Adaption of COBRA Method for The Investigation of Nutrition-Based DNA Methylation Mechanism in Escherichia coli

Year 2020, , 2383 - 2393, 15.12.2020

Taha Yasin Koç , Medine Güllüce , Burak Alaylar , Mehmet Karadayı

https://doi.org/10.21597/jist.719873

Abstract

Epigenetics are changes that occur in the DNA sequence due to environmental conditions. In last few decades epigenetics has been one of the most important advances in biology and related fields. It is very important in that it offers a new approach to all relevant disciplines, especially biology, to explain how DNA sequencing in an epigenetic organism is affected by environmental conditions and phenotype changes that may result from this interaction. Although there are many environmental factors affecting organisms, starvation is one of the most important factors. In our study, epigenetic changes in Escherichia coli due to carbon starvation in the sprE (rssB) gene region were investigated by COBRA (Combined Bisulfite Restriction Analysis) technique, which is one of the quantitative methylation analyzes. As a result of the current results, it has been shown that the methylation status of the 16th CpG islet located in the sprE gene region does not play a role in the regulation of fasting metabolism in E. coli due to the restriction of the carbon level.

Keywords

COBRA, DNA methylation, Capillary gel electrophresis, Escherichia coli, sprE gene

References

• Alaylar B, 2014. Determination of Epigenetic Changes Depending on Presence of Sucrose and Glucose in Related Gene Regions of Saccharomyces cerevısıae. Atatürk University Graduate School of Natural and Applied Sciences, Master Thesis (Printed).
• Alaylar B, Gulluce M, Karadayı M, 2019. Development and Evaluation of Epigenetic Regulation of Sucrose Metabolism in Saccharomyces cerevisiae by Using COBRA Technique and Selected CpG Islands in HXT10 and SUC2 genes. Eastern Anatolian Journal of Science, 5, 50-55.
• Bozoğlu C, 2014. Purification of Laccase Enzyme of Thermophilic Brevibacillus sp. Isolated from Agri Diyadin Hot Spring and Determination of Potential Industrial Usage of the Enzyme. Atatürk University Graduate School of Natural and Applied Sciences, Master Thesis (Printed).
• Carabetta, V.J., Mohanty, B.K., Kushner, S.R., Silhavy, T.J., 2009. The Response Regulator sprE (rssB) Modulates Polyadenylation and mRNA Stability in Escherichia coli. Journal of Bacteriology, 22, 6812 – 6821.
• Casadesûs J, Low DA, 2013. Programmed Heterogeneity: Epigenetic Mechanisms in Bacteria. The Journal of Biological Chemistry, 288, 13929-13935.
• Choi SW, Friso S, 2010. Epigenetics: A New Bridge between Nutrition and Health. Advances in Nutrition-An International Review Journal, 1, 8-16.
• Choi SW, Corrocher R, Friso S, 2009. Nutrients and DNA Methylation. Nutrients and Epigenetics, Ed: Choi, S.W., Friso, S. CRC Press Taylor & Francis Group, Boca Raton, 105-125.
• Goedecke S, Schlosser S, Mühlisch J, Hempel G, Frühwald MC, Wünsch B, 2009. Determination of DNA methylation by COBRA: A comparative study of CGE with LIF detection and conventional gel electrophoresis. Electrophoresis, 30, 3063 – 3070.
• Gulluce M, Alaylar B, Koc TY, Karadayı M, 2014. Epigenetics: An Innovative Approach for Biotechnology and Food Science. International Journal of Bioscience, Biochemistry and Bioinformatics, 4 (3), 195-199.
• Handy DE, Castro R, Loscalzo J, 2011. Epigenetic Modifications Basic Mechanisms and Role in Cardiovascular Disease. Circulation Journal of American Heart Association, 123, 2145-2156.
• Jurkowski TP, Ravichandran M, Stepper P, 2015. Synthetic Epigenetics—Towards Intelligent Control of Epigenetic States and Cell Identity. Clinical Epigenetics, 7 (18), 1 – 11.
• Karadayı M, 2010. Determination of Mutagenic and Antimutagenic Properties of Some Active Compounds from Origanum vulgare L. ssp. vulgare Using Ames/Salmonella and E. coli Wp2 Test Systems. Atatürk University Graduate School of Natural and Applied Sciences, Master Thesis (Printed).
• Karakaş B, Certel M, 2006. Kapiler Elektroforez Tekniği ve Gıda Analizlerinde Kullanım Olanakları - Tahıl Proteinlerinin Analizine Getirdiği Açılımlar. Türkiye 9. Gıda Kongresi, Bolu.
• Kosova B, Özel R, Aktan Ç, 2011. Has DNA Methylation any Impact in Prostate Cancer Diagnosis? Bulletin of Urooncology, 2, 33 - 40.
• Lillycrop KA, Burdge GC, 2015. Maternal Diet as a Modifier of Offspring Epigenetics. Journal of Developmental Origins of Health and Disease, 6 (2), 88 -95.
• Mortelmans K, Zeiger E, 2000. The Ames Salmonella/Microsome Mutagenicity Assay. Mutation Research, 455, 29 – 60.
• Szarc vel Szic K, Declerck K, Vidakovic M, Berghe WV, 2015. From Inflammaging to Healthy Aging by Dietary Lifestyle Choices: Is Epigenetics the Key to Personalized Nutrition? Clinical Epigenetics, 7 (33), 1 – 18.
• Takahashi K, 2013. Influence of Bacteria on Epigenetic Gene Control. Cellular and Molecular Life Sciences, 71, 1045- 1054.
• Tollefsbol TO, 2011. Epigenetics: The New Science of Genetics, Chapter 1. Handbook of Epigenetics-The New Molecular and Medical Genetics, Ed: Trygve Tollefsbol. University of Alabama at Birmingham, Birmingham, 1 - 6.
• Tollefsbol, TO, 2004. Methods of Epigenetic Analysis, Cahapter 1. Epigenetics Protocols, Ed: Trygve Tollefsbol. Humana Press, New Jersey, 1 – 9.
• Warzak DA, Johnson SA, Ellersieck MR, Roberts RM, Zhang X, Ho Shuk-Mei, Rosenfeld CS, 2015. Effects of Post-Weaning Diet on Metabolic Parameters and DNA Methylation Status of the Cryptic Promoter in the Avy Allele of Viable Yellow Mice. Journal of Nutritional Biochemistry, 26, 667 - 674.
• Xiong Z, Laird PW, 1997. COBRA: A Sensitive and Quantitative DNA Methylation Assay. Nucleic Acids Research, 25 (12), 2532 – 2534.
• Yaykaşlı KO, Hatipoğlu ÖF, Kaya E, Yaykaşlı E, 2012. Epigenetics Mechanisms and Cancer. Düzce Medical Journal, 14 (3), 58 - 68.