechnology progress.

[3]  T. Sampson,et al.  Exploiting CRISPR/Cas systems for biotechnology , 2014, BioEssays : news and reviews in molecular, cellular and developmental biology.

[4]  Joshua K. Michener,et al.  High-throughput enzyme evolution in Saccharomyces cerevisiae using a synthetic RNA switch. , 2012, Metabolic engineering.

[5]  B. Bassler,et al.  Quorum sensing in bacteria. , 2001, Annual review of microbiology.

[6]  Jeffrey J. Tabor,et al.  Characterizing bacterial gene circuit dynamics with optically programmed gene expression signals , 2014, Nature Methods.

[7]  Christopher A. Voigt,et al.  Realizing the potential of synthetic biology , 2014, Nature Reviews Molecular Cell Biology.

[8]  T. Hughes,et al.  Signals and systems , 2006, Genome Biology.

[9]  Xuefeng Lu,et al.  Photosynthesis driven conversion of carbon dioxide to fatty alcohols and hydrocarbons in cyanobacteria. , 2011, Metabolic engineering.

[10]  Martin Fussenegger,et al.  Synthetic mammalian gene circuits for biomedical applications. , 2013, Current opinion in chemical biology.

[11]  Christian R. Boehm,et al.  Unique nucleotide sequence–guided assembly of repetitive DNA parts for synthetic biology applications , 2014, Nature Protocols.

[12]  C. Chuck,et al.  Low-cost lipid production by an oleaginous yeast cultured in non-sterile conditions using model waste resources , 2014, Biotechnology for Biofuels.

[13]  H. Sauro,et al.  Standard Biological Parts Knowledgebase , 2011, PloS one.

[14]  M H Porteus,et al.  Zinc-finger nuclease-mediated gene correction using single AAV vector transduction and enhancement by Food and Drug Administration-approved drugs , 2012, Gene Therapy.

[15]  V. Wendisch,et al.  Carotenoid biosynthesis and overproduction in Corynebacterium glutamicum , 2012, BMC Microbiology.

[16]  Z. Zhao,et al.  Mechanistic studies of IspH in the deoxyxylulose phosphate pathway: heterolytic C-O bond cleavage at C4 position. , 2008, Journal of the American Chemical Society.

[17]  Drew Endy,et al.  Amplifying Genetic Logic Gates , 2013, Science.

[18]  J. Liao,et al.  Photosynthetic production of 2-methyl-1-butanol from CO2 in cyanobacterium Synechococcus elongatus PCC7942 and characterization of the native acetohydroxyacid synthase , 2012 .

[19]  Drew Endy,et al.  Precise and reliable gene expression via standard transcription and translation initiation elements , 2013, Nature Methods.

[20]  Drew Endy,et al.  Measuring the activity of BioBrick promoters using an in vivo reference standard , 2009, Journal of biological engineering.

[21]  D. Clark,et al.  The fermentation pathways of Escherichia coli. , 1989, FEMS microbiology reviews.

[22]  Adam P Arkin,et al.  An adaptor from translational to transcriptional control enables predictable assembly of complex regulation , 2012, Nature Methods.

[23]  D. Hanahan.  Studies on transformation of Escherichia coli with plasmids. , 1983, Journal of molecular biology.

[24]  Mattijs K. Julsing,et al.  Functional analysis of genes involved in the biosynthesis of isoprene in Bacillus subtilis , 2006 .

[25]  C. Wittmann,et al.  Characterization of the metabolic shift between oxidative and fermentative growth in Saccharomyces cerevisiae by comparative 13C flux analysis , 2005, Microbial cell factories.

[26]  J. Rood,et al.  Conjugative transfer of RP4-oriT shuttle vectors from Escherichia coli to Clostridium perfringens. , 1998, Plasmid.

[27]  V. de Lorenzo,et al.  Transposon-based and plasmid-based genetic tools for editing genomes of gram-negative bacteria. , 2012, Methods in molecular biology.

[28]  Thomas H Segall-Shapiro,et al.  Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome , 2010, Science.

[29]  C. Laluce,et al.  Advances and Developments in Strategies to Improve Strains of Saccharomyces cerevisiae and Processes to Obtain the Lignocellulosic Ethanol−A Review , 2012, Applied Biochemistry and Biotechnology.

[30]  S Omura,et al.  Inhibition of fatty acid synthesis by the antibiotic cerulenin. Specific inactivation of beta-ketoacyl-acyl carrier protein synthetase. , 1973, Biochimica et biophysica acta.

[31]  J. Keasling,et al.  Microbial engineering for the production of advanced biofuels , 2012, Nature.

[32]  O. Adachi,et al.  Quinoproteins: structure, function, and biotechnological applications , 2001, Applied Microbiology and Biotechnology.

[33]  Nian Liu,et al.  Effects of heme precursors on CYP1A2 and POR expression in the baculovirus/Spodoptera frugiperda system , 2010, Journal of biomedical research.

[34]  Jingwen Zhou,et al.  Metabolic engineering of Escherichia coli for (2S)-pinocembrin production from glucose by a modular metabolic strategy. , 2013, Metabolic engineering.

[35]  Ron Milo,et al.  Spanning high-dimensional expression space using ribosome-binding site combinatorics , 2013, Nucleic acids research.

[36]  L. Eberl,et al.  N-acyl homoserinelactone-mediated gene regulation in gram-negative bacteria. , 1999, Systematic and applied microbiology.

[37]  A. Steinbüchel,et al.  Biochemical and molecular basis of microbial synthesis of polyhydroxyalkanoates in microorganisms. , 2001, Advances in biochemical engineering/biotechnology.

[38]  Martin Fussenegger,et al.  Synthetic two-way communication between mammalian cells , 2012, Nature Biotechnology.

[39]  Zhengxiang Wang,et al.  Metabolic engineering of Escherichia coli: a sustainable industrial platform for bio-based chemical production. , 2013, Biotechnology advances.

[40]  Ryan T Gill,et al.  Strategy for directing combinatorial genome engineering in Escherichia coli , 2012, Proceedings of the National Academy of Sciences.

[41]  Kyongbum Lee,et al.  Engineering E. coli for triglyceride accumulation through native and heterologous metabolic reactions , 2013, Applied Microbiology and Biotechnology.

[42]  Huimin Zhao,et al.  Recent advances in DNA assembly technologies. , 2014, FEMS yeast research.

[43]  K. Shanmugam,et al.  Simplified process for ethanol production from sugarcane bagasse using hydrolysate-resistant Escherichia coli strain MM160. , 2011, Bioresource technology.

[44]  U. Bornscheuer,et al.  Multistep enzymatic synthesis of long-chain α,ω-dicarboxylic and ω-hydroxycarboxylic acids from renewable fatty acids and plant oils. , 2013, Angewandte Chemie.

[45]  Fuzhong Zhang,et al.  Biosensors and their applications in microbial metabolic engineering. , 2011, Trends in microbiology.

[46]  Mauricio Barahona,et al.  A modular cell-based biosensor using engineered genetic logic circuits to detect and integrate multiple environmental signals , 2013, Biosensors & bioelectronics.

[47]  D. Brat,et al.  Functional Expression of a Bacterial Xylose Isomerase in Saccharomyces cerevisiae , 2009, Applied and Environmental Microbiology.

[48]  Dong-Woo Lee,et al.  Cytochrome c biogenesis: the Ccm system. , 2010, Trends in microbiology.

[49]  P. Nikel,et al.  Elimination of d-Lactate Synthesis Increases Poly(3-Hydroxybutyrate) and Ethanol Synthesis from Glycerol and Affects Cofactor Distribution in Recombinant Escherichia coli , 2010, Applied and Environmental Microbiology.

[50]  Mo Xian,et al.  Biosynthesis of isoprene in Escherichia coli via methylerythritol phosphate (MEP) pathway , 2011, Applied Microbiology and Biotechnology.

[51]  H. Chang,et al.  The effect of volatile fatty acids as a sole carbon source on lipid accumulation by Cryptococcus albidus for biodiesel production. , 2011, Bioresource technology.

[52]  M. Urbanowski,et al.  The Quorum Sensing Negative Regulators EsaR and ExpREcc, Homologues within the LuxR Family, Retain the Ability To Function as Activators of Transcription , 2003, Journal of bacteriology.

[53]  Sang Yup Lee,et al.  Genome engineering and gene expression control for bacterial strain development , 2015, Biotechnology journal.

[54]  Akihiko Kondo,et al.  Xylose isomerase from polycentric fungus Orpinomyces: gene sequencing, cloning, and expression in Saccharomyces cerevisiae for bioconversion of xylose to ethanol , 2009, Applied Microbiology and Biotechnology.

[55]  Jacob Beal,et al.  Automated selection of synthetic biology parts for genetic regulatory networks. , 2012, ACS synthetic biology.

[56]  Jae-Seong Yang,et al.  Predictive design of mRNA translation initiation region to control prokaryotic translation efficiency. , 2013, Metabolic engineering.

[57]  M. Berhow,et al.  Adaptive response of yeasts to furfural and 5-hydroxymethylfurfural and new chemical evidence for HMF conversion to 2,5-bis-hydroxymethylfuran , 2004, Journal of Industrial Microbiology and Biotechnology.

[58]  Rajib Saha,et al.  Synthetic biology of cyanobacteria: unique challenges and opportunities , 2013, Front. Microbiol..

[59]  Vladimir Larionov,et al.  Selective isolation of genomic loci from complex genomes by transformation-associated recombination cloning in the yeast Saccharomyces cerevisiae , 2008, Nature Protocols.

[60]  Pablo Carbonell,et al.  A retrosynthetic biology approach to metabolic pathway design for therapeutic production , 2011, BMC Systems Biology.

[61]  Alfonso Jaramillo,et al.  AutoBioCAD: full biodesign automation of genetic circuits. , 2013, ACS synthetic biology.

[62]  H. Krisch,et al.  The stability of bacteriophage T4 gene 32 mRNA: A 5′ leader sequence that can stabilize mRNA transcripts , 1985, Cell.

[63]  B. Suess,et al.  A theophylline responsive riboswitch based on helix slipping controls gene expression in vivo. , 2004, Nucleic acids research.

[64]  M. Inui,et al.  Effect of Lignocellulose-Derived Inhibitors on Growth of and Ethanol Production by Growth-Arrested Corynebacterium glutamicum R , 2007, Applied and Environmental Microbiology.

[65]  T. Ramseier.  Cra and the control of carbon flux via metabolic pathways. , 1996, Research in microbiology.

[66]  M. Silverman,et al.  Identification of genes and gene products necessary for bacterial bioluminescence. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

[67]  Jef Boeke,et al.  The Saccharomyces cerevisiae SCRaMbLE system and genome minimization , 2012, Bioengineered bugs.

[68]  D. Mazel,et al.  Silent Mischief: Bacteriophage Mu Insertions Contaminate Products of Escherichia coli Random Mutagenesis Performed Using Suicidal Transposon Delivery Plasmids Mobilized by Broad-Host-Range RP4 Conjugative Machinery , 2010, Journal of bacteriology.

[69]  Oscar Ces,et al.  Design of a prototype flow microreactor for synthetic biology in vitro. , 2013, Lab on a chip.

[70]  Hao Yan,et al.  DNA Origami with Complex Curvatures in Three-Dimensional Space , 2011, Science.

[71]  G. Silverman,et al.  C. elegans in high-throughput drug discovery. , 2014, Advanced drug delivery reviews.

[72]  Lee Põllumaa,et al.  Quorum Sensing and Expression of Virulence in Pectobacteria , 2012, Sensors.

[73]  Mario A Marchisio,et al.  In silico design and in vivo implementation of yeast gene Boolean gates , 2014, Journal of Biological Engineering.

[74]  Andrés Moya,et al.  The Calculus of Life , 2015, SpringerBriefs in Biology.

[75]  R. Cortese,et al.  The crystal structure of the quorum sensing protein TraR bound to its autoinducer and target DNA , 2002, The EMBO journal.

[76]  G. Church,et al.  Accurate multiplex gene synthesis from programmable DNA microchips , 2004, Nature.

[77]  Alejandro Buschiazzo,et al.  Structural basis of lipid biosynthesis regulation in Gram‐positive bacteria , 2006, The EMBO journal.

[78]  V. Wendisch,et al.  Improving putrescine production by Corynebacterium glutamicum by fine-tuning ornithine transcarbamoylase activity using a plasmid addiction system , 2012, Applied Microbiology and Biotechnology.

[79]  S. Elledge,et al.  Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC , 2007, Nature Methods.

[80]  Wei Zhang,et al.  Hydrogen peroxide-independent production of α-alkenes by OleTJE P450 fatty acid decarboxylase , 2014, Biotechnology for Biofuels.

[81]  Nathan J Hillson,et al.  j5 DNA assembly design automation software. , 2012, ACS synthetic biology.

[82]  M. Itaya,et al.  Bottom-up genome assembly using the Bacillus subtilis genome vector , 2008, Nature Methods.

[83]  Brian F. Pfleger,et al.  Modular Synthase-Encoding Gene Involved in α-Olefin Biosynthesis in Synechococcus sp. Strain PCC 7002 , 2011, Applied and Environmental Microbiology.

[84]  F. Bordes,et al.  Metabolic engineering for ricinoleic acid production in the oleaginous yeast Yarrowia lipolytica , 2013, Applied Microbiology and Biotechnology.

[85]  S. Papanikolaou,et al.  Single cell oil production by Yarrowia lipolytica growing on an industrial derivative of animal fat in batch cultures , 2002, Applied Microbiology and Biotechnology.

[86]  G. Stephanopoulos,et al.  Improving fatty acids production by engineering dynamic pathway regulation and metabolic control , 2014, Proceedings of the National Academy of Sciences.

[87]  Cornelis P. Hollenberg,et al.  Isolation and characterization of the Pichia stipitis xylitol dehydrogenase gene, XYL2, and construction of a xylose-utilizing Saccharomyces cerevisiae transformant , 1990, Current Genetics.

[88]  A. Steinbüchel.  Production of rubber-like polymers by microorganisms. , 2003, Current opinion in microbiology.

[89]  Guoqiang Chen,et al.  Polyhydroxyalkanoates, challenges and opportunities. , 2014, Current opinion in biotechnology.

[90]  R. Doi,et al.  In vitro expression of a Tn9-derived chloramphenicol acetyltransferase gene fusion by using a Bacillus subtilis system , 1987, Journal of bacteriology.

[91]  Guillaume Charras,et al.  Spatiotemporal control of gene expression using microfluidics. , 2014, Lab on a chip.

[92]  Daoyi Guo,et al.  Metabolic engineering of Escherichia coli for production of fatty acid short-chain esters through combination of the fatty acid and 2-keto acid pathways. , 2014, Metabolic engineering.

[93]  Faisal A. Aldaye,et al.  Identity : Key to Children ’ s Understanding of Belief , 2013 .

[94]  N. Linden,et al.  Self-Assembling Cages from Coiled-Coil Peptide Modules , 2013, Science.

[95]  L. Eggeling,et al.  Looking for the pick of the bunch: high-throughput screening of producing microorganisms with biosensors. , 2014, Current opinion in biotechnology.

[96]  Harold G. Craighead,et al.  High-throughput binding characterization of RNA aptamer selections using a microplate-based multiplex microcolumn device , 2014, Analytical and Bioanalytical Chemistry.

