TapScan - v4


OFP	Hackbusch et al (2005): OFPs are characterized by a conserved C-terminal domain shared with the tomato OVATE protein, and most members of this family contain a predicted nuclear localization signal.	Hackbusch, J; Richter, K; Müller, J; Salamini, F; Uhrig, JF. 2005. A central role of Arabidopsis thaliana ovate family proteins in networking and subcellular localization of 3-aa loop extension homeodomain proteins. Proc. Natl. Acad. Sci. U.S.A. 102(13):4908-12	TR
NZZ	Schiefthaler et al (1999): Sexual reproduction is a salient aspect of plants, and elaborate structures, such as the flowers of angiosperms, have evolved that aid in this process. Within the flower the corresponding sex organs, the anther and the ovule, form the male and female sporangia, the pollen sac and the nucellus, respectively. However, despite their central role for sexual reproduction little is known about the mechanisms that control the establishment of these important structures. Here we present the identification and molecular characterization of the NOZZLE (NZZ) gene in the flowering plant Arabidopsis thaliana. In several nzz mutants the nucellus and the pollen sac fail to form. It indicates that NZZ plays an early and central role in the development of both types of sporangia and that the mechanisms controlling these processes share a crucial factor. In addition, NZZ may have an early function during male and female sporogenesis as well. The evolutionary aspects of these findings are discussed. NZZ encodes a putative protein of unknown function. However, based on sequence analysis we speculate that NZZ is a nuclear protein and possibly a transcription factor.	Schiefthaler, U; Balasubramanian, S; Sieber, P; Chevalier, D; Wisman, E; Schneitz, K. 1999. Molecular analysis of NOZZLE, a gene involved in pattern formation and early sporogenesis during sex organ development in Arabidopsis thaliana. Proc. Natl. Acad. Sci. U.S.A. 96(20):11664-9,"Wilson, ZA; Yang, C. 2004. Plant gametogenesis: conservation and contrasts in development. Reproduction 128(5):483-92"	TF
NLP	According to (Chardin et al., 2014), the plant specific RWP-RK TF Family can be divided into the two subfamilies NLP (NIN-like proteins) and RKD (RWP-RK domain proteins). Proteins belonging to the subfamily NLP provide an additional PB1 (Phox and Bem 1) domain at their C-terminus (Chardin et al., 2014; Wu et al., 2020). RWP-RK proteins are involved in response to nitrate availability and in nodule interception (Wu et al., 2020).	Chardin, C., Girin, T., Roudier, F., Meyer, C., & Krapp, A. (2014). The plant RWP-RK transcription factors: key regulators of nitrogen responses and of gametophyte development. Journal of Experimental Botany, 65(19), 5577–5587. https://doi.org/10.1093/jxb/eru261,"Wu, Z., Liu, H., Huang, W., Yi, L., Qin, E., Yang, T., Wang, J., & Qin, R. (2020). Genome-Wide Identification, Characterization, and Regulation of RWP-RK Gene Family in the Nitrogen-Fixing Clade. Plants, 9(9), 1178. https://doi.org/10.3390/plants9091178"	TF
NF-YC	Bernadt et al (2005): NF-Y is a bifunctional transcription factor capable of activating or repressing transcription. NF-Y specifically recognizes CCAAT box motifs present in many eukaryotic promoters. The mechanisms involved in regulating its activity are poorly understood.	Zanetti, ME; Rípodas, C; Niebel, A. 2017. Plant NF-Y transcription factors: Key players in plant-microbe interactions, root development and adaptation to stress. Biochim Biophys Acta. 1860(5):645-654,"Lang, D; Weiche, B; Timmerhaus, G; Richardt, S; Riano-Pachon, DM; Correa, LG; Reski, R; Mueller-Roeber, B; Rensing, SA. 2010. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2: 488-503","Bernadt, CT; Nowling, T; Wiebe, MS; Rizzino, A. 2005. NF-Y behaves as a bifunctional transcription factor that can stimulate or repress the FGF-4 promoter in an enhancer-dependent manner. Gene Expr. 12(3):193-212","Li, XY; Mantovani, R; Hooft van Huijsduijnen, R; Andre, I; Benoist, C; Mathis, D. 1992. Evolutionary variation of the CCAAT-binding transcription factor NF-Y. Nucleic Acids Res. 20(5):1087-91"	TF
NF-YB	Bernadt et al (2005): NF-Y is a bifunctional transcription factor capable of activating or repressing transcription. NF-Y specifically recognizes CCAAT box motifs present in many eukaryotic promoters. The mechanisms involved in regulating its activity are poorly understood.	Zanetti, ME; Rípodas, C; Niebel, A. 2017. Plant NF-Y transcription factors: Key players in plant-microbe interactions, root development and adaptation to stress. Biochim Biophys Acta. 1860(5):645-654,"Lang, D; Weiche, B; Timmerhaus, G; Richardt, S; Riano-Pachon, DM; Correa, LG; Reski, R; Mueller-Roeber, B; Rensing, SA. 2010. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2: 488-503","Bernadt, CT; Nowling, T; Wiebe, MS; Rizzino, A. 2005. NF-Y behaves as a bifunctional transcription factor that can stimulate or repress the FGF-4 promoter in an enhancer-dependent manner. Gene Expr. 12(3):193-212","Li, XY; Mantovani, R; Hooft van Huijsduijnen, R; Andre, I; Benoist, C; Mathis, D. 1992. Evolutionary variation of the CCAAT-binding transcription factor NF-Y. Nucleic Acids Res. 20(5):1087-91"	TF
NF-YA	Bernadt et al (2005): NF-Y is a bifunctional transcription factor capable of activating or repressing transcription. NF-Y specifically recognizes CCAAT box motifs present in many eukaryotic promoters. The mechanisms involved in regulating its activity are poorly understood.	Zanetti, ME; Rípodas, C; Niebel, A. 2017. Plant NF-Y transcription factors: Key players in plant-microbe interactions, root development and adaptation to stress. Biochim Biophys Acta. 1860(5):645-654,"Lang, D; Weiche, B; Timmerhaus, G; Richardt, S; Riano-Pachon, DM; Correa, LG; Reski, R; Mueller-Roeber, B; Rensing, SA. 2010. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2: 488-503","Bernadt, CT; Nowling, T; Wiebe, MS; Rizzino, A. 2005. NF-Y behaves as a bifunctional transcription factor that can stimulate or repress the FGF-4 promoter in an enhancer-dependent manner. Gene Expr. 12(3):193-212","Li, XY; Mantovani, R; Hooft van Huijsduijnen, R; Andre, I; Benoist, C; Mathis, D. 1992. Evolutionary variation of the CCAAT-binding transcription factor NF-Y. Nucleic Acids Res. 20(5):1087-91"	TF
