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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    Specification and regulation of vascular tissue identity in the Arabidopsis embryo
    Smit, Margot E. ; Llavata-Peris, Cristina I. ; Roosjen, Mark ; Beijnum, Henriette van; Novikova, Daria ; Levitsky, Victor ; Sevilem, Iris ; Roszak, Pawel ; Slane, Daniel ; Jürgens, Gerd ; Mironova, Victoria ; Brady, Siobhan M. ; Weijers, Dolf - \ 2020
    Development 147 (2020)8. - ISSN 0950-1991
    Arabidopsis - Auxin - Embryo - Gene regulatory network - Vascular development

    Development of plant vascular tissues involves tissue identity specification, growth, pattern formation and cell-type differentiation. Although later developmental steps are understood in some detail, it is still largely unknown how the tissue is initially specified. We used the early Arabidopsis embryo as a simple model to study this process. Using a large collection of marker genes, we found that vascular identity was specified in the 16-cell embryo. After a transient precursor state, however, there was no persistent uniform tissue identity. Auxin is intimately connected to vascular tissue development. We found that, although an AUXIN RESPONSE FACTOR5/MONOPTEROS (ARF5/MP)-dependent auxin response was required, it was not sufficient for tissue specification. We therefore used a large-scale enhanced yeast one-hybrid assay to identify potential regulators of vascular identity. Network and functional analysis of candidate regulators suggest that vascular identity is under robust, complex control. We found that one candidate regulator, the G-class bZIP transcription factor GBF2, can modulate vascular gene expression by tuning MP output through direct interaction. Our work uncovers components of a gene regulatory network that controls the initial specification of vascular tissue identity.

    A coherent feed-forward loop drives vascular regeneration in damaged aerial organs of plants growing in a normal developmental context
    Radhakrishnan, Dhanya ; Shanmukhan, Anju Pallipurath ; Kareem, Abdul ; Aiyaz, Mohammed ; Varapparambathu, Vijina ; Toms, Ashna ; Kerstens, Merijn ; Valsakumar, Devisree ; Landge, Amit N. ; Shaji, Anil ; Mathew, Mathew K. ; Sawchuk, Megan G. ; Scarpella, Enrico ; Krizek, Beth A. ; Efroni, Idan ; Mähönen, Ari Pekka ; Willemsen, Viola ; Scheres, Ben ; Prasad, Kalika - \ 2020
    Development 147 (2020)6. - ISSN 0950-1991
    Arabidopsis - Auxin - CUC2 - PIN1 - PLT - Vascular regeneration - Wound repair

    Aerial organs of plants, being highly prone to local injuries, require tissue restoration to ensure their survival. However, knowledge of the underlying mechanism is sparse. In this study, we mimicked natural injuries in growing leaves and stems to study the reunion between mechanically disconnected tissues. We show that PLETHORA (PLT) and AINTEGUMENTA (ANT) genes, which encode stem cell-promoting factors, are activated and contribute to vascular regeneration in response to these injuries. PLT proteins bind to and activate the CUC2 promoter. PLT proteins and CUC2 regulate the transcription of the local auxin biosynthesis gene YUC4 in a coherent feed-forward loop, and this process is necessary to drive vascular regeneration. In the absence of this PLT-mediated regeneration response, leaf ground tissue cells can neither acquire the early vascular identity marker ATHB8, nor properly polarise auxin transporters to specify new venation paths. The PLT-CUC2 module is required for vascular regeneration, but is dispensable for midvein formation in leaves. We reveal the mechanisms of vascular regeneration in plants and distinguish between the wound-repair ability of the tissue and its formation during normal development.

