Methods and applications for assembling large DNA constructs.

The construction of large DNA molecules that encode pathways, biological machinery, and entire genomes has been limited to the reproduction of natural sequences. However, now that robust methods for assembling hundreds of DNA fragments into constructs > 20 kb are readily available, optimization of large genetic elements for metabolic engineering purposes is becoming more routine. Here, various DNA assembly methodologies are reviewed and some of their potential applications are discussed. We tested the potential of DNA assembly to install rational changes in complex biosynthetic pathways, their potential for generating complex libraries, and consider how various strategies are applicable to metabolic engineering.

[1]  Shankar Mukherji,et al.  Synthetic biology: understanding biological design from synthetic circuits , 2009, Nature Reviews Genetics.

[2]  K. Novak The complete genome sequence… , 1998, Nature Medicine.

[3]  G. O’Toole,et al.  Saccharomyces cerevisiae-Based Molecular Tool Kit for Manipulation of Genes from Gram-Negative Bacteria , 2006, Applied and Environmental Microbiology.

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

[5]  Engineering a Ligand-Dependent RNA , 2004 .

[6]  Alcino J. Silva,et al.  Multiple genetic modifications of the erythromycin polyketide synthase to produce a library of novel ‘ ‘ unnatural ’ ’ natural products , 1999 .

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

[8]  A. Paul,et al.  Chemical Synthesis of Poliovirus cDNA: Generation of Infectious Virus in the Absence of Natural Template , 2002, Science.

[9]  Sarah J Kodumal,et al.  Total synthesis of long DNA sequences: synthesis of a contiguous 32-kb polyketide synthase gene cluster. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[10]  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.

[11]  D. Endy,et al.  Refactoring bacteriophage T7 , 2005, Molecular systems biology.

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

[13]  R. Baric,et al.  Systematic Assembly of a Full-Length Infectious cDNA of Mouse Hepatitis Virus Strain A59 , 2002, Journal of Virology.

[14]  Stephan Ladisch,et al.  Construction of long DNA molecules using long PCR-based fusion of several fragments simultaneously. , 2004, Nucleic acids research.

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

[16]  Pamela A. Silver,et al.  Eukaryotic systems broaden the scope of synthetic biology , 2009, The Journal of cell biology.

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

[18]  X. Chen,et al.  Specific cloning of human DNA as yeast artificial chromosomes by transformation-associated recombination. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[19]  K. A. Noren,et al.  Construction of high-complexity combinatorial phage display peptide libraries. , 2001, Methods.

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

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

[22]  R. D'Amato,et al.  Exogenous control of mammalian gene expression through modulation of RNA self-cleavage , 2004, Nature.

[23]  D. G. Gibson,et al.  Isolation of circular yeast artificial chromosomes for synthetic biology and functional genomics studies , 2011, Nature Protocols.

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

[25]  Fernando Geu-Flores,et al.  USER fusion: a rapid and efficient method for simultaneous fusion and cloning of multiple PCR products , 2007, Nucleic acids research.

[26]  Jay D Keasling,et al.  Microbial sensors for small molecules: development of a mevalonate biosensor. , 2007, Metabolic engineering.

[27]  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.

[28]  W. Szybalski,et al.  RecA-AC: single-site cleavage of plasmids and chromosomes at any predetermined restriction site. , 1992, Nucleic acids research.

[29]  Jun Ishikawa,et al.  Genome Sequence of the Streptomycin-Producing Microorganism Streptomyces griseus IFO 13350 , 2008, Journal of bacteriology.

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

[31]  J Craig Venter,et al.  Generating a synthetic genome by whole genome assembly: φX174 bacteriophage from synthetic oligonucleotides , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[32]  R. Fleischmann,et al.  Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. , 1995, Science.

[33]  J. Doyle,et al.  Bow Ties, Metabolism and Disease , 2022 .

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

[35]  L. Serrano,et al.  Engineering stability in gene networks by autoregulation , 2000, Nature.

[36]  Claes Gustafsson,et al.  Optimizing the search algorithm for protein engineering by directed evolution. , 2003, Protein engineering.

[37]  S. Beale,et al.  The Biosynthesis of delta-Aminolevulinic Acid in Higher Plants: I. Accumulation of delta-Aminolevulinic Acid in Greening Plant Tissues. , 1974, Plant physiology.

