TY  - JOUR
AB  - BACKGROUND: Apple replant disease (ARD) represents a dysbiotic rhizosphere condition potentially driven by root exudates including phytoalexins at the root-soil interface. A promising mitigation strategy could be the application of bioinoculants that reduce these compounds and foster a diverse microbiome. This study investigated the effects of Rhodococcus pseudokoreensis R79T, a strain with benzoate-degrading capabilities and genetic potential to degrade biphenyls, on the rhizosphere microbiome of apple plantlets grown in ARD-affected soil in a greenhouse experiment. RESULTS: We applied R79T at 10⁶ to 10⁹ CFU/ml, assessing its impact on bacterial 16S rRNA diversity and abundance, as well as the abundance of biphenyl dioxygenase (bphd) genes. Eight weeks post-inoculation reads of strain R79T persisted in the rhizosphere, particularly at higher inoculation levels. Inoculation enhanced bacterial diversity and bphd gene abundance, with significant shifts in community composition. Key responders included members of Gaiellales, which increased, and Streptomyces, which decreased. Co-occurrence network analysis revealed that inoculation promoted positive interactions, more homogeneous connectivity, and a higher degree of connections. Effects on bacterial community structure varied significantly with inoculation concentration. CONCLUSIONS: The fact that R79T enhanced rhizosphere bacterial diversity and modulated community composition in ARD-affected soil highlights the potential of R79T to reshape microbial interactions. Further research is needed to elucidate the mechanisms underlying these effects, including studies on in situ degradation of phytoalexins and inoculation of R79T alongside bacteria for plant growth promotion (PGP) in synthetic communities for elevated efficiency against ARD.
AU  - Benning, S.
AU  - Mahmoud, F.M.
AU  - Espíndola-Hernández, P.
AU  - Liu, B.*
AU  - Pritsch, K.
AU  - Radl, V.
AU  - Winkler, J.B.
AU  - Winkelmann, T.*
AU  - Beerhues, L.*
AU  - Schloter, M.
C1  - 74826
C2  - 57616
CY  - Campus, 4 Crinan St, London N1 9xw, England
TI  - Inoculation of apple plantlets with Rhodococcus pseudokoreensis R79T enhances diversity and modulates the structure of bacterial rhizosphere communities in soil affected by apple replant disease.
JO  - BMC Plant Biol.
VL  - 25
IS  - 1
PB  - Bmc
PY  - 2025
SN  - 1471-2229
ER  - 

TY  - JOUR
AB  - The physical appearance of date palm (Phoenix dactylifera) fruit (dates) is important for its market value. Many date-producing countries experience significant financial losses due to the poor appearance of the fruit, skin separation or puffiness being a major reason. Previous research showed evidence linking the skin separation phenotype to environmental conditions. To investigate this further, a genome-wide association study was conducted using genome data from 199 samples collected from 14 countries. Here, we identified nine genetic loci associated with this phenotype and investigated genes in these regions that may contribute to the phenotype overall. Multiple genes in the associated regions have functional responses to growth regulators and are involved in cell wall development and modification. Analysis of gene expression data shows many are expressed during fruit development. We show that there are both environmental and genetic contributions to the fruit skin separation phenotype. Our results indicate that different date cultivars exhibit varying degrees of skin separation despite genetic similarities or differences. However, genetically different cultivars show extreme differences compared to the phenotype variation between genetically similar cultivars. We demonstrate that beyond environmental factors, genetics is a strong contributor to the most extreme skin separation in some cultivars. Identifying the genetic factors may help better understand the biology and pathways that lead to the environmental effects on skin separation and improve commercial date production. In conclusion, our key finding is that both environmental and genetic factors contribute to skin separation variation, and improvements in environmental factors alone cannot overcome the extreme level of variation observed in some cultivars.
AU  - Younuskunju, S.*
AU  - Mohamoud, Y.A.*
AU  - Mathew, L.S.*
AU  - Mayer, K.F.X.
AU  - Suhre, K.*
AU  - Malek, J.A.*
C1  - 72255
C2  - 56534
TI  - The genetics of fruit skin separation in date palm.
JO  - BMC Plant Biol.
VL  - 24
IS  - 1
PY  - 2024
SN  - 1471-2229
ER  - 

