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HD_TALE_BEL
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The homeobox TF superfamily is defined by an occurrence of the characteristic homeodomain (HD) and can be defined as pan-eukaryotic since it is found in all eukaryotic organisms (Catarino et al., 2016; Romani et al., 2018). According to different references (e.g., (Catarino et al., 2016; Mukherjee et al., 2009; Que et al., 2018)), the HD superfamily is divided into 11 subfamilies, namely BEL, DDT, HDZ, KNOX, LD, NDX, PHD, PINTOX, PLINC, SAWADEE and WOX. Interestingly, all subfamilies evolved in the common ancestor, before terrestrialization and diversification of land plants (Catarino et al., 2016). Furthermore, the broad distribution and high conservation of domains induces a common highly conserved functional role in plants and whenever members are present, also in algae (Mukherjee et al., 2009). In general, homeobox TFs show diverse functions in developmental and physiological mechanisms (Romani et al., 2018). In members of the LD subfamily, the conserved LUMI domain is expected in addition to the homeodomain (Mukherjee et al., 2009).
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Catarino, B., Hetherington, A. J., Emms, D. M., Kelly, S., & Dolan, L. (2016). The Stepwise Increase in the Number of Transcription Factor Families in the Precambrian Predated the Diversification of Plants On Land. Molecular Biology and Evolution, 33(11), 2815–2819. https://doi.org/10.1093/molbev/msw155,"Romani, F., Reinheimer, R., Florent, S. N., Bowman, J. L., & Moreno, J. E. (2018). Evolutionary history of HOMEODOMAIN LEUCINE ZIPPER transcription factors during plant transition to land. New Phytologist, 219(1), 408–421. https://doi.org/10.1111/nph.15133","Que, F., Wang, G.-L., Li, T., Wang, Y.-H., Xu, Z.-S., & Xiong, A.-S. (2018). Genome-wide identification, expansion, and evolution analysis of homeobox genes and their expression profiles during root development in carrot. Functional & Integrative Genomics, 18(6), 685–700. https://doi.org/10.1007/s10142-018-0624-x", "Mukherjee, K., Brocchieri, L., & Burglin, T. R. (2009). A Comprehensive Classification and Evolutionary Analysis of Plant Homeobox Genes. Molecular Biology and Evolution, 26(12), 2775–2794. https://doi.org/10.1093/molbev/msp201"
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TF
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HD_TALE_KNOX1
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The homeobox TF superfamily is defined by an occurrence of the characteristic homeodomain (HD) and can be defined as pan-eukaryotic since it is found in all eukaryotic organisms (Catarino et al., 2016; Romani et al., 2018). According to different references (e.g., (Catarino et al., 2016; Mukherjee et al., 2009; Que et al., 2018)), the HD superfamily is divided into 11 subfamilies, namely BEL, DDT, HDZ, KNOX, LD, NDX, PHD, PINTOX, PLINC, SAWADEE and WOX. Interestingly, all subfamilies evolved in the common ancestor, before terrestrialization and diversification of land plants (Catarino et al., 2016). Furthermore, the broad distribution and high conservation of domains induces a common highly conserved functional role in plants and whenever members are present, also in algae (Mukherjee et al., 2009). In general, homeobox TFs show diverse functions in developmental and physiological mechanisms (Romani et al., 2018). In members of the LD subfamily, the conserved LUMI domain is expected in addition to the homeodomain (Mukherjee et al., 2009).