[97]  C. Walsh,et al.  Biosynthetic thiolase from Zoogloea ramigera. Evidence for a mechanism involving Cys-378 as the active site base. , 1991, The Journal of biological chemistry.

[98]  Peter Ruhdal Jensen,et al.  Synthetic promoter libraries for Corynebacterium glutamicum , 2014, Applied Microbiology and Biotechnology.

[99]  J. Nicaud,et al.  Catabolism of hydroxyacids and biotechnological production of lactones by Yarrowia lipolytica , 2003, Applied Microbiology and Biotechnology.

[100]  A. Anschau,et al.  Optimization of lipid production by the oleaginous yeast Lipomyces starkeyi by random mutagenesis coupled to cerulenin screening , 2012, AMB Express.

[101]  J. Cregg,et al.  Recombinant protein expression in Pichia pastoris , 2000, Molecular biotechnology.

[102]  Naheed Kaderbhai,et al.  Gene-dose-dependent expression of soluble mammalian cytochrome b5 in Escherichia coli , 1992, Applied Microbiology and Biotechnology.

[103]  A. Danchin,et al.  The logic of metabolism and its fuzzy consequences. , 2014, Environmental microbiology.

[104]  T. Conway,et al.  The Entner-Doudoroff pathway: history, physiology and molecular biology. , 1992, FEMS microbiology reviews.

[105]  Jacob Beal,et al.  Model-driven engineering of gene expression from RNA replicons. , 2015, ACS synthetic biology.

[106]  P. Nikel,et al.  Escherichia coli redox mutants as microbial cell factories for the synthesis of reduced biochemicals , 2012, Computational and structural biotechnology journal.

[107]  C. Schmidt-Dannert,et al.  Metabolic engineering towards biotechnological production of carotenoids in microorganisms , 2002, Applied Microbiology and Biotechnology.

[108]  M. Fontecave,et al.  Mechanisms of iron–sulfur cluster assembly: the SUF machinery , 2005, JBIC Journal of Biological Inorganic Chemistry.

[109]  Matthew J. Moscou,et al.  A Simple Cipher Governs DNA Recognition by TAL Effectors , 2009, Science.

[110]  J. Keasling,et al.  Integrating Biological Redesign: Where Synthetic Biology Came From and Where It Needs to Go , 2014, Cell.

[111]  Pamela A. Silver,et al.  Rapid construction of insulated genetic circuits via synthetic sequence-guided isothermal assembly , 2013, Nucleic acids research.

[112]  Jens Nielsen,et al.  Functional expression and characterization of five wax ester synthases in Saccharomyces cerevisiae and their utility for biodiesel production , 2012, Biotechnology for Biofuels.

[113]  K. Shanmugam,et al.  Increased Furfural Tolerance Due to Overexpression of NADH-Dependent Oxidoreductase FucO in Escherichia coli Strains Engineered for the Production of Ethanol and Lactate , 2011, Applied and Environmental Microbiology.

[114]  Anil Wipat,et al.  Bacillus subtilis: Model Gram-Positive Synthetic Biology Chassis , 2013 .

[115]  Christina D Smolke,et al.  Synthetic RNA switches as a tool for temporal and spatial control over gene expression. , 2012, Current opinion in biotechnology.

[116]  M. Hamberg,et al.  A prokaryotic acyl‐CoA reductase performing reduction of fatty acyl‐CoA to fatty alcohol , 2011, FEBS letters.

[117]  P. Rogers,et al.  High-productivity alcohol fermentations using Zymomonas mobilis. , 1983, Biochemical Society symposium.

[118]  Timothy B. Stockwell,et al.  Complete Chemical Synthesis, Assembly, and Cloning of a Mycoplasma genitalium Genome , 2008, Science.

[119]  M Hasebe,et al.  Tagged mutagenesis and gene-trap in the moss, Physcomitrella patens by shuttle mutagenesis. , 2000, DNA research : an international journal for rapid publication of reports on genes and genomes.

[120]  Jingdong Tian,et al.  Circular Polymerase Extension Cloning of Complex Gene Libraries and Pathways , 2009, PloS one.

[121]  Andreas Schirmer,et al.  Terminal Olefin (1-Alkene) Biosynthesis by a Novel P450 Fatty Acid Decarboxylase from Jeotgalicoccus Species , 2011, Applied and Environmental Microbiology.

[122]  Christian Cole,et al.  The Jpred 3 secondary structure prediction server , 2008, Nucleic Acids Res..

[123]  Wendell A Lim,et al.  Engineering synthetic signaling proteins with ultrasensitive input/output control , 2007, Nature Biotechnology.

[124]  Jeff Hasty,et al.  A synthetic gene network for tuning protein degradation in Saccharomyces cerevisiae , 2007, Molecular systems biology.

[125]  M. Boutros,et al.  E-CRISP: fast CRISPR target site identification , 2014, Nature Methods.

[126]  F. Lienert,et al.  Synthetic biology in mammalian cells: next generation research tools and therapeutics , 2014, Nature Reviews Molecular Cell Biology.

[127]  Lianglin Qiu,et al.  Optimization of heme precursors for the expression of human cytochrome P450 2A13 and its co-expression with oxidoreductase in baculovirus/sf9 system. , 2013, Journal of biochemistry.

[128]  Ryan T Gill,et al.  SCALEs: multiscale analysis of library enrichment , 2007, Nature Methods.

[129]  J. Cregg,et al.  New yeast expression platforms based on methylotrophic Hansenula polymorpha and Pichia pastoris and on dimorphic Arxula adeninivorans and Yarrowia lipolytica - a comparison. , 2005, FEMS yeast research.

[130]  B. Bassler,et al.  Structural identification of a bacterial quorum-sensing signal containing boron , 2002, Nature.

[131]  B. Hahn-Hägerdal,et al.  Comparing the xylose reductase/xylitol dehydrogenase and xylose isomerase pathways in arabinose and xylose fermenting Saccharomyces cerevisiae strains , 2008, Biotechnology for biofuels.

[132]  Víctor de Lorenzo,et al.  pBAM1: an all-synthetic genetic tool for analysis and construction of complex bacterial phenotypes , 2011, BMC Microbiology.

[133]  J. Y. Lee,et al.  Engineering butanol‐tolerance in escherichia coli with artificial transcription factor libraries , 2011, Biotechnology and bioengineering.

[134]  Claire Marris,et al.  Open Engagement: Exploring Public Participation in the Biosciences , 2010, PLoS biology.

[135]  H. Boyer,et al.  A complementation analysis of the restriction and modification of DNA in Escherichia coli. , 1969, Journal of molecular biology.

[136]  Merja Penttilä,et al.  Xylose transport studies with xylose-utilizing Saccharomyces cerevisiae strains expressing heterologous and homologous permeases , 2007, Applied Microbiology and Biotechnology.

[137]  Jeff Hasty,et al.  Genetic Circuits in Salmonella typhimurium , 2012, ACS synthetic biology.

[138]  W. Eisenreich,et al.  Biosynthesis of terpenes: Studies on 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[139]  Rui Gan,et al.  A combined cell-free transcription-translation system from Saccharomyces cerevisiae for rapid and robust protein synthe. , 2014, Biotechnology journal.

[140]  J. Keasling.  Manufacturing Molecules Through Metabolic Engineering , 2010, Science.

[141]  J. Collins,et al.  DIVERSITY-BASED, MODEL-GUIDED CONSTRUCTION OF SYNTHETIC GENE NETWORKS WITH PREDICTED FUNCTIONS , 2009, Nature Biotechnology.

[142]  J. Nicaud,et al.  Lipid particle composition of the yeast Yarrowia lipolytica depends on the carbon source , 2006, Proteomics.

[143]  J. Keasling,et al.  Metabolic pathway optimization using ribosome binding site variants and combinatorial gene assembly , 2014, Applied Microbiology and Biotechnology.

[144]  L. Jarboe,et al.  Genetic changes that increase 5-hydroxymethyl furfural resistance in ethanol-producing Escherichia coli LY180 , 2010, Biotechnology Letters.

[145]  Bastian Blombach,et al.  Current knowledge on isobutanol production with Escherichia coli, Bacillus subtilis and Corynebacterium glutamicum , 2011, Bioengineered bugs.

[146]  V. Wendisch,et al.  Optimization of the IPP Precursor Supply for the Production of Lycopene, Decaprenoxanthin and Astaxanthin by Corynebacterium glutamicum , 2014, Front. Bioeng. Biotechnol..

[147]  V. Wendisch,et al.  Putrescine production by engineered Corynebacterium glutamicum , 2010, Applied Microbiology and Biotechnology.

[148]  Gunnar Lidén,et al.  Control of xylose consumption by xylose transport in recombinant Saccharomyces cerevisiae. , 2003, Biotechnology and bioengineering.

[149]  A. Anderson,et al.  Occurrence, metabolism, metabolic role, and industrial uses of bacterial polyhydroxyalkanoates. , 1990, Microbiological reviews.

[150]  H. Salis.  The ribosome binding site calculator. , 2011, Methods in enzymology.

[151]  T. Schäfer,et al.  Acetyl-CoA synthetase (ADP forming) in archaea, a novel enzyme involved in acetate formation and ATP synthesis , 2004, Archives of Microbiology.

[152]  Maxime Durot,et al.  Rapid and reliable DNA assembly via ligase cycling reaction. , 2014, ACS synthetic biology.

[153]  Edward J. O'Brien,et al.  Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction , 2013, Molecular systems biology.

[154]  K. Kretz,et al.  SanDI, a new type-II restriction endonuclease that recognizes 5'-GG/GWCCC-3'. , 1995, Gene.

[155]  Yong-Su Jin,et al.  Engineered Saccharomyces cerevisiae capable of simultaneous cellobiose and xylose fermentation , 2010, Proceedings of the National Academy of Sciences.

[156]  J. McCaffery,et al.  Furfural induces reactive oxygen species accumulation and cellular damage in Saccharomyces cerevisiae , 2010, Biotechnology for biofuels.

[157]  Shawn M. Douglas,et al.  Self-assembly of DNA into nanoscale three-dimensional shapes , 2009, Nature.

[158]  R. Bazzo,et al.  Molecular Insights into Quorum Sensing in the Human Pathogen Pseudomonas aeruginosa from the Structure of the Virulence Regulator LasR Bound to Its Autoinducer* , 2007, Journal of Biological Chemistry.

[159]  Volker F Wendisch,et al.  Crude glycerol-based production of amino acids and putrescine by Corynebacterium glutamicum. , 2013, Bioresource technology.

[160]  Tajalli Keshavarz,et al.  Polyhydroxyalkanoates: bioplastics with a green agenda. , 2010, Current opinion in microbiology.

[161]  J. Keasling,et al.  Genes Involved in Long-Chain Alkene Biosynthesis in Micrococcus luteus , 2009, Applied and Environmental Microbiology.

[162]  J. Brosius,et al.  Precise location of two promoters for the beta-lactamase gene of pBR322. S1 mapping of ribonucleic acid isolated from Escherichia coli or synthesized in vitro. , 1982, The Journal of biological chemistry.

[163]  Christopher A. Voigt,et al.  Robust multicellular computing using genetically encoded NOR gates and chemical ‘wires’ , 2011, Nature.

[164]  R. Stewart,et al.  Quantitative selection and parallel characterization of aptamers , 2013, Proceedings of the National Academy of Sciences.

[165]  J. Ness,et al.  Biosynthesis of monomers for plastics from renewable oils. , 2010, Journal of the American Chemical Society.

[166]  A. Steinbüchel,et al.  Pilot-Scale Production of Fatty Acid Ethyl Esters by an Engineered Escherichia coli Strain Harboring the p(Microdiesel) Plasmid , 2010, Applied and Environmental Microbiology.

[167]  Y. Takahashi,et al.  Hyperproduction of recombinant ferredoxins in escherichia coli by coexpression of the ORF1-ORF2-iscS-iscU-iscA-hscB-hs cA-fdx-ORF3 gene cluster. , 1999, Journal of biochemistry.

[168]  Tom Ellis,et al.  GeneGuard: A modular plasmid system designed for biosafety. , 2015, ACS synthetic biology.

[169]  R. Breaker,et al.  Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes , 2005, Nature Biotechnology.

[170]  Hana El-Samad,et al.  Dynamic Characterization of Growth and Gene Expression Using High-throughput Automated Flow cytometry , 2014, Nature Methods.

[171]  T. Gerngross,et al.  Glycosylation engineering in yeast: the advent of fully humanized yeast. , 2007, Current opinion in biotechnology.

[172]  M. Rizzi,et al.  Xylose fermentation by yeasts. 5. Use of ATP balances for modeling oxygen‐limited growth and fermentation of yeast Pichia stipitis with xylose as carbon source , 1989, Biotechnology and bioengineering.

[173]  Peng Xu,et al.  ePathBrick: a synthetic biology platform for engineering metabolic pathways in E. coli. , 2012, ACS synthetic biology.

[174]  Ertugrul M. Ozbudak,et al.  Regulation of noise in the expression of a single gene , 2002, Nature Genetics.

[175]  Tom Ellis,et al.  DNA assembly for synthetic biology: from parts to pathways and beyond. , 2011, Integrative biology : quantitative biosciences from nano to macro.

[176]  E. Greenberg,et al.  Census and consensus in bacterial ecosystems: the LuxR-LuxI family of quorum-sensing transcriptional regulators. , 1996, Annual review of microbiology.

[177]  Christopher A. Voigt,et al.  Automated design of synthetic ribosome binding sites to control protein expression , 2016 .

[178]  J M Berger,et al.  Divalent metal cofactor binding in the kinetic folding trajectory of Escherichia coli ribonuclease HI , 2000, Protein science : a publication of the Protein Society.

[179]  William E. Ortyn,et al.  Cellular image analysis and imaging by flow cytometry. , 2007, Clinics in laboratory medicine.

[180]  Maurizio Labbate,et al.  AHL-driven quorum-sensing circuits: their frequency and function among the Proteobacteria , 2008, The ISME Journal.

[181]  G. Sandmann,et al.  Multiple improvement of astaxanthin biosynthesis in Xanthophyllomyces dendrorhous by a combination of conventional mutagenesis and metabolic pathway engineering , 2012, Biotechnology Letters.

[182]  Ryan T Gill,et al.  Cellulosic hydrolysate toxicity and tolerance mechanisms in Escherichia coli , 2009, Biotechnology for biofuels.

[183]  Xueli Zhang,et al.  Metabolic Engineering for Production of Biorenewable Fuels and Chemicals: Contributions of Synthetic Biology , 2010, Journal of biomedicine & biotechnology.

[184]  Jared R. Leadbetter,et al.  Dual selection enhances the signaling specificity of a variant of the quorum-sensing transcriptional activator LuxR , 2006, Nature Biotechnology.

[185]  Lingchong You,et al.  Engineered cell-cell communication and its applications. , 2014, Advances in biochemical engineering/biotechnology.

[186]  J. Beckerich,et al.  Heterologous protein expression and secretion in the non-conventional yeast Yarrowia lipolytica: a review. , 2004, Journal of biotechnology.

[187]  L. Hood,et al.  Reverse Engineering of Biological Complexity , 2007 .

