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Data from: The origin of floral organ identity quartets
Ruelens, Philip ; Zhang, Zhicheng ; Mourik, H. van; Maere, Steven ; Kaufmann, K. ; Geuten, Koen - \ 2017
evolution - angiosperms - flower development - MADS-domain - ancestral sequence rteconstruction
The origin of flowers has puzzled plant biologists ever since Darwin referred to their sudden appearance in the fossil record as an abominable mystery. Flowers are considered to be an assembly of protective, attractive and reproductive male and female leaf-like organs. Their origin cannot be understood by a morphological comparison to gymnosperms, their closest relatives, which develop separate male or female cones. Despite these morphological differences, gymnosperms and angiosperms possess a similar genetic toolbox consisting of phylogenetically related MADS-domain proteins. Using ancestral MADS-domain protein reconstruction, we trace the evolution of organ identity quartets along the stem lineage of crown angiosperms. We provide evidence that current floral quartets specifying male organ identity, which consist of four types of subunits, evolved from ancestral complexes of two types of subunits through gene duplication and integration of SEPALLATA proteins just before the origin of flowering plants. Our results suggest that protein interaction changes underlying this compositional shift were the result of a gradual and reversible evolutionary trajectory. Modelling shows that such compositional changes may have facilitated the evolution of the perfect, bisexual flower.
Tetramer formation in Arabidopsis MADS domain proteins: analysis of a protein-protein interaction network
Espinosa-Soto, C. ; Immink, R.G.H. ; Angenent, G.C. ; Alvarez-Buylla, E.R. ; Folter, de, S. - \ 2014
BMC Systems Biology 8 (2014). - ISSN 1752-0509 - 17 p.
box transcription factors - floral organ identity - flower development - gene duplication - adaptive evolution - homeotic proteins - factor family - in-vitro - dna - complexes
Background: MADS domain proteins are transcription factors that coordinate several important developmental processes in plants. These proteins interact with other MADS domain proteins to form dimers, and it has been proposed that they are able to associate as tetrameric complexes that regulate transcription of target genes. Whether the formation of functional tetramers is a widespread property of plant MADS domain proteins, or it is specific to few of these transcriptional regulators remains unclear. Results: We analyzed the structure of the network of physical interactions among MADS domain proteins in Arabidopsis thaliana. We determined the abundance of subgraphs that represent the connection pattern expected for a MADS domain protein heterotetramer. These subgraphs were significantly more abundant in the MADS domain protein interaction network than in randomized analogous networks. Importantly, these subgraphs are not significantly frequent in a protein interaction network of TCP plant transcription factors, when compared to expectation by chance. In addition, we found that MADS domain proteins in tetramer-like subgraphs are more likely to be expressed jointly than proteins in other subgraphs. This effect is mainly due to proteins in the monophyletic MIKC clade, as there is no association between tetramer-like subgraphs and co-expression for proteins outside this clade. Conclusions: Our results support that the tendency to form functional tetramers is widespread in the MADS domain protein-protein interaction network. Our observations also suggest that this trend is prevalent, or perhaps exclusive, for proteins in the MIKC clade. Because it is possible to retrodict several experimental results from our analyses, our work can be an important aid to make new predictions and facilitates experimental research on plant MADS domain proteins.
Structural determinants of DNA recognition by plant MADS-domain transcription factors
Muino Acuna, J.M. ; Smaczniak, C. ; Angenent, G.C. ; Kaufmann, K. ; Dijk, A.D.J. van - \ 2014
Nucleic acids research 42 (2014)4. - ISSN 0305-1048 - p. 2138 - 2146.
in-vitro - binding properties - flower development - antirrhinum-majus - homeotic proteins - crystal-structure - ternary complex - floral organs - box proteins - chip-chip
Plant MADS-domain transcription factors act as key regulators of many developmental processes. Despite the wealth of information that exists about these factors, the mechanisms by which they recognize their cognate DNA-binding site, called CArG-box (consensus CCW6GG), and how different MADS-domain proteins achieve DNA-binding specificity, are still largely unknown. We used information from in vivo ChIP-seq experiments, in vitro DNA-binding data and evolutionary conservation to address these important questions. We found that structural characteristics of the DNA play an important role in the DNA binding of plant MADS-domain proteins. The central region of the CArG-box largely resembles a structural motif called ‘A-tract’, which is characterized by a narrow minor groove and may assist bending of the DNA by MADS-domain proteins. Periodically spaced A-tracts outside the CArG-box suggest additional roles for this structure in the process of DNA binding of these transcription factors. Structural characteristics of the CArG-box not only play an important role in DNA-binding site recognition of MADS-domain proteins, but also partly explain differences in DNA-binding specificity of different members of this transcription factor family and their heteromeric complexes.