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Catarino, B., Hetherington, A. J., Emms, D. M., Kelly, S., & Dolan, L. (2016). The Stepwise Increase in the Number of Transcription Factor Families in the Precambrian Predated the Diversification of Plants On Land. Molecular Biology and Evolution, 33(11), 2815–2819. https://doi.org/10.1093/molbev/msw155,"Romani, F., Reinheimer, R., Florent, S. N., Bowman, J. L., & Moreno, J. E. (2018). Evolutionary history of HOMEODOMAIN LEUCINE ZIPPER transcription factors during plant transition to land. New Phytologist, 219(1), 408–421. https://doi.org/10.1111/nph.15133","Que, F., Wang, G.-L., Li, T., Wang, Y.-H., Xu, Z.-S., & Xiong, A.-S. (2018). Genome-wide identification, expansion, and evolution analysis of homeobox genes and their expression profiles during root development in carrot. Functional & Integrative Genomics, 18(6), 685–700. https://doi.org/10.1007/s10142-018-0624-x", "Mukherjee, K., Brocchieri, L., & Burglin, T. R. (2009). A Comprehensive Classification and Evolutionary Analysis of Plant Homeobox Genes. Molecular Biology and Evolution, 26(12), 2775–2794. https://doi.org/10.1093/molbev/msp201"
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TF
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HD_TALE_KNOX2
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The homeobox TF superfamily is defined by an occurrence of the characteristic homeodomain (HD) and can be defined as pan-eukaryotic since it is found in all eukaryotic organisms (Catarino et al., 2016; Romani et al., 2018). According to different references (e.g., (Catarino et al., 2016; Mukherjee et al., 2009; Que et al., 2018)), the HD superfamily is divided into 11 subfamilies, namely BEL, DDT, HDZ, KNOX, LD, NDX, PHD, PINTOX, PLINC, SAWADEE and WOX. Interestingly, all subfamilies evolved in the common ancestor, before terrestrialization and diversification of land plants (Catarino et al., 2016). Furthermore, the broad distribution and high conservation of domains induces a common highly conserved functional role in plants and whenever members are present, also in algae (Mukherjee et al., 2009). In general, homeobox TFs show diverse functions in developmental and physiological mechanisms (Romani et al., 2018). In members of the LD subfamily, the conserved LUMI domain is expected in addition to the homeodomain (Mukherjee et al., 2009).
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Catarino, B., Hetherington, A. J., Emms, D. M., Kelly, S., & Dolan, L. (2016). The Stepwise Increase in the Number of Transcription Factor Families in the Precambrian Predated the Diversification of Plants On Land. Molecular Biology and Evolution, 33(11), 2815–2819. https://doi.org/10.1093/molbev/msw155,"Romani, F., Reinheimer, R., Florent, S. N., Bowman, J. L., & Moreno, J. E. (2018). Evolutionary history of HOMEODOMAIN LEUCINE ZIPPER transcription factors during plant transition to land. New Phytologist, 219(1), 408–421. https://doi.org/10.1111/nph.15133","Que, F., Wang, G.-L., Li, T., Wang, Y.-H., Xu, Z.-S., & Xiong, A.-S. (2018). Genome-wide identification, expansion, and evolution analysis of homeobox genes and their expression profiles during root development in carrot. Functional & Integrative Genomics, 18(6), 685–700. https://doi.org/10.1007/s10142-018-0624-x", "Mukherjee, K., Brocchieri, L., & Burglin, T. R. (2009). A Comprehensive Classification and Evolutionary Analysis of Plant Homeobox Genes. Molecular Biology and Evolution, 26(12), 2775–2794. https://doi.org/10.1093/molbev/msp201"
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TF
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HD_WOX
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The homeobox TF superfamily is defined by an occurrence of the characteristic homeodomain (HD) and can be defined as pan-eukaryotic since it is found in all eukaryotic organisms (Catarino et al., 2016; Romani et al., 2018). According to different references (e.g., (Catarino et al., 2016; Mukherjee et al., 2009; Que et al., 2018)), the HD superfamily is divided into 11 subfamilies, namely BEL, DDT, HDZ, KNOX, LD, NDX, PHD, PINTOX, PLINC, SAWADEE and WOX. Interestingly, all subfamilies evolved in the common ancestor, before terrestrialization and diversification of land plants (Catarino et al., 2016). Furthermore, the broad distribution and high conservation of domains induces a common highly conserved functional role in plants and whenever members are present, also in algae (Mukherjee et al., 2009). In general, homeobox TFs show diverse functions in developmental and physiological mechanisms (Romani et al., 2018). In members of the LD subfamily, the conserved LUMI domain is expected in addition to the homeodomain (Mukherjee et al., 2009).
