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.

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The heat shock transcription factor PsHSF1 of Phytophthora sojae is required for oxidative stress tolerance and detoxifying the plant oxidative burst
Sheng, Yuting ; Wang, Yonglin ; Meijer, H.J.G. ; Yang, Xinyu ; Hua, C. ; Ye, Wenwu ; Tao, Kai ; Liu, Xiaoyun ; Govers, F. ; Wang, Yuanchao - \ 2015
Environmental Microbiology 17 (2015)4. - ISSN 1462-2912 - p. 1351 - 1364.
signal-transduction - in-vivo - pathogen - infestans - expression - sequence - defense - laccase - binding - yeast
In the interaction between plant and microbial pathogens, reactive oxygen species (ROS) rapidly accumulate upon pathogen recognition at the infection site and play a central role in plant defence. However, the mechanisms that plant pathogens use to counteract ROS are still poorly understood especially in oomycetes, filamentous organisms that evolved independently from fungi. ROS detoxification depends on transcription factors (TFs) that are highly conserved in fungi but much less conserved in oomycetes. In this study, we identified the TF PsHSF1 that acts as a modulator of the oxidative stress response in the soybean stem and root rot pathogen Phytophthora sojae. We found that PsHSF1 is critical for pathogenicity in P.¿sojae by detoxifying the plant oxidative burst. ROS produced in plant defence can be detoxified by extracellular peroxidases and laccases which might be regulated by PsHSF1. Our study extends the understanding of ROS detoxification mechanism mediated by a heat shock TF in oomycetes.
Investigation of sporulation in the Desulfotomaculum genus: a genomic comparison with the genera Bacillus and Clostridium
Vecchia, E. Dalla; Visser, M. ; Stams, A.J.M. ; Bernier-Latmani, R. - \ 2014
Environmental Microbiology Reports 6 (2014)6. - ISSN 1758-2229 - p. 756 - 766.
signal-transduction - endospore formation - spore formation - surface-layers - cell-division - subtilis - proteins - initiation - phosphorelay - reveals
The genus Desulfotomaculum, belonging to the Firmicutes, comprises strictly anaerobic and endospore-forming bacteria capable of dissimilatory sulfate reduction. These microorganisms are metabolically versatile and are widely distributed in the environment. Spore formation allows them to survive prolonged environmental stress. Information on the mechanism of sporulation in Desulfotomaculum species is scarce. Herein, this process was probed from a genomic standpoint, using the Bacillus subtilis model system as a reference and clostridial sporulation for comparison. Desulfotomaculum falls somewhere in between the Bacillus and Clostridium in terms of conservation of sporulation proteins. Furthermore, it showcased the conservation of a core regulatory cascade throughout genera, while uncovering variability in the initiation of sporulation and the structural characteristics of spores from different genera. In particular, while in Clostridium species sporulation is not initiated by a phosphorelay, Desulfotomaculum species harbour homologues of the B.¿subtilis proteins involved in this process. Conversely, both Clostridium and Desulfotomaculum species conserve very few B.¿subtilis structural proteins, particularly those found in the outer layers of the spore. Desulfotomaculum species seem to share greater similarity to the outer layers of Clostridium difficile.
Mechanisms involved in apoptosis of carp leukocytes upon in vitro and in vivo immunostimulation
Kepka, M. ; Verburg-van Kemenade, B.M.L. ; Homa, J. ; Chadzinska, M.K. - \ 2014
Fish and Shellfish Immunology 39 (2014)2. - ISSN 1050-4648 - p. 386 - 395.
