A PUTATIVE β-GLUCOSIDASE AND AN ENDO-1,4-β-GLUCANASE FROM POME METAGENOMIC DNA

Abstract views: 96 / PDF downloads: 237

Authors

  • Farah Fadwa Benbelgacem International Islamic University Malaysia
  • Adibah Parman
  • Oualid Abdelkader Bellag
  • Nabila Akhyar
  • Md Zahangir Alam
  • Hamzah Mohd. Salleh International Islamic University Malaysia

Keywords:

metagenomics; palm oil mill effluent (POME); high-throughput screening; next-generation sequencing; glucosidase; glucanase

Abstract

Functional metagenomic approach with high-throughput screening can be used to identify tapped and untapped biocatalysts. Metagenomic DNA libraries of 4.49 Gbase were constructed from microbes in Malaysian palm oil mill effluent (POME). After culture experiment based on natural selection metagenomic DNA was extracted and cloned to pCC1FOS vector and transformed into EPI300T1R. Cellulose-degrading enzyme activity was screened with microtiter assay using methylumbelliferyl-β-D-glucopyranoside (MUGlc) and methylumbelliferyl-β-D-cellobioside (MUC) as fluorogenic substrates. Reads were normalized using robust z-score and 100 highly rated clones were selected. Fosmids of these clones were isolated and sequenced with Hiseq strategy. Using Solexa, Velvet, SSPACE, Prodigal and Blastp, genes IDs of 96 putative cellulose-degrading enzymes were identified. Two putative metagenomic cellulose-degrading enzymes, MCDE1 with β-glucosidase activity and MCDE3 with endo-1,4-β-glucanase activity were produced, purified, and partially biochemically characterized.

References

Kuhad, R. C., Gupta, R., & Singh, A. (2011): Microbial Cellulases and Their Industrial Applications. Enzyme Research, pp. 1–10.

Ghimire, A., Kumar, G., Sivagurunathan, P., Shobana, S., Saratale, G. D., Kim, H. W., … Munoz, R. (2017): Bio-hythane production from microalgae biomass: Key challenges and potential opportunities for algal bio-refineries. Bioresource Technology. 241: 525–536.

Armstrong, Z., Liu, F., Kheirandish, S., Chen, H.-M., Mewis, K., Duo, T., Morgan-Lang, C., Hallam, S.J., & Withers, S. G. (2019): High-Throughput Recovery and Characterization of Metagenome-Derived Glycoside Hydrolase-Containing Clones as a Resource for Biocatalyst Development. MSystems. 4(4). https://doi.org/10.1128/mSystems.00082-19.

Amann, R. I., Ludwig, W., & Schleifer, K. H. (1995): Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Phylogenetic Identification and In Situ Detection of Individual Microbial Cells without Cultivation. Microbiological Reviews. 59(1): 143–169.

Kumar, A. K. (2015): UV mutagenesis treatment for improved production of endoglucanase and β-glucosidase from newly isolated thermotolerant actinomycetes, Streptomyces griseoaurantiacus. Bioresources and Bioprocessing. 2(1): 22. https://doi.org/10.1186/s40643-015-0052-x.

Riesenfeld, C. S., Schloss, P. D., & Handelsman, J. (2004): Metagenomics: genomic analysis of microbial communities. Annual Review of Genetics. 38: 525–552.

Martin, M., Biver, S., Steels, S., Barbeyron, T., Jam, M., Portetelle, D., van Michel, G., & Vandenbol, M. (2014): Identification and Characterization of a Halotolerant, Cold-Active Marine Endo-β-1,4-Glucanase by Using Functional Metagenomics of Seaweed-Associated Microbiota. Applied and Environmental Microbiology. 80(16): 4958–4967. https://doi.org/10.1128/AEM.01194-14.

Vester, J., Glaring, M., & Stougaard, P. (2014): Discovery of novel enzymes with industrial potential from a cold and alkaline environment by a combination of functional metagenomics and culturing. Microbial Cell Factories. 13(1): 72. doi: 10.1186/1475-2859-13-72.

Lewin, A., Zhou, J., Pham, V. T. T., Haugen, T., Zeiny, M. El, Aarstad, O., Leibl, W., Wenzel, A., & Liles, M. R. (2017): Novel archaeal thermostable cellulases from an oil reservoir metagenome. AMB Express. 7(1): 183. doi: 10.1186/s13568-017-0485-z.

