Pathway Assembly and Optimization

Abstract With the current advancements in DNA technology, from cheap synthesis to synthetic biology, it is now possible to design, in a modular and combinatorial fashion, not only the genes that will structure the heterologous metabolic pathways, but also the regulatory elements that will ensure the optimal expression levels of such genes. In the realm of biofuels, such biotechnologies have established a clear path toward successfully engineering microbes with features like high yields, titers, and productivities, which are the main goal in any industrial production. This chapter summarizes outstanding technologies that have shown capability to assemble pathways in a standard, quick, and efficient manner. Combinatorial pathway assembly, a trend that has been enabled by exponential emergence of synthetic biology tools will be discussed in the main body of this chapter. To finalize, we discuss the current challenges revolving around the availability of high-throughput screening techniques and automated processes. These technologies aim to potentiate the assembly of pathways for the production of biofuels and other metabolites of interest.

[1]  Jun Ishii,et al.  Increased isobutanol production in Saccharomyces cerevisiae by eliminating competing pathways and resolving cofactor imbalance , 2013, Microbial Cell Factories.

[2]  Laura R. Jarboe,et al.  The damaging effects of short chain fatty acids on Escherichia coli membranes , 2013, Applied Microbiology and Biotechnology.

[3]  Joeri Beauprez,et al.  One step DNA assembly for combinatorial metabolic engineering. , 2014, Metabolic engineering.

[4]  Shuliang Gao,et al.  One-step integration of multiple genes into the oleaginous yeast Yarrowia lipolytica , 2014, Biotechnology Letters.

[5]  S. Elledge,et al.  MAGIC, an in vivo genetic method for the rapid construction of recombinant DNA molecules , 2005, Nature Genetics.

[6]  Burckhard Seelig,et al.  Advances in the directed evolution of proteins. , 2014, Current opinion in chemical biology.

[7]  Jay D. Keasling,et al.  High-Level Production of Amorpha-4,11-Diene, a Precursor of the Antimalarial Agent Artemisinin, in Escherichia coli , 2009, PloS one.

[8]  Hal S Alper,et al.  The synthetic biology toolbox for tuning gene expression in yeast. , 2014, FEMS yeast research.

[9]  Hamilton O. Smith,et al.  Single-step linker-based combinatorial assembly of promoter and gene cassettes for pathway engineering , 2011, Biotechnology Letters.

[10]  Abdul Jabbar,et al.  Antimicrobial natural products: an update on future antibiotic drug candidates. , 2010, Natural product reports.

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

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

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

[14]  Huimin Zhao,et al.  DNA assembly techniques for next-generation combinatorial biosynthesis of natural products , 2014, Journal of Industrial Microbiology & Biotechnology.

[15]  S. Horinouchi,et al.  Synthesis of unnatural flavonoids and stilbenes by exploiting the plant biosynthetic pathway in Escherichia coli. , 2007, Chemistry & biology.

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

[17]  R. Stevens,et al.  Structure-function of the G protein-coupled receptor superfamily. , 2013, Annual review of pharmacology and toxicology.

[18]  Yanhe Ma,et al.  Activating transhydrogenase and NAD kinase in combination for improving isobutanol production. , 2013, Metabolic engineering.

[19]  Martin Dufva,et al.  Bioelectrochemical probing of intracellular redox processes in living yeast cells—application of redox polymer wiring in a microfluidic environment , 2013, Analytical and Bioanalytical Chemistry.

[20]  Huimin Zhao,et al.  Rapid characterization and engineering of natural product biosynthetic pathways via DNA assembler. , 2011, Molecular bioSystems.

[21]  James M Clomburg,et al.  Engineered reversal of the β-oxidation cycle for the synthesis of fuels and chemicals , 2011, Nature.

[22]  Meng Wang,et al.  Activation and Characterization of a Cryptic Polycyclic Tetramate Macrolactam Biosynthetic Gene Cluster , 2013, Nature Communications.

[23]  C. Schmidt-Dannert,et al.  Construction of a Chimeric Biosynthetic Pathway for the De Novo Biosynthesis of Rosmarinic Acid in Escherichia coli , 2014, Chembiochem : a European journal of chemical biology.

