@phdthesis{Geigenberger2006,
  author    = {Geigenberger, Peter Ludwig},
  title     = {Untersuchungen zur Regulation der Kohlenstoffspeicherung in Pflanzen},
  publisher = {Golm},
  pages     = {45 S. : graph. Darst.},
  year      = {2006},
  language  = {de}
}
@article{OliverLunnUrbanczykWochniaketal.2008,
  author    = {Oliver, Sandra N. and Lunn, John Edward and Urbanczyk-Wochniak, Ewa and Lytovchenko, Anna and van Dongen, Joost T. and Faix, Benjamin and Schm{\"a}lzlin, Elmar and Fernie, Alisdair R. and Schm{\"a}elzlin, E. and Geigenberger, Peter},
  title     = {Decreased expression of cytosolic pyruvate kinase in potato tubers leads to a decline in pyruvate resulting in an in vivo repression of the alternative oxidase},
  doi       = {10.1104/pp.108.126516},
  year      = {2008},
  abstract  = {The aim of this work was to investigate the effect of decreased cytosolic pyruvate kinase (PKc) on potato (Solanum tuberosum) tuber metabolism. Transgenic potato plants with strongly reduced levels of PKc were generated by RNA interference gene silencing under the control of a tuber-specific promoter. Metabolite profiling showed that decreased PKc activity led to a decrease in the levels of pyruvate and some other organic acids involved in the tricarboxylic acid cycle. Flux analysis showed that this was accompanied by changes in carbon partitioning, with carbon flux being diverted from glycolysis toward starch synthesis. However, this metabolic shift was relatively small and hence did not result in enhanced starch levels in the tubers. Although total respiration rates and the ATP to ADP ratio were largely unchanged, transgenic tubers showed a strong decrease in the levels of alternative oxidase (AOX) protein and a corresponding decrease in the capacity of the alternative pathway of respiration. External feeding of pyruvate to tuber tissue or isolated mitochondria resulted in activation of the AOX pathway, both in the wild type and the PKc transgenic lines, providing direct evidence for the regulation of AOX by changes in pyruvate levels. Overall, these results provide evidence for a crucial role of PKc in the regulation of pyruvate levels as well as the level of the AOX in heterotrophic plant tissue, and furthermore reveal that these parameters are interlinked in vivo.},
  language  = {en}
}
@article{ZabalzavanDongenFroehlichetal.2009,
  author    = {Zabalza, Ana and van Dongen, Joost T. and Fr{\"o}hlich, Anja and Oliver, Sandra N. and Faix, Benjamin and Gupta, Kapuganti Jagadis and Schmalzlin, Elmar and Igal, Maria and Orcaray, Luis and Royuela, Mercedes and Geigenberger, Peter},
  title     = {Regulation of respiration and fermentation to control the plant internal oxygen concentration},
  issn      = {0032-0889},
  doi       = {10.1104/pp.108.129288},
  year      = {2009},
  abstract  = {Plant internal oxygen concentrations can drop well below ambient even when the plant grows under optimal conditions. Using pea (Pisum sativum) roots, we show how amenable respiration adapts to hypoxia to save oxygen when the oxygen availability decreases. The data cannot simply be explained by oxygen being limiting as substrate but indicate the existence of a regulatory mechanism, because the oxygen concentration at which the adaptive response is initiated is independent of the actual respiratory rate. Two phases can be discerned during the adaptive reaction: an initial linear decline of respiration is followed by a nonlinear inhibition in which the respiratory rate decreased progressively faster upon decreasing oxygen availability. In contrast to the cytochrome c pathway, the inhibition of the alternative oxidase pathway shows only the linear component of the adaptive response. Feeding pyruvate to the roots led to an increase of the oxygen consumption rate, which ultimately led to anoxia. The importance of balancing the in vivo pyruvate availability in the tissue was further investigated. Using various alcohol dehydrogenase knockout lines of Arabidopsis (Arabidopsis thaliana), it was shown that even under aerobic conditions, alcohol fermentation plays an important role in the control of the level of pyruvate in the tissue. Interestingly, alcohol fermentation appeared to be primarily induced by a drop in the energy status of the tissue rather than by a low oxygen concentration, indicating that sensing the energy status is an important component of optimizing plant metabolism to changes in the oxygen availability.},
