TapScan - v4


ZPR	ZPR proteins are a group of transcriptional regulators that were derived by a duplication event of a C3HDZ protein in the common ancestor of ferns and seed plants and subsequent degenerative mutations. They are involved in the regulation of C3HDZ and in the regulation of plant form and growth (Floyd et al., 2014). Furthermore, ZPR regulators display the important role of gene duplications in the complexity of land plant developmental complexity (Floyd et al., 2014).	Floyd, S. K., Ryan, J. G., Conway, S. J., Brenner, E., Burris, K. P., Burris, J. N., Chen, T., Edger, P. P., Graham, S. W., Leebens-Mack, J. H., Pires, J. C., Rothfels, C. J., Sigel, E. M., Stevenson, D. W., Neal Stewart, C., Wong, G. K.-S., & Bowman, J. L. (2014). Origin of a novel regulatory module by duplication and degeneration of an ancient plant transcription factor. Molecular Phylogenetics and Evolution, 81, 159–173. https://doi.org/10.1016/j.ympev.2014.06.017	TR
Zn_clus	Pan & Coleman (1990): The DNA-binding domain of the transcription factor GAL4, consisting of the 62 N-terminal residues and denoted GAL4(62), contains a Cys-Xaa2-Cys-Xaa6-Cys-Xaa6-Cys-Xaa2-Cys-Xaa6+ ++-Cys motif, which has been shown previously to bind two Zn(II) or Cd(II) ions. Binding of Zn(II) or Cd(II) is essential for the recognition by GAL4 of the specific palindromic DNA sequence to which it binds upstream of genes for galactose-metabolizing enzymes, the UASG sequence. On the basis of the 113Cd NMR chemical shifts of the two bound 113Cd(II) ions, we propose a binuclear cluster model for this Zn(II)-binding subdomain. 1H-113Cd heteronuclear multiple-quantum NMR spectroscopy and phase-sensitive double-quantum filtered 1H correlation spectroscopy of the 112Cd(II)- and 113Cd(II)-substituted GAL4(62) derivatives provide direct evidence that the two bound 113Cd(II) ions are coordinated only by the six cysteine residues, two of which form bridging ligands between the two 113Cd(II) ions. The latter can be identified from the pattern of 1H-113Cd J coupling. Thus a binuclear metal ion cluster rather than a "zinc finger" is formed by the six cysteine residues of the GAL4 DNA-binding domain. This model can be directly applied to eight other fungal transcription factors which have been shown to contain similarly spaced Cys6 clusters. 1H NMR spectra of apo-GAL4(62*) suggest conformational fluctuation of the metal-binding subdomain upon removal of Zn(II) or Cd(II). Both Cd(II)2- and Zn(II)2-containing species of GAL4 can be formed, and the similar 1H NMR spectra suggest similar conformations.	Pan, T; Coleman, JE. 1990. GAL4 transcription factor is not a zinc finger" but forms a Zn(II)2Cys6 binuclear cluster. Proc. Natl. Acad. Sci. U.S.A. 87(6):2077-81"	TF
Zinc finger, ZPR1	<a target="_blank" class="awithout" href="http://pfam.xfam.org/family/PF03367">PFAM</a> (0): The zinc-finger protein ZPR1 is localised to the cytoplasm in quiescent cells; in proliferating cells treated with EGF or with other mitogens it accumulates in the nucleolus. Upon stimulation by EGF, ZPR1 directly binds the eukaryotic translation elongation factor-1alpha (eEF-1alpha) to form ZPR1/eEF-1alpha complexes. These move into the nucleus, localising particularly at the nucleolus. ZPR1 is thought to be involved in pre-ribosomal RNA expression. The ZPR1 domain consists of an elongation initiation factor 2-like zinc finger and a double-stranded beta helix with a helical hairpin insertion.	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,"Gangwani, L1; Mikrut, M; Galcheva-Gargova, Z; Davis, RJ. 1998. Interaction of ZPR1 with translation elongation factor-1alpha in proliferating cells. J Cell Biol 143(6):1471-84","Galcheva-Gargova, Z; Gangwani, L; Konstantinov, KN; Mikrut, M; Theroux, SJ; Enoch, T; Davis RJ. 1998. The cytoplasmic zinc finger protein ZPR1 accumulates in the nucleolus of proliferating cells. Mol Biol Cell 9(10):2963-71"	TR
Zinc finger, MIZ type	<a target="_blank" class="awithout" href="http://pfam.xfam.org/family/PF02891">PFAM</a> (0): The MIZ-type zinc finger domain is a sequence specific DNA binding domain that is part of proteins like Miz1 that can function as a positive-acting transcription factor. The name MIZ is derived from Msx-interacting-zinc finger.	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
Zinc finger, AN1 and A20 type	<a target="_blank" class="awithout" href="http://pfam.xfam.org/family/PF01428">PFAM</a> (0): The AN1-type zinc finger domain has a dimetal (zinc)-bound alpha/beta fold. Certain stress-associated proteins contain the AN1 domain, often in combination with A20 zinc finger domains or C2H2 domains.	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,"Vij, S; Tyagi, AK. 2006. Genome-wide analysis of the stress associated protein (SAP) gene family containing A20/AN1 zinc-finger(s) in rice and their phylogenetic relationship with Arabidopsis. Mol Genet Genomics 276(6):565-75"	TR
WRKY	Wu et al (2005): WRKY transcription factors, originally isolated from plants contain one or two conserved WRKY domains, about 60 amino acid residues with the WRKYGQK sequence followed by a C2H2 or C2HC zinc finger motif. Evidence is accumulating to suggest that the WRKY proteins play significant roles in responses to biotic and abiotic stresses, and in development. In this research, we identified 102 putative WRKY genes from the rice genome and compared them with those from Arabidopsis. The WRKY genes from rice and Arabidopsis were divided into three groups with several subgroups on the basis of phylogenies and the basic structure of the WRKY domains (WDs). The phylogenetic trees generated from the WDs and the genes indicate that the WRKY gene family arose during evolution through duplication and that the dramatic amplification of rice WRKY genes in group III is due to tandem and segmental gene duplication compared with those of Arabidopsis. The result suggests that some of the rice WRKY genes in group III are evolutionarily more active than those in Arabidopsis, and may have specific roles in monocotyledonous plants. Further, it was possible to identify the presence of WRKY-like genes in protists (Giardia lamblia and Dictyostelium discoideum) and green algae Chlamydomonas reinhardtii through database research, demonstrating the ancient origin of the gene family. The results obtained by alignments of the WDs from different species and other analysis imply that domain gain and loss is a divergent force for expansion of the WRKY gene family, and that a rapid amplification of the WRKY genes predate the divergence of monocots and dicots. On the basis of these results, we believe that genes encoding a single WD may have been derived from the C-terminal WD of the genes harboring two WDs. The conserved intron splicing positions in the WDs of higher plants offer clues about WRKY gene evolution, annotation, and classification.	Eulgem, T; Rushton, PJ; Robatzek, S; Somssich, IE. 2000. The WRKY superfamily of plant transcription factors. Trends Plant Sci. 5(5):199-206,"Ulker, B; Somssich, IE. 2004. WRKY transcription factors: from DNA binding towards biological function. Curr. Opin. Plant Biol. 7(5):491-8","Wu, KL; Guo, ZJ; Wang, HH; Li, J. 2005. The WRKY family of transcription factors in rice and Arabidopsis and their origins. DNA Res. 12(1):9-26","Zhang, Y; Wang, L. 2005. The WRKY transcription factor superfamily: its origin in eukaryotes and expansion in plants. BMC Evol. Biol. 5(1):1"	TF
