Applied Microbiology and Biotechnology

, Volume 99, Issue 5, pp 2093–2104 | Cite as

Combinatorial and high-throughput screening approaches for strain engineering



Microbes have long been used in the industry to produce valuable biochemicals. Combinatorial engineering approaches, new strain engineering tools derived from inverse metabolic engineering, have started to attract attention in recent years, including genome shuffling, error-prone DNA polymerase, global transcription machinery engineering (gTME), random knockout/overexpression libraries, ribosome engineering, multiplex automated genome engineering (MAGE), customized optimization of metabolic pathways by combinatorial transcriptional engineering (COMPACTER), and library construction of “tunable intergenic regions” (TIGR). Since combinatorial approaches and high-throughput screening methods are fundamentally interconnected, color/fluorescence-based, growth-based, and biosensor-based high-throughput screening methods have been reviewed. We believe that with the help of metabolic engineering tools and new combinatorial approaches, plus effective high-throughput screening methods, researchers will be able to achieve better results on improving microorganism performance under stress or enhancing biochemical yield.


Strain engineering Combinatorial engineering Transcriptional engineering High-throughput screening Global transcription machinery engineering Multiplex automated genome engineering Fine tuning of gene expression 



This work is supported by the National Research Foundation (NRF-CRP-5-2009-03) and the Ministry of Education (MOE2012-T2-2-117), Singapore.


  1. Abe H, Fujita Y, Takaoka Y, Kurita E, Yano S, Tanaka N, Nakayama K (2009a) Ethanol-tolerant Saccharomyces cerevisiae strains isolated under selective conditions by over-expression of a proofreading-deficient DNA polymerase delta. J Biosci Bioeng 108(3):199–204. doi:10.1016/j.jbiosc.2009.03.019 PubMedGoogle Scholar
  2. Abe H, Takaoka Y, Chiba Y, Sato N, Ohgiya S, Itadani A, Hirashima M, Shimoda C, Jigami Y, Nakayama KI (2009b) Development of valuable yeast strains using a novel mutagenesis technique for the effective production of therapeutic glycoproteins. Glycobiology 19(4):428–436. doi:10.1093/glycob/cwn157 PubMedGoogle Scholar
  3. Alper H, Stephanopoulos G (2007) Global transcription machinery engineering: a new approach for improving cellular phenotype. Metab Eng 9(3):258–267. doi:10.1016/j.ymben.2006.12.002 PubMedGoogle Scholar
  4. Alper H, Miyaoku K, Stephanopoulos G (2005) Construction of lycopene-overproducing E. coli strains by combining systematic and combinatorial gene knockout targets. Nat Biotechnol 23(5):612–616. doi:10.1038/Nbt1083 PubMedGoogle Scholar
  5. Alper H, Moxley J, Nevoigt E, Fink GR, Stephanopoulos G (2006) Engineering yeast transcription machinery for improved ethanol tolerance and production. Science 314(5805):1565–1568. doi:10.1126/science.1131969 PubMedGoogle Scholar
  6. Bailey JE, Shurlati A, Hatzimanikatis V, Lee K, Renner WA, Tsai PS (1996) Inverse metabolic engineering: a strategy for directed genetic engineering of useful phenotypes. Biotechnol Bioeng 52(1):109–121. doi:10.1002/(Sici)1097-0290(19961005)52:1<109::Aid-Bit11>3.0.Co;2-J PubMedGoogle Scholar
  7. Basak S, Jiang R (2012) Enhancing E. coli tolerance towards oxidative stress via engineering its global regulator cAMP receptor protein (CRP). PLoS One 7(12):e51179. doi:10.1371/journal.pone.0051179 PubMedCentralPubMedGoogle Scholar
