|
ABI3/VP1
|
Suzuki et al (1997): When expressed and purified as a separate peptide, the B3 domain has a highly cooperative DNA binding activity that is specific for the Sph sequence. We find that the properties of this activity are in compelling agreement with the functional analyses of VP1 and regulatory sequences in the C7 promoter. These results identify a new class of DNA binding proteins, which thus far are known only in the plant kingdom, that have critical functions in 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,"Nag, R; Maity, MK; Dasgupta, M. 2005. Dual DNA binding property of ABA insensitive 3 like factors targeted to promoters responsive to ABA and auxin. Plant Mol. Biol. 59(5):821-38","Suzuki, M; Kao, CY; McCarty, DR. 1997. The conserved B3 domain of VIVIPAROUS1 has a cooperative DNA binding activity. Plant Cell 9(5):799-807"
|
TF
|
|
ADA2
|
SWIRM domain proteins can be subdivided into 3 subfamilies, namely SWI3-type, LSD1-type (Lysine-specific demethylase 1), and Ada2-type (Adenosine deaminase isoenzymes 2), based on their domain architectures and sequence homology (Gao et al., 2012). ADA2-type proteins are known to be involved in lysine activation and transcriptional activation (Sterner et al., 2002).
|
Gao, Y., Yang, S., Yuan, L., Cui, Y., & Wu, K. (2012). Comparative Analysis of SWIRM Domain-Containing Proteins in Plants. Comparative and Functional Genomics, 2012, 1–8. https://doi.org/10.1155/2012/310402,"Sterner, D. E., Wang, X., Bloom, M. H., Simon, G. M., & Berger, S. L. (2002). The SANT Domain of Ada2 Is Required for Normal Acetylation of Histones by the Yeast SAGA Complex. Journal of Biological Chemistry, 277(10), 8178–8186. https://doi.org/10.1074/jbc.M108601200"
|
TR
|
|
Alfin-like
|
Bastola et al (1998): Alfin1 cDNA, obtained by differential screening of a poly(A)+ library from salt-tolerant alfalfa cells, encodes a novel protein with a Cys4 and His/Cys3 putative zinc-binding domain that suggests a possible role for this protein in transcriptional regulation. We have expressed the cDNA in Escherichia coli and show that the recombinant Alfin1 protein binds DNA in a sequence-specific manner. The DNA recognition sequence was determined from individual clones isolated after four rounds of random oligonucleotide selection in gel retardation assays, coupled with PCR amplification of the selected sequences. The consensus binding site for Alfin1 is shown to contain two to five G-rich triplets with the conserved core of GNGGTG or GTGGNG in clones showing high-efficiency binding. DNA binding of the recombinant Alfin1 was inhibited by EDTA. Alfin1 mRNA was found predominantly in alfalfa roots. Growth of salt-sensitive Medicago sativa L on 171 mM NaCl led to a slight decrease in Alfin1 mRNA, while the salt-tolerant plants showed no decrease in Alfin1 mRNA levels. Interestingly, recombinant Alfin1 binds efficiently to three fragments of the MsPRP2 promoter, each containing consensus sequences identified by the random oligonucleotide selection. Since MsPRP2 transcripts were shown to be root-specific and accumulated in alfalfa roots in a salt-inducible manner, Alfin1 may play a role in the regulated expression of MsPRP2 in alfalfa roots and contribute to salt tolerance in these plants.
