Skip to main content
SpringerLink
Log in
Book cover

Functional Metagenomics: Tools and Applications pp 75–94Cite as

Enhancing Metagenomic Approaches Through Synthetic Biology

  • Chapter
  • First Online:

Abstract

Bioactive compounds and enzymes with tolerance to process-specific parameters or improved catalytic performance play a crucial role in the development of applications in the chemical and pharmaceutical industry or energy production. Metagenomics takes advantage of the wealth of biochemical diversity present in the genomes of microorganisms found in environmental samples and provides a set of new technologies directed toward screening for new genes with potential in biotechnological applications. However, despite the vast number of published successful studies using this approach, metagenomic strategies typically have low rates of target discovery, and a number of issues need to be addressed in order to improve the screening efficiency of metagenomic libraries. Current limitations include biases imposed by expression in foreign host organisms, low vector performance in particular hosts, and the absence of suitable screening strategies for many targets. These restrictions cannot be overcome by using a single approach but rather require the synergetic implementation of multiple methodologies. In this chapter, we review some of the principal constraints regarding the discovery of new genes with potential use in biotechnology in metagenomic libraries and discuss how these might be resolved using synthetic biology methods. In addition, we review the state of art of synthetic biology approaches directed to improve the recovery of target genes in metagenomic screenings.

This is a preview of subscription content, log in via an institution.

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

References

  • Ajikumar PK, Tyo K, Carlsen S, Mucha O, Phon TH, Stephanopoulos G (2008) Terpenoids: opportunities for biosynthesis of natural product drugs using engineered microorganisms. Mol Pharm 5(2):167–190. doi:10.1021/mp700151b

    Article  CAS  PubMed  Google Scholar 

  • Alcaide M, Tornes J, Stogios PJ, Xu X, Gertler C, Di Leo R, Bargiela R, Lafraya A, Guazzaroni ME, Lopez-Cortes N, Chernikova TN, Golyshina OV, Nechitaylo TY, Plumeier I, Pieper DH, Yakimov MM, Savchenko A, Golyshin PN, Ferrer M (2013) Single residues dictate the co-evolution of dual esterases: MCP hydrolases from the alpha/beta hydrolase family. Biochem J 454(1):157–166

    Article  CAS  PubMed  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 

  • Arkin A (2008) Setting the standard in synthetic biology. Nat Biotechnol 26(7):771–774. doi:10.1038/nbt0708-771

    Article  CAS  PubMed  Google Scholar 

  • Banik JJ, Brady SF (2010) Recent application of metagenomic approaches toward the discovery of antimicrobials and other bioactive small molecules. Curr Opin Microbiol 13(5):603–609. doi:10.1016/j.mib.2010.08.012

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bharate SB, Sawant SD, Singh PP, Vishwakarma RA (2013) Kinase inhibitors of marine origin. Chem Rev 113(8):6761–6815. doi:10.1021/cr300410v

    Article  CAS  PubMed  Google Scholar 

  • Bhat MK (2000) Cellulases and related enzymes in biotechnology. Biotechnol Adv 18(5):355–383

    Article  CAS  PubMed  Google Scholar 

  • Bhat A, Riyaz-Ul-Hassan S, Ahmad N, Srivastava N, Johri S (2013) Isolation of cold-active, acidic endocellulase from Ladakh soil by functional metagenomics. Extremophiles 17(2):229–239

    Article  CAS  PubMed  Google Scholar 

  • Bhatnagar I, Kim SK (2010) Immense essence of excellence: marine microbial bioactive compounds. Mar Drugs 8(10):2673–2701. doi:10.3390/md8102673

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Blunt JW, Copp BR, Keyzers RA, Munro MH, Prinsep MR (2015) Marine natural products. Nat Prod Rep 32(2):116–211. doi:10.1039/c4np00144c

    Article  CAS  PubMed  Google Scholar 

  • Brady SF, Simmons L, Kim JH, Schmidt EW (2009) Metagenomic approaches to natural products from free-living and symbiotic organisms. Nat Prod Rep 26(11):1488–1503. doi:10.1039/b817078a

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen HL, Chen YC, Lu MY, Chang JJ, Wang HT, Ke HM, Wang TY, Ruan SK, Wang TY, Hung KY, Cho HY, Lin WT, Shih MC, Li WH (2012) A highly efficient beta-glucosidase from the buffalo rumen fungus Neocallimastix patriciarum W5. Biotechnol Biofuels 5(1):24

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cieslinski H, Bialkowskaa A, Tkaczuk K, Dlugolecka A, Kur J, Turkiewicz M (2009) Identification and molecular modeling of a novel lipase from an Antarctic soil metagenomic library. Pol J Microbiol 58(3):199–204

    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. [pii].