    GH3 Auxin-Amido Synthetases Alter the Ratio of Indole-3-Acetic Acid and Phenylacetic Acid in Arabidopsis
    Aoi, Yuki ; Tanaka, Keita ; Cook, Sam David ; Hayashi, Ken Ichiro ; Kasahara, Hiroyuki - \ 2020
    Plant and Cell Physiology 61 (2020)3. - ISSN 0032-0781 - p. 596 - 605.
    Arabidopsis - Auxin - Biosynthesis - Inactivation - Indole-3-acetic acid - Phenylacetic acid

    Auxin is the first discovered plant hormone and is essential for many aspects of plant growth and development. Indole-3-acetic acid (IAA) is the main auxin and plays pivotal roles in intercellular communication through polar auxin transport. Phenylacetic acid (PAA) is another natural auxin that does not show polar movement. Although a wide range of species have been shown to produce PAA, its biosynthesis, inactivation and physiological significance in plants are largely unknown. In this study, we demonstrate that overexpression of the CYP79A2 gene, which is involved in benzylglucosinolate synthesis, remarkably increased the levels of PAA and enhanced lateral root formation in Arabidopsis. This coincided with a significant reduction in the levels of IAA. The results from auxin metabolite quantification suggest that the PAA-dependent induction of GRETCHEN HAGEN 3 (GH3) genes, which encode auxin-amido synthetases, promote the inactivation of IAA. Similarly, an increase in IAA synthesis, via the indole-3-acetaldoxime pathway, significantly reduced the levels of PAA. The same adjustment of IAA and PAA levels was also observed by applying each auxin to wild-type plants. These results show that GH3 auxin-amido synthetases can alter the ratio of IAA and PAA in plant growth and development.

    Seed maturation and post-harvest ripening negatively affect arabidopsis somatic embryogenesis
    Wu, Han ; Chen, Baojian ; Fiers, Martijn ; Wróbel-Marek, Justyna ; Kodde, Jan ; Groot, Steven P.C. ; Angenent, Gerco ; Feng, Hui ; Bentsink, Leónie ; Boutilier, Kim - \ 2019
    Plant Cell, Tissue and Organ Culture: an international journal on in vitro culture of higher plants 139 (2019)1. - ISSN 0167-6857 - p. 17 - 27.
    ABA - Arabidopsis - Auxin - Post-harvest ripening - ROS - Seed maturation - Somatic embryogenesis

    Plant development is highly malleable, as evidenced by the ability of cultured cells, tissues and organs to regenerate into whole plants in vitro. The ability of plants to regenerate in vitro is influenced by many different factors, including the donor plant growth conditions and the type of explant. Empirical trial and error manipulation of these and other culture parameters is the basis for improving plant regeneration protocols, but the mechanisms underlying the effects of these parameters on plant regeneration are unknown. Somatic embryogenesis (SE) is a type of in vitro plant regeneration where somatic/vegetative cells are induced to form embryos. Here we show that seed maturation is one of the parameters that affects the ability of germinating embryos to undergo auxin-induced somatic embryogenesis in Arabidopsis thaliana. Late maturation stage seeds harvested from yellow siliques have a higher capacity for somatic embryogenesis than seeds harvested later from brown siliques, a process that can be mimicked by post-harvest storage. Physiological and genetic analyses suggest that an oxidizing environment and ABA metabolism enhance the rate at which germinating embryos lose capacity to reactivate embryogenic growth. Our data suggest that there is a narrow window during late seed maturation in which embryogenic competence is reduced, and that this process also takes place, albeit more slowly, during seed storage. This knowledge provides a framework for identifying new plant totipotency factors and for directing efficient SE in systems that make use of mature seed explants.

