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Yang X, Wu F, Lin X, Du X, Chong K, Gramzow L, Schilling S, Becker A, Theißen G, Meng Z. Live and let die - the B(sister) MADS-box gene OsMADS29 controls the degeneration of cells in maternal tissues during seed development of rice (Oryza sativa). PLoS One 2012; 7:e51435. [PMID: 23251532 PMCID: PMC3520895 DOI: 10.1371/journal.pone.0051435] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Accepted: 11/01/2012] [Indexed: 11/19/2022] Open
Abstract
Bsister genes have been identified as the closest relatives of class B floral homeotic genes. Previous studies have shown that Bsister genes from eudicots are involved in cell differentiation during ovule and seed development. However, the complete function of Bsister genes in eudicots is masked by redundancy with other genes and little is known about the function of Bsister genes in monocots, and about the evolution of Bsister gene functions. Here we characterize OsMADS29, one of three MADS-box Bsister genes in rice. Our analyses show that OsMADS29 is expressed in female reproductive organs including the ovule, ovule vasculature, and the whole seed except for the outer layer cells of the pericarp. Knock-down of OsMADS29 by double-stranded RNA-mediated interference (RNAi) results in shriveled and/or aborted seeds. Histological analyses of the abnormal seeds at 7 days after pollination (DAP) indicate that the symplastic continuity, including the ovular vascular trace and the nucellar projection, which is the nutrient source for the filial tissue at early development stages, is affected. Moreover, degeneration of all the maternal tissues in the transgenic seeds, including the pericarp, ovular vascular trace, integuments, nucellar epidermis and nucellar projection, is blocked as compared to control plants. Our results suggest that OsMADS29 has important functions in seed development of rice by regulating cell degeneration of maternal tissues. Our findings provide important insights into the ancestral function of Bsister genes.
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Affiliation(s)
- Xuelian Yang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, People’s Republic of China
- Graduate School, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Feng Wu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Xuelei Lin
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, People’s Republic of China
- Graduate School, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Xiaoqiu Du
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Kang Chong
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Lydia Gramzow
- Department of Genetics, Friedrich Schiller University Jena, Jena, Germany
| | - Susanne Schilling
- Department of Genetics, Friedrich Schiller University Jena, Jena, Germany
| | - Annette Becker
- Plant Evo-Devo Group, The Institute of Botany, Justus-Liebig-University Gießen, Gießen, Germany
| | - Günter Theißen
- Department of Genetics, Friedrich Schiller University Jena, Jena, Germany
- * E-mail: (GT); (ZM)
| | - Zheng Meng
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, People’s Republic of China
- * E-mail: (GT); (ZM)
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Smaczniak C, Immink RGH, Angenent GC, Kaufmann K. Developmental and evolutionary diversity of plant MADS-domain factors: insights from recent studies. Development 2012; 139:3081-98. [PMID: 22872082 DOI: 10.1242/dev.074674] [Citation(s) in RCA: 340] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Members of the MADS-box transcription factor family play essential roles in almost every developmental process in plants. Many MADS-box genes have conserved functions across the flowering plants, but some have acquired novel functions in specific species during evolution. The analyses of MADS-domain protein interactions and target genes have provided new insights into their molecular functions. Here, we review recent findings on MADS-box gene functions in Arabidopsis and discuss the evolutionary history and functional diversification of this gene family in plants. We also discuss possible mechanisms of action of MADS-domain proteins based on their interactions with chromatin-associated factors and other transcriptional regulators.
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Affiliation(s)
- Cezary Smaczniak
- Laboratory of Molecular Biology, Wageningen University, 6708PB Wageningen, The Netherlands
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Deng W, Chen G, Peng F, Truksa M, Snyder CL, Weselake RJ. Transparent testa16 plays multiple roles in plant development and is involved in lipid synthesis and embryo development in canola. PLANT PHYSIOLOGY 2012; 160:978-89. [PMID: 22846192 PMCID: PMC3461570 DOI: 10.1104/pp.112.198713] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Transparent Testa16 (TT16), a transcript regulator belonging to the B(sister) MADS box proteins, regulates proper endothelial differentiation and proanthocyanidin accumulation in the seed coat. Our understanding of its other physiological roles, however, is limited. In this study, the physiological and developmental roles of TT16 in an important oil crop, canola (Brassica napus), were dissected by a loss-of-function approach. RNA interference (RNAi)-mediated down-regulation of tt16 in canola caused dwarf phenotypes with a decrease in the number of inflorescences, flowers, siliques, and seeds. Fluorescence microscopy revealed that tt16 deficiency affects pollen tube guidance, resulting in reduced fertility and negatively impacting embryo and seed development. Moreover, Bntt16 RNAi plants had reduced oil content and altered fatty acid composition. Transmission electron microscopy showed that the seeds of the RNAi plants had fewer oil bodies than the nontransgenic plants. In addition, tt16 RNAi transgenic lines were more sensitive to auxin. Further analysis by microarray showed that tt16 down-regulation alters the expression of genes involved in gynoecium and embryo development, lipid metabolism, auxin transport, and signal transduction. The broad regulatory function of TT16 at the transcriptional level may explain the altered phenotypes observed in the transgenic lines. Overall, the results uncovered important biological roles of TT16 in plant development, especially in fatty acid synthesis and embryo development.