NAC	Olsen et al (2005): NAC proteins constitute one of the largest families of plant-specific transcription factors, and the family is present in a wide range of land plants. Here, we summarize the biological and molecular functions of the NAC family, paying particular attention to the intricate regulation of NAC protein level and localization, and to the first indications of NAC participation in transcription factor networks. The recent determination of the DNA and protein binding NAC domain structure offers insight into the molecular functions of the protein family. Research into NAC transcription factors has demonstrated the importance of this protein family in the biology of plants and the need for further studies.	Olsen, AN; Ernst, HA; Leggio, LL; Skriver, K. 2005. NAC transcription factors: structurally distinct, functionally diverse. Trends Plant Sci. 10(2):79-87	TF
MYST	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). The HAT subfamily MYST can be found with an average of two members in green algae, land plants, heterokonts and other photosynthetic eukaryotes involved for instances in transcriptional activation and silencing, apoptosis and in the process of the cell cycle (Latrasse et al., 2008; Uhrig et al., 2017).	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","Latrasse, D., Benhamed, M., Henry, Y., Domenichini, S., Kim, W., Zhou, D.-X., & Delarue, M. (2008). The MYST histone acetyltransferases are essential for gametophyte development in Arabidopsis. BMC Plant Biology, 8(1), 121. https://doi.org/10.1186/1471-2229-8-121"	TR
MYB-related	Martin & Paz-Ares (1997): The cloning of the first transcription factor from plants, the C1 gene of maize, indicated that plants use transcription factors that are structurally related to those of animals in their control of gene expression, because C1 showed significant structural homology to the vertebrate cellular proto-oncogene c-MYB. Since 1987, the catalogue of MYB-related transcription factors has increased considerably in size due, primarily, to the ever-expanding number of MYB genes identified in higher plants (Arabidopsis thaliana is estimated to contain more than a hundred MYB genes). In vertebrates, the MYB-related proto-oncogenes comprise a small family with a central role in controlling cellular proliferation and commitment to development. However, while the functions of some plant MYB genes are relatively well understood they are, at present, quite distinct from their animal counterparts.	Jin, H; Martin, C. 1999. Multifunctionality and diversity within the plant MYB-gene family. Plant Mol. Biol. 41(5):577-85,"Klempnauer, KH; Sippel, AE. 1987. The highly conserved amino-terminal region of the protein encoded by the v-myb oncogene functions as a DNA-binding domain. EMBO J. 6(9):2719-25","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","Martin, C; Paz-Ares, J. 1997. MYB transcription factors in plants. Trends Genet. 13(2):67-73"	TF
MYB-4R	Martin & Paz-Ares (1997): The cloning of the first transcription factor from plants, the C1 gene of maize, indicated that plants use transcription factors that are structurally related to those of animals in their control of gene expression, because C1 showed significant structural homology to the vertebrate cellular proto-oncogene c-MYB. Since 1987, the catalogue of MYB-related transcription factors has increased considerably in size due, primarily, to the ever-expanding number of MYB genes identified in higher plants (Arabidopsis thaliana is estimated to contain more than a hundred MYB genes). In vertebrates, the MYB-related proto-oncogenes comprise a small family with a central role in controlling cellular proliferation and commitment to development. However, while the functions of some plant MYB genes are relatively well understood they are, at present, quite distinct from their animal counterparts. MYB TFs exhibit a highly conserved N-terminal MYB domain, which consists of one to four imperfect sequence repeats (Cao et al., 2020; Dubos et al., 2010). Based on the occurrence of these repeats, proteins belonging to the MYB family can be classified into four subfamilies, namely MYB-1R, MYB-2R, MYB-3R and MYB-4R (Cao et al., 2020).	Jin, H; Martin, C. 1999. Multifunctionality and diversity within the plant MYB-gene family. Plant Mol. Biol. 41(5):577-85,"Klempnauer, KH; Sippel, AE. 1987. The highly conserved amino-terminal region of the protein encoded by the v-myb oncogene functions as a DNA-binding domain. EMBO J. 6(9):2719-25","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","Martin, C; Paz-Ares, J. 1997. MYB transcription factors in plants. Trends Genet. 13(2):67-73"	TF
MYB-3R	Martin & Paz-Ares (1997): The cloning of the first transcription factor from plants, the C1 gene of maize, indicated that plants use transcription factors that are structurally related to those of animals in their control of gene expression, because C1 showed significant structural homology to the vertebrate cellular proto-oncogene c-MYB. Since 1987, the catalogue of MYB-related transcription factors has increased considerably in size due, primarily, to the ever-expanding number of MYB genes identified in higher plants (Arabidopsis thaliana is estimated to contain more than a hundred MYB genes). In vertebrates, the MYB-related proto-oncogenes comprise a small family with a central role in controlling cellular proliferation and commitment to development. However, while the functions of some plant MYB genes are relatively well understood they are, at present, quite distinct from their animal counterparts. MYB TFs exhibit a highly conserved N-terminal MYB domain, which consists of one to four imperfect sequence repeats (Cao et al., 2020; Dubos et al., 2010). Based on the occurrence of these repeats, proteins belonging to the MYB family can be classified into four subfamilies, namely MYB-1R, MYB-2R, MYB-3R and MYB-4R (Cao et al., 2020).	Jin, H; Martin, C. 1999. Multifunctionality and diversity within the plant MYB-gene family. Plant Mol. Biol. 41(5):577-85,"Klempnauer, KH; Sippel, AE. 1987. The highly conserved amino-terminal region of the protein encoded by the v-myb oncogene functions as a DNA-binding domain. EMBO J. 6(9):2719-25","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","Martin, C; Paz-Ares, J. 1997. MYB transcription factors in plants. Trends Genet. 13(2):67-73"	TF