    A disturbed auxin signaling affects adventitious root outgrowth in Solanum dulcamara under complete submergence
    Yang, Xinping ; Jansen, Martijn J. ; Zhang, Qian ; Sergeeva, Lidiya ; Ligterink, Wilco ; Mariani, Celestina ; Rieu, Ivo ; Visser, Eric J.W. - \ 2018
    Journal of Plant Physiology 224-225 (2018). - ISSN 0176-1617 - p. 11 - 18.
    ABA - Adventitious roots - Auxin - Complete submergence - JA - Signaling
    Flooding negatively affects the growth and even survival of most terrestrial plants. Upon flooding, the excess water quickly decreases the gas exchange between atmosphere and the submerged plant tissues, which leads to oxygen deficiency resulting in a plant cell energy crisis, and eventually plant death. Solanum dulcamara survives flooding by producing aerenchymatous adventitious roots (ARs) from pre-formed primordia on the stem, which replace the original flood-sensitive root system. However, we found that under complete submergence, AR outgrowth was impaired in S. dulcamara. In the present work, we tried to elucidate the mechanisms behind this phenomenon in particular the involvement of the phytohormones auxin, abscisic acid and jasmonic acid. Abscisic acid (ABA) is a negative regulator of AR outgrowth, but surprisingly the ABA content and signaling were decreased to a similar extent under both partial and complete submergence, suggesting that ABA might not be responsible for the difference in AR outgrowth. Auxin, which is necessary for AR outgrowth, was at similar concentrations in either partially or completely submerged primordia, but complete submergence resulted in a decrease of auxin signaling in the primordia. Application of 1-naphthaleneacetic acid (NAA) to completely submerged plants restored AR outgrowth, implying that auxin response in the rooting tissues of completely submerged plants was reduced. Furthermore, jasmonic acid (JA) concentrations did not differ between partial and complete submergence. To conclude, a disruption in the auxin signaling within S. dulcamara AR primordia may result in the abortion of AR outgrowth under complete submergence.
    Auxin Response Factors : Output control in auxin biology
    Roosjen, Mark ; Paque, Sébastien ; Weijers, Dolf - \ 2018
    Journal of Experimental Botany 69 (2018)2. - ISSN 0022-0957 - p. 179 - 188.
    Auxin - auxin response - gene regulation - plant development - signal transduction - transcription factors
    The phytohormone auxin is involved in almost all developmental processes in land plants. Most, if not all, of these processes are mediated by changes in gene expression. Auxin acts on gene expression through a short nuclear pathway that converges upon the activation of a family of DNA-binding transcription factors. These AUXIN RESPONSE FACTORS (ARFs) are thus the effector of auxin response and translate the chemical signal into the regulation of a defined set of genes. Given the limited number of dedicated components in auxin signaling, distinct properties among the ARF family probably contribute to the establishment of multiple unique auxin responses in plant development. In the two decades following the identification of the first ARF in Arabidopsis, much has been learnt about how these transcription factors act, and how they generate unique auxin responses. Progress in genetics, biochemistry, genomics, and structural biology has helped to develop mechanistic models for ARF action. However, despite intensive efforts, many central questions are yet to be addressed. In this review, we highlight what has been learnt about ARF transcription factors, and identify outstanding questions and challenges for the near future.
    Auxin: Small molecule, big impact
    Weijers, Dolf ; Nemhauser, Jennifer ; Yang, Zhenbiao - \ 2018
    Journal of Experimental Botany 69 (2018)2. - ISSN 0022-0957 - p. 133 - 136.
    Auxin - AUXIN RESPONSE FACTOR (ARF) - cell wall acidification - indole-3-Acetic acid (IAA) - lateral root formation - pin-formed1 - PIN1 - shoot meristem development
    Diversity of cis-regulatory elements associated with auxin response in Arabidopsis thaliana
    Cherenkov, Pavel ; Novikova, Daria ; Omelyanchuk, Nadya ; Levitsky, Victor ; Grosse, Ivo ; Weijers, Dolf ; Mironova, Victoria - \ 2018
    Journal of Experimental Botany 69 (2018)2. - ISSN 0022-0957 - p. 329 - 339.
    ARF - Auxin - AuxRE - bHLH - bioinformatics - bZIP - chromatin states - transcriptional regulation
    The phytohormone auxin regulates virtually every developmental process in land plants. This regulation is mediated via de-repression of DNA-binding auxin response factors (ARFs). ARFs bind TGTC-containing auxin response cis-elements (AuxREs), but there is growing evidence that additional cis-elements occur in auxin-responsive regulatory regions. The repertoire of auxin-related cis-elements and their involvement in different modes of auxin response are not yet known. Here we analyze the enrichment of nucleotide hexamers in upstream regions of auxin-responsive genes associated with auxin up-or down-regulation, with early or late response, ARF-binding domains, and with different chromatin states. Intriguingly, hexamers potentially bound by basic helix-loop-helix (bHLH) and basic leucine zipper (bZIP) factors as well as a family of A/T-rich hexamers are more highly enriched in auxin-responsive regions than canonical TGTC-containing AuxREs. We classify and annotate the whole spectrum of enriched hexamers and discuss their patterns of enrichment related to different modes of auxin response.
    Divergent regulation of Arabidopsis SAUR genes : A focus on the SAUR10-clade
    Mourik, Hilda van; Dijk, Aalt D.J. van; Stortenbeker, Niek ; Angenent, Gerco C. ; Bemer, Marian - \ 2017
    BMC Plant Biology 17 (2017). - ISSN 1471-2229
    ABA - Auxin - Brassinosteroids - Cell elongation - Growth - Hormones - Regulatory region - SAUR - Shade response

