TapScan - v4


CudA	Yamada et al (2008): The CudA and ECudA DNA-binding sites contain a dyad and, consistent with a symmetrical binding site, CudA forms a homodimer in the yeast two-hybrid system. The CudA and ECudA proteins share a 120 amino acid core of homology, and clustered point mutations introduced into two highly conserved motifs within the ECudA core region decrease its specific DNA binding in vitro. This region, the presumptive DNA-binding domain, is similar in sequence to domains in two Arabidopsis proteins and one Oryza protein. Significantly, these are the only proteins in the two plant species that contain an SH2 domain. Such a structure, with a DNA-binding domain located upstream of an SH2 domain, suggests that the plant proteins are orthologous to metazoan STATs.	Lang, D; Weiche, B; Timmerhaus, G; Richardt, S; Riano-Pachon, DM; Correa, LG; Reski, R; Mueller-Roeber, B; Rensing, SA. 2010. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2: 488-503,"Yamada, Y; Wang, HY; Fukuzawa, M; Barton, GJ; Williams, JG. 2008. A new family of transcription factors. Development. 135(18):3093-101"	TF
CSD	Karlson & Imai (2003): In this paper, we report the widespread occurrence of the nucleic acid-binding cold shock domain (CSD) in plants and identify the first eukaryotic homologs that are nearly identical to bacterial cold shock proteins (CSP). Using Arabidopsis as a model system, we determined that its four unique CSD genes are differentially regulated in response to low temperature.	Coles, LS; Diamond, P; Lambrusco, L; Hunter, J; Burrows, J; Vadas, MA; Goodall, GJ. 2002. A novel mechanism of repression of the vascular endothelial growth factor promoter, by single strand DNA binding cold shock domain (Y-box) proteins in normoxic fibroblasts. Nucleic Acids Res. 30(22):4845-54,"Coles, LS; Diamond, P; Occhiodoro, F; Vadas, MA; Shannon, MF. 1996. Cold shock domain proteins repress transcription from the GM-CSF promoter. Nucleic Acids Res. 24(12):2311-7","Karlson, D; Imai, R. 2003. Conservation of the cold shock domain protein family in plants. Plant Physiol. 131(1):12-5","Karlson, D; Nakaminami, K; Toyomasu, T; Imai, R. 2002. A cold-regulated nucleic acid-binding protein of winter wheat shares a domain with bacterial cold shock proteins. J. Biol. Chem. 277(38):35248-56","Nakaminami, K; Karlson, DT; Imai, R. 2006. Functional conservation of cold shock domains in bacteria and higher plants. Proc. Natl. Acad. Sci. U.S.A. 103(26):10122-7"	TF
CRF	(Rashotte & Goertzen, 2010) specify Cytokinin Response Factors (CRFs) as a subset of the AP2/ERF TF family. These proteins can be characterized by a N-terminal CRF domain relative to the AP2 DNA binding domain and by a CRF specific C-terminal region (Powell et al., 2019; Rashotte & Goertzen, 2010). CRF TFs are included in the cytokinin signal transduction pathway in the course of leaf development (Rashotte & Goertzen, 2010). (Rashotte & Goertzen, 2010) performed database searches, motif, and phylogenetic analyses to identify CRF genes in representatives of all major land plant lineages.	Rashotte, A. M., & Goertzen, L. R. (2010). The CRF domain defines Cytokinin Response Factor proteins in plants. BMC Plant Biology, 10(1), 74. https://doi.org/10.1186/1471-2229-10-74,"Powell, R. V., Willett, C. R., Goertzen, L. R., & Rashotte, A. M. (2019). Lineage specific conservation of cis-regulatory elements in Cytokinin Response Factors. Scientific Reports, 9(1), 13387. https://doi.org/10.1038/s41598-019-49741-6"	TF
CPP	Cvitanich et al (2000): Nodulin genes are specifically expressed in the nitrogen-fixing root nodules. We have identified a novel type of DNA-binding protein (CPP1) interacting with the promoter of the soybean leghemoglobin gene Gmlbc3. The DNA-binding domain of CPP1 contains two similar Cys-rich domains with 9 and 10 Cys, respectively. Genes encoding similar domains have been identified in Arabidopsis thaliana, Caenorhabditis elegans, the mouse, and human. The domains also have some homology to a Cys-rich region present in some polycomb proteins. The cpp1 gene is induced late in nodule development and the expression is confined to the distal part of the central infected tissue of the nodule. A constitutively expressed cpp1 gene reduces the expression of a Gmlbc3 promoter-gusA reporter construct in Vicia hirsuta roots. These data therefore suggest that CPP1 might be involved in the regulation of the leghemoglobin genes in the symbiotic root nodule.	Cvitanich, C; Pallisgaard, N; Nielsen, KA; Hansen, AC; Larsen, K; Pihakaski-Maunsbach, K; Marcker, KA; Jensen, EO. 2000. CPP1, a DNA-binding protein involved in the expression of a soybean leghemoglobin c3 gene. Proc. Natl. Acad. Sci. U.S.A. 97(14):8163-8	TF
Coactivator p15	Kretzschmar et al (1994): Functional deletion analyses revealed a bipartite structure of p15 comprising an amino-terminal regulatory domain and a carboxy-terminal cryptic DNA-binding domain. We provide evidence that activity of p15 is controlled by protein kinases that target the regulatory domain. Structural and functional similarities, including sequence homology to domains essential for cofactor function, cofactor activity, promiscuity with respect to transcriptional activators, and interactions with components of the basal transcription machinery, relate this novel cellular cofactor to viral immediate-early transcriptional regulators.	Kretzschmar, M; Kaiser, K; Lottspeich, F; Meisterernst, M. 1994. A novel mediator of class II gene transcription with homology to viral immediate-early transcriptional regulators. Cell 78(3):525-34	TR
CCAAT_Dr1	Bernadt et al (2005): NF-Y is a bifunctional transcription factor capable of activating or repressing transcription. NF-Y specifically recognizes CCAAT box motifs present in many eukaryotic promoters. The mechanisms involved in regulating its activity are poorly understood.	Lang, D; Weiche, B; Timmerhaus, G; Richardt, S; Riano-Pachon, DM; Correa, LG; Reski, R; Mueller-Roeber, B; Rensing, SA. 2010. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2: 488-503,"Bernadt, CT; Nowling, T; Wiebe, MS; Rizzino, A. 2005. NF-Y behaves as a bifunctional transcription factor that can stimulate or repress the FGF-4 promoter in an enhancer-dependent manner. Gene Expr. 12(3):193-212","Li, XY; Mantovani, R; Hooft van Huijsduijnen, R; Andre, I; Benoist, C; Mathis, D. 1992. Evolutionary variation of the CCAAT-binding transcription factor NF-Y. Nucleic Acids Res. 20(5):1087-91"	TF