TY  - JOUR
AB  - BACKGROUND: Tansy plants (Tanacetum vulgare L.) are known for their high intraspecific chemical variation, especially of volatile organic compounds (VOC) from the terpenoid compound group. These VOCs are closely involved in plant-insect interactions and, when profiled, can be used to classify plants into groups known as chemotypes. Tansy chemotypes have been shown to influence plant-aphid interactions, however, to date no information is available on the response of different tansy chemotypes to simultaneous herbivory by more than one insect species. RESULTS: Using a multi-cuvette system, we investigated the responses of five tansy chemotypes to feeding by sucking and/or chewing herbivores (aphids and caterpillars; Metopeurum fuscoviride Stroyan and Spodoptera littoralis Boisduval). Herbivory by caterpillars following aphid infestation led to a plant chemotype-specific change in the patterns of terpenoids stored in trichome hairs and in VOC emissions. The transcriptomic analysis of a plant chemotype represents the first de novo assembly of a transcriptome in tansy and demonstrates priming effects of aphids on a subsequent herbivory. Overall, we show that the five chemotypes do not react in the same way to the two herbivores. As expected, we found that caterpillar feeding increased VOC emissions, however, a priori aphid infestation only led to a further increase in VOC emissions for some chemotypes. CONCLUSIONS: We were able to show that different chemotypes respond to the double herbivore attack in different ways, and that pre-treatment with aphids had a priming effect on plants when they were subsequently exposed to a chewing herbivore. If neighbouring chemotypes in a field population react differently to herbivory/dual herbivory, this could possibly have effects from the individual level to the group level. Individuals of some chemotypes may respond more efficiently to herbivory stress than others, and in a group environment these "louder" chemotypes may affect the local insect community, including the natural enemies of herbivores, and other neighbouring plants.
AU  - Clancy, M.V.
AU  - Haberer, G.
AU  - Jud, W.
AU  - Niederbacher, B.
AU  - Niederbacher, S.
AU  - Senft, M.*
AU  - Zytynska, S.E.
AU  - Weisser, W. W.*
AU  - Schnitzler, J.-P.
C1  - 60769
C2  - 49530
CY  - Campus, 4 Crinan St, London N1 9xw, England
TI  - Under fire-simultaneous volatilome and transcriptome analysis unravels fine-scale responses of tansy chemotypes to dual herbivore attack.
JO  - BMC Plant Biol.
VL  - 20
IS  - 1
PB  - Bmc
PY  - 2020
SN  - 1471-2229
ER  - 

TY  - JOUR
AB  - Background: Nitrogen dioxide (NO2) triggers hypersensitive response (HR)-like cell death in Arabidopsis thaliana. A high-throughput mutant screen was established to identify genes involved in this type of programmed cell death.Results: Altogether 14,282 lines of SALK T-DNA insertion mutants were screened. Growing 1000 pooled mutant lines per tray and simultaneous NO2 fumigation of 4 trays in parallel facilitated high-throughput screening. Candidate mutants were selected based on visible symptoms. Sensitive mutants showed lesions already after fumigation for 1 h with 10 ppm (ppm) NO2 whereas tolerant mutants were hardly damaged even after treatment with 30 ppm NO2. Identification of T-DNA insertion sites by adapter ligation-mediated PCR turned out to be successful but rather time consuming. Therefore, next generation sequencing after T-DNA-specific target enrichment was tested as an alternative screening method. The targeted genome sequencing was highly efficient due to (1.) combination of the pooled DNA from 124 candidate mutants in only two libraries, (2.) successful target enrichment using T-DNA border-specific 70mer probes, and (3.) stringent filtering of the sequencing reads. Seventy mutated genes were identified by at least 3 sequencing reads. Ten corresponding mutants were re-screened of which 8 mutants exhibited NO2-sensitivity or -tolerance confirming that the screen yielded reliable results. Identified candidate genes had published functions in HR, pathogen resistance, and stomata regulation.Conclusions: The presented NO2 dead-or-alive screen combined with next-generation sequencing after T-DNAspecific target enrichment was highly efficient. Two researchers finished the screen within 3 months. Moreover, the target enrichment approach was cost-saving because of the limited number of DNA libraries and sequencing runs required. The experimental design can be easily adapted to other screening approaches e.g. involving high-throughput treatments with abiotic stressors or phytohormones.
AU  - Frank, U.
AU  - Kublik, S.
AU  - Mayer, D.
AU  - Engel, M.
AU  - Schloter, M.
AU  - Durner, J.
AU  - Gaupels, F.
C1  - 57526
C2  - 47832
CY  - Campus, 4 Crinan St, London N1 9xw, England
TI  - A T-DNA mutant screen that combines high-throughput phenotyping with the efficient identification of mutated genes by targeted genome sequencing.
JO  - BMC Plant Biol.
VL  - 19
IS  - 1
PB  - Bmc
PY  - 2019
SN  - 1471-2229
ER  - 