cytochrome-c release - molecular-cloning - cyprinus-carpio - nitric-oxide - transgenic zebrafish - signal-transduction - ceramide generation - respiratory burst - human neutrophils - oxidative stress
During inflammation leukocyte activity must be carefully regulated, as high concentrations and/or prolonged action of pro-inflammatory mediators e.g. reactive oxygen species (ROS) can be detrimental not only for pathogens but also for host tissues. Programmed cell death – apoptosis is a most effective regulatory mechanism for down regulation of leukocyte activity, but little is known about this process in fish. We aimed to reveal the mechanisms of initiation and regulation of apoptosis in carp neutrophilic granulocytes and macrophages. During zymosan-induced peritonitis in carp, activated inflammatory neutrophilic granulocytes and monocytes/macrophages died by apoptosis. This correlated with a strong production of ROS, but pretreatment of the fish with NADPH oxidase inhibitor only slightly decreased late apoptosis. Interestingly in vitro incubation with zymosan or phorbol ester, but not lipopolisaccharide and poli I:C induced apoptosis of head kidney neutrophilic granulocytes. This coincided with loss of mitochondrial membrane potential. Moreover, in zymosan-stimulated neutrophilic granulocytes NADPH oxidase inhibitor not only reduced the production of ROS but also apoptosis. A similar effect was not observed in cells stimulated with phorbol ester, where DPI reduced ROS production, but not apoptosis. In PMA-stimulated neutrophilic granulocytes both the respiratory burst and apoptosis were reduced by protein kinase inhibitor. Furthermore, a short neutrophil stimulation either with PMA or with zymosan did induce caspase-independent apoptosis. These results show that in carp, apoptosis is an important regulatory process during in vitro and in vivo immunostimulation. In neutrophils, protein kinase, but not NADPH oxidase, is involved in PMA-induced apoptosis while apoptosis induced by zymosan is ROS-dependent.
Abscisic acid (ABA) sensitivity regulates desiccation tolerance in germinated Arabidopsis seeds
Maia de Oliveira, J. ; Dekkers, S.J.W. ; Dolle, M. ; Ligterink, W. ; Hilhorst, H.W.M. - \ 2014
New Phytologist 203 (2014)1. - ISSN 0028-646X - p. 81 - 93.
bzip transcription factors - medicago-truncatula seeds - 2c protein phosphatases - signal-transduction - drought tolerance - thaliana - stress - gene - maturation - expression
During germination, orthodox seeds lose their desiccation tolerance (DT) and become sensitive to extreme drying. Yet, DT can be rescued, in a well-defined developmental window, by the application of a mild osmotic stress before dehydration. A role for abscisic acid (ABA) has been implicated in this stress response and in DT re-establishment. However, the path from the sensing of an osmotic cue and its signaling to DT re-establishment is still largely unknown. Analyses of DT, ABA sensitivity, ABA content and gene expression were performed in desiccation- sensitive (DS) and desiccation-tolerant Arabidopsis thaliana seeds. Furthermore, loss and re-establishment of DT in germinated Arabidopsis seeds was studied in ABA-deficient and ABA-insensitive mutants. We demonstrate that the developmental window in which DT can be re-established correlates strongly with the window in which ABA sensitivity is still present. Using ABA biosynthesis and signaling mutants, we show that this hormone plays a key role in DT re-establishment. Surprisingly, re-establishment of DT depends on the modulation of ABA sensitivity rather than enhanced ABA content. In addition, the evaluation of several ABA-insensitive mutants, which can still produce normal desiccation-tolerant seeds, but are impaired in the re-establishment of DT, shows that the acquisition of DT during seed development is genetically different from its re-establishment during germination.
Identification and mapping of a novel dominant resistance gene, TuRB07 to Turnip mosaic virus in Brassica rapa
Jin, M. ; Lee, S.S. ; Ke, L. ; Kim, J.S. ; Seo, M.S. ; Sohn, S.H. ; Park, B.S. ; Bonnema, A.B. - \ 2014
Theoretical and Applied Genetics 127 (2014). - ISSN 0040-5752 - p. 509 - 519.
