Genome scale engineering techniques for metabolic engineering

Metabolic Engineering

Volumn 32, Issue , 2015, Pages 143-154

  Liu, Rongming ^a   Bassalo, Marcelo C ^b   Zeitoun, Ramsey I ^a   Gill, Ryan T ^a  

^a UCB 450   (United States)

^b UNIVERSITY OF COLORADO   (United States)

Author keywords

Design Build Test Learn; Genome scale engineering; Metabolic engineering; Synthetic biology

Indexed keywords

ENGINEERING EDUCATION; GENES; ITERATIVE METHODS; METABOLISM; MODEL BUILDINGS; OPTICAL TESTING;

DESIGN BUILD; ENGINEERING APPLICATIONS; ENGINEERING FIELDS; ENGINEERING TECHNIQUES; GENETIC MODIFICATIONS; GENOME MODIFICATION; HYPOTHESIS GENERATION; SYNTHETIC BIOLOGY;

METABOLIC ENGINEERING;

4 HYDROXYBUTYRIC ACID; COMPLEMENTARY DNA; DNA FRAGMENT; FUEL; MALONYL COENZYME A; POLYHYDROXYALKANOIC ACID; RESVERATROL; DNA;

ALGORITHM; ARTICLE; BACILLUS SUBTILIS; CLOSTRIDIUM ACETOBUTYLICUM; CLOSTRIDIUM BEIJERINCKII; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; CODON USAGE; CORYNEBACTERIUM GLUTAMICUM; CRISPR CAS SYSTEM; CRYSTAL STRUCTURE; DESIGN BUILD TEST LEARN CYCLE; DNA DENATURATION; DNA END JOINING REPAIR; DNA SYNTHESIS; DOWN REGULATION; FATTY ACID METABOLISM; GENE DELETION; GENE INACTIVATION; GENE OVEREXPRESSION; GENOME SCALE ENGINEERING; GENOTYPE; HIGH THROUGHPUT SEQUENCING; HOMOLOGOUS RECOMBINATION; KOMAGATAELLA PASTORIS; LABORATORY AUTOMATION; LACTOCOCCUS LACTIS; MACHINE LEARNING; MANNHEIMIA; METABOLIC ENGINEERING; MICROBIAL GENOME; MICROBIAL METABOLISM; MITOCHONDRIAL GENOME; NONHUMAN; PHENOTYPE; POINT MUTATION; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN SECONDARY STRUCTURE; PSEUDOMONAS PUTIDA; RESTRICTION SITE; SACCHAROMYCES CEREVISIAE; ANIMAL; GENETICS; GENOME; HUMAN; PROCEDURES; SYNTHETIC BIOLOGY; TRENDS;

ANIMALS; DNA; GENOME; HUMANS; METABOLIC ENGINEERING; SYNTHETIC BIOLOGY;

EID: 84945276317     PISSN: 10967176     EISSN: 10967184     Source Type: Journal    
DOI: 10.1016/j.ymben.2015.09.013     Document Type: Review

References (167)