[188]  Yingjin Yuan,et al.  Temporal quantitative proteomics of Saccharomyces cerevisiae in response to a nonlethal concentration of furfural , 2009, Proteomics.

[189]  Yi Li,et al.  A simple, rapid, high-fidelity and cost-effective PCR-based two-step DNA synthesis method for long gene sequences. , 2004, Nucleic acids research.

[190]  G. Stephanopoulos,et al.  Improvement of Xylose Uptake and Ethanol Production in Recombinant Saccharomyces cerevisiae through an Inverse Metabolic Engineering Approach , 2005, Applied and Environmental Microbiology.

[191]  Guillermo Gosset,et al.  Growth‐rate recovery of Escherichia coli cultures carrying a multicopy plasmid, by engineering of the pentose‐phosphate pathway , 2004, Biotechnology and bioengineering.

[192]  Jens Boch,et al.  Breaking the Code of DNA Binding Specificity of TAL-Type III Effectors , 2009, Science.

[193]  H. Alper,et al.  Directed Evolution of Xylose Isomerase for Improved Xylose Catabolism and Fermentation in the Yeast Saccharomyces cerevisiae , 2012, Applied and Environmental Microbiology.

[194]  S. Papanikolaou,et al.  Accumulation of a Cocoa-Butter-Like Lipid by Yarrowia lipolytica Cultivated on Agro-Industrial Residues , 2003, Current Microbiology.

[195]  J Craig Venter,et al.  Chemical synthesis of the mouse mitochondrial genome , 2010, Nature Methods.

[196]  Christopher A. Voigt,et al.  A Synthetic Genetic Edge Detection Program , 2009, Cell.

[197]  C. Collins,et al.  Peptide‐based communication system enables Escherichia coli to Bacillus megaterium interspecies signaling , 2013, Biotechnology and bioengineering.

[198]  H. Ernst,et al.  The chemistry of novel xanthophyll carotenoids. , 2008, The American journal of cardiology.

[199]  Brian F Pfleger,et al.  Microbial production of fatty acid-derived fuels and chemicals. , 2013, Current opinion in biotechnology.

[200]  B. Py,et al.  Iron/sulfur proteins biogenesis in prokaryotes: formation, regulation and diversity. , 2013, Biochimica et biophysica acta.

[201]  D. Knorr,et al.  Rapid monitoring of cell size, vitality and lipid droplet development in the oleaginous yeast Waltomyces lipofer. , 2009, Journal of microbiological methods.

[202]  B. Hahn-Hägerdal,et al.  Expression of the Gxf1 transporter from Candida intermedia improves fermentation performance in recombinant xylose-utilizing Saccharomyces cerevisiae , 2009, Applied Microbiology and Biotechnology.

[203]  V. de Lorenzo,et al.  Engineering an anaerobic metabolic regime in Pseudomonas putida KT2440 for the anoxic biodegradation of 1,3-dichloroprop-1-ene. , 2013, Metabolic engineering.

[204]  L. T. Angenent,et al.  Prolonged conversion of n‐butyrate to n‐butanol with Clostridium saccharoperbutylacetonicum in a two‐stage continuous culture with in‐situ product removal , 2012, Biotechnology and bioengineering.

[205]  Volker F. Wendisch,et al.  Engineering of a Glycerol Utilization Pathway for Amino Acid Production by Corynebacterium glutamicum , 2008, Applied and Environmental Microbiology.

[206]  Jens Meiler,et al.  New algorithms and an in silico benchmark for computational enzyme design , 2006, Protein science : a publication of the Protein Society.

[207]  Sung Kuk Lee,et al.  Engineered Escherichia coli capable of co-utilization of cellobiose and xylose. , 2012, Enzyme and microbial technology.

[208]  Hua Zhao,et al.  Furfural and hydroxymethylfurfural tolerance in Escherichia coli ΔacrR regulatory mutants , 2015, Biotechnology and applied biochemistry.

[209]  Jane Calvert,et al.  Ownership and sharing in synthetic biology: A ‘diverse ecology’ of the open and the proprietary? , 2012, BioSocieties.

[210]  Jay D Keasling,et al.  Transcription factor-based screens and synthetic selections for microbial small-molecule biosynthesis. , 2013, ACS synthetic biology.

[211]  M. Ballesteros,et al.  Pretreatment technologies for an efficient bioethanol production process based on enzymatic hydrolysis: A review. , 2010, Bioresource technology.

[212]  Hal S Alper,et al.  Heterologous production of pentane in the oleaginous yeast Yarrowia lipolytica. , 2013, Journal of biotechnology.

[213]  Peter Lindblad,et al.  Synthetic biology in cyanobacteria engineering and analyzing novel functions. , 2011, Methods in enzymology.

[214]  W. Eisenreich,et al.  Biochemistry of the non-mevalonate isoprenoid pathway , 2011, Cellular and Molecular Life Sciences.

[215]  Charles Darwin,et al.  Experiments , 1800, The Medical and physical journal.

[216]  K. Winzer,et al.  Look who's talking: communication and quorum sensing in the bacterial world , 2007, Philosophical Transactions of the Royal Society B: Biological Sciences.

[217]  Wei-Hua Chen,et al.  The MASTER (methylation-assisted tailorable ends rational) ligation method for seamless DNA assembly , 2013, Nucleic acids research.

[218]  Joseph A Ross,et al.  Hfq restructures RNA-IN and RNA-OUT and facilitates antisense pairing in the Tn10/IS10 system. , 2013, RNA.

[219]  S. Papanikolaou,et al.  Biotechnological valorization of biodiesel derived glycerol waste through production of single cell oil and citric acid by Yarrowia lipolytica , 2009 .

[220]  D. Schaefer,et al.  Efficient gene targeting in the moss Physcomitrella patens. , 1997, The Plant journal : for cell and molecular biology.

[221]  Ahmad S. Khalil,et al.  Synthetic biology: applications come of age , 2010, Nature Reviews Genetics.

[222]  Richard M. Murray,et al.  Protocols for Implementing an Escherichia coli Based TX-TL Cell-Free Expression System for Synthetic Biology , 2013, Journal of visualized experiments : JoVE.

[223]  R. Weiss,et al.  Automatic Compilation from High-Level Biologically-Oriented Programming Language to Genetic Regulatory Networks , 2011, PloS one.

[224]  L. Jarboe,et al.  Silencing of NADPH-Dependent Oxidoreductase Genes (yqhD and dkgA) in Furfural-Resistant Ethanologenic Escherichia coli , 2009, Applied and Environmental Microbiology.

[225]  J H Hendry,et al.  Development of synthetic promoters for radiation-mediated gene therapy , 2000, Gene Therapy.

[226]  K. Murphy,et al.  Lambda Red-mediated recombinogenic engineering of enterohemorrhagic and enteropathogenic E. coli , 2003, BMC Molecular Biology.

[227]  M Kalim Akhtar,et al.  Engineering of a synthetic hydF-hydE-hydG-hydA operon for biohydrogen production. , 2008, Analytical biochemistry.

[228]  Jeffrey W. Roberts,et al.  Mechanism of intrinsic transcription termination and antitermination. , 1999, Science.

[229]  Min Zhang,et al.  Metabolic Engineering of a Pentose Metabolism Pathway in Ethanologenic Zymomonas mobilis , 1995, Science.

[230]  Jian-Kang Zhu,et al.  De novo-engineered transcription activator-like effector (TALE) hybrid nuclease with novel DNA binding specificity creates double-strand breaks , 2011, Proceedings of the National Academy of Sciences.

[231]  Eric A. Althoff,et al.  De Novo Computational Design of Retro-Aldol Enzymes , 2008, Science.

[232]  A. Gilep,et al.  The development of an efficient system for heterologous expression of cytochrome P450s in Escherichia coli using hemA gene co-expression. , 2006, Protein expression and purification.

[233]  Michael Zuker,et al.  UNAFold: software for nucleic acid folding and hybridization. , 2008, Methods in molecular biology.

[234]  L. Lynd.  Large-scale fuel ethanol from lignocellulose , 1990 .

[235]  V. Wendisch,et al.  Metabolic engineering for the microbial production of carotenoids and related products with a focus on the rare C50 carotenoids , 2014, Applied Microbiology and Biotechnology.

[236]  Ivan Razinkov,et al.  Sensing array of radically coupled genetic biopixels , 2011, Nature.

[237]  Yu Tanouchi,et al.  Generic metric to quantify quorum sensing activation dynamics. , 2014, ACS synthetic biology.

[238]  P. Swain,et al.  Gene Regulation at the Single-Cell Level , 2005, Science.

[239]  R. Kwok.  Five hard truths for synthetic biology , 2010, Nature.

[240]  A. Pardi,et al.  High-resolution molecular discrimination by RNA. , 1994, Science.

[241]  J. Cregg,et al.  Heterologous protein expression in the methylotrophic yeast Pichia pastoris. , 2000, FEMS microbiology reviews.

[242]  R. Kolter,et al.  Genetic analysis of Escherichia coli biofilm formation: roles of flagella, motility, chemotaxis and type I pili , 1998, Molecular microbiology.

[243]  Alison Downham,et al.  Colouring our foods in the last and next millennium , 2000 .

[244]  Qian Wang,et al.  Lipid production from corn stover by the oleaginous yeast Cryptococcus curvatus , 2014, Biotechnology for Biofuels.

[245]  B. Wanner,et al.  One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[246]  J. Keasling,et al.  Microbial production of fatty-acid-derived fuels and chemicals from plant biomass , 2010, Nature.

[247]  James C. Liao,et al.  ATP drives direct photosynthetic production of 1-butanol in cyanobacteria , 2012, Proceedings of the National Academy of Sciences.

[248]  Christina D Smolke,et al.  Synthetic RNA switches for yeast metabolic engineering: screening recombinant enzyme libraries. , 2014, Methods in molecular biology.

[249]  N. Dunn,et al.  Expression of cloned Xanthomonasd-xylose catabolic genes in Zymomonas mobilis , 1988 .

[250]  C. Smolke,et al.  Advancing secondary metabolite biosynthesis in yeast with synthetic biology tools. , 2012, FEMS yeast research.

[251]  Jacob Beal,et al.  A Method for Fast, High-Precision Characterization of Synthetic Biology Devices , 2012 .

[252]  G. Crooks,et al.  WebLogo: a sequence logo generator. , 2004, Genome research.

[253]  D. W. Cheng,et al.  The minimal genome: a metabolic and environmental comparison. , 2011, Briefings in functional genomics.

[254]  Scott B. Selleck,et al.  GREAT METALLOCLUSTERS IN ENZYMOLOGY , 2005 .

[255]  B. Hall,et al.  Activation of the bgl operon by adaptive mutation. , 1998, Molecular biology and evolution.

[256]  Irene A. Chen,et al.  The Emergence of Competition Between Model Protocells , 2004, Science.

[257]  J. Nielsen,et al.  Metabolic Engineering of Saccharomyces cerevisiae , 2000, Microbiology and Molecular Biology Reviews.

[258]  Tom Ellis,et al.  Building-in biosafety for synthetic biology. , 2013, Microbiology.

[259]  K. Houmiel,et al.  Multiple β-Ketothiolases Mediate Poly(β-Hydroxyalkanoate) Copolymer Synthesis in Ralstonia eutropha , 1998 .

[260]  A. W. M. van den Enden,et al.  Discrete Time Signal Processing , 1989 .

[261]  V. de Lorenzo,et al.  Analysis and construction of stable phenotypes in gram-negative bacteria with Tn5- and Tn10-derived minitransposons. , 1994, Methods in enzymology.

[262]  Laura R. Jarboe,et al.  YqhC regulates transcription of the adjacent Escherichia coli genes yqhD and dkgA that are involved in furfural tolerance , 2011, Journal of Industrial Microbiology & Biotechnology.

[263]  E. Greenberg,et al.  Overproduction and purification of the luxR gene product: Transcriptional activator of the Vibrio fischeri luminescence system. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[264]  L. Tong,et al.  Crystal Structure of 1-Deoxy-d-xylulose 5-Phosphate Synthase, a Crucial Enzyme for Isoprenoids Biosynthesis* , 2007, Journal of Biological Chemistry.

[265]  S. Lewenza,et al.  Interspecies communication between Burkholderia cepacia and Pseudomonas aeruginosa. , 2002, Canadian journal of microbiology.

[266]  Sylvestre Marillonnet,et al.  Generation of families of construct variants using golden gate shuffling. , 2011, Methods in molecular biology.

[267]  B. Hahn-Hägerdal,et al.  The Streptomyces rubiginosus xylose isomerase is misfolded when expressed in Saccharomyces cerevisiae , 2003 .

[268]  A. Sinskey,et al.  Poly-beta-hydroxybutyrate (PHB) biosynthesis in Alcaligenes eutrophus H16. Identification and characterization of the PHB polymerase gene (phbC). , 1989, The Journal of biological chemistry.

[269]  William S Reznikoff.  Transposon Tn5. , 2008, Annual review of genetics.

[270]  Jef D Boeke,et al.  RADOM, an efficient in vivo method for assembling designed DNA fragments up to 10 kb long in Saccharomyces cerevisiae. , 2015, ACS synthetic biology.

[271]  Rahul Sarpeshkar,et al.  Synthetic analog computation in living cells , 2013, Nature.

[272]  K. San,et al.  Synthesis of methyl ketones by metabolically engineered Escherichia coli , 2012, Journal of Industrial Microbiology & Biotechnology.

[273]  R. Barrangou,et al.  CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes , 2007, Science.

[274]  Erin L. Doyle,et al.  Targeting DNA Double-Strand Breaks with TAL Effector Nucleases , 2010, Genetics.

[275]  Margrith E. Mattmann,et al.  Evaluation of a focused library of N-aryl L-homoserine lactones reveals a new set of potent quorum sensing modulators. , 2008, Bioorganic & medicinal chemistry letters.

[276]  Sylvia Daunert,et al.  Biosensing systems for the detection of bacterial quorum signaling molecules. , 2006, Analytical chemistry.

[277]  Tom Ellis,et al.  R2oDNA designer: computational design of biologically neutral synthetic DNA sequences. , 2014, ACS synthetic biology.

[278]  V. Wendisch,et al.  Production and glucosylation of C50 and C40 carotenoids by metabolically engineered Corynebacterium glutamicum , 2013, Applied Microbiology and Biotechnology.

[279]  J. Lodge,et al.  Transposon Tn5 target specificity: preference for insertion at G/C pairs. , 1988, Genetics.

[280]  Ryan T Gill,et al.  Comparison of genome‐wide selection strategies to identify furfural tolerance genes in Escherichia coli , 2015, Biotechnology and bioengineering.

[281]  Martyn Amos,et al.  Multicellular Computing Using Conjugation for Wiring , 2013, PloS one.

[282]  K. Shanmugam,et al.  Engineering furfural tolerance in Escherichia coli improves the fermentation of lignocellulosic sugars into renewable chemicals , 2013, Proceedings of the National Academy of Sciences.

[283]  V. Wendisch,et al.  Glucosamine as carbon source for amino acid-producing Corynebacterium glutamicum , 2012, Applied Microbiology and Biotechnology.

[284]  Daniel J Nicholson,et al.  Organisms ≠ Machines. , 2013, Studies in history and philosophy of biological and biomedical sciences.

