Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Identification, cloning and characterization of the tomato TCP transcription factor family
Parapunova, V.A. ; Busscher, M. ; Busscher-Lange, J. ; Lammers, M. ; Karlova, R.B. ; Bovy, A.G. ; Angenent, G.C. ; Maagd, R.A. de - \ 2014
BMC Plant Biology 14 (2014). - ISSN 1471-2229
mads-box gene - arabidopsis-thaliana - fruit-development - leaf development - high-throughput - plant-growth - dna-binding - expression - time - interference
Background: TCP proteins are plant-specific transcription factors, which are known to have a wide range of functions in different plant species such as in leaf development, flower symmetry, shoot branching, and senescence. Only a small number of TCP genes has been characterised from tomato (Solanum lycopersicum). Here we report several functional features of the members of the entire family present in the tomato genome. Results: We have identified 30 Solanum lycopersicum SlTCP genes, most of which have not been described before. Phylogenetic analysis clearly distinguishes two homology classes of the SlTCP transcription factor family - class I and class II. Class II differentiates in two subclasses, the CIN-TCP subclass and the CYC/TB1 subclass, involved in leaf development and axillary shoots formation, respectively. The expression patterns of all members were determined by quantitative PCR. Several SlTCP genes, like SlTCP12, SlTCP15 and SlTCP18 are preferentially expressed in the tomato fruit, suggesting a role during fruit development or ripening. These genes are regulated by RIN (RIPENING INHIBITOR), CNR (COLORLESS NON-RIPENING) and SlAP2a (APETALA2a) proteins, which are transcription factors with key roles in ripening. With a yeast one-hybrid assay we demonstrated that RIN binds the promoter fragments of SlTCP12, SlTCP15 and SlTCP18, and that CNR binds the SlTCP18 promoter. This data strongly suggests that these class I SlTCP proteins are involved in ripening. Furthermore, we demonstrate that SlTCPs bind the promoter fragments of members of their own family, indicating that they regulate each other. Additional yeast one-hybrid studies performed with Arabidopsis transcription factors revealed binding of the promoter fragments by proteins involved in the ethylene signal transduction pathway, contributing to the idea that these SlTCP genes are involved in the ripening process. Yeast two-hybrid data shows that SlTCP proteins can form homo and heterodimers, suggesting that they act together in order to form functional protein complexes and together regulate developmental processes in tomato.
Towards modelling the flexible timing of shoot development: simulation of maize organogenesis based on coordination within and between phytomers
Zhu, J. ; Andrieu, B. ; Vos, J. ; Werf, W. van der; Fournier, C. ; Evers, J.B. - \ 2014
Annals of Botany 114 (2014)4. - ISSN 0305-7364 - p. 753 - 762.
functional-structural model - zea-mays l. - perennial ryegrass - leaf development - sheath tube - grass leaf - elongation - growth - phyllochron - internodes
* Background and Aims: Experimental evidence challenges the approximation, central in crop models, that developmental events followa fixed thermal time schedule, and indicates that leaf emergence events play a role in the timing of development. The objective of this studywas to build a structural development model of maize (Zeamays) based on a set of coordination rules at organ level that regulate duration of elongation, and to show how the distribution of leaf sizes emerges from this. * Methods: A model of maize developmentwas constructed based on three coordination rules between leaf emergence events and the dynamics of organ extension. The model was parameterized with data frommaize grown at a low plant population density and tested using data from maize grown at high population density. * Key Results: The model gave a good account of the timing and duration of organ extension. By using initial conditions associated with high population density, the model reproduced well the increase in blade elongation duration and the delay in sheath extension in high-density populations compared with low-density populations. Predictions of the sizes of sheaths at high densitywere accurate, whereas predictions of the dynamics of blade length were accurate up to rank 9; moderate overestimation of blade length occurred at higher ranks. * Conclusions: A set of simple rules for coordinated growth of organs is sufficient to simulate the development of maize plant structure without taking into account any regulation by assimilates. In this model, whole-plant architecture is shaped through initial conditions that feed a cascade of coordination events.