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54
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Immink RGH, Posé D, Ferrario S, Ott F, Kaufmann K, Valentim FL, de Folter S, van der Wal F, van Dijk ADJ, Schmid M, Angenent GC. Characterization of SOC1's central role in flowering by the identification of its upstream and downstream regulators. PLANT PHYSIOLOGY 2012; 160:433-49. [PMID: 22791302 PMCID: PMC3440217 DOI: 10.1104/pp.112.202614] [Citation(s) in RCA: 148] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Accepted: 07/10/2012] [Indexed: 05/18/2023]
Abstract
The transition from vegetative to reproductive development is one of the most important phase changes in the plant life cycle. This step is controlled by various environmental signals that are integrated at the molecular level by so-called floral integrators. One such floral integrator in Arabidopsis (Arabidopsis thaliana) is the MADS domain transcription factor SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1). Despite extensive genetic studies, little is known about the transcriptional control of SOC1, and we are just starting to explore the network of genes under the direct control of SOC1 transcription factor complexes. Here, we show that several MADS domain proteins, including SOC1 heterodimers, are able to bind SOC1 regulatory sequences. Genome-wide target gene analysis by ChIP-seq confirmed the binding of SOC1 to its own locus and shows that it also binds to a plethora of flowering-time regulatory and floral homeotic genes. In turn, the encoded floral homeotic MADS domain proteins appear to bind SOC1 regulatory sequences. Subsequent in planta analyses revealed SOC1 repression by several floral homeotic MADS domain proteins, and we show that, mechanistically, this depends on the presence of the SOC1 protein. Together, our data show that SOC1 constitutes a major hub in the regulatory networks underlying floral timing and flower development and that these networks are composed of many positive and negative autoregulatory and feedback loops. The latter seems to be crucial for the generation of a robust flower-inducing signal, followed shortly after by repression of the SOC1 floral integrator.
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Affiliation(s)
- Richard G H Immink
- Plant Research International, Bioscience, 6708 PB Wageningen, The Netherlands.
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55
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Danisman S, van der Wal F, Dhondt S, Waites R, de Folter S, Bimbo A, van Dijk ADJ, Muino JM, Cutri L, Dornelas MC, Angenent GC, Immink RG. Arabidopsis class I and class II TCP transcription factors regulate jasmonic acid metabolism and leaf development antagonistically. PLANT PHYSIOLOGY 2012; 159:1511-23. [PMID: 22718775 PMCID: PMC3425195 DOI: 10.1104/pp.112.200303] [Citation(s) in RCA: 214] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Accepted: 06/18/2012] [Indexed: 05/18/2023]
Abstract
TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR1 (TCP) transcription factors control developmental processes in plants. The 24 TCP transcription factors encoded in the Arabidopsis (Arabidopsis thaliana) genome are divided into two classes, class I and class II TCPs, which are proposed to act antagonistically. We performed a detailed phenotypic analysis of the class I tcp20 mutant, showing an increase in leaf pavement cell sizes in 10-d-old seedlings. Subsequently, a glucocorticoid receptor induction assay was performed, aiming to identify potential target genes of the TCP20 protein during leaf development. The LIPOXYGENASE2 (LOX2) and class I TCP9 genes were identified as TCP20 targets, and binding of TCP20 to their regulatory sequences could be confirmed by chromatin immunoprecipitation analyses. LOX2 encodes for a jasmonate biosynthesis gene, which is also targeted by class II TCP proteins that are under the control of the microRNA JAGGED AND WAVY (JAW), although in an antagonistic manner. Mutation of TCP9, the second identified TCP20 target, resulted in increased pavement cell sizes during early leaf developmental stages. Analysis of senescence in the single tcp9 and tcp20 mutants and the tcp9tcp20 double mutants showed an earlier onset of this process in comparison with wild-type control plants in the double mutant only. Both the cell size and senescence phenotypes are opposite to the known class II TCP mutant phenotype in JAW plants. Altogether, these results point to an antagonistic function of class I and class II TCP proteins in the control of leaf development via the jasmonate signaling pathway.
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Chen G, Deng W, Truksa M, Peng FY, Weselake RJ. The Bsister MADS-box proteins have multiple regulatory functions in plant development. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2012. [DOI: 10.1016/j.bcab.2012.03.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Mizzotti C, Mendes MA, Caporali E, Schnittger A, Kater MM, Battaglia R, Colombo L. The MADS box genes SEEDSTICK and ARABIDOPSIS Bsister play a maternal role in fertilization and seed development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 70:409-20. [PMID: 22176531 DOI: 10.1111/j.1365-313x.2011.04878.x] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The haploid generation of flowering plants develops within the sporophytic tissues of the ovule. After fertilization, the maternal seed coat develops in a coordinated manner with formation of the embryo and endosperm. In the arabidopsis bsister (abs) mutant, the endothelium, which is the most inner cell layer of the integuments that surround the haploid embryo sac, does not accumulate proanthocyanidins and the cells have an abnormal morphology. However, fertility is not affected in abs single mutants. SEEDSTICK regulates ovule identity redundantly with SHATTERPROOF 1 (SHP1) and SHP2 while a role in the control of fertility was not reported previously. Here we describe the characterization of the abs stk double mutant. This double mutant develops very few seeds due to both a reduced number of fertilized ovules and seed abortions later during development. Morphological analysis revealed a total absence of endothelium in this double mutant. Additionally, massive starch accumulation was observed in the embryo sac. The phenotype of the abs stk double mutant highlights the importance of the maternal-derived tissues, particularly the endothelium, for the development of the next generation.
