Short Communication: Preliminary phylogenetic analysis of bacteria producing laccase isolated from Gunung Pancar, Bogor, Indonesia
##plugins.themes.bootstrap3.article.sidebar##
Issue
Section
Articles
##plugins.themes.bootstrap3.article.main##
Abstract
Abstract. Mar WW, Rohman A, Muwafiqi NH, Laras GA, Agustina D, Asmarani O, Puspaningsih NNT. 2020. Short Communication: Preliminary phylogenetic analysis of bacteria producing laccase isolated from Gunung Pancar, Bogor, Indonesia. Biodiversitas 21: 2113-2118. Interpretation of phylogenetic trees is essential in understanding relationships between organisms, as well as their characteristics, bionetwork, and even their genomic and developmental ecology. The aim of this research is to analyze the phylogenetic bacteria producing laccase isolated from Gunung Pancar Bogor, Indonesia. Phylogenetic analysis of Geobacillus kaustophilus TP-02 producing laccase was performed using alignments with all Bacillus clusters. A phylogenetic tree was constructed by the neighbor-joining (NJ) method, using the maximum likelihood parameter. Laccase was purified using ammonium sulfate precipitation to 2.67-fold. The activity of crude laccase was determined to be 93.39 U/ml using 2,2-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) as the substrate. Moreover, Geobacillus related to counting some Geobacillus genus such as Geobacillus thermocatenulatus, Geobacillus sp. MAS1, Geobacillus thermoleovorans, and Geobacillus zalihae, having similarity under 91% with comparison to the Geobacillus kaustophilius sequence in GenBank. Therefore, results show that G. kaustophilus TP-02 does not have any closeness with other Geobacillus genera, even though these species have the same ancestor.
##plugins.themes.bootstrap3.article.details##
References
Agrawal, Komal et al. 2019. “Process Optimization, Purification and Characterization of Alkaline Stable White Laccase from Myrothecium Verrucaria ITCC-8447 and Its Application in Delignification of Agroresidues.” International Journal of Biological Macromolecules 125: 1042–55. https://doi.org/10.1016/j.ijbiomac.2018.12.108. URL: http://www.elsevier.com/locate/issn/0141-8130
Altschul, Stephen F. et al. 2005. “Protein Database Searches Using Compositionally Adjusted Substitution Matrices.” FEBS Journal 272(20): 5101–9. DOI: 10.1111/j.1742-4658.2005.04945.x
Baltaci, Mustafa Ozkan et al. 2017. “Isolation and Characterization of Thermophilic Bacteria from Geothermal Areas in Turkey and Preliminary Research on Biotechnologically Important Enzyme Production.” Geomicrobiology Journal 34(1): 53–62. URL: http://dx.doi.org/10.1080/01490450701436489
Hamuro, Yuhi et al. 2017. “Characterization of a Thermostable Mutant of Agaricus Brasiliensis Laccase Created by Phylogeny-Based Design.” Journal of Bioscience and Bioengineering 124(6): 623–29. URL: http://www.sbj.or.jp/e/jbb/jbb_instructions.html
Harnelly, Essy, Zairin Thomy, and Nir Fathiya. 2018. “Phylogenetic Analysis of Dipterocarpaceae in Ketambe Research Station, Gunung Leuser National Park (Sumatra, Indonesia) Based on RbcL and MatK Genes.” Biodiversitas 19(3): 1074–80. URL: https://smujo.id/biodiv/
Hoegger, Patrik J. et al. 2006. “Phylogenetic Comparison and Classification of Laccase and Related Multicopper Oxidase Protein Sequences.” FEBS Journal 273(10): 2308–26. DOI: 10.1111/j.1742-4658.2005.04945.x
Indi, N, L, P, Dharmayanti. 2011. “Filogenetika Molekuler: Metode Taksonomi Organisme Berdasarkan Sejarah Evolusi.” Jl. R.E. Martadinata No. Bogor 30(16114): 1–10.
Jones DT, Taylor WR & Thornton JM (1992) The rapid generation of mutation data matrices from protein sequences. Computer Applications in the Biosciences 8: 275-282. URL http:/(/)bioc-www.uia.ac.be/u/ yvdp/treeconw.html.