[285]  Dominic Esposito,et al.  A novel cell-free protein synthesis system. , 2004, Journal of biotechnology.

[286]  Engineering E. coli strain for conversion of short chain fatty acids to bioalcohols , 2013, Biotechnology for Biofuels.

[287]  Charles Y. Lin,et al.  DHODH modulates transcriptional elongation in the neural crest and melanoma , 2011, Nature.

[288]  Noah Linden,et al.  A de novo peptide hexamer with a mutable channel , 2011, Nature chemical biology.

[289]  E. Ruby,et al.  Symbiotic association of Photobacterium fischeri with the marine luminous fish Monocentris japonica; a model of symbiosis based on bacterial studies. , 1976, The Biological bulletin.

[290]  P. Nikel,et al.  Poly(3-hydroxybutyrate) synthesis from glycerol by a recombinant Escherichia coli arcA mutant in fed-batch microaerobic cultures , 2008, Applied Microbiology and Biotechnology.

[291]  D. Block,et al.  Simultaneous consumption of pentose and hexose sugars: an optimal microbial phenotype for efficient fermentation of lignocellulosic biomass , 2010, Applied Microbiology and Biotechnology.

[292]  J. W. Peters,et al.  Insights into [FeFe]-hydrogenase structure, mechanism, and maturation. , 2011, Structure.

[293]  Christopher A. Voigt,et al.  Genomic Mining of Prokaryotic Repressors for Orthogonal Logic Gates , 2013, Nature chemical biology.

[294]  Christopher A. Voigt,et al.  Ribozyme-based insulator parts buffer synthetic circuits from genetic context , 2012, Nature Biotechnology.

[295]  Vincent Noireaux,et al.  Linear DNA for rapid prototyping of synthetic biological circuits in an Escherichia coli based TX-TL cell-free system. , 2014, ACS synthetic biology.

[296]  Zachary L. Fowler,et al.  Genome-scale metabolic network modeling results in minimal interventions that cooperatively force carbon flux towards malonyl-CoA. , 2011, Metabolic engineering.

[297]  Sean V. Taylor,et al.  Thiamin biosynthesis in prokaryotes , 1999, Archives of Microbiology.

[298]  U. Sauer,et al.  Coordination of microbial metabolism , 2014, Nature Reviews Microbiology.

[299]  M. Bennett,et al.  A fast, robust, and tunable synthetic gene oscillator , 2008, Nature.

[300]  S. M. Waheed,et al.  Nitric oxide blocks cellular heme insertion into a broad range of heme proteins. , 2010, Free radical biology & medicine.

[301]  Jeffrey E. Barrick,et al.  The distributions, mechanisms, and structures of metabolite-binding riboswitches , 2007, Genome Biology.

[302]  David K. Karig,et al.  Expression optimization and synthetic gene networks in cell-free systems , 2011, Nucleic acids research.

[303]  Vivek K. Mutalik,et al.  Predicting strength and function for promoters of the Escherichia coli alternative sigma factor, σE , 2010, Proceedings of the National Academy of Sciences.

[304]  Michael A Speer,et al.  Amplified insert assembly: an optimized approach to standard assembly of BioBrickTM genetic circuits , 2011, Journal of biological engineering.

[305]  Keith E. J. Tyo,et al.  Engineering of vesicle trafficking improves heterologous protein secretion in Saccharomyces cerevisiae. , 2012, Metabolic engineering.

[306]  P. Galzy,et al.  Study of lipids in Lipomyces and Waltomyces , 1994 .

[307]  Jay D. Keasling,et al.  Engineering Static and Dynamic Control of Synthetic Pathways , 2010, Cell.

[308]  Gabriel C. Wu,et al.  Synthetic protein scaffolds provide modular control over metabolic flux , 2009, Nature Biotechnology.

[309]  M. Rohmer.  The discovery of a mevalonate-independent pathway for isoprenoid biosynthesis in bacteria, algae and higher plants. , 1999, Natural product reports.

[310]  Zengyi Shao,et al.  DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways , 2008, Nucleic acids research.

[311]  C. Testa,et al.  The methylerythritol phosphate pathway and its significance as a novel drug target. , 2003, Current pharmaceutical biotechnology.

[312]  Chueh Loo Poh,et al.  Engineering microbes to sense and eradicate Pseudomonas aeruginosa, a human pathogen , 2011, Molecular systems biology.

[313]  Patrik R. Jones,et al.  Constructing and testing the thermodynamic limits of synthetic NAD(P)H:H2 pathways , 2008, Microbial biotechnology.

[314]  M. Fling,et al.  Nucleotide sequence of the transposon Tn7 gene encoding an aminoglycoside-modifying enzyme, 3"(9)-O-nucleotidyltransferase. , 1985, Nucleic acids research.

[315]  L. Gold,et al.  Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. , 1990, Science.

[316]  Ron Weiss,et al.  Genetically programmable pathogen sense and destroy. , 2013, ACS synthetic biology.

[317]  Christopher A. Voigt,et al.  Genetic programs constructed from layered logic gates in single cells , 2012, Nature.

[318]  María Martín,et al.  Activities at the Universal Protein Resource (UniProt) , 2013, Nucleic Acids Res..

[319]  Thomas Landrain,et al.  Do-it-yourself biology: challenges and promises for an open science and technology movement , 2013, Systems and Synthetic Biology.

[320]  D. G. Gibson,et al.  Enzymatic assembly of DNA molecules up to several hundred kilobases , 2009, Nature Methods.

[321]  R. Service.  Biofuel Researchers Prepare to Reap a New Harvest , 2007, Science.

[322]  N. Ho,et al.  Genetically Engineered SaccharomycesYeast Capable of Effective Cofermentation of Glucose and Xylose , 1998, Applied and Environmental Microbiology.

[323]  Merja Penttilä,et al.  Endogenous Xylose Pathway in Saccharomyces cerevisiae , 2004, Applied and Environmental Microbiology.

[324]  J. Hahn,et al.  Roles of the Yap1 Transcription Factor and Antioxidants in Saccharomyces cerevisiae's Tolerance to Furfural and 5-Hydroxymethylfurfural, Which Function as Thiol-Reactive Electrophiles Generating Oxidative Stress , 2013, Applied and Environmental Microbiology.

[325]  J. Thevelein,et al.  Bioengineering of plant (tri)terpenoids: from metabolic engineering of plants to synthetic biology in vivo and in vitro. , 2013, The New phytologist.

[326]  Jingdong Tian,et al.  Circular polymerase extension cloning for high-throughput cloning of complex and combinatorial DNA libraries , 2011, Nature Protocols.

[327]  J. Bao,et al.  Biological removal of inhibitors leads to the improved lipid production in the lipid fermentation of corn stover hydrolysate by Trichosporon cutaneum. , 2011, Bioresource technology.

[328]  Trevor Douglas,et al.  Biological Containers: Protein Cages as Multifunctional Nanoplatforms , 2007 .

[329]  L. Eggeling,et al.  Characterization of a Corynebacterium glutamicum Lactate Utilization Operon Induced during Temperature-Triggered Glutamate Production , 2005, Applied and Environmental Microbiology.

[330]  Zhen Xie,et al.  Modular construction of mammalian gene circuits using TALE transcriptional repressors , 2014, Nature chemical biology.

[331]  A. Kondo,et al.  Glutamate production from β-glucan using endoglucanase-secreting Corynebacterium glutamicum , 2011, Applied Microbiology and Biotechnology.

[332]  C. Collins,et al.  Modular optimization of multi-gene pathways for fatty acids production in E. coli , 2013, Nature Communications.

[333]  Andre Levchenko,et al.  Microfluidic technologies for studying synthetic circuits. , 2012, Current opinion in chemical biology.

[334]  M. Rodríguez-Concepcíon,et al.  Elucidation of the Methylerythritol Phosphate Pathway for Isoprenoid Biosynthesis in Bacteria and Plastids. A Metabolic Milestone Achieved through Genomics1 , 2002, Plant Physiology.

[335]  Ryan T Gill,et al.  Rapid profiling of a microbial genome using mixtures of barcoded oligonucleotides , 2010, Nature Biotechnology.

[336]  C. Williams,et al.  Bacterial synthesis of biodegradable polyhydroxyalkanoates , 2007, Journal of applied microbiology.

[337]  Yong‐Su Jin,et al.  Strain engineering of Saccharomyces cerevisiae for enhanced xylose metabolism. , 2013, Biotechnology advances.

[338]  Stacie A Meaux,et al.  Yeast transcripts cleaved by an internal ribozyme provide new insight into the role of the cap and poly(A) tail in translation and mRNA decay. , 2006, RNA.

[339]  Derek N. Woolfson,et al.  More than Just Bare Scaffolds: Towards Multi-Component and Decorated Fibrous Biomaterials , 2010 .

[340]  F M Gírio,et al.  Hemicelluloses for fuel ethanol: A review. , 2010, Bioresource technology.

[341]  Jens Boch,et al.  Regulation of selected genome loci using de novo-engineered transcription activator-like effector (TALE)-type transcription factors , 2010, Proceedings of the National Academy of Sciences.

[342]  W. Eisenreich,et al.  Perspectives in anti-infective drug design. The late steps in the biosynthesis of the universal terpenoid precursors, isopentenyl diphosphate and dimethylallyl diphosphate. , 2004, Bioorganic chemistry.

[343]  Michael Bott,et al.  A high-throughput approach to identify genomic variants of bacterial metabolite producers at the single-cell level , 2012, Genome Biology.

[344]  Dong-Myung Kim,et al.  Applications of cell‐free protein synthesis in synthetic biology: Interfacing bio‐machinery with synthetic environments , 2013, Biotechnology journal.

[345]  M. Chang,et al.  Transporter engineering for improved tolerance against alkane biofuels in Saccharomyces cerevisiae , 2013, Biotechnology for Biofuels.

[346]  R. Larossa,et al.  Chromosomal promoter replacement of the isoprenoid pathway for enhancing carotenoid production in E. coli. , 2006, Metabolic engineering.

[347]  W. R. Farmer,et al.  Improving lycopene production in Escherichia coli by engineering metabolic control , 2000, Nature Biotechnology.

[348]  K. Shanmugam,et al.  Increase in Furfural Tolerance in Ethanologenic Escherichia coli LY180 by Plasmid-Based Expression of thyA , 2012, Applied and Environmental Microbiology.

[349]  Adam P Arkin,et al.  RNA processing enables predictable programming of gene expression , 2012, Nature Biotechnology.

[350]  Riccardo Zecchina,et al.  Entropy landscape and non-Gibbs solutions in constraint satisfaction problems , 2008, Physical review. E, Statistical, nonlinear, and soft matter physics.

[351]  Z. Lewis Liu,et al.  Biomass Conversion Inhibitors and In Situ Detoxification , 2010 .

[352]  J. Barredo,et al.  Xanthophyllomyces dendrorhous for the industrial production of astaxanthin , 2010, Applied Microbiology and Biotechnology.

[353]  R. Weiss,et al.  Programmed population control by cell–cell communication and regulated killing , 2004, Nature.

[354]  Emma Frow,et al.  Opening up the future(s) of synthetic biology , 2013 .

[355]  Chris J Myers,et al.  A methodology to annotate systems biology markup language models with the synthetic biology open language. , 2014, ACS synthetic biology.

[356]  Tom Ellis,et al.  One-pot DNA construction for synthetic biology: the Modular Overlap-Directed Assembly with Linkers (MODAL) strategy , 2013, Nucleic acids research.

[357]  Nir Friedman,et al.  Linking stochastic dynamics to population distribution: an analytical framework of gene expression. , 2006, Physical review letters.

[358]  Michael Z. Lin,et al.  Optobiology: optical control of biological processes via protein engineering. , 2013, Biochemical Society transactions.

[359]  Víctor de Lorenzo,et al.  Metabolic and regulatory rearrangements underlying glycerol metabolism in Pseudomonas putida KT2440. , 2014, Environmental microbiology.

[360]  J. Stelling,et al.  Computational design tools for synthetic biology. , 2009, Current opinion in biotechnology.

[361]  James H Naismith,et al.  An efficient one-step site-directed deletion, insertion, single and multiple-site plasmid mutagenesis protocol , 2008, BMC biotechnology.

[362]  Takayuki Kohchi,et al.  Plastid transformation of sporelings and suspension-cultured cells from the liverwort Marchantia polymorpha L. , 2014, Methods in molecular biology.

[363]  G. Lidén,et al.  NADH- vs NADPH-coupled reduction of 5-hydroxymethyl furfural (HMF) and its implications on product distribution in Saccharomyces cerevisiae , 2008, Applied Microbiology and Biotechnology.

[364]  E. Boles,et al.  Characterization of the xylose-transporting properties of yeast hexose transporters and their influence on xylose utilization. , 2002, Microbiology.

[365]  Verena Siewers,et al.  Engineering of chromosomal wax ester synthase integrated Saccharomyces cerevisiae mutants for improved biosynthesis of fatty acid ethyl esters , 2014, Biotechnology and bioengineering.

[366]  T. Jeffries.  Utilization of xylose by bacteria, yeasts, and fungi. , 1983, Advances in biochemical engineering/biotechnology.

[367]  S. Sauret-Güeto,et al.  Identification of lethal mutations in Escherichia coli genes encoding enzymes of the methylerythritol phosphate pathway. , 2003, Biochemical and biophysical research communications.

[368]  Hideki Kobayashi,et al.  Analysis and design of a genetic circuit for dynamic metabolic engineering. , 2013, ACS synthetic biology.

[369]  Dirk Stemerding,et al.  Challenges for the European governance of synthetic biology for human health , 2014, Life Sciences, Society and Policy.

[370]  Diego A. Oyarzún,et al.  Synthetic gene circuits for metabolic control: design trade-offs and constraints , 2013, Journal of The Royal Society Interface.

[371]  K. Shanmugam,et al.  Deletion of methylglyoxal synthase gene (mgsA) increased sugar co-metabolism in ethanol-producing Escherichia coli , 2009, Biotechnology Letters.

[372]  B. Hahn-Hägerdal,et al.  Identification of an NADH‐dependent 5‐hydroxymethylfurfural‐reducing alcohol dehydrogenase in Saccharomyces cerevisiae , 2008, Yeast.

[373]  Patrik R. Jones,et al.  Carboxylic acid reductase is a versatile enzyme for the conversion of fatty acids into fuels and chemical commodities , 2012, Proceedings of the National Academy of Sciences.

[374]  A. C. Chang,et al.  Construction of biologically functional bacterial plasmids in vitro. , 1973, Proceedings of the National Academy of Sciences of the United States of America.

[375]  Yajun Yan,et al.  Conversion of proteins into biofuels by engineering nitrogen flux , 2011, Nature Biotechnology.

[376]  H Sahm,et al.  Cloning, sequence analysis, expression, and inactivation of the Corynebacterium glutamicum icd gene encoding isocitrate dehydrogenase and biochemical characterization of the enzyme , 1995, Journal of bacteriology.

[377]  M. Tesar,et al.  Phylogeny and polyphasic taxonomy of Caulobacter species. Proposal of Maricaulis gen. nov. with Maricaulis maris (Poindexter) comb. nov. as the type species, and emended description of the genera Brevundimonas and Caulobacter. , 1999, International journal of systematic bacteriology.