  8. Basak S, Song H, Jiang RR (2012) Error-prone PCR of global transcription factor cyclic AMP receptor protein for enhanced organic solvent (toluene) tolerance. Process Biochem 47(12):2152–2158. doi:10.1016/j.procbio.2012.08.006 Google Scholar
  9. Basak S, Geng H, Jiang R (2014) Rewiring global regulator cAMP receptor protein (CRP) to improve E. coli tolerance towards low pH. J Biotechnol 173:68–75. doi:10.1016/j.jbiotec.2014.01.015 PubMedGoogle Scholar
  10. Binder S, Siedler S, Marienhagen J, Bott M, Eggeling L (2013) Recombineering in Corynebacterium glutamicum combined with optical nanosensors: a general strategy for fast producer strain generation. Nucleic Acids Res 41(12):6360–6369. doi:10.1093/nar/gkt312 PubMedCentralPubMedGoogle Scholar
  11. Biot-Pelletier D, Martin VJ (2014) Evolutionary engineering by genome shuffling. Appl Microbiol Biotechnol 98(9):3877–3887. doi:10.1007/s00253-014-5616-8 PubMedGoogle Scholar
  12. Bonde MT, Klausen MS, Anderson MV, Wallin AI, Wang HH, Sommer MO (2014) MODEST: a web-based design tool for oligonucleotide-mediated genome engineering and recombineering. Nucleic acids research 42(Web Server issue):W408-15 doi: 10.1093/nar/gku428Google Scholar
  13. Bonomo J, Lynch MD, Warnecke T, Price JV, Gill RT (2008) Genome-scale analysis of anti-metabolite directed strain engineering. Metab Eng 10(2):109–120. doi:10.1016/j.ymben.2007.10.002 PubMedGoogle Scholar
  14. Borden JR, Jones SW, Indurthi D, Chen YL, Papoutsakis ET (2010) A genomic-library based discovery of a novel, possibly synthetic, acid-tolerance mechanism in Clostridium acetobutylicum involving non-coding RNAs and ribosomal RNA processing. Metab Eng 12(3):268–281. doi:10.1016/j.ymben.2009.12.004 PubMedCentralPubMedGoogle Scholar
  15. Bro C, Nielsen J (2004) Impact of ‘ome’ analyses on inverse metabolic engineering. Metab Eng 6(3):204–211. doi:10.1016/j.ymben.2003.11.005 PubMedGoogle Scholar
  16. Camps M, Naukkarinen J, Johnson BP, Loeb LA (2003) Targeted gene evolution in Escherichia coli using a highly error-prone DNA polymerase I. Proc Natl Acad Sci U S A 100(17):9727–9732. doi:10.1073/pnas.1333928100 PubMedCentralPubMedGoogle Scholar
  17. Carr PA, Wang HH, Sterling B, Isaacs FJ, Lajoie MJ, Xu G, Church GM, Jacobson JM (2012) Enhanced multiplex genome engineering through co-operative oligonucleotide co-selection. Nucleic Acids Res 40(17):e132. doi:10.1093/nar/gks455 PubMedCentralPubMedGoogle Scholar
  18. Chalova VI, Kim WK, Woodward CL, Ricke SC (2007) Quantification of total and bioavailable lysine in feed protein sources by a whole-cell green fluorescent protein growth-based Escherichia coli biosensor. Appl Microbiol Biot 76(1):91–99. doi:10.1007/s00253-007-0989-6 Google Scholar
  19. Chen T, Wang J, Yang R, Li J, Lin M, Lin Z (2011) Laboratory-evolved mutants of an exogenous global regulator, IrrE from Deinococcus radiodurans, enhance stress tolerances of Escherichia coli. PLoS One 6(1):e16228. doi:10.1371/journal.pone.0016228 PubMedCentralPubMedGoogle Scholar
  20. Chong H, Huang L, Yeow J, Wang I, Zhang H, Song H, Jiang R (2013a) Improving ethanol tolerance of Escherichia coli by rewiring its global regulator cAMP receptor protein (CRP). PLoS One 8(2):e57628. doi:10.1371/journal.pone.0057628 PubMedCentralPubMedGoogle Scholar
  21. Chong H, Yeow J, Wang I, Song H, Jiang R (2013b) Improving acetate tolerance of Escherichia coli by rewiring its global regulator cAMP receptor protein (CRP). PLoS One 8(10):e77422. doi:10.1371/journal.pone.0077422 PubMedCentralPubMedGoogle Scholar
  22. Chong H, Geng H, Zhang H, Song H, Huang L, Jiang R (2014) Enhancing E. coli isobutanol tolerance through engineering its global transcription factor cAMP receptor protein (CRP). Biotechnol Bioeng 111(4):700–708. doi:10.1002/bit.25134 PubMedGoogle Scholar