Whirly	Desveaux et al (2002): The single-stranded DNA (ssDNA) binding subunit of the plant transcription factor p24 is representative of a novel family of ubiquitous plant-specific proteins that we refer to as the Whirly family because of their quaternary structure.	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,"Desveaux, D; Allard, J; Brisson, N; Sygusch, J. 2002. A new family of plant transcription factors displays a novel ssDNA-binding surface. Nat Struct Biol. 9(7):512-7"	TF
VOZ	Mitsuda et al (2004): A 38-bp pollen-specific cis-acting region of the AVP1 gene is involved in the expression of the Arabidopsis thaliana V-PPase during pollen development. Here, we report the isolation and structural characterization of AtVOZ1 and AtVOZ2, novel transcription factors that bind to the 38-bp cis-acting region of A. thaliana V-PPase gene, AVP1. AtVOZ1 and AtVOZ2 show 53% amino acid sequence similarity. Homologs of AtVOZ1 and AtVOZ2 are found in various vascular plants as well as a moss, Physcomitrella patens. Promoter-beta-glucuronidase reporter analysis shows that AtVOZ1 is specifically expressed in the phloem tissue and AtVOZ2 is strongly expressed in the root. In vivo transient effector-reporter analysis in A. thaliana suspension-cultured cells demonstrates that AtVOZ1 and AtVOZ2 function as transcriptional activators in the Arabidopsis cell. Two conserved regions termed Domain-A and Domain-B were identified from an alignment of AtVOZ proteins and their homologs of O. sativa and P. patens. AtVOZ2 binds as a dimer to the specific palindromic sequence, GCGTNx7ACGC, with Domain-B, which is comprised of a functional novel zinc coordinating motif and a conserved basic region. Domain-B is shown to function as both the DNA-binding and the dimerization domains of AtVOZ2. From highly the conservative nature among all identified VOZ proteins, we conclude that Domain-B is responsible for the DNA binding and dimerization of all VOZ-family proteins and designate it as the VOZ-domain.	Mitsuda, N; Hisabori, T; Takeyasu, K; Sato, MH. 2004. VOZ; isolation and characterization of novel vascular plant transcription factors with a one-zinc finger from Arabidopsis thaliana. Plant Cell Physiol. 45(7):845-54	TF
VARL	Duncan et al (2007): Chlamydomonas reinhardtii, Volvox carteri, and their relatives in the family Volvocaceae provide an excellent opportunity for studying how multicellular organisms with differentiated cell types evolved from unicellular ancestors. While C. reinhardtii is unicellular, V. carteri is multicellular with two cell types, one of which resembles C. reinhardtii cytologically but is terminally differentiated. Maintenance of this "somatic cell" fate is controlled by RegA, a putative transcription factor. We recently showed that RegA shares a conserved region with several predicted V. carteri and C. reinhardtii proteins and that this region, the VARL domain, is likely to include a DNA-binding SAND domain. As the next step toward understanding the evolutionary origins of the regA gene, we analyzed the genome sequences of C. reinhardtii and V. carteri to identify additional genes with the potential to encode VARL domain proteins. Here we report that the VARL gene family, which consists of 12 members in C. reinhardtii and 14 in V. carteri, has experienced a complex evolutionary history in which members of the family have been both gained and lost over time, although several pairs of potentially orthologous genes can still be identified. We find that regA is part of a tandem array of four VARL genes in V. carteri but that a similar array is absent in C. reinhardtii. Most importantly, our phylogenetic analysis suggests that a proto-regA gene was present in a common unicellular ancestor of V. carteri and C. reinhardtii and that this gene was lost in the latter lineage.	Duncan, L; Nishii, I; Harryman, A; Buckley, S; Howard, A; Friedman, NR; Miller, SM. 2007. The VARL gene family and the evolutionary origins of the master cell-type regulatory gene, regA, in Volvox carteri. J. Mol. Evol. 65(1):1-11	TF
ULT	Carles et al (2005): The higher-plant shoot apical meristem is a dynamic structure continuously producing cells that become incorporated into new leaves, stems and flowers. The maintenance of a constant flow of cells through the meristem depends on coordination of two antagonistic processes: self-renewal of the stem cell population and initiation of the lateral organs. This coordination is stringently controlled by gene networks that contain both positive and negative components. We have previously defined the ULTRAPETALA1 (ULT1) gene as a key negative regulator of cell accumulation in Arabidopsis shoot and floral meristems, because mutations in ULT1 cause the enlargement of inflorescence and floral meristems, the production of supernumerary flowers and floral organs, and a delay in floral meristem termination. Here, we show that ULT1 negatively regulates the size of the WUSCHEL (WUS)-expressing organizing center in inflorescence meristems. We have cloned the ULT1 gene and find that it encodes a small protein containing a B-box-like motif and a SAND domain, a DNA-binding motif previously reported only in animal transcription factors. ULT1 and its Arabidopsis paralog ULT2 define a novel small gene family in plants. ULT1 and ULT2 are expressed coordinately in embryonic shoot apical meristems, in inflorescence and floral meristems, and in developing stamens, carpels and ovules. Additionally, ULT1 is expressed in vegetative meristems and leaf primordia. ULT2 protein can compensate for mutant ULT1 protein when overexpressed in an ult1 background, indicating that the two genes may regulate a common set of targets during plant development. Downregulation of both ULT genes can lead to shoot apical meristem arrest shortly after germination, revealing a requirement for ULT activity in early development.	Carles, CC; Choffnes-Inada, D; Reville, K; Lertpiriyapong, K; Fletcher, JC. 2005. ULTRAPETALA1 encodes a SAND domain putative transcriptional regulator that controls shoot and floral meristem activity in Arabidopsis. Development 132(5):897-911	TF
