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Expression Platforms for Functional Metagenomics: Emerging Technology Options Beyond Escherichia coli

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Functional Metagenomics: Tools and Applications

Abstract

Escherichia coli is the prime workhorse for various metagenomic applications due to the multitude of efficient tools available for genetic manipulation and controlled heterologous gene expression. However, metagenome-based bioprospecting efforts continuously target a wider spectrum of ecological niches in order to harvest new enzymes and bioactive compounds for industrial and medical applications from the enormous pool of natural microbial diversity. Consequently, the development of robust and flexible screening platforms that allow functional evaluation of an expanded fraction of the highly diverse metagenomic information is widely addressed in Functional Metagenomics research. The heterologous recognition of transcriptional regulators and promotors, diverse codon usages among environmental microorganisms, and sufficient supply of precursors for secondary metabolite formation are major challenges that are addressed by an increasing spectrum of alternative expression and host systems. This includes optimized broad host-range transfer and expression vectors, screening hosts for improved gene expression and metabolite formation, as well as cell-free expression systems to cover proteins that due to toxicity are inaccessible by in vivo screening methods. In this chapter, we provide a current overview of the state of the art of selected expression systems and host organisms useful for functional metagenome screening for new enzymes and bioactive metabolites, as emerging options beyond what is currently available in and for E. coli.

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References

  • Aakvik T, Degnes KF, Dahlsrud R, Schmidt F, Dam R, Yu L, Volker U, Ellingsen TE, Valla S (2009) A plasmid RK2-based broad-host-range cloning vector useful for transfer of metagenomic libraries to a variety of bacterial species. FEMS Microbiol Lett 296(2):149–158. doi:10.1111/j.1574-6968.2009.01639.x

    Article  CAS  PubMed  Google Scholar 

  • Ahn JH, Chu HS, Kim TW, Oh IS, Choi CY, Hahn GH, Park CG, Kim DM (2005) Cell-free synthesis of recombinant proteins from PCR-amplified genes at a comparable productivity to that of plasmid-based reactions. Biochem Biophys Res Commun 338(3):1346–1352. doi:10.1016/j.bbrc.2005.10.094

    Article  CAS  PubMed  Google Scholar 

  • Alam MT, Merlo ME, Consortium S, Hodgson DA, Wellington EM, Takano E, Breitling R (2010) Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor. BMC Genomics 11:202. doi:10.1186/1471-2164-11-202

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Angelov A, Mientus M, Liebl S, Liebl W (2009) A two-host fosmid system for functional screening of (meta)genomic libraries from extreme thermophiles. Syst Appl Microbiol 32(3):177–185. doi:10.1016/j.syapm.2008.01.003

    Article  CAS  PubMed  Google Scholar 

  • Baltz RH (2008) Renaissance in antibacterial discovery from actinomycetes. Curr Opin Pharmacol 8(5):557–563. doi:10.1016/j.coph.2008.04.008

    Article  CAS  PubMed  Google Scholar 

  • Baltz RH (2010) Streptomyces and Saccharopolyspora hosts for heterologous expression of secondary metabolite gene clusters. J Ind Microbiol Biotechnol 37(8):759–772. doi:10.1007/s10295-010-0730-9

    Article  CAS  PubMed  Google Scholar 

  • Barka EA, Vatsa P, Sanchez L, Gaveau-Vaillant N, Jacquard C, Klenk HP, Clement C, Ouhdouch Y, van Wezel GP (2016) Taxonomy, physiology, and natural products of actinobacteria. Microbiol Mol Biol Rev 80(1):1–43. doi:10.1128/MMBR.00019-15

    Article  PubMed  Google Scholar 

  • Battke F, Herbig A, Wentzel A, Jakobsen ØM, Bonin M, Hodgson DA, Wohlleben W, Ellingsen TE, Consortium S, Nieselt K (2011) A technical platform for generating reproducible expression data from Streptomyces coelicolor batch cultivations. In: Arabnia HR, Tran QN (eds) Software tools and algorithms for biological systems. Springer, New York, pp 3–15. doi:10.1007/978-1-4419-7046-6_1

    Chapter  Google Scholar 

  • Bentley SD, Chater KF, Cerdeno-Tarraga AM, Challis GL, Thomson NR, James KD, Harris DE, Quail MA, Kieser H, Harper D, Bateman A, Brown S, Chandra G, Chen CW, Collins M, Cronin A, Fraser A, Goble A, Hidalgo J, Hornsby T, Howarth S, Huang CH, Kieser T, Larke L, Murphy L, Oliver K, O'Neil S, Rabbinowitsch E, Rajandream MA, Rutherford K, Rutter S, Seeger K, Saunders D, Sharp S, Squares R, Squares S, Taylor K, Warren T, Wietzorrek A, Woodward J, Barrell BG, Parkhill J, Hopwood DA (2002) Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 417(6885):141–147. doi:10.1038/417141a

    Article  PubMed  Google Scholar 

  • Bibb MJ (2005) Regulation of secondary metabolism in streptomycetes. Curr Opin Microbiol 8(2):208–215. doi:10.1016/j.mib.2005.02.016

    Article  CAS  PubMed  Google Scholar 

  • Biver S, Steels S, Portetelle D, Vandenbol M (2013) Bacillus subtilis as a tool for screening soil metagenomic libraries for antimicrobial activities. J Microbiol Biotechnol 23(6):850–855. doi:10.4014/jmb.1212.12008

    Article  CAS  PubMed  Google Scholar 

  • Bjerga GEK, Williamson AK (2015) Cold shock induction of recombinant Arctic environmental genes. BMC Biotechnol 15(1):1–12. doi:10.1186/s12896-015-0185-1

    Article  CAS  Google Scholar 

  • Brady SF (2007) Construction of soil environmental DNA cosmid libraries and screening for clones that produce biologically active small molecules. Nat Protoc 2(5):1297–1305. doi:10.1038/nprot.2007.195

    Article  CAS  PubMed  Google Scholar 

  • Brouns SJ, Wu H, Akerboom J, Turnbull AP, de Vos WM, van der Oost J (2005) Engineering a selectable marker for hyperthermophiles. J Biol Chem 280(12):11422–11431. doi:10.1074/jbc.M413623200

    Article  CAS  PubMed  Google Scholar 

  • Calhoun KA, Swartz JR (2007) Energy systems for ATP regeneration in cell-free protein synthesis reactions. Methods Mol Biol 375:3–17. doi:10.1007/978-1-59745-388-2_1

    CAS  PubMed  Google Scholar 

  • Catherine C, Lee KH, Oh SJ, Kim DM (2013) Cell-free platforms for flexible expression and screening of enzymes. Biotechnol Adv 31(6):797–803. doi:10.1016/j.biotechadv.2013.04.009

    Article  CAS  PubMed  Google Scholar 

  • Cava F, Laptenko O, Borukhov S, Chahlafi Z, Blas-Galindo E, Gomez-Puertas P, Berenguer J (2007) Control of the respiratory metabolism of Thermus thermophilus by the nitrate respiration conjugative element NCE. Mol Microbiol 64(3):630–646. doi:10.1111/j.1365-2958.2007.05687.x

    Article  CAS  PubMed  Google Scholar 

  • Cava F, Hidalgo A, Berenguer J (2009) Thermus thermophilus as biological model. Extremophiles 13(2):213–231. doi:10.1007/s00792-009-0226-6

    Article  CAS  PubMed  Google Scholar 

  • Cavicchioli R, Charlton T, Ertan H, Mohd Omar S, Siddiqui KS, Williams TJ (2011) Biotechnological uses of enzymes from psychrophiles. Microb Biotechnol 4(4):449–460. doi:10.1111/j.1751-7915.2011.00258.x

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cheng J, Pinnell L, Engel K, Neufeld JD, Charles TC (2014) Versatile broad-host-range cosmids for construction of high quality metagenomic libraries. J Microbiol Methods 99:27–34. doi:10.1016/j.mimet.2014.01.015