  23. Dai MH, Ziesman S, Ratcliffe T, Gill RT, Copley SD (2005) Visualization of protoplast fusion and quantitation of recombination in fused protoplasts of auxotrophic strains of Escherichia coli. Metab Eng 7(1):45–52. doi:10.1016/j.ymben.2004.09.002 PubMedGoogle Scholar
  24. Dietrich JA, McKee AE, Keasling JD (2010) High-throughput metabolic engineering: advances in small-molecule screening and selection. Annu Rev Biochem 79:563–590. doi:10.1146/annurev-biochem-062608-095938 PubMedGoogle Scholar
  25. Dietrich JA, Shis DL, Alikhani A, Keasling JD (2013) Transcription factor-based screens and synthetic selections for microbial small-molecule biosynthesis. ACS Synth Biol 2(1):47–58. doi:10.1021/Sb300091d PubMedGoogle Scholar
  26. Du J, Yuan Y, Si T, Lian J, Zhao H (2012) Customized optimization of metabolic pathways by combinatorial transcriptional engineering. Nucleic Acids Res 40(18):e142. doi:10.1093/nar/gks549 PubMedCentralPubMedGoogle Scholar
  27. Esvelt KM, Carlson JC, Liu DR (2011) A system for the continuous directed evolution of biomolecules. Nature 472(7344):499–503. doi:10.1038/nature09929 PubMedCentralPubMedGoogle Scholar
  28. Glebes TY, Sandoval NR, Reeder PJ, Schilling KD, Zhang M, Gill RT (2014) Genome-wide mapping of furfural tolerance genes in Escherichia coli. PLoS One 9(1):e87540. doi:10.1371/journal.pone.0087540 PubMedCentralPubMedGoogle Scholar
  29. Glick BR (1995) Metabolic load and heterologous gene-expression. Biotechnol Adv 13(2):247–261. doi:10.1016/0734-9750(95)00004-A PubMedGoogle Scholar
  30. Gong J, Zheng H, Wu Z, Chen T, Zhao X (2009) Genome shuffling: progress and applications for phenotype improvement. Biotechnol Adv 27(6):996–1005. doi:10.1016/j.biotechadv.2009.05.016 PubMedGoogle Scholar
  31. Hong ME, Lee KS, Yu BJ, Sung YJ, Park SM, Koo HM, Kweon DH, Park JC, Jin YS (2010a) Identification of gene targets eliciting improved alcohol tolerance in Saccharomyces cerevisiae through inverse metabolic engineering. J Biotechnol 149(1–2):52–59. doi:10.1016/j.jbiotec.2010.06.006 PubMedGoogle Scholar
  32. Hong SH, Lee J, Wood TK (2010b) Engineering global regulator Hha of Escherichia coli to control biofilm dispersal. Microb Biotechnol 3(6):717–728. doi:10.1111/j.1751-7915.2010.00220.x PubMedCentralPubMedGoogle Scholar
  33. Hong SH, Wang XX, Wood TK (2010c) Controlling biofilm formation, prophage excision and cell death by rewiring global regulator H-NS of Escherichia coli. Microb Biotechnol 3(3):344–356. doi:10.1111/j.1751-7915.2010.00164.x PubMedCentralPubMedGoogle Scholar
  34. Hosaka T, Ohnishi-Kameyama M, Muramatsu H, Murakami K, Tsurumi Y, Kodani S, Yoshida M, Fujie A, Ochi K (2009) Antibacterial discovery in actinomycetes strains with mutations in RNA polymerase or ribosomal protein S12. Nat Biotechnol 27(5):462–464. doi:10.1038/Nbt.1538 PubMedGoogle Scholar
  35. Hotchkiss RD, Gabor MH (1980) Biparental products of bacterial protoplast fusion showing unequal parental chromosome expression. P Natl Acad Sci-Biol 77(6):3553–3557. doi:10.1073/pnas.77.6.3553 Google Scholar
  36. Itakura M, Tabata K, Eda S, Mitsui H, Murakami K, Yasuda J, Minamisawa K (2008) Generation of Bradyrhizobium japonicum mutants with increased N2O reductase activity by selection after introduction of a mutated dnaQ gene. Appl Environ Microbiol 74(23):7258–7264. doi:10.1128/AEM. 01850-08 PubMedCentralPubMedGoogle Scholar