TUB	Lai et al (2004): In mammals, TUBBY-like proteins play an important role in maintenance and function of neuronal cells during postdifferentiation and development. We have identified a TUBBY-like protein gene family with 11 members in Arabidopsis, named AtTLP1-11. Although seven of the AtTLP genes are located on chromosome I, no local tandem repeats or gene clusters are identified. Except for AtTLP4, reverse transcription-PCR analysis indicates that all these genes are expressed in various organs in 6-week-old Arabidopsis. AtTLP1, 2, 3, 6, 7, 9, 10, and 11 are expressed ubiquitously in all the organs tested, but the expression of AtTLP5 and 8 shows dramatic organ specificity. These 11 family members share 30% to 80% amino acid similarities across their conserved C-terminal tubby domains. Unlike the highly diverse N-terminal region of animal TUBBY-like proteins, all AtTLP members except AtTLP8 contain a conserved F-box domain (51-57 residues). The interaction between AtTLP9 and ASK1 (Arabidopsis Skp1-like 1) is confirmed via yeast (Saccharomyces cerevisiae) two-hybrid assays. Abscisic acid (ABA)-insensitive phenotypes are observed for two independent AtTLP9 mutant lines, whereas transgenic plants overexpressing AtTLP9 are hypersensitive to ABA. These results suggest that AtTLP9 may participate in the ABA signaling pathway.	Boggon, TJ; Shan, WS; Santagata, S; Myers, SC; Shapiro, L. 1999. Implication of tubby proteins as transcription factors by structure-based functional analysis. Science 286(5447):2119-25,"Lai, CP; Lee, CL; Chen, PH; Wu, SH; Yang, CC; Shaw, JF. 2004. Molecular analyses of the Arabidopsis TUBBY-like protein gene family. Plant Physiol. 134(4):1586-97","Santagata, S; Boggon, TJ; Baird, CL; Gomez, CA; Zhao, J; Shan, WS; Myszka, DG; Shapiro, L. 2001. G-protein signaling through tubby proteins. Science 292(5524):2041-50"	TF
Trihelix	Kaplan-Levy et al (2012): GT factors are the founding members of the trihelix transcription factor family. Genomic studies have revealed 30 members of this family in Arabidopsis and 31 in rice, falling into five clades. Newly discovered functions involve responses to salt and pathogen stresses, the development of perianth organs, trichomes, stomata and the seed abscission layer, and the regulation of late embryogenesis.	Kaplan-Levy, RN; Brewer, PB; Quon, T; Smyth, DR. 2012. The trihelix family of transcription factors--light, stress and development. Trends Plant Sci. 17(3):163-71,"Nagano, Y. 2000. Several features of the GT-factor trihelix domain resemble those of the Myb DNA-binding domain. Plant Physiol. 124(2):491-4","Nagano, Y; Inaba, T; Furuhashi, H; Sasaki, Y. 2001. Trihelix DNA-binding protein with specificities for two distinct cis-elements: both important for light down-regulated and dark-inducible gene expression in higher plants. J. Biol. Chem. 276(25):22238-43","Smalle, J; Kurepa, J; Haegman, M; Gielen, J; Van Montagu, M; Van Der Straeten, D. 1998. The trihelix DNA-binding motif in higher plants is not restricted to the transcription factors GT-1 and GT-2. Proc. Natl. Acad. Sci. U.S.A. 95(6):3318-22","Zhou, DX. 1999. Regulatory mechanism of plant gene transcription by GT-elements and GT-factors. Trends Plant Sci 4(6):210-214","Kaplan-Levy, RN; Brewer, PB; Quon, T; Smyth, DR. 2012. The trihelix family of transcription factors--light, stress and development. Trends Plant Sci. 17(3):163-71","Nagano, Y. 2000. Several features of the GT-factor trihelix domain resemble those of the Myb DNA-binding domain. Plant Physiol. 124(2):491-4","Nagano, Y; Inaba, T; Furuhashi, H; Sasaki, Y. 2001. Trihelix DNA-binding protein with specificities for two distinct cis-elements: both important for light down-regulated and dark-inducible gene expression in higher plants. J. Biol. Chem. 276(25):22238-43","Smalle, J; Kurepa, J; Haegman, M; Gielen, J; Van Montagu, M; Van Der Straeten, D. 1998. The trihelix DNA-binding motif in higher plants is not restricted to the transcription factors GT-1 and GT-2. Proc. Natl. Acad. Sci. U.S.A. 95(6):3318-22","Zhou, DX. 1999. Regulatory mechanism of plant gene transcription by GT-elements and GT-factors. Trends Plant Sci 4(6):210-214"	TF
TRAF	Stogios et al (2005): The BTB domain (also known as the POZ domain) is a versatile protein-protein interaction motif that participates in a wide range of cellular functions, including transcriptional regulation, cytoskeleton dynamics, ion channel assembly and gating, and targeting proteins for ubiquitination. Several BTB domain structures have been experimentally determined, revealing a highly conserved core structure. The BTB domain is typically found as a single copy in proteins that contain only one or two other types of domain, and this defines the BTB-zinc finger (BTB-ZF), BTB-BACK-kelch (BBK), voltage-gated potassium channel T1 (T1-Kv), MATH-BTB, BTB-NPH3 and BTB-BACK-PHR (BBP) families of proteins, among others. BTB-ZF proteins are also known as the POK (POZ and Krüppel zinc finger) proteins. Many members of this large family have been characterized as important transcriptional factors, and several are implicated in development and cancer, most notably BCL6, leukemia/lymphoma related factor (LRF)/Pokemon, PLZF, hypermethylated in cancer (HIC)1 and Myc interacting zinc finger (MIZ)1.	Deweindt, C; Albagli, O; Bernardin, F; Dhordain, P; Quief, S; Lantoine, D; Kerckaert, JP; Leprince, D. 1995. The LAZ3/BCL6 oncogene encodes a sequence-specific transcriptional inhibitor: a novel function for the BTB/POZ domain as an autonomous repressing domain. Cell Growth Differ. 6(12):1495-503,"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","Stogios, PJ; Downs, GS; Jauhal, JJ; Nandra, SK; Privé, GG. 2005. Sequence and structural analysis of BTB domain proteins. Genome Biol. 6(10):R82"	TR
tify	Nishii et al (2000): By differential screening of an arrayed normalized cDNA library from the inflorescence apex in Arabidopsis, a cDNA clone having a deduced amino acid sequence with a motif for a zinc finger was isolated as one of the genes expressed specifically in the reproductive phase. The deduced protein has a modular structure with a putative single C2-C2 zinc-finger motif distantly related to a GATA-1-type finger, a basic region with a sequence resembling a nuclear localization signal, and an acidic region. The gene seemed to have been formed by the exon-shuffling during its molecular evolution, since individual domains are encoded by discrete exons. RNA gel blot analysis showed its expression in shoot apex and flowers in the reproductive phase. The gene was named ZIM for Zinc-finger protein expressed in Inflorescence Meristem. The nuclear localization of ZIM was detected using GFP as a reporter. These results suggest that ZIM is a putative transcription factor involved in inflorescence and flower 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,"Nishii, A; Takemura, M; Fujita, H; Shikata, M; Yokota, A; Kohchi, T. 2000. Characterization of a novel gene encoding a putative single zinc-finger protein, ZIM, expressed during the reproductive phase in Arabidopsis thaliana. Biosci. Biotechnol. Biochem. 64(7):1402-9","Vanholme, B; Grunewald, W; Bateman, A; Kohchi, T; Gheysen, G. 2007. The tify family previously known as ZIM. Trends Plant Sci. 12(6):239-44"	TF
TFb2	<a target="_blank" class="awithout" href="https://www.ebi.ac.uk/interpro/entry/IPR004598">InterPro</a> (0): This domain represents the p52/Tfb2 subunit in the TFIIH complex, which is not only required for transcription but also plays a central role in DNA repair.	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	TR
