Damla KIZILKAYA, Ayşe Gül KASAPOĞLU, Arash HOSSEİNPOUR, Kamil HALİLOĞLU, Selman MUSLU, Emre İLHAN

Sorghum bicolor L. CAMTA Transkripsiyon Faktörlerinin Genom Çaplı Analizi

Kalmodulin bağlayıcı transkripsiyon aktivatörü olan CAMTA gen ailesi, bitki familyasında karakterize edilmiş kalmodulin bağlayıcı transkripsiyon faktörleridir. CAMTA gen ailesi hastalıklara karşı direnç, biyotik ve abiyotik stres etmenlerine karşı yanıt gibi çeşitli biyolojik süreçlerde önemli roller üstlenmektedir. Bu çalışmada, sorgum (Sorghum bicolor L.) genomunda 7 CAMTA geni belirlendi ve kök ve sürgün dokularında Sobic-CAMTA genlerinin ifade profilleri analiz edildi. Sobic-CAMTA proteinlerinin moleküler ağılıkları ve uzunlukları sırasıyla 95,22 kDa (Sobic-CAMTA-6) ile 114,86 kDa (Sobic-CAMTA-5) ve 845 (Sobic-CAMTA-6) ila 1030 (Sobic-CAMTA-5) amino asit arasındadır. Sobic-CAMTA genleri arasında tahmini olarak belirlenen ekzonların sayısı en düşük 10 en yüksek 13’tür. İzoelektrik noktaları ise 5,55 (Sobic-CAMTA-5.) ila 8,36 (Sobic-CAMTA-4) arasında değişmektedir. Sobic-CAMTA-2/Sobic-CAMTA-3 tandem duplike genler iken, Sobic-CAMTA-3/Sobic-CAMTA-5 ve Sobic-CAMTA-6/Sobic-CAMTA-7 ise segmental duplike genler olarak tespit edilmiştir. S. bicolor L., Arabidopsis thaliana (L.) Heynh ve Zea mays L. CAMTA proteinleri kullanılarak çizilen filogenetik ağaca göre 3 ana grup (A, B ve C) elde edilmiştir. Sobic-CAMTA genlerinin ifade profilleri, S. bicolor L. bitkisinin farklı dokularına farklı azot kaynağı uygulaması ile belirlenmiştir. Bu çalışmanın sonuçları, sorgum bitkisinde CAMTA transkripsiyon faktörü gen ailesinin moleküler yapısının anlaşılması için önemli bilgiler sağlayacaktır.

Anahtar Kelimeler:

Ankrin, Kalmodulin, CG-1 DNA bağlanma domaini, IQ motifi, Sorghum bicolor L.

Genome wide analysis of Sorghum bicolor L. CAMTA Transcription Factors

Calmodulin binding transcription activators (CAMTAs) are well-characterized in the plants. The CAMTA gene family plays an important role in a variety of biological processes, such as resistance to diseases or response to biotic and abiotic factors. In this study, 7 CAMTA genes were identified in the Sorghum bicolor L. genome and expression profiles of Sobic-CAMTA genes in root and shoot tissues were analyzed. The molecular weight and length of Sobic-CAMTA proteins ranged from 95.22 kDa (Sobic-CAMTA-6) to 114.86 kDa (Sobic-CAMTA-5) and 845 (Sobic-CAMTA-6) to 1030 (Sobic-CAMTA-5) amino acids, respectively. Estimated number of exons determined among Sobic-CAMTA genes was between 10 and 13. The isoelectric points ranged from 5.55 (Sobic-CAMTA-5.) to 8.36 (Sobic-CAMTA-4). Sobic-CAMTA-2/Sobic-CAMTA-3 tandem duplicated genes, while Sobic-CAMTA-3/Sobic-CAMTA-5 and Sobic-CAMTA-6/Sobic-CAMTA-7 were identified as segmentally-duplicated genes. According to the phylogenetic tree, which drawn using CAMTA proteins of S. bicolor L., Arabidopsis thaliana (L.) Heynh and Zea mays L., three main groups (A, B and C) were obtained. The expression profiles of Sobic-CAMTA genes were determined by applying different nitrogen sources to different tissues of S. bicolor L. The results of this study would provide important information to understand the molecular structure of the CAMTA transcription factor gene family in sorghum.

