@article{LissoAltmannMuessig2006, author = {Lisso, Janina and Altmann, Thomas and M{\"u}ssig, Carsten}, title = {The AtNFXL1 gene encodes a NF-X1 type zinc finger protein required for growth under salt stress}, series = {FEBS letters : the journal for rapid publication of short reports in molecular biosciences}, volume = {580}, journal = {FEBS letters : the journal for rapid publication of short reports in molecular biosciences}, number = {22}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0014-5793}, doi = {10.1016/j.febslet.2006.07.079}, pages = {4851 -- 4856}, year = {2006}, abstract = {The human NF-X1 protein and homologous proteins in eukaryotes represent a class of transcription factors which are characterised. by NF-X1 type zinc finger motifs. The Arabidopsis genome encodes two NF-X1 homologs, which we termed AtNFXL1 and AtNFXL2. Growth and survival was impaired in atnfxl1 knock-out mutants and AtNFXL1-antisense plants under salt stress in comparison to wild-type plants. In contrast, 35S: :AtNFXL1 plants showed higher survival rates. The AtNFXL2 protein potentially plays an antagonistic role. The Arabidopsis NF-X1 type zinc finger proteins likely are part of regulatory mechanisms, which protect major processes such as photosynthesis.}, language = {en} } @phdthesis{Bielecka2007, author = {Bielecka, Monika}, title = {Analysis of transcription factors under sulphur deficiency stress}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-14812}, school = {Universit{\"a}t Potsdam}, year = {2007}, abstract = {Sulphur, a macronutrient essential for plant growth, is among the most versatile elements in living organisms. Unfortunately, little is known about regulation of sulphate uptake and assimilation by plants. Identification of sulphate signalling processes will allow to control sulphate acquisition and assimilation and may prove useful in the future to improve sulphur-use efficiency in agriculture. Many of genes involved in sulphate metabolism are regulated on transcriptional level by products of other genes called transcription factors (TF). Several published experiments revealed TF genes that respond to sulphate deprivation, but none of these have been so far been characterized functionally. Thus, we aimed at identifying and characterising transcription factors that control sulphate metabolism in the model plant Arabidopsis thaliana. To achieve that goal we postulated that factors regulating Arabidopsis responses to inorganic sulphate deficiency change their transcriptional levels under sulphur-limited conditions. By comparing TF transcript profiles from plants grown on different sulphate regimes, we identified TF genes that may specifically induce or repress changes in expression of genes that allow plants to adapt to changes in sulphate availability. Candidate genes obtained from this screening were tested by reverse genetics approaches. Transgenic plants constitutively overproducing selected TF genes and mutant plants, lacking functional selected TF genes (knock out), were used. By comparing metabolite and transcript profiles from transgenic and wild type plants we aimed at confirming the role of selected AP2 TF candidate genes in plant adaptation to sulphur unavailability. After preliminary characterisation of WRKY24 and MYB93 TF genes, we postulate that these factors are involved in a complex multifactorial regulatory network, in which WRKY24 and MYB93 would act as superior factors regulating other transcription factors directly involved in the regulation of S-metabolism genes. Results obtained for plants overproducing TOE1 and TOE2 TF genes suggests that these factors may be involved in a mechanism, which is promoting synthesis of an essential amino acid, methionine, over synthesis of another amino acid, cysteine. Thus, TOE1 and TOE2 genes might be a part of transcriptional regulation of methionine synthesis. Approaches creating genetically manipulated plants may produce plant phenotypes of immediate biotechnological interest, such as plants with increased sulphate or sulphate-containing amino acid content, or better adapted to the sulphate unavailability.}, language = {en} } @phdthesis{Kryvych2007, author = {Kryvych, Sergiy}, title = {Gene expression profiling in different stages of development of Arabidopsis thaliana leaftrichomes at the single cell level}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-17474}, school = {Universit{\"a}t Potsdam}, year = {2007}, abstract = {Each organ of a multicellular organism is unique at the level of its tissues and cells. Furthermore, responses to environmental stimuli or developmental signals occur differentially at the single cell or tissue level. This underlines the necessity of precise investigation of the "building block of life" -the individual cell. Although recently large amount of data concerning different aspects of single cell performance