MYB-2R	Martin & Paz-Ares (1997): The cloning of the first transcription factor from plants, the C1 gene of maize, indicated that plants use transcription factors that are structurally related to those of animals in their control of gene expression, because C1 showed significant structural homology to the vertebrate cellular proto-oncogene c-MYB. Since 1987, the catalogue of MYB-related transcription factors has increased considerably in size due, primarily, to the ever-expanding number of MYB genes identified in higher plants (Arabidopsis thaliana is estimated to contain more than a hundred MYB genes). In vertebrates, the MYB-related proto-oncogenes comprise a small family with a central role in controlling cellular proliferation and commitment to development. However, while the functions of some plant MYB genes are relatively well understood they are, at present, quite distinct from their animal counterparts. MYB TFs exhibit a highly conserved N-terminal MYB domain, which consists of one to four imperfect sequence repeats (Cao et al., 2020; Dubos et al., 2010). Based on the occurrence of these repeats, proteins belonging to the MYB family can be classified into four subfamilies, namely MYB-1R, MYB-2R, MYB-3R and MYB-4R (Cao et al., 2020).	Jin, H; Martin, C. 1999. Multifunctionality and diversity within the plant MYB-gene family. Plant Mol. Biol. 41(5):577-85,"Klempnauer, KH; Sippel, AE. 1987. The highly conserved amino-terminal region of the protein encoded by the v-myb oncogene functions as a DNA-binding domain. EMBO J. 6(9):2719-25","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","Martin, C; Paz-Ares, J. 1997. MYB transcription factors in plants. Trends Genet. 13(2):67-73"	TF
MYB	Martin & Paz-Ares (1997): The cloning of the first transcription factor from plants, the C1 gene of maize, indicated that plants use transcription factors that are structurally related to those of animals in their control of gene expression, because C1 showed significant structural homology to the vertebrate cellular proto-oncogene c-MYB. Since 1987, the catalogue of MYB-related transcription factors has increased considerably in size due, primarily, to the ever-expanding number of MYB genes identified in higher plants (Arabidopsis thaliana is estimated to contain more than a hundred MYB genes). In vertebrates, the MYB-related proto-oncogenes comprise a small family with a central role in controlling cellular proliferation and commitment to development. However, while the functions of some plant MYB genes are relatively well understood they are, at present, quite distinct from their animal counterparts. MYB TFs exhibit a highly conserved N-terminal MYB domain, which consists of one to four imperfect sequence repeats (Cao et al., 2020; Dubos et al., 2010). Based on the occurrence of these repeats, proteins belonging to the MYB family can be classified into four subfamilies, namely MYB-1R, MYB-2R, MYB-3R and MYB-4R (Cao et al., 2020).	Jin, H; Martin, C. 1999. Multifunctionality and diversity within the plant MYB-gene family. Plant Mol. Biol. 41(5):577-85,"Klempnauer, KH; Sippel, AE. 1987. The highly conserved amino-terminal region of the protein encoded by the v-myb oncogene functions as a DNA-binding domain. EMBO J. 6(9):2719-25","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","Martin, C; Paz-Ares, J. 1997. MYB transcription factors in plants. Trends Genet. 13(2):67-73"	TF
mTERF	Roberti et al (2009): The MTERF family is a wide protein family, identified in Metazoa and plants, which consists of 4 subfamilies named MTERF1-4. Proteins belonging to this family are localized in mitochondria and have a modular architecture based on repetitions of a 30 amino acid module, the mTERF motif, containing leucine zipper-like heptads. The MTERF family includes the characterized transcription termination factors human mTERF, sea urchin mtDBP and Drosophila DmTTF. In vitro and in vivo studies show that these factors play different roles which are not restricted to transcription termination, but concern also transcription inititiation and the control of mtDNA replication. The multiplicity of functions could be related to the differences in the gene organization of the mitochondrial genomes. Studies on the function of human and Drosophila MTERF3 factor showed that the protein acts as negative regulator of mitochondrial transcription, possibly in cooperation with other still unknown factors. The complete elucidation of the role of the MTERF family members will allow to unravel the molecular mechanisms of mtDNA transcription and replication.	Roberti, M; Polosa, PL; Bruni, F; Manzari, C; Deceglie, S; Gadaleta, MN; Cantatore, P. 2009. The MTERF family proteins: Mitochondrial transcription regulators and beyond. Biochim. Biophys. Acta	TR
Med7	Koschubs et al (2009): Mediator is a modular multiprotein complex required for regulated transcription by RNA polymerase (Pol) II. Here, we show that the middle module of the Mediator core contains a submodule of unique structure and function that comprises the N-terminal part of subunit Med7 (Med7N) and the highly conserved subunit Med31 (Soh1). The Med7N/31 submodule shows a conserved novel fold, with two proline-rich stretches in Med7N wrapping around the right-handed four-helix bundle of Med31. In vitro, Med7N/31 is required for activated transcription and can act in trans when added exogenously. In vivo, Med7N/31 has a predominantly positive function on the expression of a specific subset of genes, including genes involved in methionine metabolism and iron transport. Comparative phenotyping and transcriptome profiling identify specific and overlapping functions of different Mediator submodules.	Koschubs, T; Seizl, M; Lariviere, L; Kurth, F; Baumli, S; Martin, DE; Cramer, P. 2009. Identification, structure, and functional requirement of the Mediator submodule Med7N/31. EMBO J. 28(1):69-80	TR