|
Bastola, DR; Pethe, VV; Winicov, I. 1998. Alfin1, a novel zinc-finger protein in alfalfa roots that binds to promoter elements in the salt-inducible MsPRP2 gene. Plant Mol. Biol. 38(6):1123-35,"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","Bastola, DR; Pethe, VV; Winicov, I. 1998. Alfin1, a novel zinc-finger protein in alfalfa roots that binds to promoter elements in the salt-inducible MsPRP2 gene. Plant Mol. Biol. 38(6):1123-35","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","Winicov, I. 1993. cDNA encoding putative zinc finger motifs from salt-tolerant alfalfa (Medicago sativa L.) cells. Plant Physiol. 102(2):681-2","Winicov, I. 2000. Alfin1 transcription factor overexpression enhances plant root growth under normal and saline conditions and improves salt tolerance in alfalfa. Planta 210(3):416-22","Winicov, I. 1993. cDNA encoding putative zinc finger motifs from salt-tolerant alfalfa (Medicago sativa L.) cells. Plant Physiol. 102(2):681-2","Winicov, I. 2000. Alfin1 transcription factor overexpression enhances plant root growth under normal and saline conditions and improves salt tolerance in alfalfa. Planta 210(3):416-22"
|
TF
|
|
ALOG
|
Arabidopsis thaliana LSH1 and Oryza G1 proteins are abbreviated with ALOG and also referred to as light-dependent short hypocotyl (LSH) proteins (Lee et al., 2020). These proteins represent a family of TFs which can be found in all land plants and some streptophyte algae (Naramoto et al., 2020). ALOG proteins are involved i.e. in the elongation of the hypocotyl, in the determination of the lateral organ identity and in the conservation of the apical meristems (e.g., (Cho & Zambryski, 2011; Naramoto et al., 2020; Zhao et al., 2004)). (Naramoto et al., 2020) identified, based on the occurrences of ALOG proteins in some streptophyte algae, that the ALOG TF family emerged before the evolution of land plants and is present in species that feature traits like apical growth, plasmodesmata and rhizoids (Naramoto et al., 2020).
|
Lee, M., Dong, X., Song, H., Yang, J. Y., Kim, S., & Hur, Y. (2020). Molecular characterization of Arabidopsis thaliana LSH1 and LSH2 genes. Genes & Genomics, 42(10), 1151–1162. https://doi.org/10.1007/s13258-020-00985-x,"Naramoto, S., Hata, Y., & Kyozuka, J. (2020). The origin and evolution of the ALOG proteins, members of a plant-specific transcription factor family, in land plants. Journal of Plant Research, 133(3), 323–329. https://doi.org/10.1007/s10265-020-01171-6","Cho, E., & Zambryski, P. C. (2011). ORGAN BOUNDARY1 defines a gene expressed at the junction between the shoot apical meristem and lateral organs. Proceedings of the National Academy of Sciences, 108(5), 2154–2159. https://doi.org/10.1073/pnas.1018542108","Zhao, L., Nakazawa, M., Takase, T., Manabe, K., Kobayashi, M., Seki, M., Shinozaki, K., & Matsui, M. (2004). Overexpression of LSH1, a member of an uncharacterised gene family, causes enhanced light regulation of seedling development. The Plant Journal, 37(5), 694–706. https://doi.org/10.1111/j.1365-313X.2003.01993.x"
|
TF
|
|
AP2
|
Riechmann & Meyerowitz (1998): AP2 (APETALA2) and EREBPs (ethylene-responsive element binding proteins) are the prototypic members of a family of transcription factors unique to plants, whose distinguishing characteristic is that they contain the so-called AP2 DNA-binding domain. AP2/ REBP genes form a large multigene family, and they play a variety of roles throughout the plant life cycle: from being key regulators of several developmental processes, like floral organ identity determination or control of leaf epidermal cell identity, to forming part of the mechanisms used by plants to respond to various types of biotic and environmental stress.