TAZ	Du & Poovaiah (2004): A novel CaM-binding protein was isolated through protein-protein interaction based screening of an Arabidopsis cDNA expression library using a 35S calmodulin (CaM) probe. There are four additional homologs in the Arabidopsis genome with similar structures: a BTB domain in the N-terminus and a Zf-TAZ domain in the C-terminus. Hence, they were designated as AtBT1-5 (Arabidopsis thaliana BTB and TAZ domain protein). CaM-binding experiments revealed that all five AtBTs are CaM-binding proteins, and their CaM-binding domains were mapped to the C-terminus. AtBT homologs are also present in rice, but are not present in human, animal, yeast or other organisms, suggesting that the BTB and TAZ domain proteins are plant-specific. The AtBT1-smGFP fusion protein expressed in tobacco BY-2 cells showed that AtBT1 targets the nucleus. Yeast two-hybrid screening using an AtBT1 fragment as bait identified two interacting proteins (AtBET10 and AtBET9) belonging to the family of fsh/Ring3 class transcription regulators. The BTB domain of the AtBTs is required for the interaction, and this protein-protein interaction was confirmed by GST pull-down. AtBET10 also interacts with AtBT2 and AtBT4, and exhibited a transcriptional activation function in yeast cells. AtBTs exhibit varying responses to different stress stimuli, but all five genes responded rapidly to H2O2 and salicylic acid (SA) treatments. These results suggest that AtBTs play a role in transcriptional regulation, and signal molecules such as Ca2+, H2O2, and SA affect transcriptional machinery by altering the expression and conformation of AtBTs which interact with transcriptional activators such as AtBET10.	Du, L; Poovaiah, BW. 2004. A novel family of Ca2+/calmodulin-binding proteins involved in transcriptional regulation: interaction with fsh/Ring3 class transcription activators. Plant Mol. Biol. 54(4):549-69	TR
TAFII250	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). In non-photosynthetic eukaryotes, monocots, and dicots an average of one to two members of the HAT subfamily TAFII250 can be found (Uhrig et al., 2017). Furthermore, they are also present in early photosynthetic eukaryotes as red algae (Uhrig et al., 2017). Functions such as participation in light response and the phytochrome pathway could be observed (Boycheva et al., 2014).	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"	TR
SWI/SNF_SWI3	Da et al (2006): The SWIRM domain is a module found in the Swi3 and Rsc8 subunits of SWI/SNF-family chromatin remodeling complexes, and the Ada2 and BHC110/LSD1 subunits of chromatin modification complexes. Here we report the high-resolution crystal structure of the SWIRM domain from Swi3 and characterize the in vitro and in vivo function of the SWIRM domains from Saccharomyces cerevisiae Swi3 and Rsc8. The Swi3 SWIRM forms a four-helix bundle containing a pseudo 2-fold axis and a helix-turn-helix motif commonly found in DNA-binding proteins. We show that the Swi3 SWIRM binds free DNA and mononucleosomes with high and comparable affinity and that a subset of Swi3 substitution mutants that display growth defects in vivo also show impaired DNA-binding activity in vitro, consistent with a nucleosome targeting function of this domain. Genetic and biochemical studies also reveal that the Rsc8 and Swi3 SWIRM domains are essential for the proper assembly and in vivo functions of their respective complexes. Together, these studies identify the SWIRM domain as an essential multifunctional module for the regulation of gene expression.	Da, G; Lenkart, J; Zhao, K; Shiekhattar, R; Cairns, BR; Marmorstein, R. 2006. Structure and function of the SWIRM domain, a conserved protein module found in chromatin regulatory complexes. Proc. Natl. Acad. Sci. U.S.A. 103(7):2057-62	TR
SWI/SNF_SNF2	Eisen et al (1995): The SNF2 family of proteins includes representatives from a variety of species with roles in cellular processes such as transcriptional regulation (e.g. MOT1, SNF2 and BRM), maintenance of chromosome stability during mitosis (e.g. lodestar) and various aspects of processing of DNA damage, including nucleotide excision repair (e.g. RAD16 and ERCC6), recombinational pathways (e.g. RAD54) and post-replication daughter strand gap repair (e.g. RAD5). This family also includes many proteins with no known function. To better characterize this family of proteins we have used molecular phylogenetic techniques to infer evolutionary relationships among the family members. We have divided the SNF2 family into multiple subfamilies, each of which represents what we propose to be a functionally and evolutionarily distinct group. We have then used the subfamily structure to predict the functions of some of the uncharacterized proteins in the SNF2 family. We discuss possible implications of this evolutionary analysis on the general properties and evolution of the SNF2 family.	Bork, P; Koonin, EV. 1993. An expanding family of helicases within the 'DEAD/H' superfamily. Nucleic Acids Res. 21(3):751-2,"Eisen, JA; Sweder, KS; Hanawalt, PC. 1995. Evolution of the SNF2 family of proteins: subfamilies with distinct sequences and functions. Nucleic Acids Res. 23(14):2715-23","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"	TR
SWI/SNF_BAF60b	Kussie et al (1996): The MDM2 oncoprotein is a cellular inhibitor of the p53 tumor suppressor in that it can bind the transactivation domain of p53 and downregulate its ability to activate transcription. In certain cancers, MDM2 amplification is a common event and contributes to the inactivation of p53. The crystal structure of the 109-residue amino-terminal domain of MDM2 bound to a 15-residue transactivation domain peptide of p53 revealed that MDM2 has a deep hydrophobic cleft on which the p53 peptide binds as an amphipathic alpha helix. The interface relies on the steric complementarity between the MDM2 cleft and the hydrophobic face of the p53 alpha helix and, in particular, on a triad of p53 amino acids-Phe19, Trp23, and Leu26-which insert deep into the MDM2 cleft. These same p53 residues are also involved in transactivation, supporting the hypothesis that MDM2 inactivates p53 by concealing its transactivation domain. The structure also suggests that the amphipathic alpha helix may be a common structural motif in the binding of a diverse family of transactivation factors to the TATA-binding protein-associated factors.	Bennett-Lovsey, R; Hart, SE; Shirai, H; Mizuguchi, K. 2002. The SWIB and the MDM2 domains are homologous and share a common fold. Bioinformatics 18(4):626-30,"Kussie, PH; Gorina, S; Marechal, V; Elenbaas, B; Moreau, J; Levine, AJ; Pavletich, NP. 1996. Structure of the MDM2 oncoprotein bound to the p53 tumor suppressor transactivation domain. Science 274(5289):948-53"	TR
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ZPR

