Araştırma Makalesi
BibTex RIS Kaynak Göster

Genome-Wide Characterization and In-silico Transcriptional Expression Analysis of PEBP Family in Solanum lycopersicum L.

Yıl 2022, , 300 - 310, 31.12.2022
https://doi.org/10.29048/makufebed.1110458

Öz

Phosphatidylethanolamine-binding proteins (PEBPs) are an important gene family with highly conserved protein sequences represented in three taxonomic divisions. In plants, PEBP genes are an important actors in the regulation of flowering time, plant architecture and seed dormancy. Despite this, PEBP genes have not been genome-wide identified and systematically analyzed in tomato. In this study, the PEBP gene family in tomato, one of the economically important Solanum species, was comprehensively identified genome-wide and characterized by bioinformatics tools. Here, 12 PEBP genes were identified, which were classified into four clades based on their phylogenetic relationships and the presence of the structurally conserved domain/motif. In addition, the gene structure, conserved protein structure, promoter regions, and digital expression levels of these PEBP genes were determined. Digital expression profiling of SlPEBP transcripts revealed their expression in most developmental and anatomical tissues. These results will provide the further functional and evolutionary characterization of PEBP genes in tomato.

Kaynakça

  • Aceituno, F.F., Moseyko, N., Rhee, S. Y., Gutiérrez, R.A. (2008). The rules of gene expression in plants: organ identity and gene body methylation are key factors for regulation of gene expression in Arabidopsis thaliana. BMC Genomics, 9(1): 1-14.
  • Altschul, S.F., Gish, W., Miller, W., Myers, E. W., Lipman, D.J. (1990). Basic local alignment search tool. Journal of Molecular Biology, 215(3): 403-410.
  • Ariel, F.D., Manavella, P.A., Dezar, C.A., Chan, R.L. (2007). The true story of the HD-Zip family. Trends In Plant Science, 12(9): 419-426.
  • Aukerman, M.J., Sakai, H. (2003). Regulation of flowering time and floral organ identity by a microRNA and its APETALA2-like target genes. The Plant Cell, 15(11): 2730-2741.
  • Bailey, T.L., Johnson, J., Grant, C.E., Noble, W.S. (2015). The MEME suite. Nucleic Acids Research, 43(W1): W39-W49.
  • Bi, Y.M., Zhang, Y., Signorelli, T., Zhao, R., Zhu, T., Rothstein, S. (2005). Genetic analysis of Arabidopsis GATA transcription factor gene family reveals a nitrate‐inducible member important for chlorophyll synthesis and glucose sensitivity. The Plant Journal, 44(4): 680-692.
  • Biłas, R., Szafran, K., Hnatuszko-Konka, K., Kononowicz, A.K. (2016). Cis-regulatory elements used to control gene expression in plants. Plant Cell, Tissue and Organ Culture, 127(2): 269-287.
  • Carmona, M.J., Calonje, M., Martínez-Zapater, J.M. (2007). The FT/TFL1 gene family in grapevine. Plant Molecular Biology, 63(5): 637-650.
  • Castelain, M., Le Hir, R., Bellini, C. (2012). The non‐DNA‐binding bHLH transcription factor PRE3/bHLH135/ATBS1/TMO7 is involved in the regulation of light signaling pathway in Arabidopsis. Physiologia Plantarum, 145(3): 450-460.
  • Chautard, H., Jacquet, M., Schoentgen, F., Bureaud, N., Bénédetti, H. (2004). Tfs1p, a member of the PEBP family, inhibits the Ira2p but not the Ira1p Ras GTPase-activating protein in Saccharomyces cerevisiae. Eukaryotic Cell, 3(2): 459-470.
  • Chen, C., Chen, H., Zhang, Y., Thomas, H.R., Frank, M.H., He, Y., Xia, R. (2020). TBtools: an integrative toolkit developed for interactive analyses of big biological data. Molecular Plant, 13(8): 1194-1202.
  • Chow, C.N., Lee, T.Y., Hung, Y.C., Li, G.Z., Tseng, K.C., Liu, Y.H., Chang, W.C. (2019). PlantPAN3. 0: a new and updated resource for reconstructing transcriptional regulatory networks from ChIP-seq experiments in plants. Nucleic Acids Research, 47(1): 1155-1163.
  • Danilevskaya, O.N., Meng, X., Hou, Z., Ananiev, E.V., Simmons, C.R. (2008). A genomic and expression compendium of the expanded PEBP gene family from maize. Plant Physiology, 146(1): 250-264.