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Daniel R (2005) The metagenomics of soil. Nat Rev Microbiol 3(6):470–478

    Article  CAS  PubMed  Google Scholar 

  • Dinsdale EA, Edwards RA, Hall D, Angly F, Breitbart M, Brulc JM, Furlan M, Desnues C, Haynes M, Li L, McDaniel L, Moran MA, Nelson KE, Nilsson C, Olson R, Paul J, Brito BR, Ruan Y, Swan BK, Stevens R, Valentine DL, Thurber RV, Wegley L, White BA, Rohwer F (2008) Functional metagenomic profiling of nine biomes. Nature 452(7187):629–632

    Article  CAS  PubMed  Google Scholar 

  • Eggeling L, Bott M, Marienhagen J (2015) Novel screening methods-biosensors. Curr Opin Biotechnol 35C:30–36. doi:10.1016/j.copbio.2014.12.021

    Article  CAS  Google Scholar 

  • Feng Y, Duan CJ, Pang H, Mo XC, Wu CF, Yu Y, Hu YL, Wei J, Tang JL, Feng JX (2007) Cloning and identification of novel cellulase genes from uncultured microorganisms in rabbit cecum and characterization of the expressed cellulases. Appl Microbiol Biotechnol 75(2):319–328

    Article  CAS  PubMed  Google Scholar 

  • Feng Z, Kallifidas D, Brady SF (2011) Functional analysis of environmental DNA-derived type II polyketide synthases reveals structurally diverse secondary metabolites. Proc Natl Acad Sci U S A 108(31):12629–12634. doi:10.1073/pnas.1103921108

    Article  CAS  PubMed  PubMed Central  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

    Article  CAS  PubMed  Google Scholar 

  • Ferrer M, Chernikova TN, Timmis KN, Golyshin PN (2004) Expression of a temperature-sensitive esterase in a novel chaperone-based Escherichia coli strain. Appl Environ Microbiol 70(8):4499–4504. doi:10.1128/AEM.70.8.4499-4504.2004

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ferrer M, Golyshina OV, Chernikova TN, Khachane AN, Martins Dos Santos VA, Yakimov MM, Timmis KN, Golyshin PN (2005) Microbial enzymes mined from the Urania deep-sea hypersaline anoxic basin. Chem Biol 12(8):895–904

    Article  CAS  PubMed  Google Scholar 

  • Ferrer M, Beloqui A, Timmis KN, Golyshin PN (2009) Metagenomics for mining new genetic resources of microbial communities. J Mol Microbiol Biotechnol 16(1–2):109–123

    Article  CAS  PubMed  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 

  • Galvao TC, de Lorenzo V (2006) Transcriptional regulators a la carte: engineering new effector specificities in bacterial regulatory proteins. Curr Opin Biotechnol 17(1):34–42

    Article  CAS  PubMed  Google Scholar 

  • Gardner TS, Cantor CR, Collins JJ (2000) Construction of a genetic toggle switch in Escherichia coli. Nature 403(6767):339–342

    Article  CAS  PubMed  Google Scholar 

  • Gloux K, Berteau O, El Oumami H, Beguet F, Leclerc M, Dore J (2010) A metagenomic beta-glucuronidase uncovers a core adaptive function of the human intestinal microbiome. Proc Natl Acad Sci U S A 108(Suppl 1):4539–4546

    PubMed  PubMed Central  Google Scholar 

  • Gong JS, Lu ZM, Li H, Zhou ZM, Shi JS, Xu ZH (2013) Metagenomic technology and genome mining: emerging areas for exploring novel nitrilases. Appl Microbiol Biotechnol 97(15):6603–6611