1. Aach, J., Mali, P., Church, G.M., 2014. CasFinder: Flexible algorithm for identifying specific Cas9 targets in genomes. bioRxiv 005074.
2. Acevedo A., Brodsky L., Andino R. Mutational and fitness landscapes of an RNA virus revealed through population sequencing. Nature 2014, 505:686-690.
3. Agren R., Liu L., Shoaie S., Vongsangnak W., Nookaew I., Nielsen J. The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum. PLoS Comput. Biol. 2013, 9:e1002980.
4. Alkan C., Coe B.P., Eichler E.E. Genome structural variation discovery and genotyping. Nat. Rev. Genet. 2011, 12:363-376.
5. Anders C., Niewoehner O., Duerst A., Jinek M. Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease. Nature 2014, 513:569-573.
6. Annaluru N., Muller H., Mitchell L.A., Ramalingam S., Stracquadanio G., et al. Total synthesis of a functional designer eukaryotic chromosome. Science 2014, 344:55-58.
7. Bae S., Park J., Kim J.-S. Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases. Bioinformatics 2014, 30:1473-1475.
8. Bates J.T., Chivian D., Arkin A.P. GLAMM: genome-linked application for metabolic maps. Nucleic Acids Res. 2011, 39:W400-W405.
9. Becker S.A., Palsson B.O. Context-specific metabolic networks are consistent with experiments. PLoS Comput. Biol. 2008, 4:e1000082.
10. Ben-Hur A., Ong C.S., Sonnenburg S., Schölkopf B., Rätsch G. Support vector machines and kernels for computational biology. PLoS Comput. Biol. 2008, 4:e1000173.
11. Bhan N., Xu P., Khalidi O., Koffas M.A.G. Redirecting carbon flux into malonyl-CoA to improve resveratrol titers: Proof of concept for genetic interventions predicted by OptForce computational framework. Chem. Eng. Sci. 2013, 103:109-114.
12. Bikard D., Jiang W., Samai P., Hochschild A., Zhang F., Marraffini L.A. Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system. Nucleic Acids Res. 2013, 41:7429-7437.
13. Blount Z.D., Barrick J.E., Davidson C.J., Lenski R.E. Genomic analysis of a key innovation in an experimental Escherichia coli population. Nature 2012, 489:513-518.
14. Boch J., Scholze H., Schornack S., Landgraf A., Hahn S., Kay S., Lahaye T., Nickstadt A., Bonas U. Breaking the code of DNA binding specificity of TAL-type III effectors. Science 2009, 326:1509-1512.
15. Bonde M.T., Klausen M.S., Anderson M.V., Wallin A.I.N., Wang H.H., Sommer M.O.A. MODEST: a web-based design tool for oligonucleotide-mediated genome engineering and recombineering. Nucleic Acids Res. 2014, 42:W408-W415.
16. Bordbar A., Mo M.L., Nakayasu E.S., Schrimpe-Rutledge A.C., Kim Y.-M., Metz T.O., Jones M.B., Frank B.C., Smith R.D., Peterson S.N., Hyduke D.R., Adkins J.N., Palsson B.O. Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation. Mol. Syst. Biol. 2012, 8:558.
17. Broeckling C.D., Reddy I.R., Duran A.L., Zhao X., Sumner L.W. MET-IDEA: data extraction tool for mass spectrometry-based metabolomics. Anal. Chem. 2006, 78:4334-4341.
18. Büchel F., Rodriguez N., Swainston N., Wrzodek C., Czauderna T., Keller R., Mittag F., Schubert M., Glont M., Golebiewski M., van Iersel M., Keating S., Rall M., Wybrow M., Hermjakob H., Hucka M., Kell D.B., Müller W., Mendes P., Zell A., Chaouiya C., Saez-Rodriguez J., Schreiber F., Laibe C., Dräger A., Le Novère N. Path2Models: large-scale generation of computational models from biochemical pathway maps. BMC Syst. Biol. 2013, 7:116.
19. Campodonico M.A., Andrews B.A., Asenjo J.A., Palsson B.O., Feist A.M. Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-Path. Metab. Eng. 2014, 25:140-158.
20. Carbonell P., Parutto P., Baudier C., Junot C., Faulon J.-L. Retropath: automated pipeline for embedded metabolic circuits. Synth. Biol. 2014, 3:565-577. ACS.
21. Carbonell P., Parutto P., Herisson J., Pandit S.B., Faulon J.-L. XTMS: pathway design in an eXTended metabolic space. Nucleic Acids Res. 2014, 42:W389-W394.
22. Castoreno A.B., Smurnyy Y., Torres A.D., Vokes M.S., Jones T.R., Carpenter A.E., Eggert U.S. Small molecules discovered in a pathway screen target the Rho pathway in cytokinesis. Nat. Chem. Biol. 2010, 6:457-463.
23. Chandrasekaran S., Price N.D. Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis. Proc. Natl. Acad. Sci. USA 2010, 107:17845-17850.
24. Choi Y.J., Park J.H., Kim T.Y., Lee S.Y. Metabolic engineering of Escherichia coli for the production of 1-propanol. Metab. Eng. 2012, 14:477-486.