was accumulated, our knowledge about development and differentiation of individual cell within specialized tissue are still far from being complete. To get more insight into processes that occur in certain individual cell during its development and differentiation changes in gene expression during life cycle of A. thaliana leaf hair cell (trichome) were explored in this work. After onset of trichome development this cell changes its cell cycle: it starts endoreduplication (a modified cell cycle in which DNA replication continues in the absence of mitosis and cytokinesis). This makes trichomes a suitable model for studying cell cycle regulation, regulation of cell development and differentiation. Cells of interest were sampled by puncturing them with glass microcapillaries. Each sample contained as few as ten single cells. At first time trichomes in initial stage of trichome development were investigated. To allow their sampling they were specifically labelled by green fluorescent protein (GFP). In total three cell types were explored: pavement cells, trichome initials and mature trichomes. Comparison of gene expression profiles of these cells allowed identification of the genes differentially expressed in subsequent stages of trichome development. Bioinformatic analysis of genes preferentially expressed in trichome initials showed their involvement in hormonal, metal, sulphur response and cell-cycle regulation. Expression pattern of three selected candidate genes, involved in hormonal response and early developmental processes was confirmed by independent method. Effects of mutations in these genes on both trichome and plant development as well as on plant metabolism were analysed. As an outcome of this work novel components in the sophisticated machinery of trichome development and cell cycle progression were identified. These factors could integrate hormone stimuli and network interactions between characterized and as yet unknown members of this machinery. I expect findings presented in this work to enhance and complement our current knowledge about cell cycle progression and trichome development, as well as about performance of the individual cell in general.}, language = {en} } @phdthesis{Nikolovski2009, author = {Nikolovski, Nino}, title = {Pectin: New insights from an old polymer through pectinase-based genetic screens}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-35255}, school = {Universit{\"a}t Potsdam}, year = {2009}, abstract = {Pectic polysaccharides, a class of plant cell wall polymers, form one of the most complex networks known in nature. Despite their complex structure and their importance in plant biology, little is known about the molecular mechanism of their biosynthesis, modification, and turnover, particularly their structure-function relationship. One way to gain insight into pectin metabolism is the identification of mutants with an altered pectin structure. Those were obtained by a recently developed pectinase-based genetic screen. Arabidopsis thaliana seedlings grown in liquid medium containing pectinase solutions exhibited particular phenotypes: they were dwarfed and slightly chlorotic. However, when genetically different A. thaliana seed populations (random T-DNA insertional populations as well as EMS-mutagenized populations and natural variations) were subjected to this treatment, individuals were identified that exhibit a different visible phenotype compared to wild type or other ecotypes and may thus contain a different pectin structure (pec-mutants). After confirming that the altered phenotype occurs only when the pectinase is present, the EMS mutants were subjected to a detailed cell wall analysis with particular emphasis on pectins. This suite of mutants identified in this study is a valuable resource for further analysis on how the pectin network is regulated, synthesized and modified. Flanking sequences of some of the T-DNA lines have pointed toward several interesting genes, one of which is PEC100. This gene encodes a putative sugar transporter gene, which, based on our data, is implicated in rhamnogalacturonan-I synthesis. The subcellular localization of PEC100 was studied by GFP fusion and this protein was found to be localized to the Golgi apparatus, the organelle where pectin biosynthesis occurs. Arabidopsis ecotype C24 was identified as a susceptible one when grown with pectinases in liquid culture and had a different oligogalacturonide mass profile when compared to ecotype Col-0. Pectic oligosaccharides have been postulated to be signal molecules involved in plant pathogen defense mechanisms. Indeed, C24 showed elevated accumulation of reactive oxygen species upon pectinase elicitation and had altered response to the pathogen Alternaria brassicicola in comparison to Col-0. Using a recombinant inbred line population three major QTLs were identified to be