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Affiliation(s)
- Chiara Mizzotti
- Dipartimento di Biologia, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy
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58
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Severing EI, van Dijk ADJ, Morabito G, Busscher-Lange J, Immink RGH, van Ham RCHJ. Predicting the impact of alternative splicing on plant MADS domain protein function. PLoS One 2012; 7:e30524. [PMID: 22295091 PMCID: PMC3266260 DOI: 10.1371/journal.pone.0030524] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Accepted: 12/18/2011] [Indexed: 11/18/2022] Open
Abstract
Several genome-wide studies demonstrated that alternative splicing (AS) significantly increases the transcriptome complexity in plants. However, the impact of AS on the functional diversity of proteins is difficult to assess using genome-wide approaches. The availability of detailed sequence annotations for specific genes and gene families allows for a more detailed assessment of the potential effect of AS on their function. One example is the plant MADS-domain transcription factor family, members of which interact to form protein complexes that function in transcription regulation. Here, we perform an in silico analysis of the potential impact of AS on the protein-protein interaction capabilities of MIKC-type MADS-domain proteins. We first confirmed the expression of transcript isoforms resulting from predicted AS events. Expressed transcript isoforms were considered functional if they were likely to be translated and if their corresponding AS events either had an effect on predicted dimerisation motifs or occurred in regions known to be involved in multimeric complex formation, or otherwise, if their effect was conserved in different species. Nine out of twelve MIKC MADS-box genes predicted to produce multiple protein isoforms harbored putative functional AS events according to those criteria. AS events with conserved effects were only found at the borders of or within the K-box domain. We illustrate how AS can contribute to the evolution of interaction networks through an example of selective inclusion of a recently evolved interaction motif in the MADS AFFECTING FLOWERING1-3 (MAF1-3) subclade. Furthermore, we demonstrate the potential effect of an AS event in SHORT VEGETATIVE PHASE (SVP), resulting in the deletion of a short sequence stretch including a predicted interaction motif, by overexpression of the fully spliced and the alternatively spliced SVP transcripts. For most of the AS events we were able to formulate hypotheses about the potential impact on the interaction capabilities of the encoded MIKC proteins.
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Affiliation(s)
- Edouard I. Severing
- Applied Bioinformatics, Plant Research International, Wageningen, The Netherlands
- Laboratory of Bioinformatics, Wageningen University, Wageningen, The Netherlands
| | - Aalt D. J. van Dijk
- Applied Bioinformatics, Plant Research International, Wageningen, The Netherlands
| | - Giuseppa Morabito
- Plant Developmental Systems, Plant Research International, Wageningen, The Netherlands
| | | | - Richard G. H. Immink
- Centre for BioSystems Genomics, Wageningen, The Netherlands
- Plant Developmental Systems, Plant Research International, Wageningen, The Netherlands
| | - Roeland C. H. J. van Ham
- Applied Bioinformatics, Plant Research International, Wageningen, The Netherlands
- Laboratory of Bioinformatics, Wageningen University, Wageningen, The Netherlands
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59
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Fujisawa M, Nakano T, Ito Y. Identification of potential target genes for the tomato fruit-ripening regulator RIN by chromatin immunoprecipitation. BMC PLANT BIOLOGY 2011; 11:26. [PMID: 21276270 PMCID: PMC3039564 DOI: 10.1186/1471-2229-11-26] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2010] [Accepted: 01/30/2011] [Indexed: 05/18/2023]
Abstract
BACKGROUND During ripening, climacteric fruits increase their ethylene level and subsequently undergo various physiological changes, such as softening, pigmentation and development of aroma and flavor. These changes occur simultaneously and are caused by the highly synchronized expression of numerous genes at the onset of ripening. In tomatoes, the MADS-box transcription factor RIN has been regarded as a key regulator responsible for the onset of ripening by acting upstream of both ethylene- and non-ethylene-mediated controls. However, except for LeACS2, direct targets of RIN have not been clarified, and little is known about the transcriptional cascade for ripening. RESULTS Using immunoprecipitated (IPed) DNA fragments recovered by chromatin immunoprecipitation (ChIP) with anti-RIN antibody from ripening tomato fruit, we analyzed potential binding sites for RIN (CArG-box sites) in the promoters of representative ripening-induced genes by quantitative PCR. Results revealed nearly a 5- to 20-fold enrichment of CArG boxes in the promoters of LeACS2, LeACS4, PG, TBG4, LeEXP1, and LeMAN4 and of RIN itself, indicating direct interaction of RIN with their promoters in vivo. Moreover, sequence analysis and genome mapping of 51 cloned IPed DNAs revealed potential RIN binding sites. Quantitative PCR revealed that four of the potential binding sites were enriched 4- to 17-fold in the IPed DNA pools compared with the controls, indicating direct interaction of RIN with these sites in vivo. Near one of the four CArG boxes we found a gene encoding a protein similar to thioredoxin y1. An increase in the transcript level of this gene was observed with ripening in normal fruit but not in the rin mutant, suggesting that RIN possibly induces its expression. CONCLUSIONS The presented results suggest that RIN controls fruit softening and ethylene production by the direct transcriptional regulation of cell-wall-modifying genes and ethylene biosynthesis genes during ripening. Moreover, the binding of RIN to its own promoter suggests the presence of autoregulation for RIN expression. ChIP-based analyses identified a novel RIN-binding CArG-box site that harbors a gene associated with RIN expression in its flanking region. These findings clarify the crucial role of RIN in the transcriptional regulation of ripening initiation and progression.
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Affiliation(s)
- Masaki Fujisawa
- National Food Research Institute, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan
| | - Toshitsugu Nakano
- National Food Research Institute, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan
| | - Yasuhiro Ito
- National Food Research Institute, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan
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60
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Shulga OA, Shchennikova AV, Angenent GC, Skryabin KG. MADS-box genes controlling inflorescence morphogenesis in sunflower. Russ J Dev Biol 2011. [DOI: 10.1134/s1062360408010025] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Mizumoto K, Hatano H, Hirabayashi C, Murai K, Takumi S. Characterization of wheat Bell1-type homeobox genes in floral organs of alloplasmic lines with Aegilops crassa cytoplasm. BMC PLANT BIOLOGY 2011; 11:2. [PMID: 21205321 PMCID: PMC3022553 DOI: 10.1186/1471-2229-11-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2010] [Accepted: 01/04/2011] [Indexed: 05/09/2023]
Abstract
BACKGROUND Alloplasmic wheat lines with Aegilops crassa cytoplasm often show homeotic conversion of stamens into pistils under long-day conditions. In the pistillody-exhibiting florets, an ectopic ovule is formed within the transformed stamens, and female sterility is also observed because of abnormal integument development. RESULTS In this study, four wheat Bell1-like homeobox (BLH) genes were isolated and named WBLH1 to WBLH4. WBLH1/WBLH3/WBLH4 expression was observed in the basal boundary region of the ovary in both normal pistils and transformed stamens. WBLH2 was also strongly expressed in integuments not only of normal ovules in pistils but also of the ectopic ovules in transformed stamens, and the WBLH2 expression pattern in the sterile pistils seemed to be identical to that in normal ovules of fertile pistils. In addition, WBLH1 and WBLH3 showed interactions with the three wheat KNOX proteins through the BEL domain. WBLH2, however, formed a complex with wheat KNOTTED1 and ROUGH SHEATH1 orthologs through SKY and BEL domains, but not with a wheat LIGULELESS4 ortholog. CONCLUSIONS Expression of the four WBLH genes is evident in reproductive organs including pistils and transformed stamens and is independent from female sterility in alloplasmic wheat lines with Ae. crassa cytoplasm. KNOX-BLH interaction was conserved among various plant species, indicating the significance of KNOX-BLH complex formation in wheat developmental processes. The functional features of WBLH2 are likely to be distinct from other BLH gene functions in wheat development.