CBP	Lysine acetyltransferases or histone acetyltransferases (HATs) together with histone deacetylases (HDACs), are responsible for reversible acetylation of histones and are found in eukaryotes in at least four TR families, namely MYST (MOZ, Ybf2/Sas3, Sas2 and TIP60), CBP (p300/CREB-binding protein), TAFII250 (TATA-binding protein associated factor) and GNAT (GCN5-related N-terminal acetyltransferase) (Boycheva et al., 2014; Pandey, 2002; Uhrig et al., 2017). HATs function as transcriptional regulators by having different regulatory effects on gene expression in plants, animals and fungi, indicating a high conservation of these proteins and their functions (Pandey, 2002). Especially in land plants, due to their sessile lifestyle, chromatin modifications provide an important mechanism in adapting to environmental stresses (Boycheva et al., 2014). CBP proteins belonging to the HAT subfamily CBP are transcriptional coactivators that play a role in tumor suppression, in further physiological events and in signal transduction (Uhrig et al., 2017; Yuan & Giordano, 2002). These TRs can be found in all photosynthetic eukaryotes with two to five members (Uhrig et al., 2017; Yuan & Giordano, 2002).	Boycheva, I., Vassileva, V., & Iantcheva, A. (2014). Histone Acetyltransferases in Plant Development and Plasticity. Current Genomics, 15(1), 28–37. https://doi.org/10.2174/138920291501140306112742,"Pandey, R. (2002). Analysis of histone acetyltransferase and histone deacetylase families of Arabidopsis thaliana suggests functional diversification of chromatin modification among multicellular eukaryotes. Nucleic Acids Research, 30(23), 5036–5055. https://doi.org/10.1093/nar/gkf660","Uhrig, R. G., Schläpfer, P., Mehta, D., Hirsch-Hoffmann, M., & Gruissem, W. (2017). Genome-scale analysis of regulatory protein acetylation enzymes from photosynthetic eukaryotes. BMC Genomics, 18(1), 514. https://doi.org/10.1186/s12864-017-3894-0","Yuan, L. W., & Giordano, A. (2002). Acetyltransferase machinery conserved in p300/CBP-family proteins. Oncogene, 21(14), 2253–2260. https://doi.org/10.1038/sj.onc.1205283"	TR
CAMTA	Bouché et al (2002): Screening of cDNA expression libraries derived from plants exposed to stress, with 35S-labeled recombinant calmodulin as a probe, revealed a new family of proteins containing a transcription activation domain and two types of DNA-binding domains designated the CG-1 domain and the transcription factor immunoglobulin domain, ankyrin repeats, and a varying number of IQ calmodulin-binding motifs. Based on domain organization and amino acid sequence comparisons, similar proteins, with the same domain organization, were identified in the genomes of other multicellular organisms including human, Drosophila, and Caenorhabditis, whereas none were found in the complete genomes of single cell eukaryotes and prokaryotes. This family of proteins was designated calmodulin-binding transcription activators (CAMTAs).	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):21851-61	TF
C4HDZ	The homeobox TF superfamily is defined by an occurrence of the characteristic homeodomain (HD) and can be defined as pan-eukaryotic since it is found in all eukaryotic organisms (Catarino et al., 2016; Romani et al., 2018). According to different references (e.g., (Catarino et al., 2016; Mukherjee et al., 2009; Que et al., 2018)), the HD superfamily is divided into 11 subfamilies, namely BEL, DDT, HDZ, KNOX, LD, NDX, PHD, PINTOX, PLINC, SAWADEE and WOX. Interestingly, all subfamilies evolved in the common ancestor, before terrestrialization and diversification of land plants (Catarino et al., 2016). Furthermore, the broad distribution and high conservation of domains induces a common highly conserved functional role in plants and whenever members are present, also in algae (Mukherjee et al., 2009). In general, homeobox TFs show diverse functions in developmental and physiological mechanisms (Romani et al., 2018). The HD-HDZ (HDZ) subfamily can be subdivided into four classes, namely classes C1HDZ, C2HDZ, C3HDZ and C4HDZ. The members of these classes exhibit a characteristic homeodomain and an additional leucine zipper (LZ) domain (Romani et al., 2018). Furthermore, in C2HDZ proteins an aromatic, large hydrophobic, acidic context (AHA)-like motif appears (Romani et al., 2018). Also, in C2HDZ proteins there are two additional exclusive motifs, in fact the C-terminal CPSCE sequence and the N-terminal ZIBEL-like motif (Romani et al., 2018). In addition, C3HDZ proteins exhibit a unique MEKHLA domain and 3HDZ and C4HDZ proteins show START/SAD domains (Romani et al., 2018).	Catarino, B., Hetherington, A. J., Emms, D. M., Kelly, S., & Dolan, L. (2016). The Stepwise Increase in the Number of Transcription Factor Families in the Precambrian Predated the Diversification of Plants On Land. Molecular Biology and Evolution, 33(11), 2815–2819. https://doi.org/10.1093/molbev/msw155,"Romani, F., Reinheimer, R., Florent, S. N., Bowman, J. L., & Moreno, J. E. (2018). Evolutionary history of HOMEODOMAIN LEUCINE ZIPPER transcription factors during plant transition to land. New Phytologist, 219(1), 408–421. https://doi.org/10.1111/nph.15133","Mukherjee, K., Brocchieri, L., & Burglin, T. R. (2009). A Comprehensive Classification and Evolutionary Analysis of Plant Homeobox Genes. Molecular Biology and Evolution, 26(12), 2775–2794. https://doi.org/10.1093/molbev/msp201","Que, F., Wang, G.-L., Li, T., Wang, Y.-H., Xu, Z.-S., & Xiong, A.-S. (2018). Genome-wide identification, expansion, and evolution analysis of homeobox genes and their expression profiles during root development in carrot. Functional & Integrative Genomics, 18(6), 685–700. https://doi.org/10.1007/s10142-018-0624-x"	TF
C3HDZ	The homeobox TF superfamily is defined by an occurrence of the characteristic homeodomain (HD) and can be defined as pan-eukaryotic since it is found in all eukaryotic organisms (Catarino et al., 2016; Romani et al., 2018). According to different references (e.g., (Catarino et al., 2016; Mukherjee et al., 2009; Que et al., 2018)), the HD superfamily is divided into 11 subfamilies, namely BEL, DDT, HDZ, KNOX, LD, NDX, PHD, PINTOX, PLINC, SAWADEE and WOX. Interestingly, all subfamilies evolved in the common ancestor, before terrestrialization and diversification of land plants (Catarino et al., 2016). Furthermore, the broad distribution and high conservation of domains induces a common highly conserved functional role in plants and whenever members are present, also in algae (Mukherjee et al., 2009). In general, homeobox TFs show diverse functions in developmental and physiological mechanisms (Romani et al., 2018). The HD-HDZ (HDZ) subfamily can be subdivided into four classes, namely classes C1HDZ, C2HDZ, C3HDZ and C4HDZ. The members of these classes exhibit a characteristic homeodomain and an additional leucine zipper (LZ) domain (Romani et al., 2018). Furthermore, in C2HDZ proteins an aromatic, large hydrophobic, acidic context (AHA)-like motif appears (Romani et al., 2018). Also, in C2HDZ proteins there are two additional exclusive motifs, in fact the C-terminal CPSCE sequence and the N-terminal ZIBEL-like motif (Romani et al., 2018). In addition, C3HDZ proteins exhibit a unique MEKHLA domain and 3HDZ and C4HDZ proteins show START/SAD domains (Romani et al., 2018).	Catarino, B., Hetherington, A. J., Emms, D. M., Kelly, S., & Dolan, L. (2016). The Stepwise Increase in the Number of Transcription Factor Families in the Precambrian Predated the Diversification of Plants On Land. Molecular Biology and Evolution, 33(11), 2815–2819. https://doi.org/10.1093/molbev/msw155,"Romani, F., Reinheimer, R., Florent, S. N., Bowman, J. L., & Moreno, J. E. (2018). Evolutionary history of HOMEODOMAIN LEUCINE ZIPPER transcription factors during plant transition to land. New Phytologist, 219(1), 408–421. https://doi.org/10.1111/nph.15133","Mukherjee, K., Brocchieri, L., & Burglin, T. R. (2009). A Comprehensive Classification and Evolutionary Analysis of Plant Homeobox Genes. Molecular Biology and Evolution, 26(12), 2775–2794. https://doi.org/10.1093/molbev/msp201","Que, F., Wang, G.-L., Li, T., Wang, Y.-H., Xu, Z.-S., & Xiong, A.-S. (2018). Genome-wide identification, expansion, and evolution analysis of homeobox genes and their expression profiles during root development in carrot. Functional & Integrative Genomics, 18(6), 685–700. https://doi.org/10.1007/s10142-018-0624-x"	TF