responsible for the susceptibility of C24 to pectinases. In a reverse genetic approach members of the qua2 (putative pectin methyltransferase) family were tested for potential target genes that affect pectin methyl-esterification. The list of these genes was determined by in silico study of the pattern of expression and co-expression of all 34 members of this family resulting in 6 candidate genes. For only for one of the 6 analyzed genes a difference in the oligogalacturonide mass profile was observed in the corresponding knock-out lines, confirming the hypothesis that the methyl-esterification pattern of pectin is fine tuned by members of this gene family. This study of pectic polysaccharides through forward and reverse genetic screens gave new insight into how pectin structure is regulated and modified, and how these modifications could influence pectin mediated signalling and pathogenicity.}, language = {en} } @phdthesis{Bieniawska2006, author = {Bieniawska, Zuzanna}, title = {Functional analysis of the sucrose synthase gene family in Arabidopsis thaliana}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-13132}, school = {Universit{\"a}t Potsdam}, year = {2006}, abstract = {Sucrose synthase (Susy) is a key enzyme of sucrose metabolism, catalysing the reversible conversion of sucrose and UDP to UDP-glucose and fructose. Therefore, its activity, localization and function have been studied in various plant species. It has been shown that Susy can play a role in supplying energy in companion cells for phloem loading (Fu and Park, 1995), provides substrates for starch synthesis (Zrenner et al., 1995), and supplies UDP-glucose for cell wall synthesis (Haigler et al., 2001). Analysis of the Arabidopsis genome identifies six Susy isoforms. The expression of these isoforms was investigated using promoter-reporter gene constructs (GUS) and real time RT-PCR. Although these isoforms are closely related at the protein level they have radically different spatial and temporal patterns of expression in the plant with no two isoforms showing the same distribution. More than one isoform is expressed in all organs examined. Some of them have high but specific expression in particular organs or developmental stages whilst others are constantly expressed throughout the whole plant and across various stages of development. The in planta function of the six Susy isoforms were explored through analysis of T-DNA insertion mutants and RNAi lines. Plants without the expression of individual isoforms show no differences in growth and development, and are not significantly different from wild type plants in soluble sugars, starch and cellulose contents under all growth conditions investigated. Analysis of T-DNA insertion mutant lacking Sus3 isoform that was exclusively expressed in stomata cells only had a minor influence on guard cell osmoregulation and/or bioenergetics. Although none of the sucrose synthases appear to be essential for normal growth under our standard growth conditions, they may be necessary for growth under stress conditions. Different isoforms of sucrose synthase respond differently to various abiotic stresses. It has been shown that oxygen deprivation up regulates Sus1 and Sus4 and increases total Susy activity. However, the analysis of the plants with reduced expression of both Sus1 and Sus4 revealed no obvious effects on plant performance under oxygen deprivation. Low temperature up regulates Sus1 expression but the loss of this isoform has no effect on the freezing tolerance of non acclimated and cold acclimated plants. These data provide a comprehensive overview of the expression of this gene family which supports some of the previously reported roles for Susy and indicates the involvement of specific isoforms in metabolism and/or signalling.}, language = {en} } @article{LiuLaemkeLinetal.2018, author = {Liu, Hsiang-chin and L{\"a}mke, J{\"o}rn and Lin, Siou-ying and Hung, Meng-Ju and Liu, Kuan-Ming and Charng, Yee-yung and B{\"a}urle, Isabel}, title = {Distinct heat shock factors and chromatin modifications mediate the organ-autonomous transcriptional memory of heat stress}, series = {The plant journal}, volume = {95}, journal = {The plant journal}, number = {3}, publisher = {Wiley}, address = {Hoboken}, issn = {0960-7412}, doi = {10.1111/tpj.13958}, pages = {401 -- 413}, year = {2018}, abstract = {Plants can be primed by a stress cue to mount a faster or stronger activation of defense mechanisms upon subsequent stress. A crucial component of such stress priming is the modified reactivation of genes upon recurring stress; however, the underlying mechanisms of this are poorly understood. Here, we report that dozens of Arabidopsis thaliana genes display transcriptional memory, i.e. stronger upregulation after a recurring heat stress, that lasts for at least 3 days. We define a set of transcription factors involved in this memory response and show that the transcriptional memory results in enhanced transcriptional activation within minutes of the onset of a heat stress cue. Further, we show that the transcriptional memory is active in all tissues. It may last for up to a week, and is associated during this time with histone H3 lysine 4 hypermethylation. This transcriptional memory is cis-encoded, as we identify a promoter fragment that confers memory onto a heterologous gene. In summary, heat-induced transcriptional memory is a widespread and sustained response, and our study provides a framework for future mechanistic studies of somatic stress memory in higher plants.