25. Choon Y.W., Mohamad M.S., Deris S., Illias R.M., Chong C.K., Chai L.E., Omatu S., Corchado J.M. Differential bees flux balance analysis with OptKnock for in silico microbial strains optimization. PLoS One 2014, 9:e102744.
26. Choulika A., Perrin A., Dujon B., Nicolas J.F. Induction of homologous recombination in mammalian chromosomes by using the I-SceI system of Saccharomyces cerevisiae. Mol. Cell. Biol. 1995, 15:1968-1973.
27. Chu V.T., Weber T., Wefers B., Wurst W., Sander S., Rajewsky K., Kühn R. Increasing the efficiency of homology-directed repair for CRISPR-Cas9-induced precise gene editing in mammalian cells. Nat. Biotechnol. 2015, 10.1038/nbt.3198.
28. Colijn C., Brandes A., Zucker J., Lun D.S., Weiner B., Farhat M.R., Cheng T.-Y., Moody D.B., Murray M., Galagan J.E. Interpreting expression data with metabolic flux models: predicting Mycobacterium tuberculosis mycolic acid production. PLoS Comput. Biol. 2009, 5:e1000489.
29. Collinet C., Stöter M., Bradshaw C.R., Samusik N., Rink J.C., Kenski D., Habermann B., Buchholz F., Henschel R., Mueller M.S., Nagel W.E., Fava E., Kalaidzidis Y., Zerial M. Systems survey of endocytosis by multiparametric image analysis. Nature 2010, 464:243-249.
30. Collins S.B., Reznik E., Segrè D. Temporal expression-based analysis of metabolism. PLoS Comput. Biol. 2012, 8:e1002781.
31. Cong L., Ran F.A., Cox D., Lin S., Barretto R., Habib N., Hsu P.D., Wu X., Jiang W., Marraffini L.A., Zhang F. Multiplex genome engineering using CRISPR/Cas systems. Science 2013, 339:819-823.
32. Cotten C., Reed J.L. Constraint-based strain design using continuous modifications (CosMos) of flux bounds finds new strategies for metabolic engineering. Biotechnol. J. 2013, 8:595-604.
33. Craig D.W., Pearson J.V., Szelinger S., Sekar A., Redman M., Corneveaux J.J., Pawlowski T.L., Laub T., Nunn G., Stephan D.A., Homer N., Huentelman M.J. Identification of genetic variants using bar-coded multiplexed sequencing. Nat. Methods 2008, 5:887-893.
34. Datsenko K.A., Wanner B.L. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl. Acad. Sci. USA 2000, 97:6640-6645.
35. Datta S., Pihur V. Feature selection and machine learning with mass spectrometry data. Methods Mol. Biol. 2010, 593:205-229.
36. De Ridder D., de Ridder J., Reinders M.J.T. Pattern recognition in bioinformatics. Brief. Bioinform. 2013, 14:633-647.
37. DiCarlo J.E., Conley A.J., Penttilä M., Jäntti J., Wang H.H., Church G.M. Yeast oligo-mediated genome engineering (YOGE). Synth. Biol. 2013, 2:741-749. ACS.
38. DiCarlo J.E., Norville J.E., Mali P., Rios X., Aach J., Church G.M. Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems. Nucleic Acids Res. 2013, 41:4336-4343.
39. Dietrich J.A., McKee A.E., Keasling J.D. High-throughput metabolic engineering: advances in small-molecule screening and selection. Annu. Rev. Biochem. 2010, 79:563-590.
40. Dillingham M.S., Kowalczykowski S.C. RecBCD enzyme and the repair of double-stranded DNA breaks. Microbiol. Mol. Biol. Rev. 2008, 72:642-671.
41. Engler C., Kandzia R., Marillonnet S. A one pot, one step, precision cloning method with high throughput capability. PLoS One 2008, 3:e3647.
42. Engler C., Marillonnet S. Golden gate cloning. Methods Mol. Biol. 2014, 1116:119-131.
43. Firnberg E., Labonte J.W., Gray J.J., Ostermeier M. A comprehensive, high-resolution map of a gene's fitness landscape. Mol. Biol. Evol. 2014, 31:1581-1592.
44. Flahaut N.A.L., Wiersma A., van de Bunt B., Martens D.E., Schaap P.J., Sijtsma L., Dos Santos V.A.M., de Vos W.M. Genome-scale metabolic model for Lactococcus lactis MG1363 and its application to the analysis of flavor formation. Appl. Microbiol. Biotechnol. 2013, 97:8729-8739.
45. Fowler D.M., Fields S. Deep mutational scanning: a new style of protein science. Nat. Methods 2014, 11:801-807.
46. Fu J., Bian X., Hu S., Wang H., Huang F., Seibert P.M., Plaza A., Xia L., Müller R., Stewart A.F., Zhang Y. Full-length RecE enhances linear-linear homologous recombination and facilitates direct cloning for bioprospecting. Nat. Biotechnol. 2012, 30:440-446.
47. Förster J., Famili I., Fu P., Palsson B.Ø., Nielsen J. Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res. 2003, 13:244-253.
48. Gaj T., Gersbach C.A., Barbas C.F. ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol. 2013, 31:397-405.