  37. Jin YS, Stephanopoulos G (2007) Multi-dimensional gene target search for improving lycopene biosynthesis in Escherichia coli. Metab Eng 9(4):337–347. doi:10.1016/j.ymben.2007.03.003 PubMedGoogle Scholar
  38. Kang JS, Kim JS (2000) Zinc finger proteins as designer transcription factors. J Biol Chem 275(12):8742–8748. doi:10.1074/jbc.275.12.8742 PubMedGoogle Scholar
  39. Keasling JD (2010) Manufacturing molecules through metabolic engineering. Science 330(6009):1355–1358. doi:10.1126/science.1193990 PubMedGoogle Scholar
  40. Kim MI, Yu BJ, Woo MA, Cho D, Dordick JS, Cho JH, Choi BO, Park HG (2010) Multiplexed amino acid array utilizing bioluminescent Escherichia coli auxotrophs. Anal Chem 82(10):4072–4077. doi:10.1021/Ac100087r PubMedGoogle Scholar
  41. Kim OC, Kim SY, Hwang DH, Oh DB, Kang HA, Kwon O (2013) Development of a genome-wide random mutagenesis system using proofreading-deficient DNA polymerase delta in the methylotrophic yeast Hansenula polymorpha. J Microbiol Biotechn 23(3):304–312. doi:10.4014/jmb.1211.11048 Google Scholar
  42. Klein-Marcuschamer D, Stephanopoulos G (2008) Assessing the potential of mutational strategies to elicit new phenotypes in industrial strains. Proc Natl Acad Sci U S A 105(7):2319–2324. doi:10.1073/pnas.0712177105 PubMedCentralPubMedGoogle Scholar
  43. Klein-Marcuschamer D, Stephanopoulos G (2010) Method for designing and optimizing random-search libraries for strain improvement. Appl Environ Microb 76(16):5541–5546. doi:10.1128/Aem. 00828-10 Google Scholar
  44. Klein-Marcuschamer D, Santos CNS, Yu HM, Stephanopoulos G (2009) Mutagenesis of the bacterial RNA polymerase alpha subunit for improvement of complex phenotypes. Appl Environ Microb 75(9):2705–2711. doi:10.1128/Aem. 01888-08 Google Scholar
  45. Lee JY, Sung BH, Yu BJ, Lee JH, Lee SH, Kim MS, Koob MD, Kim SC (2008) Phenotypic engineering by reprogramming gene transcription using novel artificial transcription factors in Escherichia coli. Nucleic Acids Res 36(16):e102. doi:10.1093/nar/gkn449 PubMedCentralPubMedGoogle Scholar
  46. Lee JY, Yang KS, Jang SA, Sung BH, Kim SC (2011) Engineering butanol-tolerance in Escherichia coli with artificial transcription factor libraries. Biotechnol Bioeng 108(4):742–749. doi:10.1002/bit.22989 PubMedGoogle Scholar
  47. Lee JH, Lee SH, Yim SS, Kang KH, Lee SY, Park SJ, Jeong KJ (2013a) Quantified high-throughput screening of Escherichia coli producing poly(3-hydroxybutyrate) based on FACS. Appl Biochem Biotech 170(7):1767–1779. doi:10.1007/s12010-013-0311-2 Google Scholar
  48. Lee SW, Kim E, Kim JS, Oh MK (2013b) Artificial transcription regulator as a tool for improvement of cellular property in Saccharomyces cerevisiae. Chem Eng Sci 103(15):42–49. doi:10.1016/j.ces.2012.09.007 Google Scholar
  49. Li L, Ma T, Liu Q, Huang Y, Hu C, Liao G (2013) Improvement of daptomycin production in Streptomyces roseosporus through the acquisition of pleuromutilin resistance. BioMed Res Int 2013:479742. doi:10.1155/2013/479742 PubMedCentralPubMedGoogle Scholar
  50. Li W, Chen G, Gu L, Zeng W, Liang Z (2014) Genome shuffling of Aspergillus niger for improving transglycosylation activity. Appl Biochem Biotechnol 172(1):50–61. doi:10.1007/s12010-013-0421-x PubMedGoogle Scholar
  51. Liu HM, Yan M, Lai CG, Xu L, Ouyang PK (2010) gTME for improved xylose fermentation of Saccharomyces cerevisiae. Appl Biochem Biotech 160(2):574–582. doi:10.1007/s12010-008-8431-9 Google Scholar
  52. Liu HM, Liu K, Yan M, Xu L, Ouyang PK (2011) gTME for improved adaptation of Saccharomyces cerevisiae to corn cob acid hydrolysate. Appl Biochem Biotech 164(7):1150–1159. doi:10.1007/s12010-011-9201-7 Google Scholar
