TapScan - v4


SRS	Fridborg et al (2001): The current model of gibberellin (GA) signal transduction is based on a derepressible system and a number of candidate negative regulators have been identified in Arabidopsis. We previously have reported the identification of the Arabidopsis gene SHORT INTERNODES (SHI) that causes suppression of GA responses when constitutively activated. In this paper, we show by using reporter gene analysis that the SHI gene is expressed in young organs, e.g. shoot apices and root tips. The model predicts a suppressor of GA responses to be active in these tissues to prevent premature growth or development. To study the effect of SHI on GA signaling, we used a functional assay that measures effects of signaling components on a well-defined GA response; the up-regulation of alpha-amylase in barley (Hordeum vulgare) aleurones in response to GA treatment. We found that SHI was able to specifically block the activity of a high-isoelectric point alpha-amylase promoter following GA(3) treatment, which further supports that SHI is a suppressor of GA responses. We have identified two putative loss-of-function insertion alleles of SHI and lines homozygous for either of the new alleles show no phenotypic deviations from wild type. Because SHI belongs to a gene family consisting of nine members, we suggest that SHI and the SHI-related genes are functionally redundant. We also show that a functional ERECTA allele is able to partly suppress the dwarfing effect of the shi gain-of-function mutation, suggesting that the erecta mutation harbored by the Landsberg erecta ecotype is an enhancer of the shi dwarf phenotype.	Fridborg, I; Kuusk, S; Robertson, M; Sundberg, E. 2001. The Arabidopsis protein SHI represses gibberellin responses in Arabidopsis and barley. Plant Physiol. 127(3):937-48	TF
SOH1	Fan et al (1996): The soh1, soh2 and soh4 mutants were isolated as suppressors of the temperature-dependent growth of the hyperrecombination mutant hpr1 of Saccharomyces cerevisiae. Cloning and sequence analysis of these suppressor genes has unexpectedly shown them to code for components of the RNA polymerase II transcription complex. SOH2 is identical to RPB2, which encodes the second largest subunit of RNA polymerase II, and SOH4 is the same as SUA7, encoding the yeast transcription initiation factor TFIIB. SOH1 encodes a novel 14-kD protein with limited sequence similarity to RNA polymerases. Interestingly, SOH1 not only interacts with factors involved in DNA repair, but transcription as well. Thus, the Soh1 protein may serve to couple these two processes. The Soh1 protein interacts with a DNA repair protein, Rad5p, in a two-hybrid system assay. Soh1p may functionally interact with components of the RNA polymerase II complex as suggested from the synthetic lethality observed in soh1 rpb delta 104, soh1 soh2-1 (rpb2), and soh1 soh4 (sua7) double mutants. Because mutations in SOH1, RPB2 and SUA7 suppress the hyperrecombination phenotype of hpr1 mutants, this suggests a link between recombination in direct repeats and transcription.	Fan, HY; Cheng, KK; Klein, HL. 1996. Mutations in the RNA polymerase II transcription machinery suppress the hyperrecombination mutant hpr1 delta of Saccharomyces cerevisiae. Genetics 142(3):749-59	TR
Sir2	<a target="_blank" class="awithout" href="http://pfam.xfam.org/family/PF02146">PFAM</a> (0): Sirtuins are a class of proteins that possess either mono-ADP-ribosyltransferase, or deacylase activity and have been implicated in a wide range of cellular processes, including transcription. The human Sirt7 is involved in rRNA transcription in the nucleolus.	Lang, D; Weiche, B; Timmerhaus, G; Richardt, S; Riano-Pachon, DM; Correa, LG; Reski, R; Mueller-Roeber, B; Rensing, SA. 2010. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2: 488-503	TF
Sin3	<a target="_blank" class="awithout" href="http://pfam.xfam.org/family/PF02671">PFAM</a> (0): This family contains the paired amphipathic helix repeat. The family contains the yeast SIN3 gene. This repeat may be distantly related to the helix-loop-helix motif, which mediates protein-protein interactions.	Lang, D; Weiche, B; Timmerhaus, G; Richardt, S; Riano-Pachon, DM; Correa, LG; Reski, R; Mueller-Roeber, B; Rensing, SA. 2010. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2: 488-503	TR
Sigma70-like	Allison (2000): Expression of plastid genes is controlled at both transcriptional and post-transcriptional levels in response to developmental and environmental signals. In many cases this regulation is mediated by nuclear-encoded proteins acting in concert with the endogenous plastid gene expression machinery. Transcription in plastids is accomplished by two distinct RNA polymerase enzymes, one of which resembles eubacterial RNA polymerases in both subunit structure and promoter recognition properties. The holoenzyme contains a catalytic core composed of plastid-encoded subunits, assembled with a nuclear-encoded promoter-specificity factor, sigma. Based on examples of transcriptional regulation in bacteria, it is proposed that differential activation of sigma factors may provide the nucleus with a mechanism to control expression of groups of plastid genes. Hence, much effort has focused on identifying and characterizing sigma-like factors in plants. While fractionation studies had identified several candidate sigma factors in purified RNA polymerase preparations, it was only 4 years ago that the first sigma factor genes were cloned from two photosynthetic eukaryotes, both of which were red algae. More recently this achievement has extended to the identification of families of sigma-like factor genes from several species of vascular plants. Now, efforts in the field are directed at understanding the roles in plastid transcription of each member of the rapidly expanding plant sigma factor gene family. Recent results suggest that accumulation of individual sigma-like factors is controlled by light, by plastid type and/or by a particular stage of chloroplast development. These data mesh nicely with accumulating evidence that the core sigma-binding regions of plastid promoters mediate regulated transcription in response to light-regime and plastid type or developmental state. In this review I will outline progress made to date in identifying and characterizing the sigma-like factors of plants, and in dissecting their potential roles in chloroplast gene expression.	