C3H	Li & Thomas (1998): We used virtual subtraction, a new gene isolation strategy, to isolate several genes of interest that are expressed in Arabidopsis embryos. These genes have demonstrated biological properties or have the potential to be involved in important biological processes. One gene isolated by virtual subtraction is PEI. It encodes a protein containing a Cys3His zinc finger domain associated with a number of animal and fungal transcription factors. In situ hybridization results showed that PEI1 is expressed throughout the embryo from globular to late cotyledon stage.	Lang, D; Weiche, B; Timmerhaus, G; Richardt, S; Riano-Pachon, DM; Correa, LG; Reski, R; Mueller-Roeber, B; Rensing, SA. 2010. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2: 488-503,"Li, Z; Thomas, TL. 1998. PEI1, an embryo-specific zinc finger protein gene required for heart-stage embryo formation in Arabidopsis. Plant Cell 10(3):383-98"	TF
C2HDZ	The homeobox TF superfamily is defined by an occurrence of the characteristic homeodomain (HD) and can be defined as pan-eukaryotic since it is found in all eukaryotic organisms (Catarino et al., 2016; Romani et al., 2018). According to different references (e.g., (Catarino et al., 2016; Mukherjee et al., 2009; Que et al., 2018)), the HD superfamily is divided into 11 subfamilies, namely BEL, DDT, HDZ, KNOX, LD, NDX, PHD, PINTOX, PLINC, SAWADEE and WOX. Interestingly, all subfamilies evolved in the common ancestor, before terrestrialization and diversification of land plants (Catarino et al., 2016). Furthermore, the broad distribution and high conservation of domains induces a common highly conserved functional role in plants and whenever members are present, also in algae (Mukherjee et al., 2009). In general, homeobox TFs show diverse functions in developmental and physiological mechanisms (Romani et al., 2018). The HD-HDZ (HDZ) subfamily can be subdivided into four classes, namely classes C1HDZ, C2HDZ, C3HDZ and C4HDZ. The members of these classes exhibit a characteristic homeodomain and an additional leucine zipper (LZ) domain (Romani et al., 2018). Furthermore, in C2HDZ proteins an aromatic, large hydrophobic, acidic context (AHA)-like motif appears (Romani et al., 2018). Also, in C2HDZ proteins there are two additional exclusive motifs, in fact the C-terminal CPSCE sequence and the N-terminal ZIBEL-like motif (Romani et al., 2018). In addition, C3HDZ proteins exhibit a unique MEKHLA domain and 3HDZ and C4HDZ proteins show START/SAD domains (Romani et al., 2018).	Catarino, B., Hetherington, A. J., Emms, D. M., Kelly, S., & Dolan, L. (2016). The Stepwise Increase in the Number of Transcription Factor Families in the Precambrian Predated the Diversification of Plants On Land. Molecular Biology and Evolution, 33(11), 2815–2819. https://doi.org/10.1093/molbev/msw155,"Romani, F., Reinheimer, R., Florent, S. N., Bowman, J. L., & Moreno, J. E. (2018). Evolutionary history of HOMEODOMAIN LEUCINE ZIPPER transcription factors during plant transition to land. New Phytologist, 219(1), 408–421. https://doi.org/10.1111/nph.15133","Mukherjee, K., Brocchieri, L., & Burglin, T. R. (2009). A Comprehensive Classification and Evolutionary Analysis of Plant Homeobox Genes. Molecular Biology and Evolution, 26(12), 2775–2794. https://doi.org/10.1093/molbev/msp201","Que, F., Wang, G.-L., Li, T., Wang, Y.-H., Xu, Z.-S., & Xiong, A.-S. (2018). Genome-wide identification, expansion, and evolution analysis of homeobox genes and their expression profiles during root development in carrot. Functional & Integrative Genomics, 18(6), 685–700. https://doi.org/10.1007/s10142-018-0624-x"	TF
C2H2_IDD	The Cys2-His2 (C2H2) zinc-finger protein family is present in all eukaryotes and among the largest families of eukaryotic transcription factors (Seetharam & Stuart, 2013). One identified plant-specific subfamily of this large protein family is the Indeterminate Domain (IDD) subfamily of TFs, which was first reported in Zea mays (Coelho et al., 2018; Prochetto & Reinheimer, 2020). Proteins belonging to the IDD subfamily can be distinguished from the remaining C2H2 members by the fact that they contain a highly conserved N-terminal IDD domain in addition to further C2H2 zinc finger domains (Prochetto & Reinheimer, 2020). Among previously identified functions controlled by C2H2-IDD proteins are metabolic and development processes like flowering time, root development, leaf differentiation and the regulation of the C4 Kranz anatomy (Coelho et al., 2018; Prochetto & Reinheimer, 2020).	Seetharam, A., & Stuart, G. W. (2013). A study on the distribution of 37 well conserved families of C2H2 zinc finger genes in eukaryotes. BMC Genomics, 14(1), 420. https://doi.org/10.1186/1471-2164-14-420,"Coelho, C. P., Huang, P., Lee, D.-Y., & Brutnell, T. P. (2018). Making Roots, Shoots, and Seeds: IDD Gene Family Diversification in Plants. Trends in Plant Science, 23(1), 66–78. https://doi.org/10.1016/j.tplants.2017.09.008","Prochetto, S., & Reinheimer, R. (2020). Step by step evolution of Indeterminate Domain (IDD) transcriptional regulators: from algae to angiosperms. Annals of Botany, 126(1), 85–101. https://doi.org/10.1093/aob/mcaa052"	TF
C2H2	Englbrecht et al (2004): C2H2 zinc fingers (ZF) display a wide range of functions, from DNA or RNA binding to the involvement in protein-protein interactions. Therefore ZFPs not only act in transcriptional regulation, either directly or through site-specific modification and/or regulation of chromatin, but also participate in RNA metabolism and in other cellular functions that probably require specific protein contacts of the ZF domain.	Ciftci-Yilmaz, S; Mittler, R. 2008. The zinc finger network of plants. Cell. Mol. Life Sci. 65(7-8):1150-60,"Englbrecht, CC; Schoof, H; Böhm. S. 2004. Conservation, diversification and expansion of C2H2 zinc finger proteins in the Arabidopsis thaliana genome. BMC Genomics. 5(1):39","Iuchi, S. 2001. Three classes of C2H2 zinc finger proteins. Cell. Mol. Life Sci. 58(4):625-35","Lang, D; Weiche, B; Timmerhaus, G; Richardt, S; Riano-Pachon, DM; Correa, LG; Reski, R; Mueller-Roeber, B; Rensing, SA. 2010. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2: 488-503","Takatsuji, H. 1999. Zinc-finger proteins: the classical zinc finger emerges in contemporary plant science. Plant Mol. Biol. 39(6):1073-8"	TF
C2C2_YABBY	Bowman (2000): The establishment of abaxial-adaxial polarity in lateral organs involves factors intrinsic to the primordia and interactions with the apical meristem from which they are derived. Recently, a small plant-specific family of genes, the YABBY gene family, has been proposed to specify abaxial cell fate. Each asymmetric above-ground lateral organ expresses at least one member of the family in a polar manner, and loss- and gain-of-function studies indicate that they are sufficient to specify abaxial cell fate and that they act in both distinct and redundant manners.	Bowman, JL. 2000. The YABBY gene family and abaxial cell fate. Curr. Opin. Plant Biol. 3(1):17-22,"Golz, JF; Hudson, A. 1999. Plant development: YABBYs claw to the fore. Curr. Biol. 9(22):R861-3"	TF