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Catarino, B., Hetherington, A. J., Emms, D. M., Kelly, S., & Dolan, L. (2016). The Stepwise Increase in the Number of Transcription Factor Families in the Precambrian Predated the Diversification of Plants On Land. Molecular Biology and Evolution, 33(11), 2815–2819. https://doi.org/10.1093/molbev/msw155,"Romani, F., Reinheimer, R., Florent, S. N., Bowman, J. L., & Moreno, J. E. (2018). Evolutionary history of HOMEODOMAIN LEUCINE ZIPPER transcription factors during plant transition to land. New Phytologist, 219(1), 408–421. https://doi.org/10.1111/nph.15133","Que, F., Wang, G.-L., Li, T., Wang, Y.-H., Xu, Z.-S., & Xiong, A.-S. (2018). Genome-wide identification, expansion, and evolution analysis of homeobox genes and their expression profiles during root development in carrot. Functional & Integrative Genomics, 18(6), 685–700. https://doi.org/10.1007/s10142-018-0624-x", "Mukherjee, K., Brocchieri, L., & Burglin, T. R. (2009). A Comprehensive Classification and Evolutionary Analysis of Plant Homeobox Genes. Molecular Biology and Evolution, 26(12), 2775–2794. https://doi.org/10.1093/molbev/msp201"
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TF
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HD-LD
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The homeobox TF superfamily is defined by an occurrence of the characteristic homeodomain (HD) and can be defined as pan-eukaryotic since it is found in all eukaryotic organisms (Catarino et al., 2016; Romani et al., 2018). According to different references (e.g., (Catarino et al., 2016; Mukherjee et al., 2009; Que et al., 2018)), the HD superfamily is divided into 11 subfamilies, namely BEL, DDT, HDZ, KNOX, LD, NDX, PHD, PINTOX, PLINC, SAWADEE and WOX. Interestingly, all subfamilies evolved in the common ancestor, before terrestrialization and diversification of land plants (Catarino et al., 2016). Furthermore, the broad distribution and high conservation of domains induces a common highly conserved functional role in plants and whenever members are present, also in algae (Mukherjee et al., 2009). In general, homeobox TFs show diverse functions in developmental and physiological mechanisms (Romani et al., 2018). In members of the LD subfamily, the conserved LUMI domain is expected in addition to the homeodomain (Mukherjee et al., 2009).
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Catarino, B., Hetherington, A. J., Emms, D. M., Kelly, S., & Dolan, L. (2016). The Stepwise Increase in the Number of Transcription Factor Families in the Precambrian Predated the Diversification of Plants On Land. Molecular Biology and Evolution, 33(11), 2815–2819. https://doi.org/10.1093/molbev/msw155,"Romani, F., Reinheimer, R., Florent, S. N., Bowman, J. L., & Moreno, J. E. (2018). Evolutionary history of HOMEODOMAIN LEUCINE ZIPPER transcription factors during plant transition to land. New Phytologist, 219(1), 408–421. https://doi.org/10.1111/nph.15133","Que, F., Wang, G.-L., Li, T., Wang, Y.-H., Xu, Z.-S., & Xiong, A.-S. (2018). Genome-wide identification, expansion, and evolution analysis of homeobox genes and their expression profiles during root development in carrot. Functional & Integrative Genomics, 18(6), 685–700. https://doi.org/10.1007/s10142-018-0624-x", "Mukherjee, K., Brocchieri, L., & Burglin, T. R. (2009). A Comprehensive Classification and Evolutionary Analysis of Plant Homeobox Genes. Molecular Biology and Evolution, 26(12), 2775–2794. https://doi.org/10.1093/molbev/msp201"
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TF
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HD-NDX
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The homeobox TF superfamily is defined by an occurrence of the characteristic homeodomain (HD) and can be defined as pan-eukaryotic since it is found in all eukaryotic organisms (Catarino et al., 2016; Romani et al., 2018). According to different references (e.g., (Catarino et al., 2016; Mukherjee et al., 2009; Que et al., 2018)), the HD superfamily is divided into 11 subfamilies, namely BEL, DDT, HDZ, KNOX, LD, NDX, PHD, PINTOX, PLINC, SAWADEE and WOX. Interestingly, all subfamilies evolved in the common ancestor, before terrestrialization and diversification of land plants (Catarino et al., 2016). Furthermore, the broad distribution and high conservation of domains induces a common highly conserved functional role in plants and whenever members are present, also in algae (Mukherjee et al., 2009). In general, homeobox TFs show diverse functions in developmental and physiological mechanisms (Romani et al., 2018). In members of the NDX subfamily, an NDX (Nodulin Homeobox genes) domain is expected in addition to the homeodomain (Mukherjee et al., 2009).