[378]  Gemma L. Holliday,et al.  The structures and physicochemical properties of organic cofactors in biocatalysis. , 2010, Journal of molecular biology.

[379]  Priscilla E. M. Purnick,et al.  The second wave of synthetic biology: from modules to systems , 2009, Nature Reviews Molecular Cell Biology.

[380]  Jason T Stevens,et al.  Designing RNA-based genetic control systems for efficient production from engineered metabolic pathways. , 2015, ACS synthetic biology.

[381]  L. Eggeling,et al.  Handbook of Corynebacterium glutamicum , 2005 .

[382]  Alistair Elfick,et al.  PaperClip: rapid multi-part DNA assembly from existing libraries , 2014, Nucleic acids research.

[383]  Christopher M. MacDermaid,et al.  Theoretical and computational protein design. , 2011, Annual review of physical chemistry.

[384]  Matthias Köppe,et al.  SBROME: a scalable optimization and module matching framework for automated biosystems design. , 2013, ACS synthetic biology.

[385]  F. Neidhardt,et al.  Physiology of the bacterial cell : a molecular approach , 1990 .

[386]  P. Venkitasubramanian,et al.  Reduction of Carboxylic Acids by Nocardia Aldehyde Oxidoreductase Requires a Phosphopantetheinylated Enzyme* , 2007, Journal of Biological Chemistry.

[387]  H. Bujard,et al.  Promoters of Escherichia coli: a hierarchy of in vivo strength indicates alternate structures. , 1986, The EMBO journal.

[388]  R. Hill,et al.  The Biogenetic Anatomy of Vitamin B6 , 1996, The Journal of Biological Chemistry.

[389]  Klaus Winzer,et al.  Making 'sense' of metabolism: autoinducer-2, LUXS and pathogenic bacteria , 2005, Nature Reviews Microbiology.

[390]  James J. Collins,et al.  Using Targeted Chromatin Regulators to Engineer Combinatorial and Spatial Transcriptional Regulation , 2014, Cell.

[391]  Ron Weiss,et al.  Rapid, modular and reliable construction of complex mammalian gene circuits , 2013, Nucleic acids research.

[392]  Michael C. Jewett,et al.  Non-standard amino acid incorporation into proteins using Escherichia coli cell-free protein synthesis , 2014, Front. Chem..

[393]  Gregory Stephanopoulos,et al.  Combinatorial Engineering of 1-Deoxy-D-Xylulose 5-Phosphate Pathway Using Cross-Lapping In Vitro Assembly (CLIVA) Method , 2013, PloS one.

[394]  Michael Seibert,et al.  Discovery of Two Novel Radical S-Adenosylmethionine Proteins Required for the Assembly of an Active [Fe] Hydrogenase* , 2004, Journal of Biological Chemistry.

[395]  James C Liao,et al.  Direct photosynthetic recycling of carbon dioxide to isobutyraldehyde , 2009, Nature Biotechnology.

[396]  Fengwu Bai,et al.  High-density cultivation of oleaginous yeast Rhodosporidium toruloides Y4 in fed-batch culture , 2007 .

[397]  R. Milo,et al.  Promoters maintain their relative activity levels under different growth conditions , 2013, Molecular systems biology.

[398]  M. Penttilä,et al.  The role of xylulokinase in Saccharomyces cerevisiae xylulose catabolism. , 2000, FEMS microbiology letters.

[399]  Michele Forlin,et al.  Gene position more strongly influences cell-free protein expression from operons than T7 transcriptional promoter strength. , 2014, ACS synthetic biology.

[400]  Ralf Reski,et al.  A red light-controlled synthetic gene expression switch for plant systems. , 2014, Molecular bioSystems.

[401]  R. Fischer,et al.  Cellulases for biomass degradation: comparing recombinant cellulase expression platforms. , 2013, Trends in biotechnology.

[402]  I. Tirosh,et al.  Coupled Evolution of Transcription and mRNA Degradation , 2011, PLoS biology.

[403]  Gerald Jay Sussman,et al.  Cellular Gate Technology , 1998 .

[404]  M. Elowitz,et al.  A synthetic oscillatory network of transcriptional regulators , 2000, Nature.

[405]  Adam E. Hendry,et al.  Chemical genetics and drug discovery in Xenopus. , 2012, Methods in molecular biology.

[406]  T. W. Jeffries,et al.  Metabolic engineering for improved fermentation of pentoses by yeasts , 2004, Applied Microbiology and Biotechnology.

[407]  C. Johnson,et al.  A bioluminescence resonance energy transfer (BRET) system: application to interacting circadian clock proteins. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[408]  B. Hall,et al.  Expression of the Escherichia coli xylose isomerase gene in Saccharomyces cerevisiae , 1987, Applied and environmental microbiology.

[409]  Z Lewis Liu,et al.  Enhanced biotransformation of furfural and hydroxymethylfurfural by newly developed ethanologenic yeast strains. , 2005, Applied biochemistry and biotechnology.

[410]  M. Sedlák,et al.  Characterization of the effectiveness of hexose transporters for transporting xylose during glucose and xylose co‐fermentation by a recombinant Saccharomyces yeast , 2004, Yeast.

[411]  Jameson K. Rogers,et al.  Evolution-guided optimization of biosynthetic pathways , 2014, Proceedings of the National Academy of Sciences.

[412]  Gerald A Tuskan,et al.  Synthetic biology as it relates to CAM photosynthesis: challenges and opportunities. , 2014, Journal of experimental botany.

[413]  P. Slininger,et al.  Multiple gene-mediated NAD(P)H-dependent aldehyde reduction is a mechanism of in situ detoxification of furfural and 5-hydroxymethylfurfural by Saccharomyces cerevisiae , 2008, Applied Microbiology and Biotechnology.

[414]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[415]  Jörg Stelling,et al.  Automatic Design of Digital Synthetic Gene Circuits , 2011, PLoS Comput. Biol..

[416]  S. Lee,et al.  Production of poly(3-hydroxybutyrate) by fed-batch culture of filamentation-suppressed recombinant Escherichia coli , 1997, Applied and environmental microbiology.

[417]  Gunnar Lidén,et al.  Metabolic effects of furaldehydes and impacts on biotechnological processes , 2009, Applied Microbiology and Biotechnology.

[418]  K. Shanmugam,et al.  Increased Furan Tolerance in Escherichia coli Due to a Cryptic ucpA Gene , 2012, Applied and Environmental Microbiology.

[419]  Y. Choi,et al.  Microbial production of short-chain alkanes , 2013, Nature.

[420]  Farren J. Isaacs,et al.  Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement , 2011, Science.

[421]  L. Jarboe,et al.  Development of ethanologenic bacteria. , 2007, Advances in biochemical engineering/biotechnology.

[422]  K. Shanmugam,et al.  Seed train development for the fermentation of bagasse from sweet sorghum and sugarcane using a simplified fermentation process. , 2013, Bioresource technology.

[423]  B. Ahmer,et al.  SdiA of Salmonella enterica Is a LuxR Homolog That Detects Mixed Microbial Communities , 2001, Journal of bacteriology.

[424]  Pernilla Wittung-Stafshede,et al.  Role of metal in folding and stability of copper proteins in vitro. , 2012, Biochimica et biophysica acta.

[425]  T. G. Villa,et al.  Oily yeasts as oleaginous cell factories , 2011, Applied Microbiology and Biotechnology.

[426]  Nick Wierckx,et al.  Identification and characterization of the furfural and 5-(hydroxymethyl)furfural degradation pathways of Cupriavidus basilensis HMF14 , 2010, Proceedings of the National Academy of Sciences.

[427]  R R Breaker,et al.  Rational design of allosteric ribozymes. , 1997, Chemistry & biology.

[428]  Eric A. Althoff,et al.  Kemp elimination catalysts by computational enzyme design , 2008, Nature.

[429]  Dong-Yup Lee,et al.  Computational codon optimization of synthetic gene for protein expression , 2012, BMC Systems Biology.

[430]  Matthias Heinemann,et al.  Synthetic biology - putting engineering into biology , 2006, Bioinform..

[431]  Paul S. Freemont,et al.  Validation of an entirely in vitro approach for rapid prototyping of DNA regulatory elements for synthetic biology , 2013, Nucleic acids research.

[432]  Gerd H. G. Moe-Behrens,et al.  Preparing synthetic biology for the world , 2013, Front. Microbio..

[433]  Vivek K. Mutalik,et al.  Predicting the strength of UP-elements and full-length E. coli σE promoters , 2011, Nucleic acids research.

[434]  D. Baker,et al.  Computational Design of Self-Assembling Protein Nanomaterials with Atomic Level Accuracy , 2012, Science.

[435]  B. M. Lange,et al.  Isoprenoid biosynthesis: the evolution of two ancient and distinct pathways across genomes. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[436]  P M Bramley,et al.  Expression of prokaryotic 1‐deoxy‐d‐xylulose‐5‐phosphatases in Escherichia coli increases carotenoid and ubiquinone biosynthesis , 1999, FEBS letters.

[437]  M. Jewett,et al.  Optimized extract preparation methods and reaction conditions for improved yeast cell‐free protein synthesis , 2013, Biotechnology and bioengineering.

[438]  G. Spiegelman,et al.  The GtaR protein negatively regulates transcription of the gtaRI operon and modulates gene transfer agent (RcGTA) expression in Rhodobacter capsulatus , 2012, Molecular microbiology.

[439]  L. Lynd,et al.  Metabolic engineering of Thermoanaerobacterium saccharolyticum for n-butanol production. , 2014, Metabolic engineering.

[440]  P. Rothemund.  Folding DNA to create nanoscale shapes and patterns , 2006, Nature.

[441]  J. Sambrook,et al.  Molecular Cloning: A Laboratory Manual , 2001 .

[442]  K. Timmis,et al.  Specific-purpose plasmid cloning vectors. II. Broad host range, high copy number, RSF1010-derived vectors, and a host-vector system for gene cloning in Pseudomonas. , 1981, Gene.

[443]  R. Weiss,et al.  CRISPR transcriptional repression devices and layered circuits in mammalian cells , 2014, Nature Methods.

[444]  Bonnie L Bassler,et al.  A strategy for antagonizing quorum sensing. , 2011, Molecular cell.

[445]  Robert M. Dirks,et al.  Selective cell death mediated by small conditional RNAs , 2010, Proceedings of the National Academy of Sciences.

[446]  K. Murphy,et al.  Use of Bacteriophage λ Recombination Functions To Promote Gene Replacement in Escherichia coli , 1998, Journal of bacteriology.

[447]  Namita Bhan,et al.  Engineering plant metabolism into microbes: from systems biology to synthetic biology. , 2013, Current opinion in biotechnology.

[448]  T. Hwa,et al.  Sequential Establishment of Stripe Patterns in an Expanding Cell Population , 2011, Science.

[449]  Jay D Keasling,et al.  BglBricks: A flexible standard for biological part assembly , 2010, Journal of biological engineering.

[450]  O. White,et al.  Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. , 2002, Environmental microbiology.

[451]  G Zacchi,et al.  Optimizing the saccharification of sugar cane bagasse using dilute phosphoric acid followed by fungal cellulases. , 2010, Bioresource technology.

[452]  Yin Li,et al.  Engineering Saccharomyces cerevisiae for efficient anaerobic xylose fermentation: Reflections and perspectives , 2012, Biotechnology journal.

[453]  V. Wendisch,et al.  Production of the sesquiterpene (+)-valencene by metabolically engineered Corynebacterium glutamicum. , 2014, Journal of biotechnology.

[454]  Dong-Yup Lee,et al.  Codon Optimization OnLine (COOL): a web-based multi-objective optimization platform for synthetic gene design , 2014, Bioinform..

[455]  C. Hollenberg,et al.  Cloning and characterization of three genes (SUT1–3 ) encoding glucose transporters of the yeast Pichia stipitis , 1999, Molecular microbiology.

[456]  Jo Maertens,et al.  Construction and model-based analysis of a promoter library for E. coli: an indispensable tool for metabolic engineering , 2007, BMC biotechnology.

[457]  J. Shear,et al.  3D printing of microscopic bacterial communities , 2013, Proceedings of the National Academy of Sciences.

[458]  W. Reznikoff,et al.  Molecular genetic analysis of transposase-end DNA sequence recognition: cooperativity of three adjacent base-pairs in specific interaction with a mutant Tn5 transposase. , 1998, Journal of molecular biology.

[459]  J. Keasling,et al.  Metabolic engineering of Saccharomyces cerevisiae for production of fatty acid-derived biofuels and chemicals. , 2014, Metabolic engineering.

[460]  Q. Qi,et al.  The production of polyhydroxyalkanoates in recombinant Escherichia coli. , 2007, Bioresource technology.

[461]  C. Ratledge.  Yeasts, moulds, algae and bacteria as sources of lipids , 1994 .

[462]  J. Szostak,et al.  In vitro selection of RNA molecules that bind specific ligands , 1990, Nature.

[463]  K. Aronsson,et al.  Influence of pH, water activity and temperature on the inactivation of Escherichia coli and Saccharomyces cerevisiae by pulsed electric fields , 2001 .

[464]  W. Eisenreich,et al.  IspH protein of Escherichia coli: studies on iron-sulfur cluster implementation and catalysis. , 2004, Journal of the American Chemical Society.

[465]  Matias D Zurbriggen,et al.  Control of gene expression using a red- and far-red light–responsive bi-stable toggle switch , 2014, Nature Protocols.

[466]  W. Eisenreich,et al.  Studies on the nonmevalonate terpene biosynthetic pathway: Metabolic role of IspH (LytB) protein , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[467]  P. Bernstein,et al.  Microbial xanthophylls , 2005, Applied Microbiology and Biotechnology.

[468]  Menake E Piyasena,et al.  The intersection of flow cytometry with microfluidics and microfabrication. , 2014, Lab on a chip.

[469]  R T Lorenz,et al.  Commercial potential for Haematococcus microalgae as a natural source of astaxanthin. , 2000, Trends in biotechnology.

[470]  John Buckingham,et al.  Biotechnological production of astaxanthin with Phaffia rhodozyma/Xanthophyllomyces dendrorhous , 2011, Applied Microbiology and Biotechnology.

[471]  Christopher Bystroff,et al.  Directed evolution of the quorum-sensing regulator EsaR for increased signal sensitivity. , 2013, ACS chemical biology.

[472]  E. Papoutsakis,et al.  Flow cytometry for bacteria: enabling metabolic engineering, synthetic biology and the elucidation of complex phenotypes. , 2010, Current opinion in biotechnology.

[473]  Rafael Artuch,et al.  Tetrahydrobiopterin responsiveness in patients with phenylketonuria. , 2004, Clinical biochemistry.

[474]  Pablo Carbonell,et al.  Validation of RetroPath, a computer-aided design tool for metabolic pathway engineering. , 2014, Biotechnology journal.

[475]  Kyoung-Rok Kim,et al.  Production of hydroxy fatty acids by microbial fatty acid-hydroxylation enzymes. , 2013, Biotechnology advances.

[476]  Luke A. Gilbert,et al.  Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression , 2013, Cell.

[477]  J. Keasling,et al.  High-throughput metabolic engineering: advances in small-molecule screening and selection. , 2010, Annual review of biochemistry.