Allison, LA. 2000. The role of sigma factors in plastid transcription. Biochimie 82(6-7):537-48,"Paget, MS; Helmann, JD. 2003. The sigma70 family of sigma factors. Genome Biol. 4(1):203","Sriraman, P; Silhavy, D; Maliga, P. 1998. Transcription from heterologous rRNA operon promoters in chloroplasts reveals requirement for specific activating factors. Plant Physiol. 117(4):1495-9"	TR
SET	Marmorstein (2003): The methylation of lysine residues on histone tails is catalyzed by proteins containing a conserved SET domain. A recent flurry of structures of SET domain proteins has revealed a new protein fold and a scaffold for understanding catalysis and substrate binding by these enzymes. The prospect that histone methylation might form an epigenetic code and the implicated involvement of SET domain proteins in cancer assures that structure-function studies of these enzymes will continue until their detailed mechanism of action is determined.	Marmorstein, R. 2003. Structure of SET domain proteins: a new twist on histone methylation. Trends Biochem. Sci. 28(2):59-62,"Lang, D; Weiche, B; Timmerhaus, G; Richardt, S; Riano-Pachon, DM; Correa, LG; Reski, R; Mueller-Roeber, B; Rensing, SA. 2010. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2: 488-503"	TR
SBP	Cardon et al (1999): The Arabidopsis thaliana SPL gene family represents a group of structurally diverse genes encoding putative transcription factors found apparently only in plants. The distinguishing characteristic of the SPL gene family is the SBP-box encoding a conserved protein domain of 76 amino acids in length, the SBP-domain, which is responsible for the interaction with DNA. We present here characterisation of 12 members of the SPL gene family. These genes show highly diverse genomic organisations and are found scattered over the Arabidopsis genome. Some SPL genes are constitutively expressed, while transcriptional activity of others is under developmental control. Based on phylogenetic reconstruction, gene structure and expression patterns, they can be divided into subfamilies. In addition to the Arabidopsis SPL genes, we isolated and determined the sequences of three SBP-box genes from Antirrhinum majus and seven from Zea mays.	Cardon, G; Höhmann, S; Klein, J; Nettesheim, K; Saedler, H; Huijser, P. 1999. Molecular characterisation of the Arabidopsis SBP-box genes. Gene. 237(1):91-104,"Guo, AY; Zhu, QH; Gu, X; Ge, S; Yang, J; Luo, J. 2008. Genome-wide identification and evolutionary analysis of the plant specific SBP-box transcription factor family. Gene 418(1-2):1-8","Klein, J; Saedler, H; Huijser, P. 1996. A new family of DNA binding proteins includes putative transcriptional regulators of the Antirrhinum majus floral meristem identity gene SQUAMOSA. Mol. Gen. Genet. 250(1):7-16"	TF
SAP	Byzova et al (1999): A recessive mutation in the Arabidopsis STERILE APETALA (SAP) causes severe aberrations in inflorescence and flower and ovule development. In sap flowers, sepals are carpelloid, petals are short and narrow or absent, and anthers are degenerated. Megasporogenesis, the process of meiotic divisions preceding the female gametophyte formation, is arrested in sap ovules during or just after the first meiotic division. More severe aberrations were observed in double mutants between sap and mutant alleles of the floral homeotic gene APETALA2 (AP2) suggesting that both genes are involved in the initiation of female gametophyte development. Together with the organ identity gene AGAMOUS (AG) SAP is required for the maintenance of floral identity acting in a manner similar to APETALA1. In contrast to the outer two floral organs in sap mutant flowers, normal sepals and petals develop in ag/sap double mutants, indicating that SAP negatively regulates AG expression in the perianth whorls. This supposed cadastral function of SAP is supported by in situ hybridization experiments showing ectopic expression of AG in the sap mutant. We have cloned the SAP gene by transposon tagging and revealed that it encodes a novel protein with sequence motifs, that are also present in plant and animal transcription regulators. Consistent with the mutant phenotype, SAP is expressed in inflorescence and floral meristems, floral organ primordia, and ovules. Taken together, we propose that SAP belongs to a new class of transcription regulators essential for a number of processes in Arabidopsis flower development.	Byzova, MV; Franken, J; Aarts, MG; de Almeida-Engler, J; Engler, G; Mariani, C; Van Lookeren Campagne, MM; Angenent, GC. 1999. Arabidopsis STERILE APETALA, a multifunctional gene regulating inflorescence, flower, and ovule development. Genes Dev. 13(8):1002-14	TF