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Catarino, B., Hetherington, A. J., Emms, D. M., Kelly, S., & Dolan, L. (2016). The Stepwise Increase in the Number of Transcription Factor Families in the Precambrian Predated the Diversification of Plants On Land. Molecular Biology and Evolution, 33(11), 2815–2819. https://doi.org/10.1093/molbev/msw155,"Romani, F., Reinheimer, R., Florent, S. N., Bowman, J. L., & Moreno, J. E. (2018). Evolutionary history of HOMEODOMAIN LEUCINE ZIPPER transcription factors during plant transition to land. New Phytologist, 219(1), 408–421. https://doi.org/10.1111/nph.15133","Que, F., Wang, G.-L., Li, T., Wang, Y.-H., Xu, Z.-S., & Xiong, A.-S. (2018). Genome-wide identification, expansion, and evolution analysis of homeobox genes and their expression profiles during root development in carrot. Functional & Integrative Genomics, 18(6), 685–700. https://doi.org/10.1007/s10142-018-0624-x","Mukherjee, K., Brocchieri, L., & Burglin, T. R. (2009). A Comprehensive Classification and Evolutionary Analysis of Plant Homeobox Genes. Molecular Biology and Evolution, 26(12), 2775–2794. https://doi.org/10.1093/molbev/msp201"
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TF
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HD-other
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The homeobox TF superfamily is defined by an occurrence of the characteristic homeodomain (HD) and can be defined as pan-eukaryotic since it is found in all eukaryotic organisms (Catarino et al., 2016; Romani et al., 2018). According to different references (e.g., (Catarino et al., 2016; Mukherjee et al., 2009; Que et al., 2018)), the HD superfamily is divided into 11 subfamilies, namely BEL, DDT, HDZ, KNOX, LD, NDX, PHD, PINTOX, PLINC, SAWADEE and WOX. Interestingly, all subfamilies evolved in the common ancestor, before terrestrialization and diversification of land plants (Catarino et al., 2016). Furthermore, the broad distribution and high conservation of domains induces a common highly conserved functional role in plants and whenever members are present, also in algae (Mukherjee et al., 2009). In general, homeobox TFs show diverse functions in developmental and physiological mechanisms (Romani et al., 2018). In members of the LD subfamily, the conserved LUMI domain is expected in addition to the homeodomain (Mukherjee et al., 2009).
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Catarino, B., Hetherington, A. J., Emms, D. M., Kelly, S., & Dolan, L. (2016). The Stepwise Increase in the Number of Transcription Factor Families in the Precambrian Predated the Diversification of Plants On Land. Molecular Biology and Evolution, 33(11), 2815–2819. https://doi.org/10.1093/molbev/msw155,"Romani, F., Reinheimer, R., Florent, S. N., Bowman, J. L., & Moreno, J. E. (2018). Evolutionary history of HOMEODOMAIN LEUCINE ZIPPER transcription factors during plant transition to land. New Phytologist, 219(1), 408–421. https://doi.org/10.1111/nph.15133","Que, F., Wang, G.-L., Li, T., Wang, Y.-H., Xu, Z.-S., & Xiong, A.-S. (2018). Genome-wide identification, expansion, and evolution analysis of homeobox genes and their expression profiles during root development in carrot. Functional & Integrative Genomics, 18(6), 685–700. https://doi.org/10.1007/s10142-018-0624-x", "Mukherjee, K., Brocchieri, L., & Burglin, T. R. (2009). A Comprehensive Classification and Evolutionary Analysis of Plant Homeobox Genes. Molecular Biology and Evolution, 26(12), 2775–2794. https://doi.org/10.1093/molbev/msp201"
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TF
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HD-SAWADEE
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The homeobox TF superfamily is defined by an occurrence of the characteristic homeodomain (HD) and can be defined as pan-eukaryotic since it is found in all eukaryotic organisms (Catarino et al., 2016; Romani et al., 2018). According to different references (e.g., (Catarino et al., 2016; Mukherjee et al., 2009; Que et al., 2018)), the HD superfamily is divided into 11 subfamilies, namely BEL, DDT, HDZ, KNOX, LD, NDX, PHD, PINTOX, PLINC, SAWADEE and WOX. Interestingly, all subfamilies evolved in the common ancestor, before terrestrialization and diversification of land plants (Catarino et al., 2016). Furthermore, the broad distribution and high conservation of domains induces a common highly conserved functional role in plants and whenever members are present, also in algae (Mukherjee et al., 2009). In general, homeobox TFs show diverse functions in developmental and physiological mechanisms (Romani et al., 2018). In members of the SAWADEE subfamily, an SAWADEE domain is expected in addition to the homeodomain.