    Article  CAS  PubMed  Google Scholar 

  • Guazzaroni M-E, Golyshin PN, Ferrer M (2010a) Analysis of complex microbial communities through metagenomic survey. In: Marco D (ed) Metagenomics: theory, methods and applications. Caister Academic, Norfolk, pp 55–77

    Google Scholar 

  • Guazzaroni ME, Beloqui A, Vieites JM, Al-ramahi Y, Cortes NL, Ghazi A, Golyshin PN, Ferrer M (2010b) Metagenomic mining of enzyme diversity. In: Timmis K (ed) Handbook of hydrocarbon and lipid microbiology. Springer, Berlin, pp 2911–2927. doi:10.1007/978-3-540-77587-4_216

    Chapter  Google Scholar 

  • Guazzaroni ME, Morgante V, Mirete S, Gonzalez-Pastor JE (2013) Novel acid resistance genes from the metagenome of the Tinto River, an extremely acidic environment. Environ Microbiol 15(4):1088–1102

    Article  CAS  PubMed  Google Scholar 

  • Hallin PF, Binnewies TT, Ussery DW (2008) The genome BLASTatlas-a GeneWiz extension for visualization of whole-genome homology. Mol Biosyst 4(5):363–371

    Article  CAS  PubMed  Google Scholar 

  • Handelsman J (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 68(4):669–685

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Heath C, Hu XP, Cary SC, Cowan D (2009) Identification of a novel alkaliphilic esterase active at low temperatures by screening a metagenomic library from Antarctic desert soil. Appl Environ Microbiol 75(13):4657–4659

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Herrera S (2004) Industrial biotechnology-a chance at redemption. Nat Biotechnol 22(6):671–675

    Article  CAS  PubMed  Google Scholar 

  • Homann MJ, Vail RB, Previte E, Tamarez M, Morgan B, Dodds DR, Zaks A (2004) Rapid identification of enantioselective ketone reductions using targeted microbial libraries, vol 60. Elsevier. First published

    Google Scholar 

  • Houssen WE, Jaspars M (2012) Isolation of marine natural products. Methods Mol Biol 864:367–392. doi:10.1007/978-1-61779-624-1_14

    Article  CAS  PubMed  Google Scholar 

  • Hu XP, Heath C, Taylor MP, Tuffin M, Cowan D (2012) A novel, extremely alkaliphilic and cold-active esterase from Antarctic desert soil. Extremophiles 16(1):79–86

    Article  CAS  PubMed  Google Scholar 

  • Jackson SA, Borchert E, O’Gara F, Dobson AD (2015) Metagenomics for the discovery of novel biosurfactants of environmental interest from marine ecosystems. Curr Opin Biotechnol 33:176–182. doi:10.1016/j.copbio.2015.03.004

    Article  CAS  PubMed  Google Scholar 

  • Jiang C, Ma G, Li S, Hu T, Che Z, Shen P, Yan B, Wu B (2009) Characterization of a novel beta-glucosidase-like activity from a soil metagenome. J Microbiol 47(5):542–548

    Article  CAS  PubMed  Google Scholar 

  • Jiang C, Yin B, Tang M, Zhao G, He J, Shen P, Wu B (2013) Identification of a metagenome-derived prephenate dehydrogenase gene from an alkaline-polluted soil microorganism. Antonie Van Leeuwenhoek 103(6):1209–1219

    Article  CAS  PubMed  Google Scholar 

  • Kirk O, Borchert TV, Fuglsang CC (2002) Industrial enzyme applications. Curr Opin Biotechnol 13(4):345–351

    Article  CAS  PubMed  Google Scholar 

  • Ko KC, Han Y, Cheong DE, Choi JH, Song JJ (2013) Strategy for screening metagenomic resources for exocellulase activity using a robotic, high-throughput screening system. J Microbiol Methods 94(3):311–316

    Article  CAS  PubMed  Google Scholar 

  • Koide T, Pang WL, Baliga NS (2009) The role of predictive modelling in rationally re-engineering biological systems. Nat Rev Microbiol 7(4):297–305. doi:10.1038/nrmicro2107

    CAS  PubMed  PubMed Central  Google Scholar 

  • Krogh KB, Harris PV, Olsen CL, Johansen KS, Hojer-Pedersen J, Borjesson J, Olsson L (2010) Characterization and kinetic analysis of a thermostable GH3 beta-glucosidase from Penicillium brasilianum. Appl Microbiol Biotechnol 86(1):143–154