C2C2_GATA	Lowry & Atchley (2000): The GATA-binding transcription factors comprise a protein family whose members contain either one or two highly conserved zinc finger DNA-binding domains. Members of this group have been identified in organisms ranging from cellular slime mold to vertebrates, including plants, fungi, nematodes, insects, and echinoderms.	Lang, D; Weiche, B; Timmerhaus, G; Richardt, S; Riano-Pachon, DM; Correa, LG; Reski, R; Mueller-Roeber, B; Rensing, SA. 2010. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2: 488-503,"Lowry, JA; Atchley, WR. 2000. Molecular evolution of the GATA family of transcription factors: conservation within the DNA-binding domain. J. Mol. Evol. 50(2):103-15","Omichinski, JG; Clore, GM; Schaad, O; Felsenfeld, G; Trainor, C; Appella, E; Stahl, SJ; Gronenborn, AM. 1993. NMR structure of a specific DNA complex of Zn-containing DNA binding domain of GATA-1. Science 261(5120):438-46","Takatsuji, H. 1998. Zinc-finger transcription factors in plants. Cell. Mol. Life Sci. 54(6):582-96"	TF
C2C2_Dof	Yanagisawa (2004): Dof (DNA-binding with one finger) domain proteins are plant-specific transcription factors with a highly conserved DNA-binding domain, which presumably includes a single C(2)-C(2) zinc finger. During the past decade, numerous Dof domain proteins have been identified in both monocots and dicots including maize, barley, wheat, rice, tobacco, Arabidopsis, pumpkin, potato, and pea. Biochemical, molecular biological and molecular genetic analyses revealed that Dof domain proteins function as a transcriptional activator or a repressor involved in diverse plant-specific biological processes. Although more physiological roles of Dof domain proteins would be elucidated in future because of numerous Dof domain proteins in plants, it is already evident that the Dof domain proteins play critical roles as transcriptional regulators in plant growth and development.	Lang, D; Weiche, B; Timmerhaus, G; Richardt, S; Riano-Pachon, DM; Correa, LG; Reski, R; Mueller-Roeber, B; Rensing, SA. 2010. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2: 488-503,"Moreno-Risueno, MA; Martínez, M; Vicente-Carbajosa, J; Carbonero, P. 2006. The family of DOF transcription factors: from green unicellular algae to vascular plants. Mol Genet Genomics","Shigyo, M; Tabei, N; Yoneyama, T; Yanagisawa, S. 2006. Evolutional processes during the formation of the plant-specific Dof transcription factor family. Plant Cell Physiol","Umemura, Y; Ishiduka, T; Yamamoto, R; Esaka, M. 2004. The Dof domain, a zinc finger DNA-binding domain conserved only in higher plants, truly functions as a Cys2/Cys2 Zn finger domain. Plant J. 37(5):741-9","Yanagisawa, S. 1997. Dof DNA-binding domains of plant transcription factors contribute to multiple protein-protein interactions. Eur. J. Biochem. 250(2):403-10","Yanagisawa, S. 2002. The Dof family of plant transcription factors. Trends Plant Sci. 7(12):555-60","Yanagisawa, S. 2004. Dof domain proteins: plant-specific transcription factors associated with diverse phenomena unique to plants. Plant Cell Physiol. 45(4):386-91","Yanagisawa, S; Schmidt, RJ. 1999. Diversity and similarity among recognition sequences of Dof transcription factors. Plant J. 17(2):209-14"	TF
C2C2_CO-like	Lagercrantz & Axelsson (2000): A family of CONSTANS LIKE genes (COLs) has recently been identified in Arabidopsis thaliana and other plant species. CONSTANS, the first isolated member, is a putative zinc finger transcription factor that promotes the induction of flowering in A. thaliana in long photoperiods.	Lagercrantz, U; Axelsson, T. 2000. Rapid evolution of the family of CONSTANS LIKE genes in plants. Mol. Biol. Evol. 17(10):1499-507,"Lang, D; Weiche, B; Timmerhaus, G; Richardt, S; Riano-Pachon, DM; Correa, LG; Reski, R; Mueller-Roeber, B; Rensing, SA. 2010. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2: 488-503"	TF
C1HDZ	The homeobox TF superfamily is defined by an occurrence of the characteristic homeodomain (HD) and can be defined as pan-eukaryotic since it is found in all eukaryotic organisms (Catarino et al., 2016; Romani et al., 2018). According to different references (e.g., (Catarino et al., 2016; Mukherjee et al., 2009; Que et al., 2018)), the HD superfamily is divided into 11 subfamilies, namely BEL, DDT, HDZ, KNOX, LD, NDX, PHD, PINTOX, PLINC, SAWADEE and WOX. Interestingly, all subfamilies evolved in the common ancestor, before terrestrialization and diversification of land plants (Catarino et al., 2016). Furthermore, the broad distribution and high conservation of domains induces a common highly conserved functional role in plants and whenever members are present, also in algae (Mukherjee et al., 2009). In general, homeobox TFs show diverse functions in developmental and physiological mechanisms (Romani et al., 2018). The HD-HDZ (HDZ) subfamily can be subdivided into four classes, namely classes C1HDZ, C2HDZ, C3HDZ and C4HDZ. The members of these classes exhibit a characteristic homeodomain and an additional leucine zipper (LZ) domain (Romani et al., 2018). Furthermore, in C2HDZ proteins an aromatic, large hydrophobic, acidic context (AHA)-like motif appears (Romani et al., 2018). Also, in C2HDZ proteins there are two additional exclusive motifs, in fact the C-terminal CPSCE sequence and the N-terminal ZIBEL-like motif (Romani et al., 2018). In addition, C3HDZ proteins exhibit a unique MEKHLA domain and 3HDZ and C4HDZ proteins show START/SAD domains (Romani et al., 2018).	Catarino, B., Hetherington, A. J., Emms, D. M., Kelly, S., & Dolan, L. (2016). The Stepwise Increase in the Number of Transcription Factor Families in the Precambrian Predated the Diversification of Plants On Land. Molecular Biology and Evolution, 33(11), 2815–2819. https://doi.org/10.1093/molbev/msw155,"Romani, F., Reinheimer, R., Florent, S. N., Bowman, J. L., & Moreno, J. E. (2018). Evolutionary history of HOMEODOMAIN LEUCINE ZIPPER transcription factors during plant transition to land. New Phytologist, 219(1), 408–421. https://doi.org/10.1111/nph.15133","Mukherjee, K., Brocchieri, L., & Burglin, T. R. (2009). A Comprehensive Classification and Evolutionary Analysis of Plant Homeobox Genes. Molecular Biology and Evolution, 26(12), 2775–2794. https://doi.org/10.1093/molbev/msp201","Que, F., Wang, G.-L., Li, T., Wang, Y.-H., Xu, Z.-S., & Xiong, A.-S. (2018). Genome-wide identification, expansion, and evolution analysis of homeobox genes and their expression profiles during root development in carrot. Functional & Integrative Genomics, 18(6), 685–700. https://doi.org/10.1007/s10142-018-0624-x"	TF
bZIP	Jakoby et al (2002): In plants, basic region/leucine zipper motif (bZIP) transcription factors regulate processes including pathogen defence, light and stress signalling, seed maturation and flower development.	Corrêa, LG; Riaño-Pachón, DM; Schrago, CG; dos Santos, RV; Mueller-Roeber, B; Vincentz, M. 2008. The role of bZIP transcription factors in green plant evolution: adaptive features emerging from four founder genes. PLoS ONE 3(8):e2944,"Foster, R; Izawa, T; Chua, NH. 1994. Plant bZIP proteins gather at ACGT elements. FASEB J. 8(2):192-200","Hurst, HC. 1995. Transcription factors 1: bZIP proteins. Protein Profile 2(2):101-68","Jakoby, M; Weisshaar, B; Dröge-Laser, W; Vicente-Carbajosa, J; Tiedemann, J; Kroj, T; Parcy, F; bZIP Research Group. 2002. bZIP transcription factors in Arabidopsis. Trends Plant Sci. 7(3):106-11","Landschulz, WH; Johnson, PF; McKnight, SL. 1988. The leucine zipper: a hypothetical structure common to a new class of DNA binding proteins. Science 240(4860):1759-64","Vinson, C; Acharya, A; Taparowsky, EJ. 2006. Deciphering B-ZIP transcription factor interactions in vitro and in vivo. Biochim. Biophys. Acta 1759(1-2):4-12"	TF
Showing results 101 to 120 on 136 ‹ 1 2 3 4 5 6 7 ›