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Catarino, B., Hetherington, A. J., Emms, D. M., Kelly, S., & Dolan, L. (2016). The Stepwise Increase in the Number of Transcription Factor Families in the Precambrian Predated the Diversification of Plants On Land. Molecular Biology and Evolution, 33(11), 2815–2819. https://doi.org/10.1093/molbev/msw155,"Romani, F., Reinheimer, R., Florent, S. N., Bowman, J. L., & Moreno, J. E. (2018). Evolutionary history of HOMEODOMAIN LEUCINE ZIPPER transcription factors during plant transition to land. New Phytologist, 219(1), 408–421. https://doi.org/10.1111/nph.15133","Que, F., Wang, G.-L., Li, T., Wang, Y.-H., Xu, Z.-S., & Xiong, A.-S. (2018). Genome-wide identification, expansion, and evolution analysis of homeobox genes and their expression profiles during root development in carrot. Functional & Integrative Genomics, 18(6), 685–700. https://doi.org/10.1007/s10142-018-0624-x","Mukherjee, K., Brocchieri, L., & Burglin, T. R. (2009). A Comprehensive Classification and Evolutionary Analysis of Plant Homeobox Genes. Molecular Biology and Evolution, 26(12), 2775–2794. https://doi.org/10.1093/molbev/msp201"
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TF
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HDZ
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The homeobox TF superfamily is defined by an occurrence of the characteristic homeodomain (HD) and can be defined as pan-eukaryotic since it is found in all eukaryotic organisms (Catarino et al., 2016; Romani et al., 2018). According to different references (e.g., (Catarino et al., 2016; Mukherjee et al., 2009; Que et al., 2018)), the HD superfamily is divided into 11 subfamilies, namely BEL, DDT, HDZ, KNOX, LD, NDX, PHD, PINTOX, PLINC, SAWADEE and WOX. Interestingly, all subfamilies evolved in the common ancestor, before terrestrialization and diversification of land plants (Catarino et al., 2016). Furthermore, the broad distribution and high conservation of domains induces a common highly conserved functional role in plants and whenever members are present, also in algae (Mukherjee et al., 2009). In general, homeobox TFs show diverse functions in developmental and physiological mechanisms (Romani et al., 2018). The HD-HDZ (HDZ) subfamily can be subdivided into four classes, namely classes C1HDZ, C2HDZ, C3HDZ and C4HDZ. The members of these classes exhibit a characteristic homeodomain and an additional leucine zipper (LZ) domain (Romani et al., 2018). Furthermore, in C2HDZ proteins an aromatic, large hydrophobic, acidic context (AHA)-like motif appears (Romani et al., 2018). Also, in C2HDZ proteins there are two additional exclusive motifs, in fact the C-terminal CPSCE sequence and the N-terminal ZIBEL-like motif (Romani et al., 2018). In addition, C3HDZ proteins exhibit a unique MEKHLA domain and 3HDZ and C4HDZ proteins show START/SAD domains (Romani et al., 2018).