Analysis of functional redundancies within the Arabidopsis TCP transcription factor family
Danisman, S. ; Dijk, A.D.J. van; Bimbo, A. ; Wal, F. van der; Hennig, L. ; Folter, S. de; Angenent, G.C. ; Immink, R.G.H. - \ 2013
Journal of Experimental Botany 64 (2013)18. - ISSN 0022-0957 - p. 5673 - 5685.
gene-expression map - leaf development - circadian clock - class-i - thaliana - evolution - proteins - growth - duplication - plants
Analyses of the functions of TEOSINTE-LIKE1, CYCLOIDEA, and ROLIFERATING CELL FACTOR1 (TCP) transcription factors have been hampered by functional redundancy between its individual members. In general, putative functionally redundant genes are predicted based on sequence similarity and confirmed by genetic analysis. In the TCP family, however, identification is impeded by relatively low overall sequence similarity. In a search for functionally redundant TCP pairs that control Arabidopsis leaf development, this work performed an integrative bioinformatics analysis, combining protein sequence similarities, gene expression data, and results of pair-wise protein–protein interaction studies for the 24 members of the Arabidopsis TCP transcription factor family. For this, the work completed any lacking gene expression and protein–protein interaction data experimentally and then performed a comprehensive prediction of potential functional redundant TCP pairs. Subsequently, redundant functions could be confirmed for selected predicted TCP pairs by genetic and molecular analyses. It is demonstrated that the previously uncharacterized class I TCP19 gene plays a role in the control of leaf senescence in a redundant fashion with TCP20. Altogether, this work shows the power of combining classical genetic and molecular approaches with bioinformatics predictions to unravel functional redundancies in the TCP transcription factor family.
Meristem temperature substantially deviates from air temperature, even in moderate environments: Is the magnitude of this deviation species-specific?
Savvides, A. ; Ieperen, W. van; Dieleman, J.A. ; Marcelis, L.F.M. - \ 2013
Plant, Cell & Environment 36 (2013)1. - ISSN 0140-7791 - p. 1950 - 1960.
shoot-tip temperature - climate-change - leaf development - effective thickness - light interception - boundary-layers - heat-transfer - crop yields - maize apex - plant
Meristem temperature (Tmeristem) drives plant development but is hardly ever quantified. Instead, air temperature (Tair) is usually used as its approximation. Meristems are enclosed within apical buds. Bud structure and function may differ across species. Therefore, Tmeristem may deviate from Tair in a species-specific way. Environmental variables (air temperature, vapour pressure deficit, radiation, and wind speed) were systematically varied to quantify the response of Tmeristem. This response was related to observations of bud structure and transpiration. Tomato and cucumber plants were used as model plants as they are morphologically distinct and usually growing in similar environments. Tmeristem substantially deviated from Tair in a species-specific manner under moderate environments. This deviation ranged between -2.6 and 3.8¿°C in tomato and between -4.1 and 3.0¿°C in cucumber. The lower Tmeristem observed in cucumber was linked with the higher transpiration of the bud foliage sheltering the meristem when compared with tomato plants. We here indicate that for properly linking growth and development of plants to temperature in future applications, for instance in climate change scenarios studies, Tmeristem should be used instead of Tair, as a species-specific trait highly reliant on various environmental factors
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
Arabidopsis E2FA stimulates proliferation and endocycle separately through RBR-bound and RBR-free complexes
Magyar, Z. ; Horvath, B. ; Khan, S. ; Scheres, B. - \ 2012
The EMBO Journal 31 (2012). - ISSN 0261-4189 - p. 1480 - 1493.
retinoblastoma-related protein - cyclin-dependent kinase - genome-wide identification - stem-cell maintenance - a-type cyclin - transcription factor - leaf development - dna-replication - plant development - follicle cells
Post-embryonic growth in plants depends on the continuous supply of undifferentiated cells within meristems. Proliferating cells maintain their competence for division by active repression of differentiation and the associated endocycle entry. We show by upregulation and downregulation of E2FA that it is required for maintaining proliferation, as well as for endocycle entry. While E2FB–RBR1 (retinoblastoma-related protein 1) complexes are reduced after sucrose addition or at elevated CYCD3;1 levels, E2FA maintains a stable complex with RBR1 in proliferating cells. Chromatin immunoprecipitation shows that RBR1 binds in the proximity of E2F promoter elements in CCS52A1 and CSS52A2 genes, central regulators for the switch from proliferation to endocycles. Overexpression of a truncated E2FA mutant (E2FA¿RB) lacking the RBR1-binding domain interferes with RBR1 recruitment to promoters through E2FA, leading to decreased meristem size in roots, premature cell expansion and hyperactivated endocycle in leaves. E2F target genes, including CCS52A1 and CCS52A2, are upregulated in E2FA¿RB and e2fa knockout lines. These data suggest that E2FA in complex with RBR1 forms a repressor complex in proliferating cells to inhibit premature differentiation and endocycle entry. Thus, E2FA regulates organ growth via two distinct, sequentially operating pathways.