S1Fa-like	Zhou et al (1995): A cDNA encoding a specific binding activity for the tissue-specific negative cis-element S1F binding site of spinach rps1 was isolated from a spinach cDNA expression library. This cDNA of 0.7 kb encodes an unusual small peptide of only 70 amino acids, with a basic domain which contains a nuclear localization signal and a putative DNA binding helix. This protein, named S1Fa, is highly conserved between dicotyledonous and monocotyledonous plants and may represent a novel class of DNA binding proteins. The corresponding mRNA is accumulated more in roots and in etiolated seedlings than in green leaves. This expression pattern is correlated with the tissue-specific function of the S1F binding site which represses the rps1 promoter preferentially in roots and in etiolated plants.	Zhou, DX; Bisanz-Seyer, C; Mache, R. 1995. Molecular cloning of a small DNA binding protein with specificity for a tissue-specific negative element within the rps1 promoter. Nucleic Acids Res. 23(7):1165-9	TF
RWP-RK	Schauser et al (2005): Genetic studies in Lotus japonicus and pea have identified Nin as a core symbiotic gene required for establishing symbiosis between legumes and nitrogen fixing bacteria collectively called Rhizobium. Sequencing of additional Lotus cDNAs combined with analysis of genome sequences from Arabidopsis and rice reveals that Nin homologues in all three species constitute small gene families. In total, the Arabidopsis and rice genomes encode nine and three NIN-like proteins (NLPs), respectively. We present here a bioinformatics analysis and prediction of NLP evolution. On a genome scale we show that in Arabidopsis, this family has evolved through segmental duplication rather than through tandem amplification. Alignment of all predicted NLP protein sequences shows a composition with six conserved modules. In addition, Lotus and pea NLPs contain segments that might characterize NIN proteins of legumes and be of importance for their function in symbiosis. The most conserved region in NLPs, the RWP-RK domain, has secondary structure predictions consistent with DNA binding properties. This motif is shared by several other small proteins in both Arabidopsis and rice. In rice, the RWP-RK domain sequences have diversified significantly more than in Arabidopsis. Database searches reveal that, apart from its presence in Arabidopsis and rice, the motif is also found in the algae Chlamydomonas and in the slime mold Dictyostelium discoideum. Thus, the origin of this putative DNA binding region seems to predate the fungus-plant divide.	Schauser, L; Roussis, A; Stiller, J; Stougaard, J. 1999. A plant regulator controlling development of symbiotic root nodules. Nature 402(6758):191-5	TF
Runt	<a target="_blank" class="awithout" href="http://pfam.xfam.org/family/PF00853">PFAM</a> (0): The Runt domain is responsible for DNA-binding and protein-protein interaction.	Kagoshima, H; Shigesada, K; Satake, M; Ito, Y; Miyoshi, H; Ohki, M; Pepling, M; Gergen, P. 1993. The Runt domain identifies a new family of heteromeric transcriptional regulators. Trends Genet. 9(10):338-41,"Lang, D; Weiche, B; Timmerhaus, G; Richardt, S; Riano-Pachon, DM; Correa, LG; Reski, R; Mueller-Roeber, B; Rensing, SA. 2010. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2: 488-503"	TF
RRN3	Yamamoto et al (1996): RRN3 is one of the RRN genes specifically required for the transcription of rDNA by RNA polymerase I (Pol I) in Saccharomyces cerevisiae.	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,"Yamamoto, RT; Nogi, Y; Dodd, JA; Nomura M. 1996. RRN3 gene of Saccharomyces cerevisiae encodes an essential RNA polymerase I transcription factor which interacts with the polymerase independently of DNA template. EMBO J. 15(15):3964-73"	TR
RKD	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
RF-X	Reith et al (1990): RFX is a regulatory factor which binds to the X box of MHC class II genes and is essential for their expression. The DNA-binding domain of RFX is the central domain of the protein and binds ssDNA as either a monomer or homodimer.	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,"Reith, W; Herrero-Sanchez, C; Kobr, M; Silacci, P; Berte, C; Barras, E; Fey, S; Mach, B. 1990. MHC class II regulatory factor RFX has a novel DNA-binding domain and a functionally independent dimerization domain. Genes Dev. 4(9):1528-40"	TF
Rel	<a target="_blank" class="awithout" href="http://pfam.xfam.org/family/PF00554">PFAM</a> (0): The Rel homology domain (RHD) is a protein domain found in a family of eukaryotic transcription factors, which includes NF-κB, NFAT, among others. The RHD is composed of two immunoglobulin-like beta barrel subdomains that grip the DNA in the major groove. The N-terminal specificity domain resembles the core domain of the p53 transcription factor, and contains a recognition loop that interacts with DNA bases. The C-terminal dimerization domain contains the site for interaction with I-kappaB.	Müller, CW; Rey, FA; Sodeoka, M; Verdine, GL; Harrison, SC. 1995. Structure of the NF-kappa B p50 homodimer bound to DNA. Nature. 373(6512):311-7,"Lang, D; Weiche, B; Timmerhaus, G; Richardt, S; Riano-Pachon, DM; Correa, LG; Reski, R; Mueller-Roeber, B; Rensing, SA. 2010. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2: 488-503"	TF