  53. Liu Z, Zhao X, Bai F (2013) Production of xylanase by an alkaline-tolerant marine-derived Streptomyces viridochromogenes strain and improvement by ribosome engineering. Appl Microbiol Biotechnol 97(10):4361–4368. doi:10.1007/s00253-012-4290-y PubMedGoogle Scholar
  54. Loh E, Salk JJ, Loeb LA (2010) Optimization of DNA polymerase mutation rates during bacterial evolution. Proc Natl Acad Sci U S A 107(3):1154–1159. doi:10.1073/pnas.0912451107 PubMedCentralPubMedGoogle Scholar
  55. Lynch MD, Warnecke T, Gill RT (2007) SCALEs: multiscale analysis of library enrichment. Nat Methods 4(1):87–93. doi:10.1038/Nmeth946 PubMedGoogle Scholar
  56. Matsuzawa T, Fujita Y, Tanaka N, Tohda H, Itadani A, Takegawa K (2011) New insights into galactose metabolism by Schizosaccharomyces pombe: isolation and characterization of a galactose-assimilating mutant. J Biosci Bioeng 111(2):158–166. doi:10.1016/j.jbiosc.2010.10.007 PubMedGoogle Scholar
  57. Michener JK, Smolke CD (2012) High-throughput enzyme evolution in Saccharomyces cerevisiae using a synthetic RNA switch. Metab Eng 14(4):306–316. doi:10.1016/j.ymben.2012.04.004 PubMedGoogle Scholar
  58. Miller JH (1996) Spontaneous mutators in bacteria: insights into pathways of mutagenesis and repair. Annu Rev Microbiol 50:625–643. doi:10.1146/annurev.micro.50.1.625 PubMedGoogle Scholar
  59. Mustafi N, Grunberger A, Kohlheyer D, Bott M, Frunzke J (2012) The development and application of a single-cell biosensor for the detection of L-methionine and branched-chain amino acids. Metab Eng 14(4):449–457. doi:10.1016/j.ymben.2012.02.002 PubMedGoogle Scholar
  60. Mutalik VK, Guimaraes JC, Cambray G, Lam C, Christoffersen MJ, Mai QA, Tran AB, Paull M, Keasling JD, Arkin AP, Endy D (2013) Precise and reliable gene expression via standard transcription and translation initiation elements. Nat Methods 10(4):354–360. doi:10.1038/nmeth.2404 PubMedGoogle Scholar
  61. Na D, Yoo SM, Chung H, Park H, Park JH, Lee SY (2013) Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs. Nat Biotechnol 31(2):170–174. doi:10.1038/nbt.2461 PubMedGoogle Scholar
  62. Nicolaou SA, Gaida SM, Papoutsakis ET (2011) Coexisting/Coexpressing Genomic Libraries (CoGeL) identify interactions among distantly located genetic loci for developing complex microbial phenotypes. Nucleic Acids Res 39(22):e152. doi:10.1093/nar/gkr817 PubMedCentralPubMedGoogle Scholar
  63. Nicolaou SA, Gaida SM, Papoutsakis ET (2012) Exploring the combinatorial genomic space in Escherichia coli for ethanol tolerance. Biotechnol J 7(11):1337–1345. doi:10.1002/biot.201200227 PubMedGoogle Scholar
  64. Ochi K (2007) From microbial differentiation to ribosome engineering. Biosci Biotech Bioch 71(6):1373–1386. doi:10.1271/Bbb.70007 Google Scholar
  65. Ochi K, Okamoto S, Tozawa Y, Inaoka T, Hosaka T, Xu J, Kurosawa K (2004) Ribosome engineering and secondary metabolite production. Adv Appl Microbiol 56:155–184. doi:10.1016/S0065-2164(04)56005-7 PubMedGoogle Scholar
  66. Ozaydin B, Burd H, Lee TS, Keasling JD (2013) Carotenoid-based phenotypic screen of the yeast deletion collection reveals new genes with roles in isoprenoid production. Metab Eng 15:174–183. doi:10.1016/j.ymben.2012.07.010 PubMedGoogle Scholar
  67. Park KS, Lee DK, Lee H, Lee Y, Jang YS, Kim YH, Yang HY, Lee SI, Seol W, Kim JS (2003) Phenotypic alteration of eukaryotic cells using randomized libraries of artificial transcription factors. Nat Biotechnol 21(10):1208–1214. doi:10.1038/Nbt868 PubMedGoogle Scholar