[478]  Tiangang Liu,et al.  In vitro reconstitution of mevalonate pathway and targeted engineering of farnesene overproduction in Escherichia coli , 2014, Biotechnology and bioengineering.

[479]  K. Timmis,et al.  A general system to integratelacZ fusions into the chromosomes of gram-negative eubacteria: regulation of thePm promoter of theTOL plasmid studied with all controlling elements in monocopy , 1992, Molecular and General Genetics MGG.

[480]  Hal S Alper,et al.  Rewiring yeast sugar transporter preference through modifying a conserved protein motif , 2013, Proceedings of the National Academy of Sciences.

[481]  Linda Thöny-Meyer,et al.  Heme Transport and Incorporation into Proteins , 2009 .

[482]  Feng Zhang,et al.  Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system , 2013, Nucleic acids research.

[483]  Huaiyu Mi,et al.  The InterPro protein families database: the classification resource after 15 years , 2014, Nucleic Acids Res..

[484]  M. Schülein.  Protein engineering of cellulases. , 2000, Biochimica et biophysica acta.

[485]  Fred J Sigworth,et al.  Synthetic Protocells to Mimic and Test Cell Function , 2010, Advanced materials.

[486]  C. Blanchet,et al.  Cofactor effects on the protein folding reaction: Acceleration of α‐lactalbumin refolding by metal ions , 2006, Protein science : a publication of the Protein Society.

[487]  Z. L. Liu,et al.  Comparative transcriptome profiling analyses during the lag phase uncover YAP1, PDR1, PDR3, RPN4, and HSF1 as key regulatory genes in genomic adaptation to the lignocellulose derived inhibitor HMF for Saccharomyces cerevisiae , 2010, BMC Genomics.

[488]  Allan Kuchinsky,et al.  The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology , 2014, Nature Biotechnology.

[489]  L. Ingram,et al.  Effect of selected aldehydes on the growth and fermentation of ethanologenic Escherichia coli. , 1999, Biotechnology and bioengineering.

[490]  V. Wendisch,et al.  Amino acid production from rice straw and wheat bran hydrolysates by recombinant pentose-utilizing Corynebacterium glutamicum , 2011, Applied Microbiology and Biotechnology.

[491]  Emma M. B. Weeding,et al.  Eugene – A Domain Specific Language for Specifying and Constraining Synthetic Biological Parts, Devices, and Systems , 2011, PloS one.

[492]  Marianne Schark,et al.  Synthetic Biology and the Distinction between Organisms and Machines , 2012 .

[493]  Nikos Kyrpides,et al.  Engineering Escherichia coli for Biodiesel Production Utilizing a Bacterial Fatty Acid Methyltransferase , 2011, Applied and Environmental Microbiology.

[494]  Helen E Blackwell,et al.  Isovaleryl-homoserine lactone, an unusual branched-chain quorum-sensing signal from the soybean symbiont Bradyrhizobium japonicum , 2011, Proceedings of the National Academy of Sciences.

[495]  E. P. Greenberg,et al.  Quorum Sensing in Vibrio fischeri: Analysis of the LuxR DNA Binding Region by Alanine-Scanning Mutagenesis , 2001, Journal of bacteriology.

[496]  Claire Marris,et al.  Synthetic Biology and Biosecurity: Challenging the “Myths” , 2014, Front. Public Health.

[497]  Hui Wu,et al.  The transport and mediation mechanisms of the common sugars in Escherichia coli. , 2014, Biotechnology advances.

[498]  Sylvestre Marillonnet,et al.  Combinatorial DNA assembly using Golden Gate cloning. , 2013, Methods in molecular biology.

[499]  Christopher A. Voigt,et al.  Environmentally controlled invasion of cancer cells by engineered bacteria. , 2006, Journal of molecular biology.

[500]  Meagan E. Sullender,et al.  Rational design of highly active sgRNAs for CRISPR-Cas9–mediated gene inactivation , 2014, Nature Biotechnology.

[501]  Peter C. Cheeseman,et al.  Where the Really Hard Problems Are , 1991, IJCAI.

[502]  John C. Anderson,et al.  Structure of a bacterial quorum-sensing transcription factor complexed with pheromone and DNA , 2002, Nature.

[503]  Vincent Noireaux,et al.  Synthesis of 2.3 mg/ml of protein with an all Escherichia coli cell-free transcription-translation system. , 2014, Biochimie.

[504]  Volker Sieber,et al.  Cell-free metabolic engineering: production of chemicals by minimized reaction cascades. , 2012, ChemSusChem.

[505]  K. Puan,et al.  fldA is an essential gene required in the 2‐C‐methyl‐D‐erythritol 4‐phosphate pathway for isoprenoid biosynthesis , 2005, FEBS letters.

[506]  L. Eggeling,et al.  Citrate synthase in Corynebacterium glutamicum is encoded by two gltA transcripts which are controlled by RamA, RamB, and GlxR. , 2011, Journal of biotechnology.

[507]  Carlos Bustamante,et al.  Introduction to single molecule imaging and mechanics: seeing and touching molecules one at a time. , 2014, Chemical reviews.

[508]  Víctor de Lorenzo,et al.  The Standard European Vector Architecture (SEVA) plasmid toolkit. , 2014, Methods in molecular biology.

[509]  Daniel P. Mulvihill,et al.  Solution structure of a bacterial microcompartment targeting peptide and its application in the construction of an ethanol bioreactor. , 2014, ACS synthetic biology.

[510]  Weihong Tan,et al.  In vitro selection with artificial expanded genetic information systems , 2013, Proceedings of the National Academy of Sciences.

[511]  S. Noack,et al.  Construction of a Prophage-Free Variant of Corynebacterium glutamicum ATCC 13032 for Use as a Platform Strain for Basic Research and Industrial Biotechnology , 2013, Applied and Environmental Microbiology.

[512]  Tyler J. Ford,et al.  Tailored fatty acid synthesis via dynamic control of fatty acid elongation , 2013, Proceedings of the National Academy of Sciences.

[513]  D. Endy,et al.  Refinement and standardization of synthetic biological parts and devices , 2008, Nature Biotechnology.

[514]  Yang Song,et al.  All-aqueous multiphase microfluidics. , 2013, Biomicrofluidics.

[515]  Erin L. Doyle,et al.  Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting , 2011, Nucleic acids research.

[516]  J. Sinclair,et al.  Generation of protein lattices by fusing proteins with matching rotational symmetry. , 2011, Nature nanotechnology.

[517]  A. Schirmer,et al.  Microbial Biosynthesis of Alkanes , 2010, Science.

[518]  Y. Chao,et al.  Systematic approach to engineer Escherichia coli pathways for co-utilization of a glucose-xylose mixture. , 2013, Journal of agricultural and food chemistry.

[519]  D. Roop,et al.  Four new derivatives of the broad-host-range cloning vector pBBR1MCS, carrying different antibiotic-resistance cassettes. , 1995, Gene.

[520]  Jacob Beal,et al.  Accurate predictions of genetic circuit behavior from part characterization and modular composition. , 2015, ACS synthetic biology.

[521]  James M Clomburg,et al.  Biofuel production in Escherichia coli: the role of metabolic engineering and synthetic biology , 2010, Applied Microbiology and Biotechnology.

[522]  Woonghee Lee,et al.  Gene2Oligo: oligonucleotide design for in vitro gene synthesis , 2004, Nucleic Acids Res..

[523]  Ana Rute Neves,et al.  Novel biosensors based on flavonoid-responsive transcriptional regulators introduced into Escherichia coli. , 2014, Metabolic engineering.

[524]  V. de Lorenzo.  From the selfish gene to selfish metabolism: revisiting the central dogma. , 2014, BioEssays : news and reviews in molecular, cellular and developmental biology.

[525]  Huimin Zhao,et al.  Utilizing an endogenous pathway for 1-butanol production in Saccharomyces cerevisiae. , 2014, Metabolic engineering.

[526]  Doheon Lee,et al.  Bioinformatics Applications Note Gene Expression Rbsdesigner: Software for Designing Synthetic Ribosome Binding Sites That Yields a Desired Level of Protein Expression , 2022 .

[527]  Tim Liedl,et al.  Nanoengineered polymer capsules: tools for detection, controlled delivery, and site-specific manipulation. , 2005, Small.

[528]  Raymond Lo,et al.  Pseudomonas Genome Database: improved comparative analysis and population genomics capability for Pseudomonas genomes , 2010, Nucleic Acids Res..

[529]  Joseph H. Davis,et al.  Design, construction and characterization of a set of insulated bacterial promoters , 2010, Nucleic acids research.

[530]  Jacob Beal,et al.  Bioengineering and Biotechnology Review Article Bridging the Gap: a Roadmap to Breaking the Biological Design Barrier , 2022 .

[531]  David Baker,et al.  Accurate design of co-assembling multi-component protein nanomaterials , 2014, Nature.

[532]  Pernilla Wittung-Stafshede,et al.  Role of cofactors in protein folding. , 2002, Accounts of chemical research.

[533]  Edgard Gnansounou,et al.  Cyanobacteria and microalgae: a positive prospect for biofuels. , 2011, Bioresource technology.

[534]  B. Hahn-Hägerdal,et al.  Putative xylose and arabinose reductases in Saccharomyces cerevisiae , 2002, Yeast.

[535]  M. Gellert,et al.  Enzymatic joining of DNA strands: a novel reaction of diphosphopyridine nucleotide. , 1967, Proceedings of the National Academy of Sciences of the United States of America.

[536]  Jens Meiler,et al.  ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. , 2011, Methods in enzymology.

[537]  Luis A. García,et al.  Application of flow cytometry to industrial microbial bioprocesses , 2010 .

[538]  Hao Yan,et al.  Interenzyme substrate diffusion for an enzyme cascade organized on spatially addressable DNA nanostructures. , 2012, Journal of the American Chemical Society.

[539]  A. Hurlburt,et al.  Escherichia coli Open Reading Frame 696 Is idi, a Nonessential Gene Encoding Isopentenyl Diphosphate Isomerase , 1999, Journal of bacteriology.

[540]  Mitsuhiro Itaya,et al.  Rearrangement of Gene Order in the phaCAB Operon Leads to Effective Production of Ultrahigh-Molecular-Weight Poly[(R)-3-Hydroxybutyrate] in Genetically Engineered Escherichia coli , 2012, Applied and Environmental Microbiology.

[541]  Niles A. Pierce,et al.  Nucleic acid sequence design via efficient ensemble defect optimization , 2011, J. Comput. Chem..

[542]  S. Kinoshita,et al.  TAXONOMICAL STUDIES ON GLUTAMIC ACID-PRODUCING BACTERIA , 1967 .

[543]  Neha P Kamat,et al.  Towards an artificial cell , 2012, FEBS letters.

[544]  J. Cronan,et al.  Overproduction of Acetyl-CoA Carboxylase Activity Increases the Rate of Fatty Acid Biosynthesis in Escherichia coli * , 2000, The Journal of Biological Chemistry.

[545]  Jack T Pronk,et al.  High-level functional expression of a fungal xylose isomerase: the key to efficient ethanolic fermentation of xylose by Saccharomyces cerevisiae? , 2003, FEMS yeast research.

[546]  B. Dien,et al.  Tolerance to furfural-induced stress is associated with pentose phosphate pathway genes ZWF1, GND1, RPE1, and TKL1 in Saccharomyces cerevisiae , 2006, Applied Microbiology and Biotechnology.

[547]  J. Nicaud,et al.  Hydrophobic substrate utilisation by the yeast Yarrowia lipolytica, and its potential applications. , 2005, FEMS yeast research.

[548]  J. Nielsen,et al.  Metabolic engineering of Saccharomyces cerevisiae for production of fatty acid ethyl esters, an advanced biofuel, by eliminating non-essential fatty acid utilization pathways , 2014 .

[549]  J. Collins,et al.  A brief history of synthetic biology , 2014, Nature Reviews Microbiology.

[550]  N. Misawa,et al.  Expression of an exogenous isopentenyl diphosphate isomerase gene enhances isoprenoid biosynthesis in Escherichia coli. , 1997, The Biochemical journal.

[551]  M. Reth,et al.  Drosophila S2 Schneider cells: a useful tool for rebuilding and redesigning approaches in synthetic biology. , 2012, Methods in molecular biology.

[552]  Jay D. Keasling,et al.  Identification and microbial production of a terpene-based advanced biofuel , 2011, Nature communications.

[553]  Andreas S Bommarius,et al.  Status of protein engineering for biocatalysts: how to design an industrially useful biocatalyst. , 2011, Current opinion in chemical biology.

[554]  V. Noireaux,et al.  An E. coli cell-free expression toolbox: application to synthetic gene circuits and artificial cells. , 2012, ACS synthetic biology.

[555]  W. Edelmann,et al.  SLiCE: a novel bacterial cell extract-based DNA cloning method , 2012, Nucleic acids research.

[556]  Fuzhong Zhang,et al.  Negative feedback regulation of fatty acid production based on a malonyl-CoA sensor-actuator. , 2015, ACS synthetic biology.

[557]  B. Saha,et al.  Hemicellulose bioconversion , 2003, Journal of Industrial Microbiology and Biotechnology.

[558]  Tomohisa Hasunuma,et al.  A review of enzymes and microbes for lignocellulosic biorefinery and the possibility of their application to consolidated bioprocessing technology. , 2013, Bioresource technology.

[559]  Laura R. Jarboe,et al.  Furfural Inhibits Growth by Limiting Sulfur Assimilation in Ethanologenic Escherichia coli Strain LY180 , 2009, Applied and Environmental Microbiology.

[560]  Jens Nielsen,et al.  Identification and treatment of heme depletion attributed to overexpression of a lineage of evolved P450 monooxygenases , 2012, Proceedings of the National Academy of Sciences.

[561]  Dieter Jahn,et al.  Structure and function of enzymes in heme biosynthesis , 2010, Protein science : a publication of the Protein Society.

[562]  P Leslie Dutton,et al.  Engineering enzymes. , 2011, Faraday discussions.

[563]  Min Zhang,et al.  Genome-Wide Mapping of Furfural Tolerance Genes in Escherichia coli , 2014, PloS one.

[564]  Stefan Bruder,et al.  Engineering of yeast hexose transporters to transport d-xylose without inhibition by d-glucose , 2014, Proceedings of the National Academy of Sciences.

[565]  Anthony G. Wedd,et al.  Parallel In Vivo DNA Assembly by Recombination: Experimental Demonstration and Theoretical Approaches , 2013, PloS one.

[566]  Maria Almira Correia,et al.  Cytochrome P450 regulation: the interplay between its heme* and apoprotein moieties in synthesis, assembly, repair, and disposal , 2011, Drug metabolism reviews.

[567]  J. Andreesen,et al.  Xanthine dehydrogenase and 2-furoyl-coenzyme A dehydrogenase from Pseudomonas putida Fu1: two molybdenum-containing dehydrogenases of novel structural composition , 1990, Journal of bacteriology.

[568]  Beth Preston,et al.  Synthetic biology as red herring. , 2013, Studies in history and philosophy of biological and biomedical sciences.

[569]  J. Liao,et al.  Driving Forces Enable High-Titer Anaerobic 1-Butanol Synthesis in Escherichia coli , 2011, Applied and Environmental Microbiology.