Rcd1-like	Okazaki et al (1998): In the fission yeast Schizosaccharomyces pombe, the onset of sexual development is controlled mainly by two external signals, nutrient starvation and mating pheromone availability. We have isolated a novel gene named rcd1+ as a key factor required for nitrogen starvation-induced sexual development. rcd1+ encodes a 283-amino-acid protein with no particular motifs. However, genes highly homologous to rcd1+ (encoding amino acids with >70% identity) are present at least in budding yeasts, plants, nematodes, and humans. Cells with rcd1+ deleted are sterile if sexual development is induced by nitrogen starvation but fertile if it is induced by glucose starvation. This results largely from a defect in nitrogen starvation-invoked induction of ste11+, a key transcriptional factor gene required for the onset of sexual development. The striking conservation of the gene throughout eukaryotes may suggest the presence of an evolutionarily conserved differentiation controlling system.	Okazaki, N; Okazaki, K; Watanabe, Y; Kato-Hayashi, M; Yamamoto, M; Okayama, H. 1998. Novel factor highly conserved among eukaryotes controls sexual development in fission yeast. Mol. Cell. Biol. 18(2):887-95	TR
RB	Bremner et al (2004): The data suggest that RB protein may not control the rate of progenitor division, but is critical for cell cycle exit when dividing retinal progenitors differentiate into postmitotic transition cells.	Bremner, R; Chen, D; Pacal, M; Livne-Bar, I; Agochiya, M. 2004. The RB protein family in retinal development and retinoblastoma: new insights from new mouse models. Dev Neurosci. 26(5-6):417-34,"Ebel, C; Mariconti, L; Gruissem, W. 2004. Plant retinoblastoma homologues control nuclear proliferation in the female gametophyte. Nature 429(6993):776-80","Bremner, R; Chen, D; Pacal, M; Livne-Bar, I; Agochiya, M. 2004. The RB protein family in retinal development and retinoblastoma: new insights from new mouse models. Dev Neurosci. 26(5-6):417-34","Ebel, C; Mariconti, L; Gruissem, W. 2004. Plant retinoblastoma homologues control nuclear proliferation in the female gametophyte. Nature 429(6993):776-80"	TF
Pseudo ARR-B	Tajima et al (2004): In Arabidopsis thaliana, a Histidine-to-Aspartate (His-->Asp) phosphorelay is involved in the signal transduction for propagation of certain stimuli, such as plant hormones. Through the phosphorelay, the type-B phospho-accepting response regulator (ARR) family members serve as DNA-binding transcriptional regulators, whose activities are most likely regulated by phosphorylation/dephosphorylation.	Aoyama, T; Oka, A. 2003. Cytokinin signal transduction in plant cells. J. Plant Res. 116(3):221-31,"D'Agostino, IB; Kieber, JJ. 1999. Phosphorelay signal transduction: the emerging family of plant response regulators. Trends Biochem. Sci. 24(11):452-6","Kakimoto, T. 2003. Perception and signal transduction of cytokinins. Annu Rev Plant Biol 54:605-27","Kolmos, E; Schoof, H; PlÃ¼mer, M; Davis, SJ. 2008. Structural insights into the function of the core-circadian factor TIMING OF CAB2 EXPRESSION 1 (TOC1). J Circadian Rhythms 6:3","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","Tajima, Y; Imamura, A; Kiba, T; Amano, Y; Yamashino, T; Mizuno, T. 2004. Comparative studies on the type-B response regulators revealing their distinctive properties in the His-to-Asp phosphorelay signal transduction of Arabidopsis thaliana. Plant Cell Physiol. 45(1):28-39"	TF
PLATZ	Nagano et al (2001): Complementary DNA encoding a DNA-binding protein, designated PLATZ1 (plant AT-rich sequence- and zinc-binding protein 1), was isolated from peas. The amino acid sequence of the protein is similar to those of other uncharacterized proteins predicted from the genome sequences of higher plants. However, no paralogous sequences have been found outside the plant kingdom. Multiple alignments among these paralogous proteins show that several cysteine and histidine residues are invariant, suggesting that these proteins are a novel class of zinc-dependent DNA-binding proteins with two distantly located regions, C-x(2)-H-x(11)-C-x(2)-C-x((4-5))-C-x(2)-C-x((3-7))-H-x(2)-H and C-x(2)-C-x((10-11))-C-x(3)-C. In an electrophoretic mobility shift assay, the zinc chelator 1,10-o-phenanthroline inhibited DNA binding, and two distant zinc-binding regions were required for DNA binding. A protein blot with (65)ZnCl(2) showed that both regions are required for zinc-binding activity. The PLATZ1 protein non-specifically binds to A/T-rich sequences, including the upstream region of the pea GTPase pra2 and plastocyanin petE genes. Expression of the PLATZ1 repressed those of the reporter constructs containing the coding sequence of luciferase gene driven by the cauliflower mosaic virus (CaMV) 35S90 promoter fused to the tandem repeat of the A/T-rich sequences. These results indicate that PLATZ1 is a novel class of plant-specific zinc-dependent DNA-binding protein responsible for A/T-rich sequence-mediated transcriptional repression.	Nagano, Y; Furuhashi, H; Inaba, T; Sasaki, Y. 2001. A novel class of plant-specific zinc-dependent DNA-binding protein that binds to A/T-rich DNA sequences. Nucleic Acids Res. 29(20):4097-105	TF
PHD	Bienz (2006): PHD proteins seem to be found universally in the nucleus, and their functions tend to lie in the control of chromatin or transcription. Increasing evidence indicates that PHD fingers bind to specific nuclear protein partners, for which they apparently use their loop 2 surface. Perhaps each PHD finger has its own cognate nuclear ligand, much like RING fingers have their cognate E2 ligases. No doubt the list of specific PHD finger ligands will grow, and the set of these ligands is likely to reveal whether PHD fingers have a common function in the nucleus.	Bienz, M. 2006. The PHD finger, a nuclear protein-interaction domain. Trends Biochem. Sci. 31(1):35-40,"Lang, D; Weiche, B; Timmerhaus, G; Richardt, S; Riano-Pachon, DM; Correa, LG; Reski, R; Mueller-Roeber, B; Rensing, SA. 2010. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2: 488-503"	TR
Showing results 21 to 40 on 136 ‹ 1 2 3 4 5 6 7 ›