Med6	Lee et al (1997): A temperature-sensitive mutation was obtained in Med6p, a component of the mediator complex from the yeast Saccharomyces cerevisiae. The mediator complex has been shown to enable transcriptional activation in vitro. This mutation in Med6p abolished activation of transcription from four of five inducible promoters tested in vivo. There was no effect, however, on uninduced transcription, transcription of constitutively expressed genes, or transcription by RNA polymerases I and III. Mediator-RNA polymerase II complex isolated from the mutant yeast strain was temperature sensitive for transcriptional activation in a reconstituted in vitro system due to a defect in initiation complex formation. A database search revealed the existence of MED6-related genes in humans and Caenorhabditis elegans, suggesting that the role of mediator in transcriptional activation is conserved throughout the evolution.	Kim, YJ; Björklund, S; Li, Y; Sayre, MH; Kornberg, RD. 1994. A multiprotein mediator of transcriptional activation and its interaction with the C-terminal repeat domain of RNA polymerase II. Cell 77(4):599-608,"Lee, YC; Min, S; Gim, BS; Kim, YJ. 1997. A transcriptional mediator protein that is required for activation of many RNA polymerase II promoters and is conserved from yeast to humans. Mol. Cell. Biol. 17(8):4622-32"	TR
MBF1	Tsuda et al (2004): Multiprotein bridging factor 1 (MBF1) is known to be a transcriptional co-activator that mediates transcriptional activation by bridging between an activator and a TATA-box binding protein (TBP). We demonstrated that expression of every three MBF1 from Arabidopsis partially rescues the yeast mbf1 mutant phenotype, indicating that all of them function as co-activators for GCN4-dependent transcriptional activation. We also report that each of their subtypes shows distinct tissue-specific expression patterns and responses to phytohormones. These observations suggest that even though they share a similar biochemical function, each MBF1 has distinct roles in various tissues and conditions.	Tsuda, K; Tsuji, T; Hirose, S; Yamazaki, K. 2004. Three Arabidopsis MBF1 homologs with distinct expression profiles play roles as transcriptional co-activators. Plant Cell Physiol. 45(2):225-31	TR
MADS	Riechmann & Meyerowitz (1997): The MADS domain (MCM1, AGAMOUS, DEFICIENS, and SRF, serum response factor) is a conserved DNA-binding/dimerization region present in a variety of transcription factors from different kingdoms. MADS box genes represent a large multigene family in vascular plants. In angiosperms, many of the genes of the MADS family are involved in different steps of flower development, most notably in the determination of floral meristem and organ identity. The roles that MADS box genes play, however, are not restricted to control the development of the plant reproductive structures. The genetic, molecular, and biochemical basis of the action of the MADS domain proteins in the plant life cycle are reviewed here.	Gramzow L.; Theissen G. 2010. A hitchhiker's guide to the MADS world of plants. Genome Biol. 11(6):214,"Jack, T. 2001. Plant development going MADS. Plant Mol. Biol. 46(5):515-20","Nam, J; dePamphilis, CW; Ma, H; Nei, M. 2003. Antiquity and evolution of the MADS-box gene family controlling flower development in plants. Mol. Biol. Evol. 20(9):1435-47","Nam, J; Kim, J; Lee, S; An, G; Ma, H; Nei, M. 2004. Type I MADS-box genes have experienced faster birth-and-death evolution than type II MADS-box genes in angiosperms. Proc. Natl. Acad. Sci. U.S.A. 101(7):1910-5","Ng, M; Yanofsky, MF. 2001. Function and evolution of the plant MADS-box gene family. Nat. Rev. Genet. 2(3):186-95","Riechmann, JL; Meyerowitz, EM. 1997. MADS domain proteins in plant development. Biol. Chem. 378(10):1079-101","Shore, P; Sharrocks, AD. 1995. The MADS-box family of transcription factors. Eur. J. Biochem. 229(1):1-13","West, AG; Sharrocks, AD. 1999. MADS-box transcription factors adopt alternative mechanisms for bending DNA. J. Mol. Biol. 286(5):1311-23"	TF
LUG	Conner & Liu (2000): Regulation of homeotic gene expression is critical for proper developmental patterns in both animals and plants. LEUNIG is a key regulator of the Arabidopsis floral homeotic gene AGAMOUS. Mutations in LEUNIG cause ectopic AGAMOUS mRNA expression in the outer two whorls of a flower, leading to homeotic transformations of floral organ identity as well as loss of floral organs. We isolated the LEUNIG gene by using a map-based approach and showed that LEUNIG encodes a glutamine-rich protein with seven WD repeats and is similar in motif structure to a class of functionally related transcriptional corepressors including Tup1 from yeast and Groucho from Drosophila. The nuclear localization of LEUNIG-GFP is consistent with a role of LEUNIG as a transcriptional regulator. The detection of LEUNIG mRNA in all floral whorls at the time of their inception suggests that the restricted activity of LEUNIG in the outer two floral whorls must depend on interactions with other spatially restricted factors or on posttranslational regulation. Our finding suggests that both animals and plants use similar repressor proteins to regulate critical developmental processes.	Conner, J; Liu, Z. 2000. LEUNIG, a putative transcriptional corepressor that regulates AGAMOUS expression during flower development. Proc. Natl. Acad. Sci. U.S.A. 97(23):12902-7	TR
LOB2	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
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OFP