CudA

Yamada et al (2008): The CudA and ECudA DNA-binding sites contain a dyad and, consistent with a symmetrical binding site, CudA forms a homodimer in the yeast two-hybrid system. The CudA and ECudA proteins share a 120 amino acid core of homology, and clustered point mutations introduced into two highly conserved motifs within the ECudA core region decrease its specific DNA binding in vitro. This region, the presumptive DNA-binding domain, is similar in sequence to domains in two Arabidopsis proteins and one Oryza protein. Significantly, these are the only proteins in the two plant species that contain an SH2 domain. Such a structure, with a DNA-binding domain located upstream of an SH2 domain, suggests that the plant proteins are orthologous to metazoan STATs.

Lang, D; Weiche, B; Timmerhaus, G; Richardt, S; Riano-Pachon, DM; Correa, LG; Reski, R; Mueller-Roeber, B; Rensing, SA. 2010. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2: 488-503,"Yamada, Y; Wang, HY; Fukuzawa, M; Barton, GJ; Williams, JG. 2008. A new family of transcription factors. Development. 135(18):3093-101"

TF

CSD

Karlson & Imai (2003): In this paper, we report the widespread occurrence of the nucleic acid-binding cold shock domain (CSD) in plants and identify the first eukaryotic homologs that are nearly identical to bacterial cold shock proteins (CSP). Using Arabidopsis as a model system, we determined that its four unique CSD genes are differentially regulated in response to low temperature.

Coles, LS; Diamond, P; Lambrusco, L; Hunter, J; Burrows, J; Vadas, MA; Goodall, GJ. 2002. A novel mechanism of repression of the vascular endothelial growth factor promoter, by single strand DNA binding cold shock domain (Y-box) proteins in normoxic fibroblasts. Nucleic Acids Res. 30(22):4845-54,"Coles, LS; Diamond, P; Occhiodoro, F; Vadas, MA; Shannon, MF. 1996. Cold shock domain proteins repress transcription from the GM-CSF promoter. Nucleic Acids Res. 24(12):2311-7","Karlson, D; Imai, R. 2003. Conservation of the cold shock domain protein family in plants. Plant Physiol. 131(1):12-5","Karlson, D; Nakaminami, K; Toyomasu, T; Imai, R. 2002. A cold-regulated nucleic acid-binding protein of winter wheat shares a domain with bacterial cold shock proteins. J. Biol. Chem. 277(38):35248-56","Nakaminami, K; Karlson, DT; Imai, R. 2006. Functional conservation of cold shock domains in bacteria and higher plants. Proc. Natl. Acad. Sci. U.S.A. 103(26):10122-7"

TF

CRF

(Rashotte & Goertzen, 2010) specify Cytokinin Response Factors (CRFs) as a subset of the AP2/ERF TF family. These proteins can be characterized by a N-terminal CRF domain relative to the AP2 DNA binding domain and by a CRF specific C-terminal region (Powell et al., 2019; Rashotte & Goertzen, 2010). CRF TFs are included in the cytokinin signal transduction pathway in the course of leaf development (Rashotte & Goertzen, 2010). (Rashotte & Goertzen, 2010) performed database searches, motif, and phylogenetic analyses to identify CRF genes in representatives of all major land plant lineages.

Rashotte, A. M., & Goertzen, L. R. (2010). The CRF domain defines Cytokinin Response Factor proteins in plants. BMC Plant Biology, 10(1), 74. https://doi.org/10.1186/1471-2229-10-74,"Powell, R. V., Willett, C. R., Goertzen, L. R., & Rashotte, A. M. (2019). Lineage specific conservation of cis-regulatory elements in Cytokinin Response Factors. Scientific Reports, 9(1), 13387. https://doi.org/10.1038/s41598-019-49741-6"

TF

CPP

Cvitanich et al (2000): Nodulin genes are specifically expressed in the nitrogen-fixing root nodules. We have identified a novel type of DNA-binding protein (CPP1) interacting with the promoter of the soybean leghemoglobin gene Gmlbc3. The DNA-binding domain of CPP1 contains two similar Cys-rich domains with 9 and 10 Cys, respectively. Genes encoding similar domains have been identified in Arabidopsis thaliana, Caenorhabditis elegans, the mouse, and human. The domains also have some homology to a Cys-rich region present in some polycomb proteins. The cpp1 gene is induced late in nodule development and the expression is confined to the distal part of the central infected tissue of the nodule. A constitutively expressed cpp1 gene reduces the expression of a Gmlbc3 promoter-gusA reporter construct in Vicia hirsuta roots. These data therefore suggest that CPP1 might be involved in the regulation of the leghemoglobin genes in the symbiotic root nodule.

Cvitanich, C; Pallisgaard, N; Nielsen, KA; Hansen, AC; Larsen, K; Pihakaski-Maunsbach, K; Marcker, KA; Jensen, EO. 2000. CPP1, a DNA-binding protein involved in the expression of a soybean leghemoglobin c3 gene. Proc. Natl. Acad. Sci. U.S.A. 97(14):8163-8

TF

Coactivator p15

Kretzschmar et al (1994): Functional deletion analyses revealed a bipartite structure of p15 comprising an amino-terminal regulatory domain and a carboxy-terminal cryptic DNA-binding domain. We provide evidence that activity of p15 is controlled by protein kinases that target the regulatory domain. Structural and functional similarities, including sequence homology to domains essential for cofactor function, cofactor activity, promiscuity with respect to transcriptional activators, and interactions with components of the basal transcription machinery, relate this novel cellular cofactor to viral immediate-early transcriptional regulators.

Kretzschmar, M; Kaiser, K; Lottspeich, F; Meisterernst, M. 1994. A novel mediator of class II gene transcription with homology to viral immediate-early transcriptional regulators. Cell 78(3):525-34

TR

CCAAT_Dr1

Bernadt et al (2005): NF-Y is a bifunctional transcription factor capable of activating or repressing transcription. NF-Y specifically recognizes CCAAT box motifs present in many eukaryotic promoters. The mechanisms involved in regulating its activity are poorly understood.

Lang, D; Weiche, B; Timmerhaus, G; Richardt, S; Riano-Pachon, DM; Correa, LG; Reski, R; Mueller-Roeber, B; Rensing, SA. 2010. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2: 488-503,"Bernadt, CT; Nowling, T; Wiebe, MS; Rizzino, A. 2005. NF-Y behaves as a bifunctional transcription factor that can stimulate or repress the FGF-4 promoter in an enhancer-dependent manner. Gene Expr. 12(3):193-212","Li, XY; Mantovani, R; Hooft van Huijsduijnen, R; Andre, I; Benoist, C; Mathis, D. 1992. Evolutionary variation of the CCAAT-binding transcription factor NF-Y. Nucleic Acids Res. 20(5):1087-91"

TF

CBP

Lysine acetyltransferases or histone acetyltransferases (HATs) together with histone deacetylases (HDACs), are responsible for reversible acetylation of histones and are found in eukaryotes in at least four TR families, namely MYST (MOZ, Ybf2/Sas3, Sas2 and TIP60), CBP (p300/CREB-binding protein), TAFII250 (TATA-binding protein associated factor) and GNAT (GCN5-related N-terminal acetyltransferase) (Boycheva et al., 2014; Pandey, 2002; Uhrig et al., 2017). HATs function as transcriptional regulators by having different regulatory effects on gene expression in plants, animals and fungi, indicating a high conservation of these proteins and their functions (Pandey, 2002). Especially in land plants, due to their sessile lifestyle, chromatin modifications provide an important mechanism in adapting to environmental stresses (Boycheva et al., 2014). CBP proteins belonging to the HAT subfamily CBP are transcriptional coactivators that play a role in tumor suppression, in further physiological events and in signal transduction (Uhrig et al., 2017; Yuan & Giordano, 2002). These TRs can be found in all photosynthetic eukaryotes with two to five members (Uhrig et al., 2017; Yuan & Giordano, 2002).