quantitative trait loci - chinese-cabbage - arabidopsis-thaliana - signal-transduction - linkage maps - host-defense - protein rx - binding - nucleotide - napus
The inheritance of resistance to Turnip mosaic virus in Brassica rapa was investigated by crossing the resistant line, VC1 with the susceptible line, SR5, and genotyping and phenotyping diverse progenies derived from this cross. Both a doubled haploid population, VCS3M-DH, an F2 and two BC1 (F1 × VC1 and F1 × SR5) populations were created. Population tests revealed that the resistance to the TuMV C4 isolate in B. rapa is controlled by a single dominant gene. This resistance gene, TuRB07 was positioned on the top of linkage group A06 of the B. rapa genome through bulk segregation analysis and fine mapping recombinants in three doubled haploid- and one backcross population using microsatellite markers developed from BAC end sequences. Within the region between the two closely linked markers flanking TuRB07, H132A24-s1, and KS10960, in the Chiifu reference genome, two genes encoding nucleotide-binding site and leucine-rich repeat proteins with a coiled-coil motif (CC-NBS-LRR), Bra018862 and Bra018863 were identified as candidate resistance genes. The gene Bra018862 is truncated, but the gene Bra018863 has all the domains to function. Furthermore, the analysis of structural variation using resequencing data of VC1 and SR5 revealed that Bra018863 might be a functional gene because the gene has no structural variation in the resistant line VC1 when compared with Chiifu, whereas at the other NBS-LRR genes large deletions were identified in the resistant line. Allelic differences of Bra018863 were found between VC1 and SR5, supporting the notion that this gene is a putative candidate gene for the virus resistance.
Immune Modulation by Different Types of ß2¿1-Fructans Is Toll-Like Receptor Dependent
Vogt, L. ; Ramasamy, U. ; Meyer, D. ; Pullens, G. ; Venema, K. ; Faas, M.M. ; Schols, H.A. ; Vos, P. de - \ 2013
PLoS ONE 8 (2013)7. - ISSN 1932-6203 - 12 p.
chain fatty-acids - nf-kappa-b - blood mononuclear-cells - dendritic cells - lactobacillus-rhamnosus - bifidobacterium-lactis - signal-transduction - innate immunity - dietary fiber - inulin
Introduction ß2¿1-fructans are dietary fibers. Main objectives of this study were 1) to demonstrate direct signalling of ß2¿1-fructans on immune cells, 2) to study whether this is mediated by the pattern recognition receptors Toll-like receptors (TLRs) and nucleotide-binding oligomerisation domain-containing proteins (NODs), and 3) to relate the observed effects to the chain length differences in ß2¿1-fructans. Methods Four different ß2¿1-fructan formulations were characterised for their chain length profile. Human peripheral blood mononuclear cells (PBMCs) were stimulated in vitro with ß2¿1-fructans, and production of IL-1Ra, IL-1ß, IL-6, IL-10, IL-12p70, and TNF-a was analysed. Reporter cells for TLRs and NODs were incubated with ß2¿1-fructans and analysed for NF-¿B/AP-1 activation. Results Cytokine production in human PBMCs was dose- and chain length-dependent. Strikingly, short chain enriched ß2¿1-fructans induced a regulatory cytokine balance compared to long chain enriched ß2¿1-fructans as measured by IL-10/IL-12 ratios. Activation of reporter cells showed that signalling was highly dependent on TLRs and their adapter, myeloid differentiation primary response protein 88 (MyD88). In human embryonic kidney reporter cells, TLR2 was prominently activated, while TLR4, 5, 7, 8, and NOD2 were mildly activated. Conclusions ß2¿1-fructans possess direct signalling capacity on human immune cells. By activating primarily TLR2, and to a lesser extent TLR4, 5, 7, 8, and NOD2, ß2¿1-fructan stimulation results in NF-¿B/AP-1 activation. Chain length of ß2¿1-fructans is important for the induced activation pattern and IL-10/IL-12 ratios.