Hackbusch et al (2005): OFPs are characterized by a conserved C-terminal domain shared with the tomato OVATE protein, and most members of this family contain a predicted nuclear localization signal.

Hackbusch, J; Richter, K; Müller, J; Salamini, F; Uhrig, JF. 2005. A central role of Arabidopsis thaliana ovate family proteins in networking and subcellular localization of 3-aa loop extension homeodomain proteins. Proc. Natl. Acad. Sci. U.S.A. 102(13):4908-12

TR

NZZ

Schiefthaler et al (1999): Sexual reproduction is a salient aspect of plants, and elaborate structures, such as the flowers of angiosperms, have evolved that aid in this process. Within the flower the corresponding sex organs, the anther and the ovule, form the male and female sporangia, the pollen sac and the nucellus, respectively. However, despite their central role for sexual reproduction little is known about the mechanisms that control the establishment of these important structures. Here we present the identification and molecular characterization of the NOZZLE (NZZ) gene in the flowering plant Arabidopsis thaliana. In several nzz mutants the nucellus and the pollen sac fail to form. It indicates that NZZ plays an early and central role in the development of both types of sporangia and that the mechanisms controlling these processes share a crucial factor. In addition, NZZ may have an early function during male and female sporogenesis as well. The evolutionary aspects of these findings are discussed. NZZ encodes a putative protein of unknown function. However, based on sequence analysis we speculate that NZZ is a nuclear protein and possibly a transcription factor.

Schiefthaler, U; Balasubramanian, S; Sieber, P; Chevalier, D; Wisman, E; Schneitz, K. 1999. Molecular analysis of NOZZLE, a gene involved in pattern formation and early sporogenesis during sex organ development in Arabidopsis thaliana. Proc. Natl. Acad. Sci. U.S.A. 96(20):11664-9,"Wilson, ZA; Yang, C. 2004. Plant gametogenesis: conservation and contrasts in development. Reproduction 128(5):483-92"

TF

NLP

According to (Chardin et al., 2014), the plant specific RWP-RK TF Family can be divided into the two subfamilies NLP (NIN-like proteins) and RKD (RWP-RK domain proteins). Proteins belonging to the subfamily NLP provide an additional PB1 (Phox and Bem 1) domain at their C-terminus (Chardin et al., 2014; Wu et al., 2020). RWP-RK proteins are involved in response to nitrate availability and in nodule interception (Wu et al., 2020).

Chardin, C., Girin, T., Roudier, F., Meyer, C., & Krapp, A. (2014). The plant RWP-RK transcription factors: key regulators of nitrogen responses and of gametophyte development. Journal of Experimental Botany, 65(19), 5577–5587. https://doi.org/10.1093/jxb/eru261,"Wu, Z., Liu, H., Huang, W., Yi, L., Qin, E., Yang, T., Wang, J., & Qin, R. (2020). Genome-Wide Identification, Characterization, and Regulation of RWP-RK Gene Family in the Nitrogen-Fixing Clade. Plants, 9(9), 1178. https://doi.org/10.3390/plants9091178"

TF

NF-YC

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

Zanetti, ME; Rípodas, C; Niebel, A. 2017. Plant NF-Y transcription factors: Key players in plant-microbe interactions, root development and adaptation to stress. Biochim Biophys Acta. 1860(5):645-654,"Lang, D; Weiche, B; Timmerhaus, G; Richardt, S; Riano-Pachon, DM; Correa, LG; Reski, R; Mueller-Roeber, B; Rensing, SA. 2010. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2: 488-503","Bernadt, CT; Nowling, T; Wiebe, MS; Rizzino, A. 2005. NF-Y behaves as a bifunctional transcription factor that can stimulate or repress the FGF-4 promoter in an enhancer-dependent manner. Gene Expr. 12(3):193-212","Li, XY; Mantovani, R; Hooft van Huijsduijnen, R; Andre, I; Benoist, C; Mathis, D. 1992. Evolutionary variation of the CCAAT-binding transcription factor NF-Y. Nucleic Acids Res. 20(5):1087-91"

TF

NF-YB

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

Zanetti, ME; Rípodas, C; Niebel, A. 2017. Plant NF-Y transcription factors: Key players in plant-microbe interactions, root development and adaptation to stress. Biochim Biophys Acta. 1860(5):645-654,"Lang, D; Weiche, B; Timmerhaus, G; Richardt, S; Riano-Pachon, DM; Correa, LG; Reski, R; Mueller-Roeber, B; Rensing, SA. 2010. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2: 488-503","Bernadt, CT; Nowling, T; Wiebe, MS; Rizzino, A. 2005. NF-Y behaves as a bifunctional transcription factor that can stimulate or repress the FGF-4 promoter in an enhancer-dependent manner. Gene Expr. 12(3):193-212","Li, XY; Mantovani, R; Hooft van Huijsduijnen, R; Andre, I; Benoist, C; Mathis, D. 1992. Evolutionary variation of the CCAAT-binding transcription factor NF-Y. Nucleic Acids Res. 20(5):1087-91"