Identification of microRNA targets in tomato fruit development using high-throughput sequencing and degradome analysis
Karlova, R.B. ; Haarst, J.C. van; Maliepaard, C.A. ; Geest, H.C. van de; Bovy, A.G. ; Lammers, M. ; Angenent, G.C. ; Maagd, R.A. de - \ 2013
Journal of Experimental Botany 64 (2013)7. - ISSN 0022-0957 - p. 1863 - 1878.
solanum-lycopersicon - small rnas - flower development - parallel analysis - seed-germination - sirna biogenesis - leaf development - mirna targets - arabidopsis - expression
MicroRNAs (miRNAs) play important roles in plant development through regulation of gene expression by mRNA degradation or translational inhibition. Despite the fact that tomato (Solanum lycopersicum) is the model system for studying fleshy fruit development and ripening, only a few experimentally proven miRNA targets are known, and the role of miRNA action in these processes remains largely unknown. Here, by using parallel analysis of RNA ends (PARE) for global identification of miRNA targets and comparing four different stages of tomato fruit development, a total of 119 target genes of miRNAs were identified. Of these, 106 appeared to be new targets. A large part of the identified targets (56) coded for transcription factors. Auxin response factors, as well as two known ripening regulators, COLORLESS NON-RIPENING (CNR) and APETALA2a (SlAP2a), with developmentally regulated degradation patterns were identified. The levels of the intact messenger of both CNR and AP2a are actively modulated during ripening, by miR156/157 and miR172, respectively. Additionally, two TAS3-mRNA loci were identified as targets of miR390. Other targets such as ARGONAUTE 1 (AGO1), shown to be involved in miRNA biogenesis in other plant species, were identified, which suggests a feedback loop regulation of this process. In this study, it is shown that miRNA-guided cleavage of mRNAs is likely to play an important role in tomato fruit development and ripening
Simulation of Organ Patterning on the Floral Meristem Using a Polar Auxin Transport Model
Mourik, S. van; Kaufmann, K. ; Dijk, A.D.J. van; Angenent, G.C. ; Merks, R.M.H. ; Molenaar, J. - \ 2012
PLoS ONE 7 (2012)1. - ISSN 1932-6203 - 9 p.
flower development - arabidopsis-thaliana - phyllotaxis - efflux - flux - canalization - initiation - leaf
An intriguing phenomenon in plant development is the timing and positioning of lateral organ initiation, which is a fundamental aspect of plant architecture. Although important progress has been made in elucidating the role of auxin transport in the vegetative shoot to explain the phyllotaxis of leaf formation in a spiral fashion, a model study of the role of auxin transport in whorled organ patterning in the expanding floral meristem is not available yet. We present an initial simulation approach to study the mechanisms that are expected to play an important role. Starting point is a confocal imaging study of Arabidopsis floral meristems at consecutive time points during flower development. These images reveal auxin accumulation patterns at the positions of the organs, which strongly suggests that the role of auxin in the floral meristem is similar to the role it plays in the shoot apical meristem. This is the basis for a simulation study of auxin transport through a growing floral meristem, which may answer the question whether auxin transport can in itself be responsible for the typical whorled floral pattern. We combined a cellular growth model for the meristem with a polar auxin transport model. The model predicts that sepals are initiated by auxin maxima arising early during meristem outgrowth. These form a pre-pattern relative to which a series of smaller auxin maxima are positioned, which partially overlap with the anlagen of petals, stamens, and carpels. We adjusted the model parameters corresponding to properties of floral mutants and found that the model predictions agree with the observed mutant patterns. The predicted timing of the primordia outgrowth and the timing and positioning of the sepal primordia show remarkable similarities with a developing flower in nature
Transcriptome and Metabolite Profiling Show That APETALA2a Is a Major Regulator of Tomato Fruit Ripening
Karlova, R.B. ; Rosin, F.M.A. ; Busscher-Lange, J. ; Parapunova, V.A. ; Do, P.T. ; Fernie, A.R. ; Fraser, P.D. ; Baxter, C. ; Angenent, G.C. ; Maagd, R.A. de - \ 2011
The Plant Cell 23 (2011)3. - ISSN 1040-4651 - p. 923 - 941.