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Affiliation(s)
- Kota Mizumoto
- Graduate School of Agricultural Science, Kobe University, Nada-ku, Kobe 657-8501, Japan
| | - Hitoshi Hatano
- Graduate School of Agricultural Science, Kobe University, Nada-ku, Kobe 657-8501, Japan
| | - Chizuru Hirabayashi
- Department of Bioscience, Fukui Prefectural University, Yoshida-gun, Fukui 910-1195, Japan
| | - Koji Murai
- Department of Bioscience, Fukui Prefectural University, Yoshida-gun, Fukui 910-1195, Japan
| | - Shigeo Takumi
- Graduate School of Agricultural Science, Kobe University, Nada-ku, Kobe 657-8501, Japan
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Abstract
Most transcription factors fulfill their role in protein complexes. As a consequence, information about their interaction capacity sheds light on a protein's function and the molecular mechanism underlying this activity. The yeast two-hybrid GAL4 (Y2H) assay is a powerful method to unravel and identify the composition of protein complexes. This in vivo based system makes use of two functional protein domains of the GAL4 transcription factor, each fused to a protein of interest. Upon interaction between the two proteins under study, a transcriptional activator gets reconstituted and reporter genes get activated, allowing the yeast to grow on selective medium. In this chapter protocols are given for Y2H library screening, directed Y2H screening, Y2H matrix screening, and YnH screening involving more than two proteins.
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Affiliation(s)
- Stefan de Folter
- Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV-IPN), Irapuato, Guanajuato, México.
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63
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Wang YQ, Melzer R, Theissen G. Molecular interactions of orthologues of floral homeotic proteins from the gymnosperm Gnetum gnemon provide a clue to the evolutionary origin of 'floral quartets'. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 64:177-90. [PMID: 21070403 DOI: 10.1111/j.1365-313x.2010.04325.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Several lines of evidence suggest that the identity of floral organs in angiosperms is specified by multimeric transcription factor complexes composed of MADS-domain proteins. These bind to specific cis-regulatory elements ('CArG-boxes') of their target genes involving DNA-loop formation, thus constituting 'floral quartets'. Gymnosperms, angiosperms' closest relatives, contain orthologues of floral homeotic genes, but when and how the interactions constituting floral quartets were established during evolution has remained unknown. We have comprehensively studied the dimerization and DNA-binding of several classes of MADS-domain proteins from the gymnosperm Gnetum gnemon. Determination of protein-protein and protein-DNA interactions by yeast two-hybrid, in vitro pull-down and electrophoretic mobility shift assays revealed complex patterns of homo- and heterodimerization among orthologues of floral homeotic class B, class C and class E proteins and B(sister) proteins. Using DNase I footprint assays we demonstrate that both orthologues of class B with C proteins, and orthologues of class C proteins alone, but not orthologues of class B proteins alone can loop DNA in floral quartet-like complexes. This is in contrast to class B and class C proteins from angiosperms, which require other factors such as class E floral homeotic proteins to 'glue' them together in multimeric complexes. Our findings suggest that the evolutionary origin of floral quartet formation is based on the interaction of different DNA-bound homodimers, does not depend on class E proteins, and predates the origin of angiosperms.
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Affiliation(s)
- Yong-Qiang Wang
- Department of Genetics, Friedrich Schiller University Jena, Philosophenweg 12, Jena, Germany
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Erdmann R, Gramzow L, Melzer R, Theissen G, Becker A. GORDITA (AGL63) is a young paralog of the Arabidopsis thaliana B(sister) MADS box gene ABS (TT16) that has undergone neofunctionalization. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 63:914-924. [PMID: 20598091 DOI: 10.1111/j.1365-313x.2010.04290.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
MIKC-type MADS domain proteins are key regulators of flower development in angiosperms. B(sister) genes constitute a clade with a close relationship to class B floral homeotic genes, and have been conserved for more than 300 million years. The loss-of-function phenotype of the A. thaliana B(sister) gene ABS is mild: mutants show reduced seed coloration and defects in endothelium development. This study focuses on GORDITA (GOA, formerly known as AGL63), the most closely related paralog of ABS in A. thaliana, which is thought to act redundantly with ABS. Phylogenetic trees reveal that the duplication leading to ABS and GOA occurred during diversification of the Brassicaceae, and further analyses show that GOA has evolved under relaxed selection pressure. The knockdown phenotype of GOA suggests a role for this gene in fruit longitudinal growth, while over-expression of GOA results in disorganized floral structure and addition of carpel-like features to sepals. Given the phylogeny and function of other B(sister) genes, our data suggest that GOA has evolved a new function as compared to ABS. Protein analysis reveals that the GOA-specific 'deviant' domain is required for protein dimerization, in contrast to other MIKC-type proteins that require the K domain for dimerization. Moreover, no shared protein interaction partners for ABS and GOA could be identified. Our experiments indicate that modification of a protein domain and a shift in expression pattern can lead to a novel gene function in a relatively short time, and highlight the molecular mechanism by which neofunctionalization following gene duplication can be achieved.
