PL EN


Preferencje help
Widoczny [Schowaj] Abstrakt
Liczba wyników
2012 | 59 | 4 |

Tytuł artykułu

Metagenomic approach in the investigation of new bioactive compounds in the marine environment

Warianty tytułu

Języki publikacji

EN

Abstrakty

EN
The marine environment is estimated to be one of the most significant sources of biological activity in the world. In the last few decades an increase in the research intensity conducted on marine microorganisms has been observed, which confirms the great potential of these organisms in the field of bioactive compounds' production. In order to efficiently use the natural resources of the marine environment, metagenomics can be applied. This powerful technique allows for efficient screening of microbial biodiversity for bioactive compounds. The primary aim of this review is to present some aspects of the construction of metagenomic libraries, and strategies of screening for novel bioactives in the marine surrounding. This paper also illustrates several examples of the application of metagenomic methods in the discovery of novel enzymes and drugs in various marine environments.

Słowa kluczowe

Wydawca

-

Rocznik

Tom

59

Numer

4

Opis fizyczny

p.501-505,fig.,ref.

Twórcy

  • Department of Molecular Biology, University of Gdańsk, Gdańsk, Poland
autor
  • Department of Molecular Biology, University of Gdańsk, Gdańsk, Poland
  • Department of Molecular Biology, University of Gdańsk, Gdańsk, Poland
autor
  • Department of Molecular Biology, University of Gdańsk, Gdańsk, Poland