}, language = {en} } @article{BaeurleBrzezinkaAltmann2018, author = {B{\"a}urle, Isabel and Brzezinka, Krzysztof and Altmann, Simone}, title = {BRUSHY1/TONSOKU/MGOUN3 is required for heat stress memory}, series = {Plant Cell \& Environment}, volume = {42}, journal = {Plant Cell \& Environment}, doi = {10.1111/pce.13365}, pages = {771 -- 781}, year = {2018}, abstract = {Plants encounter biotic and abiotic stresses many times during their life cycle and this limits their productivity. Moderate heat stress (HS) primes a plant to survive higher temperatures that are lethal in the na{\"i}ve state. Once temperature stress subsides, the memory of the priming event is actively retained for several days preparing the plant to better cope with recurring HS. Recently, chromatin regulation at different levels has been implicated in HS memory. Here, we report that the chromatin protein BRUSHY1 (BRU1)/TONSOKU/MGOUN3 plays a role in the HS memory in Arabidopsis thaliana. BRU1 is also involved in transcriptional gene silencing and DNA damage repair. This corresponds with the functions of its mammalian orthologue TONSOKU-LIKE/NFΚBIL2. During HS memory, BRU1 is required to maintain sustained induction of HS memory-associated genes, whereas it is dispensable for the acquisition of thermotolerance. In summary, we report that BRU1 is required for HS memory in A. thaliana, and propose a model where BRU1 mediates the epigenetic inheritance of chromatin states across DNA replication and cell division.}, language = {en} } @article{TejosRodriguezFurlanAdamowskietal.2018, author = {Tejos, Ricardo and Rodriguez-Furlan, Cecilia and Adamowski, Maciej and Sauer, Michael and Norambuena, Lorena and Friml, Jiri}, title = {PATELLINS are regulators of auxin-mediated PIN1 relocation and plant development in Arabidopsis thaliana}, series = {Journal of cell science}, volume = {131}, journal = {Journal of cell science}, number = {2}, publisher = {Company of Biologists Limited}, address = {Cambridge}, issn = {0021-9533}, doi = {10.1242/jcs.204198}, pages = {10}, year = {2018}, abstract = {Coordinated cell polarization in developing tissues is a recurrent theme in multicellular organisms. In plants, a directional distribution of the plant hormone auxin is at the core of many developmental programs. A feedback regulation of auxin on the polarized localization of PIN auxin transporters in individual cells has been proposed as a self-organizing mechanism for coordinated tissue polarization, but the molecular mechanisms linking auxin signalling to PIN-dependent auxin transport remain unknown. We used a microarray-based approach to find regulators of the auxin-induced PIN relocation in Arabidopsis thaliana root, and identified a subset of a family of phosphatidylinositol transfer proteins (PITPs), the PATELLINs (PATLs). Here, we show that PATLs are expressed in partially overlapping cell types in different tissues going through mitosis or initiating differentiation programs. PATLs are plasma membrane-associated proteins accumulated in Arabidopsis embryos, primary roots, lateral root primordia and developing stomata. Higher order patl mutants display reduced PIN1 repolarization in response to auxin, shorter root apical meristem, and drastic defects in embryo and seedling development. This suggests that PATLs play a redundant and crucial role in polarity and patterning in Arabidopsis.}, language = {en} } @phdthesis{CastroMarin2007, author = {Castro Marin, Inmaculada}, title = {Nitrate: metabolism and development}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-18827}, school = {Universit{\"a}t Potsdam}, year = {2007}, abstract = {The major aim of this thesis was to study the effect of nitrate on primary metabolism and in development of the model plant Arabidopsis thaliana. The present work has two separate topics. First, to investigate the GDH family, a small gene family at the interface between nitrogen and carbon metabolisms. Second, to investigate the mechanisms whereby nitrogen is regulating the transition to flowering time in Arabidopsis thaliana. To gain more insights into the regulation of primary metabolism by the functional characterization of the glutamate dehydrogenase (GDH) family, an