|
Gutterson, N; Reuber, TL. 2004. Regulation of disease resistance pathways by AP2/ERF transcription factors. Curr. Opin. Plant Biol. 7(4):465-71,"Liu, Y; Zhao, TJ; Liu, JM; Liu, WQ; Liu, Q; Yan, YB; Zhou, HM. 2006. The conserved Ala37 in the ERF/AP2 domain is essential for binding with the DRE element and the GCC box. FEBS Lett. 580(5):1303-8","Riechmann, JL; Meyerowitz, EM. 1998. The AP2/EREBP family of plant transcription factors. Biol. Chem. 379(6):633-46","Shigyo, M; Hasebe, M; Ito, M. 2006. Molecular evolution of the AP2 subfamily. Gene 366(2):256-65","Shigyo, M; Ito, M. 2004. Analysis of gymnosperm two-AP2-domain-containing genes. Dev. Genes Evol. 214(3):105-14","Magnani, E; Sjölander, K; Hake, S. 2004. From endonucleases to transcription factors: evolution of the AP2 DNA binding domain in plants. Plant Cell 16(9):2265-77","Ohme-Takagi, M; Shinshi, H. 1995. Ethylene-inducible DNA binding proteins that interact with an ethylene-responsive element. Plant Cell 7(2):173-82","Weigel, D. 1995. The APETALA2 domain is related to a novel type of DNA binding domain. Plant Cell 7(4):388-9","Gutterson, N; Reuber, TL. 2004. Regulation of disease resistance pathways by AP2/ERF transcription factors. Curr. Opin. Plant Biol. 7(4):465-71","Liu, Y; Zhao, TJ; Liu, JM; Liu, WQ; Liu, Q; Yan, YB; Zhou, HM. 2006. The conserved Ala37 in the ERF/AP2 domain is essential for binding with the DRE element and the GCC box. FEBS Lett. 580(5):1303-8","Magnani, E; Sjölander, K; Hake, S. 2004. From endonucleases to transcription factors: evolution of the AP2 DNA binding domain in plants. Plant Cell 16(9):2265-77","Ohme-Takagi, M; Shinshi, H. 1995. Ethylene-inducible DNA binding proteins that interact with an ethylene-responsive element. Plant Cell 7(2):173-82","Riechmann, JL; Meyerowitz, EM. 1998. The AP2/EREBP family of plant transcription factors. Biol. Chem. 379(6):633-46","Shigyo, M; Hasebe, M; Ito, M. 2006. Molecular evolution of the AP2 subfamily. Gene 366(2):256-65","Shigyo, M; Ito, M. 2004. Analysis of gymnosperm two-AP2-domain-containing genes. Dev. Genes Evol. 214(3):105-14","Weigel, D. 1995. The APETALA2 domain is related to a novel type of DNA binding domain. Plant Cell 7(4):388-9"
|
TF
|
|
ARF
|
Li et al (2016): Auxin is a key regulator of virtually every aspect of plant growth and development from embryogenesis to senescence. Previous studies have indicated that auxin regulates these processes by controlling gene expression via a family of functionally distinct DNA-binding auxin response factors (ARFs). ARFs are likely components that confer specificity to auxin response through selection of target genes as transcription factors. They bind to auxin response DNA elements (AuxRE) in the promoters of auxin-regulated genes and either activate or repress transcription of these genes depending on a specific domain in the middle of the protein. Recent advances have provided information on the regulation of ARF gene expression, the role of ARFs in growth and developmental processes, protein–protein interactions of ARFs and target genes regulated by ARFs in plants. The canonical auxin response pathway evolved at the origin of Streptophyta (Mutte et al., 2018). In land plants, canonical plant ARFs contain an N-terminal B3-type DNA binding domain (Li et al., 2016), and/or an AUX_IAA domain. However, the analysis of TAP complements across brown algae (Denoeud et al., 2024) showed the presence of an auxin_resp domain but the lack of a B3 domain within most examined brown algal species. With the current TAPscan version 4, we cannot say with certainty whether the nature of these proteins is ARF-like. A revised classification of ARF TFs in TAPscan also including sub-family classification of ARFs will be included in the next TAPscan version, taking into account recent work, e.g. Rienstra et al., 2023.