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Affiliation(s)
- Robert Erdmann
- University of Bremen, Department of Biology and Chemistry, Plant Evo-Devo Group, Leobener Straße, 28359 Bremen, Germany
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65
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Prasad K, Zhang X, Tobón E, Ambrose BA. The Arabidopsis B-sister MADS-box protein, GORDITA, represses fruit growth and contributes to integument development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 62:203-214. [PMID: 20088901 DOI: 10.1111/j.1365-313x.2010.04139.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The MADS-box family of transcription factors have diverse developmental roles in flower pattern formation, gametophyte cell division and fruit differentiation. The B-sister MADS-box proteins are most similar to the B-class floral homeotic proteins, and are expressed in female reproductive organs. The Arabidopsis B-sister MADS-box protein, TT16, is necessary for inner integument differentiation. We have functionally characterized the only other B-sister MADS-box gene in Arabidopsis, AGL63, renamed here as GORDITA (GOA). A loss-of-function mutation in goa or reduction of endogenous GOA expression results in larger fruits, illustrating its novel function in regulating fruit growth. Consistent with its function, GOA expression is detected in the walls of the valves and throughout the replum of the fruit. Our phenotypic and molecular analyses of 35S::GOA and goa plants show that GOA controls organ size via cell expansion. Further, functional studies of goa tt16 double mutants have shown their additive role in controlling seed coat development, and have revealed the importance of GOA expression in the outer integument. Together, our studies provide evidence of a new regulatory role for a B-sister MADS-box gene in the control of organ growth.
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Affiliation(s)
- Kalika Prasad
- Institute of Molecular BioSciences, Massey University, Palmerston North, New Zealand
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66
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Immink RG, Kaufmann K, Angenent GC. The ‘ABC’ of MADS domain protein behaviour and interactions. Semin Cell Dev Biol 2010; 21:87-93. [DOI: 10.1016/j.semcdb.2009.10.004] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2009] [Accepted: 10/23/2009] [Indexed: 02/05/2023]
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67
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Ferrándiz C, Fourquin C, Prunet N, Scutt CP, Sundberg E, Trehin C, Vialette-Guiraud AC. Carpel Development. ADVANCES IN BOTANICAL RESEARCH 2010. [PMID: 0 DOI: 10.1016/b978-0-12-380868-4.00001-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
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68
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Zhao YH, Möller M, Yang JB, Liu TS, Zhao JF, Dong LN, Zhang JP, Li CY, Wang GY, Li DZ. Extended expression of B-class MADS-box genes in the paleoherb Asarum caudigerum. PLANTA 2010; 231:265-276. [PMID: 19904556 PMCID: PMC7088318 DOI: 10.1007/s00425-009-1048-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2009] [Accepted: 10/23/2009] [Indexed: 05/28/2023]
Abstract
Asarum caudigerum (Aristolochiaceae) is a paleoherb species that is important for research in origin and evolution of angiosperm flowers due to its basal position in the angiosperm phylogeny. In this study, a subtracted floral cDNA library from floral buds of A. caudigerum was constructed and cDNA arrays by suppression subtractive hybridization were generated. cDNAs of floral buds at different stages before flower opening and of leaves at the seedling stage were used. The macroarray analyses of expression profiles of isolated floral genes showed that 157 genes out of the 612 unique ESTs tested revealed higher transcript abundance in the floral buds and uppermost leaves. Among them, 78 genes were determined to be differentially expressed in the perianth, 62 in the stamens, and 100 genes in the carpels. Quantitative real-time PCR of selected genes validated the macroarray results. Remarkably, APETALA3 (AP3) B-class genes isolated from A. caudigerum were upregulated in the perianth, stamens and carpels, implying that the expression domain of B-class genes in this basal angiosperm was broader than those in their eudicot counterparts.
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Affiliation(s)
- Yin-He Zhao
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, 650204 Kunming, China
- College of Agronomy and Key Laboratory for Plant Pathology of Yunnan Province, Yunnan Agricultural University, 650201 Kunming, China
| | - Michael Möller
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR Scotland, UK
| | - Jun-Bo Yang
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, 650204 Kunming, China
| | - Ting-Song Liu
- State Key Laboratory of Agrobiotechnology, China Agricultural University, 100094 Beijing, China
| | - Jin-Feng Zhao
- State Key Laboratory of Agrobiotechnology, China Agricultural University, 100094 Beijing, China
| | - Li-Na Dong
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, 650204 Kunming, China
| | - Jin-Peng Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Zhongguancun Nandajie 12, 100081 Beijing, China
| | - Cheng-Yun Li
- College of Agronomy and Key Laboratory for Plant Pathology of Yunnan Province, Yunnan Agricultural University, 650201 Kunming, China
| | - Guo-Ying Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Zhongguancun Nandajie 12, 100081 Beijing, China
| | - De-Zhu Li
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, 650204 Kunming, China
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69
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Yamada K, Saraike T, Shitsukawa N, Hirabayashi C, Takumi S, Murai K. Class D and B(sister) MADS-box genes are associated with ectopic ovule formation in the pistil-like stamens of alloplasmic wheat (Triticum aestivum L.). PLANT MOLECULAR BIOLOGY 2009; 71:1-14. [PMID: 19488678 DOI: 10.1007/s11103-009-9504-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2008] [Accepted: 05/19/2009] [Indexed: 05/10/2023]
Abstract
Homeotic transformation of stamens into pistil-like structures (pistillody) has been reported in cytoplasmic substitution (alloplasmic) lines of bread wheat (Triticum aestivum L.) that have the cytoplasm of a related wild species, Aegilops crassa. An ectopic ovule differentiates in the pistil-like stamen in the alloplasmic wheat. The SEEDSTICK (STK)-like class D MADS-box gene, wheat STK (WSTK), was expressed in the primordia of ectopic ovules in the pistil-like stamens as well as in the true pistil, suggesting that ectopic ovule formation results from WSTK expression in the pistil-like stamens of alloplasmic wheat. The ectopic ovule is abnormal as it fails to form complete integuments. Based on the expression pattern of WSTK and B(sister) MADS-box gene, WBsis (wheat B ( sister )), we conclude that WSTK plays a role in determination of ovule identity in the pistil-like stamen, but complete ovule development fails due to aberrant expression of WBsis.