  language  = {en}
}
@article{LicausiGiorgiSchmaelzlinetal.2011,
  author    = {Licausi, Francesco and Giorgi, Federico Manuel and Schmaelzlin, Elmar and Usadel, Bj{\"o}rn and Perata, Pierdomenico and van Dongen, Joost Thomas and Geigenberger, Peter},
  title     = {HRE-Type Genes are regulated by Growth-Related Changes in internal Oxygen Concentrations During the normal development of Potato (Solanum tuberosum) Tubers},
  series = {Plant \& cell physiology},
  volume    = {52},
  journal   = {Plant \& cell physiology},
  number    = {11},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {0032-0781},
  doi       = {10.1093/pcp/pcr128},
  pages     = {1957 -- 1972},
  year      = {2011},
  abstract  = {The occurrence of hypoxic conditions in plants not only represents a stress condition but is also associated with the normal development and growth of many organs, leading to adaptive changes in metabolism and growth to prevent internal anoxia. Internal oxygen concentrations decrease inside growing potato tubers, due to their active metabolism and increased resistance to gas diffusion as tubers grow. In the present work, we identified three hypoxia-responsive ERF (StHRE) genes whose expression is regulated by the gradual decrease in oxygen tensions that occur when potato tubers grow larger. Increasing the external oxygen concentration counteracted the modification of StHRE expression during tuber growth, supporting the idea that the actual oxygen levels inside the organs, rather than development itself, are responsible for the regulation of StHRE genes. We identified several sugar metabolism-related genes co-regulated with StHRE genes during tuber development and possibly involved in starch accumulation. All together, our data suggest a possible role for low oxygen in the regulation of sugar metabolism in the potato tuber, similar to what happens in storage tissues during seed development.},
  language  = {en}
}
@misc{SchmaelzlinDongenKlimantetal.2005,
  author    = {Schm{\"a}lzlin, Elmar and Dongen, Joost T. van and Klimant, Ingo and Marmod{\´e}e, Bettina and Steup, Martin and Fishahn, Joachim and Geigenberger, Peter and L{\"o}hmannsr{\"o}ben, Hans-Gerd},
  title     = {An optical multifrequency phase-modulation method using microbeads for measuring intracellular oxygen concentrations in plants},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-12232},
  year      = {2005},
  abstract  = {A technique has been developed to measure absolute intracellular oxygen concentrations in green plants. Oxygen-sensitive phosphorescent microbeads were injected into the cells and an optical multifrequency phase-modulation technique was used to discriminate the sensor signal from the strong autofluorescence of the plant tissue. The method was established using photosynthesis-competent cells of the giant algae Chara corallina L., and was validated by application to various cell types of other plant species.},
  language  = {en}
}
@article{FettkeEckermannTiessenetal.2005,
  author    = {Fettke, J{\"o}rg and Eckermann, Nora and Tiessen, Axel and Geigenberger, Peter Ludwig and Steup, Martin},
  title     = {Identification, subcellular localization and biochemical characterization of water-soluble heteroglycans (SHG) in leaves of Arabidopsis thaliana L. : distinct SHG reside in the cytosol and in the apoplast},
  issn      = {0960-7412},
  year      = {2005},