  68. Park KS, Jang YS, Lee H, Kim JS (2005) Phenotypic alteration and target gene identification using combinatorial libraries of zinc finger proteins in prokaryotic cells. J Bacteriol 187(15):5496–5499. doi:10.1128/Jb.187.15.5496-5499.2005 PubMedCentralPubMedGoogle Scholar
  69. Park EY, Ito Y, Nariyama M, Sugimoto T, Lies D, Kato T (2011) The improvement of riboflavin production in Ashbya gossypii via disparity mutagenesis and DNA microarray analysis. Appl Microbiol Biot 91(5):1315–1326. doi:10.1007/s00253-011-3325-0 Google Scholar
  70. Pfleger BF, Pitera DJ, Smolke D, Keasling CJD (2006) Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes. Nat Biotechnol 24(8):1027–1032. doi:10.1038/Nbt1226 PubMedGoogle Scholar
  71. Pfleger BF, Pitera DJ, Newman JD, Martin VJJ, Keasling JD (2007) Microbial sensors for small molecules: development of a mevalonate biosensor. Metab Eng 9(1):30–38. doi:10.1016/j.ymben.2006.08.002 PubMedGoogle Scholar
  72. Qin X, Qian J, Yao G, Zhuang Y, Zhang S, Chu J (2011) GAP promoter library for fine-tuning of gene expression in Pichia pastoris. Appl Environ Microbiol 77(11):3600–3608. doi:10.1128/AEM.%2002843-10
  73. Sandoval NR, Mills TY, Zhang M, Gill RT (2011) Elucidating acetate tolerance in E. coli using a genome-wide approach. Metab Eng 13(2):214–224. doi:10.1016/j.ymben.2010.12.001 PubMedGoogle Scholar
  74. Santos CNS, Stephanopoulos G (2008) Combinatorial engineering of microbes for optimizing cellular phenotype. Curr Opin Chem Biol 12(2):168–176. doi:10.1016/j.cbpa.2008.01.017 PubMedGoogle Scholar
  75. Seo SW, Yang JS, Kim I, Yang J, Min BE, Kim S, Jung GY (2013) Predictive design of mRNA translation initiation region to control prokaryotic translation efficiency. Metab Eng 15:67–74. doi:10.1016/j.ymben.2012.10.006 PubMedGoogle Scholar
  76. Shimoda C, Itadani A, Sugino A, Furusawa M (2006) Isolation of thermotolerant mutants by using proofreading-deficient DNA polymerase delta as an effective mutator in Saccharomyces cerevisiae. Genes Genet Syst 81(6):391–397. doi:10.1266/Ggs.81.391 PubMedGoogle Scholar
  77. Shiwa Y, Fukushima-Tanaka S, Kasahara K, Horiuchi T, Yoshikawa H (2012) Whole-genome profiling of a novel mutagenesis technique using proofreading-deficient DNA polymerase. Int J Evol Biol 2012:860797. doi:10.1155/2012/860797 PubMedCentralPubMedGoogle Scholar
  78. Siedler S, Stahlhut SG, Malla S, Maury J, Neves AR (2013) Novel biosensors based on flavonoid-responsive transcriptional regulators introduced into Escherichia coli. Metab Eng 21:2–8. doi:10.1016/j.ymben.2013.10.011 PubMedGoogle Scholar
  79. Singh A, Lynch MD, Gill RT (2009) Genes restoring redox balance in fermentation-deficient E. coli NZN111. Metab Eng 11(6):347–354. doi:10.1016/j.ymben.2009.07.002 PubMedGoogle Scholar
  80. Stephanopoulos G (2008) Metabolic engineering: enabling technology for biofuels production. Metab Eng 10(6):293–294. doi:10.1016/j.ymben.2008.10.003 PubMedGoogle Scholar
  81. Struble JM, Gill RT (2009) Genome-scale identification method applied to find cryptic aminoglycoside resistance genes in Pseudomonas aeruginosa. PLoS One 4(11):e6576. doi:10.1371/journal.pone.0006576 PubMedCentralPubMedGoogle Scholar
  82. Suzuki T, Seta K, Nishikawa C, Hara E, Shigeno T, Nakajima-Kambe T (2015) Improved ethanol tolerance and ethanol production from glycerol in a streptomycin-resistant Klebsiella variicola mutant obtained by ribosome engineering. Bioresour Technol 176:156–162. doi:10.1016/j.biortech.2014.10.153 PubMedGoogle Scholar
  83. Tanaka Y, Komatsu M, Okamoto S, Tokuyama S, Kaji A, Ikeda H, Ochi K (2009) Antibiotic overproduction by rpsL and rsmG mutants of various actinomycetes. Appl Environ Microb 75(14):4919–4922. doi:10.1128/Aem. 00681-09 Google Scholar