TF

NF-YA

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

Zanetti, ME; Rípodas, C; Niebel, A. 2017. Plant NF-Y transcription factors: Key players in plant-microbe interactions, root development and adaptation to stress. Biochim Biophys Acta. 1860(5):645-654,"Lang, D; Weiche, B; Timmerhaus, G; Richardt, S; Riano-Pachon, DM; Correa, LG; Reski, R; Mueller-Roeber, B; Rensing, SA. 2010. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2: 488-503","Bernadt, CT; Nowling, T; Wiebe, MS; Rizzino, A. 2005. NF-Y behaves as a bifunctional transcription factor that can stimulate or repress the FGF-4 promoter in an enhancer-dependent manner. Gene Expr. 12(3):193-212","Li, XY; Mantovani, R; Hooft van Huijsduijnen, R; Andre, I; Benoist, C; Mathis, D. 1992. Evolutionary variation of the CCAAT-binding transcription factor NF-Y. Nucleic Acids Res. 20(5):1087-91"

TF

NAC

Olsen et al (2005): NAC proteins constitute one of the largest families of plant-specific transcription factors, and the family is present in a wide range of land plants. Here, we summarize the biological and molecular functions of the NAC family, paying particular attention to the intricate regulation of NAC protein level and localization, and to the first indications of NAC participation in transcription factor networks. The recent determination of the DNA and protein binding NAC domain structure offers insight into the molecular functions of the protein family. Research into NAC transcription factors has demonstrated the importance of this protein family in the biology of plants and the need for further studies.

Olsen, AN; Ernst, HA; Leggio, LL; Skriver, K. 2005. NAC transcription factors: structurally distinct, functionally diverse. Trends Plant Sci. 10(2):79-87

TF

MYST

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). The HAT subfamily MYST can be found with an average of two members in green algae, land plants, heterokonts and other photosynthetic eukaryotes involved for instances in transcriptional activation and silencing, apoptosis and in the process of the cell cycle (Latrasse et al., 2008; Uhrig et al., 2017).

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","Latrasse, D., Benhamed, M., Henry, Y., Domenichini, S., Kim, W., Zhou, D.-X., & Delarue, M. (2008). The MYST histone acetyltransferases are essential for gametophyte development in Arabidopsis. BMC Plant Biology, 8(1), 121. https://doi.org/10.1186/1471-2229-8-121"

TR

MYB-related

Martin & Paz-Ares (1997): The cloning of the first transcription factor from plants, the C1 gene of maize, indicated that plants use transcription factors that are structurally related to those of animals in their control of gene expression, because C1 showed significant structural homology to the vertebrate cellular proto-oncogene c-MYB. Since 1987, the catalogue of MYB-related transcription factors has increased considerably in size due, primarily, to the ever-expanding number of MYB genes identified in higher plants (Arabidopsis thaliana is estimated to contain more than a hundred MYB genes). In vertebrates, the MYB-related proto-oncogenes comprise a small family with a central role in controlling cellular proliferation and commitment to development. However, while the functions of some plant MYB genes are relatively well understood they are, at present, quite distinct from their animal counterparts.

Jin, H; Martin, C. 1999. Multifunctionality and diversity within the plant MYB-gene family. Plant Mol. Biol. 41(5):577-85,"Klempnauer, KH; Sippel, AE. 1987. The highly conserved amino-terminal region of the protein encoded by the v-myb oncogene functions as a DNA-binding domain. EMBO J. 6(9):2719-25","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","Martin, C; Paz-Ares, J. 1997. MYB transcription factors in plants. Trends Genet. 13(2):67-73"

TF

MYB-4R

Martin & Paz-Ares (1997): The cloning of the first transcription factor from plants, the C1 gene of maize, indicated that plants use transcription factors that are structurally related to those of animals in their control of gene expression, because C1 showed significant structural homology to the vertebrate cellular proto-oncogene c-MYB. Since 1987, the catalogue of MYB-related transcription factors has increased considerably in size due, primarily, to the ever-expanding number of MYB genes identified in higher plants (Arabidopsis thaliana is estimated to contain more than a hundred MYB genes). In vertebrates, the MYB-related proto-oncogenes comprise a small family with a central role in controlling cellular proliferation and commitment to development. However, while the functions of some plant MYB genes are relatively well understood they are, at present, quite distinct from their animal counterparts. MYB TFs exhibit a highly conserved N-terminal MYB domain, which consists of one to four imperfect sequence repeats (Cao et al., 2020; Dubos et al., 2010). Based on the occurrence of these repeats, proteins belonging to the MYB family can be classified into four subfamilies, namely MYB-1R, MYB-2R, MYB-3R and MYB-4R (Cao et al., 2020).

Jin, H; Martin, C. 1999. Multifunctionality and diversity within the plant MYB-gene family. Plant Mol. Biol. 41(5):577-85,"Klempnauer, KH; Sippel, AE. 1987. The highly conserved amino-terminal region of the protein encoded by the v-myb oncogene functions as a DNA-binding domain. EMBO J. 6(9):2719-25","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","Martin, C; Paz-Ares, J. 1997. MYB transcription factors in plants. Trends Genet. 13(2):67-73"

TF

MYB-3R

Martin & Paz-Ares (1997): The cloning of the first transcription factor from plants, the C1 gene of maize, indicated that plants use transcription factors that are structurally related to those of animals in their control of gene expression, because C1 showed significant structural homology to the vertebrate cellular proto-oncogene c-MYB. Since 1987, the catalogue of MYB-related transcription factors has increased considerably in size due, primarily, to the ever-expanding number of MYB genes identified in higher plants (Arabidopsis thaliana is estimated to contain more than a hundred MYB genes). In vertebrates, the MYB-related proto-oncogenes comprise a small family with a central role in controlling cellular proliferation and commitment to development. However, while the functions of some plant MYB genes are relatively well understood they are, at present, quite distinct from their animal counterparts. MYB TFs exhibit a highly conserved N-terminal MYB domain, which consists of one to four imperfect sequence repeats (Cao et al., 2020; Dubos et al., 2010). Based on the occurrence of these repeats, proteins belonging to the MYB family can be classified into four subfamilies, namely MYB-1R, MYB-2R, MYB-3R and MYB-4R (Cao et al., 2020).

