Tec1 Proteininin NTH1 Promotoruna Bağlanmasının Moleküler Modellemesi

Year 2019, , 1109 - 1116, 01.06.2019

Tulay Turgut Genç , Selen Çakas

https://doi.org/10.21597/jist.456544

Abstract

Saccharomyces cerevisiae maya hücrelerinde trehaloz molekülü enerji kaynağı ve stres metaboliti olarak görev yapmaktadır. Trehalozun sentezinde ve yıkımında görevli proteinlerin ve ilgili genlerinin ekspresyonları sıkı bir şekilde kontrol edilmektedir. Stres koşullarında sentezlenen trehalozun yıkımında görev alan NTH1 geni transkrispsiyonel ve post-translasyonel olarak regüle edilmektedir. Özellikle transkripsiyonel regülasyonda rol alan transkripsiyon faktörlerinin tümü henüz bilinmemektedir. Bu nedenle çalışmada öncelikle NTH1 promotor bölgesinin biyoinformatik analizi yapıldı ve bağlanma olasılığı bulunan transkripsiyon faktörleri belirlendi. Bu faktörlerden Tec1 transkripsiyon faktörünün NTH1 promotoruna potansiyel üç boyutlu NTH1 promotor-Tec1p bağlanma modeli farklı veri tabanları ve DNA-protein docking programları kullanılarak oluşturuldu. Elde edilen modelleme üzerinde yapılan ölçümlerde Tec1 proteinin NTH1 promotoruna bağlanma olasılığının kuvvetli olduğu belirlendi. Ayrıca Tec1 proteininin TEA-DNA bağlanma bölgesinin S. cerevisiae ve diğer canlılarda yapılan BLAST analizi sonucunda TEA-DNA bağlanma bölgesinde bulunan 22 amino asitin tüm canlılarda % 100 korunduğu tespit edildi.

Keywords

NTH1, Tec1p, DNA-Protein 3D modelleme, Saccharomyces cerevisiae

The Molecular Modelling of Tec1 Protein Binding to NTH1 Promoter

Abstract

The trehalose molecule acts as an energy source and stress metabolite in Saccharomyces cerevisiae yeast cells. The proteins and their encoded genes involved in the synthesis and breakdown of trehalose are tightly controlled. NTH1 gene that is responsible from the degradation of stress accumulated-trehalose, is regulated transcriptionally and post-translationally. Not all of the transcription factors involved in transcriptional regulation are yet to be known. For this reasons, in this study the bioinformatic analysis of NTH1 promoter region was performed and transcription factors that are likely to bind were identified. Of these factors, Tec1 transcription factor was used to construct the potential three-dimensional NTH1 promoter-Tec1p binding model by using different databases and DNA-protein docking programs. The measurements in the obtained three dimensional model revealed that the probability of Tec1 protein binding to the NTH1 promoter was too high. In addition, BLAST analysis of the TEA-DNA binding site in S. cerevisiae and other organisms revealed that 22 amino acids in the TEA-DNA binding region were 100% conserved in all living organisms.

Keywords

NTH1, Tec1p, DNA-Protein 3D modelling, Saccharomyces cerevisiae

References

• Brückner S., Kern S., Birke R., Saugar I., Ulrich HD., Mösch HU., 2011. The TEA Transcription Factor Tec1 Links TOR and MAPK Pathways to Coordinate Yeast Development. Genetics, 189(2): 479-494.
• Cooper TG., 2002. Transmitting the Signal of Excess Nitrogen in Saccharomyces cerevisiae from the Tor Proteins to the GATA Factors: Connecting the Dots. Federation of European Microbiological Societies (FEMS), Microbiological Reviews, 26(3): 223-238.
• Köhler T., Wesche S., Taheri N., Braus GH., Mösch HU., 2002. Dual Role of the Saccharomyces cerevisiae TEA/ATTS Family Transcription Factor Tec1p in Regulation of Gene Expression and Cellular Development. Eukaryotic Cell, 1(5): 673-686.
• Lillie SH., Pringle JR., 1980. Reserve Carbohydrate Metabolism in Saccharomyces cerevisiae: Responses to Nutrient Limitation. Journal of Bacteriology, 143: 1384-1394.
• Madhani H. D., Fink G. R., 1997. Combinatorial Control Required for the Specificity of Yeast MAPK Signaling. Science, 275 (5304): 1314-1317.
• Martinez-Pastor MT., Marchler G., Schuller C., Marchler-Bauer A., Ruis H., Estruch F., 1996. The Saccharomyces cerevisiae Zinc Finger Proteins Msn2p And Msn4p are Required for Transcriptional Induction Through the Stress-Response Element (STRE). The EMBO Journal, 15: 2227–2235.
• Nwaka S., Kopp M., Holzer H., 1995a. Expression and Function of the Trehalase Genes Nth1 and Ybr0106 in Saccharomyces cerevisiae. The Journal of Biological Chemistry, 270: 10193-10198.
• Nwaka S., Mechler B., Destruelle M., Holzer H., 1995b. Phenotipic Features of Trehalase Mutants in Saccharomyces cerevisiae. FEBS Letters, 360(3): 286-290.
• Nwaka S., Holzer H., 1998. Molecular Biology of Trehalose and the Trehalases in the Yeast Saccharomyces cerevisiae. Progress in Nucleic Acid Research Molecular Biology, 58: 197-237.
• Ruis H., Schüller C., 1995. Stress Signaling in Yeast. Bioassays, 17(11): 959-965.