|
Denoeud, F., Godfroy, O., Cruaud, C., Heesch, S., Nehr, Z., Tadrent, N., Couloux, A., Brillet-Guéguen, L., Delage, L., Mckeown, D., Motomura, T., Sussfeld, D., Fan, X., Mazéas, L., Terrapon, N., Barrera-Redondo, J., Petroll, R., Reynes, L., Choi, S.-W., … Cock, J. M. (2024). Evolutionary genomics of the emergence of brown algae as key components of coastal ecosystems. BioRxiv, 2024.02.19.579948. https://doi.org/10.1101/2024.02.19.579948,"Li, S.-B., Xie, Z.-Z., Hu, C.-G., & Zhang, J.-Z. (2016). A Review of Auxin Response Factors (ARFs) in Plants. Frontiers in Plant Science, 7. https://doi.org/10.3389/fpls.2016.00047","Mutte, S. K., Kato, H., Rothfels, C., Melkonian, M., Wong, G. K.-S., & Weijers, D. (2018). Origin and evolution of the nuclear auxin response system. ELife, 7. https://doi.org/10.7554/eLife.33399","Rienstra, J., Hernández-García, J., Weijers, D. (2023) To bind or not to bind: how AUXIN RESPONSE FACTORs select their target genes. J Exp Bot 2023 Dec 1;74(22):6922-6932. doi: 10.1093/jxb/erad259."
|
TF
|
|
Argonaute
|
Rogers & Weiche (2013): MicroRNAs (miRNAs) are small RNAs that control gene expression through silencing of target mRNAs. Mature miRNAs are processed from primary miRNA transcripts by the endonuclease activity of the DICER-LIKE1 (DCL1) protein complex. Mechanisms exist that allow the DCL1 complex to precisely excise the miRNA from its precursor. Our understanding of miRNA biogenesis, particularly its intersection with transcription and other aspects of RNA metabolism such as splicing, is still evolving. Mature miRNAs are incorporated into an ARGONAUTE (AGO) effector complex competent for target gene silencing but are also subjected to turnover through a degradation mechanism that is beginning to be understood. The mechanisms of miRNA target silencing in plants are no longer limited to AGO-catalyzed slicing, and the contribution of translational inhibition is increasingly appreciated. Here, we review the mechanisms underlying the biogenesis, turnover, and activities of plant miRNAs.
|
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,"Rogers K; Chen X. 2013. Biogenesis, turnover, and mode of action of plant microRNAs. Plant Cell 25(7):2383-99"
|
TR
|
|
ARID
|
Kortschak et al (2000): Members of the recently discovered ARID (AT-rich interaction domain) family of DNA-binding proteins are found in fungi and invertebrate and vertebrate metazoans. ARID-encoding genes are involved in a variety of biological processes including embryonic development, cell lineage gene regulation and cell cycle control. Although the specific roles of this domain and of ARID-containing proteins in transcriptional regulation are yet to be elucidated, they include both positive and negative transcriptional regulation and a likely involvement in the modification of chromatin structure.
|
Kortschak, RD; Tucker, PW; Saint, R. 2000. ARID proteins come in from the desert. Trends Biochem. Sci. 25(6):294-9,"Patsialou, A; Wilsker, D; Moran, E. 2005. DNA-binding properties of ARID family proteins. Nucleic Acids Res. 33(1):66-80","Wilsker, D; Patsialou, A; Dallas, PB; Moran, E. 2002. ARID proteins: a diverse family of DNA binding proteins implicated in the control of cell growth, differentiation, and development. Cell Growth Differ. 13(3):95-106","Wilsker, D; Probst, L; Wain, HM; Maltais, L; Tucker, PW; Moran, E. 2005. Nomenclature of the ARID family of DNA-binding proteins. Genomics 86(2):242-51","Kortschak, RD; Tucker, PW; Saint, R. 2000. ARID proteins come in from the desert. Trends Biochem. Sci. 25(6):294-9","Patsialou, A; Wilsker, D; Moran, E. 2005. DNA-binding properties of ARID family proteins. Nucleic Acids Res. 33(1):66-80","Wilsker, D; Patsialou, A; Dallas, PB; Moran, E. 2002. ARID proteins: a diverse family of DNA binding proteins implicated in the control of cell growth, differentiation, and development. Cell Growth Differ. 13(3):95-106","Wilsker, D; Probst, L; Wain, HM; Maltais, L; Tucker, PW; Moran, E. 2005. Nomenclature of the ARID family of DNA-binding proteins. Genomics 86(2):242-51"