49. Gao Y., Zhao Y. Specific and heritable gene editing in Arabidopsis. Proc. Natl. Acad. Sci. USA 2014, 111:4357-4358.
50. Gawand P., Hyland P., Ekins A., Martin V.J.J., Mahadevan R. Novel approach to engineer strains for simultaneous sugar utilization. Metab. Eng. 2013, 20:63-72.
51. Gerosa L., Sauer U. Regulation and control of metabolic fluxes in microbes. Curr. Opin. Biotechnol. 2011, 22:566-575.
52. Gibson D.G., Benders G.A., Andrews-Pfannkoch C., Denisova E.A., Baden-Tillson H., Zaveri J., Stockwell T.B., Brownley A., Thomas D.W., Algire M.A., Merryman C., Young L., Noskov V.N., Glass J.I., Venter J.C., Hutchison C.A., Smith H.O. Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science 2008, 319:1215-1220.
53. Gibson D.G., Smith H.O., Hutchison C.A., Craig Venter J., Merryman C. Chemical synthesis of the mouse mitochondrial genome. Nat. Methods 2010, 7:901-903.
54. Gibson D.G., Young L., Chuang R.-Y., Venter J.C., Hutchison C.A., Smith H.O. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat. Methods 2009, 6:343-345.
55. Gong B., Shin M., Sun J., Jung C.-H., Bolt E.L., van der Oost J., Kim J.-S. Molecular insights into DNA interference by CRISPR-associated nuclease-helicase Cas3. Proc. Natl. Acad. Sci. USA 2014, 111:16359-16364.
56. Goodman D.B., Church G.M., Kosuri S. Causes and effects of N-terminal codon bias in bacterial genes. Science 2013, 342:475-479.
57. Hastie T., Tibshirani R., Friedman J. The Elements of Statistical Learning: Data Mining, Inference, and Prediction 2009, Springer Science & Business Media, New York, Philadelphia. Second Edition.
58. Hatzimanikatis V., Li C., Ionita J.A., Henry C.S., Jankowski M.D., Broadbelt L.J. Exploring the diversity of complex metabolic networks. Bioinformatics 2005, 21:1603-1609.
59. Heigwer F., Kerr G., Boutros M. E-CRISP: fast CRISPR target site identification. Nat. Methods 2014, 11:122-123.
60. Henry C.S., DeJongh M., Best A.A., Frybarger P.M., Linsay B., Stevens R.L. High-throughput generation, optimization and analysis of genome-scale metabolic models. Nat. Biotechnol. 2010, 28:977-982.
61. Henry C.S., Zinner J.F., Cohoon M.P., Stevens R.L. iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations. Genome Biol. 2009, 10:R69.
62. Hilton I.B., D'Ippolito A.M., Vockley C.M., Thakore P.I., Crawford G.E., Reddy T.E., Gersbach C.A. Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers. Nat. Biotechnol. 2015, 10.1038/nbt.3199.
63. Hou Y., Braun D.R., Michel C.R., Klassen J.L., Adnani N., Wyche T.P., Bugni T.S. Microbial strain prioritization using metabolomics tools for the discovery of natural products. Anal. Chem. 2012, 84:4277-4283.
64. Isaacs F.J., Carr P.A., Wang H.H., Lajoie M.J., Sterling B., Kraal L., Tolonen A.C., Gianoulis T.A., Goodman D.B., Reppas N.B., Emig C.J., Bang D., Hwang S.J., Jewett M.C., Jacobson J.M., Church G.M. Precise manipulation of chromosomes in vivo enables genome-wide codon replacement. Science 2011, 333:348-353.
65. Jakočiunas T., Rajkumar A.S., Zhang J., Arsovska D., Rodriguez A., Jendresen C.B., Skjødt M.L., Nielsen A.T., Borodina I., Jensen M.K., Keasling J.D. CasEMBLR: Cas9-facilitated multiloci genomic integration of in vivo assembled DNA parts in saccharomyces cerevisiae. ACS Synth. Biol. 2015, 10.1021/acssynbio.5b00007.
66. Jang Y.-S., Lee J.Y., Lee J., Park J.H., Im J.A., Eom M.-H., Lee J., Lee S.-H., Song H., Cho J.-H., Seung D.Y., Lee S.Y. Enhanced butanol production obtained by reinforcing the direct butanol-forming route in clostridium acetobutylicum. MBio 2012, 3. e00314-12-e00314-12.
67. Janga S.C., Díaz-Mejía J.J., Moreno-Hagelsieb G. Network-based function prediction and interactomics: the case for metabolic enzymes. Metab. Eng. 2011, 13:1-10.
68. Jensen P.A., Lutz K.A., Papin J.A. TIGER: toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks. BMC Syst. Biol. 2011, 5:147.
69. Jensen P.A., Papin J.A. Functional integration of a metabolic network model and expression data without arbitrary thresholding. Bioinformatics 2011, 27:541-547.
70. Jiang W., Bikard D., Cox D., Zhang F., Marraffini L.A. RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat. Biotechnol. 2013, 31:233-239.
71. Jiang Y., Chen B., Duan C., Sun B., Yang J., Yang S. Multigene editing in the Escherichia coli genome via the CRISPR-Cas9 System. Appl. Environ. Microbiol. 2015, 81:2506-2514.