Keywords:

Ankyrin, Calmodulin, CG-1 DNA binding domain, IQ motif, Sorghum bicolor L.,

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Anonymous, 2018a. Phytozome Database. https://phytozome.jgi.doe.gov/pz/portal.html (Erişim tarihi: 20.02.2018).
Anonymous, 2018b. Hidden Markov Model (HMM). http://www.ebi.ac.uk (Erişim tarihi: 20.02.2018).
Anonymous, 2018c. Decrease Redundancy Tool. http://web.expasy.org/decrease_redundancy/ (Erişim tarihi: 20.02.2018).
Anonymous, 2018d. HMMER. http://www.ebi.ac.uk (Erişim tarihi: 20.02.2018).
Anonymous, 2018e. ProtParam. http://web. expasy.org/protparam (Erişim tarihi: 20.02.2018).
Anonymous, 2018f. Plant Genome Duplication Database. http://chibba.agtec.uga.edu/duplication/ index/locus (Erişim Tarihi: 26.02.2018).
Anonymous, 2018g. CIMMiner http://discover.nci.nih. gov/cimminer (Erişim tarihi: 01.03.2018).
Bailey, T.L., Williams, N., Misleh, C., Li, W.W., 2006. MEME: Discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Research, 34: W369 W373.
Bouché, N., Scharlat, A., Snedden, W., Bouchez, D., Fromm, H., 2002. A novel family of calmodulin-binding transcription activators in multicellular organisms. J. Biol. Chem., 277(24): 21851–21861.
Büyük, İ., İlhan, E., Şener, D., Özsoy, A. U., Aras, S., 2019. Genome-wide identification of CAMTA gene family members in Phaseolus vulgaris L. and their expression profiling during salt stress. Molecular biology reports, 46(3): 2721-2732.
Choi, M.S., Kim, M.C., Yoo, J.H., Moon, B.C., Koo, S.C., Park, B.O., Lee, J.H., Koo, Y.D., Han, H.J., Lee, S.Y., Chung, W. S., Lim, C. O., Cho, M. J., 2005. Isolation of a calmodulin-binding transcription factor from rice (Oryza sativa L.). J. Biol. Chem., 280: 40820–40831.
Crooks, G.E., Hon, G., Chandonia, J.M., Brenner, S.E., 2004. WebLogo: A sequence logo generator. Genome Research, 14(6): 1188-1190.
de Mendoza, A., Sebé-Pedrós, A., Šestak, M. S., Matejčić, M., Torruella, G., Domazet-Lošo, T., Ruiz-Trillo, I., 2013. Transcription factor evolution in eukaryotes and the assembly of the regulatory toolkit in multicellular lineages. Proceedings of the National Academy of Sciences, 110(50): E4858-E4866.
Du, L., Ali, G.S., Simons, K.A., Hou, J., Yang, T., Reddy, A.S.N., Poovaiah, B.W., 2009. Ca(2+)/calmodulin regulates salicylic-acid-mediated plant immunity. Nature, 457: 1154–1158.
Du, L., Poovaiah, B. W., 2004. A novel family of Ca2+/calmodulin-binding proteins involved in transcriptional regulation: Interaction with fsh/Ring3 class transcription activators. Plant. Mol. Biol., 54(4): 549–569.
Finkler, A., Kaplan, B., Fromm, H., 2007. Ca2+-responsive cis-elements in plants. Plant Signaling and Behavior, 2(1): 17–19.
Guo, A., Zhu, Q., Chen, X., Luo, J., 2007. GSDS: a gene structure display server. Yi Chuan= Hereditas, 29(8): 1023-1026.
Hu, R., Wang, Z., Wu, P., Tang, J., Hou, X., 2015. Identification and abiotic stress analysis of calmodulin-binding transcription activator/signal responsive genes in non-heading Chinese cabbage (Brassica campestris ssp. chinensis Makino). Plant Omics J., 8(2): 141-147.
Juretic, N., Hoen, D.R., Huynh, M.L., Harrison, P.M., Bureau, T.E., 2005. The evolutionary fate of MULE-mediated duplications of host gene fragments in rice. Genome Research, 15(9): 1292- 1297.
Kim, Y., Park, S., Gilmour, S.J., Thomashow, M.F., 2013. Roles of CAMTA transcription factors and salicylic acid in configuring the low temperature transcriptome and freezing tolerance of Arabidopsis. Plant J., 75(3): 364–376.
Lee, T.H., Tang, H.B., Wang, X.Y., Paterson, A.H., 2013. PGDD: A database of gene and genome duplication in plants. Nucleic Acids Research, 41(D1): 1152-1158.
Letunic, I., Bork, P., 2011. Interactive tree of life v2: Online annotation and display of phylogenetic trees made easy. Nucleic Acids Research, 39: W475- W478.
