전체메뉴
검색
Article Search

JMB Journal of Microbiolog and Biotechnology

QR Code QR Code

Note

References

  1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J. Mol. Biol. 215: 403-410.
    CrossRef
  2. Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, et al. 2009. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 37: W202-W208.
    Pubmed PMC CrossRef
  3. Barriuso J, Ramos Solano B, Santamaría C, Daza A, Gutierrez Mañero FJ. 2008. Effect of inoculation with putative PGPR isolated from Pinus sp. on Pinus pinea growth, mycorrhization and rhizosphere microbial communities. J. Appl. Microbiol. 105: 1298-1309.
    Pubmed CrossRef
  4. Barriuso J, Valverde JR, Mellado RP. 2011. Estimation of bacterial diversity using next generation sequencing of 16S rDNA: a comparison of different workflows. BMC Bioinformatics 14: 473.
    Pubmed PMC CrossRef
  5. Barriuso J, Prieto A, Martínez M J. 2 013. F ungal geno mes mining to discover novel sterol esterases and lipases as catalysts. BMC Genomics 18: 712.
  6. Bolduc B, Shaughnessy DP, Wolf YI, Koonin EV, Roberto FF, Young M. 2012. Identification of novel positive-strand RNA viruses by metagenomic analysis of archaea-dominated Yellowstone hot springs. J. Virol. 6: 5562-5573.
    Pubmed PMC CrossRef
  7. Calero-Rueda O, Plou FJ, Ballesteros A, Martínez AT, Martínez MJ. 2002. Production, isolation and characterization of a sterol esterase from Ophiostoma piceae. BBA Proteins Proteomics 1599: 28-35.
    CrossRef
  8. Finn RD, Clements J, Eddy SR. 2011. HMMER web server:interactive sequence similarity searching. Nucleic Acids Res. 39: W29-W37.
    Pubmed PMC CrossRef
  9. Gango iti J, S antos M, P rieto MA, d e la M ata I, S erra J L, Llama MJ. 2012. Characterization of a novel subgroup of extracellular medium-chain-length polyhydroxyalkanoate depolymerases from actinobacteria. Appl. Environ. Microbiol. 78: 7229-7237.
  10. Jaeger KE, Eggert T. 2002. Lipases for biotechnology. Curr. Opin. Biotechnol. 13: 390-397.
    CrossRef
  11. Jiang Y, Ye J, Wu H, Zhang H. 2004. Cloning and expression of the polyhydroxyalkanoate depolymerase gene from Pseudomonas putida, and characterization of the gene product. Biotechnol. Lett. 26: 1585-1588.
    Pubmed CrossRef
  12. Kiefer F, Arnold K, Künzli M, Bordoli L, Schwede T. 2009. The SWISS-MODEL repository and associated resources. Nucleic Acids Res. 37: D387-D392.
    Pubmed PMC CrossRef
  13. Kontkanen H, Tenkanen M, Reinikainen T. 2006. Purification and characterisation of a novel steryl esterase from Melanocarpus albomyces. Enzyme Microb. Technol. 39: 265-273.
    CrossRef
  14. Lee SY. 1996. Bacterial polyhydroxyalkanoates. Biotechnol. Bioeng. 49: 1-14.
    CrossRef
  15. Lotti M, Tramontano A, Longhi S, Fusetti F, Brocca S, Pizzi E, Alberghina L. 1994. Variability within the Candida rugosa lipases family. Protein Eng. 7: 531-535.
    Pubmed CrossRef
  16. Mancheño JM, Pernas MA, Martínez MJ, Ochoa B, Rua ML, Hermoso JA. 2003. Structural insights into the lipase/esterase behavior in the Candida rugosa lipases family: crystal structure of the lipase 2 isoenzyme at 1.97A resolution. J. Mol. Biol. 332: 1059-1069.
    CrossRef
  17. Markowitz VM, Chen IM, Chu K, Szeto E, Palaniappan K, Grechkin Y, et al. 2012. IMG/M: the integrated metagenome data management and comparative analysis system. Nucleic Acids Res. 40: D123-D129.
    Pubmed PMC CrossRef
  18. Medek P, Benes P, Sochor J. 2007. Computation of tunnels in protein molecules using Delaunay triangulation. J. WSCG 15: 107-114.
  19. Meyer F, Paarmann D, D’Souza M, Olson R, Glass EM, Kubal M, et al. 2008. The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 19: 386.
    Pubmed PMC CrossRef
  20. Olson SA. 2002. EMBOSS opens up sequence analysis. European molecular biology open software suite. Brief Bioinform. 3: 87-91.
    Pubmed CrossRef
  21. Pleiss J, Fischer M, Peiker M, Thiele C, Schmid RD. 2000. Lipase engineering database: understanding and exploiting sequence-structure-function relationships. J. Mol. Catal. B Enzym. 10: 491-508.
    CrossRef
  22. Schmeisser C, Steele H, Streit WR. 2007. Metagenomics, biotechnology with non-culturable microbes. Appl. Microbiol. Biotechnol. 75: 955-962.
    Pubmed CrossRef
  23. Sun S, Chen J, Li W, Altintas I, Lin A, Peltier S, et al. 2011. Community cyberinfrastructure for advanced microbial ecology research and analysis: the CAMERA resource. Nucleic Acids Res. 39: D546-D551.
    Pubmed PMC CrossRef
  24. Voget S, Leggewie C, Uesbeck A, Raasch C, Jaeger KE, Streit WR. 2003. Prospecting for novel biocatalysts in a soil metagenomes. Appl. Environ. Microbiol. 69: 6235-6242.
    Pubmed PMC CrossRef
  25. Wei Y, Contreras JA, Sheffield P, Osterlund T, Derewenda U, Kneusel RE, et al. 1999. Crystal structure of brefeldin A esterase, a bacterial homolog of the mammalian hormonesensitive lipase. Nat. Struct. Biol. 6: 340-345.
    Pubmed CrossRef