    Background: Small Auxin-Upregulated RNA (SAUR) genes encode growth regulators that induce cell elongation. Arabidopsis contains more than 70 SAUR genes, of which the growth-promoting function has been unveiled in seedlings, while their role in other tissues remained largely unknown. Here, we focus on the regulatory regions of Arabidopsis SAUR genes, to predict the processes in which they play a role, and understand the dynamics of plant growth. Results: In this study, we characterized in detail the entire SAUR10-clade: SAUR8, SAUR9, SAUR10, SAUR12, SAUR16, SAUR50, SAUR51 and SAUR54. Overexpression analysis revealed that the different proteins fulfil similar functions, while the SAUR expression patterns were highly diverse, showing expression throughout plant development in a variety of tissues. In addition, the response to application of different hormones largely varied between the different genes. These tissue-specific and hormone-specific responses could be linked to transcription factor binding sites using in silico analyses. These analyses also supported the existence of two groups of SAURs in Arabidopsis: Class I genes can be induced by combinatorial action of ARF-BZR-PIF transcription factors, while Class II genes are not regulated by auxin. Conclusions:SAUR10-clade genes generally induce cell-elongation, but exhibit diverse expression patterns and responses to hormones. Our experimental and in silico analyses suggest that transcription factors involved in plant development determine the tissue specific expression of the different SAUR genes, whereas the amplitude of this expression can often be controlled by hormone response transcription factors. This allows the plant to fine tune growth in a variety of tissues in response to internal and external signals.

    The roles of the sole activator-type auxin response factor in pattern formation of marchantia polymorpha
    Kato, Hirotaka ; Kouno, Masaru ; Takeda, Mayuko ; Suzuki, Hidemasa ; Ishizaki, Kimitsune ; Nishihama, Ryuichi ; Kohchi, Takayuki - \ 2017
    Plant and Cell Physiology 58 (2017)10. - ISSN 0032-0781 - p. 1642 - 1651.
    ARF - Auxin - Bryophyte - Cell division - Pattern formation
    Cell division patterning is important to determine body shape in plants. Nuclear auxin signaling mediated by AUXIN RESPONSE FACTOR (ARF) transcription factors affects plant growth and development through regulation of cell division, elongation and differentiation. The evolutionary origin of the ARF-mediated pathway dates back to at least the common ancestor of bryophytes and other land plants. The liverwort Marchantia polymorpha has three phylogenetically distinct ARFs: MpARF1, the sole ‘activator’ ARF; and MpARF2 and MpARF3, two ‘repressor’ ARFs. Genetic screens for auxin-resistant mutants revealed that loss of MpARF1 function conferred auxin insensitivity. Mparf1 mutants showed reduced auxin-inducible gene expression and various developmental defects, including thallus twisting and gemma malformation. We further investigated the role of MpARF1 in gemma development, which is traceable at the cellular level. In wild-type plants, a gemma initial first undergoes several transverse divisions to generate a single-celled stalk and a gemma proper, followed by rather synchronous longitudinal divisions in the latter. Mparf1 mutants often contained multicelled stalks and showed defects in the execution and timing of the longitudinal divisions. While wild-type gemmae finally generate two meristem notches, Mparf1 gemmae displayed various numbers of ectopic meristems. These results suggest that MpARF1 regulates formative cell divisions and axis formation through auxin responses. The mechanism for activator ARF regulation of pattern formation may be shared in land plants and therefore important for the general acquisition of three-dimensional body plans.
    BEN3/BIG2 ARF GEF is involved in brefeldin a-sensitive trafficking at the trans-golgi network/early endosome in arabidopsis thaliana
    Kitakura, Saeko ; Adamowski, Maciek ; Matsuura, Yuki ; Santuari, Luca ; Kouno, Hirotaka ; Arima, Kohei ; Hardtke, Christian S. ; Friml, Jiř ; Kakimoto, Tatsuo ; Tanaka, Hirokazu - \ 2017
    Plant and Cell Physiology 58 (2017)10. - ISSN 0032-0781 - p. 1801 - 1811.
    Arabidopsis - ARF GEF - Auxin - Brefeldin A - PIN-FORMED1 - Trans-Golgi network