[24]  N. Pasco,et al.  Detection of two distinct substrate-dependent catabolic responses in yeast cells using a mediated electrochemical method , 2002, Applied Microbiology and Biotechnology.

[25]  James R Broach,et al.  Creation of GPCR-based chemical sensors by directed evolution in yeast. , 2006, Protein engineering, design & selection : PEDS.

[26]  Robert L. Mach,et al.  Regulation of transcription of cellulases- and hemicellulases-encoding genes in Aspergillus niger and Hypocrea jecorina (Trichoderma reesei) , 2008, Applied Microbiology and Biotechnology.

[27]  S. Atsumi,et al.  Synthetic biology and metabolic engineering approaches to produce biofuels. , 2013, Chemical reviews.

[28]  Sylvestre Marillonnet,et al.  Assembly of Designer TAL Effectors by Golden Gate Cloning , 2011, PloS one.

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

[30]  W. Frommer,et al.  Optical sensors for measuring dynamic changes of cytosolic metabolite levels in yeast , 2011, Nature Protocols.

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

[32]  David C. Cantu,et al.  Phylogenetic and experimental characterization of an acyl-ACP thioesterase family reveals significant diversity in enzymatic specificity and activity , 2011, BMC Biochemistry.

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

[34]  Drew Endy,et al.  A survey of enabling technologies in synthetic biology , 2013, Journal of biological engineering.

[35]  Nathan J Hillson,et al.  PR-PR: cross-platform laboratory automation system. , 2014, ACS synthetic biology.

[36]  A. Granell,et al.  GoldenBraid: An Iterative Cloning System for Standardized Assembly of Reusable Genetic Modules , 2011, PloS one.

[37]  Wei Chen,et al.  Biochemical characterization of GDP-L-fucose de novo synthesis pathway in fungus Mortierella alpina. , 2010, Biochemical and biophysical research communications.

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

[39]  Karen N. Allen,et al.  Enzyme Promiscuity: Engine of Evolutionary Innovation* , 2014, The Journal of Biological Chemistry.

[40]  J. Boeke,et al.  GeneDesign: rapid, automated design of multikilobase synthetic genes. , 2006, Genome research.

[41]  John R Carney,et al.  Combinatorial polyketide biosynthesis by de novo design and rearrangement of modular polyketide synthase genes , 2005, Nature Biotechnology.

[42]  Brad A. Chapman,et al.  Pairwise selection assembly for sequence-independent construction of long-length DNA , 2010, Nucleic acids research.

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

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

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

[46]  Yu Shen,et al.  Fine-tuning of NADH oxidase decreases byproduct accumulation in respiration deficient xylose metabolic Saccharomyces cerevisiae , 2014, BMC Biotechnology.

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

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

[49]  Guoping Zhao,et al.  Tandem assembly of the epothilone biosynthetic gene cluster by in vitro site-specific recombination , 2011, Scientific reports.

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

[51]  P. Cirino,et al.  Recent advances in engineering proteins for biocatalysis , 2014, Biotechnology and bioengineering.

[52]  Huimin Zhao,et al.  Refactoring the silent spectinabilin gene cluster using a plug-and-play scaffold. , 2013, ACS synthetic biology.

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

[54]  A. Abate,et al.  Ultrahigh-throughput screening in drop-based microfluidics for directed evolution , 2010, Proceedings of the National Academy of Sciences.

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

[56]  Elliott M. Ross,et al.  Activation Biosensor for G Protein-Coupled Receptors: A FRET-Based m1 Muscarinic Activation Sensor That Regulates Gq , 2012, PloS one.

[57]  Lei Wang,et al.  Rapid assembly of multiple DNA fragments through direct transformation of PCR products into E. coli and Lactobacillus. , 2014, Plasmid.

[58]  Akihiko Kondo,et al.  Cocktail δ-integration: a novel method to construct cellulolytic enzyme expression ratio-optimized yeast strains , 2010, Microbial cell factories.

[59]  Mitsuhiro Itaya,et al.  One step assembly of multiple DNA fragments with a designed order and orientation in Bacillus subtilis plasmid. , 2003, Nucleic acids research.