Jin, H; Martin, C. 1999. Multifunctionality and diversity within the plant MYB-gene family. Plant Mol. Biol. 41(5):577-85,"Klempnauer, KH; Sippel, AE. 1987. The highly conserved amino-terminal region of the protein encoded by the v-myb oncogene functions as a DNA-binding domain. EMBO J. 6(9):2719-25","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","Martin, C; Paz-Ares, J. 1997. MYB transcription factors in plants. Trends Genet. 13(2):67-73"

TF

MYB-2R

Martin & Paz-Ares (1997): The cloning of the first transcription factor from plants, the C1 gene of maize, indicated that plants use transcription factors that are structurally related to those of animals in their control of gene expression, because C1 showed significant structural homology to the vertebrate cellular proto-oncogene c-MYB. Since 1987, the catalogue of MYB-related transcription factors has increased considerably in size due, primarily, to the ever-expanding number of MYB genes identified in higher plants (Arabidopsis thaliana is estimated to contain more than a hundred MYB genes). In vertebrates, the MYB-related proto-oncogenes comprise a small family with a central role in controlling cellular proliferation and commitment to development. However, while the functions of some plant MYB genes are relatively well understood they are, at present, quite distinct from their animal counterparts. MYB TFs exhibit a highly conserved N-terminal MYB domain, which consists of one to four imperfect sequence repeats (Cao et al., 2020; Dubos et al., 2010). Based on the occurrence of these repeats, proteins belonging to the MYB family can be classified into four subfamilies, namely MYB-1R, MYB-2R, MYB-3R and MYB-4R (Cao et al., 2020).

Jin, H; Martin, C. 1999. Multifunctionality and diversity within the plant MYB-gene family. Plant Mol. Biol. 41(5):577-85,"Klempnauer, KH; Sippel, AE. 1987. The highly conserved amino-terminal region of the protein encoded by the v-myb oncogene functions as a DNA-binding domain. EMBO J. 6(9):2719-25","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","Martin, C; Paz-Ares, J. 1997. MYB transcription factors in plants. Trends Genet. 13(2):67-73"

TF

MYB

Martin & Paz-Ares (1997): The cloning of the first transcription factor from plants, the C1 gene of maize, indicated that plants use transcription factors that are structurally related to those of animals in their control of gene expression, because C1 showed significant structural homology to the vertebrate cellular proto-oncogene c-MYB. Since 1987, the catalogue of MYB-related transcription factors has increased considerably in size due, primarily, to the ever-expanding number of MYB genes identified in higher plants (Arabidopsis thaliana is estimated to contain more than a hundred MYB genes). In vertebrates, the MYB-related proto-oncogenes comprise a small family with a central role in controlling cellular proliferation and commitment to development. However, while the functions of some plant MYB genes are relatively well understood they are, at present, quite distinct from their animal counterparts. MYB TFs exhibit a highly conserved N-terminal MYB domain, which consists of one to four imperfect sequence repeats (Cao et al., 2020; Dubos et al., 2010). Based on the occurrence of these repeats, proteins belonging to the MYB family can be classified into four subfamilies, namely MYB-1R, MYB-2R, MYB-3R and MYB-4R (Cao et al., 2020).

Jin, H; Martin, C. 1999. Multifunctionality and diversity within the plant MYB-gene family. Plant Mol. Biol. 41(5):577-85,"Klempnauer, KH; Sippel, AE. 1987. The highly conserved amino-terminal region of the protein encoded by the v-myb oncogene functions as a DNA-binding domain. EMBO J. 6(9):2719-25","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","Martin, C; Paz-Ares, J. 1997. MYB transcription factors in plants. Trends Genet. 13(2):67-73"

TF

mTERF

Roberti et al (2009): The MTERF family is a wide protein family, identified in Metazoa and plants, which consists of 4 subfamilies named MTERF1-4. Proteins belonging to this family are localized in mitochondria and have a modular architecture based on repetitions of a 30 amino acid module, the mTERF motif, containing leucine zipper-like heptads. The MTERF family includes the characterized transcription termination factors human mTERF, sea urchin mtDBP and Drosophila DmTTF. In vitro and in vivo studies show that these factors play different roles which are not restricted to transcription termination, but concern also transcription inititiation and the control of mtDNA replication. The multiplicity of functions could be related to the differences in the gene organization of the mitochondrial genomes. Studies on the function of human and Drosophila MTERF3 factor showed that the protein acts as negative regulator of mitochondrial transcription, possibly in cooperation with other still unknown factors. The complete elucidation of the role of the MTERF family members will allow to unravel the molecular mechanisms of mtDNA transcription and replication.

Roberti, M; Polosa, PL; Bruni, F; Manzari, C; Deceglie, S; Gadaleta, MN; Cantatore, P. 2009. The MTERF family proteins: Mitochondrial transcription regulators and beyond. Biochim. Biophys. Acta

TR

Med7

Koschubs et al (2009): Mediator is a modular multiprotein complex required for regulated transcription by RNA polymerase (Pol) II. Here, we show that the middle module of the Mediator core contains a submodule of unique structure and function that comprises the N-terminal part of subunit Med7 (Med7N) and the highly conserved subunit Med31 (Soh1). The Med7N/31 submodule shows a conserved novel fold, with two proline-rich stretches in Med7N wrapping around the right-handed four-helix bundle of Med31. In vitro, Med7N/31 is required for activated transcription and can act in trans when added exogenously. In vivo, Med7N/31 has a predominantly positive function on the expression of a specific subset of genes, including genes involved in methionine metabolism and iron transport. Comparative phenotyping and transcriptome profiling identify specific and overlapping functions of different Mediator submodules.