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

[39]  H. D. de Boer,et al.  Specialized ribosome system: preferential translation of a single mRNA species by a subpopulation of mutated ribosomes in Escherichia coli. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

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

[41]  Pavel A Pevzner,et al.  Imaging mass spectrometry of intraspecies metabolic exchange revealed the cannibalistic factors of Bacillus subtilis , 2010, Proceedings of the National Academy of Sciences.

[42]  Tomer Shlomi,et al.  Computational Design of Auxotrophy-Dependent Microbial Biosensors for Combinatorial Metabolic Engineering Experiments , 2011, PloS one.

[43]  J. Chin,et al.  A network of orthogonal ribosome·mRNA pairs , 2005, Nature chemical biology.

[44]  D. G. Gibson,et al.  Synthesis of DNA fragments in yeast by one-step assembly of overlapping oligonucleotides , 2009, Nucleic acids research.

[45]  J. Vederas,et al.  [Drug discovery and natural products: end of era or an endless frontier?]. , 2011, Biomeditsinskaia khimiia.

[46]  H. G. Khorana Total synthesis of the gene for an alanine transfer ribonucleic acid from yeast , 1971, Nature.

[47]  Herbert M. Sauro,et al.  In-Fusion BioBrick assembly and re-engineering , 2010, Nucleic acids research.

[48]  Clay C C Wang,et al.  Total biosynthesis of antitumor nonribosomal peptides in Escherichia coli , 2006, Nature chemical biology.

[49]  D. Newman,et al.  Impact of natural products on developing new anti-cancer agents. , 2009, Chemical reviews.

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

[51]  C R Hutchinson,et al.  A multiplasmid approach to preparing large libraries of polyketides. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[52]  Martin Fussenegger,et al.  Mammalian synthetic biology – from tools to therapies , 2010, BioEssays : news and reviews in molecular, cellular and developmental biology.

[53]  F. Neidhardt,et al.  The road from The Microbial world to Microbe. , 2007, International microbiology : the official journal of the Spanish Society for Microbiology.

[54]  D. Newman,et al.  Natural products as sources of new drugs over the last 25 years. , 2007, Journal of natural products.

[55]  M. Itaya,et al.  Combining two genomes in one cell: stable cloning of the Synechocystis PCC6803 genome in the Bacillus subtilis 168 genome. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[56]  M. Caruthers,et al.  Studies on polynucleotides. 103. Total synthesis of the structural gene for an alanine transfer ribonucleic acid from yeast. , 1972, Journal of molecular biology.

[57]  Yoshiyuki Sakaki,et al.  Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis , 2003, Nature Biotechnology.

[58]  R. Johnston,et al.  Synthetic recombinant bat SARS-like coronavirus is infectious in cultured cells and in mice , 2008, Proceedings of the National Academy of Sciences.

[59]  O. White,et al.  Global transposon mutagenesis and a minimal Mycoplasma genome. , 1999, Science.

[60]  Wei Niu,et al.  Microbial synthesis of the energetic material precursor 1,2,4-butanetriol. , 2003, Journal of the American Chemical Society.

[61]  C. Rosen,et al.  A rapid method for the construction of synthetic genes using the polymerase chain reaction. , 1990, BioTechniques.

[62]  Christopher A. Voigt,et al.  Prokaryotic gene clusters: A rich toolbox for synthetic biology , 2010, Biotechnology journal.

[63]  A. Riggs,et al.  Expression in Escherichia coli of a chemically synthesized gene for the hormone somatostatin. , 1977, Science.

[64]  B. Barrell,et al.  Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2) , 2002, Nature.

[65]  Robert A. Holt,et al.  Constructing large DNA segments by iterative clone recombination , 2008, Systems and Synthetic Biology.

[66]  C. Raymond,et al.  General method for plasmid construction using homologous recombination. , 1999, BioTechniques.

[67]  Alan Villalobos,et al.  Design Parameters to Control Synthetic Gene Expression in Escherichia coli , 2009, PloS one.

[68]  David R. Liu,et al.  Engineering a ligand-dependent RNA transcriptional activator. , 2004, Chemistry & biology.

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

[70]  발레 페르난도,et al.  Process for the biological production of 1,3-propanediol with high yield , 2003 .

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

[72]  J Craig Venter,et al.  One-step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic Mycoplasma genitalium genome , 2008, Proceedings of the National Academy of Sciences.