  abstract  = {Water-soluble heteroglycans (SHG) were isolated from leaves of wild-type Arabidopsis thaliana L. and from two starch-deficient mutants. Major constituents of the SHG are arabinose, galactose, rhamnose, and glucose. SHG was separated into low (< 10 kDa; SHG(S)) and high (> 10 kDa; SHG(L)) molecular weight compounds. SHG(S) was resolved into approximately 25 distinct oligoglycans by ion exchange chromatography. SHG(L) was further separated into two subfractions, designated as subfraction I and II, by field flow fractionation. For the intracellular localization of the various SHG compounds several approaches were chosen: first, leaf material was subjected to non-aqueous fractionation. The apolar gradient fractions were characterized by monitoring markers and were used as starting material for the SHG isolation. Subfraction I and SHG(S) exhibited a distribution similar to that of cytosolic markers whereas subfraction II cofractionated with crystalline cellulose. Secondly, intact organelles were isolated and used for SHG isolation. Preparations of intact organelles (mitochondria plus peroxisomes) contained no significant amount of any heteroglycan. In isolated intact microsomes a series of oligoglycans was recovered but neither subfraction I nor II. In in vitro assays using glucose 1-phosphate and recombinant cytosolic (Pho 2) phosphorylase both SHG(S) and subfraction I acted as glucosyl acceptor whereas subfraction II was essentially inactive. Rabbit muscle phosphorylase a did not utilize any of the plant glycans indicating a specific Pho 2-glycan interaction. As revealed by in vivo labeling experiments using (CO2)-C-14 carbon fluxes into subfraction I and II differed. Furthermore, in leaves the pool size of subfraction I varied during the light-dark regime},
  language  = {en}
}
@article{SteinfathStrehmelPetersetal.2010,
  author    = {Steinfath, Matthias and Strehmel, Nadine and Peters, Rolf and Schauer, Nicolas and Groth, Detlef and Hummel, Jan and Steup, Martin and Selbig, Joachim and Kopka, Joachim and Geigenberger, Peter and Dongen, Joost T. van},
  title     = {Discovering plant metabolic biomarkers for phenotype prediction using an untargeted approach},
  issn      = {1467-7644},
  doi       = {10.1111/j.1467-7652.2010.00516.x},
  year      = {2010},
  abstract  = {Biomarkers are used to predict phenotypical properties before these features become apparent and, therefore, are valuable tools for both fundamental and applied research. Diagnostic biomarkers have been discovered in medicine many decades ago and are now commonly applied. While this is routine in the field of medicine, it is of surprise that in agriculture this approach has never been investigated. Up to now, the prediction of phenotypes in plants was based on growing plants and assaying the organs of interest in a time intensive process. For the first time, we demonstrate in this study the application of metabolomics to predict agronomic important phenotypes of a crop plant that was grown in different environments. Our procedure consists of established techniques to screen untargeted for a large amount of metabolites in parallel, in combination with machine learning methods. By using this combination of metabolomics and biomathematical tools metabolites were identified that can be used as biomarkers to improve the prediction of traits. The predictive metabolites can be selected and used subsequently to develop fast, targeted and low-cost diagnostic biomarker assays that can be implemented in breeding programs or quality assessment analysis. The identified metabolic biomarkers allow for the prediction of crop product quality. Furthermore, marker-assisted selection can benefit from the discovery of metabolic biomarkers when other molecular markers come to its limitation. The described marker selection method was developed for potato tubers, but is generally applicable to any crop and trait as it functions independently of genomic information.},
  language  = {en}
}
@article{KoettingPuschTiessenetal.2005,
  author    = {K{\"o}tting, Oliver and Pusch, Kerstin and Tiessen, Axel and Geigenberger, Peter Ludwig and Steup, Martin and Ritte, Gerhard},
  title     = {Identification of a novel enzyme required for starch metabolism in Arabidopsis leaves : the phosphoglucan, water dikinase},
  year      = {2005},