    Membrane traffic at the trans-Golgi network (TGN) is crucial for correctly distributing various membrane proteins to their destination. Polarly localized auxin efflux proteins, including PIN-FORMED1 (PIN1), are dynamically transported between the endosomes and the plasma membrane (PM) in the plant cells. The intracellular trafficking of PIN1 protein is sensitive to the fungal toxin brefeldin A (BFA), which is known to inhibit guanine nucleotide exchange factors for ADP ribosylation factors (ARF GEFs) such as GNOM. However, the molecular details of the BFA-sensitive trafficking pathway have not been fully revealed. In a previous study, we identified an Arabidopsis mutant BFA-visualized endocytic trafficking defective 3 (ben3) which exhibited reduced sensitivity to BFA in terms of BFA-induced intracellular PIN1 agglomeration. Here, we show that BEN3 encodes a member of BIG family ARF GEFs, BIG2. BEN3/BIG2 tagged with fluorescent proteins co-localized with markers for the TGN/early endosome (EE). Inspection of conditionally induced de novo synthesized PIN1 confirmed that its secretion to the PM is BFA sensitive, and established BEN3/BIG2 as a crucial component of this BFA action at the level of the TGN/EE. Furthermore, ben3 mutation alleviated BFAinduced agglomeration of another TGN-localized ARF GEF, BEN1/MIN7. Taken together, our results suggest that BEN3/BIG2 is an ARF GEF component, which confers BFA sensitivity to the TGN/EE in Arabidopsis.

    Plant phenotypic and transcriptional changes induced by volatiles from the fungal root pathogen Rhizoctonia solani
    Cordovez da Cunha, Viviane ; Mommer, Liesje ; Moisan, Kay ; Lucas Gomes Marques Barbosa, Dani ; Pierik, Ronald ; Mumm, Roland ; Carrion, Victor J. ; Raaijmakers, Jos M. - \ 2017
    Frontiers in Plant Science 8 (2017). - ISSN 1664-462X
    Auxin - Fungal volatiles - Plant growth promotion - Plant resistance - Plant transcriptome

    Beneficial soil microorganisms can affect plant growth and resistance by the production of volatile organic compounds (VOCs). Yet, little is known on how VOCs from soil-borne plant pathogens affect plant growth and resistance. Here we show that VOCs released from mycelium and sclerotia of the fungal root pathogen Rhizoctonia solani enhance growth and accelerate development of Arabidopsis thaliana. Seedlings briefly exposed to the fungal VOCs showed similar phenotypes, suggesting that enhanced biomass and accelerated development are primed already at early developmental stages. Fungal VOCs did not affect plant resistance to infection by the VOC-producing pathogen itself but reduced aboveground resistance to the herbivore Mamestra brassicae. Transcriptomics of A. thaliana revealed that genes involved in auxin signaling were up-regulated, whereas ethylene and jasmonic acid signaling pathways were down-regulated by fungal VOCs. Mutants disrupted in these pathways showed similar VOC-mediated growth responses as the wild-type A. thaliana, suggesting that other yet unknown pathways play a more prominent role. We postulate that R. solani uses VOCs to predispose plants for infection from a distance by altering root architecture and enhancing root biomass. Alternatively, plants may use enhanced root growth upon fungal VOC perception to sacrifice part of the root biomass and accelerate development and reproduction to survive infection.

