DOI: https://doi.org/10.14710/jksa.23.5.183-188

Polymerization Domain Translated from 0.9 kb Gene Fragment of DNA Polymerase I from a Thermo-Halophilic PLS A Strain

Biomolecules Application Research Group, Chemistry Department, Faculty of Mathematics and Natural Sciences, Universitas Syiah Kuala, Indonesia

Received: 24 Feb 2020; Revised: 7 Apr 2020; Accepted: 30 Apr 2020; Published: 31 May 2020.
Open Access Copyright 2020 Jurnal Kimia Sains dan Aplikasi under http://creativecommons.org/licenses/by-sa/4.0.

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Abstract
The search for novel DNA Polymerases I, with higher fidelity and better polymerization rate, is essential to improve the Polymerase Chain Reaction method. A thermo-halophilic bacterium has been isolated from an undersea hot spring, dubbed Pria Laot Sabang (PLS) A strain. The 0.9 kb DNA Polymerase I gene fragments from the isolate were amplified, sequenced, and identified. The fragments were part of the polymerization domain of the enzyme. Homological analysis of the gene sequence showed that the PLS A strain was closely related to Bacillus caldolyticusstrain XM. However, Swissprot structural analysis reveals that PLS A strain had high homology to Geobacillus stearathermophilus. Full sequence analysis is still needed to identify the species and evaluate the intact enzyme structure.
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Keywords: DNA polymerase; Geobacillus; halophilic; thermophilic; Sabang
Funding: Universitas Syiah Kuala