  • Abeles, F.B., Morgan, P.W., Saltveit Jr, M.E. (2012). Ethylene in plant biology. Academic Press; DOI:10.1016/C2009-0-03226-7
  • Dong, L., Lu, Y., Liu, S. (2020). Genome-wide member identification, phylogeny and expression analysis of PEBP gene family in wheat and its progenitors. PeerJ, 8: 10483; DOI: 10.7717/peerj.10483
  • Dong, T., Hu, Z., Deng, L., Wang, Y., Zhu, M., Zhang, J., Chen, G. (2013). A tomato MADS-box transcription factor, SlMADS1, acts as a negative regulator of fruit ripening. Plant Physiology, 163(2): 1026-1036.
  • Faure, S., Higgins, J., Turner, A., Laurie, D.A. (2007). The FLOWERING LOCUS T-like gene family in barley (Hordeum vulgare). Genetics, 176(1): 599-609.
  • Fernandez-Pozo, N., Menda, N., Edwards, J.D., Saha, S., Tecle, I.Y., Strickler, S.R., Mueller, L.A. (2015). The Sol Genomics Network (SGN)—from genotype to phenotype to breeding. Nucleic Acids Research, 43: 1036-1041.
  • Fukazawa, J., Sakai, T., Ishida, S., Yamaguchi, I., Kamiya, Y., Takahashi, Y. (2000). Repression of shoot growth, a bZIP transcriptional activator, regulates cell elongation by controlling the level of gibberellins. The Plant Cell, 12(6): 901-915.
  • Gallavotti, A., Malcomber, S., Gaines, C., Stanfield, S., Whipple, C., Kellogg, E., Schmidt, R.J. (2011). BARREN STALK FASTIGIATE1 is an AT-hook protein required for the formation of maize ears. The Plant Cell, 23(5): 1756-1771.
  • Goodstein, D. M., Shu, S., Howson, R., Neupane, R., Hayes, R.D., Fazo, J., Rokhsar, D.S. (2012). Phytozome: a comparative platform for green plant genomics. Nucleic Acids Research, 40: 1178-1186.
  • Hecht, V., Laurie, R.E., Vander Schoor, J.K., Ridge, S., Knowles, C.L., Liew, L.C., Weller, J.L. (2011). The pea GIGAS gene is a FLOWERING LOCUS T homolog necessary for graft-transmissible specification of flowering but not for responsiveness to photoperiod. The Plant Cell, 23:147-161.
  • Hegedus, D., Yu, M., Baldwin, D., Gruber, M., Sharpe, A., Parkin, I., Lydiate, D. (2003). Molecular characterization of Brassica napus NAC domain transcriptional activators induced in response to biotic and abiotic stress. Plant Molecular Biology, 53(3): 383-397.
  • Hengst, U., Albrecht, H., Hess, D., Monard, D. (2001). The phosphatidylethanolamine-binding protein is the prototype of a novel family of serine protease inhibitors. Journal of Biological Chemistry, 276(1): 535-540.
  • Hu, B., Jin, J., Guo, A. Y., Zhang, H., Luo, J., Gao, G. (2015). GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics, 31(8): 1296-1297.
  • Huang, N.C., Jane, W.N., Chen, J., Yu, T.S. (2012). Arabidopsis thaliana CENTRORADIALIS homologue (ATC) acts systemically to inhibit floral initiation in Arabidopsis. The Plant Journal, 72(2): 175-184.
  • Jin, S., Nasim, Z., Susila, H., Ahn, J.H. (2021). Evolution and functional diversification of FLOWERING LOCUS T/TERMINAL FLOWER 1 family genes in plants. In Seminars in Cell & Developmental Biology, 109: 20-30.
  • Johnson, C.S., Kolevski, B., Smyth, D.R. (2002). TRANSPARENT TESTA GLABRA2, a trichome and seed coat development gene of Arabidopsis, encodes a WRKY transcription factor. The Plant Cell, 14(6): 1359-1375.
  • Kardailsky, I., Shukla, V.K., Ahn, J.H., Dagenais, N., Christensen, S.K., Nguyen, J.T., Weigel, D. (1999). Activation tagging of the floral inducer FT. Science, 286: 1962-1965.
  • Karlgren, A., Gyllenstrand, N., Källman, T., Sundström, J.F., Moore, D., Lascoux, M., Lagercrantz, U. (2011). Evolution of the PEBP gene family in plants: functional diversification in seed plant evolution. Plant Physiology, 156(4): 1967-1977.
  • Kobayashi, Y., Kaya, H., Goto, K., Iwabuchi, M., Araki, T. (1999). A pair of related genes with antagonistic roles in mediating flowering signals. Science, 286(5446): 1960-1962.