    Article  CAS  PubMed  Google Scholar 

  • Leis B, Angelov A, Li H, Liebl W (2014) Genetic analysis of lipolytic activities in Thermus thermophilus HB27. J Biotechnol 191:150–157. doi:10.1016/j.jbiotec.2014.07.448

    Article  CAS  PubMed  Google Scholar 

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

    Article  PubMed  PubMed Central  Google Scholar 

  • Lorenz P, Eck J (2005) Metagenomics and industrial applications. Nat Rev Microbiol 3(6):510–516

    Article  CAS  PubMed  Google Scholar 

  • Lorenz P, Liebeton K, Niehaus F, Eck J (2002) Screening for novel enzymes for biocatalytic processes: accessing the metagenome as a resource of novel functional sequence space. Curr Opin Biotechnol 13(6):572–577

    Article  CAS  PubMed  Google Scholar 

  • Lynd LR, Weimer PJ, van Zyl WH, Pretorius IS (2002) Microbial cellulose utilization: fundamentals and biotechnology. Microbiol Mol Biol Rev 66(3):506–577

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Martinez-Garcia E, Nikel PI, Chavarria M, de Lorenzo V (2014) The metabolic cost of flagellar motion in Pseudomonas putida KT2440. Environ Microbiol 16(1):291–303. doi:10.1111/1462-2920.12309

    Article  CAS  PubMed  Google Scholar 

  • Martinez-Martinez M, Alcaide M, Tchigvintsev A, Reva O, Polaina J, Bargiela R, Guazzaroni ME, Chicote A, Canet A, Valero F, Rico Eguizabal E, Guerrero Mdel C, Yakunin AF, Ferrer M (2013) Biochemical diversity of carboxyl esterases and lipases from Lake Arreo (Spain): a metagenomic approach. Appl Environ Microbiol 79(12):3553–3562

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Martinez-Martinez M, Lores I, Pena-Garcia C, Bargiela R, Reyes-Duarte D, Guazzaroni ME, Pelaez AI, Sanchez J, Ferrer M (2014) Biochemical studies on a versatile esterase that is most catalytically active with polyaromatic esters. Microb Biotechnol 7(2):184–191

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Maurer KH (2004) Detergent proteases. Curr Opin Biotechnol 15(4):330–334

    Article  CAS  PubMed  Google Scholar 

  • Medini D, Donati C, Tettelin H, Masignani V, Rappuoli R (2005) The microbial pan-genome. Curr Opin Genet Dev 15(6):589–594. doi:10.1016/j.gde.2005.09.006

    Article  CAS  PubMed  Google Scholar 

  • Mohn WW, Garmendia J, Galvao TC, de Lorenzo V (2006) Surveying biotransformations with a la carte genetic traps: translating dehydrochlorination of lindane (gamma-hexachlorocyclohexane) into lacZ-based phenotypes. Environ Microbiol 8(3):546–555. doi:10.1111/j.1462-2920.2006.00983.x

    Article  CAS  PubMed  Google Scholar 

  • Moon TS, Clarke EJ, Groban ES, Tamsir A, Clark RM, Eames M, Kortemme T, Voigt CA (2011) Construction of a genetic multiplexer to toggle between chemosensory pathways in Escherichia coli. J Mol Biol 406(2):215–227. doi:10.1016/j.jmb.2010.12.019

    Article  CAS  PubMed  Google Scholar 

  • Morimoto S, Fujii T (2009) A new approach to retrieve full lengths of functional genes from soil by PCR-DGGE and metagenome walking. Appl Microbiol Biotechnol 83(2):389–396

    Article  CAS  PubMed  Google Scholar 

  • Nasuno E, Kimura N, Fujita MJ, Nakatsu CH, Kamagata Y, Hanada S (2012) Phylogenetically novel LuxI/LuxR-type quorum sensing systems isolated using a metagenomic approach. Appl Environ Microbiol 78(22):8067–8074

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nikel PI, de Lorenzo V (2013) Implantation of unmarked regulatory and metabolic modules in Gram-negative bacteria with specialised mini-transposon delivery vectors. J Biotechnol 163(2):143–154. doi:10.1016/j.jbiotec.2012.05.002