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Section: 8th - International Conference of the Indonesian Chemical Society (ICICS)
Language : EN
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  1. Kary B. Mullis and Fred A. Faloona, [21] Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction, in: Methods in Enzymology, Academic Press, 1987, pp. 335-350 https://doi.org/10.1016/0076-6879(87)55023-6
  2. Joos Aschenbrenner and Andreas Marx, DNA polymerases and biotechnological applications, Current Opinion in Biotechnology, 48, (2017), 187-195 https://doi.org/10.1016/j.copbio.2017.04.005
  3. Premal H. Patel, Motoshi Suzuki, Elinor Adman, Akeo Shinkai and Lawrence A. Loeb, Prokaryotic DNA polymerase I: evolution, structure, and “base flipping” mechanism for nucleotide selection11Edited by J. H. Miller, Journal of Molecular Biology, 308, 5, (2001), 823-837 https://doi.org/10.1006/jmbi.2001.4619
  4. Jonathan Filée, Patrick Forterre, Tang Sen-Lin and Jacqueline Laurent, Evolution of DNA Polymerase Families: Evidences for Multiple Gene Exchange Between Cellular and Viral Proteins, Journal of Molecular Evolution, 54, 6, (2002), 763-773 https://doi.org/10.1007/s00239-001-0078-x
  5. I. R. Lehman, Discovery of DNA Polymerase, Journal of Biological Chemistry, 278, 37, (2003), 34733-34738 http://doi.org/10.1074/jbc.X300002200
  6. Anna Bębenek and Izabela Ziuzia-Graczyk, Fidelity of DNA replication—a matter of proofreading, Current Genetics, 64, 5, (2018), 985-996 https://doi.org/10.1007/s00294-018-0820-1
  7. Sonoko Ishino and Yoshizumi Ishino, DNA polymerases as useful reagents for biotechnology – the history of developmental research in the field, Frontiers in Microbiology, 5, 465, (2014), 1-8 https://doi.org/10.3389/fmicb.2014.00465
  8. Roberto Laos, Ryan W. Shaw and Steven A. Benner, Engineered DNA Polymerases, in: K.S. Murakami, M.A. Trakselis (Eds.) Nucleic Acid Polymerases, Springer Berlin Heidelberg, Berlin, Heidelberg, 2014, pp. 163-187 https://doi.org/10.1007/978-3-642-39796-7_7
  9. G. D. Haki and S. K. Rakshit, Developments in industrially important thermostable enzymes: a review, Bioresource Technology, 89, 1, (2003), 17-34 https://doi.org/10.1016/S0960-8524(03)00033-6
  10. Akhmaloka, Hendro Pramono, Laksmi Ambarsari, Evi Susanti, Santi Nurbaiti and Fida Madayanti, Cloning, homological analysis, and expression of DNA Pol I from Geobacillus thermoleovorans, International Journal of Integrative Biology, 1, 3, (2007), 206-215
  11. N. V. Bhagavan and Chung-Eun Ha, Chapter 22 - DNA Replication, Repair, and Mutagenesis, in: N.V. Bhagavan, C.-E. Ha (Eds.) Essentials of Medical Biochemistry, Academic Press, San Diego, 2011, pp. 287-299 https://doi.org/10.1016/B978-0-12-095461-2.00022-9
  12. Febriani Febriani, Hira Helwati, Muhammad Velayati and Teuku Iqbalsyah, Identification of a DNA polymerase i gene fragment from a local isolate (PLS 80) from an underwater hot spring, Research Journal of Chemistry and Environment, 22, Special issue II, (2018), 189-192
  13. J. Zhou, M. A. Bruns and J. M. Tiedje, DNA recovery from soils of diverse composition, Applied and Environmental Microbiology, 62, 2, (1996), 316-322
  14. Koichiro Tamura, Glen Stecher, Daniel Peterson, Alan Filipski and Sudhir Kumar, MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0, Molecular Biology and Evolution, 30, 12, (2013), 2725-2729 https://doi.org/10.1093/molbev/mst197
  15. William Humphrey, Andrew Dalke and Klaus Schulten, VMD: Visual molecular dynamics, Journal of Molecular Graphics, 14, 1, (1996), 33-38 https://doi.org/10.1016/0263-7855(96)00018-5
  16. P. D. Gutman, P. Fuchs, L. Ouyang and K. W. Minton, Identification, sequencing, and targeted mutagenesis of a DNA polymerase gene required for the extreme radioresistance of Deinococcus radiodurans, Journal of Bacteriology, 175, 11, (1993), 3581 http://doi.org/10.1128/jb.175.11.3581-3590.1993
  17. Teuku M. Iqbalsyah, Malahayati, Atikah and Febriani, Purification and partial characterization of a thermo-halostable protease produced by Geobacillus sp. strain PLS A isolated from undersea fumaroles, Journal of Taibah University for Science, 13, 1, (2019), 850-857 https://doi.org/10.1080/16583655.2019.1650489
  18. Jose Castresana, Topological variation in single-gene phylogenetic trees, Genome Biology, 8, 6, (2007), 216 https://doi.org/10.1186/gb-2007-8-6-216
  19. Thorsten Thiergart, Giddy Landan and William F. Martin, Concatenated alignments and the case of the disappearing tree, BMC Evolutionary Biology, 14, 1, (2014), 266 https://doi.org/10.1186/s12862-014-0266-0
  20. Marc Delarue, Olivier Poch, Noel Tordo, Dino Moras and Patrick Argos, An attempt to unify the structure of polymerases, Protein Engineering, Design and Selection, 3, 6, (1990), 461-467 https://doi.org/10.1093/protein/3.6.461
  21. Marco Biasini, Stefan Bienert, Andrew Waterhouse, Konstantin Arnold, Gabriel Studer, Tobias Schmidt, Florian Kiefer, Tiziano Gallo Cassarino, Martino Bertoni, Lorenza Bordoli and Torsten Schwede, SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information, Nucleic Acids Research, 42, W1, (2014), W252-W258 https://doi.org/10.1093/nar/gku340
  22. F. C. Lawyer, S. Stoffel, R. K. Saiki, K. Myambo, R. Drummond and D. H. Gelfand, Isolation, characterization, and expression in Escherichia coli of the DNA polymerase gene from Thermus aquaticus, Journal of Biological Chemistry, 264, 11, (1989), 6427-6437

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