    Neighbor detection at the leaf tip adaptively regulates upward leaf movement through spatial auxin dynamics
    Pantazopoulou, Chrysoula K. ; Bongers, Franca J. ; Küpers, Jesse J. ; Reinen, Emilie ; Das, Debatosh ; Evers, Jochem B. ; Anten, Niels P.R. ; Pierik, Ronald - \ 2017
    Proceedings of the National Academy of Sciences of the United States of America 114 (2017)28. - ISSN 0027-8424 - p. 7450 - 7455.
    Auxin - Functional-structural plant model - Leaf movement - Phytochrome - Shade avoidance
    Vegetation stands have a heterogeneous distribution of light quality, including the red/far-red light ratio (R/FR) that informs plants about proximity of neighbors. Adequate responses to changes in R/FR are important for competitive success. How the detection and response to R/FR are spatially linked and how this spatial coordination between detection and response affects plant performance remains unresolved. We show in Arabidopsis thaliana and Brassica nigra that localized FR enrichment at the lamina tip induces upward leaf movement (hyponasty) from the petiole base. Using a combination of organ-level transcriptome analysis, molecular reporters, and physiology, we show that PIF-dependent spatial auxin dynamics are key to this remote response to localized FR enrichment. Using computational 3D modeling, we show that remote signaling of R/FR for hyponasty has an adaptive advantage over local signaling in the petiole, because it optimizes the timing of leaf movement in response to neighbors and prevents hyponasty caused by self-shading.
    Theoretical approaches to understanding root vascular patterning : A consensus between recent models
    Mellor, Nathan ; Adibi, Milad ; El-Showk, Sedeer ; Rybel, Bert De; King, John ; Mähönen, Ari Pekka ; Weijers, Dolf ; Bishopp, Anthony ; Etchells, Peter - \ 2017
    Journal of Experimental Botany 68 (2017)1. - ISSN 0022-0957 - p. 5 - 16.
    Auxin - Cytokinin - Mathematical modeling - Organ patterning - Systems biology - Vascular development

    The root vascular tissues provide an excellent system for studying organ patterning, as the specification of these tissues signals a transition from radial symmetry to bisymmetric patterns. The patterning process is controlled by the combined action of hormonal signaling/transport pathways, transcription factors, and miRNA that operate through a series of non-linear pathways to drive pattern formation collectively. With the discovery of multiple components and feedback loops controlling patterning, it has become increasingly difficult to understand how these interactions act in unison to determine pattern formation in multicellular tissues. Three independent mathematical models of root vascular patterning have been formulated in the last few years, providing an excellent example of how theoretical approaches can complement experimental studies to provide new insights into complex systems. In many aspects these models support each other; however, each study also provides its own novel findings and unique viewpoints. Here we reconcile these models by identifying the commonalities and exploring the differences between them by testing how transferable findings are between models. New simulations herein support the hypothesis that an asymmetry in auxin input can direct the formation of vascular pattern. We show that the xylem axis can act as a sole source of cytokinin and specify the correct pattern, but also that broader patterns of cytokinin production are also able to pattern the root. By comparing the three modeling approaches, we gain further insight into vascular patterning and identify several key areas for experimental investigation.

    Auxin synthesis gene tms1 driven by tuber-specific promoter alters hormonal status of transgenic potato plants and their responses to exogenous phytohormones
    Kolachevskaya, Oksana O. ; Sergeeva, Lidia ; Floková, Kristyna ; Getman, Irina A. ; Lomin, Sergey N. ; Alekseeva, Valeriya V. ; Rukavtsova, Elena B. ; Buryanov, Yaroslav I. ; Romanov, Georgy A. - \ 2017
    Plant Cell Reports 36 (2017)3. - ISSN 0721-7714 - p. 419 - 435.
    Auxin - Cytokinin - Hormonal status - Phytohormones - Potato - Solanum tuberosum - Transformants - Tuberization
    Key message: Ectopic auxin overproduction in transgenic potato leads to enhanced productivity accompanied with concerted and occasional changes in hormonal status, and causing altered response of transformants to exogenous auxin or cytokinin.Abstract: Previously, we generated potato transformants expressing Agrobacterium-derived auxin synthesis gene tms1 driven by tuber-specific patatin gene promoter (B33-promoter). Here, we studied the endogenous hormonal status and the response to exogenous phytohormones in tms1 transformants cultured in vitro. Adding indole-3-acetic acid (IAA) or kinetin to culture medium affected differently tuberization of tms1-transformed and control plants, depending also on sucrose content in the medium. Exogenous phytohormones ceased to stimulate the tuber initiation in transformants at high (5–8%) sucrose concentration, while in control plants the stimulation was observed in all experimental settings. Furthermore, exogenous auxin partly inhibited the tuber initiation, and exogenous cytokinin reduced the average tuber weight in most transformants at high sucrose content. The elevated auxin level in tubers of the transformants was accompanied with a decrease in content of cytokinin bases and their ribosides in tubers and most shoots. No concerted changes in contents of abscisic, jasmonic, salicylic acids and gibberellins in tubers were detected. The data on hormonal status indicated that the enhanced productivity of tms1 transformants was due to auxin and not mediated by other phytohormones. In addition, exogenous cytokinin was shown to upregulate the expression of genes encoding orthologs of auxin receptors. Overall, the results showed that tms1 expression and local increase in IAA level in transformants affect both the balance of endogenous cytokinins and the dynamics of tuberization in response to exogenous hormones (auxin, cytokinin), the latter reaction depending also on the carbohydrate supply. We introduce a basic model for the hormonal network controlling tuberization.
    Knocking down expression of the auxin-amidohydrolase IAR3 alters defense responses in Solanaceae family plants
    Ippolito, Sebastian D'; Vankova, Radomira ; Joosten, Matthieu H.A.J. ; Casalongué, Claudia A. ; Fiol, Diego F. - \ 2016
    Plant Science 253 (2016). - ISSN 0168-9452 - p. 31 - 39.
    Auxin - Biotic stress - Cladosporium fulvum - Indole-3-acetic acid amido hydrolases - Nicotiana benthamiana - Phytophthora infestans - Solanum lycopersicum

