Patatesde (Solanum tuberosum L.) kurağa tepki veren transpozonların ve transkripsiyon faktörlerin in siliko analizi

Yıl 2019, Cilt: 23 Sayı: 2, 189 - 195, 18.06.2019

Ebru Derelli Tüfekçi Behcet İnal

https://doi.org/10.29050/harranziraat.439682

Öz

Patates (Solanum tuberosum L.) tahıl grubundan olmayan önemli bir kültür
bitkisidir ve küresel gıda güvenliği açısından büyük bir öneme sahiptir.
Kuraklık, tarımsal üretimde büyük verim kayıplarına neden olan başlıca abiyotik
stres faktörlerinden biridir ve patatesde yumru oluşumu, yumru verimi ve
yumruların kalitesini olumsuz yönde etkilemektedir. Birçok ökaryotik türdeki
genomun büyük bir bölümünü hareketli elementler oluşturmaktadır. Transpozon
elementlerin (TE) stres altında nasıl aktive olduklarının moleküler mekanızması
birçok çalışmada tanımlamıştır. Stres ve çevresel zorlukların, özellikle
bitkilerde hareketli elementlerin ekspresyonunu veya transpozisyonunu uyardığı
bilinmektedir. Strese tepki
veren bu genlerin transkripsiyonu büyük ölçüde transkripsiyon faktörleri
tarafından kontrol edilmektedir. Son yıllarda, bitkilerin kurağa tepkilerinin
düzenlenmesinde önemli role sahip bazı transkripsiyon faktörleri
belirlenmiştir. Bu çalışmada, transkripsiyon homolojisi ve anotasyon yaklaşımı
kullanılarak yumru büyütme dönemindeki patateste kuraklığa tepki veren
hareketli elementler ve transkripsiyon faktörü aileleri tanımlanmıştır.
Sonuçlarımız, hareketli elementlerin alt aileleri için okuma sayılarının DNA ve
RNA transpozonları arasında farklı
dağılımlar sağladığını ve bHLH, WRKY, NAC, AP2/ERF transkripsiyon faktörlerini
kodlayan çok sayıda genin, kuraklık stresine
tepkinin düzenlenmesinde önemli işlevlere sahip olabileceğini göstermiştir. Strese tepkide yer alan hareketli
elementlerin ve transkripsiyon faktörlerin tanımlanması ve bunların beraber değerlendirilmesi, işlevsel genomik
çalışmaları ve strese dirençli bitkilerin geliştirilmesinde yeni ıslah
stratejilerinin tasarlanması için yararlı bilgiler sağlayabilir.

Anahtar Kelimeler

Kuraklık, Patates, Transkripsiyon, Transpozon, Transkripsiyon faktör

In silico analysis of drought responsive transposons and transcription factors in Solanum tuberosum L.

Öz

Potato (Solanum tuberosum L.) is the most
important non-grainfood crop and is essential for global food security. Drought
is one of the major abiotic stress factors resulting in huge yield loss in the
production of crops and similarly, it negativelly affects the tuberization, tuber
yield and tuber quality of potato. Transposable elements (TEs) account for a
large portion of the genome in many eukaryotic species. Several studies have
identified the molecular mechanism that cause the activation of TEs under
stress. Stresses and environmental challenges, in particular, are known to
alter the expression or stimulate the transposition of mobile elements in
plants. Transcription of these stress-responsive genes is largely controlled by
transcription factors (TFs). A number of transcription factors playing an
essential role in drought tolerance of plants have been identified in the past
few years. In this work, a subset of drought responsive TE families and TFs in
potato at tuber bulking stage was defined, based on genome-wide transposon homology
and annotation. Our results indicated that, the read numbers for TE subfamilies
yielded different distributions between DNA and RNA transposons. In addition,
many TFs such as bHLH, WRKY, NAC, AP2/ERF may have important functions in
regulation of drought tolerance in potato. Identification of TEs and TFs which
are taking part in stress can offer useful information for functional genomics
and designing novel breeding strategies for developing stress tolerant plants.