    Article  CAS  PubMed  Google Scholar 

  • Osterberg S, del Peso-Santos T, Shingler V (2011) Regulation of alternative sigma factor use. Annu Rev Microbiol 65:37–55. doi:10.1146/annurev.micro.112408.134219

    Article  PubMed  CAS  Google Scholar 

  • Otte KB, Hauer B (2015) Enzyme engineering in the context of novel pathways and products. Curr Opin Biotechnol 35C:16–22. doi:10.1016/j.copbio.2014.12.011

    Article  CAS  Google Scholar 

  • Percival Zhang YH, Himmel ME, Mielenz JR (2006) Outlook for cellulase improvement: screening and selection strategies. Biotechnol Adv 24(5):452–481

    Article  CAS  PubMed  Google Scholar 

  • Posfai G, Plunkett G 3rd, Feher T, Frisch D, Keil GM, Umenhoffer K, Kolisnychenko V, Stahl B, Sharma SS, de Arruda M, Burland V, Harcum SW, Blattner FR (2006) Emergent properties of reduced-genome Escherichia coli. Science 312(5776):1044–1046. doi:10.1126/science.1126439

    Article  CAS  PubMed  Google Scholar 

  • Purnick PE, Weiss R (2009) The second wave of synthetic biology: from modules to systems. Nat Rev Mol Cell Biol 10(6):410–422

    Article  CAS  PubMed  Google Scholar 

  • Regot S, Macia J, Conde N, Furukawa K, Kjellen J, Peeters T, Hohmann S, de Nadal E, Posas F, Sole R (2011) Distributed biological computation with multicellular engineered networks. Nature 469(7329):207–211. doi:10.1038/nature09679

    Article  CAS  PubMed  Google Scholar 

  • Rhee JK, Ahn DG, Kim YG, Oh JW (2005) New thermophilic and thermostable esterase with sequence similarity to the hormone-sensitive lipase family, cloned from a metagenomic library. Appl Environ Microbiol 71(2):817–825

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rhodius VA, Segall-Shapiro TH, Sharon BD, Ghodasara A, Orlova E, Tabakh H, Burkhardt DH, Clancy K, Peterson TC, Gross CA, Voigt CA (2013) Design of orthogonal genetic switches based on a crosstalk map of sigmas, anti-sigmas, and promoters. Mol Syst Biol 9:702. doi:10.1038/msb.2013.58

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Robertson DE, Chaplin JA, DeSantis G, Podar M, Madden M, Chi E, Richardson T, Milan A, Miller M, Weiner DP, Wong K, McQuaid J, Farwell B, Preston LA, Tan X, Snead MA, Keller M, Mathur E, Kretz PL, Burk MJ, Short JM (2004) Exploring nitrilase sequence space for enantioselective catalysis. Appl Environ Microbiol 70(4):2429–2436

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rocha-Martin J, Harrington C, Dobson AD, O’Gara F (2014) Emerging strategies and integrated systems microbiology technologies for biodiscovery of marine bioactive compounds. Mar Drugs 12(6):3516–3559. doi:10.3390/md12063516

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Schloss PD, Handelsman J (2003) Biotechnological prospects from metagenomics. Curr Opin Biotechnol 14(3):303–310

    Article  CAS  PubMed  Google Scholar 

  • Schloss PD, Handelsman J (2006) Toward a census of bacteria in soil. PLoS Comput Biol 2(7):e92

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Schmidt M, de Lorenzo V (2012) Synthetic constructs in/for the environment: managing the interplay between natural and engineered Biology. FEBS Lett 586(15):2199–2206. doi:10.1016/j.febslet.2012.02.022

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schnoes AM, Brown SD, Dodevski I, Babbitt PC (2009) Annotation error in public databases: misannotation of molecular function in enzyme superfamilies. PLoS Comput Biol 5(12):e1000605

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Shetty RP, Endy D, Knight TF Jr (2008) Engineering BioBrick vectors from BioBrick parts. J Biol Eng 2:5. doi:10.1186/1754-1611-2-5

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Silva-Rocha R, de Lorenzo V (2011) Implementing an OR-NOT (ORN) logic gate with components of the SOS regulatory network of Escherichia coli. Mol Biosyst 7(8):2389–2396. doi:10.1039/c1mb05094j