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Catarino, B., Hetherington, A. J., Emms, D. M., Kelly, S., & Dolan, L. (2016). The Stepwise Increase in the Number of Transcription Factor Families in the Precambrian Predated the Diversification of Plants On Land. Molecular Biology and Evolution, 33(11), 2815–2819. https://doi.org/10.1093/molbev/msw155,"Romani, F., Reinheimer, R., Florent, S. N., Bowman, J. L., & Moreno, J. E. (2018). Evolutionary history of HOMEODOMAIN LEUCINE ZIPPER transcription factors during plant transition to land. New Phytologist, 219(1), 408–421. https://doi.org/10.1111/nph.15133","Mukherjee, K., Brocchieri, L., & Burglin, T. R. (2009). A Comprehensive Classification and Evolutionary Analysis of Plant Homeobox Genes. Molecular Biology and Evolution, 26(12), 2775–2794. https://doi.org/10.1093/molbev/msp201","Que, F., Wang, G.-L., Li, T., Wang, Y.-H., Xu, Z.-S., & Xiong, A.-S. (2018). Genome-wide identification, expansion, and evolution analysis of homeobox genes and their expression profiles during root development in carrot. Functional & Integrative Genomics, 18(6), 685–700. https://doi.org/10.1007/s10142-018-0624-x"
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TF
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HMG
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Griess et al (1993): HMG boxes were initially identified as DNA-binding domains of the human RNA polymerase I (pol I) transcription factor hUBF and the animal high-mobility-group (HMG) protein family HMG1.
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Grasser, KD; Teo, SH; Lee, KB; Broadhurst, RW; Rees, C; Hardman, CH; Thomas, JO. 1998. DNA-binding properties of the tandem HMG boxes of high-mobility-group protein 1 (HMG1). Eur. J. Biochem. 253(3):787-95,"Griess, EA; Rensing, SA; Grasser, KD; Maier, UG; Feix, G. 1993. Phylogenetic relationships of HMG box DNA-binding domains. J. Mol. Evol. 37(2):204-10","Wissmüller, S; Kosian, T; Wolf, M; Finzsch, M; Wegner, M. 2006. The high-mobility-group domain of Sox proteins interacts with DNA-binding domains of many transcription factors. Nucleic Acids Res. 34(6):1735-44"
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TR
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HRT
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Raventós et al (1998): A barley gene encoding a novel DNA-binding protein (HRT) was identified by southwestern screening with baits containing a gibberellin phytohormone response element from an alpha-amylase promoter. The HRT gene contains two introns, the larger of which (5722 base pairs (bp)) contains a 3094-bp LINE-like element with homology to maize Colonist1. In vitro mutagenesis and zinc- and DNA-binding assays demonstrate that HRT contains three unusual zinc fingers with a CX8-9CX10CX2H consensus sequence. HRT is targeted to nuclei, and homologues are expressed in other plants. In vivo, functional tests in plant cells indicate that full-length HRT can repress expression from certain promoters including the Amy1/6-4 and Amy2/32 alpha-amylase promoters. In contrast, truncated forms of HRT containing DNA-binding domains can activate, or derepress, transcription from these promoters. Northern hybridizations indicate that HRT mRNA accumulates to low levels in various tissues. Roles for HRT in mediating developmental and phytohormone-responsive gene expression are discussed.
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Raventós, D; Skriver, K; Schlein, M; Karnahl, K; Rogers, SW; Rogers, JC; Mundy, J. 1998. HRT, a novel zinc finger, transcriptional repressor from barley. J. Biol. Chem. 273(36):23313-20
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TF
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HSF
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Wu (1995): Organisms respond to elevated temperatures and to chemical and physiological stresses by an increase in the synthesis of heat shock proteins. The regulation of heat shock gene expression in eukaryotes is mediated by the conserved heat shock transcription factor (HSF). HSF is present in a latent state under normal conditions; it is activated upon heat stress by induction of trimerization and high-affinity binding to DNA and by exposure of domains for transcriptional activity. Analysis of HSF cDNA clones from many species has defined structural and regulatory regions responsible for the inducible activities. The heat stress signal is thought to be transduced to HSF by changes in the physical environment, in the activity of HSF-modifying enzymes, or by changes in the intracellular level of heat shock proteins.
