Biopython: Comparing the DNA Polymerase I (polA) Gene of Thermophilic, Mesophilic, and Psychrophilic Bacteria


  • Chaidir Adam Department of Biology Education, Faculty of Teacher Training and Education, University of Palangka Raya



Biopython, Python, Bioinformatics, Computational Biology


Biopython is a specialized Python tool for computational molecular biology. Various computational molecular analysis that can be performed using Biopython, such as reconstructing phylogenetic trees, multiple sequence analysis, generating complementary sequences, counting amino acids, etc. This technical notes paper describes in detail the procedures computational DNA sequence analysis using Biopython. The DNA polymerase I (polA) gene sequences of bacteria were used in this study to compare the differences between Thermophilic, Mesophilic, and Psychrophilic bacteria.


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Allen, J. M., Simcha, D. M., Ericson, N. G., Alexander, D. L., Marquette, J. T., Van Biber, B. P., Troll, C. J., Karchin, R., Bielas, J. H., Loeb, L. A., & Camps, M. (2011). Roles of DNA polymerase I in leading and lagging-strand replication defined by a high-resolution mutation footprint of ColE1 plasmid replication. Nucleic Acids Research, 39(16), 7020–7033.
Bayat, A. (2002). Science, medicine, and the future: Bioinformatics. BMJ (Clinical Research Ed.), 324(7344), 1018–1022. PubMed.
Brown, W. E., Stump, K. H., & Kelley, W. S. (1982). Escherichia coli DNA polymerase I. Sequence characterization and secondary structure prediction. The Journal of Biological Chemistry, 257(4), 1965–1972.
Caetano-Anollés, D. (2013). Polymerase Chain Reaction. In S. Maloy & K. Hughes (Eds.), Brenner’s Encyclopedia of Genetics (Second Edition) (pp. 392–395). Academic Press.
Cavicchioli, R. (2016). On the concept of a psychrophile. The ISME Journal, 10(4), 793–795. PubMed.
Chang, J., Chapman, B., Friedberg, I., Hamelryck, T., de Hoon, M., Cock, P., Antao, T., Talevich, E., & Wilczynski, B. (2020). Biopython Tutorial and Cookbook.
Chapman, B., & Chang, J. (2000). Biopython: Python Tools for Computational Biology. SIGBIO Newsl., 20(2), 15–19.
Chen, C.-H., & Berns, D. S. (1980). Thermotropic Properties of Thermophilic, Mesophilic, and Psychrophilic Blue-green Algae. Plant Physiology, 66(4), 596–599.
Chien, A., Edgar, D. B., & Trela, J. M. (1976). Deoxyribonucleic acid polymerase from the extreme thermophile Thermus aquaticus. Journal of Bacteriology, 127(3), 1550–1557. PubMed.
Cock, P. J. A., Antao, T., Chang, J. T., Chapman, B. A., Cox, C. J., Dalke, A., Friedberg, I., Hamelryck, T., Kauff, F., Wilczynski, B., & de Hoon, M. J. L. (2009). Biopython: Freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics, 25(11), 1422–1423.
Erlich, H. A. (1989). Polymerase chain reaction. Journal of Clinical Immunology, 9(6), 437–447.
Fourment, M., & Gillings, M. R. (2008). A comparison of common programming languages used in bioinformatics. BMC Bioinformatics, 9(1), 82.
Gao, F., & Zhang, C.-T. (2006). GC-Profile: A web-based tool for visualizing and analyzing the variation of GC content in genomic sequences. Nucleic Acids Research, 34(suppl_2), W686–W691.
Garcia-Diaz, M., & Bebenek, K. (2007). Multiple functions of DNA polymerases. Critical Reviews in Plant Sciences, 26(2), 105–122. PubMed.
Irwin, J. A. (2020). Chapter 6—Overview of extremophiles and their food and medical applications. In R. Salwan & V. Sharma (Eds.), Physiological and Biotechnological Aspects of Extremophiles (pp. 65–87). Academic Press.
Ishino, S., & Ishino, Y. (2014). DNA polymerases as useful reagents for biotechnology—The history of developmental research in the field. Frontiers in Microbiology, 5, 465–465. PubMed.
Kagawa, Y., Nojima, H., Nukiwa, N., Ishizuka, M., Nakajima, T., Yasuhara, T., Tanaka, T., & Oshima, T. (1984). High guanine plus cytosine content in the third letter of codons of an extreme thermophile. DNA sequence of the isopropylmalate dehydrogenase of Thermus thermophilus. The Journal of Biological Chemistry, 259(5), 2956–2960.
Kotzekidou, P. (1999). BACILLUS | Bacillus Stearothermophilus. In R. K. Robinson (Ed.), Encyclopedia of Food Microbiology (pp. 124–129). Elsevier.
LaPelusa, A., & Kaushik, R. (2021). Physiology, Proteins. In StatPearls. StatPearls Publishing.