Anahtar Kelimeler

Drought, Potato, Transcription, Transposon, Transcription factor

Kaynakça

• Agarwal, P.K., Agarwal, P., Reddy, M.K., Sopory, S.K., 2006. Role of DREB transcription factors in abiotic and biotic stress tolerance in plants. Plant Cell Reports, 25(12):1263-1274.
• Beguiristain, T., Grandbastien, M.A., Puigdomènech, P., Casacuberta, J.M., 2001. Three Tnt1 subfamilies show different stress-associated patterns of expression in tobacco.Consequences for retrotransposon control and evolution in plants. Plant Physiology, 127(1):212-221.
• Biémont, C., 2010. A brief history of the status of transposable elements: from junk DNA to major players in evolution. Genetics, 186(4):1085-1093.
• Capy, P., Gasperi, G., Biémont, C., Bazin, C., 2000. Stress and transposable elements: co‐evolution or useful parasites? Heredity, 85(2):101-106.
• Charfeddine, M., Saidi, M.N., Charfeddine, S., Hammami, A., Bouzid, R.G., 2015. Genome-Wide Analysis and Expression Profiling of the ERF Transcription Factor Family in Potato (Solanum tuberosum L.). Molecular Biotechnology, 57(4):348-358.
• Choi, H., Hong, J., Ha, J., Kang, J., Kim, S.Y., 2000. ABFs, a family of ABA-responsive element binding factors. Journal of Biological Chemistry, 275(3):1723-1730. Cowley, M., Oakey, R.J., 2013. Transposable elements re-wire and fine-tune the transcriptome. PLoS Genetics, 9(1):1-7.
• Draffehn, A.M., Meller, S., Li, L., Gebhardt, C., 2010. Natural diversity of potato (Solanum tuberosum) invertases. BMC Plant Biology, 10(271):2-15.
• Felcher, K.J., Coombs, J.J., Massa, A.N., Hansey, C.N., Hamilton, J.P., Veilleux, R.E., Buell, C.R., Douches, D.S., 2012. Integration of Two Diploid Potato Linkage Maps with the Potato Genome Sequence. PLoS ONE, 7(4):1-11.
• Golldack, D., Lüking, I., Yang, O., 2011. Plant tolerance to drought and salinity: stress regulating transcription factors and their functional significance in the cellular transcriptional network. Plant Cell Reports, 30(8):1383-1391.
• Gong, P., Zhang, J., Li, H., Yang, C., Zhang, C., Zhang, X., Khurram, Z., Zhang, Y, Wang, T., Fei, Z., Ye, Z., 2010. Transcriptional profiles of drought-responsive genes in modulating transcription signal transduction, and biochemical pathways in tomato. Journal Experimental Botany, 61(13):3563-3575.
• Gong, L., Zhang, H., Gan, X., Zhang, L., Chen, Y., Nie, F., Shi, L., Li, M., Guo, Z., Zhang, G., Song, Y., 2015. Transcriptome Profiling of the Potato (Solanum tuberosum L.) Plant under Drought Stress and Water-Stimulus Conditions. PLoS ONE, 10(5):1-20.
• Govind, G., Harshavardhan, V.T., Patricia, J.K., Dhanalakshmi, R., Senthil Kumar, M., Sreenivasulu, N., Udayakumar, M., 2009. Identification and functional validation of a unique set of drought induced genes preferentially expressed in response to gradual water stress in peanut. Molecular Genetics and Genomics, 281(6):591-605.
• Grabherr, M.G., Haas, B.J., Yassour, M., Levin, J.Z., Thompson, D.A., Amit, I., Adiconis, X., Fan, L., Raychowdhury, R., Zeng, Q., Chen, Z., Mauceli, E., Hacohen, N., Gnirke, A., Rhind, N., di Palma, F., Birren, B.W., Nusbaum, C., Lindblad-Toh, K., Regev, A., 2011. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology, 29(7):644-652.
• Grandbastien, M.A., Lucas, H., More, J.B., Mhiri, C., Vernhettes, S., Casacuberta, J.M., 1997. The expression of the tobacco Tnt1 is linked to the plant defence responses. Genetica, 100(1):241-252.
• Hirayama, T., Shinozaki, K., 2010. Research on plant abiotic stress responses in the post-genome era: past, present and future. Plant Journal, 61(6):1041-1052.