    Article  CAS  PubMed  Google Scholar 

  • Cheng J, Romantsov T, Engel K, Doxey AC, Rose DR, Neufeld JD, Charles TC (2017) Functional metagenomics reveals novel beta-galactosidases not predictable from gene sequences. PLOS ONE 12(3):e0172545. doi:10.1371/journal.pone.0172545

  • Chu SF, Shu HY, Lin LC, Chen MY, Tsay SS, Lin GH (2006) Characterization of a rolling-circle replication plasmid from Thermus aquaticus NTU103. Plasmid 56(1):46–52. doi:10.1016/j.plasmid.2006.01.005

    Article  CAS  PubMed  Google Scholar 

  • Cobb RE, Wang YJ, Zhao HM (2015) High-efficiency multiplex genome editing of streptomyces species using an engineered crispr/cas system. ACS Synth Biol 4(6):723–728. doi:10.1021/sb500351f

    Article  CAS  PubMed  Google Scholar 

  • Courtois F, Olguin LF, Whyte G, Bratton D, Huck WT, Abell C, Hollfelder F (2008) An integrated device for monitoring time-dependent in vitro expression from single genes in picolitre droplets. Chembiochem 9(3):439–446. doi:10.1002/cbic.200700536

    Article  CAS  PubMed  Google Scholar 

  • Craig JW, Chang FY, Kim JH, Obiajulu SC, Brady SF (2010) Expanding small-molecule functional metagenomics through parallel screening of broad-host-range cosmid environmental dna libraries in diverse proteobacteria. Appl Environ Microbiol 76(5):1633–1641. doi:10.1128/Aem.02169-09

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Daly R, Hearn MT (2005) Expression of heterologous proteins in Pichia pastoris: a useful experimental tool in protein engineering and production. J Mol Recognit 18(2):119–138. doi:10.1002/jmr.687

    Article  CAS  PubMed  Google Scholar 

  • Damon C, Vallon L, Zimmermann S, Haider MZ, Galeote V, Dequin S, Luis P, Fraissinet-Tachet L, Marmeisse R (2011) A novel fungal family of oligopeptide transporters identified by functional metatranscriptomics of soil eukaryotes. ISME J 5(12):1871–1880. doi:10.1038/ismej.2011.67

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Danhorn T, Young CR, DeLong EF (2012) Comparison of large-insert, small-insert and pyrosequencing libraries for metagenomic analysis. ISME J 6:2056–2066. doi:10.1038/ismej.2012.35

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • de Grado M, Castan P, Berenguer J (1999) A high-transformation-efficiency cloning vector for Thermus thermophilus. Plasmid 42(3):241–245. doi:10.1006/plas.1999.1427

    Article  PubMed  CAS  Google Scholar 

  • Drew D, Kim H (2012) Preparation of saccharomyces cerevisiae expression plasmids. Methods Mol Biol 866:41–46. doi:10.1007/978-1-61779-770-5_4

    Article  CAS  PubMed  Google Scholar 

  • Du D, Zhu Y, Wei JH, Tian YQ, Niu G, Tan HR (2013) Improvement of gougerotin and nikkomycin production by engineering their biosynthetic gene clusters. Appl Microbiol Biotechnol 97(14):6383–6396. doi:10.1007/s00253-013-4836-7

    Article  CAS  PubMed  Google Scholar 

  • Ekkers DM, Cretoiu MS, Kielak AM, van Elsas JD (2012) The great screen anomaly-a new frontier in product discovery through functional metagenomics. Appl Microbiol Biotechnol 93(3):1005–1020. doi:10.1007/s00253-011-3804-3

    Article  CAS  PubMed  Google Scholar 

  • Endo Y, Sawasaki T (2004) High-throughput, genome-scale protein production method based on the wheat germ cell-free expression system. J Struct Funct Genom 5(1–2):45–57. doi:10.1023/B:JSFG.0000029208.83739.49

    Article  CAS  Google Scholar 

  • Endoh T, Kanai T, Imanaka T (2007) A highly productive system for cell-free protein synthesis using a lysate of the hyperthermophilic archaeon, Thermococcus kodakaraensis. Appl Microbiol Biotechnol 74(5):1153–1161. doi:10.1007/s00253-006-0753-3

    Article  CAS  PubMed  Google Scholar 

  • Feitelson JS, Malpartida F, Hopwood DA (1985) Genetic and biochemical characterization of the red gene cluster of Streptomyces coelicolor A3(2). J Gen Microbiol 131(9):2431–2441. doi:10.1099/00221287-131-9-2431

    CAS  PubMed  Google Scholar 

  • Feller G (2013) Psychrophilic enzymes: from folding to function and biotechnology. Scientifica (Cairo) 2013:28. doi:10.1155/2013/512840

    Google Scholar 

  • Fernandez-Arrojo L, Guazzaroni ME, Lopez-Cortes N, Beloqui A, Ferrer M (2010) Metagenomic era for biocatalyst identification. Curr Opin Biotechnol 21(6):725–733. doi:10.1016/j.copbio.2010.09.006

    Article  CAS  PubMed  Google Scholar 

  • Ferrer M, Chernikova TN, Yakimov MM, Golyshin PN, Timmis KN (2003) Chaperonins govern growth of Escherichia coli at low temperatures. Nat Biotechnol 21(11):1266–1267. doi:10.1038/nbt1103-1266b

    Article  CAS  PubMed  Google Scholar 

  • Ferrer M, Beloqui A, Golyshina OV, Plou FJ, Neef A, Chernikova TN, Fernandez-Arrojo L, Ghazi I, Ballesteros A, Elborough K, Timmis KN, Golyshin PN (2007) Biochemical and structural features of a novel cyclodextrinase from cow rumen metagenome. Biotechnol J 2(2):207–213. doi:10.1002/biot.200600183

    Article  CAS  PubMed  Google Scholar 

  • Ferrer M, Martinez-Martinez M, Bargiela R, Streit WR, Golyshina OV, Golyshin PN (2016) Estimating the success of enzyme bioprospecting through metagenomics: current status and future trends. Microb Biotechnol 9(1):22–34. doi:10.1111/1751-7915.12309

    Article  CAS  PubMed  Google Scholar 

  • Foulston LC, Bibb MJ (2010) Microbisporicin gene cluster reveals unusual features of lantibiotic biosynthesis in actinomycetes. Proc Natl Acad Sci U S A 107(30):13461–13466. doi:10.1073/pnas.1008285107

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gabor EM, Alkema WB, Janssen DB (2004) Quantifying the accessibility of the metagenome by random expression cloning techniques. Environ Microbiol 6(9):879–886. doi:10.1111/j.1462-2920.2004.00640.x

    Article  CAS  PubMed  Google Scholar 

  • Gaida SM, Sandoval NR, Nicolaou SA, Chen Y, Venkataramanan KP, Papoutsakis ET (2015) Expression of heterologous sigma factors enables functional screening of metagenomic and heterologous genomic libraries. Nat Commun 6:7045. doi:10.1038/ncomms8045

    Article  PubMed  PubMed Central  Google Scholar 

  • Garneau JE, Dupuis ME, Villion M, Romero DA, Barrangou R, Boyaval P, Fremaux C, Horvath P, Magadan AH, Moineau S (2010) The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature 468(7320):67–71. doi:10.1038/nature09523

    Article  CAS  PubMed  Google Scholar 

  • Geng A, Zou G, Yan X, Wang Q, Zhang J, Liu F, Zhu B, Zhou Z (2012) Expression and characterization of a novel metagenome-derived cellulase Exo2b and its application to improve cellulase activity in Trichoderma reesei. Appl Microbiol Biotechnol 96(4):951–962. doi:10.1007/s00253-012-3873-y

    Article  CAS  PubMed  Google Scholar 

  • Godiska R, Mead D, Dhodda V, Wu C, Hochstein R, Karsi A, Usdin K, Entezam A, Ravin N (2010) Linear plasmid vector for cloning of repetitive or unstable sequences in Escherichia coli. Nucleic Acids Res 38(6):e88. doi:10.1093/nar/gkp1181