[570]  F. Rosso,et al.  From crude glycerol to carotenoids by using a Rhodotorula glutinis mutant , 2013, World Journal of Microbiology and Biotechnology.

[571]  Jingwen Zhou,et al.  Stepwise metabolic engineering of Gluconobacter oxydans WSH-003 for the direct production of 2-keto-L-gulonic acid from D-sorbitol. , 2014, Metabolic engineering.

[572]  Jürgen Kurths,et al.  Timing Cellular Decision Making Under Noise via Cell–Cell Communication , 2009, PloS one.

[573]  Ryan Tappel,et al.  Development of a New Strategy for Production of Medium-Chain-Length Polyhydroxyalkanoates by Recombinant Escherichia coli via Inexpensive Non-Fatty Acid Feedstocks , 2011, Applied and Environmental Microbiology.

[574]  Adam M. Feist,et al.  Reconstruction of biochemical networks in microorganisms , 2009, Nature Reviews Microbiology.

[575]  B. Hahn-Hägerdal,et al.  Ethanolic fermentation of xylose with Saccharomyces cerevisiae harboring the Thermus thermophilus xylA gene, which expresses an active xylose (glucose) isomerase , 1996, Applied and environmental microbiology.

[576]  Masaru Tomita,et al.  Serial assembly of Thermus megaplasmid DNA in the genome of Bacillus subtilis 168: a BAC-based domino method applied to DNA with a high GC content. , 2012, Biotechnology journal.

[577]  F. Ceroni,et al.  The spinach RNA aptamer as a characterization tool for synthetic biology. , 2014, ACS synthetic biology.

[578]  V. de Lorenzo,et al.  Mini-Tn5 transposon derivatives for insertion mutagenesis, promoter probing, and chromosomal insertion of cloned DNA in gram-negative eubacteria , 1990, Journal of bacteriology.

[579]  J. Keasling.  Synthetic biology for synthetic chemistry. , 2008, ACS chemical biology.

[580]  H. Lichtenthaler,et al.  Inhibitors of the nonmevalonate pathway of isoprenoid biosynthesis as antimalarial drugs. , 1999, Science.

[581]  T. Kitten,et al.  An improved arbitrary primed PCR method for rapid characterization of transposon insertion sites. , 2005, Journal of microbiological methods.

[582]  J. Bao,et al.  Analysis of biodegradation performance of furfural and 5-hydroxymethylfurfural by Amorphotheca resinae ZN1 , 2014, Biotechnology for Biofuels.

[583]  Xuefeng Lu,et al.  De novo Biosynthesis of Biodiesel by Escherichia coli in Optimized Fed-Batch Cultivation , 2011, PloS one.

[584]  A. D. Kaiser,et al.  Enzymatic end-to end joining of DNA molecules. , 1973, Journal of molecular biology.

[585]  Michael L Shuler,et al.  Modeling a minimal cell. , 2012, Methods in molecular biology.

[586]  Toshiomi Yoshida,et al.  Genetic Improvement of Saccharomyces cerevisiae for Ethanol Production from Xylosea , 1994, Annals of the New York Academy of Sciences.

[587]  Rob Lee,et al.  Synthesis of customized petroleum-replica fuel molecules by targeted modification of free fatty acid pools in Escherichia coli , 2013, Proceedings of the National Academy of Sciences.

[588]  Anders S Hansen,et al.  Promoter decoding of transcription factor dynamics involves a trade-off between noise and control of gene expression , 2013 .

[589]  Ahmad S. Khalil,et al.  A Synthetic Biology Framework for Programming Eukaryotic Transcription Functions , 2012, Cell.

[590]  W. Miki,et al.  Biological functions and activities of animal carotenoids , 1991 .

[591]  Marc Weber,et al.  Dynamics of the quorum sensing switch: stochastic and non-stationary effects , 2013, BMC Systems Biology.

[592]  Joe C. Liang,et al.  Engineering biological systems with synthetic RNA molecules. , 2011, Molecular cell.

[593]  Harris H. Wang,et al.  MODEST: a web-based design tool for oligonucleotide-mediated genome engineering and recombineering , 2014, Nucleic Acids Res..

[594]  Ron Weiss,et al.  Engineered bidirectional communication mediates a consensus in a microbial biofilm consortium , 2007, Proceedings of the National Academy of Sciences.

[595]  Hyo-Jick Choi,et al.  Artificial organelle: ATP synthesis from cellular mimetic polymersomes. , 2005, Nano letters.

[596]  R. Kolter,et al.  Trans-complementation-dependent replication of a low molecular weight origin fragment from plasmid R6K , 1978, Cell.

[597]  L. Gustafsson,et al.  Physiological effects of 5-hydroxymethylfurfural on Saccharomyces cerevisiae , 2000, Applied Microbiology and Biotechnology.

[598]  Melissa M. Harrison,et al.  A CRISPR view of development , 2014, Genes & development.

[599]  Pamela A. Silver,et al.  Engineering synthetic TAL effectors with orthogonal target sites , 2012, Nucleic acids research.

[600]  Mat E. Barnet,et al.  A synthetic Escherichia coli predator–prey ecosystem , 2008, Molecular systems biology.

[601]  Y. Waché.  Production of Dicarboxylic Acids and Flagrances by Yarrowia lipolytica , 2013 .

[602]  D. Baker,et al.  Principles for designing ideal protein structures , 2012, Nature.

[603]  H. Mori,et al.  Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection , 2006, Molecular systems biology.

[604]  J. Parajó,et al.  Improved astaxanthin production by Xanthophyllomyces dendrorhous growing on enzymatic wood hydrolysates containing glucose and cellobiose , 1998 .

[605]  Seung-Pyo Hong,et al.  Production of omega-3 eicosapentaenoic acid by metabolic engineering of Yarrowia lipolytica , 2013, Nature Biotechnology.

[606]  Juhyun Kim,et al.  The Standard European Vector Architecture (SEVA): a coherent platform for the analysis and deployment of complex prokaryotic phenotypes , 2012, Nucleic Acids Res..

[607]  Jeffrey W. Smith,et al.  Stochastic Gene Expression in a Single Cell , .

[608]  P. Nikel,et al.  Two-component System Crebc Are Supplemental Material , 2008 .

[609]  Min Lin,et al.  Global regulator engineering significantly improved Escherichia coli tolerances toward inhibitors of lignocellulosic hydrolysates , 2012, Biotechnology and bioengineering.

[610]  M. M. Bradford.  A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. , 1976, Analytical biochemistry.

[611]  L. Ingram,et al.  Advances in ethanol production. , 2011, Current opinion in biotechnology.

[612]  R. Guthke,et al.  High-cell-density cultivation of microorganisms , 1999, Applied Microbiology and Biotechnology.

[613]  Jennifer E. Padilla,et al.  Nanohedra: Using symmetry to design self assembling protein cages, layers, crystals, and filaments , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[614]  L. Banaszynski,et al.  A Rapid, Reversible, and Tunable Method to Regulate Protein Function in Living Cells Using Synthetic Small Molecules , 2006, Cell.

[615]  Robert Verpoorte,et al.  Zebrafish as a model for systems biology , 2013, Biotechnology & genetic engineering reviews.

[616]  K N Houk,et al.  Theozymes and compuzymes: theoretical models for biological catalysis. , 1998, Current opinion in chemical biology.

[617]  Le Cong,et al.  Multiplex Genome Engineering Using CRISPR/Cas Systems , 2013, Science.

[618]  Jeroen S. Dickschat,et al.  Quorum sensing and bacterial biofilms. , 2010, Natural product reports.

[619]  A Martinez,et al.  Effect of alcohol compounds found in hemicellulose hydrolysate on the growth and fermentation of ethanologenic Escherichia coli , 2000, Biotechnology and bioengineering.

[620]  Y. Usuda,et al.  Identification of succinate exporter in Corynebacterium glutamicum and its physiological roles under anaerobic conditions. , 2011, Journal of biotechnology.

[621]  Georg Fritz,et al.  The Bacillus BioBrick Box: generation and evaluation of essential genetic building blocks for standardized work with Bacillus subtilis , 2013, Journal of Biological Engineering.

[622]  D. Molenaar,et al.  A heat shock following electroporation induces highly efficient transformation of Corynebacterium glutamicum with xenogeneic plasmid DNA , 1999, Applied Microbiology and Biotechnology.

[623]  S. Papanikolaou,et al.  Control of Lipid Accumulation in the Yeast Yarrowia lipolytica , 2008, Applied and Environmental Microbiology.

[624]  J. Keasling,et al.  Rapid metabolic pathway assembly and modification using serine integrase site-specific recombination , 2013, Nucleic acids research.

[625]  R. Breaker,et al.  The structural and functional diversity of metabolite-binding riboswitches. , 2009, Annual review of biochemistry.

[626]  Cormac Sheridan.  Big oil turns on biofuels , 2013, Nature Biotechnology.

[627]  T. Maoka,et al.  Detailed biosynthetic pathway to decaprenoxanthin diglucoside in Corynebacterium glutamicum and identification of novel intermediates , 2001, Archives of Microbiology.

[628]  C Toumazou,et al.  Selective hydrophilic modification of Parylene C films: a new approach to cell micro-patterning for synthetic biology applications , 2014, Biofabrication.

[629]  C. Nakatsu,et al.  Phylogenetically Novel LuxI/LuxR-Type Quorum Sensing Systems Isolated Using a Metagenomic Approach , 2012, Applied and Environmental Microbiology.

[630]  Farren J. Isaacs,et al.  Programming cells by multiplex genome engineering and accelerated evolution , 2009, Nature.

[631]  P. Nikel,et al.  Metabolic selective pressure stabilizes plasmids carrying biosynthetic genes for reduced biochemicals in Escherichia coli redox mutants , 2010, Applied Microbiology and Biotechnology.

[632]  Bruce E Dale,et al.  'Cradle-to-grave' assessment of existing lignocellulose pretreatment technologies. , 2009, Current opinion in biotechnology.

[633]  Goksel Misirli,et al.  Standard virtual biological parts: a repository of modular modeling components for synthetic biology , 2010, Bioinform..

[634]  Gregory Stephanopoulos,et al.  Synthetic biology and metabolic engineering. , 2012, ACS synthetic biology.

[635]  Chris J. Myers,et al.  Tablet—next generation sequence assembly visualization , 2009, Bioinform..

[636]  S. Howorka.  Rationally engineering natural protein assemblies in nanobiotechnology. , 2011, Current opinion in biotechnology.

[637]  David R. Liu,et al.  A System for the Continuous Directed Evolution of Biomolecules , 2011, Nature.

[638]  Andrew D Ellington,et al.  Design and selection of a synthetic operon. , 2014, ACS synthetic biology.

[639]  Stephen R. Hughes,et al.  Expression of a heterologous xylose transporter in a Saccharomyces cerevisiae strain engineered to utilize xylose improves aerobic xylose consumption , 2008, Applied Microbiology and Biotechnology.

[640]  Kumaran Narayanan,et al.  Bacterial Artificial Chromosome Mutagenesis Using Recombineering , 2010, Journal of biomedicine & biotechnology.

[641]  Julio Collado-Vides,et al.  RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units) , 2010, Nucleic Acids Res..

[642]  Florent Krzakala,et al.  A Landscape Analysis of Constraint Satisfaction Problems , 2007, Physical review. E, Statistical, nonlinear, and soft matter physics.

[643]  P. Postma,et al.  Escherichia coli is unable to produce pyrroloquinoline quinone (PQQ). , 1997, Microbiology.

[644]  Kristala L J Prather,et al.  Controlled biosynthesis of odd-chain fuels and chemicals via engineered modular metabolic pathways , 2012, Proceedings of the National Academy of Sciences.

[645]  U. Sauer,et al.  Fermentation performance of engineered and evolved xylose‐fermenting Saccharomyces cerevisiae strains , 2004, Biotechnology and bioengineering.

[646]  Engineered high content of ricinoleic acid in fission yeast Schizosaccharomyces pombe , 2012, Applied Microbiology and Biotechnology.

[647]  Babu Raman,et al.  Engineered microbial systems for enhanced conversion of lignocellulosic biomass. , 2010, Current opinion in biotechnology.

[648]  J. Mielenz,et al.  Metabolic Engineering of Candida Tropicalis for the Production of Long–Chain Dicarboxylic Acids , 1992, Bio/Technology.

[649]  Diego de Mendoza,et al.  FapR, a bacterial transcription factor involved in global regulation of membrane lipid biosynthesis. , 2003, Developmental cell.

[650]  S. Sawayama,et al.  Ethanol production from xylose in engineered Saccharomyces cerevisiae strains: current state and perspectives , 2009, Applied Microbiology and Biotechnology.

[651]  K. Shanmugam,et al.  Improving Escherichia coli FucO for Furfural Tolerance by Saturation Mutagenesis of Individual Amino Acid Positions , 2013, Applied and Environmental Microbiology.

[652]  J. Collins,et al.  Construction of a genetic toggle switch in Escherichia coli , 2000, Nature.

[653]  J. Keasling,et al.  Metabolic engineering of the nonmevalonate isopentenyl diphosphate synthesis pathway in Escherichia coli enhances lycopene production. , 2001, Biotechnology and bioengineering.

[654]  J. Mekalanos,et al.  A novel suicide vector and its use in construction of insertion mutations: osmoregulation of outer membrane proteins and virulence determinants in Vibrio cholerae requires toxR , 1988, Journal of bacteriology.

[655]  A Martinez,et al.  Effects of Ca(OH)(2) treatments ("overliming") on the composition and toxicity of bagasse hemicellulose hydrolysates. , 2000, Biotechnology and bioengineering.

[656]  P. Matthews,et al.  Metabolic engineering of carotenoid accumulation in Escherichia coli by modulation of the isoprenoid precursor pool with expression of deoxyxylulose phosphate synthase , 2000, Applied Microbiology and Biotechnology.

[657]  Beatrix Suess,et al.  Engineered riboswitches: Expanding researchers' toolbox with synthetic RNA regulators , 2012, FEBS letters.

[658]  N. Misawa,et al.  Elucidation of the Erwinia uredovora carotenoid biosynthetic pathway by functional analysis of gene products expressed in Escherichia coli , 1990, Journal of bacteriology.

[659]  M. Hatsu,et al.  Metabolic Engineering of Corynebacterium glutamicum for Cadaverine Fermentation , 2007, Bioscience, biotechnology, and biochemistry.

[660]  J. Jarrett,et al.  Loss of iron-sulfur clusters from biotin synthase as a result of catalysis promotes unfolding and degradation. , 2008, Archives of biochemistry and biophysics.

[661]  Michael C Jewett,et al.  Cell-free biology: exploiting the interface between synthetic biology and synthetic chemistry. , 2012, Current opinion in biotechnology.

[662]  Gunvor Røkke,et al.  BioBrick assembly standards and techniques and associated software tools. , 2014, Methods in molecular biology.

[663]  Robert Carlson,et al.  The changing economics of DNA synthesis , 2009, Nature Biotechnology.

[664]  Seon-Won Kim,et al.  An update on microbial carotenoid production: application of recent metabolic engineering tools , 2007, Applied Microbiology and Biotechnology.