  • Kumar, S., Stecher, G., Li, M., Knyaz, C., Tamura, K. (2018). MEGA X: molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution, 35(6): 1547; DOI: 10.1093/molbev/msy096 Lara, P., Oñate-Sánchez, L., Abraham, Z., Ferrándiz, C., Díaz, I., Carbonero, P., Vicente-Carbajosa, J. (2003). Synergistic activation of seed storage protein gene expression in Arabidopsis by ABI3 and two bZIPs related to OPAQUE2. Journal of Biological Chemistry, 278(23): 21003-21011.
  • Le, D.T., Nishiyama, R., Watanabe, Y., Vankova, R., Tanaka, M., Seki, M., Tran, L.S.P. (2012). Identification and expression analysis of cytokinin metabolic genes in soybean under normal and drought conditions in relation to cytokinin levels. Plos One, 7(8): 42411; DOI: 10.1371/journal.pone.0042411
  • Lee, C., Kim, S.J., Jin, S., Susila, H., Youn, G., Nasim, Z., Ahn, J.H. (2019). Genetic interactions reveal the antagonistic roles of FT/TSF and TFL1 in the determination of inflorescence meristem identity in Arabidopsis. The Plant Journal, 99(3): 452-464.
  • Li, H., Gao, W., Xue, C., Zhang, Y., Liu, Z., Zhang, Y., Zhao, J. (2019). Genome-wide analysis of the bHLH gene family in Chinese jujube (Ziziphus jujuba Mill.) and wild jujube. BMC Genomics, 20(1): 1-13; DOI:10.1186/s12864-019-5936-2
  • Li, Q., Fan, C., Zhang, X., Wang, X., Wu, F., Hu, R., Fu, Y. (2014). Identification of a soybean MOTHER OF FT AND TFL1 homolog involved in regulation of seed germination. PLoS One, 9(6): 99642; DOI: 10.1371/journal.pone.0099642
  • Liu, P.P., Koizuka, N., Martin, R.C., Nonogaki, H. (2005). The BME3 (Blue Micropylar End 3) GATA zinc finger transcription factor is a positive regulator of Arabidopsis seed germination. The Plant Journal, 44(6): 960-971.
  • Liu, Y.Y., Yang, K.Z., Wei, X.X., Wang, X.Q. (2016). Revisiting the phosphatidylethanolamine‐binding protein (PEBP) gene family reveals cryptic FLOWERING LOCUS T gene homologs in gymnosperms and sheds new light on functional evolution. New Phytologist, 212(3): 730-744.
  • Luo, X. M., Lin, W. H., Zhu, S., Zhu, J.Y., Sun, Y., Fan, X.Y., Wang, Z.Y. (2010). Integration of light-and brassinosteroid-signaling pathways by a GATA transcription factor in Arabidopsis. Developmental Cell, 19(6): 872-883.
  • Michaels, S.D., Ditta, G., Gustafson‐Brown, C., Pelaz, S., Yanofsky, M., Amasino, R.M. (2003). AGL24 acts as a promoter of flowering in Arabidopsis and is positively regulated by vernalization. The Plant Journal, 33(5): 867-874.
  • Mimida, N., Goto, K., Kobayashi, Y., Araki, T., Ahn, J.H., Weigel, D., Sakamoto, W. (2001). Functional divergence of the TFL1‐like gene family in Arabidopsis revealed by characterization of a novel homologue. Genes to Cells, 6(4): 327-336.
  • Mistry, J., Chuguransky, S., Williams, L., Qureshi, M., Salazar, G.A., Sonnhammer, E.L., Bateman, A. (2021). Pfam: The protein families database in 2021. Nucleic Acids Research, 49: 412-419.
  • Odabaei G, Chatterjee D, Jazirehi A.R. (2004). Raf-1 kinase inhibitor protein: structure, function, regulation of cell signaling, and pivotal role in apoptosis. Advances in Cancer Research, 91: 169; DOI: 10.1016/S0065-230X(04)91005-6
  • Ohyanagi, H., Takano, T., Terashima, S., Kobayashi, M., Kanno, M., Morimoto, K., Yano, K. (2015). Plant Omics Data Center: an integrated web repository for interspecies gene expression networks with NLP-based curation. Plant and Cell Physiology, 56(1): 9; DOI: 10.1093/pcp/pcu188
  • Pnueli, L., Carmel-Goren, L., Hareven, D., Gutfinger, T., Alvarez, J., Ganal, M., Lifschitz, E. (1998). The SELF-PRUNING gene of tomato regulates vegetative to reproductive switching of sympodial meristems and is the ortholog of CEN and TFL1. Development, 125(11): 1979-1989.
  • Sato, S., Tabata, S., Hirakawa, H. (2012). The tomato genome sequence provides insights into fleshy fruit evolution. Nature, 485(7400): 635–641.
  • Serre, L., Vallée, B., Bureaud, N., Schoentgen, F., Zelwer, C. (1998). Crystal structure of the phosphatidylethanolamine-binding protein from bovine brain: a novel structural class of phospholipid-binding proteins. Structure, 6(10): 1255-1265.