TY  - JOUR
AB  - BACKGROUND: Elevated temperature and reduced water availability are frequently linked abiotic stresses that may provoke distinct as well as interacting molecular responses. Based on non-targeted metabolomic and transcriptomic measurements from Arabidopsis rosettes, this study aims at a systematic elucidation of relevant components in different drought and heat scenarios as well as relationships between molecular players of stress response. RESULTS: In combined drought-heat stress, the majority of single stress responses are maintained. However, interaction effects between drought and heat can be discovered as well; these relate to protein folding, flavonoid biosynthesis and growth inhibition, which are enhanced, reduced or specifically induced in combined stress, respectively. Heat stress experiments with and without supplementation of air humidity for maintenance of vapor pressure deficit suggest that decreased relative air humidity due to elevated temperature is an important component of heat stress, specifically being responsible for hormone-related responses to water deprivation. Remarkably, this "dry air effect" is the primary trigger of the metabolomic response to heat. In contrast, the transcriptomic response has a substantial temperature component exceeding the dry air component and including up-regulation of many transcription factors and protein folding-related genes. Data level integration independent of prior knowledge on pathways and condition labels reveals shared drought and heat responses between transcriptome and metabolome, biomarker candidates and co-regulation between genes and metabolic compounds, suggesting novel players in abiotic stress response pathways. CONCLUSIONS: Drought and heat stress interact both at transcript and at metabolite response level. A comprehensive, non-targeted view of this interaction as well as non-interacting processes is important to be taken into account when improving tolerance to abiotic stresses in breeding programs. Transcriptome and metabolome may respond with different extent to individual stress components. Their contrasting behavior in response to temperature stress highlights that the protein folding machinery effectively shields the metabolism from stress. Disentangling the complex relationships between transcriptome and metabolome in response to stress is an enormous challenge. As demonstrated by case studies with supporting evidence from additional data, the large dataset provided in this study may assist in determining linked genetic and metabolic features as candidates for future mechanistic analyses.
AU  - Georgii, E.
AU  - Jin, M.
AU  - Zhao, J.
AU  - Kanawati, B.
AU  - Schmitt-Kopplin, P.
AU  - Albert, A.
AU  - Winkler, J.B.
AU  - Schäffner, A.
C1  - 51509
C2  - 43180
CY  - London
TI  - Relationships between drought, heat and air humidity responses revealed by transcriptome-metabolome co-analysis.
JO  - BMC Plant Biol.
VL  - 17
IS  - 1
PB  - Biomed Central Ltd
PY  - 2017
SN  - 1471-2229
ER  - 

TY  - JOUR
AB  - BACKGROUND: Physical maps created from large insert DNA libraries, typically cloned in BAC vector, are valuable resources for map-based cloning and de novo genome sequencing. The maps are most useful if contigs of overlapping DNA clones are anchored to chromosome(s), and ordered along them using molecular markers. Here we present a novel approach for anchoring physical maps, based on sequencing three-dimensional pools of BAC clones from minimum tilling path. RESULTS: We used physical map of wheat chromosome arm 3DS to validate the method with two different DNA sequence datasets. The first comprised 567 genes ordered along the chromosome arm based on syntenic relationship of wheat with the sequenced genomes of Brachypodium, rice and sorghum. The second dataset consisted of 7,136 SNP-containing sequences, which were mapped genetically in Aegilops tauschii, the donor of the wheat D genome. Mapping of sequence reads from individual BAC pools to the first and the second datasets enabled unambiguous anchoring 447 and 311 3DS-specific sequences, respectively, or 758 in total. CONCLUSIONS: We demonstrate the utility of the novel approach for BAC contig anchoring based on mass parallel sequencing of three-dimensional pools prepared from minimum tilling path of physical map. The existing genetic markers as well as any other DNA sequence could be mapped to BAC clones in a single in silico experiment. The approach reduces significantly the cost and time needed for anchoring and is applicable to any genomic project involving the construction of anchored physical map.
AU  - Cvikova, K.*
AU  - Cattonaro, F.*
AU  - Alaux, M.*
AU  - Stein, N.*
AU  - Mayer, K.F.X.
AU  - Dolezel, J.*
AU  - Bartos, J.*
C1  - 44438
C2  - 36833
CY  - London
TI  - High-throughput physical map anchoring via BAC-pool sequencing.
JO  - BMC Plant Biol.
VL  - 15
IS  - 1
PB  - Biomed Central Ltd
PY  - 2015
SN  - 1471-2229
ER  - 