SRS

Fridborg et al (2001): The current model of gibberellin (GA) signal transduction is based on a derepressible system and a number of candidate negative regulators have been identified in Arabidopsis. We previously have reported the identification of the Arabidopsis gene SHORT INTERNODES (SHI) that causes suppression of GA responses when constitutively activated. In this paper, we show by using reporter gene analysis that the SHI gene is expressed in young organs, e.g. shoot apices and root tips. The model predicts a suppressor of GA responses to be active in these tissues to prevent premature growth or development. To study the effect of SHI on GA signaling, we used a functional assay that measures effects of signaling components on a well-defined GA response; the up-regulation of alpha-amylase in barley (Hordeum vulgare) aleurones in response to GA treatment. We found that SHI was able to specifically block the activity of a high-isoelectric point alpha-amylase promoter following GA(3) treatment, which further supports that SHI is a suppressor of GA responses. We have identified two putative loss-of-function insertion alleles of SHI and lines homozygous for either of the new alleles show no phenotypic deviations from wild type. Because SHI belongs to a gene family consisting of nine members, we suggest that SHI and the SHI-related genes are functionally redundant. We also show that a functional ERECTA allele is able to partly suppress the dwarfing effect of the shi gain-of-function mutation, suggesting that the erecta mutation harbored by the Landsberg erecta ecotype is an enhancer of the shi dwarf phenotype.

Fridborg, I; Kuusk, S; Robertson, M; Sundberg, E. 2001. The Arabidopsis protein SHI represses gibberellin responses in Arabidopsis and barley. Plant Physiol. 127(3):937-48

TF

SOH1

Fan et al (1996): The soh1, soh2 and soh4 mutants were isolated as suppressors of the temperature-dependent growth of the hyperrecombination mutant hpr1 of Saccharomyces cerevisiae. Cloning and sequence analysis of these suppressor genes has unexpectedly shown them to code for components of the RNA polymerase II transcription complex. SOH2 is identical to RPB2, which encodes the second largest subunit of RNA polymerase II, and SOH4 is the same as SUA7, encoding the yeast transcription initiation factor TFIIB. SOH1 encodes a novel 14-kD protein with limited sequence similarity to RNA polymerases. Interestingly, SOH1 not only interacts with factors involved in DNA repair, but transcription as well. Thus, the Soh1 protein may serve to couple these two processes. The Soh1 protein interacts with a DNA repair protein, Rad5p, in a two-hybrid system assay. Soh1p may functionally interact with components of the RNA polymerase II complex as suggested from the synthetic lethality observed in soh1 rpb delta 104, soh1 soh2-1 (rpb2), and soh1 soh4 (sua7) double mutants. Because mutations in SOH1, RPB2 and SUA7 suppress the hyperrecombination phenotype of hpr1 mutants, this suggests a link between recombination in direct repeats and transcription.

Fan, HY; Cheng, KK; Klein, HL. 1996. Mutations in the RNA polymerase II transcription machinery suppress the hyperrecombination mutant hpr1 delta of Saccharomyces cerevisiae. Genetics 142(3):749-59

TR

Sir2

<a target="_blank" class="awithout" href="http://pfam.xfam.org/family/PF02146">PFAM</a> (0): Sirtuins are a class of proteins that possess either mono-ADP-ribosyltransferase, or deacylase activity and have been implicated in a wide range of cellular processes, including transcription. The human Sirt7 is involved in rRNA transcription in the nucleolus.

Lang, D; Weiche, B; Timmerhaus, G; Richardt, S; Riano-Pachon, DM; Correa, LG; Reski, R; Mueller-Roeber, B; Rensing, SA. 2010. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2: 488-503

TF

Sin3

<a target="_blank" class="awithout" href="http://pfam.xfam.org/family/PF02671">PFAM</a> (0): This family contains the paired amphipathic helix repeat. The family contains the yeast SIN3 gene. This repeat may be distantly related to the helix-loop-helix motif, which mediates protein-protein interactions.

Lang, D; Weiche, B; Timmerhaus, G; Richardt, S; Riano-Pachon, DM; Correa, LG; Reski, R; Mueller-Roeber, B; Rensing, SA. 2010. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2: 488-503

TR

Sigma70-like

Allison (2000): Expression of plastid genes is controlled at both transcriptional and post-transcriptional levels in response to developmental and environmental signals. In many cases this regulation is mediated by nuclear-encoded proteins acting in concert with the endogenous plastid gene expression machinery. Transcription in plastids is accomplished by two distinct RNA polymerase enzymes, one of which resembles eubacterial RNA polymerases in both subunit structure and promoter recognition properties. The holoenzyme contains a catalytic core composed of plastid-encoded subunits, assembled with a nuclear-encoded promoter-specificity factor, sigma. Based on examples of transcriptional regulation in bacteria, it is proposed that differential activation of sigma factors may provide the nucleus with a mechanism to control expression of groups of plastid genes. Hence, much effort has focused on identifying and characterizing sigma-like factors in plants. While fractionation studies had identified several candidate sigma factors in purified RNA polymerase preparations, it was only 4 years ago that the first sigma factor genes were cloned from two photosynthetic eukaryotes, both of which were red algae. More recently this achievement has extended to the identification of families of sigma-like factor genes from several species of vascular plants. Now, efforts in the field are directed at understanding the roles in plastid transcription of each member of the rapidly expanding plant sigma factor gene family. Recent results suggest that accumulation of individual sigma-like factors is controlled by light, by plastid type and/or by a particular stage of chloroplast development. These data mesh nicely with accumulating evidence that the core sigma-binding regions of plastid promoters mediate regulated transcription in response to light-regime and plastid type or developmental state. In this review I will outline progress made to date in identifying and characterizing the sigma-like factors of plants, and in dissecting their potential roles in chloroplast gene expression.