  • Song, C., Li, G., Dai, J., Deng, H. (2021). Genome-Wide Analysis of PEBP Genes in Dendrobium huoshanense: Unveiling the Antagonistic Functions of FT/TFL1 in Flowering Time. Frontiers in Genetics, 12: 687689; DOI: 10.3389/fgene.2021.687689
  • Tamaki, S., Matsuo, S., Wong, H.L., Yokoi, S., Shimamoto, K. (2007). Hd3a protein is a mobile flowering signal in rice. Science, 316(5827): 1033-1036.
  • Tao, Y. B., Luo, L., He, L.L., Ni, J., Xu, Z.F. (2014). A promoter analysis of MOTHER OF FT AND TFL1 1 (JcMFT1), a seed-preferential gene from the biofuel plant Jatropha curcas. Journal of Plant Research, 127(4): 513-524.
  • Tranbarger, T.J., Fooyontphanich, K., Roongsattham, P., Pizot, M., Collin, M., Jantasuriyarat, C., Morcillo, F. (2017). Transcriptome analysis of cell wall and NAC domain transcription factor genes during Elaeis guineensis fruit ripening: evidence for widespread conservation within monocot and eudicot lineages. Frontiers in Plant Science, 8: 603; DOI: 10.3389/fpls.2017.00603
  • Vallee, B.S., Coadou, G., Labbe, H., Sy, D., Vovelle, F., Schoentgen, F. (2003). Peptides corresponding to the N‐and C‐terminal parts of PEBP are well‐structured in solution: new insights into their possible interaction with partners in vivo. The Journal of Peptide Research, 61(2): 47-57.
  • Wang, L., Zhu, W., Fang, L., Sun, X., Su, L., Liang, Z., Xin, H. (2014). Genome-wide identification of WRKY family genes and their response to cold stress in Vitis vinifera. BMC Plant Biology, 14(1): 1-14; DOI: 10.1186/1471-2229-14-103
  • Wang, M., Tan, Y., Cai, C., Zhang, B. (2019). Identification and expression analysis of phosphatidy ethanolamine-binding protein (PEBP) gene family in cotton. Genomics, 111(6): 1373-1380.
  • Wang, Z., Zhou, Z., Liu, Y., Liu, T., Li, Q., Ji, Y., Tian, Z. (2015). Functional evolution of phosphatidylethanolamine binding proteins in soybean and Arabidopsis. The Plant Cell, 27(2): 323-336.
  • Wickland, D.P., & Hanzawa, Y. (2015). The FLOWERING LOCUS T/TERMINAL FLOWER 1 gene family: functional evolution and molecular mechanisms. Molecular Plant, 8(7): 983-997.
  • Wilkins, M.R., Gasteiger, E., Bairoch, A. (1999). Protein identification and analysis tools in the ExPASy server. Methods in Molecular Biology, 112: 531–552.
  • Xi, W., Liu, C., Hou, X., Yu, H. (2010). MOTHER OF FT AND TFL1 regulates seed germination through a negative feedback loop modulating ABA signaling in Arabidopsis. The Plant Cell, 22(6): 1733-1748.
  • Xie, Q., Sanz-Burgos, A.P., Guo, H., García, J. A., Gutiérrez, C. (1999). GRAB proteins, novel members of the NAC domain family, isolated by their interaction with a geminivirus protein. Plant Molecular Biology, 39(4): 647-656.
  • Yoo, S.J., Chung, K.S., Jung, S.H., Yoo, S.Y., Lee, J.S., Ahn, J.H. (2010). BROTHER OF FT AND TFL1 (BFT) has TFL1‐like activity and functions redundantly with TFL1 in inflorescence meristem development in Arabidopsis. The Plant Journal, 63(2): 241-253.
  • Yu, C.S., Chen, Y.C., Lu, C.H., Hwang, J.K. (2006). Prediction of protein subcellular localization. Proteins: Structure, Function, and Bioinformatics, 64(3): 643-651.
  • Zhang, Z.L., Xie, Z., Zou, X., Casaretto, J., Ho, T.H.D., Shen, Q.J. (2004). A rice WRKY gene encodes a transcriptional repressor of the gibberellin signaling pathway in aleurone cells. Plant Physiology, 134(4): 1500-1513.
  • Zhao, S., Wei, Y., Pang, H., Xu, J., Li, Y., Zhang, H., Zhang, Y. (2020). Genome-wide identification of the PEBP genes in pears and the putative role of PbFT in flower bud differentiation. PeerJ, 8: 8928; DOI: 10.7717/peerj.8928
  • Zheng, X.M., Wu, F. Q., Zhang, X., Lin, Q.B., Wang, J., Guo, X.P., Wan, J.M. (2016). Evolution of the PEBP gene family and selective signature on FT‐like clade. Journal of Systematics and Evolution, 54(5): 502-510.