  abstract  = {The phosphorylation of amylopectin by the glucan, water dikinase (GWD; EC 2.7.9.4) is an essential step within starch metabolism. This is indicated by the starch excess phenotype of GWD-deficient plants, such as the sex1-3 mutant of Arabidopsis (Arabidopsis thaliana). To identify starch-related enzymes that rely on glucan-bound phosphate, we studied the binding of proteins extracted from Arabidopsis wild-type leaves to either phosphorylated or nonphosphorylated starch granules. Granules prepared from the sex1-3 mutant were prephosphorylated in vitro using recombinant potato (Solanum tuberosum) GWD. As a control, the unmodified, phosphate free granules were used. An as-yet uncharacterized protein was identified that preferentially binds to the phosphorylated starch. The C-terminal part of this protein exhibits similarity to that of GWD. The novel protein phosphorylates starch granules, but only following prephosphorylation with GWD. The enzyme transfers the beta-P of ATP to the phosphoglucan, whereas the gamma-P is released as orthophosphate. Therefore, the novel protein is designated as phosphoglucan, water dikinase (PWD). Unlike GWD that phosphorylates preferentially the C6 position of the glucose units, PWD phosphorylates predominantly (or exclusively) the C3 position. Western-blot analysis of protoplast and chloroplast fractions from Arabidopsis leaves reveals a plastidic location of PWD. Binding of PWD to starch granules strongly increases during net starch breakdown. Transgenic Arabidopsis plants in which the expression of PWD was reduced by either RNAi or a T-DNA insertion exhibit a starch excess phenotype. Thus, in Arabidopsis leaves starch turnover requires a close collaboration of PWD and GWD},
  language  = {en}
}
@article{FettkePoesteEckermannetal.2005,
  author    = {Fettke, J{\"o}rg and Poeste, Simon and Eckermann, Nora and Tiessen, Axel and Pauly, Markus and Geigenberger, Peter Ludwig and Steup, Martin},
  title     = {Analysis of cytosolic heteroglycans from leaves of transgenic potato (Solanum tuberosum L.) plants that under- or overexpress the Pho 2 phosphorylase isozyme},
  year      = {2005},
  abstract  = {During starch degradation, chloroplasts export neutral sugars into the cytosol where they appear to enter a complex glycan metabolism. Interactions between glycans and glucosyl transferases residing in the cytosol were studied by analyzing transgenic potato (Solanum tuberosum L.) plants that possess either decreased or elevated levels of the cytosolic (Pho 2) phosphorylase isoform. Water-soluble heteroglycans (SHGs) were isolated from these plants and were characterized. SHG contains, as major constituents, arabinose, rhamnose, galactose and glucose. Non-aqueous fractionation combined with other separation techniques revealed a distinct pool of the SHG that is located in the cytosol. Under in vitro conditions, the cytosolic heteroglycans act as glucosyl acceptor selectively for Pho 2. Acceptor sites were characterized by a specific hydrolytic degradation following the Pho 2-catalyzed glucosyl transfer. The size distribution of the cytosolic SHG increased during the dark period, indicating a distinct metabolic activity related to net starch degradation. Antisense inhibition of Pho 2 resulted in increased glucosyl and rhamnosyl contents of the glycans. Overexpression of Pho 2 decreased the content of both residues. Compared with the wild type, in both types of transgenic plants the size of the cytosolic glycans was increased},
  language  = {en}
}
@article{SchmalzlinvanDongenKlimantetal.2005,
  author    = {Schmalzlin, E. and van Dongen, J. T. and Klimant, I. and Marmodee, Bettina and Steup, Martin and Fisahn, Joachim and Geigenberger, Peter Ludwig and L{\"o}hmannsr{\"o}ben, Hans-Gerd},
  title     = {An optical multifrequency phase-modulation method using microbeads for measuring intracellular oxygen concentrations in plants},
  issn      = {0006-3495},
  year      = {2005},
  abstract  = {A technique has been developed to measure absolute intracellular oxygen concentrations in green plants. Oxygen- sensitive phosphorescent microbeads were injected into the cells and an optical multifrequency phase-modulation technique was used to discriminate the sensor signal from the strong auto fluorescence of the plant tissue. The method was established using photosynthesis- competent cells of the giant algae Chara corallina L., and was validated by application to various cell types of other plant species},
  language  = {en}
}