    Article  PubMed  CAS  Google Scholar 

  • Gomez-Escribano JP, Bibb MJ (2011) Engineering Streptomyces coelicolor for heterologous expression of secondary metabolite gene clusters. Microb Biotechnol 4(2):207–215. doi:10.1111/j.1751-7915.2010.00219.x

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gomez-Escribano JP, Bibb MJ (2012) Streptomyces coelicolor as an expression host for heterologous gene clusters. Methods Enzymol 517:279–300. doi:10.1016/B978-0-12-404634-4.00014-0

    Article  CAS  PubMed  Google Scholar 

  • Gomez-Escribano JP, Bibb MJ (2014) Heterologous expression of natural product biosynthetic gene clusters in Streptomyces coelicolor: from genome mining to manipulation of biosynthetic pathways. J Ind Microbiol Biotechnol 41(2):425–431. doi:10.1007/s10295-013-1348-5

    Article  CAS  PubMed  Google Scholar 

  • Gomez-Escribano JP, Song LJ, Fox DJ, Yeo V, Bibb MJ, Challis GL (2012) Structure and biosynthesis of the unusual polyketide alkaloid coelimycin P1, a metabolic product of the cpk gene cluster of Streptomyces coelicolor M145. Chem Sci 3(9):2716–2720. doi:10.1039/c2sc20410j

    Article  CAS  Google Scholar 

  • Gruber S, Schwab H, Koefinger P (2015) Versatile plasmid-based expression systems for gram-negative bacteria—general essentials exemplified with the bacterium ralstonia eutropha H16. New Biotechnol 32(6):552–558. doi:10.1016/j.nbt.2015.03.015

    Article  CAS  Google Scholar 

  • Guazzaroni M-E, Silva-Rocha R, Ward RJ (2015) Synthetic biology approaches to improve biocatalyst identification in metagenomic library screening. Microb Biotechnol 8(1):52–64. doi:10.1111/1751-7915.12146

    Article  CAS  PubMed  Google Scholar 

  • Gust B, Chandra G, Jakimowicz D, Tian YQ, Bruton CJ, Chater KF (2004) Lambda red-mediated genetic manipulation of antibiotic-producing Streptomyces. Adv Appl Microbiol 54:107–128. doi:10.1016/S0065-2164(04)54004-2

    Article  CAS  PubMed  Google Scholar 

  • Hain T, Otten S, von Both U, Chatterjee SS, Technow U, Billion A, Ghai R, Mohamed W, Domann E, Chakraborty T (2008) Novel bacterial artificial chromosome vector pUvBBAC for use in studies of the functional genomics of Listeria spp. Appl Environ Microbiol 74(6):1892–1901. doi:10.1128/AEM.00415-07

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Handelsman J, Rondon MR, Brady SF, Clardy J, Goodman RM (1998) Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol 5(10):R245–R249. doi:10.1016/S1074-5521(98)90108-9

    Article  CAS  PubMed  Google Scholar 

  • Heil JR, Cheng J, Charles TC (2012) Site-specific bacterial chromosome engineering: PhiC31 integrase mediated cassette exchange (IMCE). J Vis Exp 61. doi:10.3791/3698

  • Hethke C, Geerling AC, Hausner W, de Vos WM, Thomm M (1996) A cell-free transcription system for the hyperthermophilic archaeon Pyrococcus furiosus. Nucleic Acids Res 24(12):2369–2376. doi:10.1093/nar/24.12.2369

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hidaka Y, Hasegawa M, Nakahara T, Hoshino T (1994) The entire population of Thermus thermophilus cells is always competent at any growth phase. Biosci Biotechnol Biochem 58(7):1338–1339. doi:10.1271/bbb.58.1338

    Article  CAS  PubMed  Google Scholar 

  • Hidalgo A, Betancor L, Moreno R, Zafra O, Cava F, Fernandez-Lafuente R, Guisan JM, Berenguer J (2004) Thermus thermophilus as a cell factory for the production of a thermophilic Mn-dependent catalase which fails to be synthesized in an active form in Escherichia coli. Appl Environ Microbiol 70(7):3839–3844. doi:10.1128/AEM.70.7.3839-3844.2004

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Holz C, Prinz B, Bolotina N, Sievert V, Büssow K, Simon B, Stahl U, Lang C (2003) Establishing the yeast Saccharomyces cerevisiae as a system for expression of human proteins on a proteome-scale. J Struct Funct Genom 4(2–3):97–108. doi:10.1023/A:1026226429429

    Article  CAS  Google Scholar 

  • Hopwood DA (2007) Streptomyces in nature and medicine: the antibiotic makers. Oxford University Press, New York

    Google Scholar 

  • Hopwood DA, Wright HM (1983) CDA is a new chromosomally determined antibiotic from Streptomyces coelicolor A3(2). J Gen Microbiol 129:3575–3579. doi:10.1099/00221287-129-12-3575

    CAS  PubMed  Google Scholar 

  • Hu H, Zhang Q, Ochi K (2002) Activation of antibiotic biosynthesis by specified mutations in the rpoB gene (encoding the RNA polymerase beta subunit) of Streptomyces lividans. J Bacteriol 184(14):3984–3991. doi:10.1128/JB.184.14.3984-3991.2002

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hu XP, Heath C, Taylor MP, Tuffin M, Cowan DA (2012) A novel extremely alkaliphilic and cold-active esterase from Antarctic desert soil. Extremophiles 16:79–86. doi:10.1007/s00792-011-0407-y

    Article  CAS  PubMed  Google Scholar 

  • Huang H, Zheng GS, Jiang WH, Hu H, Lu YH (2015) One-step high-efficiency CRISPR/Cas9-mediated genome editing in Streptomyces. Acta Biochim Biophys Sin 47(4):231–243. doi:10.1093/abbs/gmv007

    Article  CAS  PubMed  Google Scholar 

  • Huo L, Rachid S, Stadler M, Wenzel SC, Muller R (2012) Synthetic biotechnology to study and engineer ribosomal bottromycin biosynthesis. Chem Biol 19(10):1278–1287. doi:10.1016/j.chembiol.2012.08.013

    Article  CAS  PubMed  Google Scholar 

  • Iqbal M, Mast Y, Amin R, Hodgson DA, Consortium S, Wohlleben W, Burroughs NJ (2012) Extracting regulator activity profiles by integration of de novo motifs and expression data: characterizing key regulators of nutrient depletion responses in Streptomyces coelicolor. Nucleic Acids Res 40(12):5227–5239. doi:10.1093/nar/gks205

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jewett MC, Swartz JR (2004) Mimicking the Escherichia coli cytoplasmic environment activates long-lived and efficient cell-free protein synthesis. Biotechnol Bioeng 86(1):19–26. doi:10.1002/bit.20026

    Article  CAS  PubMed  Google Scholar 

  • Jones AC, Gust B, Kulik A, Heide L, Buttner MJ, Bibb MJ (2013) Phage p1-derived artificial chromosomes facilitate heterologous expression of the FK506 gene cluster. PLoS One 8(7):e69319. doi:10.1371/journal.pone.0069319

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kakirde KS, Parsley LC, Liles MR (2010) Size does matter: application-driven approaches for soil metagenomics. Soil Biol Biochem 42(11):1911–1923. doi:10.1016/j.soilbio.2010.07.021

  • Kennedy J, Marchesi JR, Dobson AD (2008) Marine metagenomics: strategies for the discovery of novel enzymes with biotechnological applications from marine environments. Microb Cell Factories 7:27. doi:10.1186/1475-2859-7-27

    Article  CAS  Google Scholar 

  • Kieser T, Bibb MJ, Buttner MJ, Chater KF, Hopwood DA (2000) Practical Streptomyces genetics. John Innes Foundation, Norwich