Allison, LA. 2000. The role of sigma factors in plastid transcription. Biochimie 82(6-7):537-48,"Paget, MS; Helmann, JD. 2003. The sigma70 family of sigma factors. Genome Biol. 4(1):203","Sriraman, P; Silhavy, D; Maliga, P. 1998. Transcription from heterologous rRNA operon promoters in chloroplasts reveals requirement for specific activating factors. Plant Physiol. 117(4):1495-9"

TR

SET

Marmorstein (2003): The methylation of lysine residues on histone tails is catalyzed by proteins containing a conserved SET domain. A recent flurry of structures of SET domain proteins has revealed a new protein fold and a scaffold for understanding catalysis and substrate binding by these enzymes. The prospect that histone methylation might form an epigenetic code and the implicated involvement of SET domain proteins in cancer assures that structure-function studies of these enzymes will continue until their detailed mechanism of action is determined.

Marmorstein, R. 2003. Structure of SET domain proteins: a new twist on histone methylation. Trends Biochem. Sci. 28(2):59-62,"Lang, D; Weiche, B; Timmerhaus, G; Richardt, S; Riano-Pachon, DM; Correa, LG; Reski, R; Mueller-Roeber, B; Rensing, SA. 2010. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2: 488-503"

TR

SBP

Cardon et al (1999): The Arabidopsis thaliana SPL gene family represents a group of structurally diverse genes encoding putative transcription factors found apparently only in plants. The distinguishing characteristic of the SPL gene family is the SBP-box encoding a conserved protein domain of 76 amino acids in length, the SBP-domain, which is responsible for the interaction with DNA. We present here characterisation of 12 members of the SPL gene family. These genes show highly diverse genomic organisations and are found scattered over the Arabidopsis genome. Some SPL genes are constitutively expressed, while transcriptional activity of others is under developmental control. Based on phylogenetic reconstruction, gene structure and expression patterns, they can be divided into subfamilies. In addition to the Arabidopsis SPL genes, we isolated and determined the sequences of three SBP-box genes from Antirrhinum majus and seven from Zea mays.

Cardon, G; Höhmann, S; Klein, J; Nettesheim, K; Saedler, H; Huijser, P. 1999. Molecular characterisation of the Arabidopsis SBP-box genes. Gene. 237(1):91-104,"Guo, AY; Zhu, QH; Gu, X; Ge, S; Yang, J; Luo, J. 2008. Genome-wide identification and evolutionary analysis of the plant specific SBP-box transcription factor family. Gene 418(1-2):1-8","Klein, J; Saedler, H; Huijser, P. 1996. A new family of DNA binding proteins includes putative transcriptional regulators of the Antirrhinum majus floral meristem identity gene SQUAMOSA. Mol. Gen. Genet. 250(1):7-16"

TF

SAP

Byzova et al (1999): A recessive mutation in the Arabidopsis STERILE APETALA (SAP) causes severe aberrations in inflorescence and flower and ovule development. In sap flowers, sepals are carpelloid, petals are short and narrow or absent, and anthers are degenerated. Megasporogenesis, the process of meiotic divisions preceding the female gametophyte formation, is arrested in sap ovules during or just after the first meiotic division. More severe aberrations were observed in double mutants between sap and mutant alleles of the floral homeotic gene APETALA2 (AP2) suggesting that both genes are involved in the initiation of female gametophyte development. Together with the organ identity gene AGAMOUS (AG) SAP is required for the maintenance of floral identity acting in a manner similar to APETALA1. In contrast to the outer two floral organs in sap mutant flowers, normal sepals and petals develop in ag/sap double mutants, indicating that SAP negatively regulates AG expression in the perianth whorls. This supposed cadastral function of SAP is supported by in situ hybridization experiments showing ectopic expression of AG in the sap mutant. We have cloned the SAP gene by transposon tagging and revealed that it encodes a novel protein with sequence motifs, that are also present in plant and animal transcription regulators. Consistent with the mutant phenotype, SAP is expressed in inflorescence and floral meristems, floral organ primordia, and ovules. Taken together, we propose that SAP belongs to a new class of transcription regulators essential for a number of processes in Arabidopsis flower development.

Byzova, MV; Franken, J; Aarts, MG; de Almeida-Engler, J; Engler, G; Mariani, C; Van Lookeren Campagne, MM; Angenent, GC. 1999. Arabidopsis STERILE APETALA, a multifunctional gene regulating inflorescence, flower, and ovule development. Genes Dev. 13(8):1002-14

TF

S1Fa-like

Zhou et al (1995): A cDNA encoding a specific binding activity for the tissue-specific negative cis-element S1F binding site of spinach rps1 was isolated from a spinach cDNA expression library. This cDNA of 0.7 kb encodes an unusual small peptide of only 70 amino acids, with a basic domain which contains a nuclear localization signal and a putative DNA binding helix. This protein, named S1Fa, is highly conserved between dicotyledonous and monocotyledonous plants and may represent a novel class of DNA binding proteins. The corresponding mRNA is accumulated more in roots and in etiolated seedlings than in green leaves. This expression pattern is correlated with the tissue-specific function of the S1F binding site which represses the rps1 promoter preferentially in roots and in etiolated plants.