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Affiliation(s)
- Kaori Yamada
- Department of Bioscience, Fukui Prefectural University, Eiheiji-cho, Fukui, Japan
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70
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Schauer SE, Schlüter PM, Baskar R, Gheyselinck J, Bolaños A, Curtis MD, Grossniklaus U. Intronic regulatory elements determine the divergent expression patterns of AGAMOUS-LIKE6 subfamily members in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2009; 59:987-1000. [PMID: 19473325 DOI: 10.1111/j.1365-313x.2009.03928.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The screening of enhancer detector lines in Arabidopsis thaliana has identified genes that are specifically expressed in the sporophytic tissue of the ovule. One such gene is the MADS-domain transcription factor AGAMOUS-LIKE6 (AGL6), which is expressed asymmetrically in the endothelial layer of the ovule, adjacent to the developing haploid female gametophyte. Transcription of AGL6 is regulated at multiple stages of development by enhancer and silencer elements located in both the upstream regulatory region and the large first intron. These include a bipartite enhancer, which requires elements in both the upstream regulatory region and the first intron, active in the endothelium. Transcription of the AGL13 locus, which encodes the other member of the AGL6 subfamily in Arabidopsis, is also regulated by elements located in the upstream regulatory region and in the first intron. There is, however, no overlapping expression of AGL6 and AGL13 except in the chalaza of the developing ovule, as was shown using a dual gene reporter system. Phylogenetic shadowing of the first intron of AGL6 and AGL13 homologs from other Brassicaceae identified four regions of conservation that probably contain the binding sites of transcriptional regulators, three of which are conserved outside Brassicaceae. Further phylogenetic analysis using the protein-encoding domains of AGL6 and AGL13 revealed that the MADS DNA-binding domain shows considerable divergence. Together, these results suggest that AGL6 and AGL13 show signs of subfunctionalization, with divergent expression patterns, regulatory sequences and possibly functions.
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Affiliation(s)
- Stephen E Schauer
- Institute of Plant Biology & Zürich-Basel Plant Science Center, University of Zürich, Zollikerstrasse 107, CH-8008 Zürich, Switzerland
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71
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Mizumoto K, Hatano H, Hirabayashi C, Murai K, Takumi S. Altered expression of wheat AINTEGUMENTA homolog, WANT-1, in pistil and pistil-like transformed stamen of an alloplasmic line with Aegilops crassa cytoplasm. Dev Genes Evol 2009; 219:175-87. [PMID: 19255779 DOI: 10.1007/s00427-009-0275-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2008] [Accepted: 02/05/2009] [Indexed: 10/21/2022]
Abstract
Homeotic transformation of stamens into pistil-like structures, called pistillody, has been reported in some alloplasmic common wheat lines with Aegilops crassa cytoplasm. An alloplasmic line of Chinese Spring ditelosomic 7BS (CSdt7BS) with Ae. crassa cytoplasm lacking the long arm of the chromosome 7B shows pistillody, and the pistils and transformed stamens are sterile due to abnormal ovule development. To elucidate the molecular mechanism of the ovule abnormality, we compared the expression profiles of floral organs between euplasmic and alloplasmic CSdt7BS lines. Two differential display methods of mRNA profiling demonstrated that Ae. crassa cytoplasm largely affects nuclear gene expression profiles of common wheat. Of the differentially expressed genes, a wheat AINTEGUMENTA (ANT) homolog, WANT-1, was preferentially expressed in pistils but not in stamens, and accumulation of the transcript was limited to ovule primordia at the floral organ development stage. In alloplasmic wheat, WANT-1 expression was patchy and weak at the ovule-development stages. On the other hand, no significant difference in gene expression patterns of wheat AGAMOUS (AG) homologs (WAG-1 and WAG-2) was observed between fertile and sterile pistils. These results indicated that alteration of gene expression after initiation of ovule primordia results in abnormal ovule development, and that the aberrant ovule formation is at least partly associated with the weak expression of WANT-1 around ovule primordia in alloplasmic wheat with Ae. crassa cytoplasm.
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Affiliation(s)
- Kota Mizumoto
- Laboratory of Plant Genetics, Graduate School of Agricultural Science, Kobe University, Nada-ku, Kobe, 657-8501, Japan
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72
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Immink RGH, Tonaco IAN, de Folter S, Shchennikova A, van Dijk ADJ, Busscher-Lange J, Borst JW, Angenent GC. SEPALLATA3: the 'glue' for MADS box transcription factor complex formation. Genome Biol 2009; 10:R24. [PMID: 19243611 PMCID: PMC2688274 DOI: 10.1186/gb-2009-10-2-r24] [Citation(s) in RCA: 205] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2008] [Revised: 12/16/2008] [Accepted: 02/25/2009] [Indexed: 11/10/2022] Open
Abstract
A yeast 3-hybrid screen in Arabidopsis reveals MADS box protein complexes: SEP3 is shown to mediate complex formation and floral timing. Background Plant MADS box proteins play important roles in a plethora of developmental processes. In order to regulate specific sets of target genes, MADS box proteins dimerize and are thought to assemble into multimeric complexes. In this study a large-scale yeast three-hybrid screen is utilized to provide insight into the higher-order complex formation capacity of the Arabidopsis MADS box family. SEPALLATA3 (SEP3) has been shown to mediate complex formation and, therefore, special attention is paid to this factor in this study. Results In total, 106 multimeric complexes were identified; in more than half of these at least one SEP protein was present. Besides the known complexes involved in determining floral organ identity, various complexes consisting of combinations of proteins known to play a role in floral organ identity specification, and flowering time determination were discovered. The capacity to form this latter type of complex suggests that homeotic factors play essential roles in down-regulation of the MADS box genes involved in floral timing in the flower via negative auto-regulatory loops. Furthermore, various novel complexes were identified that may be important for the direct regulation of the floral transition process. A subsequent detailed analysis of the APETALA3, PISTILLATA, and SEP3 proteins in living plant cells suggests the formation of a multimeric complex in vivo. Conclusions Overall, these results provide strong indications that higher-order complex formation is a general and essential molecular mechanism for plant MADS box protein functioning and attribute a pivotal role to the SEP3 'glue' protein in mediating multimerization.