Bibliografia

  • Aakvik T, Degnes KF, Dahlsrud R, Schmidt F, Dam R, Yu L, Völker 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: 149-158. 
  • Andersen RJ, Wolfe MS, Faulkner DJ (1974) Autotoxic antibiotic production by a marine Chromobacterium. Mar Biol 27: 281-285.
  • Angelov A, Liebl W (2010) Heterologous gene expression in the hyperthermophilic archaeon Sulfolobus solfataricus. Methods Mol Biol 668: 109-116. 
  • Carola S, Rolf D (2011) Achievements and new knowledge unraveled by metagenomic approaches. Appl Microbiol Biotechnol 85: 265-276. 
  • Cooper EL (2004) Drug discovery, CAM and natural products. Evid Based Complement Alternat Med 1: 215-217. 
  • 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: 1633-1641. 
  • de Lorenzo V (2005) Problems with metagenomic screening. Nat Biotechnol 23: 1045-1046. 
  • Ekkers DM, Cretoiu MS, Kielak AM, Elsas JD (2012) The great screen anomaly - a new frontier in product discovery through functional metagenomics. Appl Microbiol Biotechnol 93: 1005-1020. 
  • Faegri A, Torsvik VL, Goksoyr J (1977) Bacterial and fungal activities in soil: separation of bacteria and fungi by a rapid fractionated centrifugation technique. Soil Biol Biochem 9: 105-112.
  • Fenical W, Jensen PR (2006) Developing a new resource for drug discovery: Marine actinomycete bacteria. Nat Chem Biol 2: 666-673 
  • Ferrer M, Martínez-Abarca F, Golyshin PN (2005) Mining genomes and 'metagenomes' for novel catalysts. Curr Opin Biotechnol 6: 588-593. 
  • Foote AD, Thomsen PF, Sveegaard S, Wahlberg M, Kielgast J, Kyhn LA, Salling AB, Galatius A, Orlando L, Gilbert TP (2012) Investigating the potential use of environmental DNA (eDNA) for genetic monitoring of marine mammals. PLoS ONE 7: e41781. 
  • Gabor EM, de Vries EJ, Janssen DB (2004a) Construction, characterization, and use of small-insert gene banks of DNA isolated from soil and enrichment cultures for the recovery of novel amidases. Environ Microbiol 6: 948-958. 
  • Gabor EM, Alkema WB, Janssen DB (2004b) Quantifying the accessibility of the metagenome by random expression cloning techniques. Environ Microbiol 6: 879-886. 
  • Gilbert JA, Zhang K, Neufeld JD (2010) Multiple Displacement Amplification. Handbook of Hydrocarbon and Lipid Microbiology, Kenneth N, eds. pp 4255-4263. Springer Press.
  • Godiska R (2008) Bias-free cloning of 'unclonable' DNA for simplified genomic finishing. DNA sequencing III: Dealing with difficult templates. Kieleczawa J, eds. Jones and Bartlett Publishers, Sudbury, MA.
  • Gurgui C, Piel J (2010) Metagenomic approaches to identify and isolate bioactive natural products from microbiota of marine sponges. Methods Mol Biol 668: 247-64. 
  • Hallam SJ, Putnam N, Preston CM, Detter JC, Rokhsar D, Richardson PM, DeLong EF (2004) Reverse methanogenesis: testing the hypothesis with environmental genomics. Science 305: 1457-1462. 
  • Handelsman J (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 68: 669-685. 
  • Handelsman J (2005) Sorting out metagenomes. Nat Biotechnol 23: 38-9. 
  • Hårdeman F, Sjöling S (2007) Metagenomic approach for the isolation of a novel low-temperature-active lipase from uncultured bacteria of marine sediment. FEMS Microbiol Ecol 59: 524-534. 
  • Jiang CJ, Hao ZY, Zeng R, Shen PH, Li JF, Wu B (2011) Characterization of a novel serine protease inhibitor gene from a marine metagenome. Mar Drugs 9: 1487-1501. 
  • Jogler C, Lin W, Meyerdierks A, Kube M, Katzmann E, Flies C, Pan Y, Amann R, Reinhardt R, Schüler D (2009) Toward cloning of the magnetotactic metagenome: Identification of magnetosome island gene clusters in uncultivated magnetotactic bacteria from different aquatic sediments. Appl Environ Microbiol 75: 3972-3979. 
  • Jones BV, Sun F, Marchesi JR (2007) Using skimmed milk agar to functionally screen a gut metagenomic library for proteases may lead to false positives Lett Appl Microbiol 45: 418-420. 
  • Jones C, Gu L, Sorrels CM, Sherman DH, Gerwick WH (2009) New tricks from ancient algae: natural products biosynthesis in marine cyanobacteria. Curr Opin Chem Biol 13: 216-223. 
  • Kennedy J, Flemer B, Jackson SA, Lejon DP, Morrissey JP, O'Gara F, Dobson AD (2010) Marine metagenomics: new tools for the study and exploitation of marine microbial metabolism. Mar Drugs 8: 608-628. 
  • Kim JY, Choi GS, Kim SB, Yoon GS, Kim YS, Ryu YW (2006) Screening and characterization of a novel esterase from a metagenomic library. Protein Expr Purif 45: 315-323. 
  • Knietsch A, Waschkowitz T, Bowien S, Henne A (2003) Construction and screening of metagenomic libraries derived from enrichment cultures: generation of a gene bank for genes conferring alcohol oxidoreductase activity on Escherichia coli. Appl Environ Microbiol 69: 1408-141. 
  • Konig GM, Kehraus S, Seibert SF, Abdel-Lateff A, Muller D (2006) Natural products from marine organisms and their associated microbes. Chembiochem 7: 229-238. 
  • Kowalchuk GA, Speksnijder AG, Zhang K, Goodman RM, van Veen JA (2007) Finding the needles in the metagenome haystack. Microb Ecol 53: 475-485. 
  • Lämmle 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: 575-592. 
  • LeCleir GR, Buchan A, Hollibaugh JT (2004) Chitinase Gene sequences retrieved from diverse aquatic habitats reveal environment-specific distributions. Appl Environ Microbiol 70: 6977-6983. 
  • Lee DG, Jeon JH, Jang MK, Kim NY, Lee JH, Lee JH, Kim SJ, Kim GD, Lee SH (2007) Screening and characterization of a novel fibrinolytic metalloprotease from a metagenomic library. Biotechnol Lett 29: 465-472. 