homeotic gene apetala2 - ethylene biosynthesis - flower development - 1-aminocyclopropane-1-carboxylate synthase - chromoplast differentiation - lycopersicon-esculentum - expression analysis - arabidopsis flower - seed development - organ identity
Fruit ripening in tomato (Solanum lycopersicum) requires the coordination of both developmental cues as well as the plant hormone ethylene. Although the role of ethylene in mediating climacteric ripening has been established, knowledge regarding the developmental regulators that modulate the involvement of ethylene in tomato fruit ripening is still lacking. Here, we show that the tomato APETALA2a (AP2a) transcription factor regulates fruit ripening via regulation of ethylene biosynthesis and signaling. RNA interference (RNAi)-mediated repression of AP2a resulted in alterations in fruit shape, orange ripe fruits, and altered carotenoid accumulation. Microarray expression analyses of the ripe AP2 RNAi fruits showed altered expression of genes involved in various metabolic pathways, such as the phenylpropanoid and carotenoid pathways, as well as in hormone synthesis and perception. Genes involved in chromoplast differentiation and other ripening-associated processes were also differentially expressed, but softening and ethylene biosynthesis occurred in the transgenic plants. Ripening regulators RIPENING-INHIBITOR, NON-RIPENING, and COLORLESS NON-RIPENING (CNR) function upstream of AP2a and positively regulate its expression. In the pericarp of AP2 RNAi fruits, mRNA levels of CNR were elevated, indicating that AP2a and CNR are part of a negative feedback loop in the regulation of ripening. Moreover, we demonstrated that CNR binds to the promoter of AP2a in vitro
MADS: the missing link between identity and growth?
Dornelas, M.C. ; Patreze, C.M. ; Angenent, G.C. ; Immink, R.G.H. - \ 2011
Trends in Plant Science 16 (2011)2. - ISSN 1360-1385 - p. 89 - 97.
floral homeotic genes - genome-wide analysis - shoot apical meristem - flower development - transcription factors - arabidopsis-thaliana - organ size - morphological novelty - cell-proliferation - stamen development
Size and shape are intrinsic characteristics of any given plant organ and, therefore, are inherently connected with its identity. How the connection between identity and growth is established at the molecular level remains one of the key questions in developmental biology. The identity of floral organs is determined by a hierarchical combination of transcription factors, most of which belong to the MADS box family. Recent progress in finding the target genes of these master regulators reopened the debate about the missing link between identity and floral organ growth. Here, we review these novel findings and integrate them into a model, to show how MADS proteins, in concert with co-factors, could fulfill their role at later stages of floral organ development when size and shape are established.
Sequence Motifs in MADS Transcription Factors Responsible for Specificity and Diversification of Protein-Protein Interaction
Dijk, A.D.J. van; Morabito, G. ; Fiers, M.A. ; Ham, R.C.H.J. van; Angenent, G.C. ; Immink, R.G.H. - \ 2010
PLoS Computational Biology 6 (2010). - ISSN 1553-734X - 11 p.