Kuisiene, Nomeda, Juozas Raugalas, Milda Stuknyte, and Donaldas Chitavichius. 2007. “Identification of the Genus Geobacillus Using Genus-Specific Primers, Based on the 16S-23S RRNA Gene Internal Transcribed Spacer.” FEMS Microbiology Letters 277(2): 165–72. URL: http://femsle.oxfordjournals.org/for_authors/manuscript_preparation_instructions.html
Kumar, Sudhir et al. 2018. “MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.” Molecular Biology and Evolution 35(6): 1547–49. URL: http://www.oxfordjournals.org/our_journals/molbev/general_author_guidelines.html
Lestari, Dewi Ayu, Rodiyati Azrianingsih, and H. Hendrian. 2018. “Filogenetik Jenis-Jenis Annonaceae Dari Jawa Timur Koleksi Kebun Raya Purwodadi Berdasarkan Coding Dan Non-Coding Sekuen DNA.” Journal of Tropical Biodiversity and Biotechnology 3(1): 1–7. URL pendek : http://u.lipi.go.id/1474130745
Lon?ar, Nikola, Nikola Gligorijevi?, Nataša Boži?, and Zoran Vuj?i?. 2014. “Congo Red Degrading Laccases from Bacillus Amyloliquefaciens Strains Isolated from Salt Spring in Serbia.” International Biodeterioration and Biodegradation 91: 18–23. https://doi.org/10.1016/j.ibiod.2014.03.008
Mallika, V., K. C. Sivakumar, and E. V. Soniya. 2011. “Evolutionary Implications and Physicochemical Analyses of Selected Proteins of Type Iii Polyketide Synthase Family.” Evolutionary Bioinformatics 2011(7): 41–53. doi: 10.4137/EBO.S6854
Moon, Soo-jung, Han-woo Kim, and Sung-jong Jeon. 2018. “Enzyme and Microbial Technology Biochemical Characterization of a Thermostable Cobalt- or Copper-Dependent Polyphenol Oxidase with Dye Decolorizing Ability from Geobacillus Sp . JS12.” Enzyme and Microbial Technology 118(May): 30–36. https://doi.org/10.1016/j.enzmictec.2018.06.011. URL: http://www.elsevier.com/locate/issn/0141-0229
Nwokorie, Charles Uzodimma. 2014. “Journal of Biotechnology Science Research (JBSR) Journal Homepage: Www.Jbsr.Issres.Net.” Journal of Biotechnology Science Research 1(3): 39–62. http://issrpublishing.com/jbsr/
Ricklefs, Esther, Nadine Winkler, Katja Koschorreck, and Vlada B. Urlacher. 2014. “Expanding the Laccase-Toolbox: A Laccase from Corynebacterium Glutamicum with Phenol Coupling and Cuprous Oxidase Activity.” Journal of Biotechnology 191: 46–53. http://dx.doi.org/10.1016/j.jbiotec.2014.05.031.
Satpathy, Raghunath. 2014. “Computational Phylogenetic Study and Data Mining Approach to Laccase Enzyme Sequences.” Journal of Phylogenetics & Evolutionary Biology 01(02). URL: http://www.esciencecentral.org/journals/phylogenetics-evolutionary-biology.php
Sharma, Vikas, Seenivasan Ayothiraman, and Vasanth Dhakshinamoorthy. 2019. “Production of Highly Thermo-Tolerant Laccase from Novel Thermophilic Bacterium Bacillus Sp. PC-3 and Its Application in Functionalization of Chitosan Film.” Journal of Bioscience and Bioengineering 127(6): 672–78. https://doi.org/10.1016/j.jbiosc.2018.11.008. URL: http://www.sbj.or.jp/e/jbb/jbb_instructions.html
Siroosi, Maryam, Mohammad Ali, and Khosro Khajeh. 2016. “Journal of Molecular Catalysis B?: Enzymatic Purification and Characterization of an Alkaline Chloride-Tolerant Laccase from a Halotolerant Bacterium , Bacillus Sp . Strain WT.” “Journal of Molecular Catalysis. B, Enzymatic” 134: 89–97. URL: http://www.elsevier.com/locate/issn/1381-1177
Staton, Joseph L. 2015. “Understanding Phylogenies?: Constructing and Interpreting Phylogenetic Trees Understanding Phylogenies?: Constructing and Interpreting Phylogenetic Trees.” Journal of the South Carolina Academy of Science 13(1): 24–29. http://scholarcommons.sc.edu/jscas
Verma, Ambika et al. 2018. “Bacterial Laccase Mediated Inhibition of Enzymatic Browning in Apple Juice and Its Sensory Evaluation.” International Journal of Current Microbiology and Applied Sciences 7(1): 3371–81. DOI: https://doi.org/10.20546/ijcmas.2018.701.399
Wang, Zhi Xin et al. 2010. “Purification and Characterization of Two Thermostable Laccases with High Cold Adapted Characteristics from Pycnoporus Sp. SYBC-L1.” Process Biochemistry 45(10): 1720–29. http://dx.doi.org/10.1016/j.procbio.2010.07.011.