Boycheva, I., Vassileva, V., & Iantcheva, A. (2014). Histone Acetyltransferases in Plant Development and Plasticity. Current Genomics, 15(1), 28–37. https://doi.org/10.2174/138920291501140306112742,"Pandey, R. (2002). Analysis of histone acetyltransferase and histone deacetylase families of Arabidopsis thaliana suggests functional diversification of chromatin modification among multicellular eukaryotes. Nucleic Acids Research, 30(23), 5036–5055. https://doi.org/10.1093/nar/gkf660","Uhrig, R. G., Schläpfer, P., Mehta, D., Hirsch-Hoffmann, M., & Gruissem, W. (2017). Genome-scale analysis of regulatory protein acetylation enzymes from photosynthetic eukaryotes. BMC Genomics, 18(1), 514. https://doi.org/10.1186/s12864-017-3894-0","Yuan, L. W., & Giordano, A. (2002). Acetyltransferase machinery conserved in p300/CBP-family proteins. Oncogene, 21(14), 2253–2260. https://doi.org/10.1038/sj.onc.1205283"

TR

CAMTA

Bouché et al (2002): Screening of cDNA expression libraries derived from plants exposed to stress, with 35S-labeled recombinant calmodulin as a probe, revealed a new family of proteins containing a transcription activation domain and two types of DNA-binding domains designated the CG-1 domain and the transcription factor immunoglobulin domain, ankyrin repeats, and a varying number of IQ calmodulin-binding motifs. Based on domain organization and amino acid sequence comparisons, similar proteins, with the same domain organization, were identified in the genomes of other multicellular organisms including human, Drosophila, and Caenorhabditis, whereas none were found in the complete genomes of single cell eukaryotes and prokaryotes. This family of proteins was designated calmodulin-binding transcription activators (CAMTAs).

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):21851-61

TF

C4HDZ

The homeobox TF superfamily is defined by an occurrence of the characteristic homeodomain (HD) and can be defined as pan-eukaryotic since it is found in all eukaryotic organisms (Catarino et al., 2016; Romani et al., 2018). According to different references (e.g., (Catarino et al., 2016; Mukherjee et al., 2009; Que et al., 2018)), the HD superfamily is divided into 11 subfamilies, namely BEL, DDT, HDZ, KNOX, LD, NDX, PHD, PINTOX, PLINC, SAWADEE and WOX. Interestingly, all subfamilies evolved in the common ancestor, before terrestrialization and diversification of land plants (Catarino et al., 2016). Furthermore, the broad distribution and high conservation of domains induces a common highly conserved functional role in plants and whenever members are present, also in algae (Mukherjee et al., 2009). In general, homeobox TFs show diverse functions in developmental and physiological mechanisms (Romani et al., 2018). The HD-HDZ (HDZ) subfamily can be subdivided into four classes, namely classes C1HDZ, C2HDZ, C3HDZ and C4HDZ. The members of these classes exhibit a characteristic homeodomain and an additional leucine zipper (LZ) domain (Romani et al., 2018). Furthermore, in C2HDZ proteins an aromatic, large hydrophobic, acidic context (AHA)-like motif appears (Romani et al., 2018). Also, in C2HDZ proteins there are two additional exclusive motifs, in fact the C-terminal CPSCE sequence and the N-terminal ZIBEL-like motif (Romani et al., 2018). In addition, C3HDZ proteins exhibit a unique MEKHLA domain and 3HDZ and C4HDZ proteins show START/SAD domains (Romani et al., 2018).

Catarino, B., Hetherington, A. J., Emms, D. M., Kelly, S., & Dolan, L. (2016). The Stepwise Increase in the Number of Transcription Factor Families in the Precambrian Predated the Diversification of Plants On Land. Molecular Biology and Evolution, 33(11), 2815–2819. https://doi.org/10.1093/molbev/msw155,"Romani, F., Reinheimer, R., Florent, S. N., Bowman, J. L., & Moreno, J. E. (2018). Evolutionary history of HOMEODOMAIN LEUCINE ZIPPER transcription factors during plant transition to land. New Phytologist, 219(1), 408–421. https://doi.org/10.1111/nph.15133","Mukherjee, K., Brocchieri, L., & Burglin, T. R. (2009). A Comprehensive Classification and Evolutionary Analysis of Plant Homeobox Genes. Molecular Biology and Evolution, 26(12), 2775–2794. https://doi.org/10.1093/molbev/msp201","Que, F., Wang, G.-L., Li, T., Wang, Y.-H., Xu, Z.-S., & Xiong, A.-S. (2018). Genome-wide identification, expansion, and evolution analysis of homeobox genes and their expression profiles during root development in carrot. Functional & Integrative Genomics, 18(6), 685–700. https://doi.org/10.1007/s10142-018-0624-x"

TF

C3HDZ

The homeobox TF superfamily is defined by an occurrence of the characteristic homeodomain (HD) and can be defined as pan-eukaryotic since it is found in all eukaryotic organisms (Catarino et al., 2016; Romani et al., 2018). According to different references (e.g., (Catarino et al., 2016; Mukherjee et al., 2009; Que et al., 2018)), the HD superfamily is divided into 11 subfamilies, namely BEL, DDT, HDZ, KNOX, LD, NDX, PHD, PINTOX, PLINC, SAWADEE and WOX. Interestingly, all subfamilies evolved in the common ancestor, before terrestrialization and diversification of land plants (Catarino et al., 2016). Furthermore, the broad distribution and high conservation of domains induces a common highly conserved functional role in plants and whenever members are present, also in algae (Mukherjee et al., 2009). In general, homeobox TFs show diverse functions in developmental and physiological mechanisms (Romani et al., 2018). The HD-HDZ (HDZ) subfamily can be subdivided into four classes, namely classes C1HDZ, C2HDZ, C3HDZ and C4HDZ. The members of these classes exhibit a characteristic homeodomain and an additional leucine zipper (LZ) domain (Romani et al., 2018). Furthermore, in C2HDZ proteins an aromatic, large hydrophobic, acidic context (AHA)-like motif appears (Romani et al., 2018). Also, in C2HDZ proteins there are two additional exclusive motifs, in fact the C-terminal CPSCE sequence and the N-terminal ZIBEL-like motif (Romani et al., 2018). In addition, C3HDZ proteins exhibit a unique MEKHLA domain and 3HDZ and C4HDZ proteins show START/SAD domains (Romani et al., 2018).

Catarino, B., Hetherington, A. J., Emms, D. M., Kelly, S., & Dolan, L. (2016). The Stepwise Increase in the Number of Transcription Factor Families in the Precambrian Predated the Diversification of Plants On Land. Molecular Biology and Evolution, 33(11), 2815–2819. https://doi.org/10.1093/molbev/msw155,"Romani, F., Reinheimer, R., Florent, S. N., Bowman, J. L., & Moreno, J. E. (2018). Evolutionary history of HOMEODOMAIN LEUCINE ZIPPER transcription factors during plant transition to land. New Phytologist, 219(1), 408–421. https://doi.org/10.1111/nph.15133","Mukherjee, K., Brocchieri, L., & Burglin, T. R. (2009). A Comprehensive Classification and Evolutionary Analysis of Plant Homeobox Genes. Molecular Biology and Evolution, 26(12), 2775–2794. https://doi.org/10.1093/molbev/msp201","Que, F., Wang, G.-L., Li, T., Wang, Y.-H., Xu, Z.-S., & Xiong, A.-S. (2018). Genome-wide identification, expansion, and evolution analysis of homeobox genes and their expression profiles during root development in carrot. Functional & Integrative Genomics, 18(6), 685–700. https://doi.org/10.1007/s10142-018-0624-x"

TF

C3H

Li & Thomas (1998): We used virtual subtraction, a new gene isolation strategy, to isolate several genes of interest that are expressed in Arabidopsis embryos. These genes have demonstrated biological properties or have the potential to be involved in important biological processes. One gene isolated by virtual subtraction is PEI. It encodes a protein containing a Cys3His zinc finger domain associated with a number of animal and fungal transcription factors. In situ hybridization results showed that PEI1 is expressed throughout the embryo from globular to late cotyledon stage.