Solanum lycopersicum L.'de PEBP Ailesinin Genom Çapında Karakterizasyonu ve In-silico Transkripsiyonel İfade Analizi

Yıl 2022, , 300 - 310, 31.12.2022
https://doi.org/10.29048/makufebed.1110458

Öz

Fosfatidiletanolamin bağlayıcı proteinler (PEBP'ler), üç taksonomik bölümde temsil edilen yüksek oranda korunmuş protein dizilerine sahip önemli bir gen ailesidir. Bitkilerde PEBP genleri, çiçeklenme zamanı, bitki mimarisi ve tohum dormansisinin düzenlenmesinin önemli bir aktörüdür. Buna rağmen, PEBP genleri bugüne kadar domateste genom çapında tanımlanmamış ve sistematik olarak analiz edilmemiştir. Bu çalışmada, ekonomik açıdan önemli Solanum türlerinden domatesteki PEBP gen ailesi, genom çapında kapsamlı bir şekilde tanımlanmış ve biyoinformatik yöntemler ile karakterize edilmiştir. Bu çalışmada, filogenetik ilişkilerine ve yapısal olarak korunan domain/motif varlığına göre dört klad halinde sınıflandırılan 12 PEBP geni tanımlanmıştır. Ayrıca bu PEBP genlerinin gen yapısı, korunmuş protein yapısı, promotör bölgeleri ve dijital ekspresyon seviyeleri belirlenmiştir. SlPEBP transkriptlerinin dijital ekspresyon profili, çoğu gelişim aşamasında ve anatomik dokularda ekspresyonlarını ortaya çıkarmıştır. Bu sonuçlar, domateste PEBP genlerinin daha ileri fonksiyonel ve evrimsel karakterizasyonunun anlaşılmasını sağlayacaktır.