ZPR proteins are a group of transcriptional regulators that were derived by a duplication event of a C3HDZ protein in the common ancestor of ferns and seed plants and subsequent degenerative mutations. They are involved in the regulation of C3HDZ and in the regulation of plant form and growth (Floyd et al., 2014). Furthermore, ZPR regulators display the important role of gene duplications in the complexity of land plant developmental complexity (Floyd et al., 2014).

Floyd, S. K., Ryan, J. G., Conway, S. J., Brenner, E., Burris, K. P., Burris, J. N., Chen, T., Edger, P. P., Graham, S. W., Leebens-Mack, J. H., Pires, J. C., Rothfels, C. J., Sigel, E. M., Stevenson, D. W., Neal Stewart, C., Wong, G. K.-S., & Bowman, J. L. (2014). Origin of a novel regulatory module by duplication and degeneration of an ancient plant transcription factor. Molecular Phylogenetics and Evolution, 81, 159–173. https://doi.org/10.1016/j.ympev.2014.06.017

TR

Zn_clus

Pan & Coleman (1990): The DNA-binding domain of the transcription factor GAL4, consisting of the 62 N-terminal residues and denoted GAL4(62*), contains a Cys-Xaa2-Cys-Xaa6-Cys-Xaa6-Cys-Xaa2-Cys-Xaa6+ ++-Cys motif, which has been shown previously to bind two Zn(II) or Cd(II) ions. Binding of Zn(II) or Cd(II) is essential for the recognition by GAL4 of the specific palindromic DNA sequence to which it binds upstream of genes for galactose-metabolizing enzymes, the UASG sequence. On the basis of the 113Cd NMR chemical shifts of the two bound 113Cd(II) ions, we propose a binuclear cluster model for this Zn(II)-binding subdomain. 1H-113Cd heteronuclear multiple-quantum NMR spectroscopy and phase-sensitive double-quantum filtered 1H correlation spectroscopy of the 112Cd(II)- and 113Cd(II)-substituted GAL4(62*) derivatives provide direct evidence that the two bound 113Cd(II) ions are coordinated only by the six cysteine residues, two of which form bridging ligands between the two 113Cd(II) ions. The latter can be identified from the pattern of 1H-113Cd J coupling. Thus a binuclear metal ion cluster rather than a "zinc finger" is formed by the six cysteine residues of the GAL4 DNA-binding domain. This model can be directly applied to eight other fungal transcription factors which have been shown to contain similarly spaced Cys6 clusters. 1H NMR spectra of apo-GAL4(62*) suggest conformational fluctuation of the metal-binding subdomain upon removal of Zn(II) or Cd(II). Both Cd(II)2- and Zn(II)2-containing species of GAL4 can be formed, and the similar 1H NMR spectra suggest similar conformations.

Pan, T; Coleman, JE. 1990. GAL4 transcription factor is not a zinc finger" but forms a Zn(II)2Cys6 binuclear cluster. Proc. Natl. Acad. Sci. U.S.A. 87(6):2077-81"

TF

Zinc finger, ZPR1

<a target="_blank" class="awithout" href="http://pfam.xfam.org/family/PF03367">PFAM</a> (0): The zinc-finger protein ZPR1 is localised to the cytoplasm in quiescent cells; in proliferating cells treated with EGF or with other mitogens it accumulates in the nucleolus. Upon stimulation by EGF, ZPR1 directly binds the eukaryotic translation elongation factor-1alpha (eEF-1alpha) to form ZPR1/eEF-1alpha complexes. These move into the nucleus, localising particularly at the nucleolus. ZPR1 is thought to be involved in pre-ribosomal RNA expression. The ZPR1 domain consists of an elongation initiation factor 2-like zinc finger and a double-stranded beta helix with a helical hairpin insertion.

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,"Gangwani, L1; Mikrut, M; Galcheva-Gargova, Z; Davis, RJ. 1998. Interaction of ZPR1 with translation elongation factor-1alpha in proliferating cells. J Cell Biol 143(6):1471-84","Galcheva-Gargova, Z; Gangwani, L; Konstantinov, KN; Mikrut, M; Theroux, SJ; Enoch, T; Davis RJ. 1998. The cytoplasmic zinc finger protein ZPR1 accumulates in the nucleolus of proliferating cells. Mol Biol Cell 9(10):2963-71"

TR

Zinc finger, MIZ type

<a target="_blank" class="awithout" href="http://pfam.xfam.org/family/PF02891">PFAM</a> (0): The MIZ-type zinc finger domain is a sequence specific DNA binding domain that is part of proteins like Miz1 that can function as a positive-acting transcription factor. The name MIZ is derived from Msx-interacting-zinc finger.

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

Zinc finger, AN1 and A20 type

<a target="_blank" class="awithout" href="http://pfam.xfam.org/family/PF01428">PFAM</a> (0): The AN1-type zinc finger domain has a dimetal (zinc)-bound alpha/beta fold. Certain stress-associated proteins contain the AN1 domain, often in combination with A20 zinc finger domains or C2H2 domains.

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,"Vij, S; Tyagi, AK. 2006. Genome-wide analysis of the stress associated protein (SAP) gene family containing A20/AN1 zinc-finger(s) in rice and their phylogenetic relationship with Arabidopsis. Mol Genet Genomics 276(6):565-75"

TR

WRKY

Wu et al (2005): WRKY transcription factors, originally isolated from plants contain one or two conserved WRKY domains, about 60 amino acid residues with the WRKYGQK sequence followed by a C2H2 or C2HC zinc finger motif. Evidence is accumulating to suggest that the WRKY proteins play significant roles in responses to biotic and abiotic stresses, and in development. In this research, we identified 102 putative WRKY genes from the rice genome and compared them with those from Arabidopsis. The WRKY genes from rice and Arabidopsis were divided into three groups with several subgroups on the basis of phylogenies and the basic structure of the WRKY domains (WDs). The phylogenetic trees generated from the WDs and the genes indicate that the WRKY gene family arose during evolution through duplication and that the dramatic amplification of rice WRKY genes in group III is due to tandem and segmental gene duplication compared with those of Arabidopsis. The result suggests that some of the rice WRKY genes in group III are evolutionarily more active than those in Arabidopsis, and may have specific roles in monocotyledonous plants. Further, it was possible to identify the presence of WRKY-like genes in protists (Giardia lamblia and Dictyostelium discoideum) and green algae Chlamydomonas reinhardtii through database research, demonstrating the ancient origin of the gene family. The results obtained by alignments of the WDs from different species and other analysis imply that domain gain and loss is a divergent force for expansion of the WRKY gene family, and that a rapid amplification of the WRKY genes predate the divergence of monocots and dicots. On the basis of these results, we believe that genes encoding a single WD may have been derived from the C-terminal WD of the genes harboring two WDs. The conserved intron splicing positions in the WDs of higher plants offer clues about WRKY gene evolution, annotation, and classification.