    Article  CAS  PubMed  Google Scholar 

  • Silva-Rocha R, Martinez-Garcia E, Calles B, Chavarria M, Arce-Rodriguez A, de Las Heras A, Paez-Espino AD, Durante-Rodriguez G, Kim J, Nikel PI, Platero R, de Lorenzo V (2013) The Standard European Vector Architecture (SEVA): a coherent platform for the analysis and deployment of complex prokaryotic phenotypes. Nucleic Acids Res 41(Database issue):D666–D675. doi:10.1093/nar/gks1119

    Article  CAS  PubMed  Google Scholar 

  • Simon C, Herath J, Rockstroh S, Daniel R (2009) Rapid identification of genes encoding DNA polymerases by function-based screening of metagenomic libraries derived from glacial ice. Appl Environ Microbiol 75(9):2964–2968

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Singhania RR, Patel AK, Sukumaran RK, Larroche C, Pandey A (2013) Role and significance of beta-glucosidases in the hydrolysis of cellulose for bioethanol production. Bioresour Technol 127:500–507

    Article  CAS  PubMed  Google Scholar 

  • Siuti P, Yazbek J, Lu TK (2013) Synthetic circuits integrating logic and memory in living cells. Nat Biotechnol 31(5):448–452. doi:10.1038/nbt.2510

    Article  CAS  PubMed  Google Scholar 

  • Sleator RD, Shortall C, Hill C (2008) Metagenomics. Lett Appl Microbiol 47(5):361–366

    Article  CAS  PubMed  Google Scholar 

  • Steele HL, Jaeger KE, Daniel R, Streit WR (2009) Advances in recovery of novel biocatalysts from metagenomes. J Mol Microbiol Biotechnol 16(1–2):25–37

    Article  CAS  PubMed  Google Scholar 

  • Strachan CR, Singh R, VanInsberghe D, Ievdokymenko K, Budwill K, Mohn WW, Eltis LD, Hallam SJ (2014) Metagenomic scaffolds enable combinatorial lignin transformation. Proc Natl Acad Sci U S A 111(28):10143–10148. doi:10.1073/pnas.1401631111

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sul WJ, Park J, Quensen JF 3rd, Rodrigues JL, Seliger L, Tsoi TV, Zylstra GJ, Tiedje JM (2009) DNA-stable isotope probing integrated with metagenomics for retrieval of biphenyl dioxygenase genes from polychlorinated biphenyl-contaminated river sediment. Appl Environ Microbiol 75(17):5501–5506

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tabor S (2001) Expression using the T7 RNA polymerase/promoter system. In: Current protocols in molecular biology. Wiley. doi:10.1002/0471142727.mb1602s11

  • Tang SY, Cirino PC (2011) Design and application of a mevalonate-responsive regulatory protein. Angew Chem Int Ed Engl 50(5):1084–1086. doi:10.1002/anie.201006083

    Article  CAS  PubMed  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 

  • Trincone A (2011) Marine biocatalysts: enzymatic features and applications. Mar Drugs 9(4):478–499. doi:10.3390/md9040478

    Article  CAS  PubMed  PubMed Central  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 

  • Uchiyama T, Miyazaki K (2010) Product-induced gene expression, a product-responsive reporter assay used to screen metagenomic libraries for enzyme-encoding genes. Appl Environ Microbiol 76(21):7029–7035

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Uchiyama T, Watanabe K (2008) Substrate-induced gene expression (SIGEX) screening of metagenome libraries. Nat Protoc 3(7):1202–1212

    Article  CAS  PubMed  Google Scholar 

  • Uchiyama T, Abe T, Ikemura T, Watanabe K (2005) Substrate-induced gene-expression screening of environmental metagenome libraries for isolation of catabolic genes. Nat Biotechnol 23(1):88–93

    Article  CAS  PubMed  Google Scholar 

  • Varaljay VA, Howard EC, Sun S, Moran MA (2010) Deep sequencing of a dimethylsulfoniopropionate-degrading gene (dmdA) by using PCR primer pairs designed on the basis of marine metagenomic data. Appl Environ Microbiol 76(2):609–617

    Article  CAS  PubMed  Google Scholar 

  • Vieites JM, Guazzaroni ME, Beloqui A, Golyshin PN, Ferrer M (2009) Metagenomics approaches in systems microbiology. FEMS Microbiol Rev 33(1):236–255