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Affiliation(s)
- Richard G H Immink
- Plant Research International, Bioscience, Droevendaalsesteeg 1, Wageningen, the Netherlands.
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73
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Urbanus SL, de Folter S, Shchennikova AV, Kaufmann K, Immink RGH, Angenent GC. In planta localisation patterns of MADS domain proteins during floral development in Arabidopsis thaliana. BMC PLANT BIOLOGY 2009; 9:5. [PMID: 19138429 PMCID: PMC2630930 DOI: 10.1186/1471-2229-9-5] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2008] [Accepted: 01/12/2009] [Indexed: 05/08/2023]
Abstract
BACKGROUND MADS domain transcription factors play important roles in various developmental processes in flowering plants. Members of this family play a prominent role in the transition to flowering and the specification of floral organ identity. Several studies reported mRNA expression patterns of the genes encoding these MADS domain proteins, however, these studies do not provide the necessary information on the temporal and spatial localisation of the proteins. We have made GREEN FLUORESCENT PROTEIN (GFP) translational fusions with the four MADS domain proteins SEPALLATA3, AGAMOUS, FRUITFULL and APETALA1 from the model plant Arabidopsis thaliana and analysed the protein localisation patterns in living plant tissues by confocal laser scanning microscopy (CLSM). RESULTS We unravelled the protein localisation patterns of the four MADS domain proteins at a cellular and subcellular level in inflorescence and floral meristems, during development of the early flower bud stages, and during further differentiation of the floral organs. The protein localisation patterns revealed a few deviations from known mRNA expression patterns, suggesting a non-cell autonomous action of these factors or alternative control mechanisms. In addition, we observed a change in the subcellular localisation of SEPALLATA3 from a predominantly nuclear localisation to a more cytoplasmic localisation, occurring specifically during petal and stamen development. Furthermore, we show that the down-regulation of the homeodomain transcription factor WUSCHEL in ovular tissues is preceded by the occurrence of both AGAMOUS and SEPALLATA3 proteins, supporting the hypothesis that both proteins together suppress WUSCHEL expression in the ovule. CONCLUSION This approach provides a highly detailed in situ map of MADS domain protein presence during early and later stages of floral development. The subcellular localisation of the transcription factors in the cytoplasm, as observed at certain stages during development, points to mechanisms other than transcriptional control. Together this information is essential to understand the role of these proteins in the regulatory processes that drive floral development and leads to new hypotheses.
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Affiliation(s)
- Susan L Urbanus
- Plant Research International, Bornsesteeg 65, 6708 PD Wageningen, The Netherlands
- Laboratory of Molecular Biology, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
| | - Stefan de Folter
- National Laboratory of Genomics for Biodiversity (Langebio), CINVESTAV-IPN, Campus Guanajuato, Apartado Postal 629, 36500 Irapuato, Guanajuato, Mexico
| | - Anna V Shchennikova
- Center "Bioengineering" RAS, prospect 60-letia Oktyabrya, 7, korp.1, 117312 Moscow, Russia
| | - Kerstin Kaufmann
- Plant Research International, Bornsesteeg 65, 6708 PD Wageningen, The Netherlands
| | - Richard GH Immink
- Plant Research International, Bornsesteeg 65, 6708 PD Wageningen, The Netherlands
- Centre for BioSystems Genomics (CBSG), PO BOX 98, 6700 AB Wageningen, The Netherlands
| | - Gerco C Angenent
- Plant Research International, Bornsesteeg 65, 6708 PD Wageningen, The Netherlands
- Centre for BioSystems Genomics (CBSG), PO BOX 98, 6700 AB Wageningen, The Netherlands
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Oomen RJFJ, Wu J, Lelièvre F, Blanchet S, Richaud P, Barbier-Brygoo H, Aarts MGM, Thomine S. Functional characterization of NRAMP3 and NRAMP4 from the metal hyperaccumulator Thlaspi caerulescens. THE NEW PHYTOLOGIST 2009; 181:637-50. [PMID: 19054339 DOI: 10.1111/j.1469-8137.2008.02694.x] [Citation(s) in RCA: 162] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The ability of metal hyperaccumulating plants to tolerate and accumulate heavy metals results from adaptations of metal homeostasis. NRAMP metal transporters were found to be highly expressed in some hyperaccumulating plant species. Here, we identified TcNRAMP3 and TcNRAMP4, the closest homologues to AtNRAMP3 and AtNRAMP4 in Thlaspi caerulescens and characterized them by expression analysis, confocal imaging and heterologous expression in yeast and Arabidopsis thaliana. TcNRAMP3 and TcNRAMP4 are expressed at higher levels than their A. thaliana homologues. When expressed in yeast TcNRAMP3 and TcNRAMP4 transport the same metals as their respective A. thaliana orthologues: iron (Fe), manganese (Mn) and cadmium (Cd) but not zinc (Zn) for NRAMP3; Fe, Mn, Cd and Zn for NRAMP4. They also localize at the vacuolar membrane in A. thaliana protoplasts. Inactivation of AtNRAMP3 and AtNRAMP4 in A. thaliana results in strong Cd and Zn hypersensitivity, which is fully rescued by TcNRAMP3 or TcNRAMP4 expression. However, metal tolerance conferred by TcNRAMP expression in nramp3nramp4 mutant does not exceed that of wild-type A. thaliana. Our data indicate that the difference between TcNRAMP3 and TcNRAMP4 and their A. thaliana orthologues does not lie in a different protein function, but probably resides in a different expression level or expression pattern.