Eulgem, T; Rushton, PJ; Robatzek, S; Somssich, IE. 2000. The WRKY superfamily of plant transcription factors. Trends Plant Sci. 5(5):199-206,"Ulker, B; Somssich, IE. 2004. WRKY transcription factors: from DNA binding towards biological function. Curr. Opin. Plant Biol. 7(5):491-8","Wu, KL; Guo, ZJ; Wang, HH; Li, J. 2005. The WRKY family of transcription factors in rice and Arabidopsis and their origins. DNA Res. 12(1):9-26","Zhang, Y; Wang, L. 2005. The WRKY transcription factor superfamily: its origin in eukaryotes and expansion in plants. BMC Evol. Biol. 5(1):1"

TF

Whirly

Desveaux et al (2002): The single-stranded DNA (ssDNA) binding subunit of the plant transcription factor p24 is representative of a novel family of ubiquitous plant-specific proteins that we refer to as the Whirly family because of their quaternary structure.

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,"Desveaux, D; Allard, J; Brisson, N; Sygusch, J. 2002. A new family of plant transcription factors displays a novel ssDNA-binding surface. Nat Struct Biol. 9(7):512-7"

TF

VOZ

Mitsuda et al (2004): A 38-bp pollen-specific cis-acting region of the AVP1 gene is involved in the expression of the Arabidopsis thaliana V-PPase during pollen development. Here, we report the isolation and structural characterization of AtVOZ1 and AtVOZ2, novel transcription factors that bind to the 38-bp cis-acting region of A. thaliana V-PPase gene, AVP1. AtVOZ1 and AtVOZ2 show 53% amino acid sequence similarity. Homologs of AtVOZ1 and AtVOZ2 are found in various vascular plants as well as a moss, Physcomitrella patens. Promoter-beta-glucuronidase reporter analysis shows that AtVOZ1 is specifically expressed in the phloem tissue and AtVOZ2 is strongly expressed in the root. In vivo transient effector-reporter analysis in A. thaliana suspension-cultured cells demonstrates that AtVOZ1 and AtVOZ2 function as transcriptional activators in the Arabidopsis cell. Two conserved regions termed Domain-A and Domain-B were identified from an alignment of AtVOZ proteins and their homologs of O. sativa and P. patens. AtVOZ2 binds as a dimer to the specific palindromic sequence, GCGTNx7ACGC, with Domain-B, which is comprised of a functional novel zinc coordinating motif and a conserved basic region. Domain-B is shown to function as both the DNA-binding and the dimerization domains of AtVOZ2. From highly the conservative nature among all identified VOZ proteins, we conclude that Domain-B is responsible for the DNA binding and dimerization of all VOZ-family proteins and designate it as the VOZ-domain.

Mitsuda, N; Hisabori, T; Takeyasu, K; Sato, MH. 2004. VOZ; isolation and characterization of novel vascular plant transcription factors with a one-zinc finger from Arabidopsis thaliana. Plant Cell Physiol. 45(7):845-54

TF

VARL

Duncan et al (2007): Chlamydomonas reinhardtii, Volvox carteri, and their relatives in the family Volvocaceae provide an excellent opportunity for studying how multicellular organisms with differentiated cell types evolved from unicellular ancestors. While C. reinhardtii is unicellular, V. carteri is multicellular with two cell types, one of which resembles C. reinhardtii cytologically but is terminally differentiated. Maintenance of this "somatic cell" fate is controlled by RegA, a putative transcription factor. We recently showed that RegA shares a conserved region with several predicted V. carteri and C. reinhardtii proteins and that this region, the VARL domain, is likely to include a DNA-binding SAND domain. As the next step toward understanding the evolutionary origins of the regA gene, we analyzed the genome sequences of C. reinhardtii and V. carteri to identify additional genes with the potential to encode VARL domain proteins. Here we report that the VARL gene family, which consists of 12 members in C. reinhardtii and 14 in V. carteri, has experienced a complex evolutionary history in which members of the family have been both gained and lost over time, although several pairs of potentially orthologous genes can still be identified. We find that regA is part of a tandem array of four VARL genes in V. carteri but that a similar array is absent in C. reinhardtii. Most importantly, our phylogenetic analysis suggests that a proto-regA gene was present in a common unicellular ancestor of V. carteri and C. reinhardtii and that this gene was lost in the latter lineage.

Duncan, L; Nishii, I; Harryman, A; Buckley, S; Howard, A; Friedman, NR; Miller, SM. 2007. The VARL gene family and the evolutionary origins of the master cell-type regulatory gene, regA, in Volvox carteri. J. Mol. Evol. 65(1):1-11

TF

ULT

Carles et al (2005): The higher-plant shoot apical meristem is a dynamic structure continuously producing cells that become incorporated into new leaves, stems and flowers. The maintenance of a constant flow of cells through the meristem depends on coordination of two antagonistic processes: self-renewal of the stem cell population and initiation of the lateral organs. This coordination is stringently controlled by gene networks that contain both positive and negative components. We have previously defined the ULTRAPETALA1 (ULT1) gene as a key negative regulator of cell accumulation in Arabidopsis shoot and floral meristems, because mutations in ULT1 cause the enlargement of inflorescence and floral meristems, the production of supernumerary flowers and floral organs, and a delay in floral meristem termination. Here, we show that ULT1 negatively regulates the size of the WUSCHEL (WUS)-expressing organizing center in inflorescence meristems. We have cloned the ULT1 gene and find that it encodes a small protein containing a B-box-like motif and a SAND domain, a DNA-binding motif previously reported only in animal transcription factors. ULT1 and its Arabidopsis paralog ULT2 define a novel small gene family in plants. ULT1 and ULT2 are expressed coordinately in embryonic shoot apical meristems, in inflorescence and floral meristems, and in developing stamens, carpels and ovules. Additionally, ULT1 is expressed in vegetative meristems and leaf primordia. ULT2 protein can compensate for mutant ULT1 protein when overexpressed in an ult1 background, indicating that the two genes may regulate a common set of targets during plant development. Downregulation of both ULT genes can lead to shoot apical meristem arrest shortly after germination, revealing a requirement for ULT activity in early development.

Carles, CC; Choffnes-Inada, D; Reville, K; Lertpiriyapong, K; Fletcher, JC. 2005. ULTRAPETALA1 encodes a SAND domain putative transcriptional regulator that controls shoot and floral meristem activity in Arabidopsis. Development 132(5):897-911

TF

TUB

Lai et al (2004): In mammals, TUBBY-like proteins play an important role in maintenance and function of neuronal cells during postdifferentiation and development. We have identified a TUBBY-like protein gene family with 11 members in Arabidopsis, named AtTLP1-11. Although seven of the AtTLP genes are located on chromosome I, no local tandem repeats or gene clusters are identified. Except for AtTLP4, reverse transcription-PCR analysis indicates that all these genes are expressed in various organs in 6-week-old Arabidopsis. AtTLP1, 2, 3, 6, 7, 9, 10, and 11 are expressed ubiquitously in all the organs tested, but the expression of AtTLP5 and 8 shows dramatic organ specificity. These 11 family members share 30% to 80% amino acid similarities across their conserved C-terminal tubby domains. Unlike the highly diverse N-terminal region of animal TUBBY-like proteins, all AtTLP members except AtTLP8 contain a conserved F-box domain (51-57 residues). The interaction between AtTLP9 and ASK1 (Arabidopsis Skp1-like 1) is confirmed via yeast (Saccharomyces cerevisiae) two-hybrid assays. Abscisic acid (ABA)-insensitive phenotypes are observed for two independent AtTLP9 mutant lines, whereas transgenic plants overexpressing AtTLP9 are hypersensitive to ABA. These results suggest that AtTLP9 may participate in the ABA signaling pathway.