|
TF
|
|
AS2/LOB
|
Conserved in a variety of evolutionarily divergent plant species, LOB DOMAIN (LBD) genes define a large, plant-specific family of largely unknown function. LBD genes have been implicated in a variety of developmental processes in plants, although to date, relatively few members have been assigned functions. LBD proteins have previously been predicted to be transcription factors, however supporting evidence has only been circumstantial. To address the biochemical function of LBD proteins, we identified a 6-bp consensus motif recognized by a wide cross-section of LBD proteins, and showed that LATERAL ORGAN BOUNDARIES (LOB), the founding member of the family, is a transcriptional activator in yeast. Thus, the LBD genes encode a novel class of DNA-binding transcription factors. Post-translational regulation of transcription factors is often crucial for control of gene expression. In our study, we demonstrate that members of the basic helix-loop-helix (bHLH) family of transcription factors are capable of interacting with LOB. The expression patterns of bHLH048 and LOB overlap at lateral organ boundaries. Interestingly, the interaction of bHLH048 with LOB results in reduced affinity of LOB for the consensus DNA motif. Thus, our studies suggest that bHLH048 post-translationally regulates the function of LOB at lateral organ boundaries (Husbands et al., 2007). According to (Huang et al., 2020) and (Zhang et al., 2020) the LBD family members can be classified into two subfamilies, namely class I and class II LBD proteins. These two classes are distinguished in their domain motifs. Compared to class I proteins, class II proteins lack an intact leucine-zipper-like domain (Zhang et al., 2020). In addition, zinc-finger motifs and GAS (Gly-Ala-Ser) blocks are present in both classes (Zhang et al., 2020).
|
Husbands, A; Bell, EM; Shuai, B; Smith, HM; Springer, PS. 2007. LATERAL ORGAN BOUNDARIES defines a new family of DNA-binding transcription factors and can interact with specific bHLH proteins. Nucleic Acids Res. 35(19):6663-71,"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","Huang, X., Yan, H., Liu, Y., & Yi, Y. (2020). Genome-wide analysis of LATERAL ORGAN BOUNDARIES DOMAIN-in Physcomitrella patens and stress responses. Genes & Genomics, 42(6), 651–662. https://doi.org/10.1007/s13258-020-00931-x,"Zhang, Y., Li, Z., Ma, B., Hou, Q., & Wan, X. (2020). Phylogeny and Functions of LOB Domain Proteins in Plants. International Journal of Molecular Sciences, 21(7), 2278. https://doi.org/10.3390/ijms21072278"
|
TF
|
|
Aux/IAA
|
Tiwari et al (2004): Aux/IAA proteins are short-lived nuclear proteins that repress expression of primary/early auxin response genes in protoplast transfection assays. Repression is thought to result from Aux/IAA proteins dimerizing with auxin response factor (ARF) transcriptional activators that reside on auxin-responsive promoter elements, referred to as AuxREs. Most Aux/IAA proteins contain four conserved domains, designated domains I, II, III, and IV. Domain II and domains III and IV play roles in protein stability and dimerization, respectively. A clear function for domain I had not been established. Results reported here indicate that domain I in Aux/IAA proteins is an active repression domain that is transferable and dominant over activation domains. An LxLxL motif within domain I is important for conferring repression. The dominance of Aux/IAA repression domains over activation domains in ARF transcriptional activators provides a plausible explanation for the repression of auxin response genes via ARF-Aux/IAA dimerization on auxin-responsive promoters.