Koschubs, T; Seizl, M; Lariviere, L; Kurth, F; Baumli, S; Martin, DE; Cramer, P. 2009. Identification, structure, and functional requirement of the Mediator submodule Med7N/31. EMBO J. 28(1):69-80

TR

Med6

Lee et al (1997): A temperature-sensitive mutation was obtained in Med6p, a component of the mediator complex from the yeast Saccharomyces cerevisiae. The mediator complex has been shown to enable transcriptional activation in vitro. This mutation in Med6p abolished activation of transcription from four of five inducible promoters tested in vivo. There was no effect, however, on uninduced transcription, transcription of constitutively expressed genes, or transcription by RNA polymerases I and III. Mediator-RNA polymerase II complex isolated from the mutant yeast strain was temperature sensitive for transcriptional activation in a reconstituted in vitro system due to a defect in initiation complex formation. A database search revealed the existence of MED6-related genes in humans and Caenorhabditis elegans, suggesting that the role of mediator in transcriptional activation is conserved throughout the evolution.

Kim, YJ; Björklund, S; Li, Y; Sayre, MH; Kornberg, RD. 1994. A multiprotein mediator of transcriptional activation and its interaction with the C-terminal repeat domain of RNA polymerase II. Cell 77(4):599-608,"Lee, YC; Min, S; Gim, BS; Kim, YJ. 1997. A transcriptional mediator protein that is required for activation of many RNA polymerase II promoters and is conserved from yeast to humans. Mol. Cell. Biol. 17(8):4622-32"

TR

MBF1

Tsuda et al (2004): Multiprotein bridging factor 1 (MBF1) is known to be a transcriptional co-activator that mediates transcriptional activation by bridging between an activator and a TATA-box binding protein (TBP). We demonstrated that expression of every three MBF1 from Arabidopsis partially rescues the yeast mbf1 mutant phenotype, indicating that all of them function as co-activators for GCN4-dependent transcriptional activation. We also report that each of their subtypes shows distinct tissue-specific expression patterns and responses to phytohormones. These observations suggest that even though they share a similar biochemical function, each MBF1 has distinct roles in various tissues and conditions.

Tsuda, K; Tsuji, T; Hirose, S; Yamazaki, K. 2004. Three Arabidopsis MBF1 homologs with distinct expression profiles play roles as transcriptional co-activators. Plant Cell Physiol. 45(2):225-31

TR

MADS

Riechmann & Meyerowitz (1997): The MADS domain (MCM1, AGAMOUS, DEFICIENS, and SRF, serum response factor) is a conserved DNA-binding/dimerization region present in a variety of transcription factors from different kingdoms. MADS box genes represent a large multigene family in vascular plants. In angiosperms, many of the genes of the MADS family are involved in different steps of flower development, most notably in the determination of floral meristem and organ identity. The roles that MADS box genes play, however, are not restricted to control the development of the plant reproductive structures. The genetic, molecular, and biochemical basis of the action of the MADS domain proteins in the plant life cycle are reviewed here.

Gramzow L.; Theissen G. 2010. A hitchhiker's guide to the MADS world of plants. Genome Biol. 11(6):214,"Jack, T. 2001. Plant development going MADS. Plant Mol. Biol. 46(5):515-20","Nam, J; dePamphilis, CW; Ma, H; Nei, M. 2003. Antiquity and evolution of the MADS-box gene family controlling flower development in plants. Mol. Biol. Evol. 20(9):1435-47","Nam, J; Kim, J; Lee, S; An, G; Ma, H; Nei, M. 2004. Type I MADS-box genes have experienced faster birth-and-death evolution than type II MADS-box genes in angiosperms. Proc. Natl. Acad. Sci. U.S.A. 101(7):1910-5","Ng, M; Yanofsky, MF. 2001. Function and evolution of the plant MADS-box gene family. Nat. Rev. Genet. 2(3):186-95","Riechmann, JL; Meyerowitz, EM. 1997. MADS domain proteins in plant development. Biol. Chem. 378(10):1079-101","Shore, P; Sharrocks, AD. 1995. The MADS-box family of transcription factors. Eur. J. Biochem. 229(1):1-13","West, AG; Sharrocks, AD. 1999. MADS-box transcription factors adopt alternative mechanisms for bending DNA. J. Mol. Biol. 286(5):1311-23"

TF

LUG

Conner & Liu (2000): Regulation of homeotic gene expression is critical for proper developmental patterns in both animals and plants. LEUNIG is a key regulator of the Arabidopsis floral homeotic gene AGAMOUS. Mutations in LEUNIG cause ectopic AGAMOUS mRNA expression in the outer two whorls of a flower, leading to homeotic transformations of floral organ identity as well as loss of floral organs. We isolated the LEUNIG gene by using a map-based approach and showed that LEUNIG encodes a glutamine-rich protein with seven WD repeats and is similar in motif structure to a class of functionally related transcriptional corepressors including Tup1 from yeast and Groucho from Drosophila. The nuclear localization of LEUNIG-GFP is consistent with a role of LEUNIG as a transcriptional regulator. The detection of LEUNIG mRNA in all floral whorls at the time of their inception suggests that the restricted activity of LEUNIG in the outer two floral whorls must depend on interactions with other spatially restricted factors or on posttranslational regulation. Our finding suggests that both animals and plants use similar repressor proteins to regulate critical developmental processes.

Conner, J; Liu, Z. 2000. LEUNIG, a putative transcriptional corepressor that regulates AGAMOUS expression during flower development. Proc. Natl. Acad. Sci. U.S.A. 97(23):12902-7

TR

LOB2

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