Boggon, TJ; Shan, WS; Santagata, S; Myers, SC; Shapiro, L. 1999. Implication of tubby proteins as transcription factors by structure-based functional analysis. Science 286(5447):2119-25,"Lai, CP; Lee, CL; Chen, PH; Wu, SH; Yang, CC; Shaw, JF. 2004. Molecular analyses of the Arabidopsis TUBBY-like protein gene family. Plant Physiol. 134(4):1586-97","Santagata, S; Boggon, TJ; Baird, CL; Gomez, CA; Zhao, J; Shan, WS; Myszka, DG; Shapiro, L. 2001. G-protein signaling through tubby proteins. Science 292(5524):2041-50"

TF

Trihelix

Kaplan-Levy et al (2012): GT factors are the founding members of the trihelix transcription factor family. Genomic studies have revealed 30 members of this family in Arabidopsis and 31 in rice, falling into five clades. Newly discovered functions involve responses to salt and pathogen stresses, the development of perianth organs, trichomes, stomata and the seed abscission layer, and the regulation of late embryogenesis.

Kaplan-Levy, RN; Brewer, PB; Quon, T; Smyth, DR. 2012. The trihelix family of transcription factors--light, stress and development. Trends Plant Sci. 17(3):163-71,"Nagano, Y. 2000. Several features of the GT-factor trihelix domain resemble those of the Myb DNA-binding domain. Plant Physiol. 124(2):491-4","Nagano, Y; Inaba, T; Furuhashi, H; Sasaki, Y. 2001. Trihelix DNA-binding protein with specificities for two distinct cis-elements: both important for light down-regulated and dark-inducible gene expression in higher plants. J. Biol. Chem. 276(25):22238-43","Smalle, J; Kurepa, J; Haegman, M; Gielen, J; Van Montagu, M; Van Der Straeten, D. 1998. The trihelix DNA-binding motif in higher plants is not restricted to the transcription factors GT-1 and GT-2. Proc. Natl. Acad. Sci. U.S.A. 95(6):3318-22","Zhou, DX. 1999. Regulatory mechanism of plant gene transcription by GT-elements and GT-factors. Trends Plant Sci 4(6):210-214","Kaplan-Levy, RN; Brewer, PB; Quon, T; Smyth, DR. 2012. The trihelix family of transcription factors--light, stress and development. Trends Plant Sci. 17(3):163-71","Nagano, Y. 2000. Several features of the GT-factor trihelix domain resemble those of the Myb DNA-binding domain. Plant Physiol. 124(2):491-4","Nagano, Y; Inaba, T; Furuhashi, H; Sasaki, Y. 2001. Trihelix DNA-binding protein with specificities for two distinct cis-elements: both important for light down-regulated and dark-inducible gene expression in higher plants. J. Biol. Chem. 276(25):22238-43","Smalle, J; Kurepa, J; Haegman, M; Gielen, J; Van Montagu, M; Van Der Straeten, D. 1998. The trihelix DNA-binding motif in higher plants is not restricted to the transcription factors GT-1 and GT-2. Proc. Natl. Acad. Sci. U.S.A. 95(6):3318-22","Zhou, DX. 1999. Regulatory mechanism of plant gene transcription by GT-elements and GT-factors. Trends Plant Sci 4(6):210-214"

TF

TRAF

Stogios et al (2005): The BTB domain (also known as the POZ domain) is a versatile protein-protein interaction motif that participates in a wide range of cellular functions, including transcriptional regulation, cytoskeleton dynamics, ion channel assembly and gating, and targeting proteins for ubiquitination. Several BTB domain structures have been experimentally determined, revealing a highly conserved core structure. The BTB domain is typically found as a single copy in proteins that contain only one or two other types of domain, and this defines the BTB-zinc finger (BTB-ZF), BTB-BACK-kelch (BBK), voltage-gated potassium channel T1 (T1-Kv), MATH-BTB, BTB-NPH3 and BTB-BACK-PHR (BBP) families of proteins, among others. BTB-ZF proteins are also known as the POK (POZ and Krüppel zinc finger) proteins. Many members of this large family have been characterized as important transcriptional factors, and several are implicated in development and cancer, most notably BCL6, leukemia/lymphoma related factor (LRF)/Pokemon, PLZF, hypermethylated in cancer (HIC)1 and Myc interacting zinc finger (MIZ)1.

Deweindt, C; Albagli, O; Bernardin, F; Dhordain, P; Quief, S; Lantoine, D; Kerckaert, JP; Leprince, D. 1995. The LAZ3/BCL6 oncogene encodes a sequence-specific transcriptional inhibitor: a novel function for the BTB/POZ domain as an autonomous repressing domain. Cell Growth Differ. 6(12):1495-503,"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","Stogios, PJ; Downs, GS; Jauhal, JJ; Nandra, SK; Privé, GG. 2005. Sequence and structural analysis of BTB domain proteins. Genome Biol. 6(10):R82"

TR

tify

Nishii et al (2000): By differential screening of an arrayed normalized cDNA library from the inflorescence apex in Arabidopsis, a cDNA clone having a deduced amino acid sequence with a motif for a zinc finger was isolated as one of the genes expressed specifically in the reproductive phase. The deduced protein has a modular structure with a putative single C2-C2 zinc-finger motif distantly related to a GATA-1-type finger, a basic region with a sequence resembling a nuclear localization signal, and an acidic region. The gene seemed to have been formed by the exon-shuffling during its molecular evolution, since individual domains are encoded by discrete exons. RNA gel blot analysis showed its expression in shoot apex and flowers in the reproductive phase. The gene was named ZIM for Zinc-finger protein expressed in Inflorescence Meristem. The nuclear localization of ZIM was detected using GFP as a reporter. These results suggest that ZIM is a putative transcription factor involved in inflorescence and flower 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,"Nishii, A; Takemura, M; Fujita, H; Shikata, M; Yokota, A; Kohchi, T. 2000. Characterization of a novel gene encoding a putative single zinc-finger protein, ZIM, expressed during the reproductive phase in Arabidopsis thaliana. Biosci. Biotechnol. Biochem. 64(7):1402-9","Vanholme, B; Grunewald, W; Bateman, A; Kohchi, T; Gheysen, G. 2007. The tify family previously known as ZIM. Trends Plant Sci. 12(6):239-44"

TF

TFb2

<a target="_blank" class="awithout" href="https://www.ebi.ac.uk/interpro/entry/IPR004598">InterPro</a> (0): This domain represents the p52/Tfb2 subunit in the TFIIH complex, which is not only required for transcription but also plays a central role in DNA repair.