72. Jinek M., Chylinski K., Fonfara I., Hauer M., Doudna J.A., Charpentier E. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 2012, 337:816-821.
73. Joung J.K., Sander J.D. TALENs: a widely applicable technology for targeted genome editing. Nat. Rev. Mol. Cell Biol. 2013, 14:49-55.
74. Karp P.D., Paley S.M., Krummenacker M., Latendresse M., Dale J.M., Lee T.J., Kaipa P., Gilham F., Spaulding A., Popescu L., Altman T., Paulsen I., Keseler I.M., Caspi R. Pathway tools version 13.0: integrated software for pathway/genome informatics and systems biology. Brief. Bioinform. 2010, 11:40-79.
75. Karr J.R., Sanghvi J.C., Macklin D.N., Gutschow M.V., Jacobs J.M., Bolival B., Assad-Garcia N., Glass J.I., Covert M.W. A whole-cell computational model predicts phenotype from genotype. Cell 2012, 150:389-401.
76. Katajamaa M., Miettinen J., Oresic M. MZmine: toolbox for processing and visualization of mass spectrometry based molecular profile data. Bioinformatics 2006, 22:634-636.
77. Kaur B., Chakraborty D., Kumar B. Metabolic engineering of Pediococcus acidilactici BD16 for production of vanillin through ferulic acid catabolic pathway and process optimization using response surface methodology. Appl. Microbiol. Biotechnol. 2014, 98:8539-8551.
78. Kim H.U., Kim W.J., Lee S.Y. Flux-coupled genes and their use in metabolic flux analysis. Biotechnol. J 2013, 8:1035-1042.
79. Kim J., Reed J.L. OptORF: optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains. BMC Syst. Biol. 2010, 4:53.
80. Kim J., Reed J.L. RELATCH: relative optimality in metabolic networks explains robust metabolic and regulatory responses to perturbations. Genome Biol. 2012, 13:R78.
81. Kim T.Y., Kim H.U., Park J.M., Song H., Kim J.S., Lee S.Y. Genome-scale analysis of Mannheimia succiniciproducens metabolism. Biotechnol. Bioeng. 2007, 97:657-671.
82. King R.D., Rowland J., Oliver S.G., Young M., Aubrey W., Byrne E., Liakata M., Markham M., Pir P., Soldatova L.N., Sparkes A., Whelan K.E., Clare A. The automation of science. Science 2009, 324:85-89.
83. King R.D., Whelan K.E., Jones F.M., Reiser P.G.K., Bryant C.H., Muggleton S.H., Kell D.B., Oliver S.G. Functional genomic hypothesis generation and experimentation by a robot scientist. Nature 2004, 427:247-252.
84. Kok S., de, Stanton L.H., Slaby T., Durot M., Holmes V.F., Patel K.G., Platt D., Shapland E.B., Serber Z., Dean J., Newman J.D., Chandran S.S. Rapid and reliable DNA assembly via ligase cycling reaction. Synth. Biol. 2014, 3:97-106. ACS.
85. Kouprina N., Larionov V. Selective isolation of genomic loci from complex genomes by transformation-associated recombination cloning in the yeast Saccharomyces cerevisiae. Nat. Protoc. 2008, 3:371-377.
86. Kuhlman T.E., Cox E.C. Site-specific chromosomal integration of large synthetic constructs. Nucleic Acids Res. 2010, 38:e92.
87. Kuscu C., Arslan S., Singh R., Thorpe J., Adli M. Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease. Nat. Biotechnol. 2014, 32:677-683.
88. Lam E.T., Hastie A., Lin C., Ehrlich D., Das S.K., Austin M.D., Deshpande P., Cao H., Nagarajan N., Xiao M., Kwok P.-Y. Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly. Nat. Biotechnol. 2012, 30:771-776.
89. Lee J., Yun H., Feist A.M., Palsson B.Ø., Lee S.Y. Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network. Appl. Microbiol. Biotechnol. 2008, 80:849-862.
90. Lee Y., Lafontaine Rivera J.G., Liao J.C. Ensemble modeling for robustness analysis in engineering non-native metabolic pathways. Metab. Eng. 2014, 25:63-71.
91. Lun D.S., Rockwell G., Guido N.J., Baym M., Kelner J.A., Berger B., Galagan J.E., Church G.M. Large-scale identification of genetic design strategies using local search. Mol. Syst. Biol. 2009, 5:296.
92. Lv L., Ren Y.-L., Chen J.-C., Wu Q., Chen G.-Q. Application of CRISPRi for prokaryotic metabolic engineering involving multiple genes, a case study: controllable P(3HB-co-4HB) biosynthesis. Metab. Eng. 2015, 29:160-168.
93. Lynch M.D., Warnecke T., Gill R.T. SCALEs: multiscale analysis of library enrichment. Nat. Methods 2007, 4:87-93.
94. Mali P., Yang L., Esvelt K.M., Aach J., Guell M., DiCarlo J.E., Norville J.E., Church G.M. RNA-guided human genome engineering via Cas9. Science 2013, 339:823-826.