[60]  Carola Engler,et al.  Golden Gate Shuffling: A One-Pot DNA Shuffling Method Based on Type IIs Restriction Enzymes , 2009, PloS one.

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

[62]  N. Becker,et al.  Mechanism of promoter repression by Lac repressor–DNA loops , 2012, Nucleic acids research.

[63]  Teruyuki Nagamune,et al.  Enhancement of mutation frequency with nucleotide triphosphate analogs in PCR random mutagenesis , 1995 .

[64]  Timothy S. Ham,et al.  Metabolic engineering of microorganisms for biofuels production: from bugs to synthetic biology to fuels. , 2008, Current opinion in biotechnology.

[65]  John Walchli,et al.  Gene Composer: database software for protein construct design, codon engineering, and gene synthesis , 2009, BMC biotechnology.

[66]  Fumio Hishinuma,et al.  Integration of heterologous genes into the chromosome of Saccharomyces cerevisiae using a delta sequence of yeast retrotransposon Ty , 1990, Applied Microbiology and Biotechnology.

[67]  Huimin Zhao,et al.  Exploiting Issatchenkia orientalis SD108 for succinic acid production , 2014, Microbial Cell Factories.

[68]  Huimin Zhao,et al.  DNA assembler method for construction of zeaxanthin-producing strains of Saccharomyces cerevisiae. , 2012, Methods in molecular biology.

[69]  Romualdas Vaisvila,et al.  USER™ friendly DNA engineering and cloning method by uracil excision , 2007, Nucleic acids research.

[70]  Huimin Zhao,et al.  Customized optimization of metabolic pathways by combinatorial transcriptional engineering , 2012, Nucleic acids research.

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

[72]  N. D. Da Silva,et al.  Sequential δ‐Integration for the Regulated Insertion of Cloned Genes in Saccharomyces cerevisiae , 1997 .

[73]  N. Kouprina,et al.  TAR cloning: insights into gene function, long-range haplotypes and genome structure and evolution , 2006, Nature Reviews Genetics.

[74]  James R. Krycer,et al.  A Practical Comparison of Ligation-Independent Cloning Techniques , 2013, PloS one.

[75]  Thomas L. Madden,et al.  Domain enhanced lookup time accelerated BLAST , 2012, Biology Direct.

[76]  Etsuko N. Moriyama,et al.  Vector NTI, a balanced all-in-one sequence analysis suite , 2004, Briefings Bioinform..

[77]  Robert S. Marks,et al.  UV and arsenate toxicity: a specific and sensitive yeast bioluminescence assay , 2011, Cell Biology and Toxicology.

[78]  Keith E. J. Tyo,et al.  Yeast-based biosensors: design and applications. , 2014, FEMS yeast research.

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

[80]  Yong-Su Jin,et al.  Genome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis , 2007, Nature Biotechnology.

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

[82]  Judy Qiu,et al.  Total Synthesis of a Functional Designer Eukaryotic Chromosome , 2014, Science.

[83]  D. Botstein,et al.  Plasmid construction by homologous recombination in yeast. , 1987, Gene.

[84]  Jay D Keasling,et al.  High‐level production of amorpha‐4,11‐diene in a two‐phase partitioning bioreactor of metabolically engineered Escherichia coli , 2006, Biotechnology and bioengineering.

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

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

[87]  J. Forment,et al.  GoldenBraid 2.0: A Comprehensive DNA Assembly Framework for Plant Synthetic Biology1[C][W][OA] , 2013, Plant Physiology.

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

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

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

[91]  T. Jeffries,et al.  Engineering yeasts for xylose metabolism. , 2006, Current opinion in biotechnology.

[92]  Huimin Zhao,et al.  Combinatorial Design of a Highly Efficient Xylose-Utilizing Pathway in Saccharomyces cerevisiae for the Production of Cellulosic Biofuels , 2012, Applied and Environmental Microbiology.

[93]  Ron Milo,et al.  Quantifying translational coupling in E. coli synthetic operons using RBS modulation and fluorescent reporters. , 2013, ACS synthetic biology.

[94]  Chi Bun Ching,et al.  Combinatorial assembly of large biochemical pathways into yeast chromosomes for improved production of value-added compounds. , 2015, ACS synthetic biology.