|
Liscum, E; Reed, JW. 2002. Genetics of Aux/IAA and ARF action in plant growth and development. Plant Mol. Biol. 49(3-4):387-400,"Tiwari, SB; Hagen, G; Guilfoyle, TJ. 2004. Aux/IAA proteins contain a potent transcriptional repression domain. Plant Cell 16(2):533-43","Tiwari, SB; Wang, XJ; Hagen, G; Guilfoyle, TJ. 2001. AUX/IAA proteins are active repressors, and their stability and activity are modulated by auxin. Plant Cell 13(12):2809-22"
|
TR
|
|
BBR/BPC
|
Santi et al (2003): The barley b recombinant (BBR) protein binds specifically to the (GA/TC)8 repeat. BBR is nuclear targeted and is a characterized nuclear localization signal (NLS) sequence, a DNA-binding domain extended up to 90 aa at the C-terminus and a putative N-terminal activation domain. The corresponding gene has no introns and is ubiquitously expressed in barley tissues. In co-transfection experiments, BBR activates (GA/TC)8-containing promoters, and its overexpression in tobacco leads to a pronounced leaf shape modification. BBR has properties of a GAGA-binding factor, but the corresponding gene has no sequence homology to Trl and Psq of Drosophila, which encode functionally analogous proteins.
|
Santi, L; Wang, Y; Stile, MR; Berendzen, K; Wanke, D; Roig, C; Pozzi, C; Müller, K; Müller, J; Rohde, W; Salamini, F. 2003. The GA octodinucleotide repeat binding factor BBR participates in the transcriptional regulation of the homeobox gene Bkn3. Plant J. 34(6):813-26
|
TF
|
|
BES1
|
Yin et al (2005): Brassinosteroids (BRs) signal through a plasma membrane-localized receptor kinase to regulate plant growth and development. We showed previously that a novel protein, BES1, accumulates in the nucleus in response to BRs, where it plays a role in BR-regulated gene expression; however, the mechanism by which BES1 regulates gene expression is unknown. In this study, we dissect BES1 subdomains and establish that BES1 is a transcription factor that binds to and activates BR target gene promoters both in vitro and in vivo. BES1 interacts with a basic helix-loop-helix protein, BIM1, to synergistically bind to E box (CANNTG) sequences present in many BR-induced promoters. Loss-of-function and gain-of-function mutants of BIM1 and its close family members display BR response phenotypes. Thus, BES1 defines a new class of plant-specific transcription factors that cooperate with transcription factors such as BIM1 to regulate BR-induced genes.
|
Li, L; Deng, XW. 2005. It runs in the family: regulation of brassinosteroid signaling by the BZR1-BES1 class of transcription factors. Trends Plant Sci. 10(6):266-8,"Vert, G; Nemhauser, JL; Geldner, N; Hong, F; Chory, J. 2005. Molecular mechanisms of steroid hormone signaling in plants. Annu. Rev. Cell Dev. Biol. 21:177-201","Yin, Y; Vafeados, D; Tao, Y; Yoshida, S; Asami, T; Chory, J. 2005. A new class of transcription factors mediates brassinosteroid-regulated gene expression in Arabidopsis. Cell 120(2):249-59"
|
TF
|
|
bHLH
|
Buck & Atchley (2003): The basic helix-loop-helix (bHLH) family of proteins is a group of functionally diverse transcription factors found in both plants and animals. These proteins evolved early in eukaryotic cells before the split of animals and plants, but appear to function in lsquoplant-specificrsquo or lsquoanimal-specificrsquo processes. In animals bHLH proteins are involved in regulation of a wide variety of essential developmental processes. On the contrary, bHLH proteins have not been extensively studied in plants. Those that have been characterized function in anthocyanin biosynthesis, phytochrome signaling, globulin expression, fruit dehiscence, carpel and epidermal development.