novo structure prediction - organ-identity proteins - box genes - flower development - floral organ - dna-binding - peptide interactions - signal-transduction - arabidopsis - dimerization
Protein sequences encompass tertiary structures and contain information about specific molecular interactions, which in turn determine biological functions of proteins. Knowledge about how protein sequences define interaction specificity is largely missing, in particular for paralogous protein families with high sequence similarity, such as the plant MADS domain transcription factor family. In comparison to the situation in mammalian species, this important family of transcription regulators has expanded enormously in plant species and contains over 100 members in the model plant species Arabidopsis thaliana. Here, we provide insight into the mechanisms that determine protein-protein interaction specificity for the Arabidopsis MADS domain transcription factor family, using an integrated computational and experimental approach. Plant MADS proteins have highly similar amino acid sequences, but their dimerization patterns vary substantially. Our computational analysis uncovered small sequence regions that explain observed differences in dimerization patterns with reasonable accuracy. Furthermore, we show the usefulness of the method for prediction of MADS domain transcription factor interaction networks in other plant species. Introduction of mutations in the predicted interaction motifs demonstrated that single amino acid mutations can have a large effect and lead to loss or gain of specific interactions. In addition, various performed bioinformatics analyses shed light on the way evolution has shaped MADS domain transcription factor interaction specificity. Identified protein-protein interaction motifs appeared to be strongly conserved among orthologs, indicating their evolutionary importance. We also provide evidence that mutations in these motifs can be a source for sub- or neo-functionalization. The analyses presented here take us a step forward in understanding protein-protein interactions and the interplay between protein sequences and network evolution.
Intercellular transport of epidermis-expressed MADS domain transcription factors and their effect on plant morphology and floral transition
Urbanus, S.L. ; Martinelli, A.P. ; Dinh, Q.D. ; Aizza, L.C.B. ; Dornelas, M. ; Angenent, G.C. ; Immink, G.H. - \ 2010
The Plant Journal 63 (2010)3. - ISSN 0960-7412 - p. 60 - 72.
homeotic gene apetala3 - stem-cell maintenance - organ identity - arabidopsis-thaliana - flower development - homeobox genes - ectopic expression - meristem identity - ovule development - pound-foolish
During the lifetime of an angiosperm plant various important processes such as floral transition, specification of floral organ identity and floral determinacy, are controlled by members of the MADS domain transcription factor family. To investigate the possible non-cell-autonomous function of MADS domain proteins, we expressed GFP-tagged clones of AGAMOUS (AG), APETALA3 (AP3), PISTILLATA (PI) and SEPALLATA3 (SEP3) under the control of the MERISTEMLAYER1 promoter in Arabidopsis thaliana plants. Morphological analyses revealed that epidermal overexpression was sufficient for homeotic changes in floral organs, but that it did not result in early flowering or terminal flower phenotypes that are associated with constitutive overexpression of these proteins. Localisations of the tagged proteins in these plants were analysed with confocal laser scanning microscopy in leaf tissue, inflorescence meristems and floral meristems. We demonstrated that only AG is able to move via secondary plasmodesmata from the epidermal cell layer to the subepidermal cell layer in the floral meristem and to a lesser extent in the inflorescence meristem. To study the homeotic effects in more detail, the capacity of trafficking AG to complement the ag mutant phenotype was compared with the capacity of the non-inwards-moving AP3 protein to complement the ap3 mutant phenotype. While epidermal expression of AG gave full complementation, AP3 appeared not to be able to drive all homeotic functions from the epidermis, perhaps reflecting the difference in mobility of these proteins
Functional Analyses of the CLAVATA2-Like Proteins and Their Domains That Contribute to CLAVATA2 Specificity
Wang, G. ; Long, Y. ; Thomma, B.P.H.J. ; Wit, P.J.G.M. de; Angenent, G.C. ; Fiers, M.A. - \ 2010
Plant Physiology 152 (2010). - ISSN 0032-0889 - p. 320 - 331.