95. Martin V.J.J., Pitera D.J., Withers S.T., Newman J.D., Keasling J.D. Engineering a mevalonate pathway in Escherichia coli for production of terpenoids. Nat. Biotechnol. 2003, 21:796-802.
96. Maruyama T., Dougan S.K., Truttmann M.C., Bilate A.M., Ingram J.R., Ploegh H.L. Increasing the efficiency of precise genome editing with CRISPR-Cas9 by inhibition of nonhomologous end joining. Nat. Biotechnol. 2015, 10.1038/nbt.3190.
97. McCloskey D., Palsson B.Ø., Feist A.M. Basic and applied uses of genomescale metabolic network reconstructions of Escherichia coli. Mol. Syst. Biol. 2013, 9:661.
98. Mercer J., Snijder B., Sacher R., Burkard C., Bleck C.K.E., Stahlberg H., Pelkmans L., Helenius A. RNAi screening reveals proteasome- and Cullin3-dependent stages in vaccinia virus infection. Cell Rep. 2012, 2:1036-1047.
99. Metzker M.L. Sequencing technologies-the next generation. Nat. Rev. Genet. 2010, 11:31-46.
100. Milne C.B., Eddy J.A., Raju R., Ardekani S., Kim P.-J., Senger R.S., Jin Y.-S., Blaschek H.P., Price N.D. Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052. BMC Syst. Biol. 2011, 5:130.
101. Minty J.J., Lesnefsky A.A., Lin F., Chen Y., Zaroff T.A., Veloso A.B., Xie B., McConnell C.A., Ward R.J., Schwartz D.R., Rouillard J.-M., Gao Y., Gulari E., Lin X.N. Evolution combined with genomic study elucidates genetic bases of isobutanol tolerance in Escherichia coli. Microb. Cell Fact. 2011, 10:18.
102. Miskovic L., Hatzimanikatis V. Production of biofuels and biochemicals: in need of an ORACLE. Trends Biotechnol. 2010, 28:391-397.
103. Mojica F.J.M., Díez-Villaseñor C., García-Martínez J., Almendros C. Short motif sequences determine the targets of the prokaryotic CRISPR defence system. Microbiology 2009, 155:733-740.
104. Moriya Y., Shigemizu D., Hattori M., Tokimatsu T., Kotera M., Goto S., Kanehisa M. PathPred: an enzyme-catalyzed metabolic pathway prediction server. Nucleic Acids Res. 2010, 38:W138-W143.
105. Mosberg J.A., Lajoie M.J., Church G.M. Lambda red recombineering in Escherichia coli occurs through a fully single-stranded intermediate. Genetics 2010, 186:791-799.
106. Murphy K.C. Use of bacteriophage lambda recombination functions to promote gene replacement in Escherichia coli. J. Bacteriol. 1998, 180:2063-2071.
107. Murphy R.F. An active role for machine learning in drug development. Nat. Chem. Biol. 2011, 7:327-330.
108. Navid A., Almaas E. Genome-level transcription data of Yersinia pestis analyzed with a new metabolic constraint-based approach. BMC Syst. Biol. 2012, 6:150.
109. Nocon J., Steiger M.G., Pfeffer M., Sohn S.B., Kim T.Y., Maurer M., Rußmayer H., Pflügl S., Ask M., Haberhauer-Troyer C., Ortmayr K., Hann S., Koellensperger G., Gasser B., Lee S.Y., Mattanovich D. Model based engineering of Pichia pastoris central metabolism enhances recombinant protein production. Metab. Eng. 2014, 24:129-138.
110. Nyerges A., Csorgo B., Nagy I., Latinovics D., Szamecz B., Posfai G., Pal C. Conditional DNA repair mutants enable highly precise genome engineering. Nucleic Acids Res. 2014, 42:e62.
111. Orth J.D., Conrad T.M., Na J., Lerman J.A., Nam H., Feist A.M., Palsson B.Ø. A comprehensive genomescale reconstruction of Escherichia coli metabolism-2011. Mol. Syst. Biol. 2011, 7:535.
112. Otto A., Bernhardt J., Hecker M., Becher D. Global relative and absolute quantitation in microbial proteomics. Curr. Opin. Microbiol. 2012, 15:364-372.
113. Paddon C.J., Keasling J.D. Semi-synthetic artemisinin: a model for the use of synthetic biology in pharmaceutical development. Nat. Rev. Microbiol. 2014, 12:355-367.
114. Paley S.M., Karp P.D. The Pathway Tools cellular overview diagram and Omics Viewer. Nucleic Acids Res. 2006, 34:3771-3778.
115. Patil K.R., Rocha I., Förster J., Nielsen J. Evolutionary programming as a platform for in silico metabolic engineering. BMC Bioinform. 2005, 6:308.
116. Pavletich N.P., Pabo C.O. Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A. Science 1991, 252:809-817.
117. Peralta-Yahya P.P., Zhang F., del Cardayre S.B., Keasling J.D. Microbial engineering for the production of advanced biofuels. Nature 2012, 488:320-328.
118. Pines G., Freed E.F., Winkler J.D., Gill R.T. Bacterial recombineering: genome engineering via phage-based homologous recombination. ACS Synth. Biol 2015, 10.1021/acssynbio.5b00009.
