Kayın Mantarı (Pleurotus ostreatus) Genomunda ABC Proteinlerinden MDR Alt Ailesinin Biyoinformatik Analizi ve İfade Profili

Year 2021, , 72 - 82, 31.12.2021

Hatice Kübra Düzel Birsen Çakır Aydemir

https://doi.org/10.53501/rteufemud.1017979

Cited By: 1

Abstract

Hücre zarında birçok farklı metabolik yolu kontrol eden yapılardan biri olan ve en büyük protein ailelerinden birini oluşturan ATP bağlayan kaset taşıyıcı proteinleri (ABC) ATP enerjisini kullanarak madde taşınımında görev alırlar. Çözünür ABC proteinleri transmembran taşınmasına dahil değildir, ancak hücresel süreçlerde, örneğin ribozom biyojenezi ve mRNA translasyonunda önemli bir rol oynamaktadır. ABC proteinlerinin bir alt ailesi olan çoklu ilaç direnci (MDR) alt ailesi, antimikrobiyal peptitler, lipit taşınması, feromon taşınması, mitokondriyal porfirin alımı, ökaryotik peptit taşınması, antijenlerin işlenmesi, oksidatif stresden korunma, ağır metal dayanıklılığı, v.b. olaylarda rol oynamaktadır. Bu çalışmada kayın mantarı (Pleurotus osteradus) genomunun biyoinformatik analizi ile ABC proteinlerinin bir alt üyesi olan ABCB gen ailesine ait 8 tane MDR protein kodlayan gen (PoMDRs) belirlenmiştir. PoMDRs genlerinin kodladığı proteinler ile filogenetik ağaç oluşturulmuştur. Ayrıca bu çalışma kapsamında ilk defa sap ve şapkada PoMDR genlerinin ifade seviyeleri incelenmiş ve bu genlerin ifade düzeylerinin benzer profillere sahip oldukları ancak bu genlerin ifade seviyelerinin şapkada daha fazla olduğu tespit edilmiştir.

Keywords

ABC Kaset Taşıyıcıları, MDR Alt Ailesi, mRNA İfadesi, Pleurotus Ostreatus, Kayın mantarı

Supporting Institution

Ege Üniversitesi Bilimsel araştırmalar proje koordinasyonluğu

Project Number

FYL-2018-20023

Thanks

Bu çalışma Kübra Düzel’in Yüksek Lisans tez çalışmasından elde edilmiştir. Kayın mantarı temini sağlayarak her türlü teknik desteği esirgemeyen Dr. Öğr. Üyesi Erkan EREN’e teşekkür ederiz. Bu çalışma Ege Üniversitesi Bilimsel Araştırma Projeleri Koordinasyon Birimi tarafından desteklenmiştir. (Proje Numarası:FY-2018-20023)

Bioinformatic Analysis and Expression Profile of MDR Subfamily of ABC Proteins from Oyster Mushroom (Pleurotus ostreatus) Genome

Abstract

ATP-binding cassette proteins (ABC), one of the largest protein families involved in the transport of substances by consuming ATP in many different metabolic reactions in the cell membrane. Soluble ABC proteins, on the other hand, are not involved in transmembrane transport, but play an important role in cellular processes, such as ribosome biogenesis and mRNA translation. Multidrug resistance (MDR) subfamily, which is a subfamily of ABC proteins, plays a role in the transport of antimicrobial peptides, lipid transport, pheromone transport, mitochondrial porphyrin uptake, multidrug resistance, eukaryotic peptide transport, antigen processing, protection from oxidative stress, heavy metal resistance, etc. In this study, 8 MDR protein-coding genes (PoMDRs) belonging to the ABCB gene family, which is a sub-class of ABC proteins, were determined by bioinformatic analysis of the beech mushroom (Pleurotus osteradus) genome. And a phylogenetic tree was formed with the proteins encoded by these genes. In addition, within the scope of this study, the expression levels of PoMDR genes in the stem and cap were examined for the first time and it was determined that the expression levels of these genes had similar profiles, but the expression levels of these genes were higher in the cap.