TY  - JOUR
AB  - BACKGROUND: Chrysomela populi (poplar leaf beetle) is a common herbivore in poplar plantations whose infestation causes major economic losses. Because plant volatiles act as infochemicals, we tested whether isoprene, the main volatile organic compound (VOC) produced by poplars (Populus x canescens), affects the performance of C. populi employing isoprene emitting (IE) and transgenic isoprene non-emitting (NE) plants. Our hypothesis was that isoprene is sensed and affects beetle orientation or that the lack of isoprene affects plant VOC profiles and metabolome with consequences for C. populi feeding. RESULTS: Electroantennographic analysis revealed that C. populi can detect higher terpenes, but not isoprene. In accordance to the inability to detect isoprene, C. populi showed no clear preference for IE or NE poplar genotypes in the choice experiments, however, the beetles consumed a little bit less leaf mass and laid fewer eggs on NE poplar trees in field experiments. Slight differences in the profiles of volatile terpenoids between IE and NE genotypes were detected by gas chromatography - mass spectrometry. Non-targeted metabolomics analysis by Fourier Transform Ion Cyclotron Resonance Mass Spectrometer revealed genotype-, time- and herbivore feeding-dependent metabolic changes both in the infested and adjacent undamaged leaves under field conditions. CONCLUSIONS: We show for the first time that C. populi is unable to sense isoprene. The detected minor differences in insect feeding in choice experiments and field bioassays may be related to the revealed changes in leaf volatile emission and metabolite composition between the IE and NE poplars. Overall our results indicate that lacking isoprene emission is of minor importance for C. populi herbivory under natural conditions, and that the lack of isoprene is not expected to change the economic losses in poplar plantations caused by C. populi infestation.
AU  - Müller, A.*
AU  - Kaling, M.
AU  - Faubert, P.
AU  - Gort, G.*
AU  - Smid, H.M.*
AU  - van Loon, J.J.*
AU  - Dicke, M.*
AU  - Kanawati, B.
AU  - Schmitt-Kopplin, P.
AU  - Polle, A.*
AU  - Schnitzler, J.-P.
AU  - Rosenkranz, M.
C1  - 45606
C2  - 37417
CY  - London
TI  - Isoprene emission by poplar is not important for the feeding behaviour of poplar leaf beetles.
JO  - BMC Plant Biol.
VL  - 15
IS  - 1
PB  - Biomed Central Ltd
PY  - 2015
SN  - 1471-2229
ER  - 

TY  - JOUR
AB  - BACKGROUND: Pollen of common ragweed (Ambrosia artemisiifolia) is a main cause of allergic diseases in Northern America. The weed has recently become spreading as a neophyte in Europe, while climate change may also affect the growth of the plant and additionally may also influence pollen allergenicity. To gain better insight in the molecular mechanisms in the development of ragweed pollen and its allergenic proteins under global change scenarios, we generated SuperSAGE libraries to identify differentially expressed transcripts. RESULTS: Ragweed plants were grown in a greenhouse under 380 ppm CO2 and under elevated level of CO2 (700 ppm). In addition, drought experiments under both CO2 concentrations were performed. The pollen viability was not altered under elevated CO2, whereas drought stress decreased its viability. Increased levels of individual flavonoid metabolites were found under elevated CO2 and/or drought. Total RNA was isolated from ragweed pollen, exposed to the four mentioned scenarios and four SuperSAGE libraries were constructed. The library dataset included 236,942 unique sequences, showing overlapping as well as clear differently expressed sequence tags (ESTs). The analysis targeted ESTs known in Ambrosia, as well as in pollen of other plants. Among the identified ESTs, those encoding allergenic ragweed proteins (Amb a) increased under elevated CO2 and drought stress. In addition, ESTs encoding allergenic proteins in other plants were also identified. CONCLUSIONS: The analysis of changes in the transcriptome of ragweed pollen upon CO2 and drought stress using SuperSAGE indicates that under global change scenarios the pollen transcriptome was altered, and impacts the allergenic potential of ragweed pollen.
AU  - El-Kelish, A.
AU  - Zhao, F.
AU  - Heller, W.
AU  - Durner, J.
AU  - Winkler, J.B.
AU  - Behrendt, H.
AU  - Traidl-Hoffmann, C.
AU  - Horres, R.*
AU  - Pfeifer, M.
AU  - Frank, U.
AU  - Ernst, D.
C1  - 31761
C2  - 34723
CY  - London
TI  - Ragweed (Ambrosia artemisiifolia) pollen allergenicity: SuperSAGE transcriptomic analysis upon elevated CO2 and drought stress.
JO  - BMC Plant Biol.
VL  - 14
IS  - 1
PB  - Biomed Central Ltd
PY  - 2014
SN  - 1471-2229
ER  - 