|
Buck, MJ; Atchley, WR. 2003. Phylogenetic analysis of plant basic helix-loop-helix proteins. J. Mol. Evol. 56(6):742-50,"Heim, MA; Jakoby, M; Werber, M; Martin, C; Weisshaar, B; Bailey, PC. 2003. The basic helix-loop-helix transcription factor family in plants: a genome-wide study of protein structure and functional diversity. Mol. Biol. Evol. 20(5):735-47","Littlewood, TD; Evan, GI. 1995. Transcription factors 2: helix-loop-helix. Protein Profile 2(6):621-702","Massari, ME; Murre, C. 2000. Helix-loop-helix proteins: regulators of transcription in eucaryotic organisms. Mol. Cell. Biol. 20(2):429-40","Quattrocchio, F; Wing, JF; van der Woude, K; Mol, JN; Koes, R. 1998. Analysis of bHLH and MYB domain proteins: species-specific regulatory differences are caused by divergent evolution of target anthocyanin genes. Plant J. 13(4):475-88"
|
TF
|
|
bHLH_TCP
|
Kosugi & Ohashi (2002): The TCP domain is a plant-specific DNA binding domain found in proteins from a diverse array of species, including the cycloidea (cyc) and teosinte branched1 (tb1) gene products and the PCF1 and PCF2 proteins. To understand the role in transcriptional regulation of proteins with this domain, we have analysed the DNA binding and dimerization specificity of the TCP protein family using rice PCF proteins, and further evaluated potential targets for the TCP protein. The seven PCF members including five newly isolated proteins, were able to be grouped into two classes, I and II, based on sequence similarity in the TCP domain. Random binding site selection experiments and electrophoretic mobility shift assays (EMSAs) revealed the consensus DNA binding sequences of these two classes to be distinct but overlapping; GGNCCCAC for class I and GTGGNCCC for class II. The TB1 protein from maize, which belongs to class II, had the same specificity as the rice class II proteins, suggesting the conservation of binding specificity between TCP domains from different species. The yeast 2-hybrid assay and EMSA revealed that these proteins tend to form a homodimer or a heterodimer between members of the same class. We searched predicted 5' flanking sequences of Arabidopsis genes for the consensus binding sequences and found that the consensus sites are distributed in the genome at a considerably lower frequency. We further analysed eight promoters containing the class I consensus TCP sites. The transcriptional activities of six promoters were decreased by a mutation of the TCP binding site, which is consistent with the observation that the class I TCP site can confer transactivation function on a heterologous promoter. These results suggest that the two classes of TCP protein are distinct in DNA binding specificity and transcriptional regulation.
|
Cubas, P; Lauter, N; Doebley, J; Coen, E. 1999. The TCP domain: a motif found in proteins regulating plant growth and development. Plant J. 18(2):215-22,"Kosugi, S; Ohashi, Y. 2002. DNA binding and dimerization specificity and potential targets for the TCP protein family. Plant J. 30(3):337-48","Reeves, PA; Olmstead, RG. 2003. Evolution of the TCP gene family in Asteridae: cladistic and network approaches to understanding regulatory gene family diversification and its impact on morphological evolution. Mol. Biol. Evol. 20(12):1997-2009"
|
TF
|
|
bHSH
|
Hilger-Eversheim et al (2000): Animal AP-2 transcription factors represent a family of three closely related and evolutionarily conserved sequence-specific DNA-binding proteins, AP-2α, -β and -γ.
|
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,"Hilger-Eversheim, K; Moser, M; Schorle, H; Buettner, R. 2000. Regulatory roles of AP-2 transcription factors in vertebrate development, apoptosis and cell-cycle control. Gene 260(1-2):1-12"
|
TF
|
|
BSD domain containing
|
Doerks et al (2002): The novel domain BSD is present in basal transcription factors, synapse-associated proteins and several hypothetical proteins. It occurs in a variety of species ranging from primal protozoan to human. The BSD domain is characterized by three predicted ? helices, which probably form a three-helical bundle, as well as by conserved tryptophan and phenylalanine residues, located at the C terminus of the domain.
|
Doerks, T; Huber, S; Buchner, E; Bork, P. 2002. BSD: a novel domain in transcription factors and synapse-associated proteins. Trends Biochem. Sci. 27(4):168-70
|
PT
|
|
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
|
|
C1HDZ
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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).
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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"
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TF
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C2C2_CO-like
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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.
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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"
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TF
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C2C2_Dof
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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.
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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"
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TF
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