leucine-rich repeat - receptor-like kinase - disease resistance - gene encodes - arabidopsis-thaliana - extracellular domain - meristem development - cladosporium-fulvum - signal-transduction - flower development
The Arabidopsis (Arabidopsis thaliana) CLAVATA2 (CLV2) gene encodes a leucine-rich repeat receptor-like protein (RLP) that is involved in controlling the stem cell population size in the shoot apical meristem. Our previous genome-wide functional analysis of 57 AtRLP genes revealed only a few phenotypes for mutant alleles, despite screening a wide range of growth and developmental stages and assaying sensitivity to various stress responses, including susceptibility toward pathogens. To gain further insight into the biological role of AtRLPs, in particular CLV2-related AtRLP genes, we tested their ability to complement the clv2 mutant phenotype. We found that out of four close CLV2 homologs tested, AtRLP2 and AtRLP12 could functionally complement the clv2 mutant when expressed under the control of the CLV2 promoter. This indicates that the functional specificity of these three genes is determined at the level of their transcriptional regulation. Single and double mutant combinations with impaired AtRLP2 and/or AtRLP12 did not show an aberrant phenotype, suggesting that other genes are redundant with these CLV2-like genes. To understand which protein domains are essential for CLV2 function and which parts are interchangeable between related CLV2-like proteins, we performed domain-deletion and domain-swap experiments. These experiments revealed that CLV2 remains functional without the island domain, whereas the C1 and C3 regions of the leucine-rich repeat domain are essential for functionality. Analysis of domain-swap constructs showed that the C3-G region of CLV2 can be replaced by that of AtRLP38, although it could not complement the clv2 mutant under control of the CLV2 promoter. This suggests that the C3-G region is conserved among related AtRLP members, whereas the C1 domain may determine the functional specificity of CLV2
SEPALLATA3: the 'glue' for MADS box transcription factor complex formation
Immink, G.H. ; Tonaco, I.A.N. ; Folter, S. de; Shchennikova, A. ; Dijk, A.D.J. van; Busscher-Lange, J. ; Borst, J.W. ; Angenent, G.C. - \ 2009
Genome Biology 10 (2009). - ISSN 1474-7596 - 16 p.
protein-protein interactions - floral organ identity - short-vegetative-phase - arabidopsis-thaliana - flower development - in-vivo - homeotic proteins - meristem identity - domain proteins - coiled coils
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
In planta localisation patterns of MADS domain proteins during floral development in Arabidopsis thaliana
Urbanus, S.L. ; Folter, S. de; Shchennikova, A. ; Kaufmann, K. ; Immink, G.H. ; Angenent, G.C. - \ 2009
BMC Plant Biology 9 (2009). - ISSN 1471-2229
green-fluorescent protein - box transcription factors - homeotic gene apetala1 - flower development - ovule development - meristem identity - cell-differentiation - negative regulation - fruit-development - organ identity
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.
MADS-box genes controlling inflorescence morphogenesis in sunflower
Shulga, O.A. ; Shchennikova, A.V. ; Angenent, G.C. ; Skryabin, K.G. - \ 2008
Russian Journal of Developmental Biology 39 (2008)1. - ISSN 1062-3604 - p. 2 - 5.
flower development - ovule development - gerbera-hybrida - arabidopsis - expression - proteins - petunia - evolution - tissues - leaves
MADS-box genes play an important role in plant ontogeny, particularly, in the regulation of floral organ induction and development. Eight full-length cDNAs of HAM genes (Helianthus annuus MADS) have been isolated from sunflower. They encode MADS-box transcription factors expressed in inflorescence tissues. In the frames of the ABCDE model, the HAM proteins were classified according to their structural homology to known MADS-box transcription factors. The HAM45 and HAM59 genes encode the homeotic C function and are involved in the control of the identity of pistil and stamens, while the HAM75 and HAM92 genes determine the A function and identity of floral and inflorescence meristems and petal identity. The HAM31, HAM2, HAM63, and HAM91 genes encode the B function and are involved in the formation of petals and stamens; and the HAM137 gene encodes the E function. Analysis of the expression of HAM genes in sunflower has demonstrated that the structural and functional differences between the ray and tubular flowers in the inflorescence could be a consequence of the lack of HAM59 expression during ray flower initiation.
A genome-wide functional investigation into the roles of receptor-like proteins in Arabidopsis
Guodong Wang, G. ; Ellendorff, U. ; Kemp, B. ; Mansfield, J.W. ; Forsyth, A. ; Mitchell, K. ; Bastas, K. ; Liu, C.M. ; Woods-Tör, A. ; Zipfel, C. ; Wit, P.J.G.M. de; Jones, J.D.G. ; Tör, M. ; Thomma, B.P.H.J. - \ 2008
Plant Physiology 147 (2008). - ISSN 0032-0889 - p. 503 - 517.