    Google Scholar 

  • Kim HC, Kim DM (2009) Methods for energizing cell-free protein synthesis. J Biosci Bioeng 108(1):1–4. doi:10.1016/j.jbiosc.2009.02.007

    Article  CAS  PubMed  Google Scholar 

  • Kim UJ, Shizuya H, de Jong PJ, Birren B, Simon MI (1992) Stable propagation of cosmid sized human DNA inserts in an F factor based vector. Nucleic Acids Res 20(5):1083–1085. doi:10.1093/nar/20.5.1083

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kim HC, Kim TW, Kim DM (2011) Prolonged production of proteins in a cell-free protein synthesis system using polymeric carbohydrates as an energy source. Process Biochem 2011(46):1366–1369. doi:10.1016/j.procbio.2011.03.008

    Article  CAS  Google Scholar 

  • King RW, Bauer JD, Brady SF (2009) An environmental DNA-derived type II polyketide biosynthetic pathway encodes the biosynthesis of the pentacyclic polyketide erdacin. Angew Chem 48:6257–6261. doi:10.1002/anie.200901209

    Article  CAS  Google Scholar 

  • Kintses B, van Vliet LD, Devenish SR, Hollfelder F (2010) Microfluidic droplets: new integrated workflows for biological experiments. Curr Opin Chem Biol 14(5):548–555. doi:10.1016/j.cbpa.2010.08.013

    Article  CAS  PubMed  Google Scholar 

  • Komatsu M, Komatsu K, Koiwai H, Yamada Y, Kozone I, Izumikawa M, Hashimoto J, Takagi M, Omura S, Shin-ya K, Cane DE, Ikeda H (2013) Engineered Streptomyces avermitilis host for heterologous expression of biosynthetic gene cluster for secondary metabolites. ACS Synth Biol 2(7):384–396. doi:10.1021/sb3001003

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kotlar HK, Lewin A, Johansen J, Throne-Holst M, Haverkamp T, Markussen S, Winnberg A, Ringrose P, Aakvik T, Ryeng E, Jakobsen K, Drabløs F, Valla S (2011) High coverage sequencing of DNA from microorganisms living in an oil reservoir 2.5 kilometres subsurface. Environ Microbiol Rep 3(6):674–681. doi:10.1111/j.1758-2229.2011.00279.x

    Article  PubMed  Google Scholar 

  • Koyama Y, Hoshino T, Tomizuka N, Furukawa K (1986) Genetic transformation of the extreme thermophile Thermus thermophilus and of other Thermus spp. J Bacteriol 166(1):338–340. doi: 0021-9193/86/040338-03$02.00/0

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Koyama Y, Okamoto S, Furukawa K (1990) Cloning of alpha- and beta-galactosidase genes from an extreme thermophile, Thermus strain T2, and their expression in Thermus thermophilus HB27. Appl Environ Microbiol 56(7):2251–2254. doi: 0099-2240/90/072251-04$02.00/0

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kumar G, Chernaya G (2009) Cell-free protein synthesis using multiply-primed rolling circle amplification products. BioTechniques 47:637–639. doi:10.2144/000113171

    Article  CAS  PubMed  Google Scholar 

  • Kwon YC, Oh IS, Lee N, Lee KH, Yoon YJ, Lee EY, Kim BG, Kim DM (2013) Integrating cell-free biosyntheses of heme prosthetic group and apoenzyme for the synthesis of functional P450 monooxygenase. Biotechnol Bioeng 110(4):1193–1200. doi:10.1002/bit.24785

    Article  CAS  PubMed  Google Scholar 

  • Lam KN, Charles TC (2015) Strong spurious transcription likely a cause of DNA insert bias in typical metagenomic clone libraries. Microbiome 3:22. doi:10.1101/013763

    Article  PubMed  PubMed Central  Google Scholar 

  • Lam KN, Cheng J, Engel K, Neufeld JD, Charles TC (2015) Current and future resources for functional metagenomics. Front Microbiol 6:1196. doi:10.3389/fmicb.2015.01196

    Article  PubMed  PubMed Central  Google Scholar 

  • Lammle K, Zipper H, Breuer M, Hauer B, Buta C, Brunner H, Rupp S (2007) Identification of novel enzymes with different hydrolytic activities by metagenome expression cloning. J Biotechnol 127(4):575–592. doi:10.1016/j.jbiotec.2006.07.036

    Article  PubMed  CAS  Google Scholar 

  • Lasa I, de Grado M, de Pedro MA, Berenguer J (1992) Development of Thermus-Escherichia shuttle vectors and their use for expression of the Clostridium thermocellum celA gene in Thermus thermophilus. J Bacteriol 174(20):6424–6431. doi: 0021-9193/92/206424-08$02.00/0

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lee KH, Lee KY, Byun JY, Kim BG, Kim DM (2012) On-bead expression of recombinant proteins in an agarose gel matrix coated on a glass slide. Lab Chip 12(9):1605–1610. doi:10.1039/c2lc21239k

    Article  CAS  PubMed  Google Scholar 

  • Leis B, Angelov A, Mientus M, Li HJ, Pham VTT, Lauinger B, Bongen P, Pietruszka J, Goncalves LG, Santos H, Liebl W (2015a) Identification of novel esterase-active enzymes from hot environments by use of the host bacterium Thermus thermophilus. Front Microbiol 6:275. doi:10.3389/frricb.2015.00275

    Article  PubMed  PubMed Central  Google Scholar 

  • Leis B, Heinze S, Angelov A, Pham VT, Thürmer A, Jebbar M, Golyshin PN, Streit WR, Daniel R, Liebl W (2015b) Functional screening of hydrolytic activities reveals an extremely thermostable cellulase from a deep-sea archaeon. Front Bioeng Biotechnol 3:95. doi:10.3389/fbioe.2015.00095

    Article  PubMed  PubMed Central  Google Scholar 

  • Lewin A, Wentzel A, Valla S (2013) Metagenomics of microbial life in extreme temperature environments. Curr Opin Biotechnol 24(3):516–525. doi:10.1016/j.copbio.2012.10.012

    Article  CAS  PubMed  Google Scholar 

  • Leza A, Palmeros B, García JO, Galindo E, Soberón-Chávez G (1996) Xanthomonas campestris as a host for the production of recombinant Pseudomonas aeruginosa lipase. J Ind Microbiol 16(1):22–28. doi:10.1007/BF01569917

    Article  CAS  Google Scholar 

  • Li C, Zhang F, Kelly WL (2011) Heterologous production of thiostrepton A and biosynthetic engineering of thiostrepton analogs. Mol Biosyst 7(1):82–90. doi:10.1039/c0mb00129e

    Article  CAS  PubMed  Google Scholar 

  • Liao H, McKenzie T, Hageman R (1986) Isolation of a thermostable enzyme variant by cloning and selection in a thermophile. Proc Natl Acad Sci U S A 83(3):576–580. doi: pnas00307-0057

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liebl W, Angelov A, Juergensen J, Chow J, Loeschcke A, Drepper T, Classen T, Pietruszka J, Ehrenreich A, Streit WR, Jaeger KE (2014) Alternative hosts for functional (meta) genome analysis. Appl Microbiol Biotechnol 98(19):8099–8109. doi:10.1007/s00253-014-5961-7

    Article  CAS  PubMed  Google Scholar 

  • Liles MR, Williamson LL, Rodbumrer J, Torsvik V, Goodman RM, Handelsman J (2008) Recovery, purification, and cloning of high-molecular-weight DNA from soil microorganisms. Appl Environ Microbiol 74(10):3302–3305. doi:10.1128/AEM.02630-07

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Loeschcke A, Thies S (2015) Pseudomonas putida—a versatile host for the production of natural products. Appl Microbiol Biotechnol 99(15):6197–6214. doi:10.1007/s00253-015-6745-4