119. Pines G., Pines A., Garst A.D., Zeitoun R.I., Lynch S.A., Gill R.T. Codon compression algorithms for saturation mutagenesis. Synth. Biol. 2015, ACS, 0, null.
120. Puchałka J., Oberhardt M.A., Godinho M., Bielecka A., Regenhardt D., Timmis K.N., Papin J.A., Martins dos Santos V.A.P. Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology. PLoS Comput. Biol. 2008, 4:e1000210.
121. Qi L.S., Larson M.H., Gilbert L.A., Doudna J.A., Weissman J.S., Arkin A.P., Lim W.A. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 2013, 152:1173-1183.
122. Quan J., Tian J. Circular polymerase extension cloning for high-throughput cloning of complex and combinatorial DNA libraries. Nat. Protoc. 2011, 6:242-251.
123. Quan J., Tian J. Circular polymerase extension cloning of complex gene libraries and pathways. PLoS One 2009, 4:e6441.
124. Raman S., Rogers J.K., Taylor N.D., Church G.M. Evolution-guided optimization of biosynthetic pathways. Proc. Natl. Acad. Sci. USA 2014, 111:17803-17808.
125. Ranganathan S., Suthers P.F., Maranas C.D. OptForce: an optimization procedure for identifying all genetic manipulations leading to targeted overproductions. PLoS Comput. Biol. 2010, 6:e1000744.
126. Rath D., Amlinger L., Hoekzema M., Devulapally P.R., Lundgren M. Efficient programmable gene silencing by cascade. Nucleic Acids Res. 2015, 43:237-246.
127. Reiter L., Rinner O., Picotti P., Hüttenhain R., Beck M., Brusniak M.-Y., Hengartner M.O., Aebersold R. mProphet: automated data processing and statistical validation for large-scale SRM experiments. Nat. Methods 2011, 8:430-435.
128. Reynolds T.S., Gill R.T. Quantifying impact of chromosome copy number on recombination in Escherichia coli. ACS Synth. Biol. 2015, 10.1021/sb500338g.
129. Rodrigo G., Carrera J., Prather K.J., Jaramillo A. DESHARKY: automatic design of metabolic pathways for optimal cell growth. Bioinformatics 2008, 24:2554-2556.
130. Rossell S., Huynen M.A., Notebaart R.A. Inferring metabolic states in uncharacterized environments using gene-expression measurements. PLoS Comput. Biol. 2013, 9:e1002988.
131. Rouet P., Smih F., Jasin M. Expression of a site-specific endonuclease stimulates homologous recombination in mammalian cells. Proc. Natl. Acad. Sci. USA 1994, 91:6064-6068.
132. Ruano G., Kidd K.K. Direct haplotyping of chromosomal segments from multiple heterozygotes via allele-specific PCR amplification. Nucleic Acids Res. 1989, 17:8392.
133. Sandoval N.R., Kim J.Y.H., Glebes T.Y., Reeder P.J., Aucoin H.R., Warner J.R., Gill R.T. Strategy for directing combinatorial genome engineering in Escherichia coli. Proc. Natl. Acad. Sci. USA 2012, 109:10540-10545.
134. Santos C.N.S., Regitsky D.D., Yoshikuni Y. Implementation of stable and complex biological systems through recombinase-assisted genome engineering. Nat. Commun. 2013, 4:2503.
135. Sawitzke J.A., Costantino N., Li X.-T., Thomason L.C., Bubunenko M., Court C., Court D.L. Probing cellular processes with oligo-mediated recombination and using the knowledge gained to optimize recombineering. J. Mol. Biol. 2011, 407:45-59.
136. Schmidt B.J., Ebrahim A., Metz T.O., Adkins J.N., Palsson B.Ø., Hyduke D.R. GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data. Bioinformatics 2013, 29:2900-2908.
137. Segrè D., Vitkup D., Church G.M. Analysis of optimality in natural and perturbed metabolic networks. Proc. Natl. Acad. Sci. 2002, 99:15112-15117.
138. Shan Q., Wang Y., Li J., Zhang Y., Chen K., Liang Z., Zhang K., Liu J., Xi J.J., Qiu J.-L., Gao C. Targeted genome modification of crop plants using a CRISPR-Cas system. Nat. Biotechnol. 2013, 31:686-688.
139. Shao Z., Zhao Hua, Zhao Huimin DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways. Nucleic Acids Res. 2009, 37:e16.
140. Sharan S.K., Thomason L.C., Kuznetsov S.G., Court D.L. Recombineering: a homologous recombination-based method of genetic engineering. Nat. Protoc. 2009, 4:206-223.
141. Shetty R.P., Endy D., Knight T.F. Engineering BioBrick vectors from BioBrick parts. J. Biol. Eng. 2008, 2:5.
142. Shinfuku Y., Sorpitiporn N., Sono M., Furusawa C., Hirasawa T., Shimizu H. Development and experimental verification of a genome-scale metabolic model for Corynebacterium glutamicum. Microb. Cell Fact. 2009, 8:43.
143. Sims D., Sudbery I., Ilott N.E., Heger A., Ponting C.P. Sequencing depth and coverage: key considerations in genomic analyses. Nat. Rev. Genet. 2014, 15:121-132.