Ben Younes, Sonia, and Sami Sayadi. 2011. “Purification and Characterization of a Novel Trimeric and Thermotolerant Laccase Produced from the Ascomycete Scytalidium Thermophilum Strain.” Journal of Molecular Catalysis B: Enzymatic 73(1–4): 35–42. http://dx.doi.org/10.1016/j.molcatb.2011.07.014.
Zheng, Fei et al. 2017. “A Novel Laccase from White Rot Fungus Trametes Orientalis: Purification, Characterization, and Application.” International Journal of Biological Macromolecules 102: 758–70.http://dx.doi.org/10.1016/j.ijbiomac.2017.04.089
Altschul, Stephen F. et al. 2005. “Protein Database Searches Using Compositionally Adjusted Substitution Matrices.” FEBS Journal 272(20): 5101–9. DOI: 10.1111/j.1742-4658.2005.04945.x
Baltaci, Mustafa Ozkan et al. 2017. “Isolation and Characterization of Thermophilic Bacteria from Geothermal Areas in Turkey and Preliminary Research on Biotechnologically Important Enzyme Production.” Geomicrobiology Journal 34(1): 53–62. URL: http://dx.doi.org/10.1080/01490450701436489
Hamuro, Yuhi et al. 2017. “Characterization of a Thermostable Mutant of Agaricus Brasiliensis Laccase Created by Phylogeny-Based Design.” Journal of Bioscience and Bioengineering 124(6): 623–29. URL: http://www.sbj.or.jp/e/jbb/jbb_instructions.html
Harnelly, Essy, Zairin Thomy, and Nir Fathiya. 2018. “Phylogenetic Analysis of Dipterocarpaceae in Ketambe Research Station, Gunung Leuser National Park (Sumatra, Indonesia) Based on RbcL and MatK Genes.” Biodiversitas 19(3): 1074–80. URL: https://smujo.id/biodiv/
Hoegger, Patrik J. et al. 2006. “Phylogenetic Comparison and Classification of Laccase and Related Multicopper Oxidase Protein Sequences.” FEBS Journal 273(10): 2308–26. DOI: 10.1111/j.1742-4658.2005.04945.x
Indi, N, L, P, Dharmayanti. 2011. “Filogenetika Molekuler: Metode Taksonomi Organisme Berdasarkan Sejarah Evolusi.” Jl. R.E. Martadinata No. Bogor 30(16114): 1–10.
Jones DT, Taylor WR & Thornton JM (1992) The rapid generation of mutation data matrices from protein sequences. Computer Applications in the Biosciences 8: 275-282. URL http:/(/)bioc-www.uia.ac.be/u/ yvdp/treeconw.html.
Kuisiene, Nomeda, Juozas Raugalas, Milda Stuknyte, and Donaldas Chitavichius. 2007. “Identification of the Genus Geobacillus Using Genus-Specific Primers, Based on the 16S-23S RRNA Gene Internal Transcribed Spacer.” FEMS Microbiology Letters 277(2): 165–72. URL: http://femsle.oxfordjournals.org/for_authors/manuscript_preparation_instructions.html
Kumar, Sudhir et al. 2018. “MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.” Molecular Biology and Evolution 35(6): 1547–49. URL: http://www.oxfordjournals.org/our_journals/molbev/general_author_guidelines.html
Lestari, Dewi Ayu, Rodiyati Azrianingsih, and H. Hendrian. 2018. “Filogenetik Jenis-Jenis Annonaceae Dari Jawa Timur Koleksi Kebun Raya Purwodadi Berdasarkan Coding Dan Non-Coding Sekuen DNA.” Journal of Tropical Biodiversity and Biotechnology 3(1): 1–7. URL pendek : http://u.lipi.go.id/1474130745
Lon?ar, Nikola, Nikola Gligorijevi?, Nataša Boži?, and Zoran Vuj?i?. 2014. “Congo Red Degrading Laccases from Bacillus Amyloliquefaciens Strains Isolated from Salt Spring in Serbia.” International Biodeterioration and Biodegradation 91: 18–23. https://doi.org/10.1016/j.ibiod.2014.03.008
Mallika, V., K. C. Sivakumar, and E. V. Soniya. 2011. “Evolutionary Implications and Physicochemical Analyses of Selected Proteins of Type Iii Polyketide Synthase Family.” Evolutionary Bioinformatics 2011(7): 41–53. doi: 10.4137/EBO.S6854
Moon, Soo-jung, Han-woo Kim, and Sung-jong Jeon. 2018. “Enzyme and Microbial Technology Biochemical Characterization of a Thermostable Cobalt- or Copper-Dependent Polyphenol Oxidase with Dye Decolorizing Ability from Geobacillus Sp . JS12.” Enzyme and Microbial Technology 118(May): 30–36. https://doi.org/10.1016/j.enzmictec.2018.06.011. URL: http://www.elsevier.com/locate/issn/0141-0229
Nwokorie, Charles Uzodimma. 2014. “Journal of Biotechnology Science Research (JBSR) Journal Homepage: Www.Jbsr.Issres.Net.” Journal of Biotechnology Science Research 1(3): 39–62. http://issrpublishing.com/jbsr/
Ricklefs, Esther, Nadine Winkler, Katja Koschorreck, and Vlada B. Urlacher. 2014. “Expanding the Laccase-Toolbox: A Laccase from Corynebacterium Glutamicum with Phenol Coupling and Cuprous Oxidase Activity.” Journal of Biotechnology 191: 46–53. http://dx.doi.org/10.1016/j.jbiotec.2014.05.031.