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Maldonado LA, Stach JE, Pathom-aree W, Ward AC, Bull AT, Goodfellow M (2005) Diversity of cultivable actinobacteria in geographically widespread marine sediments. Antonie Van Leeuwenhoek 87(1):11–18. doi:10.1007/s10482-004-6525-0

    Article  PubMed  Google Scholar 

  • Marcone GL, Foulston L, Binda E, Marinelli F, Bibb M, Beltrametti F (2010) Methods for the genetic manipulation of Nonomuraea sp. ATCC 39727. J Ind Microbiol Biotechnol 37(10):1097–1103. doi:10.1007/s10295-010-0807-5

    Article  CAS  PubMed  Google Scholar 

  • Martin JF, Santos-Beneit F, Rodriguez-Garcia A, Sola-Landa A, Smith MC, Ellingsen TE, Nieselt K, Burroughs NJ, Wellington EM (2012) Transcriptomic studies of phosphate control of primary and secondary metabolism in Streptomyces coelicolor. Appl Microbiol Biotechnol 95(1):61–75. doi:10.1007/s00253-012-4129-6

    Article  CAS  PubMed  Google Scholar 

  • Martinez A, Kolvek SJ, Yip CL, Hopke J, Brown KA, MacNeil IA, Osburne MS (2004) Genetically modified bacterial strains and novel bacterial artificial chromosome shuttle vectors for constructing environmental libraries and detecting heterologous natural products in multiple expression hosts. Appl Environ Microbiol 70(4):2452–2463. doi:10.1128/AEM.70.4.2452-2463.2004

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Martinez A, Kolvek SJ, Hopke J, Yip CL, Osburne MS (2005) Environmental DNA fragment conferring early and increased sporulation and antibiotic production in Streptomyces species. Appl Environ Microbiol 71(3):1638–1641. doi:10.1128/AEM.71.3.1638-1641.2005

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mather MW, Fee JA (1992) Development of plasmid cloning vectors for Thermus thermophilus HB8: expression of a heterologous, plasmid-borne kanamycin nucleotidyltransferase gene. Appl Environ Microbiol 58(1):421–425. doi: 0099-2240/92/010421-05$02.0O/O

    CAS  PubMed  PubMed Central  Google Scholar 

  • Matsumura M, Aiba S (1985) Screening for thermostable mutant of kanamycin nucleotidyltransferase by the use of a transformation system for a thermophile, Bacillus stearothermophilus. J Biol Chem 260(28):15298–15303. doi: 260/28/15298

    CAS  PubMed  Google Scholar 

  • Matthaei JH, Nirenberg MW (1961) The dependence of cell-free protein synthesis in E. coli upon RNA prepared from ribosomes. Biochem Biophys Res Commun 28(4):404–408. doi: pnas00214-0066

    Article  Google Scholar 

  • McMahon MD, Guan C, Handelsman J, Thomas MG (2012) Metagenomic analysis of Streptomyces lividans reveals host-dependent functional expression. Appl Environ Microbiol 78(10):3622–3629. doi:10.1128/AEM.00044-12

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Medema MH, Breitling R, Bovenberg R, Takano E (2011) Exploiting plug-and-play synthetic biology for drug discovery and production in microorganisms. Nat Rev Microbiol 9(2):131–137. doi:10.1038/nrmicro2478

    Article  CAS  PubMed  Google Scholar 

  • Mergeay M, Monchy S, Vallaeys T, Auquier V, Benotmane A, Bertin P, Taghavi S, Dunn J, van der Lelie D, Wattiez R (2003) Ralstonia metallidurans, a bacterium specifically adapted to toxic metals: towards a catalogue of metal-responsive genes. FEMS Microbiol Rev 27(2–3):385–410. doi:10.1016/s0168-6445(03)00045-7

    Article  CAS  PubMed  Google Scholar 

  • Michel-Reydellet N, Woodrow K, Swartz J (2005) Increasing PCR fragment stability and protein yields in a cell-free system with genetically modified Escherichia coli extracts. J Mol Microbiol Biotechnol 9(1):26–34. doi:10.1159/000088143

    Article  CAS  PubMed  Google Scholar 

  • Miteva V, Lantz S, Brenchley J (2008) Characterization of a cryptic plasmid from a Greenland ice core Arthrobacter isolate and construction of a shuttle vector that replicates in psychrophilic high G+C Gram-positive recipients. Extremophiles 12(3):441–449. doi:10.1007/s00792-008-0149-7

    Article  CAS  PubMed  Google Scholar 

  • Miyake R, Kawamoto J, Wei YL, Kitagawa M, Kato I, Kurihara T, Esaki N (2007) Construction of a low-temperature protein expression system using a cold-adapted bacterium, Shewanella sp. strain Ac10, as the host. Appl Environ Microbiol 73(15):4849–4856. doi:10.1128/AEM.00824-07

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Moreno R, Haro A, Castellanos A, Berenguer J (2005) High-level overproduction of His-tagged Tth DNA polymerase in Thermus thermophilus. Appl Environ Microbiol 71(1):591–593. doi:10.1128/AEM.71.1.591-593.2005

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mullany P (2014) Functional metagenomics for the investigation of antibiotic resistance. Virulence 5(3):443–447. doi:10.4161/viru.28196

    Article  PubMed  PubMed Central  Google Scholar 

  • Murai N (2013) Review: plant binary vectors of Ti plasmid in agrobacterium tumefaciens with a broad host-range replicon of pRK2, pRi, pSa or pVS1. AJPS 4:932–939. doi:10.4236/ajps.2013.44115

    Article  CAS  Google Scholar 

  • Nakamura A, Takakura Y, Kobayashi H, Hoshino T (2005) In vivo directed evolution for thermostabilization of Escherichia coli hygromycin B phosphotransferase and the use of the gene as a selection marker in the host-vector system of Thermus thermophilus. J Biosci Bioeng 100(2):158–163. doi:10.1263/jbb.100.158

    Article  CAS  PubMed  Google Scholar 

  • Nett M, Ikeda H, Moore BS (2009) Genomic basis for natural product biosynthetic diversity in the actinomycetes. Nat Prod Rep 26(11):1362–1384. doi:10.1039/b817069j

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nevalainen KM, Te'o VS, Bergquist PL (2005) Heterologous protein expression in filamentous fungi. Trends Biotechnol 23(9):468–474. doi:10.1016/j.tibtech.2005.06.002

    Article  CAS  PubMed  Google Scholar 

  • Nieselt K, Battke F, Herbig A, Bruheim P, Wentzel A, Jakobsen OM, Sletta H, Alam MT, Merlo ME, Moore J, Omara WA, Morrissey ER, Juarez-Hermosillo MA, Rodriguez-Garcia A, Nentwich M, Thomas L, Iqbal M, Legaie R, Gaze WH, Challis GL, Jansen RC, Dijkhuizen L, Rand DA, Wild DL, Bonin M, Reuther J, Wohlleben W, Smith MC, Burroughs NJ, Martin JF, Hodgson DA, Takano E, Breitling R, Ellingsen TE, Wellington EM (2010) The dynamic architecture of the metabolic switch in Streptomyces coelicolor. BMC Genomics 11:10. doi:10.1186/1471-2164-11-10

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Novakova J, Farkasovsky M (2013) Bioprospecting microbial metagenome for natural products. Biologia 68(6):1079–1086. doi:10.2478/s11756-013-0246-7

    Article  CAS  Google Scholar 

  • Ochi K, Hosaka T (2013) New strategies for drug discovery: activation of silent or weakly expressed microbial gene clusters. Appl Microbiol Biotechnol 97(1):87–98. doi:10.1007/s00253-012-4551-9

    Article  CAS  PubMed  Google Scholar 

  • Ochi K, Tanaka Y, Tojo S (2014) Activating the expression of bacterial cryptic genes by rpoB mutations in RNA polymerase or by rare earth elements. J Ind Microbiol Biotechnol 41(2):403–414. doi:10.1007/s10295-013-1349-4

