Directed evolution of metabolic pathways.

The modification of cellular metabolism is of biotechnological and commercial significance because naturally occurring metabolic pathways are the source of diverse compounds used in fields ranging from medicine to bioremediation. Directed evolution is the experimental improvement of biocatalysts or cellular properties through iterative genetic diversification and selection procedures. The creation of novel metabolic functions without disrupting the balanced intracellular pool of metabolites is the primary challenge of pathway manipulation. The introduction of coordinated changes across multiple genetic elements, in conjunction with functional selection, presents an integrated approach for the modification of metabolism with benign physiological consequences. Directed evolution formats take advantage of the dynamic structures of genomes and genomic sub-structures and their ability to evolve in multiple directions in response to external stimuli. The elucidation, design and application of genome-restructuring mechanisms are key elements in the directed evolution of cellular metabolic pathways.

[1]  Jon E. Ness,et al.  Synthetic shuffling expands functional protein diversity by allowing amino acids to recombine independently , 2002, Nature Biotechnology.

[2]  V. Gavrilovic,et al.  Genome shuffling of Lactobacillus for improved acid tolerance , 2002, Nature Biotechnology.

[3]  Barry G. Hall,et al.  Predicting the evolution of antibiotic resistance genes , 2004, Nature Reviews Microbiology.

[4]  C. Gustafsson,et al.  Directed evolution: the 'rational' basis for 'irrational' design. , 2000, Current opinion in structural biology.

[5]  J R Roth,et al.  Evolution of coenzyme B12 synthesis among enteric bacteria: evidence for loss and reacquisition of a multigene complex. , 1996, Genetics.

[6]  Pilar Blancafort,et al.  In vivo selection of combinatorial libraries and designed affinity maturation of polydactyl zinc finger transcription factors for ICAM-1 provides new insights into gene regulation. , 2004, Journal of molecular biology.

[7]  D. Baker,et al.  Design of a Novel Globular Protein Fold with Atomic-Level Accuracy , 2003, Science.

[8]  Joshua A Bittker,et al.  Directed evolution of protein enzymes using nonhomologous random recombination. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[9]  D. Pompon,et al.  High efficiency family shuffling based on multi-step PCR and in vivo DNA recombination in yeast: statistical and functional analysis of a combinatorial library between human cytochrome P450 1A1 and 1A2. , 2000, Nucleic acids research.

[10]  M. Gerstein,et al.  Structure and evolution of transcriptional regulatory networks. , 2004, Current opinion in structural biology.

[11]  Volker Sieber,et al.  Libraries of hybrid proteins from distantly related sequences , 2001, Nature Biotechnology.

[12]  Peter D. Karp,et al.  EcoCyc: a comprehensive database resource for Escherichia coli , 2004, Nucleic Acids Res..

[13]  W. Stemmer,et al.  Genome shuffling leads to rapid phenotypic improvement in bacteria , 2002, Nature.

[14]  S. Salipante,et al.  GeneHunter, a Transposon Tool for Identification and Isolation of Cryptic Antibiotic Resistance Genes , 2003, Antimicrobial Agents and Chemotherapy.

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

[16]  B. Hall Evolution of a regulated operon in the laboratory. , 1982, Genetics.

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

[18]  Vos,et al.  Molecular mechanisms of genetic adaptation to xenobiotic compounds , 1992, Microbiological reviews.

[19]  Pilar Blancafort,et al.  Promoter-targeted phage display selections with preassembled synthetic zinc finger libraries for endogenous gene regulation. , 2004, Journal of molecular biology.

[20]  W. Strohl,et al.  Biochemical engineering of natural product biosynthesis pathways. , 2001, Metabolic engineering.

[21]  J. Noel,et al.  Gene library synthesis by structure-based combinatorial protein engineering. , 2004, Methods in enzymology.

[22]  Philip T. Pienkos,et al.  DNA shuffling method for generating highly recombined genes and evolved enzymes , 2001, Nature Biotechnology.

[23]  W. Stemmer,et al.  Directed evolution of proteins by exon shuffling , 2001, Nature Biotechnology.

