Abstract
Nitrilase is one of the most important members in the nitrilase superfamily and it is widely used for bioproduction of commodity chemicals and pharmaceutical intermediates as well as bioremediation of nitrile-contaminated wastes. However, its application was hindered by several limitations. Searching for new nitrilases and improving their application performances are the driving force for researchers. Genetic data resources in various databases are quite rich in post-genomic era. Besides, more than 99 % of microbes in the environment are unculturable. Metagenomic technology and genome mining are thus becoming burgeoning areas and provide unprecedented opportunities for searching more useful novel nitrilases due to the abundance of already existing but unexplored gene resources, namely uncharacterized genome information in the database and unculturable microbes in the natural environment. These techniques seem to be innovative and highly efficient. This study reviews the current status and future directions of metagenomics and genome mining in nitrilase exploration. Moreover, it discussed their utilization in coping with the challenges for nitrilase application. In the next several years, with the rapid development of nitrile biocatalysis, these two techniques would be bound to attract increasing attentions and even become a dominant trend for finding more novel nitrilases. Also, this review would provide guidance for exploitation of other commercially important enzymes.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Bayer S, Birkemeyer C, Ballschmiter M (2011) A nitrilase from a metagenomic library acts regioselectively on aliphatic dinitriles. Appl Microbiol Biotechnol 89(1):91–98
Bornscheuer UT, Huisman GW, Kazlauskas RJ, Lutz S, Moore JC, Robins K (2012) Engineering the third wave of biocatalysis. Nature 485(7397):185–194
Chauhan S, Wu S, Blumerman S, Fallon RD, Gavagan JE, DiCosimo R, Payne MS (2003) Purification, cloning, sequencing and over-expression in Escherichia coli of a regioselective aliphatic nitrilase from Acidovorax facilis 72W. Appl Microbiol Biotechnol 61(2):118–122
Chen J, Zheng R-C, Zheng Y-G, Shen Y-C (2009) Microbial transformation of nitriles to high-value acids or amides. Adv Biochem Eng Biotechnol 113:33–77
Debabov V, Yanenko A (2011) Biocatalytic hydrolysis of nitriles. Rev J Chem 1(4):385–402
DeSantis G, Zhu Z, Greenberg WA, Wong K, Chaplin J, Hanson SR, Farwell B, Nicholson LW, Rand CL, Weiner DP, Robertson DE, Burk MJ (2002) An enzyme library approach to biocatalysis:development of nitrilases for enantioselective production of carboxylic acid derivatives. J Am Chem Soc 124(31):9024–9025
Feng L-L, Zhang J-F, Luo H, Li Z (2011) Surface modification of acrylonitrile fibers and membrane by nitrilase from Escherichia coli BL21 (DE3)/pET-Nit. Adv Mater Res 175–176:651–655
Gong J-S, Lu Z-M, Shi J-S, Dou W-F, Xu H-Y, Zhou Z-M, Xu Z-H (2011) Isolation, identification, and culture optimization of a novel glycinonitrile-hydrolyzing fungus—Fusarium oxysporum H3. Appl Biochem Biotechnol 165(3–4):963–977
Gong J-S, Li H, Zhu X-Y, Lu Z-M, Wu Y, Shi J-S, Xu Z-H (2012a) Fungal His-tagged nitrilase from Gibberella intermedia: Gene cloning, heterologous expression and biochemical properties. PLoS One 7(11):e50622
Gong J-S, Lu Z-M, Li H, Shi J-S, Zhou Z-M, Xu Z-H (2012b) Nitrilases in nitrile biocatalysis: recent progress and forthcoming research. Microb Cell Fact 11:142
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
Huisman GW, Collier SJ (2013) On the development of new biocatalytic processes for practical pharmaceutical synthesis. Curr Opin Chem Biol:In press
Kaplan O, Bezouška K, Malandra A, Veselá A, Petříčková A, Felsberg J, Rinágelová A, Křen V, Martínková L (2011) Genome mining for the discovery of new nitrilases in filamentous fungi. Biotechnol Lett 33(2):309–312
Kaplan O, Veselá A, Petříčková A, Pasquarelli F, Pičmanová M, Rinágelová A, Bhalla T, Pátek M, Martínková L (2013) A comparative study of nitrilases identified by genome mining. Mol Biotechnol. doi:10.1007/s12033-013-9656-6
Kimura N (2006) Metagenomics: Access to unculturable microbes in the environment. Microbes Environ 21(4):201–215
Liu ZQ, Zhou M, Zhang XH, Xu JM, Xue YP, Zheng YG (2012) Biosynthesis of iminodiacetic acid from iminodiacetonitrile by immobilized recombinant Escherichia coli harboring nitrilase. J Mol Microbiol Biotechnol 22(1):35–47