WalK, the path towards new antibacterials with low potential for resistance development
Velikova, N.R. ; Bem, A.E. ; Baarlen, P. van; Wells, J. ; Marina, A. - \ 2013
ACS Medicical Chemistry Letters 4 (2013)10. - ISSN 1948-5875 - p. 891 - 894.
streptococcus-pneumoniae - signal-transduction - histidine kinase - discovery - inhibitors - system - genes
Resistance to antibiotics used in the treatment of bacterial infectious diseases is a global health problem. More than a decade ago, two-component systems such as WalKR were proposed as ideal targets for the development of new antibiotics. Biochemical screens for WalKR inhibitors using compound libraries have identified many hits, some of which were shown to have non-specific effects. The recently published structures of the S. mutans and B. subtilis WalK provide the opportunity to study inhibitors of WalK autophosphorylation at the atomic level and means to design compounds with improved specificity and affinity using a structure-based approach.
Diacylglycerol kinase counteracts protein kinase C-mediated inactivation of the EGF receptor
Baal, J. van; Widt, J. de; Divecha, N. ; Blitterswijk, W.J. van - \ 2012
International Journal of Biochemistry and Cell Biology 44 (2012)11. - ISSN 1357-2725 - p. 1791 - 1799.
growth-factor receptor - signal-transduction - coupled receptors - phosphorylation - cells - src - transactivation - activation - mechanisms - expression
Epidermal growth factor receptor (EGFR) activation is negatively regulated by protein kinase C (PKC)signaling. Stimulation of A431 cells with EGF, bradykinin or UTP increased EGFR phosphorylation at Thr654 in a PKC-dependent manner. Inhibition of PKC signaling enhanced EGFR activation, as assessed by increased phosphorylation of Tyr845 and Tyr1068 residues of the EGFR. Diacylglycerol is a physiological activator of PKC that can be removed by diacylglycerol kinase (DGK) activity. We found, in A431 and HEK293 cells, that the DGK isozyme translocated from the cytosol to the plasma membrane, where it co-localized with the EGFR and subsequently moved into EGFR-containing intracellular vesicles. This translocation was dependent on both activation of EGFR and PKC signaling. Furthermore, DGK physically interacted with the EGFR and became tyrosine-phosphorylated upon EGFR stimulation. Overexpression of DGK attenuated the bradykinin-stimulated, PKC-mediated EGFR phosphorylation at Thr654, and enhanced the phosphorylation at Tyr845 and Tyr1068. SiRNA-induced DGK downregulation enhanced this PKC-mediated Thr654 phosphorylation. Our data indicate that DGK translocation and activity is regulated by the concerted activity of EGFR and PKC and that DGK attenuates PKC-mediated Thr654 phosphorylation that is linked to desensitisation of EGFR signaling
The Arabidopsis thaliana SERK1 kinase domain spontaneously refolds to an active state in vitro
Toorn, M. aan den; Huijbers, M.M.E. ; Vries, S.C. de; Mierlo, C.P.M. van - \ 2012
PLoS ONE 7 (2012)12. - ISSN 1932-6203
embryogenesis receptor kinase-1 - intrinsically disordered proteins - smooth-muscle myosin - to-order transition - molecular recognition - signal-transduction - structural basis - activation loop - gras proteins - phosphorylation
Auto-phosphorylating kinase activity of plant leucine-rich-repeat receptor-like kinases (LRR-RLK's) needs to be under tight negative control to avoid unscheduled activation. One way to achieve this would be to keep these kinase domains as intrinsically disordered protein (IDP) during synthesis and transport to its final location. Subsequent folding, which may depend on chaperone activity or presence of interaction partners, is then required for full activation of the kinase domain. Bacterially produced SERK1 kinase domain was previously shown to be an active Ser/Thr kinase. SERK1 is predicted to contain a disordered region in kinase domains X and XI. Here, we show that loss of structure of the SERK1 kinase domain during unfolding is intimately linked to loss of activity. Phosphorylation of the SERK1 kinase domain neither changes its structure nor its stability. Unfolded SERK1 kinase has no autophosphorylation activity and upon removal of denaturant about one half of the protein population spontaneously refolds to an active protein in vitro. Thus, neither chaperones nor interaction partners are required during folding of this protein to its catalytically active state.
