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Cloning and Characterization of a Novel Agarase from a Newly Isolated Bacterium Simiduia sp. Strain TM-2 Able to Degrade Various Seaweeds

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Abstract

A new bacterial strain capable of reducing thalli of various seaweeds (red, green, and brown algae) was isolated from marine sediments of Uozu in Toyama Prefecture, Japan. We designated the strain Simiduia sp. TM-2 based on analyses of the 16S rRNA gene and gyrB gene sequences and its biochemical and morphological characteristics. Zymography methods revealed numerous active bands of alginate lyases, cellulases, and agarases in the cells and culture supernatants of TM-2, showing that the strain possessed multiple polysaccharide lyases. A novel agarase gene (agaTM2) was cloned from TM-2 and expressed in Escherichia coli. The resulting DNA sequence contained an open reading frame of 1764 bp that encoded a protein of 587 amino acids with an estimated molecular mass of 64 kDa and pI of 4.62. The deduced amino acid sequence, AgaTM2, had a typical signal peptide followed by a glycoside hydrolase family 16 catalytic domain and two carbohydrate-binding modules 6. A BLAST search indicated that AgaTM2 shared 75.5 % amino acid sequence identity with agarase from Simiduia agarivorans SA1. The cloned and purified AgaTM2 protein showed optimal activity at 35 °C and pH 8.0, and its thermostability increased in the presence of calcium ions. AgaTM2 degraded agarose to tetraose and hexaose.

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Acknowledgments

This study was supported in part by a Grant-in-Aid for Scientific Research (C) (No. 25340121) from the Ministry of Education, Science and Culture in Japan (to SN).

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Authors and Affiliations

  1. Graduate School of Science and Engineering, University of Toyama, Toyama, 930-8555, Japan

    Mika Tawara, Akihiro Sakatoku, Rosine E. Tiodjio, Daisuke Tanaka & Shogo Nakamura

  2. Graduate School of Science and Engineering, Department of Environmental and Energy Science, Faculty of Earth and Environmental Systems, University of Toyama, Toyama, 930-8555, Japan

    Akihiro Sakatoku

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  1. Mika Tawara
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Correspondence to Akihiro Sakatoku.

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Tawara, M., Sakatoku, A., Tiodjio, R.E. et al. Cloning and Characterization of a Novel Agarase from a Newly Isolated Bacterium Simiduia sp. Strain TM-2 Able to Degrade Various Seaweeds. Appl Biochem Biotechnol 177, 610–623 (2015). https://doi.org/10.1007/s12010-015-1765-1

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