[24]  Claes Gustafsson,et al.  Semi-synthetic DNA shuffling of aveC leads to improved industrial scale production of doramectin by Streptomyces avermitilis. , 2005, Metabolic engineering.

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

[26]  Carl O. Pabo,et al.  Drug discovery with engineered zinc-finger proteins , 2003, Nature Reviews Drug Discovery.

[27]  G. Stephanopoulos,et al.  Metabolic Engineering: Principles And Methodologies , 1998 .

[28]  E. Grotewold Plant metabolic diversity: a regulatory perspective. , 2005, Trends in plant science.

[29]  Michael J E Sternberg,et al.  Evolution of enzymes in metabolism: a network perspective. , 2002, Journal of molecular biology.

[30]  W. Stemmer DNA shuffling by random fragmentation and reassembly: in vitro recombination for molecular evolution. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[31]  Ling Yuan,et al.  Laboratory-Directed Protein Evolution , 2005, Microbiology and Molecular Biology Reviews.

[32]  W. Arber Elements in microbial evolution , 1991, Journal of Molecular Evolution.

[33]  J. Bailey,et al.  Toward a science of metabolic engineering , 1991, Science.

[34]  W. Stemmer,et al.  Molecular evolution of an arsenate detoxification pathway by DNA shuffling , 1997, Nature Biotechnology.

[35]  S. Taguchi,et al.  Enhanced Accumulation and Changed Monomer Composition in Polyhydroxyalkanoate (PHA) Copolyester by In Vitro Evolution of Aeromonas caviae PHA Synthase , 2002, Applied and Environmental Microbiology.

[36]  Claudia Schmidt-Dannert,et al.  Dealing with complexity: evolutionary engineering and genome shuffling. , 2004, Current opinion in biotechnology.

[37]  W. Reznikoff,et al.  Tn5 in Vitro Transposition* , 1998, The Journal of Biological Chemistry.

[38]  J. Shapiro Observations on the formation of clones containing araB-lacZ cistron fusions , 2004, Molecular and General Genetics MGG.

[39]  A. Steinbüchel,et al.  In vivo evolution of the Aeromonas punctata polyhydroxyalkanoate (PHA) synthase: isolation and characterization of modified PHA synthases with enhanced activity , 2002, Applied Microbiology and Biotechnology.

[40]  Marc Ostermeier,et al.  Finding Cinderella's slipper—proteins that fit , 1999, Nature Biotechnology.

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

[42]  U. Sauer High-throughput phenomics: experimental methods for mapping fluxomes. , 2004, Current opinion in biotechnology.

[43]  J. Shapiro,et al.  Genome organization, natural genetic engineering and adaptive mutation. , 1997, Trends in genetics : TIG.

[44]  J. Broadbent,et al.  Genetic construction of nisin-producing Lactococcus lactis subsp. cremoris and analysis of a rapid method for conjugation , 1991, Applied and environmental microbiology.

[45]  Gavin J. Williams,et al.  Directed evolution of enzymes for biocatalysis and the life sciences , 2004, Cellular and Molecular Life Sciences CMLS.

[46]  Sarah Kaines,et al.  Gene transfer to plants by diverse species of bacteria , 2005, Nature.

[47]  Frances H. Arnold,et al.  Molecular evolution by staggered extension process (StEP) in vitro recombination , 1998, Nature Biotechnology.

[48]  D. Mills,et al.  An extracellular Darwinian experiment with a self-duplicating nucleic acid molecule. , 1967, Proceedings of the National Academy of Sciences of the United States of America.

[49]  Dan S. Tawfik,et al.  The 'evolvability' of promiscuous protein functions , 2005, Nature Genetics.

[50]  Tony Romeo,et al.  Disruption of a Global Regulatory Gene to Enhance Central Carbon Flux into Phenylalanine Biosynthesis in Escherichia coli , 2001, Current Microbiology.

[51]  S. Copley,et al.  Genome Shuffling Improves Degradation of the Anthropogenic Pesticide Pentachlorophenol by Sphingobium chlorophenolicum ATCC 39723 , 2004, Applied and Environmental Microbiology.

