Acta Biologica

Previously: Zeszyty Naukowe Uniwersytetu Szczecińskiego. Acta Biologica

ISSN: 2450-8330     eISSN: 2353-3013    OAI    DOI: 10.18276/ab.2018.25-11
CC BY-SA   Open Access   DOAJ

Issue archive / No. 25
Bioinformatics analysis of the promoter sequence of the 9f-2.8 gene encoding germin

Authors: Izabela Szućko
University of Szczecin, Institute for Research on Biodiversity, Faculty of Biology, Department of Molecular Biology and Cytology

Urszula Kowalska
University of Szczecin, Institute for Research on Biodiversity, Faculty of Biology, Department of Molecular Biology and Cytology

Lidia Skuza
University of Szczecin, Institute for Research on Biodiversity, Faculty of Biology, Department of Molecular Biology and Cytology
Keywords: Triticum aestivum L. bioinformatic tools germin protein in silico analyse
Data publikacji całości:2018
Page range:9 (131-139)
Cited-by (Crossref) ?:

Abstract

Bioinformatics is a field of study having an enormous potential, allowing to solve a number of problems arising as a result of dynamic development of natural sciences with the use of computer science methodologies. It is widely used and constitutes a basis for most scientific research conducted in the field of molecular biology. The aim of this study was in silico analysis of the promoter sequence of the 9f-2.8 gene encoding isoform of the germin protein considered as a germination marker in common wheat’s (Triticum aestivum L.). The gene mentioned above has already been characterized, however, with the use of experimental methods instead of bioinformatics. Analysis with the use of TSSP and TSSPlant software identified the promoter region and classified it as the TATA-box containing promoter. For 9f-2.8 gene including 2.8 kbp, the TSSP software indicated that the TATA-box sequence was located in the position 1665 nt, while the TSSPlant tool showed that TSS [+1] was located in the position 1699 nt. At the second stage, transcription factors were analyzed. Four main families of transcription factors were detected within the analyzed region: MADS, AP2, bZIP and NAC. The most common were MADS-box and bZIP motifs. In the final step of analysis the presence of CpG islands have been checked using the PlantPAN software. The region which could be potentially considered as CpG island have been detected and localized. Software used in analysis above is free online tool.
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Bibliography