  84. Tanaka Y, Kasahara K, Hirose Y, Murakami K, Kugimiya R, Ochi K (2013) Activation and products of the cryptic secondary metabolite biosynthetic gene clusters by rifampin resistance (rpoB) mutations in actinomycetes. J Bacteriol 195(13):2959–2970. doi:10.1128/JB.00147-13 PubMedCentralPubMedGoogle Scholar
  85. Tang SY, Cirino PC (2011) Design and application of a mevalonate-responsive regulatory protein. Angew Chem Int Edit 50(5):1084–1086. doi:10.1002/anie.201006083 Google Scholar
  86. Tang SY, Qian S, Aldnterinwa O, Frei CS, Gredell JA, Cirino PC (2013) Screening for enhanced triacetic acid lactone production by recombinant Escherichia coli expressing a designed triacetic acid lactone reporter. J Am Chem Soc 135(27):10099–10103. doi:10.1021/Ja402654z PubMedGoogle Scholar
  87. Tannler S, Zamboni N, Kiraly C, Aymerich S, Sauer U (2008) Screening of Bacillus subtilis transposon mutants with altered riboflavin production. Metab Eng 10(5):216–226. doi:10.1016/j.ymben.2008.06.002 PubMedGoogle Scholar
  88. Tepper N, Shlomi T (2011) Computational design of auxotrophy-dependent microbial biosensors for combinatorial metabolic engineering experiments. PLoS One 6(1):e16274. doi:10.1371/journal.pone.0016274 PubMedCentralPubMedGoogle Scholar
  89. Tyo KEJ, Espinoza FA, Stephanopoulos G, Jin YS (2009) Identification of gene disruptions for increased poly-3-hydroxybutyrate accumulation in Synechocystis PCC 6803. Biotechnol Progr 25(5):1236–1243. doi:10.1002/Btpr.228 Google Scholar
  90. Wang G, Hosaka T, Ochi K (2008) Dramatic activation of antibiotic production in Streptomyces coelicolor by cumulative drug resistance mutations. Appl Environ Microbiol 74(9):2834–2840. doi:10.1128/AEM.%2002800-07
  91. Wang G, Inaoka T, Okamoto S, Ochi K (2009a) A novel insertion mutation in Streptomyces coelicolor ribosomal s12 protein results in paromomycin resistance and antibiotic overproduction. Antimicrob Agents Ch 53(3):1019–1026. doi:10.1128/Aac.%2000388-08
  92. Wang HH, Isaacs FJ, Carr PA, Sun ZZ, Xu G, Forest CR, Church GM (2009b) Programming cells by multiplex genome engineering and accelerated evolution. Nature 460(7257):894–898. doi:10.1038/nature08187 PubMedGoogle Scholar
  93. Wang HH, Kim H, Cong L, Jeong J, Bang D, Church GM (2012a) Genome-scale promoter engineering by coselection MAGE. Nat Methods 9(6):591–593. doi:10.1038/nmeth.1971 PubMedCentralPubMedGoogle Scholar
  94. Wang JQ, Zhang Y, Chen YL, Lin M, Lin ZL (2012b) Global regulator engineering significantly improved Escherichia coli tolerances toward inhibitors of lignocellulosic hydrolysates. Biotechnol Bioeng 109(12):3133–3142. doi:10.1002/Bit.24574 PubMedGoogle Scholar
  95. Wang H, Yang L, Wu K, Li G (2014a) Rational selection and engineering of exogenous principal sigma factor (sigma(HrdB)) to increase teicoplanin production in an industrial strain of Actinoplanes teichomyceticus. Microb Cell Factories 13:10. doi:10.1186/1475-2859-13-10 Google Scholar
  96. Wang Q, Zhang D, Li Y, Zhang F, Wang C, Liang X (2014b) Genome shuffling and ribosome engineering of Streptomyces actuosus for high-yield nosiheptide production. Appl Biochem Biotechnol 173(6):1553–1563. doi:10.1007/s12010-014-0948-5 PubMedGoogle Scholar
  97. Warnecke TE, Lynch MD, Karimpour-Fard A, Sandoval N, Gill RT (2008) A genomics approach to improve the analysis and design of strain selections. Metab Eng 10(3–4):154–165. doi:10.1016/j.ymben.2008.04.004 PubMedGoogle Scholar