Lang, D; Weiche, B; Timmerhaus, G; Richardt, S; Riano-Pachon, DM; Correa, LG; Reski, R; Mueller-Roeber, B; Rensing, SA. 2010. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2: 488-503,"Li, Z; Thomas, TL. 1998. PEI1, an embryo-specific zinc finger protein gene required for heart-stage embryo formation in Arabidopsis. Plant Cell 10(3):383-98"

TF

C2HDZ

The homeobox TF superfamily is defined by an occurrence of the characteristic homeodomain (HD) and can be defined as pan-eukaryotic since it is found in all eukaryotic organisms (Catarino et al., 2016; Romani et al., 2018). According to different references (e.g., (Catarino et al., 2016; Mukherjee et al., 2009; Que et al., 2018)), the HD superfamily is divided into 11 subfamilies, namely BEL, DDT, HDZ, KNOX, LD, NDX, PHD, PINTOX, PLINC, SAWADEE and WOX. Interestingly, all subfamilies evolved in the common ancestor, before terrestrialization and diversification of land plants (Catarino et al., 2016). Furthermore, the broad distribution and high conservation of domains induces a common highly conserved functional role in plants and whenever members are present, also in algae (Mukherjee et al., 2009). In general, homeobox TFs show diverse functions in developmental and physiological mechanisms (Romani et al., 2018). The HD-HDZ (HDZ) subfamily can be subdivided into four classes, namely classes C1HDZ, C2HDZ, C3HDZ and C4HDZ. The members of these classes exhibit a characteristic homeodomain and an additional leucine zipper (LZ) domain (Romani et al., 2018). Furthermore, in C2HDZ proteins an aromatic, large hydrophobic, acidic context (AHA)-like motif appears (Romani et al., 2018). Also, in C2HDZ proteins there are two additional exclusive motifs, in fact the C-terminal CPSCE sequence and the N-terminal ZIBEL-like motif (Romani et al., 2018). In addition, C3HDZ proteins exhibit a unique MEKHLA domain and 3HDZ and C4HDZ proteins show START/SAD domains (Romani et al., 2018).

Catarino, B., Hetherington, A. J., Emms, D. M., Kelly, S., & Dolan, L. (2016). The Stepwise Increase in the Number of Transcription Factor Families in the Precambrian Predated the Diversification of Plants On Land. Molecular Biology and Evolution, 33(11), 2815–2819. https://doi.org/10.1093/molbev/msw155,"Romani, F., Reinheimer, R., Florent, S. N., Bowman, J. L., & Moreno, J. E. (2018). Evolutionary history of HOMEODOMAIN LEUCINE ZIPPER transcription factors during plant transition to land. New Phytologist, 219(1), 408–421. https://doi.org/10.1111/nph.15133","Mukherjee, K., Brocchieri, L., & Burglin, T. R. (2009). A Comprehensive Classification and Evolutionary Analysis of Plant Homeobox Genes. Molecular Biology and Evolution, 26(12), 2775–2794. https://doi.org/10.1093/molbev/msp201","Que, F., Wang, G.-L., Li, T., Wang, Y.-H., Xu, Z.-S., & Xiong, A.-S. (2018). Genome-wide identification, expansion, and evolution analysis of homeobox genes and their expression profiles during root development in carrot. Functional & Integrative Genomics, 18(6), 685–700. https://doi.org/10.1007/s10142-018-0624-x"

TF

C2H2_IDD

The Cys2-His2 (C2H2) zinc-finger protein family is present in all eukaryotes and among the largest families of eukaryotic transcription factors (Seetharam & Stuart, 2013). One identified plant-specific subfamily of this large protein family is the Indeterminate Domain (IDD) subfamily of TFs, which was first reported in Zea mays (Coelho et al., 2018; Prochetto & Reinheimer, 2020). Proteins belonging to the IDD subfamily can be distinguished from the remaining C2H2 members by the fact that they contain a highly conserved N-terminal IDD domain in addition to further C2H2 zinc finger domains (Prochetto & Reinheimer, 2020). Among previously identified functions controlled by C2H2-IDD proteins are metabolic and development processes like flowering time, root development, leaf differentiation and the regulation of the C4 Kranz anatomy (Coelho et al., 2018; Prochetto & Reinheimer, 2020).

Seetharam, A., & Stuart, G. W. (2013). A study on the distribution of 37 well conserved families of C2H2 zinc finger genes in eukaryotes. BMC Genomics, 14(1), 420. https://doi.org/10.1186/1471-2164-14-420,"Coelho, C. P., Huang, P., Lee, D.-Y., & Brutnell, T. P. (2018). Making Roots, Shoots, and Seeds: IDD Gene Family Diversification in Plants. Trends in Plant Science, 23(1), 66–78. https://doi.org/10.1016/j.tplants.2017.09.008","Prochetto, S., & Reinheimer, R. (2020). Step by step evolution of Indeterminate Domain (IDD) transcriptional regulators: from algae to angiosperms. Annals of Botany, 126(1), 85–101. https://doi.org/10.1093/aob/mcaa052"

TF

C2H2

Englbrecht et al (2004): C2H2 zinc fingers (ZF) display a wide range of functions, from DNA or RNA binding to the involvement in protein-protein interactions. Therefore ZFPs not only act in transcriptional regulation, either directly or through site-specific modification and/or regulation of chromatin, but also participate in RNA metabolism and in other cellular functions that probably require specific protein contacts of the ZF domain.

Ciftci-Yilmaz, S; Mittler, R. 2008. The zinc finger network of plants. Cell. Mol. Life Sci. 65(7-8):1150-60,"Englbrecht, CC; Schoof, H; Böhm. S. 2004. Conservation, diversification and expansion of C2H2 zinc finger proteins in the Arabidopsis thaliana genome. BMC Genomics. 5(1):39","Iuchi, S. 2001. Three classes of C2H2 zinc finger proteins. Cell. Mol. Life Sci. 58(4):625-35","Lang, D; Weiche, B; Timmerhaus, G; Richardt, S; Riano-Pachon, DM; Correa, LG; Reski, R; Mueller-Roeber, B; Rensing, SA. 2010. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2: 488-503","Takatsuji, H. 1999. Zinc-finger proteins: the classical zinc finger emerges in contemporary plant science. Plant Mol. Biol. 39(6):1073-8"

TF

C2C2_YABBY

Bowman (2000): The establishment of abaxial-adaxial polarity in lateral organs involves factors intrinsic to the primordia and interactions with the apical meristem from which they are derived. Recently, a small plant-specific family of genes, the YABBY gene family, has been proposed to specify abaxial cell fate. Each asymmetric above-ground lateral organ expresses at least one member of the family in a polar manner, and loss- and gain-of-function studies indicate that they are sufficient to specify abaxial cell fate and that they act in both distinct and redundant manners.

Bowman, JL. 2000. The YABBY gene family and abaxial cell fate. Curr. Opin. Plant Biol. 3(1):17-22,"Golz, JF; Hudson, A. 1999. Plant development: YABBYs claw to the fore. Curr. Biol. 9(22):R861-3"

TF

C2C2_GATA

Lowry & Atchley (2000): The GATA-binding transcription factors comprise a protein family whose members contain either one or two highly conserved zinc finger DNA-binding domains. Members of this group have been identified in organisms ranging from cellular slime mold to vertebrates, including plants, fungi, nematodes, insects, and echinoderms.