enzyme putatively involved in the metabolism of amino acids and thus suggested to play different and essential roles in carbon and nitrogen metabolism in plants, knock out mutants and transgenic plants carrying RNA interference construct were generated and characterized. The effect of silencing GDH on carbon and nitrogen metabolisms was investigated, especially the level of carbohydrates and the amino acid pool were further analysed. It has been shown that GDH expression is regulated by light and/or sugar status therefore, phenotypic and metabolic analysis were developed in plants grown at different points of the diurnal rhythm and in response to an extended night period. In addition, we are interested in the effect of nutrient availability in the transition from vegetative growth to flowering and especially in nitrate as a metabolite that triggers widespread and coordinated changes in metabolism and development. Nutrient availability has a dramatic effect on flowering time, with a marked delay of flowering when nitrate is supplied (Stitt, 1999). The use of different mutants and transgenic plants impaired in flowering signalling pathways was crucial to evaluate the impact of different nitrate concentrations on flowering time and to better understand the interaction of nitrate-dependent signals with other main flowering signalling pathways. Plants were grown on glutamine as a constitutive source of nitrogen, and the nitrate supply varied. Low nitrate led to earlier flowering. The response to nitrate is accentuated in short days and in the CONSTANS deficient co2 mutant, whereas long days or overexpression of CONSTANS overrides the nitrate response. These results indicate that nitrates acts downstream of the known flowering signalling pathways for photoperiod, autonomy, vernalization and gibberellic acid. Global analyses of gene expression of two independent flowering systems, a light impaired mutant (co2tt4) and a constitutive over-expresser of the potent repressor of flowering (35S::FLC), were to be investigated under two different concentrations of nitrate in order to identify candidate genes that may be involved in the regulation of flowering time by nitrate.}, language = {en} } @phdthesis{Lisec2008, author = {Lisec, Jan}, title = {Identification and characterization of metabolic Quantitative Trait Loci (QTL) in Arabidopsis thaliana}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-25903}, school = {Universit{\"a}t Potsdam}, year = {2008}, abstract = {Plants are the primary producers of biomass and thereby the basis of all life. Many varieties are cultivated, mainly to produce food, but to an increasing amount as a source of renewable energy. Because of the limited acreage available, further improvements of cultivated species both with respect to yield and composition are inevitable. One approach to further progress in developing improved plant cultivars is a systems biology oriented approach. This work aimed to investigate the primary metabolism of the model plant A.thaliana and its relation to plant growth using quantitative genetics methods. A special focus was set on the characterization of heterosis, the deviation of hybrids from their parental means for certain traits, on a metabolic level. More than 2000 samples of recombinant inbred lines (RILs) and introgression lines (ILs) developed from the two accessions Col-0 and C24 were analyzed for 181 metabolic traces using gas-chromatography/ mass-spectrometry (GC-MS). The observed variance allowed the detection of 157 metabolic quantitative trait loci (mQTL), genetic regions carrying genes, which are relevant for metabolite abundance. By analyzing several hundred test crosses of RILs and ILs it was further possible to identify 385 heterotic metabolic QTL (hmQTL). Within the scope of this work a robust method for large scale GC-MS analyses was developed. A highly significant canonical correlation between biomass and metabolic profiles (r = 0.73) was found. A comparable analysis of the results of the two independent experiments using RILs and ILs showed a large agreement. The confirmation rate for RIL QTL in ILs was 56 \% and 23 \% for mQTL and hmQTL respectively. Candidate genes from available databases could be identified for 67 \% of the mQTL. To validate some of these candidates, eight genes were re-sequenced and in total 23 polymorphisms could be found. In the hybrids, heterosis is small for most metabolites (< 20\%). Heterotic QTL gave rise to less candidate genes and a lower overlap between both populations than was determined for mQTL. This hints that regulatory loci and epistatic effects contribute to metabolite heterosis. The data described in this thesis present a rich source for further investigation and annotation of relevant genes and may pave the way towards a better understanding of plant biology on a system level.}, language = {en} }