leucine-rich repeat - disease resistance genes - cladosporium-fulvum - pseudomonas-syringae - microbial pathogens - systemic resistance - flower development - plant-pathogen - kinase - thaliana
Receptor-like proteins (RLPs) are cell surface receptors that typically consist of an extracellular leucine-rich repeat domain, a transmembrane domain, and a short cytoplasmatic tail. In several plant species, RLPs have been found to play a role in disease resistance, such as the tomato (Solanum lycopersicum) Cf and Ve proteins and the apple (Malus domestica) HcrVf2 protein that mediate resistance against the fungal pathogens Cladosporium fulvum, Verticillium spp., and Venturia inaequalis, respectively. In addition, RLPs play a role in plant development; Arabidopsis (Arabidopsis thaliana) TOO MANY MOUTHS (TMM) regulates stomatal distribution, while Arabidopsis CLAVATA2 (CLV2) and its functional maize (Zea mays) ortholog FASCINATED EAR2 regulate meristem maintenance. In total, 57 RLP genes have been identified in the Arabidopsis genome and a genome-wide collection of T-DNA insertion lines was assembled. This collection was functionally analyzed with respect to plant growth and development and sensitivity to various stress responses, including susceptibility toward pathogens. A number of novel developmental phenotypes were revealed for our CLV2 and TMM insertion mutants. In addition, one AtRLP gene was found to mediate abscisic acid sensitivity and another AtRLP gene was found to influence nonhost resistance toward Pseudomonas syringae pv phaseolicola. This genome-wide collection of Arabidopsis RLP gene T-DNA insertion mutants provides a tool for future investigations into the biological roles of RLPs
Tagging of MADS domain proteins for chromatin immunoprecipitation
Folter, S. de; Urbanus, S.L. ; Zuijlen, L. ; Kaufmann, K. ; Angenent, G.C. - \ 2007
BMC Plant Biology (2007). - ISSN 1471-2229 - p. 7 - 47.
floral homeotic gene - arabidopsis fruit-development - box gene - recombinant proteins - regulatory elements - negative regulation - ectopic expression - flower development - organ identity - purification
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.
A Bsister MADS-box gene involved in ovule and seed development in petunia and Arabidopsis.
Folter, S. de; Shchennikova, A.V. ; Franken, J. ; Busscher, M. ; Baskar, R. ; Grossniklaus, U. ; Angenent, G.C. ; Immink, G.H. - \ 2006
The Plant Journal 47 (2006)6. - ISSN 0960-7412 - p. 934 - 946.
protein-protein interactions - floral organ identity - transcription factor family - flower development - wild-type - plant transformation - coat development - homeotic genes - thaliana - encodes
MADS-domain transcription factors are essential for proper flower and seed development in angiosperms and their role in determination of floral organ identity can be described by the 'ABC model' of flower development. Recently, close relatives of the B-type genes were identified by phylogenetic studies, which are referred to as Bsister (Bs) genes. Here, we report the isolation and characterization of a MADS-box Bs member from petunia, designated FBP24. An fbp24 knock-down line appeared to closely resemble the Arabidopsis Bs mutant abs and a detailed and comparative analysis led to the conclusion that both FBP24 and ABS are necessary to determine the identity of the endothelial layer within the ovule. Protein interaction studies revealed the formation of higher-order complexes between Bs¿C¿E and Bs¿D¿E type MADS-box proteins, suggesting involvement of these specific complexes in determination of endothelium identity. However, although there are many similarities between the two genes and their products and functions, interestingly FBP24 cannot replace ABS in Arabidopsis. The results presented here demonstrate the importance of the comparative analysis of key regulatory genes in various model systems to fully understand all aspects of plant development
Trans meets cis in MADS science
Folter, S. de; Angenent, G.C. - \ 2006
Trends in Plant Science 11 (2006)5. - ISSN 1360-1385 - p. 224 - 231.
floral organ identity - transcriptional regulatory networks - ternary complex-formation - homeotic gene apetala3 - dna-binding specificities - cell-fate determination - box genes - flower development - in-vitro - chromatin immunoprecipitation
The interaction between a transcription factor and its binding site at the DNA is an integral part of transcriptional regulatory networks, which is fundamental for an understanding of biological processes. An example is the family of MADS domain transcription factors, which represent key regulators of processes in yeast, animals and plants. However, despite our extensive knowledge of these transcription factors, limited information is available on the cis-elements to which these proteins bind or how these elements are defined. Here, we discuss the current understanding of MADS protein binding sites and compare data from various organisms. This information can help us in developing algorithms to predict binding sites for MADS domain transcription factors, which would be a significant step forward in the identification of `down-stream¿ target genes and the elucidation of transcriptional networks
The influence of temperature on growth and development of chrysanthemum cultivars: a review
Ploeg, A. van der; Heuvelink, E. - \ 2006
Journal of Horticultural Science and Biotechnology 81 (2006)2. - ISSN 1462-0316 - p. 174 - 182.