1.Ashikawa, I. (2001). Gene-associated CpG islands in plants as revealed by analyses of genomic sequences.
2.The Plant Journal, 26 (6), 617–25
3.Baxevanisa, A.D., Ouellette`a, B.F.F. (2004). Bioinformatyka. Podręcznik do analizy genów i białek.
4.Warszawa: Wydawnictwo Naukowe PWN.
5.Butler, J.E.F., Kadonaga, J.T. (2002). The RNA polymerase II core promoter: a key component in the regulation
6.of gene expression. Genes & Development, 16, 2583–2592.
7.Davidson, R.M., Reeves, P.A., Manosalva, P.M., Leach, J.E. (2009). Germins: A diverse protein family
8.important for corp improvement. Plant Science, 177, 499–510.
9.Heijmans, K., Morel, P., Vandenbussche, M. (2012). MADS-box genes and floral development: the dark
10.side. Journal of Experimental Botany, 63 (15), 5397–5404.
11.Hernandez-Garcia, C.M., Finer, J.J. (2014). Identification and validation of promoters and cis-acting regulatory
12.elements. Plant Science, 2017–2018, 109–119.
13.Higgs, P.G., Attwood, T.K. (2008). Bioinformatyka i ewolucja molekularna. Warszawa: Wydawnictwo
14.Naukowe PWN.
15.Jakoby, M., Weisshaar, B., Dröge-Laser, W., Vicente-Carbajosa, J., Tiedemann, J., Kroj, T., Parcy, F. (2002).
16.bZIP transcription factors in Arabidopsis. Trends in Plant Science, 7 (3), 106–111.
17.Kaur, A., Pati, P.K., Pati, A.M., Nagpal, A.K. (2017). In-silico analysis of cis-acting regulatory elements
18.of pathogenesis-related proteins of Arabidopsis thaliana and Oryza sativa. Plos one, 12 (9), e0184523.
19.https://doi.org/10.1371/journal.pone.0184523.
20.Lane, B.G., Bernier, F., Dratewka-Kos, E., Shafai, R., Kennedy, T.D., Pyne, C., Munro, J.R., Vaughan,
21.T., Walters, D., Altomare, F. (1991). Homologie between Members of the Germin Gene Family in
22.Hexaploid Wheat and Similarities between These Wheat Germins and Certain Physarum Spherulins.
23.The American Society for Biochemistry and Molecular Biology, 266 (16), 10461–104696.
24.Lane, B.G. (2000). Oxalate oxidases and differentiating surface structure in wheat: germins. Biochemical
25.Journal, 349, 309–321.
26.Molina, C., Grotewold, E. (2005). Genome wide analysis of Arabidopsis core promoters. BMC Genomics,
27.6, 25.
28.Morton, T., Petricka, J., Corcoran, D.L., Li, S., Winter, C.M., Carda, A., Benfey, P.N., Ohler, U., Megraw,
29.M. (2014). Paired-End analysis of Transcription Start Sites in Arabidopsis reveals plant-specific promoter
30.signature. The Plant Cell, 26, 2746–2760.
31.Nowakowska, J. (1998). Gene expression and oxalate oxidase activity of two germin isoforms induced by
32.stress. Acta Physiologiae Plantarum, 20 (01), 10–33.
33.Nowakowska, J. (2001). Germiny u roślin wyższych. Biuletyn Instytutu Hodowli i Aklimatyzacji Roślin,
34.217, 19–27.
35.Pandey, S.P., Krishnamachari, A. (2006). Computational analysis of plant RNA Pol-II promoters. Biosystems,
36.83, 38–50.
37.Porto, M.S., Pinheiro, M.P.N.P., Batista, V.G.L.B., dos Santos, C., Albuquerque Melo Filko, P., de Lima,
38.L.M. (2014). Plant Promoters: an approach of structure and function. Molecular Biotechnology, 56,
39.38–49.
40.Riva, A. (2012). The MAPPER2 Database: a multi-genome catalog of putative transcription factor binding
41.sites. Nucleic Acids Research, 40, 155–161.
42.Rombauts, S., Florquin, K., Lescot, M., Marchal, K., Rouze´,P., Van de Peer, Y. (2003). Computational
43.Approaches to Identify Promoters and cis Regulatory Elements in Plant Genomes. American Society
44.of Plant Biologists, 132, 1162–1176.
45.Roy, A.L., Singer, D. (2015). Core promoters in transcription: old problem, new insights. Trends in Biochemical
46.Sciences, 40 (3), 165–171.
47.Sakowicz, T., Frasiński, S. (2014). Roślinne promotory polimerazy RNA II – struktura i identyfikacja.
48.Postępy Biologii Komórki, 21 (2), 347–360.
49.Schütze, K., Harter, K., Chaban, C. (2008). Post-translational regulation of plant bZIP factors. Trends in
50.Plant Science, 13 (5), 247–255.
51.Shahmuradov, I.A., Gammerman, A.J., Hancock, J.M., Bramley, P.M., Solovyev, V.V. (2003). PlantProm:
52.a database of plant promoter sequences. Nucleic Acids Research, 31 (1), 114–117.
53.Smale, S.T., Kadonaga, J.T. (2003). The RNA Polymerase II core promoter. Annual Review of Biochemistry,
54.72, 449–479.
55.Szopa, J., Czuj, T., Łukaszewicz, M. (2003). Analiza genów rodziny 14-3-3. Biotechnologia, 3 (62), 95–106.
56.Tran, L.P., Nakashima, K., Sakuma, Y., Simpson, S.D., Fujita, Y., Maruyama, K., Fujita, M., Seki, M.,
57.Shinozaki, K., Yamaguchi-Shinozak, K. (2004). Isolation and Functional Analysis of Arabidopsis
58.Stress-Inducible NAC Transcription Factors That Bind to a Drought-Responsive cis-Element in the
59.early responsive to dehydration stress 1 Promoter. The Plant Cell, 16, 2481–2498.
60.Xiong, J. (2006). Podstawy bioinformatyki. Warszawa: UW.
61.Yaish, M.W., El-kereamy, A., Zhu, T., Beatty, P.H., Good, A.G., Bi, Y., Rothstein, S.J. (2010). The APETALA-
62.2-Like Transcription Factor OsAP2-39 Controls Key Interactions between Abscisic Acid and Gibberellin
63.in Rice. PLoS Genetics, 6 (9).