• Hollister, J.D., Gaut, B.S., 2009. Epigenetic silencing of transposable elements: a trade-off between reduced transposition and deleterious effects on neighboring gene expression. Genome Research, 19(8), 1419-1428.
• Ito, H., Gaubert, H., Bucher, E., Mirouze, M., Vaillant, I., Paszkowski, J., 2011. An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress. Nature, 472(7341):115-119.
• Ito, H., Yoshida, T., Tsukahara, S., Kawabe, A., 2013. Evolution of the ONSEN retrotransposon family activated upon heat stress in Brassicaceae. Gene, 518(2): 256-261.
• Junakovic, N., Di Franco, C., Best-Belpomme, M., Echalier, G., 1988. On the transposition of copia-like nomadic elements in cultured Drosophila cells. Chromosoma, 97(3):212-218.
• Kang, J.Y., Choi, H.I., Im, M.Y., Kim, S.Y., 2002. Arabidopsis basic leucine zipper proteins that mediate stress-responsive abscisic acid signaling. The Plant Cell, 14(2):343-357.
• Langmead, B., Salzberg, S.L., 2012. Fast gapped-read alignment with Bowtie 2. Nature Methods, 9(4):357-359.
• Li, C., Ng, C.K.Y., Fan, L.M., 2015. MYB transcription factors, active players in abiotic stress signaling, Environmental Experimental Botany, 114(3):80-91.
• Lisch, D., 2013. How important are transposons for plant evolution?, Nature Reviews Genetics, 14(1):9-61.
• Mahajan, S., Tuteja, N., 2005. Cold, salinity and drought stresses: An overview. Archieves Biochemistry and Biophysics, 444(2):139-158.
• Makarevitch, I., Waters, A.J., West, P.T., Stitzer, M., Hirsch, C.N., Ross-Ibarra, J., Springer, N.M., 2015. Transposable Elements Contribute to Activation of Maize Genes in Response to Abiotic Stress. PLoS Genetics, 11(10):1-12.
• Mao, H., Wang, H., Liu, S., Li, Z., Yang, X., Yan, J., Li, J., Tran, L.S.P., Qin, F,A., 2015. transposable element in a NAC gene is associated with drought tolerance in maize seedlings. Nature Communications, 6(8326):1-13.
• McClintock, B., 1950. The origin and behavior of mutable loci in maize. Proceedings of the National Academy of Sciences, 36(6):344-355.
• Meng, X., Li, F., Liu, C., Zhang, C., Wu, Z., Chen, Y., 2010. Isolation and characterization of an ERF transcription factor gene from cotton (Gossypium barbadense L.). Plant Molecular Biology Reporter, 28(3):176-183.
• Negi, P., Rai, A.N., Suprasanna, P., 2016. Moving through the Stressed Genome: Emerging Regulatory Roles for Transposons in Plant Stress Response. Frontiers in Plant Science, 7(1448):1-20.
• Paquin, C.E., Williamson, V.M., 1988. Effect of temperature on Ty transposition. In: Lambert ME, McDonald JF, Weinstein IB (eds) Eukaryotic Transposable Element as Mutagenic Agents. Cold Spring Harbor Press, NY, 235-244pp.
• Qin, F., Shinozaki, K., Yamaguchi-Shinozaki, K., 2011. Achievements and challenges in understanding plant abiotic stress responses and tolerance. Plant Cell Physiology, 52(9):1569-1582.
• Ranjan, A., Nigam, D., Asif, M.H., Singh, R., Ranjan S., Mantri, S., Pandey, N., Trivedi, I., Rai, K.M., Jena, S.N., Koul, B., Tuli, R., Pathre, U.V., Sawant, S.V., 2012. Genome wide expression profiling of two accession of G. herbaceum L. in response to drought. BMC Genomics, 13(94):1-18.
• Rofte, M., Spanos, A., Banks, G., 1986. Induction of yeast Ty element transcription by ultraviolet light. Nature, 319(1):339-340.
• Schafleitner, R., Gutierrez, R., Espino, R., Gaudin, A., Pérez, J., Martínez, M., Domínguez, A., Tincopa, L., Alvarado, C., Numberto, G., Bonierbale, M., 2007. Field Screening for Variation of Drought Tolerance in Solanum tuberosum L. by Agronomical, Physiological and Genetic Analysis. Potato Research, 50(1):71-85.