Comparative analyses imply that the enigmatic sigma factor 54 is a central controller of the bacterial exterior
Francke, C. ; Groot Kormelink, T. ; Hagemeijer, Y. ; Overmars, L. ; Sluijter, V. ; Moezelaar, R. ; Siezen, R.J. - \ 2011
BMC Genomics 12 (2011). - ISSN 1471-2164 - 21 p.
enhancer-binding proteins - gram-positive bacteria - termite group 1 - escherichia-coli - bacillus-subtilis - phosphotransferase-system - gene-expression - transcription-factor - signal-transduction - listeria-monocytogenes
Background - Sigma-54 is a central regulator in many pathogenic bacteria and has been linked to a multitude of cellular processes like nitrogen assimilation and important functional traits such as motility, virulence, and biofilm formation. Until now it has remained obscure whether these phenomena and the control by Sigma-54 share an underlying theme. Results - We have uncovered the commonality by performing a range of comparative genome analyses. A) The presence of Sigma-54 and its associated activators was determined for all sequenced prokaryotes. We observed a phylum-dependent distribution that is suggestive of an evolutionary relationship between Sigma-54 and lipopolysaccharide and flagellar biosynthesis. B) All Sigma-54 activators were identified and annotated. The relation with phosphotransfer-mediated signaling (TCS and PTS) and the transport and assimilation of carboxylates and nitrogen containing metabolites was substantiated. C) The function annotations, that were represented within the genomic context of all genes encoding Sigma-54, its activators and its promoters, were analyzed for intra-phylum representation and inter-phylum conservation. Promoters were localized using a straightforward scoring strategy that was formulated to identify similar motifs. We found clear highly-represented and conserved genetic associations with genes that concern the transport and biosynthesis of the metabolic intermediates of exopolysaccharides, flagella, lipids, lipopolysaccharides, lipoproteins and peptidoglycan. Conclusion - Our analyses directly implicate Sigma-54 as a central player in the control over the processes that involve the physical interaction of an organism with its environment like in the colonization of a host (virulence) or the formation of biofilm
Quantification of the BRI1 receptor in planta
Esse, G.W. van; Westphal, A.H. ; SURENDRAN, R.P. ; Albrecht, C. ; Veen, M.B. van; Borst, J.W. ; Vries, S.C. de - \ 2011
Plant Physiology 156 (2011)4. - ISSN 0032-0889 - p. 1691 - 1700.
green fluorescent protein - plasma-membrane receptor - growth-factor receptors - signal-transduction - arabidopsis-thaliana - kinase bri1 - gene-expression - erbb receptors - cell - root
In plants, green fluorescent protein (GFP) is routinely used to determine the subcellular location of fusion proteins. Here, we show that confocal imaging can be employed to approximate the number of GFP-labeled protein molecules present in living Arabidopsis (Arabidopsis thaliana) root cells. The technique involves calibration with soluble GFP to provide a usable protein concentration range within the confocal volume of the microscope. As a proof of principle, we quantified the Brassinosteroid Insensitive1 (BRI1) receptor fused to GFP, under control of its own promoter. The number of BRI1-GFP molecules per root epidermal cell ranges from 22,000 in the meristem and 130,000 in the elongation zone to 80,000 in the maturation zone, indicating that up to 6-fold differences in BRI1 receptor content exist. In contrast, when taking into account differences in cell size, BRI1-GFP receptor density in the plasma membrane is kept constant at 12 receptors µm-2 in all cells throughout the meristem and elongation zone. Only the quiescent center and columella cells deviate from this pattern and have 5 to 6 receptors µm-2. Remarkably, root cell sensitivity toward brassinosteroids appears to coincide with uniform meristem receptor density
The Medicago genome provides insight into the evolution of rhizobial symbioses
Geurts, R. ; Mitani, S. ; Bisseling, T. ; Franken, C. ; Hartog, M.V. ; Lang, C. - \ 2011
Nature 480 (2011). - ISSN 0028-0836 - p. 520 - 524.
