Metagenomic insights into lignocellulose-degrading genes through Illuminabased de novo sequencing of the microbiome in vietnamese native goats’ rumen

Thi Huyen Do, Ngoc Giang Le, Trong Khoa Dao, Thi Mai Phuong Nguyen, Tung Lam Le, Han Ly Luu, Khanh Hoang Viet Nguyen, Van Lam Nguyen, Lan Anh Le, Thu Nguyet Phung, Nico M van Straalen, Dick Roelofs, Nam Hai Truong*

*Corresponding author for this work

    Research output: Contribution to JournalArticleAcademicpeer-review

    Abstract

    The scarcity of enzymes having an optimal activity in lignocellulose deconstruction is an obstacle for industrial-scale conversion of cellulosic biomass into biofuels. With the aim of mining novel lignocellulolytic enzymes, a ~9 Gb metagenome of bacteria in Vietnamese native goats’ rumen was sequenced by Illumina platform. From the data, 821 ORFs encoding carbohydrate esterases (CEs) and polysaccharide lyases (PLs) serving for lignocellulose pre-treatment, 816 ORFs encoding 11 glycoside hydrolase families (GHs) of cellulases, and 2252 ORFs encoding 22 GHs of hemicellulases, were mined. The carbohydrate binding module (CBM) was also abundant with 763 ORFs, of which 480 ORFs are located with lignocellulolytic enzymes. The enzyme modularity analysis showed that CBMs are usually present in endoglucanase, endo 1,3-beta-D-glucosidase, and endoxylanase, whereas fibronectin 3-like module (FN3) mainly represents in GH3 and immunoglobulin-like domain (Ig) was located in GH9 only. Every domain located in each ORF was analyzed in detail to contribute enzymes’ modularity which is valuable for modelling, to study the structure, and for recombinant production. With the aim of confirming the annotated results, a mined ORF encoding CBM63 was highly expressed in E. coli in soluble form. The purified recombinant CBM63 exhibited no cellulase activity, but enhanced a commercial cellulase activity in the destruction of a paper filter.

    Original languageEnglish
    Pages (from-to)108-116
    Number of pages9
    JournalThe Journal of general and applied microbiology
    Volume64
    Issue number3
    Early online date12 Mar 2018
    DOIs
    Publication statusPublished - Mar 2018

    Funding

    We would like to acknowledge Dr. S. V. N. Vijayendra (Food Microbiology Dept., Central Food Technological Research Institute, Mysore-570020, India) for proofreading and correcting the English of this manuscript. The study was carried out with the financial support of the Project “Metagenome of some potential mini-ecologies for mining novel genes encoding effective lignocellulolytic enzymes” code DTDLCN.15/14, managed by the Ministry of Science and Technology, Vietnam, in collaboration with the Department of Ecological Science, Vrije Universiteit Amsterdam, The Netherlands, supported by the BE-BASIC consortium project numbers F07.003.05 and F07.003.07. We thank the National Key Laboratory of Gene Technology, Institute of Biotechnology, VAST, Vietnam, for the use of their facilities. We are also grateful to the Editor of JGAM for valuable comments to improve the manuscript.

    FundersFunder number
    Ministry of Science and Technology
    Vietnam Academy of Science and Technology
    Vrije Universiteit AmsterdamF07.003.05, F07.003.07
    Ministerio de Ciencia y Tecnología

      Keywords

      • Carbohydrate binding model
      • Cellulase
      • Hemicellulase
      • Illumina de novo sequencing
      • Metagenome
      • Pretreatment
      • Vietnamese native goat

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