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

TR

TAZ

Du & Poovaiah (2004): A novel CaM-binding protein was isolated through protein-protein interaction based screening of an Arabidopsis cDNA expression library using a 35S calmodulin (CaM) probe. There are four additional homologs in the Arabidopsis genome with similar structures: a BTB domain in the N-terminus and a Zf-TAZ domain in the C-terminus. Hence, they were designated as AtBT1-5 (Arabidopsis thaliana BTB and TAZ domain protein). CaM-binding experiments revealed that all five AtBTs are CaM-binding proteins, and their CaM-binding domains were mapped to the C-terminus. AtBT homologs are also present in rice, but are not present in human, animal, yeast or other organisms, suggesting that the BTB and TAZ domain proteins are plant-specific. The AtBT1-smGFP fusion protein expressed in tobacco BY-2 cells showed that AtBT1 targets the nucleus. Yeast two-hybrid screening using an AtBT1 fragment as bait identified two interacting proteins (AtBET10 and AtBET9) belonging to the family of fsh/Ring3 class transcription regulators. The BTB domain of the AtBTs is required for the interaction, and this protein-protein interaction was confirmed by GST pull-down. AtBET10 also interacts with AtBT2 and AtBT4, and exhibited a transcriptional activation function in yeast cells. AtBTs exhibit varying responses to different stress stimuli, but all five genes responded rapidly to H2O2 and salicylic acid (SA) treatments. These results suggest that AtBTs play a role in transcriptional regulation, and signal molecules such as Ca2+, H2O2, and SA affect transcriptional machinery by altering the expression and conformation of AtBTs which interact with transcriptional activators such as AtBET10.

Du, L; Poovaiah, BW. 2004. A novel family of Ca2+/calmodulin-binding proteins involved in transcriptional regulation: interaction with fsh/Ring3 class transcription activators. Plant Mol. Biol. 54(4):549-69

TR

TAFII250

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). In non-photosynthetic eukaryotes, monocots, and dicots an average of one to two members of the HAT subfamily TAFII250 can be found (Uhrig et al., 2017). Furthermore, they are also present in early photosynthetic eukaryotes as red algae (Uhrig et al., 2017). Functions such as participation in light response and the phytochrome pathway could be observed (Boycheva et al., 2014).

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"

TR

SWI/SNF_SWI3

Da et al (2006): The SWIRM domain is a module found in the Swi3 and Rsc8 subunits of SWI/SNF-family chromatin remodeling complexes, and the Ada2 and BHC110/LSD1 subunits of chromatin modification complexes. Here we report the high-resolution crystal structure of the SWIRM domain from Swi3 and characterize the in vitro and in vivo function of the SWIRM domains from Saccharomyces cerevisiae Swi3 and Rsc8. The Swi3 SWIRM forms a four-helix bundle containing a pseudo 2-fold axis and a helix-turn-helix motif commonly found in DNA-binding proteins. We show that the Swi3 SWIRM binds free DNA and mononucleosomes with high and comparable affinity and that a subset of Swi3 substitution mutants that display growth defects in vivo also show impaired DNA-binding activity in vitro, consistent with a nucleosome targeting function of this domain. Genetic and biochemical studies also reveal that the Rsc8 and Swi3 SWIRM domains are essential for the proper assembly and in vivo functions of their respective complexes. Together, these studies identify the SWIRM domain as an essential multifunctional module for the regulation of gene expression.

Da, G; Lenkart, J; Zhao, K; Shiekhattar, R; Cairns, BR; Marmorstein, R. 2006. Structure and function of the SWIRM domain, a conserved protein module found in chromatin regulatory complexes. Proc. Natl. Acad. Sci. U.S.A. 103(7):2057-62

TR

SWI/SNF_SNF2

Eisen et al (1995): The SNF2 family of proteins includes representatives from a variety of species with roles in cellular processes such as transcriptional regulation (e.g. MOT1, SNF2 and BRM), maintenance of chromosome stability during mitosis (e.g. lodestar) and various aspects of processing of DNA damage, including nucleotide excision repair (e.g. RAD16 and ERCC6), recombinational pathways (e.g. RAD54) and post-replication daughter strand gap repair (e.g. RAD5). This family also includes many proteins with no known function. To better characterize this family of proteins we have used molecular phylogenetic techniques to infer evolutionary relationships among the family members. We have divided the SNF2 family into multiple subfamilies, each of which represents what we propose to be a functionally and evolutionarily distinct group. We have then used the subfamily structure to predict the functions of some of the uncharacterized proteins in the SNF2 family. We discuss possible implications of this evolutionary analysis on the general properties and evolution of the SNF2 family.

Bork, P; Koonin, EV. 1993. An expanding family of helicases within the 'DEAD/H' superfamily. Nucleic Acids Res. 21(3):751-2,"Eisen, JA; Sweder, KS; Hanawalt, PC. 1995. Evolution of the SNF2 family of proteins: subfamilies with distinct sequences and functions. Nucleic Acids Res. 23(14):2715-23","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"

TR

SWI/SNF_BAF60b

Kussie et al (1996): The MDM2 oncoprotein is a cellular inhibitor of the p53 tumor suppressor in that it can bind the transactivation domain of p53 and downregulate its ability to activate transcription. In certain cancers, MDM2 amplification is a common event and contributes to the inactivation of p53. The crystal structure of the 109-residue amino-terminal domain of MDM2 bound to a 15-residue transactivation domain peptide of p53 revealed that MDM2 has a deep hydrophobic cleft on which the p53 peptide binds as an amphipathic alpha helix. The interface relies on the steric complementarity between the MDM2 cleft and the hydrophobic face of the p53 alpha helix and, in particular, on a triad of p53 amino acids-Phe19, Trp23, and Leu26-which insert deep into the MDM2 cleft. These same p53 residues are also involved in transactivation, supporting the hypothesis that MDM2 inactivates p53 by concealing its transactivation domain. The structure also suggests that the amphipathic alpha helix may be a common structural motif in the binding of a diverse family of transactivation factors to the TATA-binding protein-associated factors.

Bennett-Lovsey, R; Hart, SE; Shirai, H; Mizuguchi, K. 2002. The SWIB and the MDM2 domains are homologous and share a common fold. Bioinformatics 18(4):626-30,"Kussie, PH; Gorina, S; Marechal, V; Elenbaas, B; Moreau, J; Levine, AJ; Pavletich, NP. 1996. Structure of the MDM2 oncoprotein bound to the p53 tumor suppressor transactivation domain. Science 274(5289):948-53"

TR