[52]  The EBG System of E. coli: Origin and Evolution of a Novel β-Galactosidase for the Metabolism of Lactose , 2003 .

[53]  W. Stemmer,et al.  DNA shuffling of a family of genes from diverse species accelerates directed evolution , 1998, Nature.

[54]  F. Arnold,et al.  Tuning the activity of an enzyme for unusual environments: sequential random mutagenesis of subtilisin E for catalysis in dimethylformamide. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[55]  Koichi Nishigaki,et al.  Construction of block-shuffled libraries of DNA for evolutionary protein engineering: Y-ligation-based block shuffling. , 2002, Protein engineering.

[56]  R. Weiss,et al.  Directed evolution of a genetic circuit , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[57]  Barbara E. Wright,et al.  Stress‐directed adaptive mutations and evolution , 2004, Molecular microbiology.

[58]  C. Kao,et al.  Reverse engineering of industrial pharmaceutical-producing actinomycete strains using DNA microarrays. , 2004, Metabolic engineering.

[59]  S. Copley,et al.  A Previously Unrecognized Step in Pentachlorophenol Degradation in Sphingobium chlorophenolicum Is Catalyzed by Tetrachlorobenzoquinone Reductase (PcpD) , 2003, Journal of bacteriology.

[60]  W. Doolittle,et al.  The role of lateral gene transfer in the evolution of isoprenoid biosynthesis pathways , 2000, Molecular microbiology.

[61]  C. Barbas,et al.  Regulation of transgene expression in plants with polydactyl zinc finger transcription factors , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[62]  Frances H. Arnold,et al.  Diversifying Carotenoid Biosynthetic Pathways by Directed Evolution , 2005, Microbiology and Molecular Biology Reviews.

[63]  Transposable elements as activators of cryptic genes in E. coli. , 2000 .

[64]  Jean-Louis Reymond,et al.  Enzyme assays for high-throughput screening. , 2004, Current opinion in biotechnology.

[65]  W. Schwab,et al.  Metabolic engineering of monoterpene biosynthesis: two-step production of (+)-trans-isopiperitenol by tobacco. , 2004, The Plant journal : for cell and molecular biology.

[66]  Manfred T Reetz,et al.  Assembly of Designed Oligonucleotides as an Efficient Method for Gene Recombination: A New Tool in Directed Evolution , 2003, Chembiochem : a European journal of chemical biology.

[67]  M. Burk,et al.  Creation of a productive, highly enantioselective nitrilase through gene site saturation mutagenesis (GSSM). , 2003, Journal of the American Chemical Society.

[68]  Construction of DNA-Shuffled and Incrementally Truncated Libraries by a Mutagenic and Unidirectional Reassembly Method: Changing from a Substrate Specificity of Phospholipase to That of Lipase , 2002, Applied and Environmental Microbiology.

[69]  C. Schmidt-Dannert Directed evolution of single proteins, metabolic pathways, and viruses. , 2001, Biochemistry.

[70]  Janet M Thornton,et al.  Pathway evolution, structurally speaking. , 2002, Current opinion in structural biology.

[71]  Marc Ostermeier,et al.  A combinatorial approach to hybrid enzymes independent of DNA homology , 1999, Nature Biotechnology.

[72]  Michael Y. Galperin,et al.  Bacterial signal transduction network in a genomic perspective. , 2004, Environmental microbiology.

[73]  P. Christou,et al.  Progress in plant metabolic engineering. , 2004, Current opinion in biotechnology.

[74]  Ramon Gonzalez,et al.  Gene Array‐Based Identification of Changes That Contribute to Ethanol Tolerance in Ethanologenic Escherichia coli: Comparison of KO11 (Parent) to LY01 (Resistant Mutant) , 2003, Biotechnology progress.

[75]  W. Atchley,et al.  Evolution of bHLH transcription factors: modular evolution by domain shuffling? , 1999, Molecular biology and evolution.

[76]  Nemat O. Keyhani,et al.  Ancient Origin of the Tryptophan Operon and the Dynamics of Evolutionary Change , 2003, Microbiology and Molecular Biology Reviews.