Zhou, DX; Bisanz-Seyer, C; Mache, R. 1995. Molecular cloning of a small DNA binding protein with specificity for a tissue-specific negative element within the rps1 promoter. Nucleic Acids Res. 23(7):1165-9

TF

RWP-RK

Schauser et al (2005): Genetic studies in Lotus japonicus and pea have identified Nin as a core symbiotic gene required for establishing symbiosis between legumes and nitrogen fixing bacteria collectively called Rhizobium. Sequencing of additional Lotus cDNAs combined with analysis of genome sequences from Arabidopsis and rice reveals that Nin homologues in all three species constitute small gene families. In total, the Arabidopsis and rice genomes encode nine and three NIN-like proteins (NLPs), respectively. We present here a bioinformatics analysis and prediction of NLP evolution. On a genome scale we show that in Arabidopsis, this family has evolved through segmental duplication rather than through tandem amplification. Alignment of all predicted NLP protein sequences shows a composition with six conserved modules. In addition, Lotus and pea NLPs contain segments that might characterize NIN proteins of legumes and be of importance for their function in symbiosis. The most conserved region in NLPs, the RWP-RK domain, has secondary structure predictions consistent with DNA binding properties. This motif is shared by several other small proteins in both Arabidopsis and rice. In rice, the RWP-RK domain sequences have diversified significantly more than in Arabidopsis. Database searches reveal that, apart from its presence in Arabidopsis and rice, the motif is also found in the algae Chlamydomonas and in the slime mold Dictyostelium discoideum. Thus, the origin of this putative DNA binding region seems to predate the fungus-plant divide.

Schauser, L; Roussis, A; Stiller, J; Stougaard, J. 1999. A plant regulator controlling development of symbiotic root nodules. Nature 402(6758):191-5

TF

Runt

<a target="_blank" class="awithout" href="http://pfam.xfam.org/family/PF00853">PFAM</a> (0): The Runt domain is responsible for DNA-binding and protein-protein interaction.

Kagoshima, H; Shigesada, K; Satake, M; Ito, Y; Miyoshi, H; Ohki, M; Pepling, M; Gergen, P. 1993. The Runt domain identifies a new family of heteromeric transcriptional regulators. Trends Genet. 9(10):338-41,"Lang, D; Weiche, B; Timmerhaus, G; Richardt, S; Riano-Pachon, DM; Correa, LG; Reski, R; Mueller-Roeber, B; Rensing, SA. 2010. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2: 488-503"

TF

RRN3

Yamamoto et al (1996): RRN3 is one of the RRN genes specifically required for the transcription of rDNA by RNA polymerase I (Pol I) in Saccharomyces cerevisiae.

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,"Yamamoto, RT; Nogi, Y; Dodd, JA; Nomura M. 1996. RRN3 gene of Saccharomyces cerevisiae encodes an essential RNA polymerase I transcription factor which interacts with the polymerase independently of DNA template. EMBO J. 15(15):3964-73"

TR

RKD

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

RF-X

Reith et al (1990): RFX is a regulatory factor which binds to the X box of MHC class II genes and is essential for their expression. The DNA-binding domain of RFX is the central domain of the protein and binds ssDNA as either a monomer or homodimer.

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,"Reith, W; Herrero-Sanchez, C; Kobr, M; Silacci, P; Berte, C; Barras, E; Fey, S; Mach, B. 1990. MHC class II regulatory factor RFX has a novel DNA-binding domain and a functionally independent dimerization domain. Genes Dev. 4(9):1528-40"

TF

Rel

<a target="_blank" class="awithout" href="http://pfam.xfam.org/family/PF00554">PFAM</a> (0): The Rel homology domain (RHD) is a protein domain found in a family of eukaryotic transcription factors, which includes NF-κB, NFAT, among others. The RHD is composed of two immunoglobulin-like beta barrel subdomains that grip the DNA in the major groove. The N-terminal specificity domain resembles the core domain of the p53 transcription factor, and contains a recognition loop that interacts with DNA bases. The C-terminal dimerization domain contains the site for interaction with I-kappaB.

Müller, CW; Rey, FA; Sodeoka, M; Verdine, GL; Harrison, SC. 1995. Structure of the NF-kappa B p50 homodimer bound to DNA. Nature. 373(6512):311-7,"Lang, D; Weiche, B; Timmerhaus, G; Richardt, S; Riano-Pachon, DM; Correa, LG; Reski, R; Mueller-Roeber, B; Rensing, SA. 2010. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2: 488-503"

TF

Rcd1-like

Okazaki et al (1998): In the fission yeast Schizosaccharomyces pombe, the onset of sexual development is controlled mainly by two external signals, nutrient starvation and mating pheromone availability. We have isolated a novel gene named rcd1+ as a key factor required for nitrogen starvation-induced sexual development. rcd1+ encodes a 283-amino-acid protein with no particular motifs. However, genes highly homologous to rcd1+ (encoding amino acids with >70% identity) are present at least in budding yeasts, plants, nematodes, and humans. Cells with rcd1+ deleted are sterile if sexual development is induced by nitrogen starvation but fertile if it is induced by glucose starvation. This results largely from a defect in nitrogen starvation-invoked induction of ste11+, a key transcriptional factor gene required for the onset of sexual development. The striking conservation of the gene throughout eukaryotes may suggest the presence of an evolutionarily conserved differentiation controlling system.