[665]  Roslyn N. Brown,et al.  USER Friendly Cloning Coupled with Chitin-Based Natural Transformation Enables Rapid Mutagenesis of Vibrio vulnificus , 2009, Applied and Environmental Microbiology.

[666]  Hak-Sung Kim,et al.  Toward a generalized and high-throughput enzyme screening system based on artificial genetic circuits. , 2014, ACS synthetic biology.

[667]  Ernst Weber,et al.  A Modular Cloning System for Standardized Assembly of Multigene Constructs , 2011, PloS one.

[668]  Alan Villalobos,et al.  Gene Designer: a synthetic biology tool for constructing artificial DNA segments , 2006, BMC Bioinformatics.

[669]  Juan E. González,et al.  Use of Sinorhizobium meliloti as an Indicator for Specific Detection of Long-Chain N-Acyl Homoserine Lactones , 2004, Applied and Environmental Microbiology.

[670]  Ruofan Yu,et al.  A Formalized Design Process for Bacterial Consortia That Perform Logic Computing , 2013, PloS one.

[671]  D. G. Gibson,et al.  Enzymatic Assembly of Overlapping DNA Fragments , 2011, Methods in Enzymology.

[672]  Antia Rodriguez-Villalon,et al.  Carotenoid accumulation in bacteria with enhanced supply of isoprenoid precursors by upregulation of exogenous or endogenous pathways. , 2008, Journal of biotechnology.

[673]  V. de Lorenzo,et al.  Implantation of unmarked regulatory and metabolic modules in Gram-negative bacteria with specialised mini-transposon delivery vectors. , 2013, Journal of biotechnology.

[674]  Carola Engler,et al.  A One Pot, One Step, Precision Cloning Method with High Throughput Capability , 2008, PloS one.

[675]  L. Tsimring,et al.  A synchronized quorum of genetic clocks , 2009, Nature.

[676]  David J. Leak,et al.  Modular system for assessment of glycosyl hydrolase secretion in Geobacillus thermoglucosidasius. , 2013, Microbiology.

[677]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[678]  Ron Weiss,et al.  Cellular computation and communications using engineered genetic regulatory networks , 2001, Cellular Computing.

[679]  C. Hutchison,et al.  Essential genes of a minimal bacterium. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[680]  W. Reznikoff.  Tn5 transposition: a molecular tool for studying protein structure-function. , 2006, Biochemical Society transactions.

[681]  D. Hanahan,et al.  Plasmid screening at high colony density. , 1980, Gene.

[682]  Marshall W. Nirenberg,et al.  The dependence of cell-free protein synthesis in E. coli upon naturally occurring or synthetic polyribonucleotides , 1961, Proceedings of the National Academy of Sciences.

[683]  Dina Petranovic,et al.  Balanced globin protein expression and heme biosynthesis improve production of human hemoglobin in Saccharomyces cerevisiae. , 2014, Metabolic engineering.

[684]  E. O’Shea,et al.  Noise in protein expression scales with natural protein abundance , 2006, Nature Genetics.

[685]  Stefanie Redemann,et al.  Codon adaptation–based control of protein expression in C. elegans , 2011, Nature Methods.

[686]  J. Nielsen,et al.  Expression of a cytoplasmic transhydrogenase in Saccharomyces cerevisiae results in formation of 2‐oxoglutarate due to depletion of the NADPH pool , 2001, Yeast.

[687]  V. de Lorenzo,et al.  Early and late responses of TOL promoters to pathway inducers: identification of postexponential promoters in Pseudomonas putida with lacZ-tet bicistronic reporters , 1993, Journal of bacteriology.

[688]  A. Hill,et al.  The possible effects of the aggregation of the molecules of haemoglobin on its dissociation curves , 1910 .

[689]  W. R. Cluett,et al.  Dynamic metabolic engineering for increasing bioprocess productivity. , 2008, Metabolic engineering.

[690]  Tom Ellis,et al.  Predicting Translation Initiation Rates for Designing Synthetic Biology , 2013, Front. Bioeng. Biotechnol..

[691]  Jay D. Keasling,et al.  Identification of Isopentenol Biosynthetic Genes from Bacillus subtilis by a Screening Method Based on Isoprenoid Precursor Toxicity , 2007, Applied and Environmental Microbiology.

[692]  H. Sahm,et al.  Isoprenoid biosynthesis in bacteria: a novel pathway for the early steps leading to isopentenyl diphosphate. , 1993, The Biochemical journal.

[693]  Keith E. J. Tyo,et al.  Isoprenoid Pathway Optimization for Taxol Precursor Overproduction in Escherichia coli , 2010, Science.

[694]  Katsuhiko Yamamoto,et al.  Genetic engineering of Escherichia coli for production of tetrahydrobiopterin. , 2003, Metabolic engineering.

[695]  Janet M. Thornton,et al.  The CoFactor database: organic cofactors in enzyme catalysis , 2010, Bioinform..

[696]  T. Jeffries,et al.  Regulation of phosphotransferases in glucose- and xylose-fermenting yeasts. , 1997, Applied biochemistry and biotechnology.

[697]  H. Sahm,et al.  Pyruvate carboxylase is a major bottleneck for glutamate and lysine production by Corynebacterium glutamicum. , 2001, Journal of molecular microbiology and biotechnology.

[698]  Hung Lee,et al.  Genetic improvement of Saccharomyces cerevisiae for xylose fermentation. , 2007, Biotechnology advances.

[699]  J. Keasling,et al.  Engineering microbial biofuel tolerance and export using efflux pumps , 2011, Molecular systems biology.

[700]  Nicholas A. Hamilton,et al.  DomainDraw: A Macromolecular Feature Drawing Program , 2007, Silico Biol..

[701]  G. A. Benders.  Cloning whole bacterial genomes in yeast. , 2012, Methods in molecular biology.

[702]  Xiaoming Tan,et al.  Fatty alcohol production in engineered E. coli expressing Marinobacter fatty acyl-CoA reductases , 2013, Applied Microbiology and Biotechnology.

[703]  Zachary L. Fowler,et al.  Increased Malonyl Coenzyme A Biosynthesis by Tuning the Escherichia coli Metabolic Network and Its Application to Flavanone Production , 2009, Applied and Environmental Microbiology.

[704]  Corey J Wilson,et al.  Role of cofactors in metalloprotein folding , 2004, Quarterly Reviews of Biophysics.

[705]  Gary Walsh,et al.  Post-translational modifications of protein biopharmaceuticals. , 2009, Drug discovery today.

[706]  J. Keasling,et al.  Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids , 2012, Nature Biotechnology.

[707]  Jeong Wook Lee,et al.  Systems metabolic engineering of microorganisms for natural and non-natural chemicals. , 2012, Nature chemical biology.

[708]  V. Lorenzo,et al.  Biotechnological domestication of pseudomonads using synthetic biology , 2014, Nature Reviews Microbiology.

[709]  Tad Hogg,et al.  Phase Transitions and the Search Problem , 1996, Artif. Intell..

[710]  Lingchong You,et al.  Optimal tuning of bacterial sensing potential , 2009, Molecular systems biology.

[711]  Ee-Been Goh,et al.  Engineering of Bacterial Methyl Ketone Synthesis for Biofuels , 2012, Applied and Environmental Microbiology.

[712]  F. Collins,et al.  Policy: NIH plans to enhance reproducibility , 2014, Nature.

[713]  Paul Freemont,et al.  Synthetic biology – the state of play , 2012, FEBS letters.

[714]  Shuwen Wang,et al.  A multi-step strategy for BAC recombineering of large DNA fragments. , 2011, International journal of biochemistry and molecular biology.

[715]  Vivek K. Mutalik,et al.  Measurement and modeling of intrinsic transcription terminators , 2013, Nucleic acids research.

[716]  F. Goycoolea,et al.  Astaxanthin: A Review of its Chemistry and Applications , 2006, Critical reviews in food science and nutrition.

[717]  R. Fall,et al.  Evidence of Isoprenoid Precursor Toxicity in Bacillus subtilis , 2011, Bioscience, biotechnology, and biochemistry.

[718]  H. Alper,et al.  Optimizing pentose utilization in yeast: the need for novel tools and approaches , 2010, Biotechnology for biofuels.

[719]  Patrik R. Jones,et al.  Construction of a synthetic YdbK-dependent pyruvate:H2 pathway in Escherichia coli BL21(DE3). , 2009, Metabolic engineering.

[720]  H. Dyson,et al.  Structure of the Escherichia coli quorum sensing protein SdiA: activation of the folding switch by acyl homoserine lactones. , 2006, Journal of molecular biology.

[721]  Hans C. Bernstein,et al.  Synthetic Escherichia coli consortia engineered for syntrophy demonstrate enhanced biomass productivity. , 2012, Journal of biotechnology.

[722]  G. Church,et al.  CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering , 2013, Nature Biotechnology.

[723]  Jamie A. Davies,et al.  Application of synthetic biology to regenerative medicine , 2011 .

[724]  Patrik R. Jones,et al.  Deletion of iscR stimulates recombinant clostridial Fe–Fe hydrogenase activity and H2-accumulation in Escherichia coli BL21(DE3) , 2008, Applied Microbiology and Biotechnology.

[725]  P. Bhalla,et al.  RNA Sequencing Analysis of the Gametophyte Transcriptome from the Liverwort, Marchantia polymorpha , 2014, PloS one.

[726]  Tom Ellis,et al.  Rational Diversification of a Promoter Providing Fine-Tuned Expression and Orthogonal Regulation for Synthetic Biology , 2012, PloS one.

[727]  Christian Matano,et al.  Engineering of Corynebacterium glutamicum for growth and l-lysine and lycopene production from N-acetyl-glucosamine , 2014, Applied Microbiology and Biotechnology.

[728]  Andrew D. Ellington,et al.  Directed evolution of genetic parts and circuits by compartmentalized partnered replication , 2013, Nature Biotechnology.

[729]  P. Silver,et al.  A tunable zinc finger-based framework for Boolean logic computation in mammalian cells , 2012, Nucleic acids research.

[730]  V. Wendisch,et al.  Ornithine cyclodeaminase-based proline production by Corynebacterium glutamicum , 2013, Microbial Cell Factories.

[731]  Anton Glieder,et al.  New opportunities by synthetic biology for biopharmaceutical production in Pichia pastoris , 2013, Current opinion in biotechnology.

[732]  D. Endy.  Foundations for engineering biology , 2005, Nature.

[733]  Alan Bridge,et al.  New and continuing developments at PROSITE , 2012, Nucleic Acids Res..

[734]  K. Shanmugam,et al.  Polyamine Transporters and Polyamines Increase Furfural Tolerance during Xylose Fermentation with Ethanologenic Escherichia coli Strain LY180 , 2014, Applied and Environmental Microbiology.

[735]  Jeffry D. Sander,et al.  CRISPR-Cas systems for editing, regulating and targeting genomes , 2014, Nature Biotechnology.

[736]  Jay D Keasling,et al.  Metabolic engineering delivers next-generation biofuels , 2008, Nature Biotechnology.

[737]  J. Hasty,et al.  Synchronizing genetic relaxation oscillators by intercell signaling , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[738]  G. Stephanopoulos,et al.  Engineering the push and pull of lipid biosynthesis in oleaginous yeast Yarrowia lipolytica for biofuel production. , 2013, Metabolic engineering.

[739]  B. Cheirsilp,et al.  Potential use of oleaginous red yeast Rhodotorula glutinis for the bioconversion of crude glycerol from biodiesel plant to lipids and carotenoids , 2011 .

[740]  J. Kalinowski,et al.  Utilization of soluble starch by a recombinant Corynebacterium glutamicum strain: growth and lysine production. , 2006, Journal of biotechnology.

[741]  V. de Lorenzo,et al.  Transposon vectors containing non-antibiotic resistance selection markers for cloning and stable chromosomal insertion of foreign genes in gram-negative bacteria , 1990, Journal of bacteriology.

[742]  M. Levin,et al.  Endogenous voltage gradients as mediators of cell-cell communication: strategies for investigating bioelectrical signals during pattern formation , 2012, Cell and Tissue Research.

[743]  J. Keasling,et al.  Engineering a mevalonate pathway in Escherichia coli for production of terpenoids , 2003, Nature Biotechnology.

[744]  A. Steinbüchel,et al.  A sensitive, viable-colony staining method using Nile red for direct screening of bacteria that accumulate polyhydroxyalkanoic acids and other lipid storage compounds , 1999, Archives of Microbiology.

[745]  M. Pátek,et al.  Metabolic engineering of the L-valine biosynthesis pathway in Corynebacterium glutamicum using promoter activity modulation. , 2009, Journal of biotechnology.

[746]  Georg A. Sprenger,et al.  Pentose metabolism in Zymomonas mobilis wild-type and recombinant strains , 1992, Applied Microbiology and Biotechnology.

[747]  Albert J. Vilella,et al.  Cellodextrin Transport in Yeast for Improved Biofuel Production , 2010, Science.

[748]  Michiel Kleerebezem,et al.  Quorum sensing by peptide pheromones and two‐component signal‐transduction systems in Gram‐positive bacteria , 1997, Molecular microbiology.

[749]  Hao Yan,et al.  Multi-enzyme complexes on DNA scaffolds capable of substrate channelling with an artificial swinging arm. , 2014, Nature nanotechnology.

[750]  Nathan J Hillson,et al.  PaR-PaR laboratory automation platform. , 2013, ACS synthetic biology.

[751]  Samie R. Jaffrey,et al.  RNA mimics of green fluorescent protein , 2013 .

[752]  Drew Endy,et al.  Quantitative estimation of activity and quality for collections of functional genetic elements , 2013, Nature Methods.

[753]  Thomas K. Wood,et al.  Engineering global regulator Hha of Escherichia coli to control biofilm dispersal , 2010, Microbial biotechnology.

[754]  Yuh Shiwa,et al.  Bacillus subtilis genome vector-based complete manipulation and reconstruction of genomic DNA for mouse transgenesis , 2013, BMC Genomics.

[755]  Yingjin Yuan,et al.  Comparative Proteomic Analysis of Tolerance and Adaptation of Ethanologenic Saccharomyces cerevisiae to Furfural, a Lignocellulosic Inhibitory Compound , 2009, Applied and Environmental Microbiology.

[756]  J. Kalinowski,et al.  Small mobilizable multi-purpose cloning vectors derived from the Escherichia coli plasmids pK18 and pK19: selection of defined deletions in the chromosome of Corynebacterium glutamicum. , 1994, Gene.

[757]  Paul S. Freemont,et al.  Computational design approaches and tools for synthetic biology. , 2011, Integrative biology : quantitative biosciences from nano to macro.

[758]  J. Schneider,et al.  Self-assembling peptides and proteins for nanotechnological applications. , 2004, Current opinion in structural biology.

[759]  A. D. de Graaf,et al.  Identification of a thiamin-dependent synthase in Escherichia coli required for the formation of the 1-deoxy-D-xylulose 5-phosphate precursor to isoprenoids, thiamin, and pyridoxol. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[760]  Hisashi Harada,et al.  Novel approaches and achievements in biosynthesis of functional isoprenoids in Escherichia coli , 2009, Applied Microbiology and Biotechnology.

[761]  Hal S Alper,et al.  Harnessing Yarrowia lipolytica lipogenesis to create a platform for lipid and biofuel production , 2014, Nature Communications.