Wierzbicka-Woś, A., Henneberger, R., Batista-García, R. A., Martínez-Ávila, L., Jackson, S. A., Kennedy, J., & Dobson, A. D. W. (2019): Biochemical Characterization of a Novel Monospecific Endo-β-1,4-Glucanase Belonging to GH Family 5 From a Rhizosphere Metagenomic Library. Frontiers in Microbiology. 10. https://doi.org/10.3389/fmicb.2019.01342.

Santana-Pereira, A. L. R., Sandoval-Powers, M., Monsma, S., Zhou, J., Santos, S. R., Mead, D. A., & Liles, M. R. (2020): Discovery of Novel Biosynthetic Gene Cluster Diversity from a Soil Metagenomic Library. Frontiers in Microbiology. 11. https://doi.org/10.3389/fmicb.2020.585398.

Birmingham, A., Selfors, L. M., Forster, T., Wrobel, D., Kennedy, C. J., Shanks, E., Santoyo-Lopez, J., Dunican, D.J., Long, A., Kelleher, D., Beijersbergen, R.L., Ghazal, P., & Shamu, C. E. (2009). Statistical methods for analysis of high-throughput RNA interference screens. Nat Methods, 6(8): 569–575.

Rees, H. C., Grant, S., Jones, B., Grant, W. D., & Heaphy, S. (2003): Detecting cellulase and esterase enzyme activities encoded by novel genes present in environmental DNA libraries. Extremophiles. 7(5): 415–421.

Voget, S., Leggewie, C., Uesbeck, A., Raasch, C., Jaeger, K. E., & Streit, W. R. (2003): Prospecting for Novel Biocatalysts in a Soil Metagenome. Applied and Environmental Microbiology. 69(10): 6235–6242.

Lee, S., & Hallam, S. J. (2009): Extraction of high molecular weight genomic DNA from soils and sediments. Journal of Visualized Experiments: JoVE. (33): 2–5.

Asli, N., Sergio, C., & Chen, T. (2013): Data Analysis Approaches in High Throughput Screening. In Drug Discovery. InTech. doi: 10.5772/52508.

Benbelgacem, F. F., Mat Isa, Mohd Noor Abdelrahim, M. A. M., Tumian, Afidalina, Abdelkader Bellag, O., Parman, Adibah Noorbatcha, I. A., & Mohd Salleh, H. (2018): Next Generation Sequencing-Data Analysis for Cellulose- and Xylan-Degrading Enzymes from POME Metagenome. Sains Malaysiana, 47(12): 2951–2960.

http://dx.doi.org/10.17576/jsm-2018-4712-03 Zerbino, D. R., & Birney, E. (2008): Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Research. 18(5): 821–829.

Boetzer, M., Henkel, C. V., Jansen, H. J., Butler, D., & Pirovano, W. (2011): Scaffolding pre-assembled contigs using SSPACE. Bioinformatics, 27(4): 578-579. doi: 10.1093/bioinformatics/btq683.

Hyatt, D., Chen, G. L., LoCascio, P. F., Land, M. L., Larimer, F. W., & Hauser, L. J. (2010): Prodigal: Prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 11(1): 119. https://doi.org/10.1186/1471-2105-11-119.

Laemmli, U. K. (1970): Cleavage of Structural Proteins during the Assembly of the Head of Bacteriophage T4. Nature. 227(5259): 680–685.

Walker, J. M. (2002): Protein Protocols Handbook, The. New Jersey: Humana Press.

Yang, J., & Zhang, Y. (2015): Protein Structure and Function Prediction Using I-TASSER. Current Protocols in Bioinformatics. 52(1): 5.8.1-5.8.15. doi: 10.1002/0471250953.bi0508s52.

Roy, A., Kucukural, A., & Zhang, Y. (2010): I-TASSER: A unified platform for automated protein structure and function prediction. Nature Protocols. 5(4): 725–738.

Y Zhang. (2008): I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, 9: 40. https://doi.org/10.1186/1471-2105-9-40.

de Castro, E., Sigrist, C. J. A., Gattiker, A., Bulliard, V., Langendijk-Genevaux, P. S., Gasteiger, E., Bairoch, A., & Hulo, N. (2006): ScanProsite: Detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins. Nucleic Acids Research. 34(Web Server), W362–W365. doi: 10.1093/nar/gkl124.