Satpathy, Raghunath. 2014. “Computational Phylogenetic Study and Data Mining Approach to Laccase Enzyme Sequences.” Journal of Phylogenetics & Evolutionary Biology 01(02). URL: http://www.esciencecentral.org/journals/phylogenetics-evolutionary-biology.php
Sharma, Vikas, Seenivasan Ayothiraman, and Vasanth Dhakshinamoorthy. 2019. “Production of Highly Thermo-Tolerant Laccase from Novel Thermophilic Bacterium Bacillus Sp. PC-3 and Its Application in Functionalization of Chitosan Film.” Journal of Bioscience and Bioengineering 127(6): 672–78. https://doi.org/10.1016/j.jbiosc.2018.11.008. URL: http://www.sbj.or.jp/e/jbb/jbb_instructions.html
Siroosi, Maryam, Mohammad Ali, and Khosro Khajeh. 2016. “Journal of Molecular Catalysis B?: Enzymatic Purification and Characterization of an Alkaline Chloride-Tolerant Laccase from a Halotolerant Bacterium , Bacillus Sp . Strain WT.” “Journal of Molecular Catalysis. B, Enzymatic” 134: 89–97. URL: http://www.elsevier.com/locate/issn/1381-1177
Staton, Joseph L. 2015. “Understanding Phylogenies?: Constructing and Interpreting Phylogenetic Trees Understanding Phylogenies?: Constructing and Interpreting Phylogenetic Trees.” Journal of the South Carolina Academy of Science 13(1): 24–29. http://scholarcommons.sc.edu/jscas
Verma, Ambika et al. 2018. “Bacterial Laccase Mediated Inhibition of Enzymatic Browning in Apple Juice and Its Sensory Evaluation.” International Journal of Current Microbiology and Applied Sciences 7(1): 3371–81. DOI: https://doi.org/10.20546/ijcmas.2018.701.399
Wang, Zhi Xin et al. 2010. “Purification and Characterization of Two Thermostable Laccases with High Cold Adapted Characteristics from Pycnoporus Sp. SYBC-L1.” Process Biochemistry 45(10): 1720–29. http://dx.doi.org/10.1016/j.procbio.2010.07.011.
Ben Younes, Sonia, and Sami Sayadi. 2011. “Purification and Characterization of a Novel Trimeric and Thermotolerant Laccase Produced from the Ascomycete Scytalidium Thermophilum Strain.” Journal of Molecular Catalysis B: Enzymatic 73(1–4): 35–42. http://dx.doi.org/10.1016/j.molcatb.2011.07.014.
Zheng, Fei et al. 2017. “A Novel Laccase from White Rot Fungus Trametes Orientalis: Purification, Characterization, and Application.” International Journal of Biological Macromolecules 102: 758–70.http://dx.doi.org/10.1016/j.ijbiomac.2017.04.089
Most read articles by the same author(s)
- NENGAH DWIANITA KUSWYTASARI, ALFIA R KURNIAWATI, NUR HIDAYATUL ALAMI, ENNY ZULAIKA, MAYA SHOVITRI, KYU MIN OH, NI NYOMAN TRI PUSPANINGSIH, NI’MATUZAHROH NI’MATUZAHROH, Short Communication: Plastic degradation by Coriolopsis byrsina, an identified white-rot, soil-borne mangrove fungal isolate from Surabaya, East Java, Indonesia , Biodiversitas Journal of Biological Diversity: Vol. 20 No. 3 (2019)
- RAHMAT EKO SANJAYA, NI NYOMAN TRI PUSPANINGSIH, ALI ROHMAN, HAKIKI RAHMASARI, ROSLI MD. ILLIAS, NAWEE JANTARIT, KAZUHITO FUJIYAMA, ANDRE PRATAMA, FATIHA KHAIRUNNISA, Production and diversity analysis of cellulases from Anoxybacillus genus , Biodiversitas Journal of Biological Diversity: Vol. 25 No. 6 (2024)