Kaynakça

  • Aceituno, F.F., Moseyko, N., Rhee, S. Y., Gutiérrez, R.A. (2008). The rules of gene expression in plants: organ identity and gene body methylation are key factors for regulation of gene expression in Arabidopsis thaliana. BMC Genomics, 9(1): 1-14.
  • Altschul, S.F., Gish, W., Miller, W., Myers, E. W., Lipman, D.J. (1990). Basic local alignment search tool. Journal of Molecular Biology, 215(3): 403-410.
  • Ariel, F.D., Manavella, P.A., Dezar, C.A., Chan, R.L. (2007). The true story of the HD-Zip family. Trends In Plant Science, 12(9): 419-426.
  • Aukerman, M.J., Sakai, H. (2003). Regulation of flowering time and floral organ identity by a microRNA and its APETALA2-like target genes. The Plant Cell, 15(11): 2730-2741.
  • Bailey, T.L., Johnson, J., Grant, C.E., Noble, W.S. (2015). The MEME suite. Nucleic Acids Research, 43(W1): W39-W49.
  • Bi, Y.M., Zhang, Y., Signorelli, T., Zhao, R., Zhu, T., Rothstein, S. (2005). Genetic analysis of Arabidopsis GATA transcription factor gene family reveals a nitrate‐inducible member important for chlorophyll synthesis and glucose sensitivity. The Plant Journal, 44(4): 680-692.
  • Biłas, R., Szafran, K., Hnatuszko-Konka, K., Kononowicz, A.K. (2016). Cis-regulatory elements used to control gene expression in plants. Plant Cell, Tissue and Organ Culture, 127(2): 269-287.
  • Carmona, M.J., Calonje, M., Martínez-Zapater, J.M. (2007). The FT/TFL1 gene family in grapevine. Plant Molecular Biology, 63(5): 637-650.
  • Castelain, M., Le Hir, R., Bellini, C. (2012). The non‐DNA‐binding bHLH transcription factor PRE3/bHLH135/ATBS1/TMO7 is involved in the regulation of light signaling pathway in Arabidopsis. Physiologia Plantarum, 145(3): 450-460.
  • Chautard, H., Jacquet, M., Schoentgen, F., Bureaud, N., Bénédetti, H. (2004). Tfs1p, a member of the PEBP family, inhibits the Ira2p but not the Ira1p Ras GTPase-activating protein in Saccharomyces cerevisiae. Eukaryotic Cell, 3(2): 459-470.
  • Chen, C., Chen, H., Zhang, Y., Thomas, H.R., Frank, M.H., He, Y., Xia, R. (2020). TBtools: an integrative toolkit developed for interactive analyses of big biological data. Molecular Plant, 13(8): 1194-1202.
  • Chow, C.N., Lee, T.Y., Hung, Y.C., Li, G.Z., Tseng, K.C., Liu, Y.H., Chang, W.C. (2019). PlantPAN3. 0: a new and updated resource for reconstructing transcriptional regulatory networks from ChIP-seq experiments in plants. Nucleic Acids Research, 47(1): 1155-1163.
  • Danilevskaya, O.N., Meng, X., Hou, Z., Ananiev, E.V., Simmons, C.R. (2008). A genomic and expression compendium of the expanded PEBP gene family from maize. Plant Physiology, 146(1): 250-264.
  • Abeles, F.B., Morgan, P.W., Saltveit Jr, M.E. (2012). Ethylene in plant biology. Academic Press; DOI:10.1016/C2009-0-03226-7
  • Dong, L., Lu, Y., Liu, S. (2020). Genome-wide member identification, phylogeny and expression analysis of PEBP gene family in wheat and its progenitors. PeerJ, 8: 10483; DOI: 10.7717/peerj.10483
  • Dong, T., Hu, Z., Deng, L., Wang, Y., Zhu, M., Zhang, J., Chen, G. (2013). A tomato MADS-box transcription factor, SlMADS1, acts as a negative regulator of fruit ripening. Plant Physiology, 163(2): 1026-1036.
  • Faure, S., Higgins, J., Turner, A., Laurie, D.A. (2007). The FLOWERING LOCUS T-like gene family in barley (Hordeum vulgare). Genetics, 176(1): 599-609.
  • Fernandez-Pozo, N., Menda, N., Edwards, J.D., Saha, S., Tecle, I.Y., Strickler, S.R., Mueller, L.A. (2015). The Sol Genomics Network (SGN)—from genotype to phenotype to breeding. Nucleic Acids Research, 43: 1036-1041.
  • Fukazawa, J., Sakai, T., Ishida, S., Yamaguchi, I., Kamiya, Y., Takahashi, Y. (2000). Repression of shoot growth, a bZIP transcriptional activator, regulates cell elongation by controlling the level of gibberellins. The Plant Cell, 12(6): 901-915.
  • Gallavotti, A., Malcomber, S., Gaines, C., Stanfield, S., Whipple, C., Kellogg, E., Schmidt, R.J. (2011). BARREN STALK FASTIGIATE1 is an AT-hook protein required for the formation of maize ears. The Plant Cell, 23(5): 1756-1771.
  • Goodstein, D. M., Shu, S., Howson, R., Neupane, R., Hayes, R.D., Fazo, J., Rokhsar, D.S. (2012). Phytozome: a comparative platform for green plant genomics. Nucleic Acids Research, 40: 1178-1186.
  • Hecht, V., Laurie, R.E., Vander Schoor, J.K., Ridge, S., Knowles, C.L., Liew, L.C., Weller, J.L. (2011). The pea GIGAS gene is a FLOWERING LOCUS T homolog necessary for graft-transmissible specification of flowering but not for responsiveness to photoperiod. The Plant Cell, 23:147-161.
  • Hegedus, D., Yu, M., Baldwin, D., Gruber, M., Sharpe, A., Parkin, I., Lydiate, D. (2003). Molecular characterization of Brassica napus NAC domain transcriptional activators induced in response to biotic and abiotic stress. Plant Molecular Biology, 53(3): 383-397.
  • Hengst, U., Albrecht, H., Hess, D., Monard, D. (2001). The phosphatidylethanolamine-binding protein is the prototype of a novel family of serine protease inhibitors. Journal of Biological Chemistry, 276(1): 535-540.