    Article  CAS  PubMed  Google Scholar 

  • Ohnishi Y, Ishikawa J, Hara H, Suzuki H, Ikenoya M, Ikeda H, Yamashita A, Hattori M, Horinouchi S (2008) Genome sequence of the streptomycin-producing microorganism Streptomyces griseus IFO 13350. J Bacteriol 190(11):4050–4060. doi:10.1128/JB.00204-08

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Okamoto-Hosoya Y, Sato TA, Ochi K (2000) Resistance to paromomycin is conferred by rpsL mutations, accompanied by an enhanced antibiotic production in Streptomyces coelicolor A3(2). J Antibiot 53(12):1424–1427. doi:10.7164/antibiotics.53.1424

    Article  CAS  PubMed  Google Scholar 

  • Oliynyk M, Samborskyy M, Lester JB, Mironenko T, Scott N, Dickens S, Haydock SF, Leadlay PF (2007) Complete genome sequence of the erythromycin-producing bacterium Saccharopolyspora erythraea NRRL23338. Nat Biotechnol 25(4):447–453. doi:10.1038/nbt1297

    Article  CAS  PubMed  Google Scholar 

  • Parachin NS, Gorwa-Grauslund MF (2011) Isolation of xylose isomerases by sequence- and function-based screening from a soil metagenomic library. Biotechnol Biofuels 4:9. doi:10.1186/1754-6834-4-9

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Parks RJ, Graham FL (1997) A helper-dependent system for adenovirus vector production helps define a lower limit for efficient dna packaging. J Virol 71(4):3293–3298. doi: 0022-538X/97/$04.0010

    CAS  PubMed  PubMed Central  Google Scholar 

  • Pel J, Broemeling D, Mai L, Poon HL, Tropini G, Warren RL, Holt RA, Marziali A (2009) Nonlinear electrophoretic response yields a unique parameter for separation of biomolecules. Proc Natl Acad Sci U S A 106(35):14796–14801. doi:10.1073/pnas.0907402106

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Potrykus K, Cashel M (2008) (p)ppGpp: still magical? Annu Rev Microbiol 62:35–51. doi:10.1146/annurev.micro.62.081307.162903

    Article  CAS  PubMed  Google Scholar 

  • Ramirez-Arcos S, Fernandez-Herrero LA, Marin I, Berenguer J (1998) Anaerobic growth, a property horizontally transferred by an Hfr-like mechanism among extreme thermophiles. J Bacteriol 180(12):3137–3143. doi: 0021-9193/98/$04.0010

    CAS  PubMed  PubMed Central  Google Scholar 

  • Retallack D, Schneider JC, Chew L, Ramseier T, Allen J, Patkar A, Squires C, Talbot H, Mitchell J (2006) Pseudomonas fluorescens—a robust expression platform for pharmaceutical protein production. Microb Cell Factories 5(1):1–1. doi:10.1186/1475-2859-5-s1-s28

    Article  CAS  Google Scholar 

  • Riesenfeld CS, Goodman RM, Handelsman J (2004) Uncultured soil bacteria are a reservoir of new antibiotic resistance genes. Environ Microbiol 6(9):981–989. doi:10.1111/j.1462-2920.2004.00664.x

    Article  CAS  PubMed  Google Scholar 

  • Rigali S, Nothaft H, Noens EE, Schlicht M, Colson S, Muller M, Joris B, Koerten HK, Hopwood DA, Titgemeyer F, van Wezel GP (2006) The sugar phosphotransferase system of Streptomyces coelicolor is regulated by the GntR-family regulator DasR and links N-acetylglucosamine metabolism to the control of development. Mol Microbiol 61(5):1237–1251. doi:10.1111/j.1365-2958.2006.05319.x

    Article  CAS  PubMed  Google Scholar 

  • Rigali S, Titgemeyer F, Barends S, Mulder S, Thomae AW, Hopwood DA, van Wezel GP (2008) Feast or famine: the global regulator DasR links nutrient stress to antibiotic production by Streptomyces. EMBO Rep 9(7):670–675. doi:10.1038/embor.2008.83

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rodrigue S, Malmstrom RR, Berlin AM, Birren BW, Henn MR, Chisholm SW (2009) Whole genome amplification and de novo assembly of single bacterial cells. PLoS One 4(9):e6864. doi:10.1371/journal.pone.0006864

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Rondon MR, August PR, Bettermann AD, Brady SF, Grossman TH, Liles MR, Loiacono KA, Lynch BA, MacNeil IA, Minor C, Tiong CL, Gilman M, Osburne MS, Clardy J, Handelsman J, Goodman RM (2000) Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl Environ Microbiol 66(6):2541–2547. doi:10.1128/AEM.66.6.2541-2547.2000

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ruan L, Xu X (2007) Sequence analysis and characterizations of two novel plasmids isolated from Thermus sp. 4C. Plasmid 58(1):84–87. doi:10.1016/j.plasmid.2007.04.001

    Article  CAS  PubMed  Google Scholar 

  • Rudd BA, Hopwood DA (1979) Genetics of actinorhodin biosynthesis by Streptomyces coelicolor A3(2). J Gen Microbiol 114(1):35–43. doi:10.1099/00221287-114-1-35

    Article  CAS  PubMed  Google Scholar 

  • Ruggero D, Creti R, Londei P (2006) In vitro translation of archaeal natural mRNAs at high temperature. FEMS Micobiol Lett 107(1):89–94. doi:10.1111/j.1574-6968.1993.tb06009.x

    Article  Google Scholar 

  • Rungpragayphan S, Nakano H, Yamane T (2003) PCR-linked in vitro expression: a novel system for high-throughput construction and screening of protein libraries. FEBS Lett 540(1–3):147–150. doi:10.1016/S0014-5793(03)00251-5

    Article  CAS  PubMed  Google Scholar 

  • Rutledge PJ, Challis GL (2015) Discovery of microbial natural products by activation of silent biosynthetic gene clusters. Nat Rev Microbiol 13(8):509–523. doi:10.1038/nrmicro3496

    Article  CAS  PubMed  Google Scholar 

  • Sabree ZL, Rondon MR, Handelsman J (2009) Metagenomics. In: Schaechter M (ed) Encyclopedia of microbiology. Elsevier, Amsterdam, pp. 622–632. doi:10.1016/B978-012373944-5.00034-1

  • Sawasaki T, Hasegawa Y, Tsuchimochi M, Kamura N, Ogasawara T, Kuroita T, Endo Y (2002) A bilayer cell-free protein synthesis system for high-throughput screening of gene products. FEBS Lett 514(1):102–105. doi:10.1016/S0014-5793(02)02329-3

    Article  CAS  PubMed  Google Scholar 

  • Schwarzenlander C, Averhoff B (2006) Characterization of DNA transport in the thermophilic bacterium Thermus thermophilus HB27. FEBS J 273(18):4210–4218. doi:10.1111/j.1742-4658.2006.05416.x

    Article  CAS  PubMed  Google Scholar 

  • Sherwood EJ, Bibb MJ (2013) The antibiotic planosporicin coordinates its own production in the actinomycete Planomonospora alba. Proc Natl Acad Sci U S A 110(27):E2500–E2509. doi:10.1073/pnas.1305392110

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shima J, Hesketh A, Okamoto S, Kawamoto S, Ochi K (1996) Induction of actinorhodin production by rpsL (encoding ribosomal protein S12) mutations that confer streptomycin resistance in Streptomyces lividans and Streptomyces coelicolor A3(2). J Bacteriol 178(24):7276–7284. doi: 0021-9193/96/$04.0010

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shizuya H, Birren B, Kim UJ, Mancino V, Slepak T, Tachiiri Y, Simon M (1992) Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector. Proc Natl Acad Sci U S A 89(18):8794–8797. doi: pnas01092-0395

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sitaraman K, Esposito D, Klarmann G, Le Grice SF, Hartley JL, Chatterjee DK (2004) A novel cell-free protein synthesis system. J Biotechnol 110(3):257–263. doi:10.1016/j.jbiotec.2004.02.014