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Baniwal, SK; Bharti, K; Chan, KY; Fauth, M; Ganguli, A; Kotak, S; Mishra, SK; Nover, L; Port, M; Scharf, KD; Tripp, J; Weber, C; Zielinski, D; von Koskull-Döring, P. 2004. Heat stress response in plants: a complex game with chaperones and more than twenty heat stress transcription factors. J. Biosci. 29(4):471-87,"Fujita, A; Kikuchi, Y; Kuhara, S; Misumi, Y; Matsumoto, S; Kobayashi, H. 1989. Domains of the SFL1 protein of yeasts are homologous to Myc oncoproteins or yeast heat-shock transcription factor. Gene 85(2):321-8","Nover, L; Scharf, KD; Gagliardi, D; Vergne, P; Czarnecka-Verner, E; Gurley, WB. 1996. The Hsf world: classification and properties of plant heat stress transcription factors. Cell Stress Chaperones 1(4):215-23","Wu, C. 1995. Heat shock transcription factors: structure and regulation. Annu. Rev. Cell Dev. Biol. 11:441-69"
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TF
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IWS1
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<a target="_blank" class="awithout" href="http://pfam.xfam.org/family/PF08711">PFAM</a> (0): This family consists of a the C terminal region of a number of eukaryotic hypothetical proteins which are homologous to the Saccharomyces cerevisiae protein IWS1. IWS1 is known to be an Pol II transcription elongation factor and interacts with Spt6 and Spt5.
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Krogan, NJ; Kim, M; Ahn, SH; Zhong, G; Kobor, MS; Cagney, G; Emili, A; Shilatifard, A; Buratowski, S; Greenblatt, JF. 2002. RNA polymerase II elongation factors of Saccharomyces cerevisiae: a targeted proteomics approach. Mol. Cell. Biol. 22(20):6979-92
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TR
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LFY
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Parcy et al (1998): The initial steps of flower development involve two classes of consecutively acting regulatory genes. Meristem-identity genes, which act early to control the initiation of flowers, are expressed throughout the incipient floral primordium. Homeotic genes, which act later to specify the identity of individual floral organs, are expressed in distinct domains within the flower. The link between the two classes of genes has remained unknown so far. Here we show that the meristem-identity gene LEAFY has a role in controlling homeotic genes that is separable from its role in specifying floral fate. On the basis of our observation that LEAFY activates different homeotic genes through distinct mechanisms, we propose a genetic framework for the control of floral patterning.
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Parcy, F; Nilsson, O; Busch, MA; Lee, I; Weigel, D. 1998. A genetic framework for floral patterning. Nature 395(6702):561-6
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TF
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LIM
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Kawaoka et al (2000): The AC-rich motif, Pal-box, is an important cis-acting element for gene expression involved in phenylpropanoid biosynthesis. A cDNA clone (Ntlim1) encoding a Pal-box binding protein was isolated by Southwestern screening. The deduced amino acid sequence is highly similar to the members of the LIM protein family that contain a zinc finger motif. Moreover, Ntlim1 had a specific DNA binding ability and transiently activated the transcription of a beta-glucuronidase reporter gene driven by the Pal-box sequence in tobacco protoplasts. The transgenic tobacco plants with antisense Ntlim1 showed low levels of transcripts from some key phenylpropanoid pathway genes such as phenylalanine ammonia-lyase, hydroxycinnamate CoA ligase and cinnamyl alcohol dehydrogenase. Furthermore, a 27% reduction of lignin content was observed in the transgenic tobacco with antisense Ntlim1.
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Eliasson, A; Gass, N; Mundel, C; Baltz, R; Kräuter, R; Evrard, JL; Steinmetz, A. 2000. Molecular and expression analysis of a LIM protein gene family from flowering plants. Mol. Gen. Genet. 264(3):257-67,"Kawaoka, A; Kaothien, P; Yoshida, K; Endo, S; Yamada, K; Ebinuma, H. 2000. Functional analysis of tobacco LIM protein Ntlim1 involved in lignin biosynthesis. Plant J. 22(4):289-301"
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TF
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LOB1
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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).
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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"
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TF
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LOB2
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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).
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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"
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TF
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LUG
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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.
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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
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TR
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MADS
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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.
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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"
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TF
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MBF1
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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.
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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
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TR
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