Sequences Analysis of a Gene Encoding Extracellular Xylanase in Streptomyces costaricanus 45I-3
https://doi.org/10.22146/ijbiotech.15274 S. Sipriyadi(1*), Aris Tri Wahyudi(2), Maggy Thenawidjaja Suhartono(3), Anja Meryandini(4)
(1) Microbiology Study Program, Graduate School of Bogor Agricultural University, Bogor, West Java, Indonesia, 16680
(2) Biology Department, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, Bogor, West Java, Indonesia, 16680
(3) Food Science and Technology Department, Bogor Agricultural University, Bogor, West Java, Indonesia, 16680
(4) Biology Department, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University, Bogor, West Java, Indonesia, 16680
(*) Corresponding Author
Abstract
Streptomyces costaricanus 45I-3 is a bacterial strain belongs to actinomycetes group isolated from peat soil. The
bacterium is known to produce extracellular xylanase. The aims of this study were to analyze DNA sequence and
sub-clone gene involved in the synthesis of extracellular xylanase. Complete DNA sequence predicted to encode
xylanase genes was isolated from bacterial genome using Inverse Polymerase Chain Reaction (I-PCR). Total DNA
sequence of 1664 bp in size obtained from I-PCR consisted of two open reading frames (ORF) in opposite direction.
ORF1 was 1029 bp and ORF2 (partial sequence) was 309 bp. Analysis sequence using BlastX indicated that ORF1
was homologous with xylanase bacterium enrichment culture clone Xyl8B8 (GenBank accession No. AFH35005.1),
i.e. 95% in identity and 99% in similarity. In addition, ORF2 was homologous with glyoxalase bacterium enrichment
culture clone Xyl8B8 (GenBank accession No. AFH35007.1), i.e. 95% in identity and 98% in similarity. Analysis of
amino acid sequence revealed that ORF1 consisted of 2 domains, i.e. glyco-hydrolase 11 (GH11) and Carbohydrate
Binding Type 2 (CBM2). Active site was found at 130th amino acid on GH11 domain. Visualization of 3-dimension
structure showed that 1029 bp fragment is of 19 areas.
bacterium is known to produce extracellular xylanase. The aims of this study were to analyze DNA sequence and
sub-clone gene involved in the synthesis of extracellular xylanase. Complete DNA sequence predicted to encode
xylanase genes was isolated from bacterial genome using Inverse Polymerase Chain Reaction (I-PCR). Total DNA
sequence of 1664 bp in size obtained from I-PCR consisted of two open reading frames (ORF) in opposite direction.
ORF1 was 1029 bp and ORF2 (partial sequence) was 309 bp. Analysis sequence using BlastX indicated that ORF1
was homologous with xylanase bacterium enrichment culture clone Xyl8B8 (GenBank accession No. AFH35005.1),
i.e. 95% in identity and 99% in similarity. In addition, ORF2 was homologous with glyoxalase bacterium enrichment
culture clone Xyl8B8 (GenBank accession No. AFH35007.1), i.e. 95% in identity and 98% in similarity. Analysis of
amino acid sequence revealed that ORF1 consisted of 2 domains, i.e. glyco-hydrolase 11 (GH11) and Carbohydrate
Binding Type 2 (CBM2). Active site was found at 130th amino acid on GH11 domain. Visualization of 3-dimension
structure showed that 1029 bp fragment is of 19 areas.
Keywords
Streptomyces costaricanus 45I-3; xylanase extracellular; Inverse-PCR
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PDF DOI: https://doi.org/10.22146/ijbiotech.15274
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