flavonoid biosynthesis - signal-transduction - genes - arabidopsis - sequence - truncatula - duplications - tetraploidy - leguminosae - expression
Legumes (Fabaceae or Leguminosae) are unique among cultivated plants for their ability to carry out endosymbiotic nitrogen fixation with rhizobial bacteria, a process that takes place in a specialized structure known as the nodule. Legumes belong to one of the two main groups of eurosids, the Fabidae, which includes most species capable of endosymbiotic nitrogen fixation1. Legumes comprise several evolutionary lineages derived from a common ancestor 60 million years ago (Myr ago). Papilionoids are the largest clade, dating nearly to the origin of legumes and containing most cultivated species2. Medicago truncatula is a long-established model for the study of legume biology. Here we describe the draft sequence of the M. truncatula euchromatin based on a recently completed BAC assembly supplemented with Illumina shotgun sequence, together capturing ~94% of all M. truncatula genes. A whole-genome duplication (WGD) approximately 58 Myr ago had a major role in shaping the M. truncatula genome and thereby contributed to the evolution of endosymbiotic nitrogen fixation. Subsequent to the WGD, the M. truncatula genome experienced higher levels of rearrangement than two other sequenced legumes, Glycine max and Lotus japonicus. M. truncatula is a close relative of alfalfa (Medicago sativa), a widely cultivated crop with limited genomics tools and complex autotetraploid genetics. As such, the M. truncatula genome sequence provides significant opportunities to expand alfalfa’s genomic toolbox
A phylogenetic strategy based on a legume-specific whole genome duplication yields symbiotic cytokinin type-A Response Regulators
Camp, R. Op den; Mita, S. De; Lillo, A. ; Cao, Q. ; Limpens, E.H.M. ; Bisseling, T. ; Geurts, R. - \ 2011
Plant Physiology 157 (2011)4. - ISSN 0032-0889 - p. 2013 - 2022.
lateral root-formation - nodule organogenesis - medicago-truncatula - lotus-japonicus - signal-transduction - diverse roles - white clover - gene family - arabidopsis - nodulation
Legumes host their rhizobium symbiont in novel root organs, called nodules. Nodules originate from differentiated root cortical cells that de-differentiate and subsequently form nodule primordia, a process controlled by cytokinin. A whole genome duplication (WGD) has occurred at the root of the legume Papilionoideae subfamily. We hypothesize that gene pairs originating from this duplication event and are conserved in distinct Papilionoideae lineages have evolved symbiotic functions. A phylogenetic strategy was applied to search for such gene pairs in order to identify novel regulators of nodulation, using the cytokinin phosphorelay pathway as a test case. In this way two paralogous type-A cytokinin Response Regulators were identified that are involved in root nodule symbiosis. MtRR9 and MtRR11 in Medicago truncatula, and an ortholog in Lotus japonicus, are rapidly induced upon rhizobium Nod factor signaling. Constitutive expression of MtRR9 results in arrested primordia that have emerged from cortical, endodermal and pericycle cells. In legumes lateral root primordia are not exclusively formed from pericycle cells, but also involves the root cortical cell layer. Therefore, the MtRR9 induced foci of cell divisions show a strong resemblance to lateral root primordia, suggesting an ancestral function of MtRR9 in this process. Together, these findings provide a proof of principle for the applied phylogenetic strategy to identify genes with a symbiotic function in legumes.