Influence of foliar phenology and shoot inclination on annual photosynthetic gain in individual beech saplings: A functional-structural modeling approach
Umeki, K. ; Kikuzawa, K. ; Sterck, F.J. - \ 2010
Forest Ecology and Management 259 (2010)11. - ISSN 0378-1127 - p. 2141 - 2150.
temperate deciduous forests - broad-leaved trees - light conditions - leaf development - fagus-crenata - woody-plants - canopy gaps - carbon gain - growth - architecture
We developed a functional-structural plant model for Fagus crenata saplings and calculated annual photosynthetic gains to determine the influences of foliar phenology and shoot inclination on the carbon economy of saplings. The model regenerated the three-dimensional shoot structure and spatial and temporal display of leaves; we calculated the hourly light interception of each leaf with a detailed light model that allowed us to estimate hourly leaf photosynthetic gain taking leaf age into account. To evaluate the importance of simultaneous foliar phenology and slanting shoots in beech saplings, we calculated the photosynthetic budgets for saplings with contrasting foliar phenologies and shoot inclinations. In our simulations, we distinguished between simultaneous and successive foliar phenologies, upright and slanting shoot inclinations, and environments with and without a vertical gradient in light intensity. Other model parameters (including photosynthesis vs. light curve, leaf size, and leaf shape) were obtained directly from live beech saplings. With no vertical gradient in light intensity, modeled saplings with simultaneous foliar phenology and slanting shoots (as in live beech) had larger annual photosynthetic gains than saplings with other combinations of traits. Hence, simultaneous foliar phenology and slanting shoots are efficient ways to display leaves in the shaded forest understory light regime where beech saplings thrive. In the presence of vertical light gradients, which can occur in canopy gaps, saplings with upright shoots had larger annual photosynthetic gains than counterparts with slanting shoots. Although mean daily photosynthetic gains of saplings with successive foliar phenology were elevated by exposing leaves to strong light when young and productive, the annual photosynthetic budget of these saplings was reduced (compared to saplings with simultaneous foliar phenology) by their relatively short leaf lifespan. Overall, our results suggest that slanting shoots with simultaneous foliar phenology are particularly successful in shaded environments, where beech often dominates, because they appear to maximize the annual carbon budget by avoiding self-shading and extending leaf lifespans.
ASYMMETRIC LEAVES2-LIKE1gene a member of the AS2/LOB family, controls proximal-distal patterning in Arabidopsis petals
Chalfun Junior, A. ; Franken, J. ; Mes, J.J. ; Marsch-Martinez, N. ; Pereira, A.B. ; Angenent, G.C. - \ 2005
Plant Molecular Biology 57 (2005)4. - ISSN 0167-4412 - p. 559 - 575.
knotted1-like homeobox gene - asymmetric interlaced pcr - inflorescence architecture - cell-differentiation - rough-sheath2 gene - leaf development - lateral organs - expression - thaliana - activation
The formation and the development of the floral organs require an intercalate expression of organ-specific genes. At the same time, meristem-specific genes are repressed to complete the differentiation of the organs in the floral whorls. In an Arabidopsis activation tagging population, a mutant affected in inflorescence architecture was identified. This gain-of-function mutant, designateddownwards siliques1 (dsl1-D), has shorter internodes and the lateral organs such as flowers are bending downwards, similar to the loss-of-function brevipedicellus (bp) mutant. The affected gene in dsl1-D appeared to be ASYMMETRIC LEAVES2-LIKE1 (ASL1)/LATERAL ORGAN BOUNDARIESdomain gene 36 (LBD36), which is a member of the ASYMMETRIC LEAVES2 (AS2)/LATERAL ORGAN BOUNDARIES (LOB) domain gene family. Analysis of the loss-of-function mutant asl1/lbd36 did not show morphological aberration. Double mutant analysis of asl1/lbd36 together with as2, the ASL1/LBD36 closest homologue, demonstrates that these two members of the AS2/LOB family act partially redundant to control cell fate determination in Arabidopsis petals. Moreover, molecular analysis revealed that overexpression of ASL1/LBD36 leads to repression of the homeobox gene BP, which supports the model that an antagonistic relationship between ASL/LBD and homeobox members is required for the differentiation of lateral organs
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