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Affiliation(s)
- Ronald J F J Oomen
- Institut des Sciences du Végétal, CNRS, Avenue de la Terrasse, Gif-sur-Yvette, France.
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Leseberg CH, Eissler CL, Wang X, Johns MA, Duvall MR, Mao L. Interaction study of MADS-domain proteins in tomato. JOURNAL OF EXPERIMENTAL BOTANY 2008; 59:2253-65. [PMID: 18487636 DOI: 10.1093/jxb/ern094] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
MADS-domain proteins are important transcription factors involved in many biological processes of plants. Interactions between MADS-domain proteins are essential for their functions. In tomato (Solanum lycopersicum), the number of MIKC(c)-type MADS-domain proteins identified has totalled 36, but a large-scale interaction assay is lacking. In this study, 22 tomato MADS-domain proteins were selected from six functionally important subfamilies of the MADS-box gene family, to create the first large-scale tomato protein interaction network. Compared with Arabidopsis and petunia (Petunia hybrida), protein interaction patterns in tomato displayed both conservation and divergence. The majority of proteins that can be identified as putative orthologues exhibited conserved interaction patterns, and modifications were mostly found in genes underlining traits unique to tomato. JOINTLESS and RIN, characterized for their roles in abscission zone development and fruit ripening, respectively, showed enlarged interaction networks in comparison with their Arabidopsis and petunia counterparts. Novel interactions were also found for members of the expanded subfamilies, such as those represented by AP1/FUL and AP3/PI MADS-domain proteins. In search for higher order complexes, TM5 was found to be the preferred bridge among the five SEP-like proteins. Additionally, 16 proteins with the MADS-domain removed were used to assess the role of the MADS-domain in protein-protein interactions. The current work provides important knowledge for further functional and evolutionary study of the MADS-box genes in tomato.
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Affiliation(s)
- Charles H Leseberg
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL 60115, USA
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de Folter S, Urbanus SL, van Zuijlen LGC, Kaufmann K, Angenent GC. Tagging of MADS domain proteins for chromatin immunoprecipitation. BMC PLANT BIOLOGY 2007; 7:47. [PMID: 17868439 PMCID: PMC2071916 DOI: 10.1186/1471-2229-7-47] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2007] [Accepted: 09/14/2007] [Indexed: 05/17/2023]
Abstract
BACKGROUND Most transcription factors fulfill their role in complexes and regulate their target genes upon binding to DNA motifs located in upstream regions or introns. To date, knowledge about transcription factor target genes and their corresponding transcription factor binding sites are still very limited. Two related methods that allow in vivo identification of transcription factor binding sites are chromatin immunoprecipitation (ChIP) and chromatin affinity purification (ChAP). For ChAP, the protein of interest is tagged with a peptide or protein, which can be used for affinity purification of the protein-DNA complex and hence, the identification of the target gene. RESULTS Here, we present the results of experiments aiming at the development of a generic tagging approach for the Arabidopsis MADS domain proteins AGAMOUS, SEPALLATA3, and FRUITFULL. For this, Arabidopsis wild type plants were transformed with constructs containing a MADS-box gene fused to either a double Strep-tag II-FLAG-tag, a triple HA-tag, or an eGFP-tag, all under the control of the constitutive double 35S Cauliflower Mosaic Virus (CaMV) promoter. Strikingly, in all cases, the number of transformants with loss-of-function phenotypes was much larger than those with an overexpression phenotype. Using endogenous promoters in stead of the 35S CaMV resulted in a dramatic reduction in the frequency of loss-of-function phenotypes. Furthermore, pleiotropic defects occasionally caused by an overexpression strategy can be overcome by using the native promoter of the gene. Finally, a ChAP result is presented using GFP antibody on plants carrying a genomic fragment of a MADS-box gene fused to GFP. CONCLUSION This study revealed that MADS-box proteins are very sensitive to fusions with small peptide tags and GFP tags. Furthermore, for the expression of chimeric versions of MADS-box genes it is favorable to use the entire genomic region in frame to the tag of choice. Interestingly, though unexpected, it appears that the use of chimeric versions of MADS-box genes under the control of the strong 35S CaMV promoter is a very efficient method to obtain dominant-negative mutants, either caused by cosuppression or by alteration of the activity of the recombinant protein. Finally, we were able to demonstrate AGAMOUS binding to one of its targets by ChAP.
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Affiliation(s)
- Stefan de Folter
- Business Unit Bioscience, Plant Research International, 6700 AA Wageningen, The Netherlands
- Current address- National Laboratory of Genomics for Biodiversity (Langebio), CINVESTAV-IPN, Campus Guanajuato, Apartado Postal 629, 36500 Irapuato, Guanajuato, Mexico
| | - Susan L Urbanus
- Business Unit Bioscience, Plant Research International, 6700 AA Wageningen, The Netherlands
| | - Lisette GC van Zuijlen
- Business Unit Bioscience, Plant Research International, 6700 AA Wageningen, The Netherlands
| | - Kerstin Kaufmann
- Business Unit Bioscience, Plant Research International, 6700 AA Wageningen, The Netherlands
| | - Gerco C Angenent
- Business Unit Bioscience, Plant Research International, 6700 AA Wageningen, The Netherlands
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