    Article  CAS  PubMed  Google Scholar 

  • Voigt CA (2006) Genetic parts to program bacteria. Curr Opin Biotechnol 17(5):548–557. doi:10.1016/j.copbio.2006.09.001

    Article  CAS  PubMed  Google Scholar 

  • Wang GY, 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. Org Lett 2(16):2401–2404

    Article  CAS  PubMed  Google Scholar 

  • Ward R (2011) Cellulase engineering for biomass saccharification. In: Buckeridge MS, Goldman GH (eds) Routes to cellulosic ethanol. Springer, New York, pp 135–151. doi:10.1007/978-0-387-92740-4_9

    Chapter  Google Scholar 

  • Warnecke F, Hess M (2009) A perspective: metatranscriptomics as a tool for the discovery of novel biocatalysts. J Biotechnol 142(1):91–95

    Article  CAS  PubMed  Google Scholar 

  • Weber W, Fussenegger M (2010) Synthetic gene networks in mammalian cells. Curr Opin Biotechnol 21(5):690–696

    Article  CAS  PubMed  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

    Article  CAS  PubMed  Google Scholar 

  • Whitman WB, Coleman DC, Wiebe WJ (1998) Prokaryotes: the unseen majority. Proc Natl Acad Sci U S A 95(12):6578–6583

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Williamson LL, Borlee BR, Schloss PD, Guan C, Allen HK, Handelsman J (2005) Intracellular screen to identify metagenomic clones that induce or inhibit a quorum-sensing biosensor. Appl Environ Microbiol 71(10):6335–6344

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yan X, Geng A, Zhang J, Wei Y, Zhang L, Qian C, Wang Q, Wang S, Zhou Z (2013) Discovery of (hemi-) cellulase genes in a metagenomic library from a biogas digester using 454 pyrosequencing. Appl Microbiol Biotechnol 97(18):8173–8182

    Article  CAS  PubMed  Google Scholar 

  • Yuhong Z, Shi P, Liu W, Meng K, Bai Y, Wang G, Zhan Z, Yao B (2009) Lipase diversity in glacier soil based on analysis of metagenomic DNA fragments and cell culture. J Microbiol Biotechnol 19(9):888–897

    Article  PubMed  CAS  Google Scholar 

  • Zaprasis A, Liu YJ, Liu SJ, Drake HL, Horn MA (2010) Abundance of novel and diverse tfdA-like genes, encoding putative phenoxyalkanoic acid herbicide-degrading dioxygenases, in soil. Appl Environ Microbiol 76(1):119–128

    Article  CAS  PubMed  Google Scholar 

  • 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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhan J, Ding B, Ma R, Ma X, Su X, Zhao Y, Liu Z, Wu J, Liu H (2010) Develop reusable and combinable designs for transcriptional logic gates. Mol Syst Biol 6:388. doi:10.1038/msb.2010.42

    Article  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgments

The study was supported by the National Council of Technological and Scientific Development (CNPq 472893/2013-0 and 441833/2014-4) and by the Sao Paulo State Foundation (FAPESP, grant number 2015/04309-1 and 2012/21922-8). MEG was a beneficiary of a CNPq Young Talent Fellowship (CNPq 370630/2013-0). Authors have no conflict of interest to declare.

Author information

Authors and Affiliations

  1. Departamento de Bioquimica, FMRP-University of São Paulo, Ribeirão Preto, SP, Brazil

    Luana de Fátima Alves & María-Eugenia Guazzaroni

  2. Departamento de Biologia Celular, FMRP—University of São Paulo, Ribeirão Preto, São Paulo, Brazil

    Rafael Silva-Rocha

Authors
  1. Luana de Fátima Alves
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Rafael Silva-Rocha
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. María-Eugenia Guazzaroni
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to María-Eugenia Guazzaroni .

Editor information

Editors and Affiliations

  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

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer International Publishing AG

About this chapter

Cite this chapter

Alves, L.d.F., Silva-Rocha, R., Guazzaroni, ME. (2017). Enhancing Metagenomic Approaches Through Synthetic Biology. 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_5

Download citation

Publish with us

Policies and ethics

Search

Navigation