Keywords

ABC cassette transporters, MDR subfamily, mRNA expression, Pleurotus ostreatus, Oyster mushroom

Project Number

FYL-2018-20023

References

• Anonim, 2018, https://genome.jgi.doe.gov/PleosPC15_1/PleosPC15_1.home.html (Erişim tarihi: 05 Nisan 2018)
• Beltran-Garcia, M.J., Estarron-Espinosa, M. and Ogura, T. (1997). Volatile Compounds Secreted by the Oyster Mushroom (Pleurotus ostreatus) and Their Antibacterial Activities, Journal of Agricultural and Food Chemistry 45 (10): 40-49pp. doi: 10.1021/jf960876i
• Carrasco-González, J.A., Serna-Saldívar, S.O., Gutiérrez-Uribe, J.A. (2017). Nutritional composition and nutraceutical properties of the Pleurotus fruiting bodies: Potential use as food ingredient, Journal of Food Composition and Analysis 58: 69-81 http://dx.doi.org/10.1016%2Fj.jfca.2017.01.016
• Chang, S. T., Miles, P.G. (1992). Mushroom biology—a new discipline, The Mycologist 6:64-65pp. http://dx.doi.org/10.1007/s00253-010-3022-4
• Correa, R.C.G., Brugnari, T., Bracht, A., Peralta, R.M., Ferreira, I.C.F.R. (2006). Biotechnological, nutritional and therapeutic uses of Pleurotus spp. (Oyster mushroom) related with its chemical composition: A review on the past decade findings, Trends in Food Science & Technology 50: 103e117 DOI: 10.1016/j.tifs.2016.01.012
• Çakır, B. ve Kılıçkaya, O. (2012) Bitkilerde atp bağlı kaset (abc) taşıyıcı proteinlerinin yapısal özellikleri. Adnan Menderes Üniversitesi Ziraat Fakültesi Dergisi 9(1):39-44pp.
• Dean, M., Rzhetsky, A., Allikmets, R. (2001).The human ATP-binding cassette (ABC) transporter superfamily. Genome Res. Jul;11(7):1156-66. doi: 10.1101/gr.184901
• Dudler, R. and Hertig, C. (1992). Structure of an mdr-like gene from Arabidopsis thaliana, Evolutionary implications, Journal of Biological Chemistry 267:5882-5888pp. DOI:https://doi.org/10.1016/S0021-9258(18)42636-1 Fath, F.J. and Kotler, R. (1993). ABC transporters: bacterial exporters. Microbiol. Rev. 57, 995-1017. DOI: 10.1128/mr.57.4.995-1017.1993
• Higgins, C.F., Linton, K.J. (2003). The ATP switch model for ABC transporters. Nat Struct Mol Biol 11:918–926 https://doi.org/10.1038/nsmb836
• Garcia, O., Bouige, P., Forestier, C., Dassa, E. (2004). Inventory and comparative analysis of rice and Arabidopsis ATP-binding cassette (ABC) systems. J Mol Biol. 2004 Oct 8;343(1):249-65. doi: 10.1016/j.jmb.2004.07.093. PMID: 15381434.
• Jungwirth, H., Kuchler, K. (2005).Yeast ABC transporters-- a tale of sex, stress, drugs and aging. FEBS Lett. 580(4):1131-8. doi: 10.1016/j.febslet.2005.12.050.
• Kang, J., Hwang, J.U., Lee, M., Kim, Y.Y., Assmann, S.M., Martinoia, E., Lee, Y. (2010). PDR-type ABC transporter mediates cellular uptake of the phyto hormone abscisic acid, Proc Natl Acad Sci USA 107:2355-2360pp. DOI: 10.1073/pnas.0909222107
• Kovalchuk, A., Kohler, A., Martin, F. and Asiegbu, F.O. (2015). Diversity and evolution of ABC proteins in mycorrhiza-forming fungi, BMC Evolutionary Biology 15:249p. https://doi.org/10.1186/s12862-015-0526-7
• Kuromori, T., Seo, M. and Shinozaki, K. (2018). ABA tranport and plant water stress responses, Trends in Plant Science, 23(6), 513-522. doi: 10.1016/j.tplants.2018.04.001 Laurent, F., Labesse, G. and Wit, P. (2000). Molecular Cloning and Partial Characterization of a Plant VAP33 Homologue with a Major Sperm Protein Domain, Biochem Biophys Res Commun. 2(1): 286-92. doi: 10.1006/bbrc.2000.2387.
• Lee, M., Lee, K., Lee, J., Noh, E. W., Lee, Y. (2005). AtPDR12 contributes to lead resistance in Arabidopsis, Plant Physiol 138:827-836pp. DOI: 10.1104/pp.104.058107
• Michaelis, S. and Barrowman, J. (2012). Biogenesis of the Saccharomyces cerevisiae pheromone a-factor, from yeast mating to human disease. Microbiol. Mol. Biol. Rev. 76: 626-651. DOI: 10.1128/MMBR.00010-12
• Noh, B., Murphy, A. S., & Spalding, E. P. (2001). Multidrug resistance-like genes of Arabidopsis required for auxin transport and auxin-mediated development. The Plant cell, 13(11), 2441–2454. https://doi.org/10.1105/tpc.010350