Article

Note

J. Microbiol. Biotechnol. 2015; 25(5): 732-737

Published online May 28, 2015 https://doi.org/10.4014/jmb.1406.06049

Copyright © The Korean Society for Microbiology and Biotechnology.

In Silico Metagenomes Mining to Discover Novel Esterases with Industrial Application by Sequential Search Strategies

Jorge Barriuso 1* and María Jesús Martínez 1

Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, 28040 Madrid, Spain

Received: June 17, 2014; Accepted: December 4, 2014

Abstract

We present here an in silico search of fungal sterol-esterase/lipase and bacterial depolymerase
sequences from environmental metagenomes. Both enzyme types contain the α/β-hydrolase
protein fold. Analysis of DNA conserved motifs, protein homology search, phylogenetic
analysis, and protein 3D modeling have been used, and the efficiency of these screening
strategies is discussed. The presence of bacterial genes in the metagenomes was higher than
those from fungi, and the sequencing depth of the metagenomes seemed to be crucial to allow
finding enough diversity of enzyme sequences. As a result, a novel putative PHAdepolymerase
is described.

Keywords: Sterol esterase, lipase, PHA-depolymerase, genome diversity

References

  1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J. Mol. Biol. 215: 403-410.
    CrossRef
  2. Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, et al. 2009. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 37: W202-W208.
    Pubmed KoreaMed CrossRef
  3. Barriuso J, Ramos Solano B, Santamaría C, Daza A, Gutierrez Mañero FJ. 2008. Effect of inoculation with putative PGPR isolated from Pinus sp. on Pinus pinea growth, mycorrhization and rhizosphere microbial communities. J. Appl. Microbiol. 105: 1298-1309.
    Pubmed CrossRef
  4. Barriuso J, Valverde JR, Mellado RP. 2011. Estimation of bacterial diversity using next generation sequencing of 16S rDNA: a comparison of different workflows. BMC Bioinformatics 14: 473.
    Pubmed KoreaMed CrossRef
  5. Barriuso J, Prieto A, Martínez M J. 2 013. F ungal geno mes mining to discover novel sterol esterases and lipases as catalysts. BMC Genomics 18: 712.
  6. Bolduc B, Shaughnessy DP, Wolf YI, Koonin EV, Roberto FF, Young M. 2012. Identification of novel positive-strand RNA viruses by metagenomic analysis of archaea-dominated Yellowstone hot springs. J. Virol. 6: 5562-5573.
    Pubmed KoreaMed CrossRef
  7. Calero-Rueda O, Plou FJ, Ballesteros A, Martínez AT, Martínez MJ. 2002. Production, isolation and characterization of a sterol esterase from Ophiostoma piceae. BBA Proteins Proteomics 1599: 28-35.
    CrossRef
  8. Finn RD, Clements J, Eddy SR. 2011. HMMER web server:interactive sequence similarity searching. Nucleic Acids Res. 39: W29-W37.
    Pubmed KoreaMed CrossRef
  9. Gango iti J, S antos M, P rieto MA, d e la M ata I, S erra J L, Llama MJ. 2012. Characterization of a novel subgroup of extracellular medium-chain-length polyhydroxyalkanoate depolymerases from actinobacteria. Appl. Environ. Microbiol. 78: 7229-7237.