Lorenz P, Eck J (2005) Metagenomics and industrial applications. Nat Rev Micro 3(6):510–516
Malandra A, Cantarella M, Kaplan O, Vejvoda V, Uhnakova B, Stepankova B, Kubac D, Martinkova L (2009) Continuous hydrolysis of 4-cyanopyridine by nitrilases from Fusarium solani O1 and Aspergillus niger K10. Appl Microbiol Biotechnol 85(2):277–284
Martínková L, Vejvoda V, Kaplan O, Kubáč D, Malandr A, Cantarella M, Bezouška K, Křen V (2009) Fungal nitrilases as biocatalysts: recent developments. Biotechnol Adv 27(6):661–670
Pace HC, Brenner C (2001) The nitrilase superfamily: classification, structure and function. Genome Biol 2(1):1–9
Raes J, Foerstner KU, Bork P (2007) Get the most out of your metagenome: computational analysis of environmental sequence data. Curr Opin Microbiol 10(5):490–498
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
Rustler S, Chmura A, Sheldon RA, Stolz A (2008) Characterisation of the substrate specificity of the nitrile hydrolyzing system of the acidotolerant black yeast Exophiala oligosperma R1. Stud Mycol 61:165–174
Seffernick JL, Samanta SK, Louie TM, Wackett LP, Subramanian M (2009) Investigative mining of sequence data for novel enzymes: a case study with nitrilases. J Biotechnol 143(1):17–26
Temperton B, Giovannoni SJ (2012) Metagenomics: microbial diversity through a scratched lens. Curr Opin Microbiol 15(5):605–612
Velankar H, Clarke KG, Rd P, Cowan DA, Burton SG (2010) Developments in nitrile and amide biotransformation processes. Trends Biotechnol 28(11):561–569
Veselá A, Franc M, Pelantová H, Kubáč D, Vejvoda V, Šulc M, Bhalla T, Macková M, Lovecká P, Janů P, Demnerová K, Martínková L (2010) Hydrolysis of benzonitrile herbicides by soil actinobacteria and metabolite toxicity. Biodegradation 21(5):761–770
Wang H, Sun H, Wei D (2013) Discovery and characterization of a highly efficient enantioselective mandelonitrile hydrolase from Burkholderia cenocepacia J2315 by phylogeny-based enzymatic substrate specificity prediction. BMC Biotechnol 13(1):14
Wohlgemuth R (2010) Biocatalysis—key to sustainable industrial chemistry. Curr Opin Biotechnol 21(6):713–724
Wu Y, Gong J-S, Lu Z-M, Li H, Zhu X-Y, Li H, Shi J-S, Xu Z-H (2012) Isolation and characterization of Gibberella intermedia CA3-1, a novel and versatile nitrilase-producing fungus. J Basic Microbiol. doi:10.1002/jobm.201200143
Xue Y-P, Xu S-Z, Liu Z-Q, Zheng Y-G, Shen Y-C (2011) Enantioselective biocatalytic hydrolysis of (R, S)-mandelonitrile for production of (R)-(-)-mandelic acid by a newly isolated mutant strain. J Ind Microbiol Biotechnol 38(2):337–345
Zhang Z-J, Xu J-H, He Y-C, Ouyang L-M, Liu Y-Y (2011) Cloning and biochemical properties of a highly thermostable and enantioselective nitrilase from Alcaligenes sp. ECU0401 and its potential for (R)-(−)-mandelic acid production. Bioproc Biosyst Eng 34(3):315–322
Zhang C-S, Zhang Z-J, Li C-X, Yu H-L, Zheng G-W, Xu J-H (2012) Efficient production of (R)-o-chloromandelic acid by deracemization of (R)-o-chloromandelonitrile with a new nitrilase mined from Labrenzia aggregata. Appl Microbiol Biotechnol 95(1):91–99
Zhu D, Mukherjee C, Biehl ER, Hua L (2007) Discovery of a mandelonitrile hydrolase from Bradyrhizobium japonicum USDA110 by rational genome mining. J Biotechnol 129:645–650
Zhu D, Mukherjee C, Yang Y, Rios BE, Gallagher DT, Smith NN, Biehl ER, Hua L (2008) A new nitrilase from Bradyrhizobium japonicum USDA 110: Gene cloning, biochemical characterization and substrate specificity. J Biotechnol 133(3):327–333
Acknowledgments
The authors would sincerely like to thank Prof. Zhi-Song Shen for his substantial support for this project. This work was financially supported by the National Natural Science Foundation of China (no. 21206055), the Social Development Funds of Scientific Committee of Jiangsu province (BE2010629), the National High Technology Research and Development Program of China (no. 2011AA02A211), the Fundamental Research Funds for the Central Universities (no. JUSRP111A51), and the Research and Innovation Project for College Graduates of Jiangsu Province (no. CXLX12_0731).
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Gong, JS., Lu, ZM., Li, H. et al. Metagenomic technology and genome mining: emerging areas for exploring novel nitrilases. Appl Microbiol Biotechnol 97, 6603–6611 (2013). https://doi.org/10.1007/s00253-013-4932-8
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00253-013-4932-8