Feeding conditions control the expression of genes involved in sterol metabolism in peripheral blood mononuclear cells of normoweight and diet-induced (cafeteria) obese rats
Caimari, A. ; Oliver, P. ; Rodenburg, W. ; Keijer, J. ; Palou, A. - \ 2010
Journal of Nutritional Biochemistry 21 (2010)11. - ISSN 0955-2863 - p. 1127 - 1133.
low-density-lipoprotein - acute regulatory protein - coa-cholesterol acyltransferase - beta-methylglutaryl-coenzyme - messenger-rna expression - signal-transduction - human-lymphocytes - lipid-synthesis - adipose-tissue - in-vivo
Peripheral blood mononuclear cells (PBMC) are easily obtainable cells from blood whose gene expression profiles have been proven to be highly robust in distinguishing a disease state from healthy state. Sterol metabolism is of physiological importance, and although its nutritional response in liver has been described, it is poorly studied in PBMC. To examine if PBMC sterol metabolism reflects diet-induced physiological responses, we analysed the whole genome gene expression response of PBMC and focused on sterol metabolism-related genes affected by different feeding conditions (ad libitum feeding, fasting, and refeeding) in normoweight (control) rats and in diet-induced (cafeteria) obese rats. Our results of microarray analysis show that, in control rats, 21 genes involved in sterol metabolism were regulated by the different feeding conditions, whereas in cafeteria-obese rats, only seven genes showed a changed expression. Most of the genes identified were classified into three pathways: sterol biosynthesis, cholesterol transport and uptake and sterol signaling. The expression profile of these genes was similar to that previously described for liver, decreasing in response to fasting conditions and recovering the levels found in fed animals after 6-h-refeeding. In addition, our data and the comparable expression pattern of sterol metabolism-related genes between PBMC and liver suggest similar sterol regulatory element-binding protein-mediated regulatory mechanisms in response to feeding conditions in both tissues. In conclusion, the expression of genes involved in sterol metabolism is highly controlled by feeding conditions in PBMC of control rats, but this control is impaired in cafeteria-obese animals. The pathophysiological significance of this impairment requires further investigation.
The hyperhydricity syndrome: waterlogging of plant tissues as a major cause
Rojas Martinez, L.I. ; Visser, R.G.F. ; Klerk, G.J.M. de - \ 2010
Propagation of ornamental plants 10 (2010)4. - ISSN 1311-9109 - p. 169 - 175.
gypsophila-paniculata l - in-vitro - oxidative stress - carnation shoots - signal-transduction - hydrogen-peroxide - vitrification - culture - potato - water
Hyperhydricity (also known as ‘vitrification’) is a physiological disorder in tissue-cultured plant material, which causes a reduction of propagation and death of tissues when transferred to ex vitro conditions. A plethora of causes has been mentioned in literature. We consider this disorder as the result of the stressful conditions brought about by waterlogging of the apoplast. This causes hypoxia and thereby leads to severe oxidative stress. We argue that hyperhydric features like vitreous appearance and wrinkled leaves are secondary events resulting from waterlogging of the apoplast. With the use of readily available technologies, the molecular components of hyperhydricity can be dissected.
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.
On the Relevance and Control of Leaf Angle
Zanten, M. van; Pons, T.L. ; Janssen, J.A.M. ; Voesenek, L.A.C.J. ; Peeters, A.J.M. - \ 2010
Critical Reviews in Plant Sciences 29 (2010)5. - ISSN 0735-2689 - p. 300 - 316.
shade-avoidance responses - differential petiole growth - arabidopsis-thaliana - rumex-palustris - abscisic-acid - shoot elongation - submergence tolerance - hypocotyl elongation - signal-transduction - ethylene production
Plants can have constitutive leaf angles that are fixed and do not vary much among different growth environments. Several species, however, have the ability to actively adjust their leaf angles. Active leaf repositioning can be functional in avoiding detrimental environmental conditions, such as avoidance of heat stress and complete submergence, or can be, for example, utilized to maximize carbon gain by positioning the leaves relative to the incoming radiation. In recent years, major advances have been made in the understanding of the molecular mechanisms, and the underlying hormonal regulation of a particular type of leaf movement: hyponastic growth. This differential petiole growth-driven upward leaf movement is now relatively well understood in model systems such as Rumex palustris and Arabidopsis thaliana. In the first part of this review we will discuss the functional consequences of leaf orientation for plant performance. Next, we will consider hyponastic growth and describe how exploitation of natural (genetic) variation can be instrumental in studying the relevance and control of leaf positioning.