Okazaki, N; Okazaki, K; Watanabe, Y; Kato-Hayashi, M; Yamamoto, M; Okayama, H. 1998. Novel factor highly conserved among eukaryotes controls sexual development in fission yeast. Mol. Cell. Biol. 18(2):887-95

TR

RB

Bremner et al (2004): The data suggest that RB protein may not control the rate of progenitor division, but is critical for cell cycle exit when dividing retinal progenitors differentiate into postmitotic transition cells.

Bremner, R; Chen, D; Pacal, M; Livne-Bar, I; Agochiya, M. 2004. The RB protein family in retinal development and retinoblastoma: new insights from new mouse models. Dev Neurosci. 26(5-6):417-34,"Ebel, C; Mariconti, L; Gruissem, W. 2004. Plant retinoblastoma homologues control nuclear proliferation in the female gametophyte. Nature 429(6993):776-80","Bremner, R; Chen, D; Pacal, M; Livne-Bar, I; Agochiya, M. 2004. The RB protein family in retinal development and retinoblastoma: new insights from new mouse models. Dev Neurosci. 26(5-6):417-34","Ebel, C; Mariconti, L; Gruissem, W. 2004. Plant retinoblastoma homologues control nuclear proliferation in the female gametophyte. Nature 429(6993):776-80"

TF

Pseudo ARR-B

Tajima et al (2004): In Arabidopsis thaliana, a Histidine-to-Aspartate (His-->Asp) phosphorelay is involved in the signal transduction for propagation of certain stimuli, such as plant hormones. Through the phosphorelay, the type-B phospho-accepting response regulator (ARR) family members serve as DNA-binding transcriptional regulators, whose activities are most likely regulated by phosphorylation/dephosphorylation.

Aoyama, T; Oka, A. 2003. Cytokinin signal transduction in plant cells. J. Plant Res. 116(3):221-31,"D'Agostino, IB; Kieber, JJ. 1999. Phosphorelay signal transduction: the emerging family of plant response regulators. Trends Biochem. Sci. 24(11):452-6","Kakimoto, T. 2003. Perception and signal transduction of cytokinins. Annu Rev Plant Biol 54:605-27","Kolmos, E; Schoof, H; PlÃ¼mer, M; Davis, SJ. 2008. Structural insights into the function of the core-circadian factor TIMING OF CAB2 EXPRESSION 1 (TOC1). J Circadian Rhythms 6:3","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","Tajima, Y; Imamura, A; Kiba, T; Amano, Y; Yamashino, T; Mizuno, T. 2004. Comparative studies on the type-B response regulators revealing their distinctive properties in the His-to-Asp phosphorelay signal transduction of Arabidopsis thaliana. Plant Cell Physiol. 45(1):28-39"

TF

PLATZ

Nagano et al (2001): Complementary DNA encoding a DNA-binding protein, designated PLATZ1 (plant AT-rich sequence- and zinc-binding protein 1), was isolated from peas. The amino acid sequence of the protein is similar to those of other uncharacterized proteins predicted from the genome sequences of higher plants. However, no paralogous sequences have been found outside the plant kingdom. Multiple alignments among these paralogous proteins show that several cysteine and histidine residues are invariant, suggesting that these proteins are a novel class of zinc-dependent DNA-binding proteins with two distantly located regions, C-x(2)-H-x(11)-C-x(2)-C-x((4-5))-C-x(2)-C-x((3-7))-H-x(2)-H and C-x(2)-C-x((10-11))-C-x(3)-C. In an electrophoretic mobility shift assay, the zinc chelator 1,10-o-phenanthroline inhibited DNA binding, and two distant zinc-binding regions were required for DNA binding. A protein blot with (65)ZnCl(2) showed that both regions are required for zinc-binding activity. The PLATZ1 protein non-specifically binds to A/T-rich sequences, including the upstream region of the pea GTPase pra2 and plastocyanin petE genes. Expression of the PLATZ1 repressed those of the reporter constructs containing the coding sequence of luciferase gene driven by the cauliflower mosaic virus (CaMV) 35S90 promoter fused to the tandem repeat of the A/T-rich sequences. These results indicate that PLATZ1 is a novel class of plant-specific zinc-dependent DNA-binding protein responsible for A/T-rich sequence-mediated transcriptional repression.

Nagano, Y; Furuhashi, H; Inaba, T; Sasaki, Y. 2001. A novel class of plant-specific zinc-dependent DNA-binding protein that binds to A/T-rich DNA sequences. Nucleic Acids Res. 29(20):4097-105

TF

PHD

Bienz (2006): PHD proteins seem to be found universally in the nucleus, and their functions tend to lie in the control of chromatin or transcription. Increasing evidence indicates that PHD fingers bind to specific nuclear protein partners, for which they apparently use their loop 2 surface. Perhaps each PHD finger has its own cognate nuclear ligand, much like RING fingers have their cognate E2 ligases. No doubt the list of specific PHD finger ligands will grow, and the set of these ligands is likely to reveal whether PHD fingers have a common function in the nucleus.

Bienz, M. 2006. The PHD finger, a nuclear protein-interaction domain. Trends Biochem. Sci. 31(1):35-40,"Lang, D; Weiche, B; Timmerhaus, G; Richardt, S; Riano-Pachon, DM; Correa, LG; Reski, R; Mueller-Roeber, B; Rensing, SA. 2010. Genome-wide phylogenetic comparative analysis of plant transcriptional regulation: a timeline of loss, gain, expansion, and correlation with complexity. Genome Biol Evol. 2: 488-503"

TR