Benbelgacem, F.F., Bellag, O.A., Ahmad, A. A., Noorbatcha, I.A., & Mohd. Salleh, H. (2017): Palm Oil Mill Effluent Metagenome for Cellulose-Degrading Enzymes. Journal of Basic and Applied Research. 3(3): 101–106.

Uchiyama, T., & Kentaro Miyazaki. (2009): Functional metagenomics for enzyme discovery: challenges to efficient screening. Current Opinion in Biotechnology. 20: 616–622.

Madhavan, A., Sindhu, R., Parameswaran, B., Sukumaran, R. K., & Pandey, A. (2017): Metagenome Analysis: a Powerful Tool for Enzyme Bioprospecting. Applied Biochemistry and Biotechnology. 183(2): 636–651.

Parks, R., & Graham, F. (1997): A helper-dependent system for adenovirus vector production helps define a lower limit for efficient DNA packaging. Journal of Virology. 71: 3293–3298.

Zhou, J., Bruns, M. A., & Tiedje, J. M. (1996): DNA recovery from soils of diverse composition. Applied and Environmental Microbiology. 62(2): 316–322.

Wexler, M., Bond, P. L., Richardson, D. J., & Johnston, A. W. B. (2005): A wide host-range metagenomic library from a waste water treatment plant yields a novel alcohol/aldehyde dehydrogenase. Environmental Microbiology. 7(12): 1917–1926.

Kakirde, K. S., Parsley, L. C., & Liles, M. R. (2010): Size does matter: Application-driven approaches for soil metagenomics. Soil Biology and Biochemistry, 42(11): 1911-1923. doi: 10.1016/j.soilbio.2010.07.021

Craig, J. W., Chang, F.-Y., Kim, J. H., Obiajulu, S. C., & Brady, S. F. (2010): Expanding Small-Molecule Functional Metagenomics through Parallel Screening of Broad-Host-Range Cosmid Environmental DNA Libraries in Diverse Proteobacteria. Applied and Environmental Microbiology. 76(5): 1633–1641.

Troeschel, S. C., Drepper, T., Leggewie, C., Streit, W. R., & Jaeger, K.-E. (2010): Novel Tools for the Functional Expression of Metagenomic DANN, pp. 117–139.

Cheng, J., Pinnell, L., Engel, K., Neufeld, J. D., & Charles, T. C. (2014): Versatile broad-host-range cosmids for construction of high quality metagenomic libraries. Journal of Microbiological Methods. 99(1): 27–34.

Lam, K. N., Cheng, J., Engel, K., Neufeld, J. D., & Charles, T. C. (2015): Current and future resources for functional metagenomics. Frontiers in Microbiology, 6. https://doi.org/10.3389/fmicb.2015.01196.

Taupp, M., Mewis, K., & Hallam, S. J. (2011): The art and design of functional metagenomic screens. Current Opinion in Biotechnology. 22(3) 465–472.

Cano-Ramírez, C., Santiago-Hernández, A., Rivera-Orduña, F. N., García-Huante, Y., Zúñiga, G., & Hidalgo-Lara, M. E. (2016): Expression, purification and characterization of an endoglucanase from Serratia proteamaculans CDBB-1961, isolated from the gut of Dendroctonus adjunctus (Coleoptera: Scolytinae). AMB Express, 6(1): 63. doi: 10.1186/s13568-016-0233-9

Cregg, J. M., Vedvick, T. S., & Raschke, W. C. (1993): Recent advances in the expression of foreign genes in Pichia pastoris. Nature Biotechnology. 11(8): 905–910.

Woon, J. S., Jie, P., King, H., Mohamed, M., Mahadi, N. M., Mohd, W., & Wan, K. (2017): Cloning, Production and Characterization of a Glycoside Hydrolase Family 7 Enzyme from the Gut Microbiota of the Termite Coptotermes curvignathus. Molecular Biotechnology. 59(7): 271–283.

Downloads

Published

2022-01-23

How to Cite

Benbelgacem, F. F., Parman, A., Bellag, O. A., Akhyar, N., Alam, M. Z., & Mohd. Salleh, H. (2022). A PUTATIVE β-GLUCOSIDASE AND AN ENDO-1,4-β-GLUCANASE FROM POME METAGENOMIC DNA. Journal of Applied Biological Sciences, 16(1), 46–61. Retrieved from https://www.jabsonline.org/index.php/jabs/article/view/918

Issue

Section

Articles