  • Hu, B., Jin, J., Guo, A. Y., Zhang, H., Luo, J., Gao, G. (2015). GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics, 31(8): 1296-1297.
  • Huang, N.C., Jane, W.N., Chen, J., Yu, T.S. (2012). Arabidopsis thaliana CENTRORADIALIS homologue (ATC) acts systemically to inhibit floral initiation in Arabidopsis. The Plant Journal, 72(2): 175-184.
  • Jin, S., Nasim, Z., Susila, H., Ahn, J.H. (2021). Evolution and functional diversification of FLOWERING LOCUS T/TERMINAL FLOWER 1 family genes in plants. In Seminars in Cell & Developmental Biology, 109: 20-30.
  • Johnson, C.S., Kolevski, B., Smyth, D.R. (2002). TRANSPARENT TESTA GLABRA2, a trichome and seed coat development gene of Arabidopsis, encodes a WRKY transcription factor. The Plant Cell, 14(6): 1359-1375.
  • Kardailsky, I., Shukla, V.K., Ahn, J.H., Dagenais, N., Christensen, S.K., Nguyen, J.T., Weigel, D. (1999). Activation tagging of the floral inducer FT. Science, 286: 1962-1965.
  • Karlgren, A., Gyllenstrand, N., Källman, T., Sundström, J.F., Moore, D., Lascoux, M., Lagercrantz, U. (2011). Evolution of the PEBP gene family in plants: functional diversification in seed plant evolution. Plant Physiology, 156(4): 1967-1977.
  • Kobayashi, Y., Kaya, H., Goto, K., Iwabuchi, M., Araki, T. (1999). A pair of related genes with antagonistic roles in mediating flowering signals. Science, 286(5446): 1960-1962.
  • Kumar, S., Stecher, G., Li, M., Knyaz, C., Tamura, K. (2018). MEGA X: molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution, 35(6): 1547; DOI: 10.1093/molbev/msy096 Lara, P., Oñate-Sánchez, L., Abraham, Z., Ferrándiz, C., Díaz, I., Carbonero, P., Vicente-Carbajosa, J. (2003). Synergistic activation of seed storage protein gene expression in Arabidopsis by ABI3 and two bZIPs related to OPAQUE2. Journal of Biological Chemistry, 278(23): 21003-21011.
  • Le, D.T., Nishiyama, R., Watanabe, Y., Vankova, R., Tanaka, M., Seki, M., Tran, L.S.P. (2012). Identification and expression analysis of cytokinin metabolic genes in soybean under normal and drought conditions in relation to cytokinin levels. Plos One, 7(8): 42411; DOI: 10.1371/journal.pone.0042411
  • Lee, C., Kim, S.J., Jin, S., Susila, H., Youn, G., Nasim, Z., Ahn, J.H. (2019). Genetic interactions reveal the antagonistic roles of FT/TSF and TFL1 in the determination of inflorescence meristem identity in Arabidopsis. The Plant Journal, 99(3): 452-464.
  • Li, H., Gao, W., Xue, C., Zhang, Y., Liu, Z., Zhang, Y., Zhao, J. (2019). Genome-wide analysis of the bHLH gene family in Chinese jujube (Ziziphus jujuba Mill.) and wild jujube. BMC Genomics, 20(1): 1-13; DOI:10.1186/s12864-019-5936-2
  • Li, Q., Fan, C., Zhang, X., Wang, X., Wu, F., Hu, R., Fu, Y. (2014). Identification of a soybean MOTHER OF FT AND TFL1 homolog involved in regulation of seed germination. PLoS One, 9(6): 99642; DOI: 10.1371/journal.pone.0099642
  • Liu, P.P., Koizuka, N., Martin, R.C., Nonogaki, H. (2005). The BME3 (Blue Micropylar End 3) GATA zinc finger transcription factor is a positive regulator of Arabidopsis seed germination. The Plant Journal, 44(6): 960-971.
  • Liu, Y.Y., Yang, K.Z., Wei, X.X., Wang, X.Q. (2016). Revisiting the phosphatidylethanolamine‐binding protein (PEBP) gene family reveals cryptic FLOWERING LOCUS T gene homologs in gymnosperms and sheds new light on functional evolution. New Phytologist, 212(3): 730-744.
  • Luo, X. M., Lin, W. H., Zhu, S., Zhu, J.Y., Sun, Y., Fan, X.Y., Wang, Z.Y. (2010). Integration of light-and brassinosteroid-signaling pathways by a GATA transcription factor in Arabidopsis. Developmental Cell, 19(6): 872-883.
  • Michaels, S.D., Ditta, G., Gustafson‐Brown, C., Pelaz, S., Yanofsky, M., Amasino, R.M. (2003). AGL24 acts as a promoter of flowering in Arabidopsis and is positively regulated by vernalization. The Plant Journal, 33(5): 867-874.
  • Mimida, N., Goto, K., Kobayashi, Y., Araki, T., Ahn, J.H., Weigel, D., Sakamoto, W. (2001). Functional divergence of the TFL1‐like gene family in Arabidopsis revealed by characterization of a novel homologue. Genes to Cells, 6(4): 327-336.
  • Mistry, J., Chuguransky, S., Williams, L., Qureshi, M., Salazar, G.A., Sonnhammer, E.L., Bateman, A. (2021). Pfam: The protein families database in 2021. Nucleic Acids Research, 49: 412-419.
  • Odabaei G, Chatterjee D, Jazirehi A.R. (2004). Raf-1 kinase inhibitor protein: structure, function, regulation of cell signaling, and pivotal role in apoptosis. Advances in Cancer Research, 91: 169; DOI: 10.1016/S0065-230X(04)91005-6
  • Ohyanagi, H., Takano, T., Terashima, S., Kobayashi, M., Kanno, M., Morimoto, K., Yano, K. (2015). Plant Omics Data Center: an integrated web repository for interspecies gene expression networks with NLP-based curation. Plant and Cell Physiology, 56(1): 9; DOI: 10.1093/pcp/pcu188
