Mining and selecting genes encoding chitinase from DNA metagenome data

Nguyen Thi Thom, Nguyen Thi Hong Ha, Pham Bich Ngoc, Chu Hoang Ha, Ho Bich Hai, Le Mai Huong
Author affiliations


  • Nguyen Thi Thom Viện Công nghệ sinh học
  • Nguyen Thi Hong Ha
  • Pham Bich Ngoc
  • Chu Hoang Ha
  • Ho Bich Hai
  • Le Mai Huong



chitinase, DNA metagenome, E. coli, new gene, recombinant


In this study, genes encoding chitinaseswere obtained by mining the rhizosphere metagenome database of
2-year-old replanted coffee trees in Dak Lak province and annotating using CAZy data. These sequences predictably are covered 90% of chitinase domains by BLASTp and range from 33% to 99% identity in comparison with published sequence data of chitinase genes. In order to find new funtional chitinase gene(s), among 8/56 chitinase genes with sequence identity less than 75%, ChiA_2 sequenceshowed the highest max score andsignificant homology (72%) was initially selected. Analysis of in silico sequence identified a protein motif for a signal peptide of 30 amino acid residues at the N- terminal using SignalP 4.1 server. By InterProscan software, the ChiA_2 gene sequence is predicted to have conserved active site FDGIDIDWE located at 134-142. The ChiA_2 sequence consisting of 1167 nucleotides, encoding for 389 amino acids with a predicted molecular mass of 43 kDa was synthesized, cloned into the pET21 a(+) vector and transformed into E. coli BL21 (DE3) by heat shock. ChiA_2 protein was specifically expressed in the recombinant E. coli BL21 (DE3) cell with an activity of 4.9 U/ml. In this study, analyzing metagenomic data from the soil sample of rhizosphere provided relatively sufficient genetic information of chitinase gene and initially successful expression and functional evaluation of ChiA_2 sequence, encoding Chitinase 2.


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How to Cite

Thi Thom, N., Thi Hong Ha, N., Bich Ngoc, P., Hoang Ha, C., Bich Hai, H., & Mai Huong, L. (2020). Mining and selecting genes encoding chitinase from DNA metagenome data. Vietnam Journal of Biotechnology, 17(3), 553–560.




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