Lehman, I., & Uyemura, D. (1976). DNA polymerase I: essential replication enzyme. Science, 193(4257), 963.
Loeb, L. A., & Monnat, R. J. (2008). DNA polymerases and human disease. Nature Reviews Genetics, 9(8), 594–604.
Lopez, M. J., & Mohiuddin, S. S. (2021). Biochemistry, Essential Amino Acids. In StatPearls. StatPearls Publishing.
Luscombe, N. M., Greenbaum, D., & Gerstein, M. (2001). What is bioinformatics? A proposed definition and overview of the field. Methods of Information in Medicine, 40(4), 346–358.
Markowetz, F. (2017). All biology is computational biology. PLOS Biology, 15(3), e2002050.
Musto, H., Naya, H., Zavala, A., Romero, H., Alvarez-Valín, F., & Bernardi, G. (2004). Correlations between genomic GC levels and optimal growth temperatures in prokaryotes. FEBS Letters, 573(1–3), 73–77.
Oshima, T., & Imahori, K. (1971). Isolation of an Extreme Thermophile and Thermostability of Its Transfer Ribonucleic Acid and Ribosomes. The Journal of General and Applied Microbiology, 17(6), 513–517.
Oshima, T., & Imahori, K. (1974). Description of Thermus thermophilus (Yoshida and Oshima) comb. Nov., a Nonsporulating Thermophilic Bacterium from a Japanese Thermal Spa. International Journal of Systematic and Evolutionary Microbiology, 24(1), 102–112.
Pánek, T., Žihala, D., Sokol, M., Derelle, R., Klimeš, V., Hradilová, M., Zadrobílková, E., Susko, E., Roger, A. J., ?epi?ka, I., & Eliáš, M. (2017). Nuclear genetic codes with a different meaning of the UAG and the UAA codon. BMC Biology, 15(1), 8.
Piovesan, A., Pelleri, M. C., Antonaros, F., Strippoli, P., Caracausi, M., & Vitale, L. (2019). On the length, weight and GC content of the human genome. BMC Research Notes, 12(1), 106.
Rother, M., & Krzycki, J. A. (2010). Selenocysteine, Pyrrolysine, and the Unique Energy Metabolism of Methanogenic Archaea. Archaea, 2010, 453642.
Saunders, N. F. W., Thomas, T., Curmi, P. M. G., Mattick, J. S., Kuczek, E., Slade, R., Davis, J., Franzmann, P. D., Boone, D., Rusterholtz, K., Feldman, R., Gates, C., Bench, S., Sowers, K., Kadner, K., Aerts, A., Dehal, P., Detter, C., Glavina, T., … Cavicchioli, R. (2003). Mechanisms of thermal adaptation revealed from the genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii. Genome Research, 13(7), 1580–1588.
Schiraldi, C., & De Rosa, M. (2016). Mesophilic Organisms. In E. Drioli & L. Giorno (Eds.), Encyclopedia of Membranes (pp. 1–2). Springer.
Shing, Y. W., Akagi, J. M., & Himes, R. H. (1975). Psychrophilic, mesophilic, and thermophilic triosephosphate isomerases from three clostridial species. Journal of Bacteriology, 122(1), 177–184.
Smith, M. (2020). MRNA Transcription, Translation, and Defects in Developmental Cognitive and Behavioral Disorders. Frontiers in Molecular Biosciences, 7.
Taylor, W. R. (2006). Transcription and translation in an RNA world. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 361(1474), 1751–1760. PubMed.
Tessari, P., Lante, A., & Mosca, G. (2016). Essential amino acids: Master regulators of nutrition and environmental footprint? Scientific Reports, 6(1), 26074.
Wages, J. M. (2005). POLYMERASE CHAIN REACTION. In P. Worsfold, A. Townshend, & C. Poole (Eds.), Encyclopedia of Analytical Science (Second Edition) (pp. 243–250). Elsevier.
Wu, G. (2009). Amino acids: Metabolism, functions, and nutrition. Amino Acids, 37(1), 1–17.
Yoon, J.-H., Roy Choudhury, J., Park, J., Prakash, S., & Prakash, L. (2014). A role for DNA polymerase ? in promoting replication through oxidative DNA lesion, thymine glycol, in human cells. The Journal of Biological Chemistry, 289(19), 13177–13185.
Yuan, J., O’Donoghue, P., Ambrogelly, A., Gundllapalli, S., Sherrer, R. L., Palioura, S., Simonovi?, M., & Söll, D. (2010). Distinct genetic code expansion strategies for selenocysteine and pyrrolysine are reflected in different aminoacyl-tRNA formation systems. FEBS Letters, 584(2), 342–349. PubMed.
Zhang, Y., Baranov, P. V., Atkins, J. F., & Gladyshev, V. N. (2005). Pyrrolysine and selenocysteine use dissimilar decoding strategies. The Journal of Biological Chemistry, 280(21), 20740–20751.



2021-06-21 — Updated on 2021-06-21

How to Cite

Adam, C. (2021). Biopython: Comparing the DNA Polymerase I (polA) Gene of Thermophilic, Mesophilic, and Psychrophilic Bacteria. BiosciED: Journal of Biological Science and Education, 2(1), 10–20.



Biological Sciences