  • Pnueli, L., Carmel-Goren, L., Hareven, D., Gutfinger, T., Alvarez, J., Ganal, M., Lifschitz, E. (1998). The SELF-PRUNING gene of tomato regulates vegetative to reproductive switching of sympodial meristems and is the ortholog of CEN and TFL1. Development, 125(11): 1979-1989.
  • Sato, S., Tabata, S., Hirakawa, H. (2012). The tomato genome sequence provides insights into fleshy fruit evolution. Nature, 485(7400): 635–641.
  • Serre, L., Vallée, B., Bureaud, N., Schoentgen, F., Zelwer, C. (1998). Crystal structure of the phosphatidylethanolamine-binding protein from bovine brain: a novel structural class of phospholipid-binding proteins. Structure, 6(10): 1255-1265.
  • Song, C., Li, G., Dai, J., Deng, H. (2021). Genome-Wide Analysis of PEBP Genes in Dendrobium huoshanense: Unveiling the Antagonistic Functions of FT/TFL1 in Flowering Time. Frontiers in Genetics, 12: 687689; DOI: 10.3389/fgene.2021.687689
  • Tamaki, S., Matsuo, S., Wong, H.L., Yokoi, S., Shimamoto, K. (2007). Hd3a protein is a mobile flowering signal in rice. Science, 316(5827): 1033-1036.
  • Tao, Y. B., Luo, L., He, L.L., Ni, J., Xu, Z.F. (2014). A promoter analysis of MOTHER OF FT AND TFL1 1 (JcMFT1), a seed-preferential gene from the biofuel plant Jatropha curcas. Journal of Plant Research, 127(4): 513-524.
  • Tranbarger, T.J., Fooyontphanich, K., Roongsattham, P., Pizot, M., Collin, M., Jantasuriyarat, C., Morcillo, F. (2017). Transcriptome analysis of cell wall and NAC domain transcription factor genes during Elaeis guineensis fruit ripening: evidence for widespread conservation within monocot and eudicot lineages. Frontiers in Plant Science, 8: 603; DOI: 10.3389/fpls.2017.00603
  • Vallee, B.S., Coadou, G., Labbe, H., Sy, D., Vovelle, F., Schoentgen, F. (2003). Peptides corresponding to the N‐and C‐terminal parts of PEBP are well‐structured in solution: new insights into their possible interaction with partners in vivo. The Journal of Peptide Research, 61(2): 47-57.
  • Wang, L., Zhu, W., Fang, L., Sun, X., Su, L., Liang, Z., Xin, H. (2014). Genome-wide identification of WRKY family genes and their response to cold stress in Vitis vinifera. BMC Plant Biology, 14(1): 1-14; DOI: 10.1186/1471-2229-14-103
  • Wang, M., Tan, Y., Cai, C., Zhang, B. (2019). Identification and expression analysis of phosphatidy ethanolamine-binding protein (PEBP) gene family in cotton. Genomics, 111(6): 1373-1380.
  • Wang, Z., Zhou, Z., Liu, Y., Liu, T., Li, Q., Ji, Y., Tian, Z. (2015). Functional evolution of phosphatidylethanolamine binding proteins in soybean and Arabidopsis. The Plant Cell, 27(2): 323-336.
  • Wickland, D.P., & Hanzawa, Y. (2015). The FLOWERING LOCUS T/TERMINAL FLOWER 1 gene family: functional evolution and molecular mechanisms. Molecular Plant, 8(7): 983-997.
  • Wilkins, M.R., Gasteiger, E., Bairoch, A. (1999). Protein identification and analysis tools in the ExPASy server. Methods in Molecular Biology, 112: 531–552.
  • Xi, W., Liu, C., Hou, X., Yu, H. (2010). MOTHER OF FT AND TFL1 regulates seed germination through a negative feedback loop modulating ABA signaling in Arabidopsis. The Plant Cell, 22(6): 1733-1748.
  • Xie, Q., Sanz-Burgos, A.P., Guo, H., García, J. A., Gutiérrez, C. (1999). GRAB proteins, novel members of the NAC domain family, isolated by their interaction with a geminivirus protein. Plant Molecular Biology, 39(4): 647-656.
  • Yoo, S.J., Chung, K.S., Jung, S.H., Yoo, S.Y., Lee, J.S., Ahn, J.H. (2010). BROTHER OF FT AND TFL1 (BFT) has TFL1‐like activity and functions redundantly with TFL1 in inflorescence meristem development in Arabidopsis. The Plant Journal, 63(2): 241-253.
  • Yu, C.S., Chen, Y.C., Lu, C.H., Hwang, J.K. (2006). Prediction of protein subcellular localization. Proteins: Structure, Function, and Bioinformatics, 64(3): 643-651.
  • Zhang, Z.L., Xie, Z., Zou, X., Casaretto, J., Ho, T.H.D., Shen, Q.J. (2004). A rice WRKY gene encodes a transcriptional repressor of the gibberellin signaling pathway in aleurone cells. Plant Physiology, 134(4): 1500-1513.
  • Zhao, S., Wei, Y., Pang, H., Xu, J., Li, Y., Zhang, H., Zhang, Y. (2020). Genome-wide identification of the PEBP genes in pears and the putative role of PbFT in flower bud differentiation. PeerJ, 8: 8928; DOI: 10.7717/peerj.8928
  • Zheng, X.M., Wu, F. Q., Zhang, X., Lin, Q.B., Wang, J., Guo, X.P., Wan, J.M. (2016). Evolution of the PEBP gene family and selective signature on FT‐like clade. Journal of Systematics and Evolution, 54(5): 502-510.
Toplam 64 adet kaynakça vardır.

Ayrıntılar

Birincil Dil İngilizce
Bölüm Araştırma Makalesi
Yazarlar

Ali Kıyak 0000-0002-6631-7778

Yayımlanma Tarihi 31 Aralık 2022
Kabul Tarihi 10 Ekim 2022
Yayımlandığı Sayı Yıl 2022

Kaynak Göster

APA Kıyak, A. (2022). Genome-Wide Characterization and In-silico Transcriptional Expression Analysis of PEBP Family in Solanum lycopersicum L. Mehmet Akif Ersoy Üniversitesi Fen Bilimleri Enstitüsü Dergisi, 13(Ek (Suppl.) 1), 300-310. https://doi.org/10.29048/makufebed.1110458