144. Smith A.M., Heisler L.E., Mellor J., Kaper F., Thompson M.J., Chee M., Roth F.P., Giaever G., Nislow C. Quantitative phenotyping via deep barcode sequencing. Genome Res. 2009, 19:1836-1842.
145. Smith A.M., Heisler L.E., St Onge R.P., Farias-Hesson E., Wallace I.M., Bodeau J., Harris A.N., Perry K.M., Giaever G., Pourmand N., Nislow C. Highly-multiplexed barcode sequencing: an efficient method for parallel analysis of pooled samples. Nucleic Acids Res. 2010, 38:e142.
146. Sohn S.B., Graf A.B., Kim T.Y., Gasser B., Maurer M., Ferrer P., Mattanovich D., Lee S.Y. Genome-scale metabolic model of methylotrophic yeast Pichia pastoris and its use for in silico analysis of heterologous protein production. Biotechnol. J. 2010, 5:705-715.
147. Song C.W., Kim D.I., Choi S., Jang J.W., Lee S.Y. Metabolic engineering of Escherichia coli for the production of fumaric acid. Biotechnol. Bioeng. 2013, 110:2025-2034.
148. Sorek R., Cossart P. Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity. Nat. Rev. Genet. 2010, 11:9-16.
149. Sorek R., Lawrence C.M., Wiedenheft B. CRISPR-mediated adaptive immune systems in bacteria and archaea. Annu. Rev. Biochem. 2013, 82:237-266.
150. Stemmer W.P., Crameri A., Ha K.D., Brennan T.M., Heyneker H.L. Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides. Gene 1995, 164:49-53.
151. Swainston N., Smallbone K., Mendes P., Kell D., Paton N. The SuBliMinaL Toolbox: automating steps in the reconstruction of metabolic networks. J. Integr. Bioinform. 2011, 8:186.
152. Töpfer N., Jozefczuk S., Nikoloski Z. Integration of time-resolved transcriptomics data with flux-based methods reveals stress-induced metabolic adaptation in Escherichia coli. BMC Syst. Biol. 2012, 6:148.
153. Tran L.M., Rizk M.L., Liao J.C. Ensemble modeling of metabolic networks. Biophys. J. 2008, 95:5606-5617.
154. Van Opijnen T., Bodi K.L., Camilli A. Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms. Nat. Methods 2009, 6:767-772.
155. Wang H.H., Church G.M. Multiplexed genome engineering and genotyping methods applications for synthetic biology and metabolic engineering. Methods Enzymol. 2011, 498:409-426.
156. Wang H.H., Isaacs F.J., Carr P.A., Sun Z.Z., Xu G., Forest C.R., Church G.M. Programming cells by multiplex genome engineering and accelerated evolution. Nature 2009, 460:894-898.
157. Wang H.H., Kim H., Cong L., Jeong J., Bang D., Church G.M. Genome-scale promoter engineering by coselection MAGE. Nat. Methods 2012, 9:591-593.
158. Wang Y., Eddy J.A., Price N.D. Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE. BMC Syst. Biol. 2012, 6:153.
159. Warner J.R., Reeder P.J., Karimpour-Fard A., Woodruff L.B.A., Gill R.T. Rapid profiling of a microbial genome using mixtures of barcoded oligonucleotides. Nat. Biotechnol. 2010, 28:856-862.
160. Yang L., Cluett W.R., Mahadevan R. EMILiO: a fast algorithm for genome-scale strain design. Metab. Eng. 2011, 13:272-281.
161. Yang H., Wang H., Shivalila C.S., Cheng A.W., Shi L., Jaenisch R. One-step generation of mice carrying reporter and conditional alleles by CRISPR/Cas-mediated genome engineering. Cell 2013, 154:1370-1379.
162. Yang J., Wang Z., Zhu N., Wang B., Chen T., Zhao X. Metabolic engineering of Escherichia coli and in silico comparing of carboxylation pathways for high succinate productivity under aerobic conditions. Microbiol. Res. 2014, 169:432-440.
163. Zhang F., Keasling J. Biosensors and their applications in microbial metabolic engineering. Trends Microbiol. 2011, 19:323-329.
164. Zhang Y., Muyrers J.P., Testa G., Stewart A.F. DNA cloning by homologous recombination in Escherichia coli. Nat. Biotechnol. 2000, 18:1314-1317.
165. Zhang Y., Werling U., Edelmann W. SLiCE: a novel bacterial cell extract-based DNA cloning method. Nucleic Acids Res. 2012, 40:e55.
166. Zeitoun R.I., Garst A.D., Degen G.D., Pines G., Mansell T.J., Glebes T.Y., Boyle N.R., Gill R.T. Multiplexed tracking of combinatorial genomic mutations in engineered cell populations. Nat. Biotechnol. 2015, 33:631-637.
167. Zomorrodi A.R., Lafontaine Rivera J.G., Liao J.C., Maranas C.D. Optimization-driven identification of genetic perturbations accelerates the convergence of model parameters in ensemble modeling of metabolic networks. Biotechnol. J. 2013, 8:1090-1104.