    Article  CAS  PubMed  Google Scholar 

  • Smanski MJ, Casper J, Peterson RM, Yu Z, Rajski SR, Shen B (2012) Expression of the platencin biosynthetic gene cluster in heterologous hosts yielding new platencin congeners. J Nat Prod 75(12):2158–2167. doi:10.1021/np3005985

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sosio M, Giusino F, Cappellano C, Bossi E, Puglia AM, Donadio S (2000) Artificial chromosomes for antibiotic-producing actinomycetes. Nat Biotechnol 18(3):343–345. doi:10.1038/73810

    Article  CAS  PubMed  Google Scholar 

  • Strausberg RL, Strausberg SL (2001) Overview of protein expression in saccharomyces cerevisiae. In: Current protocols in protein science. Wiley, Hoboken. doi:10.1002/0471140864.ps0506s02

    Google Scholar 

  • Struvay C, Feller G (2012) Optimization to low temperature activity in psychrophilic enzymes. Int J Mol Sci 13(9):11643–11665. doi:10.3390/ijms130911643

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tabata K, Kosuge T, Nakahara T, Hoshino T (1993) Physical map of the extremely thermophilic bacterium Thermus thermophilus HB27 chromosome. FEBS Lett 331(1–2):81–85. doi:10.1016/0014-5793(93)80301-A

    Article  CAS  PubMed  Google Scholar 

  • Tachibana A, Tanaka T, Taniguchi M, Oi S (1996) Evidence for farnesol-mediated isoprenoid synthesis regulation in a halophilic archaeon, Haloferax volcanii. FEBS Lett 379(1):43–46. doi:10.1016/0014-5793(95)01479-9

    Article  CAS  PubMed  Google Scholar 

  • Takai K, Sawasaki T, Endo Y (2010) The wheat-germ cell-free expression system. Curr Pharm Biotechnol 11(3):272–278. doi:10.1016/j.febslet.2014.05.061

    Article  CAS  PubMed  Google Scholar 

  • Tamakoshi M, Uchida M, Tanabe K, Fukuyama S, Yamagishi A, Oshima T (1997) A new Thermus-Escherichia coli shuttle integration vector system. J Bacteriol 179(15):4811–4814. doi: 0021-9193/97/$04.0010

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Taupp M, Mewis K, Hallam SJ (2011) The art and design of functional metagenomic screens. Curr Opin Biotechnol 22(3):465–472. doi:10.1016/j.copbio.2011.02.010

    Article  CAS  PubMed  Google Scholar 

  • Tebbe CC, Vahjen W (1993) Interference of humic acids and DNA extracted directly from soil in detection and transformation of recombinant-DNA from bacteria and a yeast. Appl Environ Microbiol 59(8):2657–2665. doi: aem00037-0325

    CAS  PubMed  PubMed Central  Google Scholar 

  • Terron-Gonzalez L, Medina C, Limon-Mortes MC, Santero E (2013) Heterologous viral expression systems in fosmid vectors increase the functional analysis potential of metagenomic libraries. Sci Rep 3:1107. doi:10.1038/srep01107

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Thomas L, Hodgson DA, Wentzel A, Nieselt K, Ellingsen TE, Moore J, Morrissey ER, Legaie R, Consortium S, Wohlleben W, Rodriguez-Garcia A, Martin JF, Burroughs NJ, Wellington EM, Smith MC (2012) Metabolic switches and adaptations deduced from the proteomes of Streptomyces coelicolor wild type and phoP mutant grown in batch culture. Mol Cell Proteomics 11(2):M111.013797. doi:10.1074/mcp.M111.013797

    Article  PubMed  CAS  Google Scholar 

  • Tong YJ, Charusanti P, Zhang LX, Weber T, Lee SY (2015) CRISPR-Cas9 based engineering of actinomycetal genomes. ACS Synth Biol 4(9):1020–1029. doi:10.1021/acssynbio.5b00038

    Article  CAS  PubMed  Google Scholar 

  • Troeschel S, Drepper T, Leggewie C, Streit W, Jaeger K-E (2010) Novel tools for the functional expression of metagenomic DNA. In: Streit WR, Daniel R (eds) Metagenomics, Methods in molecular biology, vol 668. Humana Press, New York, pp 117–139. doi:10.1007/978-1-60761-823-2_8

    Chapter  Google Scholar 

  • Tutino ML, Duilio A, Moretti MA, Sannia G, Marino G (2000) A rolling-circle plasmid from Psychrobacter sp. TA144: evidence for a novel rep subfamily. Biochem Biophys Res Commun 274(2):488–495. doi:10.1006/bbrc.2000.3148

    Article  CAS  PubMed  Google Scholar 

  • Tutino ML, Duilio A, Parrilli E, Remaut E, Sannia G, Marino G (2001) A novel replication element from an Antarctic plasmid as a tool for the expression of proteins at low temperature. Extremophiles 5(4):257–264. doi:10.1007/s007920100203

    Article  CAS  PubMed  Google Scholar 

  • Uchiyama T, Miyazaki K (2009) Functional metagenomics for enzyme discovery: challenges to efficient screening. Curr Opin Biotechnol 20(6):616–622. doi:10.1016/j.copbio.2009.09.010

    Article  CAS  PubMed  Google Scholar 

  • Udwary DW, Zeigler L, Asolkar RN, Singan V, Lapidus A, Fenical W, Jensen PR, Moore BS (2007) Genome sequencing reveals complex secondary metabolome in the marine actinomycete Salinispora tropica. Proc Natl Acad Sci U S A 104(25):10376–10381. doi:10.1073/pnas.0700962104

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • van Wezel GP, McDowall KJ (2011) The regulation of the secondary metabolism of Streptomyces: new links and experimental advances. Nat Prod Rep 28(7):1311–1333. doi:10.1039/c1np00003a

    Article  PubMed  CAS  Google Scholar 

  • van Wezel GP, McKenzie NL, Nodwell JR (2009) Chapter 5. Applying the genetics of secondary metabolism in model actinomycetes to the discovery of new antibiotics. Methods Enzymol 458:117–141. doi:10.1016/S0076-6879(09)04805-8

    Article  PubMed  CAS  Google Scholar 

  • Vester JK, Glaring MA, Stougaard P (2015) Improved cultivation and metagenomics as new tools for bioprospecting in cold environments. Extremophiles 19(1):17–29. doi:10.1007/s00792-014-0704-3

    Article  CAS  PubMed  Google Scholar 

  • Waldvogel E, Herbig A, Battke F, Amin R, Nentwich M, Nieselt K, Ellingsen TE, Wentzel A, Hodgson DA, Wohlleben W, Mast Y (2011) The PII protein GlnK is a pleiotropic regulator for morphological differentiation and secondary metabolism in Streptomyces coelicolor. Appl Microbiol Biotechnol 92(6):1219–1236. doi:10.1007/s00253

    Article  CAS  PubMed  Google Scholar 

  • Wang F, Hao J, Yang C, Sun M (2010) Cloning, expression, and identification of a novel extracellular cold-adapted alkaline protease gene of the marine bacterium strain YS-80-122. Appl Biochem Biotechnol 162(5):1497–1505. doi:10.1007/s12010-010-8927-y

    Article  CAS  PubMed  Google Scholar 

  • Wang GYS, Graziani E, Waters B, Pan W, Li X, McDermott J, Meurer G, Saxena G, Andersen RJ, Davies J (2000) Novel natural products from soil DNA libraries in a Streptomycete host. Organic Letters 2(16):2401–2404. doi: 10.1021/ol005860z

  • Wang Y, Zhang YH (2009) Cell-free protein synthesis energized by slowly-metabolized maltodextrin. BMC Biotechnol 9:58. doi:10.1186/1472-6750-9-58

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Warburton P, Roberts AP, Allan E, Seville L, Lancaster H, Mullany P (2009) Characterization of tet(32) genes from the oral metagenome. Antimicrob Agents Chemother 53(1):273–276. doi:10.1128/AAC.00788-08