  10. Jaeger KE, Eggert T. 2002. Lipases for biotechnology. Curr. Opin. Biotechnol. 13: 390-397.
    CrossRef
  11. Jiang Y, Ye J, Wu H, Zhang H. 2004. Cloning and expression of the polyhydroxyalkanoate depolymerase gene from Pseudomonas putida, and characterization of the gene product. Biotechnol. Lett. 26: 1585-1588.
    Pubmed CrossRef
  12. Kiefer F, Arnold K, Künzli M, Bordoli L, Schwede T. 2009. The SWISS-MODEL repository and associated resources. Nucleic Acids Res. 37: D387-D392.
    Pubmed KoreaMed CrossRef
  13. Kontkanen H, Tenkanen M, Reinikainen T. 2006. Purification and characterisation of a novel steryl esterase from Melanocarpus albomyces. Enzyme Microb. Technol. 39: 265-273.
    CrossRef
  14. Lee SY. 1996. Bacterial polyhydroxyalkanoates. Biotechnol. Bioeng. 49: 1-14.
    CrossRef
  15. Lotti M, Tramontano A, Longhi S, Fusetti F, Brocca S, Pizzi E, Alberghina L. 1994. Variability within the Candida rugosa lipases family. Protein Eng. 7: 531-535.
    Pubmed CrossRef
  16. Mancheño JM, Pernas MA, Martínez MJ, Ochoa B, Rua ML, Hermoso JA. 2003. Structural insights into the lipase/esterase behavior in the Candida rugosa lipases family: crystal structure of the lipase 2 isoenzyme at 1.97A resolution. J. Mol. Biol. 332: 1059-1069.
    CrossRef
  17. Markowitz VM, Chen IM, Chu K, Szeto E, Palaniappan K, Grechkin Y, et al. 2012. IMG/M: the integrated metagenome data management and comparative analysis system. Nucleic Acids Res. 40: D123-D129.
    Pubmed KoreaMed CrossRef
  18. Medek P, Benes P, Sochor J. 2007. Computation of tunnels in protein molecules using Delaunay triangulation. J. WSCG 15: 107-114.
  19. Meyer F, Paarmann D, D’Souza M, Olson R, Glass EM, Kubal M, et al. 2008. The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 19: 386.
    Pubmed KoreaMed CrossRef
  20. Olson SA. 2002. EMBOSS opens up sequence analysis. European molecular biology open software suite. Brief Bioinform. 3: 87-91.
    Pubmed CrossRef
  21. Pleiss J, Fischer M, Peiker M, Thiele C, Schmid RD. 2000. Lipase engineering database: understanding and exploiting sequence-structure-function relationships. J. Mol. Catal. B Enzym. 10: 491-508.
    CrossRef
  22. Schmeisser C, Steele H, Streit WR. 2007. Metagenomics, biotechnology with non-culturable microbes. Appl. Microbiol. Biotechnol. 75: 955-962.
    Pubmed CrossRef
  23. Sun S, Chen J, Li W, Altintas I, Lin A, Peltier S, et al. 2011. Community cyberinfrastructure for advanced microbial ecology research and analysis: the CAMERA resource. Nucleic Acids Res. 39: D546-D551.
    Pubmed KoreaMed CrossRef
  24. Voget S, Leggewie C, Uesbeck A, Raasch C, Jaeger KE, Streit WR. 2003. Prospecting for novel biocatalysts in a soil metagenomes. Appl. Environ. Microbiol. 69: 6235-6242.
    Pubmed KoreaMed CrossRef
  25. Wei Y, Contreras JA, Sheffield P, Osterlund T, Derewenda U, Kneusel RE, et al. 1999. Crystal structure of brefeldin A esterase, a bacterial homolog of the mammalian hormonesensitive lipase. Nat. Struct. Biol. 6: 340-345.
    Pubmed CrossRef