Lang, D; Weiche, B; Timmerhaus, G; Richardt, S; Riano-Pachon, DM; Correa, LG; Reski, R; Mueller-Roeber, B; Rensing, SA. 2010. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2: 488-503,"Lowry, JA; Atchley, WR. 2000. Molecular evolution of the GATA family of transcription factors: conservation within the DNA-binding domain. J. Mol. Evol. 50(2):103-15","Omichinski, JG; Clore, GM; Schaad, O; Felsenfeld, G; Trainor, C; Appella, E; Stahl, SJ; Gronenborn, AM. 1993. NMR structure of a specific DNA complex of Zn-containing DNA binding domain of GATA-1. Science 261(5120):438-46","Takatsuji, H. 1998. Zinc-finger transcription factors in plants. Cell. Mol. Life Sci. 54(6):582-96"

TF

C2C2_Dof

Yanagisawa (2004): Dof (DNA-binding with one finger) domain proteins are plant-specific transcription factors with a highly conserved DNA-binding domain, which presumably includes a single C(2)-C(2) zinc finger. During the past decade, numerous Dof domain proteins have been identified in both monocots and dicots including maize, barley, wheat, rice, tobacco, Arabidopsis, pumpkin, potato, and pea. Biochemical, molecular biological and molecular genetic analyses revealed that Dof domain proteins function as a transcriptional activator or a repressor involved in diverse plant-specific biological processes. Although more physiological roles of Dof domain proteins would be elucidated in future because of numerous Dof domain proteins in plants, it is already evident that the Dof domain proteins play critical roles as transcriptional regulators in plant growth and development.

Lang, D; Weiche, B; Timmerhaus, G; Richardt, S; Riano-Pachon, DM; Correa, LG; Reski, R; Mueller-Roeber, B; Rensing, SA. 2010. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2: 488-503,"Moreno-Risueno, MA; Martínez, M; Vicente-Carbajosa, J; Carbonero, P. 2006. The family of DOF transcription factors: from green unicellular algae to vascular plants. Mol Genet Genomics","Shigyo, M; Tabei, N; Yoneyama, T; Yanagisawa, S. 2006. Evolutional processes during the formation of the plant-specific Dof transcription factor family. Plant Cell Physiol","Umemura, Y; Ishiduka, T; Yamamoto, R; Esaka, M. 2004. The Dof domain, a zinc finger DNA-binding domain conserved only in higher plants, truly functions as a Cys2/Cys2 Zn finger domain. Plant J. 37(5):741-9","Yanagisawa, S. 1997. Dof DNA-binding domains of plant transcription factors contribute to multiple protein-protein interactions. Eur. J. Biochem. 250(2):403-10","Yanagisawa, S. 2002. The Dof family of plant transcription factors. Trends Plant Sci. 7(12):555-60","Yanagisawa, S. 2004. Dof domain proteins: plant-specific transcription factors associated with diverse phenomena unique to plants. Plant Cell Physiol. 45(4):386-91","Yanagisawa, S; Schmidt, RJ. 1999. Diversity and similarity among recognition sequences of Dof transcription factors. Plant J. 17(2):209-14"

TF

C2C2_CO-like

Lagercrantz & Axelsson (2000): A family of CONSTANS LIKE genes (COLs) has recently been identified in Arabidopsis thaliana and other plant species. CONSTANS, the first isolated member, is a putative zinc finger transcription factor that promotes the induction of flowering in A. thaliana in long photoperiods.

Lagercrantz, U; Axelsson, T. 2000. Rapid evolution of the family of CONSTANS LIKE genes in plants. Mol. Biol. Evol. 17(10):1499-507,"Lang, D; Weiche, B; Timmerhaus, G; Richardt, S; Riano-Pachon, DM; Correa, LG; Reski, R; Mueller-Roeber, B; Rensing, SA. 2010. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2: 488-503"

TF

C1HDZ

The homeobox TF superfamily is defined by an occurrence of the characteristic homeodomain (HD) and can be defined as pan-eukaryotic since it is found in all eukaryotic organisms (Catarino et al., 2016; Romani et al., 2018). According to different references (e.g., (Catarino et al., 2016; Mukherjee et al., 2009; Que et al., 2018)), the HD superfamily is divided into 11 subfamilies, namely BEL, DDT, HDZ, KNOX, LD, NDX, PHD, PINTOX, PLINC, SAWADEE and WOX. Interestingly, all subfamilies evolved in the common ancestor, before terrestrialization and diversification of land plants (Catarino et al., 2016). Furthermore, the broad distribution and high conservation of domains induces a common highly conserved functional role in plants and whenever members are present, also in algae (Mukherjee et al., 2009). In general, homeobox TFs show diverse functions in developmental and physiological mechanisms (Romani et al., 2018). The HD-HDZ (HDZ) subfamily can be subdivided into four classes, namely classes C1HDZ, C2HDZ, C3HDZ and C4HDZ. The members of these classes exhibit a characteristic homeodomain and an additional leucine zipper (LZ) domain (Romani et al., 2018). Furthermore, in C2HDZ proteins an aromatic, large hydrophobic, acidic context (AHA)-like motif appears (Romani et al., 2018). Also, in C2HDZ proteins there are two additional exclusive motifs, in fact the C-terminal CPSCE sequence and the N-terminal ZIBEL-like motif (Romani et al., 2018). In addition, C3HDZ proteins exhibit a unique MEKHLA domain and 3HDZ and C4HDZ proteins show START/SAD domains (Romani et al., 2018).

Catarino, B., Hetherington, A. J., Emms, D. M., Kelly, S., & Dolan, L. (2016). The Stepwise Increase in the Number of Transcription Factor Families in the Precambrian Predated the Diversification of Plants On Land. Molecular Biology and Evolution, 33(11), 2815–2819. https://doi.org/10.1093/molbev/msw155,"Romani, F., Reinheimer, R., Florent, S. N., Bowman, J. L., & Moreno, J. E. (2018). Evolutionary history of HOMEODOMAIN LEUCINE ZIPPER transcription factors during plant transition to land. New Phytologist, 219(1), 408–421. https://doi.org/10.1111/nph.15133","Mukherjee, K., Brocchieri, L., & Burglin, T. R. (2009). A Comprehensive Classification and Evolutionary Analysis of Plant Homeobox Genes. Molecular Biology and Evolution, 26(12), 2775–2794. https://doi.org/10.1093/molbev/msp201","Que, F., Wang, G.-L., Li, T., Wang, Y.-H., Xu, Z.-S., & Xiong, A.-S. (2018). Genome-wide identification, expansion, and evolution analysis of homeobox genes and their expression profiles during root development in carrot. Functional & Integrative Genomics, 18(6), 685–700. https://doi.org/10.1007/s10142-018-0624-x"

TF

bZIP

Jakoby et al (2002): In plants, basic region/leucine zipper motif (bZIP) transcription factors regulate processes including pathogen defence, light and stress signalling, seed maturation and flower development.

Corrêa, LG; Riaño-Pachón, DM; Schrago, CG; dos Santos, RV; Mueller-Roeber, B; Vincentz, M. 2008. The role of bZIP transcription factors in green plant evolution: adaptive features emerging from four founder genes. PLoS ONE 3(8):e2944,"Foster, R; Izawa, T; Chua, NH. 1994. Plant bZIP proteins gather at ACGT elements. FASEB J. 8(2):192-200","Hurst, HC. 1995. Transcription factors 1: bZIP proteins. Protein Profile 2(2):101-68","Jakoby, M; Weisshaar, B; Dröge-Laser, W; Vicente-Carbajosa, J; Tiedemann, J; Kroj, T; Parcy, F; bZIP Research Group. 2002. bZIP transcription factors in Arabidopsis. Trends Plant Sci. 7(3):106-11","Landschulz, WH; Johnson, PF; McKnight, SL. 1988. The leucine zipper: a hypothetical structure common to a new class of DNA binding proteins. Science 240(4860):1759-64","Vinson, C; Acharya, A; Taparowsky, EJ. 2006. Deciphering B-ZIP transcription factor interactions in vitro and in vivo. Biochim. Biophys. Acta 1759(1-2):4-12"

TF