    Article  CAS  PubMed  Google Scholar 

  • Warren RL, Freeman JD, Levesque RC, Smailus DE, Flibotte S, Holt RA (2008) Transcription of foreign DNA in Escherichia coli. Genome Res 18(11):1798–1805. doi:10.1101/gr.080358.108

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wayne J, Xu SY (1997) Identification of a thermophilic plasmid origin and its cloning within a new Thermus-E. coli shuttle vector. Gene 195(2):321–328. doi:10.1016/S0378-1119(97)00191-1

    Article  CAS  PubMed  Google Scholar 

  • Wentzel A, Bruheim P, Overby A, Jakobsen OM, Sletta H, Omara WA, Hodgson DA, Ellingsen TE (2012a) Optimized submerged batch fermentation strategy for systems scale studies of metabolic switching in Streptomyces coelicolor A3(2). BMC Syst Biol 6:59. doi:10.1186/1752-0509-6-59

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wentzel A, Sletta H, Consortium S, Ellingsen TE, Bruheim P (2012b) Intracellular metabolite pool changes in response to nutrient depletion induced metabolic switching in streptomyces coelicolor. Metabolites 2(1):178–194. doi:10.3390/metabo2010178

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wexler M, Bond PL, Richardson DJ, Johnston AW (2005) A wide host-range metagenomic library from a waste water treatment plant yields a novel alcohol/aldehyde dehydrogenase. Environ Microbiol 7(12):1917–1926. doi:10.1111/j.1462-2920.2005.00854.x

    Article  CAS  PubMed  Google Scholar 

  • Wietzorrek A, Bibb M (1997) A novel family of proteins that regulates antibiotic production in streptomycetes appears to contain an OmpR-like DNA-binding fold. Mol Microbiol 25(6):1181–1184. doi:10.1046/j.1365-2958.1997.5421903.x

    Article  CAS  PubMed  Google Scholar 

  • Wild J, Hradecna Z, Szybalski W (2002) Conditionally amplifiable BACs: switching from single-copy to high-copy vectors and genomic clones. Genome Res 12:1434–1444. doi:10.1101/gr.130502

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wilson MC, Mori T, Ruckert C, Uria AR, Helf MJ, Takada K, Gernert C, Steffens UA, Heycke N, Schmitt S, Rinke C, Helfrich EJ, Brachmann AO, Gurgui C, Wakimoto T, Kracht M, Crusemann M, Hentschel U, Abe I, Matsunaga S, Kalinowski J, Takeyama H, Piel J (2014) An environmental bacterial taxon with a large and distinct metabolic repertoire. Nature 506(7486):58–62. doi:10.1038/nature12959

    Article  CAS  PubMed  Google Scholar 

  • Wong S-L (1995) Advances in the use of Bacillus subtilis for the expression and secretion of heterologous proteins. Curr Opin Biotechnol 6(5):517–522. doi:10.1016/0958-1669(95)80085-9

    Article  CAS  PubMed  Google Scholar 

  • Wright LF, Hopwood DA (1976) Identification of the antibiotic determined by the SCP1 plasmid of Streptomyces coelicolor A3(2). J Gen Microbiol 95(1):96–106. doi:10.1099/00221287-95-1-96

    Article  CAS  PubMed  Google Scholar 

  • Yoon V, Nodwell JR (2014) Activating secondary metabolism with stress and chemicals. J Ind Microbiol Biotechnol 41(2):415–424. doi:10.1007/s10295-013-1387-y

    Article  CAS  PubMed  Google Scholar 

  • Yoon MY, Lee KM, Yoon Y, Go J, Park Y, Cho YJ, Tannock GW, Yoon SS (2013) Functional screening of a metagenomic library reveals operons responsible for enhanced intestinal colonization by gut commensal microbes. Appl Environ Microbiol 79(12):3829–3838. doi:10.1128/AEM.00581-13

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zemella A, Thoring L, Hoffmeister C, Kubick S (2015) Cell-free protein synthesis: pros and cons of prokaryotic and eukaryotic systems. Chembiochem 16(17):2420–2431. doi:10.1002/cbic.201500340

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zengler K, Toledo G, Rappe M, Elkins J, Mathur EJ, Short JM, Keller M (2002) Cultivating the uncultured. Proc Natl Acad Sci U S A 99(24):15681–15686. doi:10.1073/pnas.252630999

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zerikly M, Challis GL (2009) Strategies for the discovery of new natural products by genome mining. Chembiochem 10(4):625–633. doi:10.1002/cbic.200800389

    Article  CAS  PubMed  Google Scholar 

  • Zhang JW, Zeng RY (2008) Molecular cloning and expression of a cold-adapted lipase gene from an Antarctic deep sea psychrotrophic bacterium Pseudomonas sp 7323. Mar Biotechnol 10(5):612–621. doi:10.1007/s10126-008-9099-4

    Article  CAS  PubMed  Google Scholar 

  • Zhang K, Martiny AC, Reppas NB, Barry KW, Malek J, Chisholm SW, Church GM (2006) Sequencing genomes from single cells by polymerase cloning. Nat Biotechnol 24(6):680–686. doi:10.1038/nbt1214

    Article  CAS  PubMed  Google Scholar 

  • Zhang G, Li Y, Fang L, Pfeifer BA (2015) Tailoring pathway modularity in the biosynthesis of erythromycin analogs heterologously engineered in E. coli. Sci Adv 1(4):e1500077. doi:10.1126/sciadv.1500077

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhou JZ, Bruns MA, Tiedje JM (1996) DNA recovery from soils of diverse composition. Appl Environ Microbiol 62(2):316–322. doi: 0099-2240/96/$04.0010

    CAS  PubMed  PubMed Central  Google Scholar 

  • Zhou Y, Asahara H, Gaucher EA, Chong S (2012) Reconstitution of translation from Thermus thermophilus reveals a minimal set of components sufficient for protein synthesis at high temperatures and functional conservation of modern and ancient translation components. Nucleic Acids Res 40(16):7932–7945. doi:10.1093/nar/gks568

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhu H, Sandiford SK, van Wezel GP (2014) Triggers and cues that activate antibiotic production by actinomycetes. J Ind Microbiol Biotechnol 41(2):371–386. doi:10.1007/s10295-013-1309-z

    Article  CAS  PubMed  Google Scholar 

  • Zobel S, Kumpfmüller J, Süssmuth R, Schweder T (2015) Bacillus subtilis as heterologous host for the secretory production of the non-ribosomal cyclodepsipeptide enniatin. Appl Microbiol Biotechnol 99(2):681–691. doi:10.1007/s00253-014-6199-0

    Article  CAS  PubMed  Google Scholar 

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Authors and Affiliations

  1. Department of Biotechnology and Nanomedicine, SINTEF Materials and Chemistry, Trondheim, Norway

    Anna Lewin & Alexander Wentzel

  2. Department of Biotechnology and Food Science, PhotoSynLab, Norwegian University of Science and Technology, Trondheim, Norway

    Rahmi Lale

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  1. Anna Lewin
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  2. Rahmi Lale
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  3. Alexander Wentzel
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Correspondence to Alexander Wentzel .

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  1. Department of Biology, University of Waterloo , Waterloo, Ontario, Canada

    Trevor C. Charles

  2. Department of Biological Sciences, Auburn University , Auburn, Alabama, USA

    Mark R. Liles

  3. Biorescources, AIT Austrian Institute of Technology Biorescources, Tulln, Austria

    Angela Sessitsch

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Lewin, A., Lale, R., Wentzel, A. (2017). Expression Platforms for Functional Metagenomics: Emerging Technology Options Beyond Escherichia coli . In: Charles, T., Liles, M., Sessitsch, A. (eds) Functional Metagenomics: Tools and Applications. Springer, Cham. https://doi.org/10.1007/978-3-319-61510-3_2

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