• Shinozaki, K., Yamaguchi-Shinozaki, K., 2007. Gene networks involved in drought stress response and tolerance. Journal Experimental Botany, 58(2):221-227.
• Singh, K.B., Foley, R.C., Onate-Sanchez, L., 2002. Transcription factors in plant defense and stress responses. Current Opinion in Plant Biology, 5(5):430-436.
• Singh, A.K., Sharma, Pal, A.K., Acharya, V., Ahuja, P.S., 2013. Genome-Wide Organization and Expression Profiling of the NAC Transcription Factor Family in Potato (Solanum tuberosum L.). DNA Research, 20(4):403-423.
• Strand, D.J., McDonald, J.F., 1985. Copia is transcriptionally responsive to environmental stress. Nucleic Acids Research, 13(12):4401-4410.
• Takeda, S., Sugimoto, K., Otsuki, H., Hirochika, H., 1998. Transcriptional activation of the tobacco retrotransposon Tto1 by wounding and methyl jasmonate. Plant Molecular Biology, 36(3):365-376.
• Tran, L.S.P., Nakashima, K., Sakuma, Y., Simpson, S.D., Fujita, Y., Maruyama, K., Fujita, M., Seki, M., Shinozaki, K., Yamaguchi-Shinozaki, K., 2004. Isolation and functional analysis of Arabidopsis stress-inducible NAC transcription factors that bind to a drought-responsive cis-element in the early responsive to dehydration stress 1 promoter. The Plant Cell, 16(9):2481, 2498.
• Tripathi, P., Rabara, R.C., Rushton, P.J., 2014. A systems biology perspective on the role of WRKY transcription factors in drought responses in plants. Planta, 239(2):255-266.
• Uno, Y., Furihata, T., Abe, H., Yoshida, R., Shinozaki, K., Yamaguchi-Shinozaki, K., 2000. Arabidopsis basic leucine zipper transcription factors involved in an abscisic acid-dependent signal transduction pathway under drought and highsalinity conditions. Proceedings of the National Academy of Sciences of the United States of America, 97(21):11632-11637.
• Vos, P.G., Uitdewilligen, J.G., Voorrips, R.E., Visser, R.F., van Eck, H.J., 2015. Development and analysis of a 20K SNP array for potato (Solanum tuberosum): an insight into the breeding history. Theoretical and Applied Genetics, 128(12):2387-2401.
• Walbot, V., 1992. Reactivation of Mutator transposable element of maize by ultraviolet light. Molecular and General Genetics, 234(3):353-360.
• Wicker, T., Sabot, F., Hua-Van, A., Bennetzen, J.L., Capy, P., Chalhoub, B., Flavell, A., Leroy, P., Morgante, M., Panaud, O., Paux, E., SanMiguel, P., Schulman, A.H., 2007. A unified classification system for eukaryotic transposable elements, Nature Review Genetics, 8(1):973-982.
• Wu, S., Hu, C., Tan, Q., Nie, Z., Sun, X., 2014. Effects of molybdenum on water utilization, antioxidative defense system and osmoticadjustment ability in winter wheat (Triticum aestivum) under drought stress. Plant Physiology and Biochemistry, 83(2014):365-374.
• Xie, Y., Wu, G., Tang, J., Luo, R., Patterson, J., Liu, S., Wang, J., 2014. SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads. Bioinformatics, 30(12):1660-1666.
• Yasuda, K., Ito, M., Sugita, T., Tsukiyama, T., Saito, H., Naito, K., Teraishi, M., Tanisaka, T., Okumoto, Y., 2013. Utilization of transposable element mPing as a novel genetic tool for modification of the stress response in rice. Molecular Breeding, 32(3), 505-516.
• Yue, G., Zhuang, Y., Li, Z., Sun, L., Zhang, J., 2008. Differential gene expression analysis of maize leaf at heading stage in response to water-deficit stress. Bioscience Reports, 28(3):125-134.
• Zhang, B., 2015. MicroRNA: a new target for improving plant tolerance to abiotic stress. Journal Experimental Botany, 66(7):1749-1761.