Ludwig, A.A., Romeis, T., Jones, J., 2004. CDPK-mediated signalling pathways: specificity and cross-talk. J. Exp. Bot., 55(395): 181–188.
McCormick, R.F., Truong, S.K., Sreedasyam, A., Jenkins, J., Shu, S., Sims, D., Kennedy, M., Amirebrahimi, M., Weers, B.D., McKinley, B., Mattison, A., Morishige, D.T., Grimwood, J., Schmutz, J., Mullet, J.E., 2018. The Sorghum bicolor reference genome: improved assembly, gene annotations, a transcriptome atlas, and signatures of genome organization. The Plant Journal, 93(2): 338-354.
Menz, M.A., Klein, R.R., Mullet, J.E., Obert, J.A., Unruh, N.C., Klein, P.E., 2002. A high-density genetic map of Sorghum bicolor (L.) Moench based on 2926 AFLP®, RFLP and SSR markers. Plant molecular biology, 48(5-6): 483-499.
Miller, A.J., Cramer, M.D., 2005. Root nitrogen acquisition and assimilation. Plant Soil, 274: 1–36.
Pant, P., Iqbal, Z., Pandey, B. K., Sawant, S. V., 2018. Genome-wide comparative and evolutionary analysis of calmodulin-binding transcription activator (CAMTA) family in Gossypium species. Scientific reports, 8(1): 5573.
Quevillon, E., Silventoinen, V., Pillai, S., Harte, N., Mulder, N., Apweiler, R., Lopez, R., 2005. InterProScan: Protein domains identifier. Nucleic Acids Research, 33(suppl_2): W116-W120.
Rahman, H., Yang, J., Xu, Y. P., Munyampundu, J. P., Cai, X. Z., 2016. Phylogeny of plant CAMTAs and role of AtCAMTAs in nonhost resistance to Xanthomonas oryzae pv. oryzae. Frontiers in plant science, 7: 177.
Reddy, A.S., Ali, G.S., Celesnik, H., Day, I.S., 2011. Coping with stresses: Roles of calcium- and calcium / calmodulin-regulated gene expression. Plant Cell, 23(6): 2010–2032.
Shangguan, L., Wang, X., Leng, X., Liu, D., Ren, G., Tao, R., Zhang, C., Fang, J., 2014. Identification and bioinformatic analysis of signal responsive/calmodulin-binding transcription activators gene models in Vitis vinifera. Mol. Biol. Rep., 41: 1573-4978.
Suyama, M., Torrents, D., Bork, P., 2006. PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Research, 34: W609-W612.
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): 2731-2739.
Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., Higgins, D.G., 1997. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research, 25(24): 4876-4882.
Trapnell, C., Roberts, A., Goffl, O., Pertea, G., Kim, D., Kelley, D.R., Pimentel, H., Salzberg, S.L., Rinn, J.L., Pachter, L., 2013. Differential gene and transcript expression analysis of RNAseq experiments with TopHat and Cufflinks. Nature Protocols, 7(3): 562-578.
Voorrips, R.E., 2002. MapChart: Software for the graphical presentation of linkage maps and QTLs. Journal of Heredity, 93(1): 77-78.
Wei, M., Xu, X., Li, C., 2017. Identification and expression of CAMTA genes in Populus trichocarpa under biotic and abiotic stress. Scientific reports, 7(1): 17910.
Xu, H., Ding, A., Chen, S., Marowa, P., Wang, D., Chen, M., Hu, R., Kong, Y., O’Neill, M., Chai, G., Zhou, G., 2018. Genome-Wide Analysis of Sorghum GT47 Family Reveals Functional Divergences of MUR3-Like Genes. Frontiers in plant science, 9: 1773.
Yang, T., Poovaiah, B.W., 2000. An early ethylene up regulated gene encoding a calmodulin binding protein involved in plant senescence and death. J. Biol. Chem., 275(49):38467-38473.
Yang, T., Poovaiah. B.W., 2002. A calmodulin-binding/CGCG box DNA-binding protein family involved in multiple signalling pathways in plants. J. Biol. Chem., 277(47): 45049–45058.
Yang, Z.H., 2007. PAML 4: Phylogenetic analysis by maximum likelihood. Molecular Biology and Evolution, 24(8): 1586-1591.
Zheng, Y., Jiao, C., Sun, H.H., Rosli, H.G., Pombo, M.A., Zhang, P.F., Banf, M., Dai, X.B., Martin, G.B., Giovannoni, J.J., Zhao, P.X., Rhee, S.Y., Fei, Z.J., 2016. iTAK: A program for genome-wide prediction and classification of plant transcription factors, transcriptional regulators, and protein kinases. Molecular Plant, 9(12): 1667-1670.