  • 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: 572-577. 
  • Lorenz P, Eck J (2005) Metagenomics and industrial applications. Nature Reviews Microbiology 3: 510-516.  
  • McMahon MD, Guan C, Handelsman J, Thomas MG (2012) Metagenomic analysis of Streptomyces lividans reveals host-dependent functional expression. Appl Environ Microbiol 78: 3622-3629  
  • Mayer AM, Rodríguez AD, Berlinck RG, Fusetani N (2011) Marine pharmacology in 2007-8: marine compounds with antibacterial, anticoagulant, antifungal, anti-inflammatory, antimalarial, antiprotozoal, antituberculosis, and antiviral activities; Affecting the immune and nervous system, and other miscellaneous mechanisms of action. Comp Biochem Physiol C Toxicol Pharmacol 153: 191-222. 
  • Mitra S, Gilbert JA, Field D, Huson DH (2010) Comparison of multiple metagenomes using phylogenetic networks based on ecological indices. ISME J 4: 1236-1242. 
  • Morgan JL, Darling AE, Eisen JA (2009) Metagenomic sequencing of an in vitro-simulated microbial community. PLoS ONE 5: e10209. 
  • Mori T, Mizuta S, Suenaga H, Miyazaki K (2008) Metagenomic screening for bleomycin resistance genes. Appl Environ Microbiol 74: 6803-6805. 
  • Neufeld JD, Chen Y, Dumont MG, Murrell JC (2008) Marine methylotrophs revealed by stable-isotope probing, multiple displacement amplification and metagenomics. Environ Microbiol 10: 1526-1535. 
  • 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. 
  • Park HJ, Jeon JH, Kang SG, Lee JH, Lee SA, Kim HK (2007) Functional expression and refolding of new alkaline esterase, EM2L8 from deep-sea sediment metagenome. Protein Expr Purif 52: 340-347. 
  • Penesyan A, Kjelleberg S, Egan S (2010) Development of novel drugs from marine surface associated microorganisms. Mar Drugs 8: 438-459. 
  • Peng Q, Zhang Z, Shang M, Wang X, Wang G, Li B, Guan G, Li J, Wang Y (2011) A novel esterase gene cloned from a metagenomic library from neritic sediments of the South China Sea. Microb Cell Fact 10: 95. 
  • Pottkämper J, Barthen P, Ilmberger N, Schwaneberg U, Schenk A, Schulte M, Ignatiev N, Streit WR (2009) Applying metagenomics for the identification of bacterial cellulases that are stable in ionic liquids. Green Chem 11: 957-965.
  • Raes J, Korbel JO, Lercher MJ, von Mering C, Bork P (2007) Prediction of effective genome size in metagenomic samples. Genome Biol 8: R10. 
  • Rheinheimer G (1992) Aquatic Microbiology, pp 56-82. Willey J & Sons, New York, USA.
  • Riesenfeld CS, Goodman RM, Handelsman J (2004) Uncultured soil bacteria are a reservoir of new antibiotic resistance genes. Environ Microbiol 6: 981-989. 
  • Roh C, Villatte F, Kim BG, Schmid RD (2006) Comparative study of methods for extraction and purification of environmental DNA from soil and sludge Samales. Appl Biochem Biotechnol 134: 97-112. 
  • Rolf D (2005) The metagenomics of soil. Nat Rev Microbiol 3: 470-478. 
  • 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: 2541-2547. 
  • Schloss PD, Handelsman J (2003) Biotechnological prospects from metagenomic. Curr Opin Biotechnol 14: 303-310. 
  • Schoenfeld T, Liles M, Wommack KE, Polson SW, Godiska R, Mead D (2010) Functional viral metagenomics and the next generation of molecular tools. Trends Microbiol 18: 20-29. 
  • Simon C, Daniel R (2011) Metagenomic analyses: past and future trends.. Appl Environ Microbiol 77: 1153-1161. 
  • Spits C, Le Caignec C, De Rycke M, Van Haute L, Van Steirteghem A, Liebaers I, Sermon K (2006) Whole-genome multiple displacement amplification from single cells. Nat Protoc 1: 1965-1970. 
  • Suenaga H, Ohnuki T, Miyazaki K (2007) Functional screening of a metagenomic library for genes involved in microbial degradation of aromatic compounds. Environ Microbiol 9: 2289-2297. 
  • Thomas T, Gilbert J, Meyer F (2012) Metagenomics - a guide from sampling to data analysis. Microb Inform Exp 2: 3. 
  • Uchiyama T, Miyazaki K (2009) Functional metagenomics for enzyme discovery: challenges to efficient screening. Curr Opin Biotechnol 20: 616-622. 
  • Weiland N, Löscher C, Metzger R, Schmitz R (2010) Construction and screening of marine metagenomic libraries. Methods Mol Biol 668: 51-65. 
  • 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: 1917-1926. 
  • Williamson LL, Borlee BR, Schloss PD, Guan CH, Allen HK, Handelsman J (2005) Intracellular screen to identify metagenomic clones that induce or inhibit a quorum-sensing biosensor. Appl Environ Microbiol 71: 6335-6344. 
  • Woyke T, Tighe D, Mavromatis K, Clum A, Copeland A, Schackwitz W, Lapidus A, Wu D, McCutcheon JP, McDonald BR, Moran NA, Bristow J, Cheng JF (2010) One bacterial cell, one complete genome. PLoS ONE 5: e10314. 
  • Xu M, Xiao X, Wang F (2008) Isolation and characterization of alkane hydroxylases from a metagenomic library of Pacific deep-sea sediment. Extremophiles 12: 255-262. 
  • Yun J, Ryu S (2005) Screening for novel enzymes from metagenome and SIGEX, as a way to improve it. Microb Cell Fact 4: 8. 
  • Zhao XQ (2011) Genome-based studies of marine microorganisms to maximize the diversity of natural products discovery for medical treatments. Evid-Based Complement Alternat Med 2011: 384572 
  • Zobell CE (1946) Characteristics of water bacteria. Sanitarian 8: 211-214. 

Uwagi

rekord w opracowaniu

Typ dokumentu

Bibliografia

Identyfikatory

Identyfikator YADDA

bwmeta1.element.agro-289b0419-9630-4833-858a-d928151e00d5
JavaScript jest wyłączony w Twojej przeglądarce internetowej. Włącz go, a następnie odśwież stronę, aby móc w pełni z niej korzystać.