  98. Warnecke TE, Lynch MD, Karimpour-Fard A, Lipscomb ML, Handke P, Mills T, Ramey CJ, Hoang T, Gill RT (2010) Rapid dissection of a complex phenotype through genomic-scale mapping of fitness altering genes. Metab Eng 12(3):241–250. doi:10.1016/j.ymben.2009.12.002 PubMedGoogle Scholar
  99. Winkler J, Kao KC (2012) Harnessing recombination to speed adaptive evolution in Escherichia coli. Metab Eng 14(5):487–495. doi:10.1016/j.ymben.2012.07.004 PubMedGoogle Scholar
  100. Woodruff LB, Boyle NR, Gill RT (2013a) Engineering improved ethanol production in Escherichia coli with a genome-wide approach. Metab Eng 17:1–11. doi:10.1016/j.ymben.2013.01.006 PubMedGoogle Scholar
  101. Woodruff LBA, Pandhal J, Ow SY, Karimpour-Fard A, Weiss SJ, Wright PC, Gill RT (2013b) Genome-scale identification and characterization of ethanol tolerance genes in Escherichia coli. Metab Eng 15:124–133. doi:10.1016/j.ymben.2012.10.007 PubMedGoogle Scholar
  102. Yang J, Seo SW, Jang S, Shin SI, Lim CH, Roh TY, Jung GY (2013) Synthetic RNA devices to expedite the evolution of metabolite-producing microbes. Nat Commun 4:1413. doi:10.1038/ncomms2404 PubMedGoogle Scholar
  103. Yu H, Tyo K, Alper H, Klein-Marcuschamer D, Stephanopoulos G (2008) A high-throughput screen for hyaluronic acid accumulation in recombinant Escherichia coli transformed by libraries of engineered sigma factors. Biotechnol Bioeng 101(4):788-796 doi:10.1002/Bit.21947Google Scholar
  104. Yu G, Hu Y, Hui M, Chen L, Wang L, Liu N, Yin Y, Zhao J (2014) Genome shuffling of Streptomyces roseosporus for improving daptomycin production. Appl Biochem Biotechnol 172(5):2661–2669. doi:10.1007/s12010-013-0687-z PubMedGoogle Scholar
  105. Zelcbuch L, Antonovsky N, Bar-Even A, Levin-Karp A, Barenholz U, Dayagi M, Liebermeister W, Flamholz A, Noor E, Amram S, Brandis A, Bareia T, Yofe I, Jubran H, Milo R (2013) Spanning high-dimensional expression space using ribosome-binding site combinatorics. Nucleic Acids Res 41(9):e98. doi:10.1093/nar/gkt151 PubMedCentralPubMedGoogle Scholar
  106. Zhang YX, Perry K, Vinci VA, Powell K, Stemmer WP, del Cardayre SB (2002) Genome shuffling leads to rapid phenotypic improvement in bacteria. Nature 415(6872):644–646. doi:10.1038/415644a PubMedGoogle Scholar
  107. Zhang F, Carothers JM, Keasling JD (2012a) Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids. Nat Biotechnol 30(4):354–359. doi:10.1038/nbt.2149 PubMedGoogle Scholar
  108. Zhang HF, Chong HQ, Ching CB, Jiang RR (2012b) Random mutagenesis of global transcription factor cAMP receptor protein for improved osmotolerance. Biotechnol Bioeng 109(5):1165–1172. doi:10.1002/Bit.24411 PubMedGoogle Scholar
  109. Zhang HF, Chong HQ, Ching CB, Song H, Jiang RR (2012c) Engineering global transcription factor cyclic AMP receptor protein of Escherichia coli for improved 1-butanol tolerance. Appl Microbiol Biot 94(4):1107–1117. doi:10.1007/s00253-012-4012-5 Google Scholar
  110. Zhao H, Li J, Han B, Li X, Chen J (2014) Improvement of oxidative stress tolerance in Saccharomyces cerevisiae through global transcription machinery engineering. J Indust Microbiol Biotechnol 41(5):869–878. doi:10.1007/s10295-014-1421-8 Google Scholar
  111. Zheng DQ, Chen J, Zhang K, Gao KH, Li O, Wang PM, Zhang XY, Du FG, Sun PY, Qu AM, Wu S, Wu XC (2014) Genomic structural variations contribute to trait improvement during whole-genome shuffling of yeast. Appl Microbiol Biotechnol 98(7):3059–3070. doi:10.1007/s00253-013-5423-7 PubMedGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  1. 1.School of Chemical and Biomedical EngineeringNanyang Technological UniversitySingaporeSingapore

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