    In plants, indole-3-acetic acid (IAA) amido hydrolases (AHs) participate in auxin homeostasis by releasing free IAA from IAA-amino acid conjugates. We investigated the role of IAR3, a member of the IAA amido hydrolase family, in the response of Solanaceous plants challenged by biotrophic and hemi-biotrophic pathogens. By means of genome inspection and phylogenic analysis we firstly identified IAA-AH sequences and putative IAR3 orthologs in Nicotiana benthamiana, tomato and potato. We evaluated the involvement of IAR3 genes in defense responses by using virus-induced gene silencing. We observed that N. benthamiana and tomato plants with knocked-down expression of IAR3 genes contained lower levels of free IAA and presented altered responses to pathogen attack, including enhanced basal defenses and higher tolerance to infection in susceptible plants. We showed that IAR3 genes are consistently up-regulated in N. benthamiana and tomato upon inoculation with Phytophthora infestans and Cladosporium fulvum respectively. However, IAR3 expression decreased significantly when hypersensitive response was triggered in transgenic tomato plants coexpressing the Cf-4 resistance gene and the avirulence factor Avr4. Altogether, our results indicate that changes in IAR3 expression lead to alteration in auxin homeostasis that ultimately affects plant defense responses.

    Molecular signals controlling the inhibition of nodulation by nitrate in Medicago truncatula
    Noorden, Giel E. Van; Verbeek, Rob ; Dinh, Peter ; Jin, Jian ; Green, Alexandra ; Ng, Jason Liang Pin ; Mathesius, Ulrike - \ 2016
    International Journal of Molecular Sciences 17 (2016)7. - ISSN 1661-6596
    Auxin - Flavonoid - Nitrate - Nodulation - Proteomics - Reactive oxygen species

    The presence of nitrogen inhibits legume nodule formation, but the mechanism of this inhibition is poorly understood. We found that 2.5 mM nitrate and above significantly inhibited nodule initiation but not root hair curling in Medicago trunatula. We analyzed protein abundance in M. truncatula roots after treatment with either 0 or 2.5 mM nitrate in the presence or absence of its symbiont Sinorhizobium meliloti after 1, 2 and 5 days following inoculation. Two-dimensional gel electrophoresis combined with mass spectrometry was used to identify 106 differentially accumulated proteins responding to nitrate addition, inoculation or time point. While flavonoid-related proteins were less abundant in the presence of nitrate, addition of Nod gene-inducing flavonoids to the Sinorhizobium culture did not rescue nodulation. Accumulation of auxin in response to rhizobia, which is also controlled by flavonoids, still occurred in the presence of nitrate, but did not localize to a nodule initiation site. Several of the changes included defense- and redox-related proteins, and visualization of reactive oxygen species indicated that their induction in root hairs following Sinorhizobium inoculation was inhibited by nitrate. In summary, the presence of nitrate appears to inhibit nodulation via multiple pathways, including changes to flavonoid metabolism, defense responses and redox changes.