• Oswald, C., Holland, I.B., Schmitt, L. (2006). The motor domains of ABC-transporters/what can structures tell us? Naunyn Schmiedebergs Arch Pharmacol 372: 385–399 https://doi.org/10.1007/s00210-005-0031-4
• Pekşen A. (2013). Mantarların insan hayatı ve sağlığındaki yeri. Bahçe Haber 2(1):10-15pp.
• Rea, P.A. (2007). Plant ATP-Binding Cassette Transporters, Annual Review of Plant Biology 58:347-375pp. https://doi.org/10.1146/annurev.arplant.57.032905.105406
• Rea, P.A., Sánchez-Fernández, R., Chen, S., Peng, M., Klein, M., Geisler, M., and Martinoia, E. (2003). The Plant ABC Transporter Superfamily: The Functions of a Few and Identities of Many, ABC Proteins, Holland, I. B., Cole, S. P. C., Kuchler, K. ve Higgins, C. F. (Eds.), Academic Press, London: 335-355pp.
• Sánchez-Fernández, R., Davies, T.G., Coleman, J.O., Rea, P.A. (2001). The Arabidopsis thaliana ABC protein superfamily, a complete inventory. Journal of Biological Chemistry. 276(32):30231-44. doi: 10.1074/jbc.M103104200. PMID: 11346655.
• Santelia, D., Vincenzetti, V., Azzarello, E., Bovet, L., Fukao, Y., Düchtig, P., Mancuso, S., Martinoia, E. ve Geisler, M. (2005). MDR-like ABC transporter AtPGP4 is involved in auxin-mediated lateral root and root hair development, FEBS Letters 579:5399-5406pp. DOI: 10.1016/j.febslet.2005.08.061
• Schulz, B. and Kolukisaoglu, H.Ü. (2006). Genomics of plant ABC transporters: The alphabet of photosynthetic life forms or just holes in membranes, FEBS letters 580(4):1010-1016pDOI: 10.1016/j.febslet.2006.01.002
• Stamets, P. and Chilton, J.S. (1985). The Mushroom Cultivator: A Practical Guide to Growing Mushrooms at Home, Richmond Publishing Co Ltd:415p.
• Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., Kumar, S. (2011). MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods, Molecular Biology and Evolution, 28(10), pp2731–2739, https://doi.org/10.1093/molbev/msr121
• Theodoulou, F.L. (2000). Plant ABC transporters, Biochimica et Biophysica Acta (BBA) – Bio membranes 1465(1-2):79-103pp. DOI: 10.1016/s0005-2736(00)00132-2
• Varadi, A., Tusnady, G. E., Sarkadi, B. (2003). Membrane Topology of the Human ABC Transporter Proteins, In ABC Proteins (I. B. Holland, P. C. C. Susan, K. Karl, S.P.C.C.K. Christopher ) Academic press pp 37-46 , London
• Vasiliou, V., Vasiliou, K., and Nebert, D. (2008). Human ATP-binding cassette (ABC) transporter family, Human Genomics 3:281-290pp. doi: 10.1186/1479-7364-3-3-281
• Wang, L., Gao, W., Wu, X., Zhao, M., Qu, J., Huang, C., and Zhang, J. (2018). Genome-Wide Characterization and Expression Analyses of Pleurotus ostreatus MYB Transcription Factors during Developmental Stages and under Heat Stress Based on de novo Sequenced Genome, International Journal of Molecular Science, 19(7), 2052. doi: 10.3390/ijms19072052
• Wang, W., Buitrago, L., and Wang, Y. (2017). ABC transporters in megakaryopoiesis and platelet activity, Thrombosis Research, 156, 126-133. DOI: 10.1016/j.thromres.2017.06.020
• Wasser, S.P. (2010). Medicinal mushroom science: history, current status, future trends, and unsolved problems. Int J Med Mushrooms 12(1):1-16pp. DOI: 10.1615/IntJMedMushr.v12.i1.10
• Wasser, S.P. (2002). Medicinal Mushrooms as a Source of Anti tumor and immuno modulating Polysaccharides. Applied Microbiolgy and Biotechnology 60:258-274pp. DOI: 10.1007/s00253-002-1076-7
• Williamson, M.P. (1994). The structure and function of proline-rich regions in proteins, Biochem J. 15(2): 249-60. DOI: 10.1042/bj2970249
• Yazaki K., Shitan N., Takanashi K. (2009). Cell and molecular biology of ATP-binding cassette proteins in plants, International Review of Cell and Molecular Biology: 263-299pp. DOI: 10.1016/S1937-6448(09)76006-X Zhu, H., Sun, X., Liu, D., Zheng, L., Chen, L., Ma, A. (2017). An Improved Total RNA Extraction Method for White Jelly Mushroom Tremella fuciformis Rich in Polysaccharides. Mycobiology. 45(4):434-437. doi:10.5941/MYCO.2017.45.4.434