TY  - JOUR
AB  - BackgroundOver the last years reference genome sequences of several economically and scientifically important cereals and model plants became available. Despite the agricultural significance of these crops only a small number of tools exist that allow users to inspect and visualize the genomic position of genes of interest in an interactive manner.DescriptionWe present chromoWIZ, a web tool that allows visualizing the genomic positions of relevant genes and comparing these data between different plant genomes. Genes can be queried using gene identifiers, functional annotations, or sequence homology in four grass species (Triticum aestivum, Hordeum vulgare, Brachypodium distachyon, Oryza sativa). The distribution of the anchored genes is visualized along the chromosomes by using heat maps. Custom gene expression measurements, differential expression information, and gene-to-group mappings can be uploaded and can be used for further filtering.ConclusionsThis tool is mainly designed for breeders and plant researchers, who are interested in the location and the distribution of candidate genes as well as in the syntenic relationships between different grass species. chromoWIZ is freely available and online accessible at http://mips.helmholtz-muenchen.de/plant/chromoWIZ/index.jsp.
AU  - Nussbaumer, T.
AU  - Kugler, K.G.
AU  - Schweiger, W.*
AU  - Bader, K.C.
AU  - Gundlach, H.
AU  - Spannagl, M.
AU  - Poursarebani, N.*
AU  - Pfeifer, M.
AU  - Mayer, K.F.X.
C1  - 42988
C2  - 35917
TI  - chromoWIZ: A web tool to query and visualize chromosome-anchored genes from cereal and model genomes.
JO  - BMC Plant Biol.
VL  - 14
IS  - 1
PY  - 2014
SN  - 1471-2229
ER  - 

TY  - JOUR
AB  - BACKGROUND: The improvement of agricultural crops with regard to yield, resistance and environmental adaptation is a perpetual challenge for both breeding and research. Exploration of the genetic potential and implementation of genome-based breeding strategies for efficient rye (Secale cereale L.) cultivar improvement have been hampered by the lack of genome sequence information. To overcome this limitation we sequenced the transcriptomes of five winter rye inbred lines using Roche/454 GS FLX technology. RESULTS: More than 2.5 million reads were assembled into 115,400 contigs representing a comprehensive rye expressed sequence tag (EST) resource. From sequence comparisons 5,234 single nucleotide polymorphisms (SNPs) were identified to develop the Rye5K high-throughput SNP genotyping array. Performance of the Rye5K SNP array was investigated by genotyping 59 rye inbred lines including the five lines used for sequencing, and five barley, three wheat, and two triticale accessions. A balanced distribution of allele frequencies ranging from 0.1 to 0.9 was observed. Residual heterozygosity of the rye inbred lines varied from 4.0 to 20.4% with higher average heterozygosity in the pollen compared to the seed parent pool. CONCLUSIONS: The established sequence and molecular marker resources will improve and promote genetic and genomic research as well as genome-based breeding in rye.
AU  - Haseneyer, G.*
AU  - Schmutzer, T.*
AU  - Seidel, M.
AU  - Zhou, R.*
AU  - Mascher, M.*
AU  - Schön, C.C.*
AU  - Taudien, S.*
AU  - Scholz, U.*
AU  - Stein, N.*
AU  - Mayer, K.F.X.
AU  - Bauer, E.*
C1  - 6664
C2  - 29068
TI  - From RNA-seq to large-scale genotyping - genomics resources for rye (Secale cereale L.).
JO  - BMC Plant Biol.
VL  - 11
PB  - BioMedCentral
PY  - 2011
SN  - 1471-2229
ER  - 