    Transcriptional Responses to the Auxin Hormone
    Weijers, Dolf ; Wagner, Doris - \ 2016
    Annual Review of Plant Biology 67 (2016). - ISSN 1543-5008 - p. 539 - 574.
    ARF - Auxin - Chromatin - Development - Gene expression - Specificity

    Auxin is arguably the most important signaling molecule in plants, and the last few decades have seen remarkable breakthroughs in understanding its production, transport, and perception. Recent investigations have focused on transcriptional responses to auxin, providing novel insight into the functions of the domains of key transcription regulators in responses to the hormonal cue and prominently implicating chromatin regulation in these responses. In addition, studies are beginning to identify direct targets of the auxin-responsive transcription factors that underlie auxin modulation of development. Mechanisms to tune the response to different auxin levels are emerging, as are first insights into how this single hormone can trigger diverse responses. Key unanswered questions center on the mechanism for auxin-directed transcriptional repression and the identity of additional determinants of auxin response specificity. Much of what has been learned in model plants holds true in other species, including the earliest land plants.

    Computational and Experimental Evidence That Auxin Accumulation in Nodule and Lateral Root Primordia Occurs by Different Mechanisms
    Deinum, Eva E. ; Geurts, René ; Hartog, Marijke ; Bisseling, Ton ; Mulder, Bela M. - \ 2015
    In: Biological Nitrogen Fixation / de Bruijn, Frans J., Wiley-Blackwell - ISBN 9781118637043 - p. 659 - 668.
    Auxin - Computer simulation - Nodule primordium - PIN efflux carriers

    The formation of root lateral organ formation typically requires the de novo generation of a primordium, initiated at the site of local auxin accumulation. Legume roots are a particularly interesting example in this respect, as they can give rise to both lateral roots and root nodules. The initiation of the latter primordium is much less understood. Using computer simulations we start with an unbiased comparison of different mechanisms that a priori seemed capable of producing local auxin accumulation. These mechanisms all produce different characteristic signatures, of which a reduction of auxin efflux best matches the morphology of nodule primordia. This leads to the prediction that root nodule positions would not be affected by root curvature - contrary to lateral root primordia that are initiated by increased influx - which we experimentally confirmed. We further investigate how changes in the in silico root segment affect the induction and shape of local auxin maxima and discuss the functional implications of these findings with respect to nodule type and bounding the developmental zone where nodulation takes place.

    Solanum lycopersicum AUXIN RESPONSE FACTOR 9 regulates cell division activity during early tomato fruit development
    Jong, Maaike De; Wolters-Arts, Mieke ; Schimmel, B.C.J. ; Tikunov, Y.M. ; Bovy, A.G. - \ 2015
    Journal of Experimental Botany 66 (2015)11. - ISSN 0022-0957 - p. 3405 - 3416.
    Auxin - AUXIN RESPONSE FACTOR 9 (ARF9) - Cell division - Fruit development - Fruit size - Tomato (Solanum lycopersicum L.)

    The transformation of the ovary into a fruit after successful completion of pollination and fertilization has been associated with many changes at transcriptomic level. These changes are part of a dynamic and complex regulatory network that is controlled by phytohormones, with a major role for auxin. One of the auxin-related genes differentially expressed upon fruit set and early fruit development in tomato is Solanum lycopersicum AUXIN RESPONSE FACTOR 9 (SlARF9). Here, the functional analysis of this ARF is described. SlARF9 expression was found to be auxin-responsive and SlARF9 mRNA levels were high in the ovules, placenta, and pericarp of pollinated ovaries, but also in other plant tissues with high cell division activity, such as the axillary meristems and root meristems. Transgenic plants with increased SlARF9 mRNA levels formed fruits that were smaller than wild-type fruits because of reduced cell division activity, whereas transgenic lines in which SlARF9 mRNA levels were reduced showed the opposite phenotype. The expression analysis, together with the phenotype of the transgenic lines, suggests that, in tomato, ARF9 negatively controls cell division during early fruit development.

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