photosynthetic photon flux - bright golden anne - night temperatures - morifolium ramat - inflorescence initiation - flower development - light-intensity - plant-density - irradiance - crop
The effects of temperature, especially in the sub-optimal temperature range, on growth and development of chrysanthemum (Dendranthema grandiflorum syn. Chrysanthemum morifolium) are reviewed with special emphasis on cultivar differences. The developmental aspects analysed in this paper are leaf unfolding rate, stem elongation, time to flowering, and the number and sizes of flowers. Growth is studied as biomass production and partitioning to different plant organs.Temperature has a significant effect on development, especially on leaf unfolding rate and time to flowering, both of which show an optimum response to temperature. The optimum for time to flowering is cultivar dependent and lies between 17º - 22ºC. Also, for the other developmental traits, there are clear differences between cultivars in their response to temperature. The effect of temperature on biomass production is less clear. When leaf area index is low, sub-optimal day temperatures decrease biomass production due to the formation of thicker leaves. Biomass produced up to flowering is highly variable and depends on cultivar and the interaction between temperature and other growing conditions. More research is required to determine whether differences in biomass produced between cultivars are related to differences in the duration of the cultivation period, growth rate, or both. The possibilities for breeding for low energy demand are also discussed.
Isolation and characterization of an AGAMOUS homologue from cocoa
Chaidamsari, T. ; Sugiarit, H. ; Santoso, D. ; Angenent, G.C. ; Maagd, R.A. de - \ 2006
Plant Science 170 (2006)5. - ISSN 0168-9452 - p. 968 - 975.
mads-box genes - ectopic expression - flower development - transcription factors - arabidopsis - plants - transformation - theobroma - evolution - cacao
We report the cloning of a cDNA from TcAG, an AG (Arabidopsis thaliana MADS-box C-type transcription factor gene AGAMOUS) homologue from cocoa (Theobroma cacao L.). TcAG was in the cocoa flower expressed primarily in stamens and ovaries, comparable to AG in Arabidopsis. Additionally, we found that TcAG is also expressed in the fruit (pod) wall and during its entire development, as well as in the fruit pulp. Ectopic expression of TcAG in transgenic A. thaliana plants resulted in a range of weak to strong apetala2 (ap2) mutant-like phenotypes as well as early flowering and curly leaves, as observed in other studies of plants overexpressing a functional AG homologue. The severity of the phenotypes correlated positively with the TcAG transcript level in the transgenic plants.
Transcriptional program controlled by the floral homeotic gene AGAMOUS during early organogenesis
Gomez-Mena, C. ; Folter, S. de; Costa, M.M.R. ; Angenent, G.C. ; Sablowski, R. - \ 2005
Development 132 (2005)3. - ISSN 0950-1991 - p. 429 - 438.
mads-box genes - arabidopsis-thaliana - flower development - organ identity - meristem identity - gibberellin 3-beta-hydroxylase - molecular characterization - expression analysis - stem elongation - target genes
Floral organs, whose identity is determined by specific combinations of homeotic genes, originate from a group of undifferentiated cells called the floral meristem. In Arabidopsis, the homeotic gene AGAMOUS (AG) terminates meristem activity and promotes development of stamens and carpels. To understand the program of gene expression activated by AG, we followed genome-wide expression during early stamen and carpel development. The AG target genes included most genes for which mutant screens revealed a function downstream of AG. Novel targets were validated by in situ hybridisation and binding to AG in vitro and in vivo. Transcription factors formed a large fraction of AG targets, suggesting that during early organogenesis, much of the genetic program is concerned with elaborating gene expression patterns. The results also suggest that AG and other homeotic proteins with which it interacts (SEPALLATA3, APETALA3, PISTILLATA) are coordinately regulated in a positive-feedback loop to maintain their own expression, and that AG activates biosynthesis of gibberellin, which has been proposed to promote the shift from meristem identity to differentiation.