TY  - JOUR
AB  - BACKGROUND: Ionic aluminum (mainly Al3+) is rhizotoxic and can be present in acid soils at concentrations high enough to inhibit root growth. Many forest tree species grow naturally in acid soils and often tolerate high concentrations of Al. Previously, we have shown that aspen (Populus tremula) releases citrate and oxalate from roots in response to Al exposure. To obtain further insights into the root responses of aspen to Al, we investigated root gene expression at Al conditions that inhibit root growth. RESULTS: Treatment of the aspen roots with 500 μM Al induced a strong inhibition of root growth within 6 h of exposure time. The root growth subsequently recovered, reaching growth rates comparable to that of control plants. Changes in gene expression were determined after 6 h, 2 d, and 10 d of Al exposure. Replicated transcriptome analyses using the Affymetrix poplar genome array revealed a total of 175 significantly up-regulated and 69 down-regulated genes, of which 70% could be annotated based on Arabidopsis genome resources. Between 6 h and 2 d, the number of responsive genes strongly decreased from 202 to 26, and then the number of changes remained low. The responses after 6 h were characterized by genes involved in cell wall modification, ion transport, and oxidative stress. Two genes with prolonged induction were closely related to the Arabidopsis Al tolerance genes ALS3 (for Al sensitive 3) and MATE (for multidrug and toxin efflux protein, mediating citrate efflux). Patterns of expression in different plant organs and in response to Al indicated that the two aspen genes are homologs of the Arabidopsis ALS3 and MATE. CONCLUSION: Exposure of aspen roots to Al results in a rapid inhibition of root growth and a large change in root gene expression. The subsequent root growth recovery and the concomitant reduction in the number of responsive genes presumably reflect the success of the roots in activating Al tolerance mechanisms. The aspen genes ALS3 and MATE may be important components of these mechanisms.
AU  - Grisel, N.*
AU  - Zoller, S.*
AU  - Künzli-Gontarczyk, M.*
AU  - Lampart, T.*
AU  - Münsterkötter, M.
AU  - Brunner, I.*
AU  - Bovet, L.*
AU  - Metraux, J.-P.*
AU  - Sperisen, C.*
C1  - 6135
C2  - 28141
SP  - 185
TI  - Transcriptome responses to aluminum stress in roots of aspen (Populus tremula).
JO  - BMC Plant Biol.
VL  - 10
PB  - BioMed Central Ltd.
PY  - 2010
SN  - 1471-2229
ER  - 

TY  - JOUR
AB  - BACKGROUND: Populus euphratica is a salt tolerant and Populus x canescens a salt sensitive poplar species. Because of low transcriptional responsiveness of P. euphratica to salinity we hypothesized that this species exhibits an innate activation of stress protective genes compared with salt sensitive poplars. To test this hypothesis, the transcriptome and metabolome of mature unstressed leaves of P. euphratica and P. x canescens were compared by whole genome microarray analyses and FT-ICR-MS metabolite profiling. RESULTS: Direct cross-species comparison of the transcriptomes of the two poplar species from phylogenetically different sections required filtering of the data set. Genes assigned to the GO slim categories 'mitochondria', 'cell wall', 'transport', 'energy metabolism' and 'secondary metabolism' were significantly enriched, whereas genes in the categories 'nucleus', 'RNA or DNA binding', 'kinase activity' and 'transcription factor activity' were significantly depleted in P. euphratica compared with P. x canescens. Evidence for a general activation of stress relevant genes in P. euphratica was not detected. Pathway analyses of metabolome and transcriptome data indicated stronger accumulation of primary sugars, activation of pathways for sugar alcohol production, and faster consumption of secondary metabolites in P. euphratica compared to P. x canescens. Physiological measurements showing higher respiration, higher tannin and soluble phenolic contents as well as enrichment of glucose and fructose in P. euphratica compared to P. x canescens corroborated the results of pathway analyses. CONCLUSION: P. euphratica does not rely on general over-expression of stress pathways to tolerate salt stress. Instead, it exhibits permanent activation of control mechanisms for osmotic adjustment (sugar and sugar alcohols), ion compartmentalization (sodium, potassium and other metabolite transporters) and detoxification of reactive oxygen species (phenolic compounds). The evolutionary adaptation of P. euphratica to saline environments is apparently linked with higher energy requirement of cellular metabolism and a loss of transcriptional regulation.
AU  - Janz, D.*
AU  - Behnke, K.*
AU  - Schnitzler, J.-P.*
AU  - Kanawati, B.
AU  - Schmitt-Kopplin, P.
AU  - Polle, A.*
C1  - 5643
C2  - 27420
TI  - Pathway analysis of the transcriptome and metabolome of salt sensitive and tolerant poplar species reveals evolutionary adaption of stress tolerance mechanisms.
JO  - BMC Plant Biol.
VL  - 10
PB  - BioMed Central Ltd.
PY  - 2010
SN  - 1471-2229
ER  - 