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
Inhibitory effect of rapamycin and dexamethasone on production of IL-17 and IFN-gamma in Vogt-Koyanagi-Harada patients
Yang, K. ; Wen, J. ; Liu, X. ; Kijlstra, A. ; Chen, L. ; Chi, W. ; Zhou, H. ; Huang, X. ; Yang, P. - \ 2009
British Journal of Ophthalmology 93 (2009)2. - ISSN 0007-1161 - p. 249 - 253.
t-cell-activation - interferon-gamma - in-vitro - autoimmune uveoretinitis - immunosuppressive drugs - signal-transduction - cytokine production - modulation - expression - disease
Aims: To evaluate the effect of rapamycin (RAPA) and dexamethasone (DEX) on the production of IL-17 and IFN-gamma by peripheral blood mononuclear cells (PBMCs) from Vogt-Koyanagi-Harada (VKH) patients and healthy individuals. Methods: Blood samples were drawn from 10 active VKH patients and 10 healthy individuals. PBMCs were cultured with or without anti-CD3 and anti-CD28 antibodies in the presence or absence of different concentrations of RAPA or DEX for 72 h. IL-17 and IFN-gamma concentrations in the supernatants were measured by enzyme-linked immunosorbent assay (ELISA). Results: The expression of IL-17 and IFN-gamma was significantly increased in active VKH patients compared with that in healthy controls. Both RAPA and DEX were able to significantly inhibit the production of IL-17 and IFN-gamma by PBMCs from patients and healthy controls. RAPA was able to completely inhibit IL-17 production at a dosage of 10 ng/ml but only partially suppressed IFN-gamma production even at a much higher concentration (1000 ng/ml). DEX inhibited the production of both IL-17 and IFN-gamma by approximately 70%. Conclusions: This study indicates that both RAPA and DEX inhibit the production of IL-17 and IFN-gamma by PBMCs. RAPA is much stronger in inhibiting the production of IL-17 than DEX.
Effect of tomato pleiotropic ripening mutations on flavour volatile biosynthesis
Kovacs, K. ; Fray, R.G. ; Tikunov, Y.M. ; Graham, N. ; Bradley, G. ; Seymour, G.B. ; Bovy, A.G. ; Grierson, D. - \ 2009
Phytochemistry 70 (2009)8. - ISSN 0031-9422 - p. 1003 - 1008.
high-pigment-1 mutant - hydroperoxide lyase - oxylipin metabolism - signal-transduction - lipoxygenase genes - fruit - ethylene - manipulation - phenotype - expression
Ripening is a tightly controlled and developmentally regulated process involving networks of genes, and metabolites that result in dramatic changes in fruit colour, texture and flavour. Molecular and genetic analysis in tomato has revealed a series of regulatory genes involved in fruit development and ripening, including MADS box and SPB box transcription factors and genes involved in ethylene synthesis, signalling and response. Volatile metabolites represent a significant part of the plant metabolome, playing an important role in plant signalling, defence strategies and probably in regulatory mechanisms. They also play an important role in fruit quality. In order to acquire a better insight into the biochemical and genetic control of flavour compound generation and links between these metabolites and the central regulators of ripening, five pleiotropic mutant tomato lines were subjected to volatile metabolite profiling in comparison with wild-type Ailsa Craig. One hundred and seventeen volatile compounds were identified and quantified using SPME (Solid Phase Microextraction) headspace extraction followed by Gas Chromatography–Mass Spectrometry (GC–MS) and the data were subjected to multivariate comparative analysis. We find that the different mutants each produce distinct volatile profiles during ripening. Through principal component analysis the volatiles most dramatically affected are those derived from fatty-acids. The results are consistent with the suggestion that specific isoforms of lipoxygenase located in the plastids and the enzymes that provide precursors and downstream metabolites play a key role in determining volatile composition.
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