TY  - JOUR
AB  - Receptor-like kinases are a prominent class of surface receptors that regulate many aspects of the plant life cycle. Despite recent advances the function of most receptor-like kinases remains elusive. Therefore, it is paramount to investigate these receptors. The task is complicated by the fact that receptor-like kinases belong to a large monophyletic family with many sub-clades. In general, functional analysis of gene family members by reverse genetics is often obscured by several issues, such as redundancy, subtle or difficult to detect phenotypes in mutants, or by decision problems regarding suitable biological and biochemical assays. Therefore, in many cases additional strategies have to be employed to allow inference of hypotheses regarding gene function.We approached the function of genes encoding the nine-member STRUBBELIG-RECEPTOR FAMILY (SRF) class of putative leucine-rich repeat receptor-like kinases. Sequence comparisons show overall conservation but also divergence in predicted functional domains among SRF proteins. Interestingly, SRF1 undergoes differential splicing. As a result, SRF1 is predicted to exist in a standard receptor configuration and in a membrane-anchored receptor-like version that lacks most of the intracellular domain. Furthermore, SRF1 is characterised by a high degree of polymorphism between the Ler and Col accessions. Two independent T-DNA-based srf4 mutants showed smaller leaves while 35S::SRF4 plants displayed enlarged leaves. This is in addition to the strubbelig phenotype which has been described before. Additional single and several key double mutant combinations did not reveal obvious mutant phenotypes. Ectopic expression of several SRF genes, using the 35S promoter, resulted in male sterility. To gain possible insights into SRF gene function we employed a computational analysis of publicly available microarray data. We performed global expression profiling, coexpression analysis, and an analysis of the enrichment of gene ontology terms among coexpressed genes. The bioinformatic analyses raise the possibility that some SRF genes affect different aspects of cell wall biology. The results also indicate that redundancy is a minor aspect of the SRF family. The results provide evidence that SRF4 is a positive regulator of leaf size. In addition, they suggest that the SRF family is characterised by functional diversity and that some SRF genes may function in cell wall biology. They also indicate that complementing reverse genetics with bioinformatical data mining of genome-wide expression data aids in inferring hypotheses on possible functions for members of a gene family.
AU  - Eyüboglu, B.*
AU  - Pfister, K.*
AU  - Haberer, G.
AU  - Chevalier, D.*
AU  - Fuchs, A.*
AU  - Mayer, K.F.X.
AU  - Schneitz, K.*
C1  - 5882
C2  - 24571
TI  - Molecular characterisation of the STRUBBELIG-RECEPTOR FAMILY of genes encoding putative leucine-rich repeat receptor-like kinases in Arabidopsis thaliana.
JO  - BMC Plant Biol.
VL  - 7
PB  - BioMed Central
PY  - 2007
SN  - 1471-2229
ER  - 

TY  - JOUR
AU  - Wendehenne, D.*
AU  - Gould, K.*
AU  - Lamotte, O.*
AU  - Durner, J.
AU  - Vandelle, E.*
AU  - Lecourieux, D.*
AU  - Courtois, C.*
AU  - Barnavon, L.*
AU  - Bentejac, M.*
AU  - Pugin, A.*
C1  - 785
C2  - 25138
TI  - NO signaling functions in the biotic and abiotic stress responses.
JO  - BMC Plant Biol.
VL  - 5
PB  - Biomed Central
PY  - 2005
SN  - 1471-2229
ER  -